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| + | [{{gmod.org.url}}?title=Special%3ANewsChannel&format=rss20&limit=5000&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed RSS] [[File:RSSIcon16x16.gif|RSS feed|link={{gmod.org.url}}?title=Special%3ANewsChannel&format=rss20&limit=5000&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed]]<br /> |
| + | [[GMOD News|Recent News Only]]<br /> |
| + | [[GMOD News#Adding a News Item|Add a news item]] |
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| The GMOD News Archive contains old news items that have been archived off of the [[GMOD News]] page/feed. The News includes anything that is relevant to the GMOD user and developer communities. This includes a wide range of topics, from GMOD meetings and releases to user success stories and GMOD related publications. | | The GMOD News Archive contains old news items that have been archived off of the [[GMOD News]] page/feed. The News includes anything that is relevant to the GMOD user and developer communities. This includes a wide range of topics, from GMOD meetings and releases to user success stories and GMOD related publications. |
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| See the [[GMOD News]] page for instruction on how to post a news item. | | See the [[GMOD News]] page for instruction on how to post a news item. |
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− | = 2010 Stories = | + | = All News Items = |
− | | + | |
− | Many of the 2010 stories are still on the [[GMOD News]] page. Items are only moved here when they are more than 6 months old.
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− | | + | |
− | == GMOD Meeting: Sept. 13-14 ==
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− | {{ImageRight|Cambridge.jpg|September 2010 GMOD Meeting||September 2010 GMOD Meeting}}
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− | Thanks to the prep work by Gos Micklem at Cambridge, I am pleased to announce that there will be a two day [[September 2010 GMOD Meeting|GMOD community meeting]] starting on Monday September 13 in Cambridge, England. This meeting occurs immediately prior to the [http://meetings.cshl.edu/meetings/infouk10.shtml Genome Informatics meeting] in Hinxton (for which the abstract deadline is [[Calendar|June 25]]). Registration information for this meeting will be available in a few weeks. In the mean time, you can [[September 2010 GMOD Meeting|post topic suggestions]] to the [[September 2010 GMOD Meeting|meeting page]].
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− | Please feel free to tell your colleagues and to post to mailing lists that you think would be interested in this meeting.
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− | I look forward to seeing you in England this Fall.
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− | [[User:Scott|Scott Cain]]
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− | | + | |
− | ''2010/06/17''
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− | == New GMOD Tutorials ==
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− | | + | |
− | {{ImageRight|2010SummerSchoolAmericas170.png|Summer School - Americas||http://gmod.org/wiki/Training_and_Outreach#Online_Tutorials}}
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− | Detailed and hands-on [[Training and Outreach#Online Tutorials|online tutorials]] are now available for the [[GMOD Components]] that were covered at the [[2010 GMOD Summer School - Americas]]. Each tutorial includes a [[VMware]] system image to work with, and detailed instructions on how to setup the component on that image. This year we have a [[Galaxy Tutorial]] for the first time.
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− | The [[:Category:Tutorials|tutorials]] are:
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− | * '''[[Apollo Tutorial]]''' - by [[User:Elee|Ed Lee]]
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− | * '''[[Chado Tutorial]]''' - by [[User:Scott|Scott Cain]], [[User:Clements|Dave Clements]], and [[User:Jorvis|Joshua Orvis]].
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− | * '''[[Galaxy Tutorial]]''' - by [[User:JamesTaylor|James Taylor]]
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− | * '''[[GBrowse Tutorial]]''' - by [[User:Scott|Scott Cain]]
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− | * '''[[GBrowse_syn Tutorial]]''' - by [[User:Mckays|Sheldon McKay]]
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− | * '''[[JBrowse Tutorial]]''' - by [[User:MitchSkinner|Mitch Skinner]]
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− | * '''[[MAKER Tutorial]]''' - by [[User:Carsonholt|Carson Holt]]
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− | * '''[[Tripal Tutorial]]''' - by [[User:Sficklin|Stephen Ficklin]]
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− | The [[2010 GMOD Summer School - Americas]] got the best [[2010 GMOD Summer School - Americas|reviews]] of any [[GMOD Summer School|course]] GMOD has ever done. I'd like to thank this year's instructors and participants for making it such a success.
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− | Thanks,
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− | [[User:Clements|Dave Clements]]<br />
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− | [[GMOD Help Desk]]
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− | | + | |
− | ''2010/06/14''
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− | | + | |
− | == ISGA Pipeline Service ==
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− | | + | |
− | {{ImageRight|ISGAHomePageThumb.png|ISGA at the Center for Genomics and Bioinformatics||http://isga.cgb.indiana.edu/}}
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− | [http://isga.cgb.indiana.edu/ Integrated Services for Genomic Analysis (ISGA)] is an [[Ergatis]]-based bioinformatics pipeline service based at [http://cgb.indiana.edu/ Indiana University's Center for Genomics and Bioinformatics]. ISGA is also a [http://sourceforge.net/projects/isga/ free, open-source software package] that you can install locally to provide a biologist-friendly web interface to your computational resources. ISGA currently provides prokaryotic annotation and prokaryotic assembly pipelines and offers an intuitive interface for biologists to run and customize pipelines. ISGA also integrates tools such as [[GBrowse]] and Blast for visualizing and analyzing pipeline results. Since ISGA utilizes the [[Ergatis]] workflow system to execute pipelines, ISGA pipeline can be submitted back to the Ergatis community and other Ergatis pipelines can be adapted to use ISGA. (See [[#Ergatis Update|Ergatis Update]] below for what's new with Ergatis.)
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− | For more on ISGA, see the manuscript [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/8/1122 "An Ergatis-based prokaryotic genome annotation web server"] in ''[http://bioinformatics.oxfordjournals.org/ Bioinformatics]'', the [http://isga.cgb.indiana.edu/Help/Tutorial ISGA pipeline and account tutorials], and the [http://isga.cgb.indiana.edu/Help/FAQ ISGA FAQ page]. For help using or installing ISGA, join the [https://lists.sourceforge.net/lists/listinfo/isga-users isga-users mailing list].
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− | [[User:Chemmeri|Chris Hemmerich]]
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− | ''2010/06/07''
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− | | + | |
− | == MAKER 2.0, AGS Workshop ==
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− | <div style="Float: right;">
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− | {|
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− | |{{ImageRight|MAKERLogo.png|MAKER 2.0 Released|170|MAKER}}<br>
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− | |-
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− | | {{ImageRight|AGSBug170.png|Arthropod Genomics Symposium|100|http://www.k-state.edu/agc/symp2010/seminar.html}}
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− | |}
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− | </div>
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− | [[MAKER]], the easy to use genome annotation pipeline, is now version 2.0.
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− | Some of the current features and other improvements
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− | * Improved gene model preparation and evidence filtering...
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− | * mRNAseq data in your annotations (use output from programs like [http://tophat.cbcb.umd.edu/ TopHat], [http://cufflinks.cbcb.umd.edu/ CuffLinks], and others in [[MAKER]])...
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− | * Annotate eukaryotes and prokayotes...
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− | * Pass through any kind of evidence evidence from any source via [[GFF3]] pass-through...
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− | * Easy single-command-line dump of MAKER output to a [[Chado]] database and to [[JBrowse]]...
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− | * Same directory parallelization - just start MAKER on top of itself, and it will share the workload with the new process...
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− | * Auto recovery - start, stop, and restart MAKER at any time; MAKER will always just pick up where it left off...
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− | * optional web base GUI for a local MAKER installation
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− | There will also be a [http://www.k-state.edu/agc/symp2010/seminar.html workshop on MAKER] on June 12 at the [http://www.k-state.edu/agc/symposium.shtml 4th Annual Arthropod Genomics Symposium] in Kansas City. If you are attending AGS and are interested in genome annotation, please consider attending.
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− | | + | |
− | Thanks,<br />
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− | [[User:Carsonholt|Carson Holt]]
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− | | + | |
− | ''2010/06/01''
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− | | + | |
− | == Load Chado into BioMart ==
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− | <div style="float: right; text-align: center">
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− | {{#icon: Biomart250.png|Load Chado into BioMart|125|http://gmod.org/wiki/BioMart#How_to_Load_a_Chado_Database_into_BioMart}}<br /><br />
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− | {{#icon: Urgi.png|INRA URGI|105|http://urgi.versailles.inra.fr/}}
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− | </div>
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− | A group at INRA URGI have documented "[[BioMart#How to Load a Chado Database into BioMart|How to load a Chado database into BioMart]]". This step by step document details what how to configure BioMart for Chado, and includes some specific use cases useful with [[Chado]]. This guide is based on experience at [http://urgi.versailles.inra.fr/ INRA URGI], and was written by Aminah Keliet, Joëlle Amselem, Sandra Derozie, and Delphine Steinbach.
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− | | + | |
− | If you are interested in loading your [[Chado]] data into a [[BioMart]] instance then I recommend starting with this guide.
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− | | + | |
− | Thanks,
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− | | + | |
− | [[User:Clements|Dave C.]]<br />
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− | [[GMOD Help Desk]]
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− | | + | |
− | ''2010/05/27''
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− | | + | |
− | == June 2010 Calendar ==
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− | | + | |
− | {{ImageLeft|calendar_icon.gif|GMOD Calendar||Calendar}}
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− | The [[Calendar|next 5 weeks]] includes the a [[MAKER]] workshop at the [http://www.k-state.edu/agc/symp2010/ Arthropod Genomics Symposium], and deadlines for [http://www.iscb.org/ismb2010-deadlines ISMB] (Boston in July), [http://www.amatameeting.org/ AMATA] (Hobart in September), [http://gi-workshop.net/ GIW] (Hangzhou in December), [http://www.eccb10.org/ ECCB] (Ghent in September), [http://incob10.hgc.jp/ InCoB] (Tokyo in September), and [http://meetings.cshl.edu/meetings/infouk10.shtml Genome Informatics] (Hinxton in September).
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− | <div style="margin-right: 26em">
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− | <embedurl>http://www.google.com/calendar/embed?src=0ajv0bm32ue3c2o2v1c8i889hk%40group.calendar.google.com&showTitle=0&showCalendars=0&height=350&mode=AGENDA&ctz=America/NewYork&dates=20100601%2F20100601</embedurl>
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− | </div>
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− | If you know of any other events or deadlines that the GMOD community would be interested in, please send them to me.
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− | | + | |
− | Thanks,
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− | | + | |
− | [[User:Clements|Dave Clements]]<br />
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− | [[GMOD Help Desk]]
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− | | + | |
− | ''2010/05/24''
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− | | + | |
− | == gmod (Chado) 1.1 Released ==
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− | | + | |
− | I am pleased to announce that we released [https://sourceforge.net/projects/gmod/ gmod-1.1] today. This release has the GMOD database [[Glossary#Schema|schema]], [[Chado]], and a variety of tools for loading and working with the database. The release can be downloaded from the [https://sourceforge.net/projects/gmod/ GMOD SourceForge site].
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− | There have been many people who have helped with getting this release done and I would like to thank all of them. I would like to especially thank [[User:RobertBuels|Rob Buels]] and [[User:NaamaMenda|Naama Menda]] and the rest of the people at the [http://solgenomics.net/ Sol Genomics Network (SGN)] for their code contributions, including a pub table loader that works with PubMed and an updated version of the script to calculate [[Chado CV Module#Transitive Closure|cvterm closures]].
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− | There have been many changes and bug fixes since the [[GMOD News Archives#GMOD 1.0 Released|1.0 release just over two years ago]], but the schema itself has changed very little.
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− | For a [[Glossary#SQL|SQL]] summary of the changes, see [http://gmod.svn.sourceforge.net/viewvc/gmod/schema/tags/gmod-1.1/chado/Changes.sql?revision=23255&view=markup <tt>Changes.sql</tt>] in the release that contains SQL statements that should take a 1.0 release of the [[Chado]] schema to the 1.1 schema. See the [http://gmod.svn.sourceforge.net/viewvc/gmod/schema/tags/gmod-1.1/chado/Changes?revision=23255&view=markup <tt>Changes</tt>] file for a full list.
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− | If you have been using Chado from a recent [[SVN|svn]] checkout, you don't need to modify your schema at all, since the last change to the schema was about a year ago.
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− | Now that this release is out, the plan going forward is for frequent, smaller releases, with an eye on the [[Chado Natural Diversity Module Working Group|Natural Diversity]] schema modifications being worked on now.
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− | Thanks for your continued support of the GMOD project,
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− | [[User:Scott|Scott]]
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− | ''2010/05/24''
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− | | + | |
− | == GMOD in Boston in July? ==
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− | | + | |
− | From Scott on 2010/05/25:
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− | <div class="emphasisbox">
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− | Due to the short notice, I've decided not to have a GMOD meeting
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− | before BOSC/ISMB in July. I am hoping to plan an informal "GMOD
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− | lunch" sometime during BOSC or ISMB for people who are going to the
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− | meetings and would like to get together to chat.
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− | </div>
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− | Scott Cain sent this question about the next [[Meetings|GMOD meeting]] out to several [[GMOD Mailing Lists|mailing lists]] on May 17:
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− | <div class="quotebox">
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− | Since the last GMOD meeting in January, I had been hoping to have a
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− | [[Meetings|GMOD meeting]] around the ISMB and BOSC meetings in Boston this July.
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− | Until this week, though, I had had a difficult time finding a place
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− | where a meeting could be held for a reasonable price. However, a kind
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− | soul at The Broad has offered a meeting space that would easily
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− | accommodate a GMOD meeting for two days before BOSC (either July 6-7
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− | or July 7-8). The only question I have is this: can people make it to
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− | a GMOD meeting with about 2 months notice? Please let me know your
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− | thoughts on this. While there would probably be a registration fee,
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− | it would be fairly low (I'm guessing in the ballpark of $50).
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− | Thanks,
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− | [[User:Scott|Scott]]
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− | </div>
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− | Scott hasn't heard back, yea or nay, from very many people so far and we need to make a decision as soon as possible. '''If you have any thoughts on this, please [mailto:scott@scottcain.net send them to Scott] before 3pm Eastern US time on Monday, May 24.''' See the GMOD [[Calendar]] for a list of what else is going on in July.
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− | Thanks,
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− | | + | |
− | [[User:Clements|Dave C.]]<br />
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− | [[GMOD Help Desk]]
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− | | + | |
− | ''2010/05/21, updated 2010/05/25''
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− | | + | |
− | == Ergatis Update ==
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− | {{ImageRight|BionformaticsCover.gif|Ergatis Paper in Bioinformatics||http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq167v1}}
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− | The paper "[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq167v1 Ergatis: A web interface and scalable software system for bioinformatics workflows]" is now available as an advance access manuscript in the journal ''[http://bioinformatics.oxfordjournals.org/ Bioinformatics]''. [[Ergatis]] "enables users to build, execute, and monitor pipelines for computational analysis of genomics data."
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− | Ergatis now includes pipeline templates for prokaryotic genome annotation and comparative genome analysis, as well as 174 modular 'components' that can be used to create custom pipelines, all of which can be executed either locally or on large compute clusters.
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− | New tools available that use Ergatis include [http://clovr.igs.umaryland.edu CloVR], which enables bioinformatic pipeline execution in compute clouds and the recently-awarded [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0959894 Data Intensive Academic Grid (DIAG)], which will provide a publicly-accessible Ergatis instance as one of its access methods. At the [[January 2010 GMOD Meeting]] Chris Hemmerich [[:Image:Jan2010ErgatisForBiologists.pdf|presented ISGA]], which provides a customized, abstract interface to Ergatis designed for biologists with specific pipeline needs.
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− | [[User:Jorvis|Joshua Orvis]]
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− | ''2010/05/20''
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− | | + | |
− | == May 2010 Calendar ==
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− | | + | |
− | {{ImageLeft|calendar_icon.gif|GMOD Calendar||Calendar}}
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− | The [[Calendar|next 5 weeks]] includes the [[2010 GMOD Summer School - Americas]] and the first [[Galaxy]] Developers Conference. Upcoming deadlines include the ISMB technology track (tomorrow), posters at Arthropod Genomics and ECCB10, and papers for GIW 2010.
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− | <embedurl>http://www.google.com/calendar/embed?src=0ajv0bm32ue3c2o2v1c8i889hk%40group.calendar.google.com&showTitle=0&showCalendars=0&height=350&mode=MONTH&ctz=America/NewYork&dates=20100501%2F20100501</embedurl>
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− | If you know of any other events or deadlines that the GMOD community would be interested in, please send them to me.
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− | | + | |
− | Thanks,
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− | | + | |
− | [[User:Clements|Dave Clements]]<br />
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− | [[GMOD Help Desk]]
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− | | + | |
− | ''2010/04/22''
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− | | + | |
− | == MaizeGDB: Choosing GBrowse ==
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− | {{ImageRight|MaizeGDB.gif|Database Paper||http://database.oxfordjournals.org/cgi/content/abstract/baq007}}
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− | A paper, "[http://database.oxfordjournals.org/cgi/content/abstract/baq007 Choosing a genome browser for a Model Organism Database: surveying the Maize community]," by the [http://maizegdb.org MaizeGDB] team has been published in ''[http://database.oxfordjournals.org/ Database].'' To prepare for the availability of a reference genome, MaizeGDB surveyed their community to assess genome visualization needs. This paper summarizes the survey and MaizeGDB's review of available browsers, and describes why they chose [[GBrowse]]. The paper finishes by describing how they implemented GBrowse, including the ''locus lookup tool'' ([http://bioinformatics.oxfordjournals.org/cgi/content/short/26/3/434 described here]), a MaizeGDB extension that uses maize's extensive physical and genetic mapping data to localize genomic regions in GBrowse. This is a great paper for anyone considering which genome browser to use.
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− | {{ImageRight|DatabaseJournal.jpg|Database Journal|265|http://database.oxfordjournals.org/}}
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− | I'd also like to highlight the journal the paper appears in: ''[http://database.oxfordjournals.org/ Database: The Journal of Biological Databases and Curation].'' "Biological Databases and Curation" are what GMOD is about and many of the papers cover issues and resources that are widely applicable in the GMOD community. The [http://database.oxfordjournals.org/content/vol2010/issue0/index.dtl current issue] also includes papers on [http://database.oxfordjournals.org/cgi/content/abstract/2010/0/baq009 community annotation using wikis], and [http://database.oxfordjournals.org/cgi/content/abstract/2010/0/baq001 a report on best practices in genome annotation] from the [http://biocurator.org/ ISB] [http://projects.eml.org/sdbv/events/BiocurationMeeting/index.html 3<sup>rd</sup> International Biocuration Conference]. ''Database'' is an open access publication, making it an even better match for GMOD.
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− | [[User:Clements|Dave Clements]]<br />
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− | [[GMOD Help Desk]]
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− | | + | |
− | ''2010/04/19''
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− | == YAPC::NA 2010 is Almost Here! ==
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− | <div style="float: right; background-color: #121315">{{#icon: Yapc2010Logo.png|YAPC::NA 2010|220|http://conferences.mongueurs.net/yn2010/}}</div>
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− | June 21st – 23rd 2010 is quickly approaching and Columbus.PM is getting very excited. Hotel reservation information is available, dorm reservation details are up and ready, the conference is quickly approaching. For everyone still looking for [http://conferences.mongueurs.net/yn2010/ YAPC::NA 2010 (Yet Another Perl Conference North America)] details, here is what we have planned. The conference will be held in the brand new beautiful [http://conferences.mongueurs.net/yn2010/wiki?node=ConferenceSummary The Ohio State Union].
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− | Larry Wall, Damian Conway, Randal Schwartz, and many others will be in attendance.
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− | The main dorm location is Morrison Tower and the Hotel conference block is in The Blackwell Inn (see [http://conferences.mongueurs.net/yn2010/wiki?node=Accommodations Accommodations]). Early registration is quickly coming to an end so make sure that you forward this to all of your friends and coworkers and get signed up
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− | today!
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− | I hope to see you all at [http://conferences.mongueurs.net/yn2010/ YAPC::NA 2010] in beautiful Columbus, Ohio.
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− | Heath Bair<br />
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− | [http://conferences.mongueurs.net/yn2010/ YAPC::NA 2010] Conference Chairman
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− | ''2010/04/13''
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− | | + | |
− | == Don Gilbert Nominated for BFA ==
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− | | + | |
− | {{ImageRight|BioinformaticsOrganization.png|Don Gilbert Nominated for Benjamin Franklin Award|140|http://www.bioinformatics.org/franklin/}}
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− | The Bioinformatics Organization has announced its nominees for the the [http://www.bioinformatics.org/forums/forum.php?forum_id=7956 2010 Benjamin Franklin Award].
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− | <div class="indent">
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− | The Benjamin Franklin Award for Open Access in the Life Sciences is a humanitarian/bioethics award presented annually by this organization to an individual who has, in his or her practice, promoted free and open access to the materials and methods used in the life sciences.
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− | </div>
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− | This year's nominees include longtime GMOD contributor [[User:Dongilbert|Don Gilbert]], of Indiana University. Other 2010 nominees are Alex Bateman, David J. Lipman, G.P.S. Raghava, and John Quakenbush. Previous winners of the BFA include [http://www.bioinformatics.org/franklin/2003/ Jim Kent], Michael Ashburner, and another long-time GMOD contributor [http://www.bioinformatics.org/franklin/2004/ Lincoln Stein].
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− | ''If you want a say on who should receive the 2010 award, please go to [http://www.bioinformatics.org/forums/forum.php?forum_id=7956 Bioinformatics.org] and cast your vote.'' If you are not already a member you will need to [http://www.bioinformatics.org/account/register.php join], but basic membership is free.
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− | [[User:Clements|Dave Clements]]<br />
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− | [[GMOD Help Desk]]
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− | | + | |
− | ''2010/04/01''
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− | | + | |
− | == April 2010 Calendar ==
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− | | + | |
− | {{ImageLeft|calendar_icon.gif|GMOD Calendar||Calendar}}
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− | There's a lot on the [[calendar]] in the next 5 weeks, including (among others) registration deadlines for Arthropod Genomics (early) and the Galaxy Developers Conference, and submission deadlines for ECCB, iEvoBio, BOSC, and ISMB.
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− | | + | |
− | <div style="margin-right: 26em">
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− | <embedurl>http://www.google.com/calendar/embed?src=0ajv0bm32ue3c2o2v1c8i889hk%40group.calendar.google.com&showTitle=0&showCalendars=0&height=350&mode=AGENDA&ctz=America/NewYork&dates=20100401%2F20100401</embedurl></div>
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− | | + | |
− | If you know of any other events or deadlines that the GMOD community would be interested in, please send them to me.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
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− | | + | |
− | ''2010/03/25''
| + | |
− | | + | |
− | == Google Summer of Code & OBF ==
| + | |
− | | + | |
− | {{ImageRight|OBF logo.png|OBF in GSoC||http://open-bio.org/wiki/Google_Summer_of_Code}}
| + | |
− | Great news: the [http://open-bio.org/wiki/Google_Summer_of_Code Open Bioinformatics Foundation (OBF)] has been accepted as a mentoring organization for this summer's Google Summer of Code!
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− | | + | |
− | GSoC is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents). Students are paid a $5000 USD stipend to work as a developer on an open-source project for the summer. For more on GSoC, see the [http://open-bio.org/wiki/Google_Summer_of_Code GSoC 2010 FAQ].
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− | | + | |
− | Student applications are due April 9, 2010 at 19:00 UTC. Students who are interested in participating should look at the [http://open-bio.org/wiki/Google_Summer_of_Code OBF's GSoC page], which lists project ideas, and who to contact about applying.
| + | |
− | | + | |
− | For current developers on OBF projects, please consider volunteering to be a mentor if you have not already, and contribute project ideas. Just list your name and project ideas on OBF wiki and on the relevant project's GSoC wiki page.
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− | | + | |
− | Thanks to all who helped make OBF's application to GSoC a success, and let's have a great, productive summer of code!
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− | | + | |
− | [[User:RobertBuels|Rob Buels]]
| + | |
− | | + | |
− | [http://open-bio.org/wiki/Google_Summer_of_Code OBF GSoC 2010 Administrator]
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− | | + | |
− | ''2010/03/21''
| + | |
− | | + | |
− | == InterMine is Hiring ==
| + | |
− | | + | |
− | {{ImageRight|InterMine.png|InterMine is hiring|180|http://intermine.org/wiki/NowHiring}}
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− | | + | |
− | We have [http://intermine.org/wiki/NowHiring four vacancies] on [[InterMine]] related projects at The University
| + | |
− | of Cambridge, UK. We are looking for a Web Developer, Bioinformatics Software Developers and a Java Developer. See [http://intermine.org/wiki/NowHiring the position descriptions] for more information.
| + | |
− | | + | |
− | The closing date for applications is 2nd April 2010.
| + | |
− | | + | |
− | The [[InterMine]] Team.
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− | | + | |
− | ''2010/03/19''
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− | | + | |
− | == Internships @ Dow AgroSciences ==
| + | |
− | | + | |
− | {{ImageRight|das_header_logo.gif|Dow AgroSciences|200}}
| + | |
− | | + | |
− | [http://www.bioinformatics.org/forums/forum.php?forum_id=7919 Dow AgroSciences has 7 Bioinformatics summer internship positions open], 2 of which are related to GMOD. We are looking for candidates with experience in installing, configuring, and uploading data into GMOD. Experience with the [[GBrowse]] source code and modifying it to create new views (e.g creating new glyphs and modifying existing glyphs as per user needs) is highly preferred. We have started the interview process. Please email your resume ASAP to Navin Elango ([mailto:nelango@dow.com nelango@dow.com]). For more information about Dow AgroSciences, please visit our [http://www.dowagro.com/homepage/index.htm website]
| + | |
− | | + | |
− | Navin Elango
| + | |
− | | + | |
− | ''2010/03/16''
| + | |
− | | + | |
− | == Sr. DB Programmer @ FlyBase ==
| + | |
− | | + | |
− | {{ImageRight|Fly_logo.png|FlyBase Opening|200}}
| + | |
− | | + | |
− | [https://sjobs.brassring.com/1033/asp/tg/cim_jobdetail.asp?partnerID=25240&siteID=5341&AReq=20510BR FlyBase has a single opening for a developer] to join the database team at Harvard University in Cambridge, Mass. The position consists of roles in two model organism database projects, [http://vectorbase.org VectorBase] and [http://flybase.org FlyBase], in the development and maintenance of production applications involving [[Chado]], [[Apollo]], Ensembl, and [[InterMine]]. For more information, see the [https://sjobs.brassring.com/1033/asp/tg/cim_jobdetail.asp?partnerID=25240&siteID=5341&AReq=20510BR job posting].
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− | | + | |
− | Dave Emmert
| + | |
− | | + | |
− | ''2010/03/09''
| + | |
− | | + | |
− | == NGS Analyses in Galaxy ==
| + | |
− | | + | |
− | {{ImageRight|GalaxyLogoSmall.png|NGS Analyses in Galaxy||http://main.g2.bx.psu.edu/u/aun1/p/ngs-analysis-service}}
| + | |
− | The Galaxy team is [http://main.g2.bx.psu.edu/u/aun1/p/ngs-analysis-service announcing the launch of the first free public resource for NGS analysis]. This service is the beginning of our campaign to provide free web-based utilities for [[Next Generation Sequencing|NGS]] analysis and later in the year will take advantage of the Cloud resources. At present, there are three main groups of tools including:
| + | |
− | | + | |
− | # '''NGS QC and manipulation''' - contains a variety of tools for dealing with all flavors of fastq datasets as well as outputs of SOLiD and 454 instruments.
| + | |
− | # '''NGS Mapping''' - currently includes [http://bowtie-bio.sourceforge.net/ Bowtie] (Illumina & SOLiD), [http://bio-bwa.sourceforge.net/ BWA] (Illumina), and [http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.01.50/README.lastz-1.01.50.html LASTZ] (454) mappers. [http://code.google.com/p/perm/ PerM] (SOLiD) is on the way and more will be added in the coming months. Transcriptome tools are also in the final stages of development.
| + | |
− | # '''NGS [http://samtools.sourceforge.net SAMTools]''' - includes a variety of utilities for SAM/BAM manipulation. Some are based on SAMtools library, some are written by [[Galaxy]] team.
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− | | + | |
− | See the [http://main.g2.bx.psu.edu/u/aun1/p/ngs-analysis-service announcement page] for more information and for links to several Galaxy ''Quickies'' (video tutorials) demonstrating the new service.
| + | |
− | | + | |
− | Anton Nekrutenko
| + | |
− | | + | |
− | ''2010/03/08''
| + | |
− | | + | |
− | == Openings @ SGD ==
| + | |
− | | + | |
− | {{ImageRight|SGD-t.gif|Scientific Application Programmers at SGD||http://recruit.trovix.com/jobhostmaster/jobhost/ListJobPosts.do?action=search&searchSectionActive=false&accountId=de85ad313f8598db1c42b567a3df24a00497ba22&searchCategory=1424&searchStatus=226&searchKeywords=Scientific+Application+Programmer}}
| + | |
− | There are [http://recruit.trovix.com/jobhostmaster/jobhost/ListJobPosts.do?action=search&searchSectionActive=false&accountId=de85ad313f8598db1c42b567a3df24a00497ba22&searchCategory=1424&searchStatus=226&searchKeywords=Scientific+Application+Programmer 3 openings for Scientific Application Programmers] at the [http://yeastgenome.org ''Saccharomyces'' Genome Database (SGD)], the model organism database for yeast. These positions will be involved in enhancing databases and data pipelines for the sharing of genomic data. See the [http://recruit.trovix.com/jobhostmaster/jobhost/ListJobPosts.do?action=search&searchSectionActive=false&accountId=de85ad313f8598db1c42b567a3df24a00497ba22&searchCategory=1424&searchStatus=226&searchKeywords=Scientific+Application+Programmer job postings] for more information.
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− | | + | |
− | [[:Category:SGD|SGD]] is both a GMOD contributor (''e.g.'', [[BLAST Graphic Viewer]]) and GMOD user.
| + | |
− | | + | |
− | ''2010/03/05''
| + | |
− | | + | |
− | == Logo Program Deadline Extended ==
| + | |
− | | + | |
− | {{ImageRight|Lbcclogo.jpg|GMOD Logo Program||GMOD Logo Program}}
| + | |
− | '''The first call to participate in the [[GMOD Logo Program]] has been extended to March 19.'''
| + | |
− | | + | |
− | We still have some room for additional participants. If you are interested, please [[GMOD Logo Program|submit an application]]. '''Participation is limited to non-profits, and costs US$75.''' Please see the [[GMOD Logo Program|program page]] for additional details and requirements, and a link to an application form.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2010/03/03''
| + | |
− | | + | |
− | == March 2010 Calendar ==
| + | |
− | | + | |
− | {{ImageLeft|calendar_icon.gif|GMOD Calendar||Calendar}}
| + | |
− | There is always a lot going on that is of interest to the GMOD community. Anything that GMOD staff knows about is added to the GMOD [[Calendar]]. I'm going to start posting the GMOD calendar here for the upcoming month.
| + | |
− | | + | |
− | <div style="margin-right: 26em">
| + | |
− | <embedurl>http://www.google.com/calendar/embed?src=0ajv0bm32ue3c2o2v1c8i889hk%40group.calendar.google.com&showTitle=0&showCalendars=0&height=350&mode=AGENDA&ctz=America/NewYork&dates=20100301%2F20100301</embedurl>
| + | |
− | </div>
| + | |
− | Please [mailto:help@gmod.org let me know] if this is useful, and I'll keep doing it. If not, I'll stop and the GMOD News will be a little less cluttered.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2010/02/22''
| + | |
− | | + | |
− | == GMOD Logo Program, Spring 2010 ==
| + | |
− | | + | |
− | <div style="float: right; text-align: center">
| + | |
− | {{#icon: Gmod_cog170.png|The GMOD Logo||GMOD Logo Program}}<br>
| + | |
− | {{#icon: Lbcclogo.jpg|GMOD Logo Program||GMOD Logo Program}}
| + | |
− | </div>
| + | |
− | I am pleased to announce the first call for participation in the [[GMOD Logo Program]]. This program is for GMOD users and developers that would like a custom designed logo for their web site, database or software. This spring we will be working with students in an advanced design class at [[GMOD Logo Program#Linn-Benton Community College|Linn-Benton Community College]]. Interested GMOD users and developers will be paired with students and meet several times (remotely) over a 3 week period this spring, with the end result being a new logo.
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− | | + | |
− | '''Participation is limited to non-profits, and costs US$75.''' If you are interested, please see the [[GMOD Logo Program|program page]] for additional details and requirements, and an application form. '''The program is accepting applications until March 1.'''
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2010/02/03''
| + | |
− | | + | |
− | == GMOD Summer School - Americas ==
| + | |
− | | + | |
− | We are now [[2010 GMOD Summer School - Americas|accepting applications]] for the [[2010 GMOD Summer School - Americas]]. This will be a hands-on multi-day course aimed at teaching new GMOD administrators how to get [[GMOD Components]] up and running. The course will introduce participants to the GMOD project and then focus on installation, configuration and integration of popular [[GMOD Components]].
| + | |
− | | + | |
− | The course will be held May 6-9, at [http://nescent.org NESCent] in Durham, NC. These [[GMOD Components]] will be covered:
| + | |
− | {|
| + | |
− | | align="center" |
| + | |
− | {{#icon: 2010SummerSchoolAmericas170.png|GMOD Summer School||2010 GMOD Summer School - Americas}}<br>
| + | |
− | <div style="font-size:120%">'''[[2010 GMOD Summer School - Americas|Apply Now]]'''</div>
| + | |
− | |
| + | |
− | |
| + | |
− | * [[Apollo]] - genome annotation editor
| + | |
− | * [[Chado]] - a modular and extensible database schema
| + | |
− | * [[Galaxy]] - workflow system
| + | |
− | * [[GBrowse]] - the Generic Genome Browser
| + | |
− | * [[GBrowse_syn]] - A generic synteny browser
| + | |
− | * [[JBrowse]] - genome browser
| + | |
− | * [[MAKER]] - Genome annotation pipeline
| + | |
− | * [[Tripal]] - Web front end for [[Chado]]
| + | |
− | |}
| + | |
− | '''The deadline for applying is the end of Friday, February 22. Admission is competitive and is based on the strength of the application (especially the statement of interest).''' In 2009 there were over 50 applications for the 25 slots. Any applications received after the deadline will be automatically placed on the waiting list.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | {|
| + | |
− | | valign="top" | PS:
| + | |
− | | We are also investigating holding a GMOD course in the Asia/Pacific region, sometime this fall. Watch the [[GMOD Mailing Lists]] and the [[GMOD News]] for updates.
| + | |
− | |}
| + | |
− | ''2010/01/29''
| + | |
− | | + | |
− | == GMOD @ February NextGenBUG ==
| + | |
− | | + | |
− | {{ImageRight|SBForumLogo.png|NextGenBUG 9 Feb Dundee|140|http://genepool.bio.ed.ac.uk:16080/nextgenbug/meeting/20100209}}
| + | |
− | If you are anywhere close to Dundee, Scotland on 9 February, consider attending the [http://genepool.bio.ed.ac.uk:16080/nextgenbug/meeting/20100209 NextGen Sequencing Bioinformatics User Group (NextGenBUG) meeting] being held at the [http://www.lifesci.dundee.ac.uk/visit University of Dundee]. The program includes two talks with GMOD related content.
| + | |
− | | + | |
− | * '''[http://insectacentral.org InsectaCentral] - assembling and annotating insect transcriptomes''', Alexie Papanicolau, Exeter
| + | |
− | *: [http://insectacentral.org InsectaCentral] uses [[GMOD Components]] (including [[Chado]] and [[GBrowse]]) extensively in its infrastructure.
| + | |
− | | + | |
− | * '''[[Galaxy]]: a stairway to [[Next Generation Sequencing|NGS]] heaven''', Chris Cole, Dundee
| + | |
− | *: Chris will be discussing how Dundee uses [[Galaxy]] to process their [[next generation sequencing]] data.
| + | |
− | | + | |
− | There will also be talks by [[User:DanBolser|Dan Bolser]] of Dundee and Darrol Baker of CLCBio. If you are interested in attending, please [http://genepool.bio.ed.ac.uk:16080/nextgenbug/meeting/20100209 add your name to the participants list].
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2010/01/29
| + | |
− | | + | |
− | == GBrowse 2.0 ==
| + | |
− | | + | |
− | {{ImageRight|GBrowse2Thumb.png|||GBrowse 2.0 HOWTO}}
| + | |
− | With thanks to the many people who have worked long and hard on this project, as well as the people who found and reported bugs during the prerelease stage, I am happy I announce that [[GBrowse 2.0 HOWTO|GBrowse 2.00]] is now available for downloading from [http://search.cpan.org/dist/GBrowse/ CPAN], and [https://sourceforge.net/projects/gmod/files/ SourceForge].
| + | |
− | | + | |
− | The following are highlights of the many new features that have been added since the 1.70 release:
| + | |
− | | + | |
− | * A completely rewritten internal rearchitecture loads tracks asynchronously, providing a more responsive user experience.
| + | |
− | * Different [[GBrowse 2.0 HOWTO#Database Definitions|database backends]] can be associated with each track, making backend management much simpler.
| + | |
− | * A revamped user interface for a less cluttered and more functional end-user experience.
| + | |
− | * A [[GBrowse 2.0 HOWTO#Themes|UI theming system]] with three predefined themes, including a cool "transparent" theme.
| + | |
− | * A custom [[GBrowse 2.0 HOWTO#Configuring the Uploaded Track Database|track upload and management system]] gives users much greater control over custom tracks.
| + | |
− | * An optional [[GBrowse 2.0 HOWTO#The Admin Interface|admin interface]] allows an authorized user to upload and manage public tracks without editing config files.
| + | |
− | * An optional [[GBrowse 2.0 HOWTO#Configuring the User Account Database|user registration and login system]] allows users to register stable GBrowse accounts and to keep their settings and custom tracks when they move from one computer to another.
| + | |
− | * Support for named subtracks (tracks within tracks) and filtering of those subtracks.
| + | |
− | * Support for [[GBrowse NGS Tutorial|next generation sequencing]] data.
| + | |
− | | + | |
− | There are also a number of features that ''didn't'' make it into the 2.00 release, most notably:
| + | |
− | | + | |
− | * The internal [[DAS]] server does not work, although the DAS client (ability to import DAS tracks) does. This will be added in a 2.01 release.
| + | |
− | * Internationalization has lagged way behind, and so most of the new features will be presented in English rather than in the user's preferred language (volunteers are needed to help with translations).
| + | |
− | | + | |
− | Please send help queries to the [https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse GBrowse mailing list], and file [https://sourceforge.net/tracker/?group_id=27707&atid=391291 bug reports at SourceForge].
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− | | + | |
− | On behalf of the GMOD team,
| + | |
− | | + | |
− | [[User:Lstein|Lincoln Stein]]
| + | |
− | | + | |
− | ''2010/01/28''
| + | |
− | | + | |
− | == WebGBrowse 2.0 ==
| + | |
− | | + | |
− | {{ImageRight|cgb_logo.png|WebGBrowse at the Center for Genomics and Bioinformatics||http://webgbrowse.cgb.indiana.edu/}}
| + | |
− | | + | |
− | [http://webgbrowse.cgb.indiana.edu/ WebGBrowse 2.0] is now available at http://webgbrowse.cgb.indiana.edu. Here is some of ''what's new'' in WebGBrowse 2.0:
| + | |
− | * [http://webgbrowse.cgb.indiana.edu/ WebGBrowse 2.0] continues to help the inexperienced users of [[GBrowse]] with hosting their [[GFF3]] data without worrying about installation or configuration semantics.
| + | |
− | * Users now have a choice of [[GBrowse]] display between versions 1.7 and 2.0.
| + | |
− | * The display from one version can be migrated to the other by simple button clicks. This helps the users to compare their data display between the two versions without much hassle. It also helps the WebGBrowse users in upgrading/migrating their existing GBrowse displays to version 2.0 seamlessly.
| + | |
− | * A few bug fixes from the earlier version.
| + | |
− | * For those interested in installing WebGBrowse locally, the current installation package is lot more easier to install and less clumsy than the previous version.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | Ram Podicheti<br />
| + | |
− | [http://cgb.indiana.edu/ Center for Genomics and Bioinformatics<br />Indiana University]
| + | |
− | | + | |
− | ''2010/01/25''
| + | |
− | | + | |
− | == Tripal v0.2 Released ==
| + | |
− | | + | |
− | {{ImageRight|TripalLogo.jpg|Triapl|120|Tripal}}
| + | |
− | I’d like to announce the release of the second version of [[Tripal]], v0.2. This version provides new support for [[Chado CV Module|controlled vocabularies]], [[Chado General Module|databases]] and several [[Chado Companalysis Module|analysis]] types. This includes better support and visualizations for [http://geneontology.org GO], new [http://www.genome.jp/kegg/pathway.html KEGG pathways] and [http://www.genome.jp/kegg/brite.html BRITE hierarchies], [http://www.ebi.ac.uk/Tools/InterProScan/ InterProScan] results and improved BLAST results.
| + | |
− | | + | |
− | [[Tripal]] has been freely and publicly available since May of 2009 and provides a PHP-based [http://drupal.org Drupal] front-end for the [[Chado]] database schema. It his highly customizable and is extendable by anyone with Drupal and PHP experience. We encourage end-users to develop new or improved modules that can be shared back with the community. We can offer assistance when needed in the development of new modules.
| + | |
− | | + | |
− | An updated [[Media:TripalUsersGuideJan2010.pdf|user’s manual]] is available, but not quite complete. An update to the manual will be added soon. If you have any questions please feel free to email the [https://lists.sourceforge.net/lists/listinfo/gmod-tripal Tripal mailing list] for assistance.
| + | |
− | | + | |
− | Tripal can be [http://www.genome.clemson.edu/software/tripal downloaded from the CUGI website] as a compressed package, or developers can retrieve the most up-to-date code from the GMOD [[SVN]].
| + | |
− | | + | |
− | Best Regards,
| + | |
− | | + | |
− | [[User:Sficklin|Stephen Ficklin]]<br />
| + | |
− | [http://www.genome.clemson.edu/ Clemson University Genomics Institute]
| + | |
− | | + | |
− | ''2010/01/23''
| + | |
− | | + | |
− | == CMap3D ==
| + | |
− | | + | |
− | {{ImageRight|CMap3DScreenshot.png|CMap3D|220|CMap3D}}
| + | |
− | [http://acpfg.imb.uq.edu.au/cmap3d.php CMap3D] is a 3D visualisation tool for comparative genetic maps that runs on top of a [[CMap]] database. [[CMap]], a [[GMOD Components|GMOD component]], is a common tool for the storage, comparison and visualisation of genetic maps. However, current map visualisation in CMap is limited to the comparison of adjacent aligned maps. CMap3D overcomes this limitation. Multiple genetic maps can now be compared in three-dimensional space. The CMap3D visualisation tool is based on a client server model ensuring operability with current [[CMap]] data repositories.
| + | |
− | | + | |
− | [[CMap3D]] can be applied to any species where genetic map information is available and enables rapid, direct comparison between multiple aligned maps. For more on [[CMap3D]] see the [http://acpfg.imb.uq.edu.au/cmap3d.php CMap3D page] at the [http://acpfg.imb.uq.edu.au/ Australian Centre for Plant Functional Genomics (ACPFG)], the [[:Image:PAG2010CMap3D.pdf|PAG 2010 presentation on CMap3D]] (and other tools), and the [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/2/273 CMap3D paper] in [http://bioinformatics.oxfordjournals.org/ Bioinformatics].
| + | |
− | | + | |
− | Chris Duran
| + | |
− | | + | |
− | ''2010/01/21''
| + | |
− | | + | |
− | == DAS Workshop 7-9 April 2010 ==
| + | |
− | | + | |
− | {{ImageRight|Das_logo_64x64.jpg|DAS Workshop||http://www.ebi.ac.uk/training/handson/DAS_070410.html}}
| + | |
− | There will be a [http://www.ebi.ac.uk/training/handson/DAS_070410.html Distributed Annotation System (DAS) Workshop] at [http://www.ebi.ac.uk/ EBI], 7-9 April 2010. In GMOD, DAS is supported by [[GBrowse]], and [[Chado]] (and DAS support in [[Apollo]] is in the works).
| + | |
− | | + | |
− | If you don't know about [[DAS]] and wish to know how to distribute your latest biological annotation to the world then the upcoming [http://www.ebi.ac.uk/training/handson/DAS_070410.html DAS workshop] may be for you.
| + | |
− | | + | |
− | If you know about [[DAS]] and are maybe a DAS client developer then the upcoming [http://www.ebi.ac.uk/training/handson/DAS_070410.html DAS workshop] is for you (as you will need to know about the upcoming DAS 1.6 Specification and how it may affect your software).
| + | |
− | | + | |
− | See the [http://www.ebi.ac.uk/training/handson/DAS_070410.html workshop page] for more information and registration details.
| + | |
− | | + | |
− | [[User:JWarren|Jonathan Warren]]
| + | |
− | | + | |
− | ''2010/01/21''
| + | |
− | | + | |
− | | + | |
− | == GBrowse.org ==
| + | |
− | | + | |
− | <div style="float:right; padding: 0em 0.5em; font-size: 110%; border: 3px #d0d0d0 solid; margin-left: 1em; margin-bottom: 1em; padding-bottom: 0.25em">
| + | |
− | {|
| + | |
− | |{{#icon: GBrowseOrgOrig.png|GBrowse.org|80|http://www.gbrowse.org/}}
| + | |
− | |-
| + | |
− | | align="center" | <span class="plainlinks">[http://www.gbrowse.org GBrowse.org]</span>
| + | |
− | |}
| + | |
− | </div>
| + | |
− | | + | |
− | [http://www.gbrowse.org GBrowse.org] is a resource for using and setting up [[GBrowse]] genome browsers. The site provides one location where biologists and bioinformaticians can find:
| + | |
− | | + | |
− | # Genome browser web sites for any organism that has them. If a species has a genome browser anywhere on the web, then we aim to link to it.
| + | |
− | # Links to sequence and annotation files that are available online.
| + | |
− | # Links to genome browser configuration files, when available
| + | |
− | # An FTP site containing genome annotation and configuration files for each annotated genome that does not have its own web site.
| + | |
− | | + | |
− | [http://www.gbrowse.org GBrowse.org] emphasizes the [[GBrowse]] genome browser in its organization, but also links to sites that use other browser packages such as UCSC, Ensembl, and [[JBrowse]].
| + | |
− | | + | |
− | <div class="emphasisbox" style="font-size: 120%; text-align: center">
| + | |
− | Also, we are currently conducting a [http://gbrowse.org/survey/index.php?sid=64264&lang=en survey] seeking input on future project direction. Please take a few minutes now to [http://gbrowse.org/survey/index.php?sid=64264&lang=en provide your feedback].
| + | |
− | </div>
| + | |
− | | + | |
− | GBrowse.org was first introduced at the [[August 2009 GMOD Meeting#GBrowse.org|August 2009 GMOD Meeting]].
| + | |
− | | + | |
− | Ciao,
| + | |
− | | + | |
− | [[User:Bilardi|Alessandra Bilardi]]<br />
| + | |
− | [http://genomics.cribi.unipd.it/Main_Page CRIBI Genomics, University of Padua]
| + | |
− | | + | |
− | ''2010/01/11''
| + | |
− | | + | |
− | == Bio::Chado::Schema 0.05 Released ==
| + | |
− | | + | |
− | I'd like to announce a new [[Bio::Chado::Schema]] release, version 0.05. Changes in this release:
| + | |
− | | + | |
− | * Got POD generation working, now all classes and methods have POD, '''including''' the embedded table and column comments! Thanks to the wonderful DBIx::Class::Schema::Loader folks.
| + | |
− | * Turned off DBIC's cascade_delete and cascade_copy on all relations (thanks to Siddhartha Basu for troubleshooting). Deletes break if these are on and you don't have every part of the schema installed.
| + | |
− | | + | |
− | I [http://search.cpan.org/dist/Bio-Chado-Schema/ uploaded] it to [http://cpan.org CPAN] a week ago, so it should have propagated by now to almost all of the CPAN mirrors.
| + | |
− | | + | |
− | See the [[Bio::Chado::Schema]] wiki page for more on what [[Bio::Chado::Schema]] is and what it's for.
| + | |
− | | + | |
− | [[User:RobertBuels|Rob Buels]]<br>
| + | |
− | [[:Category:SGN|SGN]]
| + | |
− | | + | |
− | ''2010/01/08''
| + | |
− | | + | |
− | == GMOD at PAG 2010 ==
| + | |
− | | + | |
− | GMOD will once again have a strong presence at the [[PAG 2010|Plant and Animal Genome Conference (PAG 2010)]], being held January 9-13 in San Diego. There will be [[PAG 2010|'''over 45 talks, workshops, demonstrations and posters''']] about [[GMOD Components]] and projects that use them. See the [[PAG 2010]] page for a full listing and a flier showing highlights. Highlights at [[PAG 2010]] include:
| + | |
− | {{ImageRight|Paglogo.gif|GMOD @ PAG||PAG 2010}}
| + | |
− | * [http://www.intl-pag.org/18/abstracts/C01_PAGXVIII_913.html Animal Genomics with Galaxy], Saturday
| + | |
− | * [[MAKER PAG 2010 Workshop|MAKER: An easy to use genome annotation pipeline]], Saturday
| + | |
− | * [http://www.intl-pag.org/18/abstracts/W26_PAGXVIII_192.html Database Resources at the EBI] (including [[BioMart]]), Sunday
| + | |
− | * [[GBrowse PAG 2010 Workshop|The Generic Genome Browser: A Hands on Workshop]], Sunday
| + | |
− | * [http://www.intl-pag.org/18/abstracts/P08b_PAGXVIII_858.html GBrowse And Next Generation Sequencing Data], Monday
| + | |
− | * [http://www.intl-pag.org/18/abstracts/C02_PAGXVIII_938.html GMOD Project Update], Monday
| + | |
− | * [http://www.intl-pag.org/18/abstracts/C01_PAGXVIII_919.html Using the JBrowse Genome Browser with Large Amounts of Data], Monday
| + | |
− | * [http://www.intl-pag.org/18/abstracts/P08b_PAGXVIII_859.html Visualizing And Comparing Genomes] ([[CMap]]), Monday
| + | |
− | * [http://www.intl-pag.org/18/abstracts/P08b_PAGXVIII_861.html Comparative Genomics Tools In GMOD], Monday
| + | |
− | * [http://www.intl-pag.org/18/18-gramene.html Using Gramene] (including [[CMap]]), Tuesday
| + | |
− | * [[GBrowse_syn PAG 2010 Workshop|Comparative Genomics with GBrowse_syn]], Wednesday
| + | |
− | * [http://www.intl-pag.org/18/abstracts/C01_PAGXVIII_931.html Tripal: a Construction Toolkit for Online Genomic Databases], Wednesday
| + | |
− | | + | |
− | Many GMOD staff and developers ([[User:Scott|Scott Cain]], [[User:Clements|Dave Clements]], [[User:Sficklin|Stephen Ficklin]], [[User:Carsonholt|Carson Holt]], [[User:Mckays|Sheldon McKay]], Anton Nekrutenko, [[User:MitchSkinner|Mitch Skinner]], Ken Youens-Clark) and even more GMOD users will be at PAG. If you are attending please keep an eye open for us.
| + | |
− | | + | |
− | Finally, the [[January 2010 GMOD Meeting]] is being held immediately after PAG. The meeting is full (you are encouraged to add your name to the short waiting list), but there will be several [[January 2010 GMOD Meeting#Satellite Meetings|Satellite Meetings]], ''held during PAG'', that you can attend even if you don't go to the main GMOD Meeting.
| + | |
− | | + | |
− | See you in San Diego,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2010/01/05''
| + | |
− | | + | |
− | = 2009 Stories =
| + | |
− | | + | |
− | == Galaxy Developer Conference ==
| + | |
− | | + | |
− | {{ImageLeft|GalaxyLogoSmall.png|Galaxy Developer Conference||http://meetings.cshl.edu/meetings/meetingsregistration_galaxy10.asp}}
| + | |
− | {{ImageRight|CSHL Logo75x75.gif|Galaxy Developer Conference||http://meetings.cshl.edu/meetings/meetingsregistration_galaxy10.asp}}
| + | |
− | | + | |
− | The [http://meetings.cshl.edu/meetings/meetingsregistration_galaxy10.asp First Galaxy Developer Conference] will be held at [http://www.cshl.edu/ Cold Spring Harbor Laboratory]
| + | |
− | May 15-17, 2010, immediately after the [http://meetings.cshl.edu/meetings/genome10.shtml Biology of Genomes] conference. [http://meetings.cshl.edu/meetings/meetingsregistration_galaxy10.asp Registration] is now open.
| + | |
− | | + | |
− | This meeting is aimed at developers of analysis tools, bioinformatics staff, and IT managers of sequencing facilities. The meeting will focus on these features of the [[Galaxy]] framework:
| + | |
− | | + | |
− | * tool integration and distributed job management
| + | |
− | * deployment of private Galaxy instances on local resources and on the cloud
| + | |
− | * management of large datasets with the Galaxy Library System
| + | |
− | * using the Galaxy LIMS functionality for managing sample submission at [[Next Generation Sequencing|NGS]] sequencing facilities.
| + | |
− | | + | |
− | Please [http://meetings.cshl.edu/meetings/meetingsregistration_galaxy10.asp register now] if you are interested in using and extending [[Galaxy]].
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/12/28''
| + | |
− | | + | |
− | == Arthropod Genomics Consortium ==
| + | |
− | | + | |
− | {{ImageRight|AGSBug170.png|Arthropod Genomics Consortium|100|http://arthropodgenomes.org}}
| + | |
− | The [http://arthropodgenomes.org Arthropod Genomics Consortium] encourages collaboration and information exchange amongst arthropod researchers. The consortium, launched at the [http://www.k-state.edu/agc/symp2009/ 2009 Arthropod Genomics Symposium], has now started [http://arthropodgenomes.org a wiki] to enable this community to self-organize:
| + | |
− | | + | |
− | : ''Our goal is to provide a central location for information about arthropod genomics projects, bioinformatics tools, and people interested in arthropod genomics. We think this is a great way to "identify the community"; information from the wiki can be used to support white papers and grant proposals. It will also serve as a central location for links to arthropod genomics resources, news releases and meeting announcements.''
| + | |
− | :: [http://www.ksu.edu/biology/faculty_pages/brown.html Sue Brown], Director, [http://www.k-state.edu/agc/ K-State Arthropod Genomics Center]
| + | |
− | | + | |
− | If you are an arthropod researcher, please consider [http://arthropodgenomes.org/wiki/Main_Page#tab=Adding_data_to_this_wiki joining this growing consortium].
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/12/18''
| + | |
− | | + | |
− | == BioPerl Podcast ==
| + | |
− | | + | |
− | {{ImageRight|BioPerl_logo.jpg|BioPerl Podcast|70|http://twit.tv/floss96}}
| + | |
− | | + | |
− | A [http://twit.tv/floss96 podcast on the BioPerl project] is available at [http://twit.tv/FLOSS FLOSS Weekly]. It's about an hour long and it's a good introduction to [[BioPerl]], a set of libraries that many popular [[GMOD Components]] are built upon. The podcast is an interview with BioPerl heavy hitters [[User:Cjfields|Chris Fields]] and [[User:Stajich|Jason Stajich]].
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | ''2009/11/23''
| + | |
− | | + | |
− | == InterMine 0.92 Released ==
| + | |
− | | + | |
− | {{ImageRight|InterMine.png|InterMine Release Notes|180|http://www.intermine.org/wiki/ReleaseNotes}}
| + | |
− | | + | |
− | We have released version 0.92 of [[InterMine]].
| + | |
− | | + | |
− | The main changes are some improvements to the way integration keys and priorities are configured and validated, a BioPax parser, performance enhancements and some webapp fixes.
| + | |
− | | + | |
− | Version 0.92 has [http://www.intermine.org/wiki/ReleaseNotes Release Notes] and [http://www.intermine.org/wiki/UpgradeInterMine upgrade information].
| + | |
− | | + | |
− | Upgrade should be quite straightforward from either 0.9 or 0.91. The
| + | |
− | only issue is compatibility of the GO enrichment widget with old
| + | |
− | databases built before 0.91.
| + | |
− | | + | |
− | [mailto:dev@mail.intermine.org Let us know] if you have problems or suggestions for the next releases.
| + | |
− | | + | |
− | The InterMine team.
| + | |
− | | + | |
− | ''2009/11/23''
| + | |
− | | + | |
− | == CMap Paper in Bioinformatics ==
| + | |
− | | + | |
− | {{ImageRight|BionformaticsCover.gif|Bioinformatics||http://bioinformatics.oxfordjournals.org/cgi/content/full/25/22/3040}}
| + | |
− | | + | |
− | A [http://bioinformatics.oxfordjournals.org/cgi/content/full/25/22/3040 paper] describing the [[CMap]] comparative map viewer is in the [http://bioinformatics.oxfordjournals.org/content/vol25/issue22/index.dtl current issue] of ''[http://bioinformatics.oxfordjournals.org/ Bioinformatics]'':
| + | |
− | | + | |
− | : [http://bioinformatics.oxfordjournals.org/cgi/content/full/25/22/3040 CMap 1.01: a comparative mapping application for the Internet], by Ken Youens-Clark, [[User:Faga|Ben Faga]], Immanuel V. Yap, [[User:Lstein|Lincoln Stein]] and Doreen Ware.
| + | |
− | | + | |
− | [[CMap]] is a web-based tool for displaying and comparing maps of any type and from any species. Users can compare an arbitrary number of maps, view pair-wise comparisons of known correspondences, and search for maps or for features by name, species, type and accession.
| + | |
− | | + | |
− | See the [[CMap|CMap page]] to learn more. CMap will also be covered in the [http://www.intl-pag.org/18/18-gramene.html Gramene workshop] and in a poster at [[PAG 2010]].
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/11/14''
| + | |
− | | + | |
− | == January 2010 GMOD Meeting ==
| + | |
− | | + | |
− | {{ImageRight|Jan2010MtgLogo170.png|January 2010 GMOD Meeting||January 2010 GMOD Meeting}}
| + | |
− | | + | |
− | | + | |
− | <div style="font-size: 140%; text-align: center">[[January 2010 GMOD Meeting|Register for the January 2010 GMOD Meeting]]</div>
| + | |
− | | + | |
− | | + | |
− | I am pleased to announce that the [[January 2010 GMOD Meeting|January GMOD meeting]] will be taking place on January 14 and 15, 2010 in San Diego at the [[January 2010 GMOD Meeting#Lodging|Best Western Seven Seas]]
| + | |
− | (the same location as last year). Please see the [[January 2010 GMOD Meeting|meeting page]] for registration information.
| + | |
− | | + | |
− | Please also take a moment to [[January 2010 GMOD Meeting#Agenda Proposals|add suggestions for the agenda]]. There is no registration fee for this meeting. However, there is limited space, so please register early.
| + | |
− | | + | |
− | The proprietors of the Best Western have given us an excellent room rate, and extended it to the previous week, so that people attending the [[January 2010 GMOD Meeting|GMOD meeting]] and the [[PAG 2010|Plant and Animal Genome meeting]] before it may stay at the Best Western the entire time.
| + | |
− | | + | |
− | Please direct follow up questions to the [https://lists.sourceforge.net/lists/listinfo/gmod-devel gmod-devel mailing list] ([mailto:gmod-devel@lists.sourceforge.net gmod-devel@lists.sourceforge.net]).
| + | |
− | | + | |
− | Thanks and I look forward to seeing you in San Diego!
| + | |
− | | + | |
− | [[User:Scott|Scott]]
| + | |
− | | + | |
− | ''2009/11/13''
| + | |
− | | + | |
− | == Long Term Database Funding ==
| + | |
− | | + | |
− | You may have heard about [http://www.arabidopsis.org/doc/about/tair_funding/410 TAIR's funding situation]. Basically, their funding is being cut by 25% per year, starting in September 2010, and NSF is encouraging them to find alternative funding sources. This news was sent to the TAIR community (and posted on the [http://mailman.tairgroup.org/mailman/listinfo/biocurator Biocurator list]) on October 22. A day later the paper "[http://database.oxfordjournals.org/cgi/content/full/2009/0/bap017 Models for financial sustainability of biological databases and resources]" appeared in ''[http://database.oxfordjournals.org/ Database: The Journal of Biological Databases and Curation]''.
| + | |
− | | + | |
− | All GMOD users need to give at least some thought to long term funding issues. A [http://biocurator.proboards.com/index.cgi?board=fundingissues discussion thread on long term database funding] has now been started on the [http://biocurator.org International Society for Biocuration]'s (ISB) [http://biocurator.proboards.com/ forum site]. | + | |
− | | + | |
− | {{ImageRight|TAIR_logo.gif|TAIR Funding Update and Discussion Forum||http://www.arabidopsis.org/doc/about/tair_funding/410}}
| + | |
− | [http://www.arabidopsis.org/ TAIR] asked people to do a couple things:
| + | |
− | # Cite TAIR in publications: as a reference, as a source of data in methods sections, and under acknowledgments.
| + | |
− | # Contribute to a [http://www.arabidopsis.org/doc/about/tair_funding/410 discussion on the TAIR web site] about
| + | |
− | ## the bioinformatics needs of the ''Arabidopsis'' and wider plant biology communities and
| + | |
− | ## how resources like TAIR should be funded.
| + | |
− | | + | |
− | The [http://www.arabidopsis.org/doc/about/tair_funding/410 discussion at TAIR] is now 19 pages long and contains mountains of praise for TAIR, and a few suggestions on alternative funding, including subscriptions, international and industrial support, and advertising. It also contains many statements that none of those options will work. The ''[http://database.oxfordjournals.org/cgi/content/full/2009/0/bap017 Database]'' paper discusses similar proposals, plus some others.
| + | |
− | | + | |
− | If you are interested in long-term funding issues, I encourage you to participate in the [http://biocurator.proboards.com/index.cgi?board=fundingissues discussion at ISB]. If you use TAIR and want to see it funded, please [http://www.arabidopsis.org/doc/about/tair_funding/410 post a comment at the TAIR web site]. And, if you aren't already doing so, make it easy for your users to cite your database by including an easy to find "Citing this resource" link on your site.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]
| + | |
− | | + | |
− | ''2009/11/06''
| + | |
− | | + | |
− | == Two Openings at Bayer CropScience ==
| + | |
− | {{ImageRight|Logo_BayerCropScience.gif|Open positions at Bayer CropScience||http://www.mybayerjob.com/en}}
| + | |
− | '''1. BioAnalyst Scientist:'''
| + | |
− | | + | |
− | You will provide support in various activities: [[Next Generation Sequencing]] (NGS) data analysis, expression data (microarrays) analysis, genomics and biological networks. The successful applicant should have a PhD or equivalent experience in (plant) genetics and/or genomics. Computer skills are not mandatory but knowledge of bioinformatics applications is required. Excellent communication skills and the ability to support and train researchers with genomics data analysis is essential.
| + | |
− | | + | |
− | More information: [https://mybayerjob.bayerbbs.com/sap(bD1lbiZjPTAwNQ==)/bc/bsp/sap/hrrcf_pinst_pbl/application.do?PARAM=UElOU1RfR1VJRD00QUE2NjQ4RkNFNjUwMDlBRTEwMDgwMDAwQUJGRDkwRQ%3d%3d BioAnalyst Scientist]
| + | |
− | | + | |
− | '''2. BioAnalyst Researcher:'''
| + | |
− | | + | |
− | You will support and foster the data management and analysis of [[Next Generation Sequencing]] (NGS) data (assembly, processing, development of analysis methods, pipelines, etc.). Candidates must be highly motivated to work on biological questions and flexible to interact with the various groups of the research center. They should have a degree (MSc or PhD) in computational biology, boinformatics, statistics or equivalent level of knowledge and possess some programming skills (e.g. [[Glossary#Perl|perl]] and/or python). The candidate should have a good background in (plant) genetics and/or genomics and/or molecular biology.
| + | |
− | | + | |
− | More information: [https://mybayerjob.bayerbbs.com/sap(bD1lbiZjPTAwNQ==)/bc/bsp/sap/hrrcf_pinst_pbl/application.do?PARAM=UElOU1RfR1VJRD00QUI3NUU2MzIzRDcwMTEyRTEwMDgwMDAwQUJGRDkwRQ%3d%3d BioAnalyst Researcher]
| + | |
− | | + | |
− | Operating language in the company is English.
| + | |
− | | + | |
− | '''Interested in any of these positions?''' You can apply [http://www.mybayerjob.com/en here] or send your CV to [mailto:Laurent.viau@bayercropscience.com Laurent Viau]
| + | |
− | | + | |
− | [[User:ErickAntezana|Erick Antezana]]
| + | |
− | | + | |
− | ''2009/11/06''
| + | |
− | | + | |
− | == GBrowse NGS Tutorial & Poster==
| + | |
− | | + | |
− | {{ImageRight|BA2009Logo.png|GBrowse NGS Tutorial|100|GBrowse NGS Tutorial}}
| + | |
− | A tutorial on using [[GBrowse NGS Tutorial|GBrowse 2 to visualize next generation sequencing (NGS) data]] is now available. The [[:Category:Tutorials|tutorial]] walks through how to configure the [[GBrowse]] 2 genome browser to display [[next generation sequencing]] (NGS) data using the [http://samtools.sourceforge.net SAMtools] GBrowse adaptor, Bio::DB::Sam. This tutorial was originally taught at the [[BA2009|Bioinformatics Australia 2009 (BA2009) GMOD Workshop]]. The tutorial includes a [[VMware]] image to work with and step-by-step instructions for visualizing the example human data that comes with the SAMtools package.
| + | |
− | | + | |
− | The tutorial includes examples showing read depth coverage, individual reads - including mismatches, using color to show alignment quality, and read-pairs.
| + | |
− | | + | |
− | A [[:Image:GBrowse_nextgen_poster.pdf|poster]] (by [[User:Scott|Scott Cain]]) demonstrating how to use the adaptor with ''GBrowse 1 and GBrowse 2'' is also available.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/11/04''
| + | |
− | | + | |
− | == Galaxy Project Hiring ==
| + | |
− | | + | |
− | {{ImageRight|GalaxyLogoSmall.png|Galaxy Project Hiring||http://bitbucket.org/galaxy/galaxy-central/wiki/job_rc2}}
| + | |
− | There are several open [http://bitbucket.org/galaxy/galaxy-central/wiki/job_rc2 software engineer and postdoc positions] with the [[Galaxy]] project. Galaxy is looking for engineers with with experience in distributed computing, visualization, and usability. The positions will initially focus on making [[next generation sequencing]] (NGS) data analysis more widely accessible, transparent, and reproducible, as well as development of bioinformatic tools in areas enabled by NGS: re-sequencing, ''de novo'' assembly, metagenomics, transcriptome analysis and epigenetics. Postdoc positions will address biological questions (''e.g.'', mutagenesis and sex chromosome evolution from NGS data) using [[Galaxy]] tools.
| + | |
− | | + | |
− | See the [http://bitbucket.org/galaxy/galaxy-central/wiki/job_rc2 official posting] for full details and contact information.
| + | |
− | | + | |
− | ''2009/11/02''
| + | |
− | | + | |
− | == Visualizing Biological Data Workshop ==
| + | |
− | | + | |
− | {{ImageRight|EMBO_Logo.png|Visualizing Biological Data (VizBi)||http://www.vizbi.org}}
| + | |
− | | + | |
− | The first [http://www.vizbi.org/ EMBO Workshop on Visualizing Biological Data (VizBi)] will be held 3-5 March 2010, at the [http://www.embl.de/training/eicat/atc/index.html EMBL Advanced Training Centre] in Heidelberg, Germany.
| + | |
− | | + | |
− | The goal of the workshop is to bring together researchers developing and using visualization systems across all areas of biology, including genomics, sequence analysis, macromolecular structures, systems biology, and imaging (including microscopy and magnetic resonance imaging). The primary focus will be on visualizing processed and annotated data in their biological context, rather than on processing of raw data.
| + | |
− | | + | |
− | The workshop is limited in the total number participants, and each participant is normally required to present a poster and to give a ''fastforward'' presentation about their work (limited to 30 seconds and 1 slide). To apply to join the workshop, please [http://vizbi.org submit an abstract and image] related to your work. Submissions close on 16 November 2009.
| + | |
− | | + | |
− | ''2009/10/21''
| + | |
− | | + | |
− | == Openings at Syngenta ==
| + | |
− | {{ImageRight|SyngentaLogo.png|Openings at Syngenta||http://www.syngentacareers.com/listing/}}
| + | |
− | There are two openings at [http://www.syngentacareers.com/listing/ Syngenta], recently named one of the top biotechnology employers by [http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2009_10_02/science.opms.r0900079 Science], in Research Triangle Park, NC.
| + | |
− | | + | |
− | [http://careers2.hiredesk.net/viewjobs/JobDetail.asp?Comp=Yoh&sPERS_ID=&TP_ID=1&JB_ID=&PROJ_ID={2258BBC6-9CD1-4991-9F4A-3099220C760D}&LAN=en-US&BackUrl=ViewJobs/Default.asp Genomic Database Specialist (#1435)]: We are currently using the [[Chado]] schema, and this individual will be responsible for maintaining and optimizing database systems for genome annotation and related information. Experience overseeing database systems is required and experience with Oracle and [[PostgreSQL]] is desirable. The ideal candidate will have a solid understanding of genomics and a background in a life sciences setting. Strong competency with Unix and Perl is required.
| + | |
− | | + | |
− | [http://careers2.hiredesk.net/viewjobs/JobDetail.asp?Comp=Yoh&sPERS_ID=&TP_ID=1&JB_ID=&PROJ_ID={D9207D76-4EFC-49B7-B4A5-E0F2988E9DF5}&LAN=en-US&BackUrl=ViewJobs/Default.asp Genome Annotation Specialist (#1434)]: This individual will be responsible for implementing automated annotation pipelines for genome, transcript, and proteins sequences. Advanced knowledge of sequence analysis tools is required. Experience with modern high throughput sequencing analytics is desirable. A strong competency with Unix and scripting in a language such as Perl is required.
| + | |
− | | + | |
− | Both positions will work with Chado and [[GBrowse]], and will help evaluate the adoption of additional GMOD tools. See the links for more details.
| + | |
− | | + | |
− | [[User:Eric.ganko|Eric Ganko]]
| + | |
− | | + | |
− | ''2009/10/21''
| + | |
− | | + | |
− | == Opening at SGD ==
| + | |
− | | + | |
− | There is an [http://recruit.trovix.com/jobhostmaster/jobhost/ViewJobPostDetails.do?action=viewDetails&accountId=de85ad313f8598db1c42b567a3df24a00497ba22&jobId=36125 opening for a Bioinformatics Analyst] at the [http://yeastgenome.org ''Saccharomyces'' Genome Database (SGD)], the model organism database for yeast.
| + | |
− | | + | |
− | {{ImageRight|SGD-t.gif|Bioinformatics Analyst at SGD||http://yeastgenome.org}}
| + | |
− | The position includes interacting with international research laboratories, working with genomic data, evaluating new technologies, analysis via computational methods created by others but integrated at SGD, knowledge of new experimental methodology, large genomic datasets and their computational analysis, and bioinformatic analysis of data types such as RNA transcription and second-generation sequencing. Experience with [[Comparative Genomics|comparative genomics]] is also desirable.
| + | |
− | | + | |
− | SGD is both a GMOD contributor (''e.g.'', [[BLAST Graphic Viewer]]) and GMOD user, and this position will work with the [[GBrowse]] genome viewer as well as other GMOD tools.
| + | |
− | | + | |
− | See the [http://jobs.stanford.edu Stanford jobs site] (search for posting [http://recruit.trovix.com/jobhostmaster/jobhost/ViewJobPostDetails.do?action=viewDetails&accountId=de85ad313f8598db1c42b567a3df24a00497ba22&jobId=36125 36125]) for more.
| + | |
− | | + | |
− | ''2009/10/20''
| + | |
− | | + | |
− | == Apollo 1.11.2 Released ==
| + | |
− | | + | |
− | I've just cut a new [[Apollo]] release that fixes some [[GFF3]] and [[Chado]] writeback issues. As usual, you can get the most current version of Apollo at:
| + | |
− | | + | |
− | : http://apollo.berkeleybop.org/current/
| + | |
− | | + | |
− | Cheers,
| + | |
− | | + | |
− | [[User:Elee|Ed Lee]]
| + | |
− | | + | |
− | ''2009/10/07''
| + | |
− | | + | |
− | == 2009 GMOD Survey Results ==
| + | |
− | | + | |
− | The [[2009 GMOD Community Survey|results of the 2009 GMOD Community Survey]] are now available online. This year's survey focused on genomic and comparative genomics visualization was taken by 45 respondents. The survey includes:
| + | |
− | * [[2009 GMOD Community Survey#Use Cases|Use Cases]] - what people would like visualization software to do.
| + | |
− | * [[2009 GMOD Community Survey#Features|Feature Ranking]] - what features are the most (and least) important to users.
| + | |
− | * Plus general feedback on [[2009 GMOD Community Survey#Other Feedback on Visualization Tools|visualization tools]], [[2009 GMOD Community Survey#Documentation|documentation]], and the [[2009 GMOD Community Survey#Other Feedback|project]].
| + | |
− | | + | |
− | The survey results will be used to improve GMOD and guide its future direction. This year's survey complements the [[2008 GMOD Community Survey]], which covered all of GMOD.
| + | |
− | | + | |
− | {{ImageRight|GMODMug150x150.jpg|GMOD Mug|100|http://www.cafepress.com/GenericMOD/}}
| + | |
− | And, finally, we have our 3 winners of [http://www.cafepress.com/GenericMOD/ GMOD Gear]:
| + | |
− | | + | |
− | * James Estill of the [http://www.genetics.uga.edu/ University of Georgia]
| + | |
− | * Philippe Lamesch of [http://www.arabidopsis.org/ TAIR]
| + | |
− | * Sandra Lövenich of [http://www.imsb.ethz.ch/ ETH Zürich]
| + | |
− | | + | |
− | Thanks to everyone who took the time to participate in the survey.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/10/05''
| + | |
− | | + | |
− | == GMOD Tutorials! GMOD Training! ==
| + | |
− | | + | |
− | {{ImageRight|GMOD2009Europe170.png|Summer School - Europe|120|http://gmod.org/wiki/Training_and_Outreach#Online_Tutorials}}
| + | |
− | {{ImageRight|2009SummerSchoolAmericas170.png|Summer School - Americas|120|http://gmod.org/wiki/Training_and_Outreach#Online_Tutorials}}
| + | |
− | | + | |
− | Detailed and hands-on [[Training and Outreach#Online Tutorials|online tutorials]] are now available for the [[GMOD Components]] that were covered at the [[GMOD Summer School|2009 GMOD Summer Schools]]. Each tutorial includes a [[VMware]] system image to work with, and detailed instructions on how to setup the component on that image.
| + | |
− | | + | |
− | The [[:Category:Tutorials|tutorials]] are:
| + | |
− | * '''[[Apollo Tutorial]]''' - by [[User:Elee|Ed Lee]]
| + | |
− | * '''[[Artemis-Chado Integration Tutorial]]''' - by [[User:RobinHouston|Robin Houston]], [[User:TimCarver|Tim Carver]] and [[User:Buggy|Giles Velarde]]
| + | |
− | * '''[[BioMart Tutorial]]''' - by [[User:Junjun|Junjun Zhang]] and [[User:SyedHaider|Syed Haider]]
| + | |
− | * '''[[Chado Tutorial]]''' - by [[User:Scott|Scott Cain]], [[User:Jorvis|Joshua Orvis]], and [[User:Clements|Dave Clements]]
| + | |
− | * '''[[GBrowse Tutorial]]''' - by [[User:Scott|Scott Cain]] and [[User:Mckays|Sheldon McKay]]'''
| + | |
− | * '''[[GBrowse_syn Tutorial]]''' - by [[User:Mckays|Sheldon McKay]]
| + | |
− | * '''[[JBrowse Tutorial]]''' - by [[User:MitchSkinner|Mitch Skinner]] and Ian Holmes
| + | |
− | * '''[[MAKER Tutorial]]''' - by [[User:Carsonholt|Carson Holt]]
| + | |
− | * '''[[Tripal Tutorial]]''' - by [[User:Sficklin|Stephen Ficklin]]
| + | |
− | | + | |
− | | + | |
− | There is also a plethora of GMOD related [[Training and Outreach|training and outreach]] going on in the next few months. Here's what I know about:
| + | |
− | {| class="wikitable"
| + | |
− | ! Date
| + | |
− | ! Topic
| + | |
− | ! Conference / Location
| + | |
− | |-
| + | |
− | ! October 12-27
| + | |
− | | '''[http://meetings.cshl.edu/courses/c-info09.shtml Programming for Biology]'''<br />This includes a session on [[GBrowse]].
| + | |
− | | [http://www.cshl.edu Cold Spring Harbor Laboratory], Cold Spring Harobr, NY, USA
| + | |
− | |-
| + | |
− | ! October 21-22
| + | |
− | | '''[http://www.ashg.org/2009meeting/pages/workshops.shtml#ucsc Interactive Workshops on the UCSC Genome Browser and Galaxy Framework]
| + | |
− | | [http://www.ashg.org/2009meeting/ The American Society of Human Genetics (AHSG)], Honolulu, Hawaii, USA
| + | |
− | |-
| + | |
− | ! October 27-30
| + | |
− | | '''[[GBrowse]] and [[Next Generation Sequencing]] Data'''
| + | |
− | | [http://meetings.cshl.edu/meetings/info09.shtml Genome Informatics], Cold Spring Harbor, New York, USA
| + | |
− | |-
| + | |
− | ! rowspan="2" | October 28-30
| + | |
− | | '''[[BA2009|Database Tools for Biologists: A Half-Day GMOD Workshop]]'''
| + | |
− | | rowspan="2" | [http://www.ausbiotech2009.com.au/bia/bia-home Bioinformatics Australia 2009 (BA2009)], Melbourne, Australia
| + | |
− | |-
| + | |
− | | '''Visualizing [[Next Generation Sequencing|Next Generation Sequence]] Data with [[GBrowse]] and [http://samtools.sourceforge.net SAMtools]''' (poster)
| + | |
− | |-
| + | |
− | | style="background-color: #cccccc" colspan="3" |
| + | |
− | |-
| + | |
− | ! rowspan="2" | November 16-17
| + | |
− | | '''[http://www.biomed.cam.ac.uk/gradschool/skills/intermine.html InterMine Data Warehouse Workshop]
| + | |
− | | Cambridge, UK
| + | |
− | |-
| + | |
− | | '''Comparative Genomics with GMOD'''
| + | |
− | | [http://colloque.inra.fr/isyip Information Systems for Insect Pests], Rennes, France
| + | |
− | |-
| + | |
− | | style="background-color: #cccccc" colspan="3" |
| + | |
− | |-
| + | |
− | ! rowspan="3" | January 9-13
| + | |
− | | '''[[GBrowse PAG 2010 Workshop|The Generic Genome Browser: A Hands on Workshop for Installing, Configuring and Using Your Own GBrowse]]'''
| + | |
− | | rowspan="3" | [[PAG 2010|Plant and Animal Genome XVII Conference (PAG 2010)]], San Diego, CA, USA<br />See '''[[PAG 2010]]''' for links to many talks and presentations.
| + | |
− | |-
| + | |
− | | '''[[GBrowse_syn PAG 2010 Workshop|Comparative Genomics with GBrowse_syn: A hands on workshop for visualizing your comparative genomics data with GBrowse_syn]]'''
| + | |
− | |-
| + | |
− | | '''[[MAKER PAG 2010 Workshop|MAKER: An easy to use genome annotation pipeline]]'''
| + | |
− | |-
| + | |
− | |}
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/10/02''
| + | |
− | | + | |
− | == modENCODE & Gramene Openings ==
| + | |
− | | + | |
− | The [http://www.modencode.org modENCODE] and [http://www.gramene.org Gramene] projects are both hiring.
| + | |
− | | + | |
− | <span style="font-size:120%">'''modENCODE'''</span>
| + | |
− | | + | |
− | {{ImageRight|ModENCODE logo.png|modENCODE Project Openings||http://blog.modencode.org/}}
| + | |
− | [http://www.modencode.org modENCODE] is [http://blog.modencode.org/?p=350 looking for a few consultants]. The project's aim is to discover and explore the genomes of ''C. elegans'' and ''D. melanogaster'', using new scientific strategies and new technologies for discovery.
| + | |
− | | + | |
− | Consultants will be responsible for interacting with several external research labs, as well as with internal software developers, to collect and collate experimental data
| + | |
− | of many different types. In addition to a strong background in biology, candidates must be knowledgeable in programming and/or software development. Candidates must also possess verbal and written communication skills, particularly for understanding requirements from biologists, and to productively work in a collaborative environment.
| + | |
− | | + | |
− | Please see the [http://blog.modencode.org/?p=350 complete job description] for details.
| + | |
− | | + | |
− | [http://www.modencode.org modENCODE] is a power GMOD user. The project uses [[GBrowse]], [[Chado]], [[InterMine]], [[JBrowse]], and [[GBrowse_syn]]. (See [[January 2009 GMOD Meeting#modENCODE: extending Chado, BIR-TAB, & GBrowse for automating data validation & display|Nicole Washington's talk]] at the [[January 2009 GMOD Meeting]] for some details on how they are used.)
| + | |
− | | + | |
− | | + | |
− | <span style="font-size: 120%">'''Gramene'''</span>
| + | |
− | | + | |
− | {{ImageRight|Gramene_logo180.jpg|Grameene Project Opening||http://news.gramene.org/}}
| + | |
− | | + | |
− | [http://www.gramene.org Gramene] has [http://news.gramene.org/?p=392 several bioinformatics openings] in the [http://www.science.oregonstate.edu/bpp/faculty/jaiswal/ Jaiswal lab] at Oregon State University.
| + | |
− | | + | |
− | The positions involve development and maintenance of the databases, software and analysis pipelines necessary for development of the Plant Gene Expression, biochemical and regulatory pathway networks, comparative genomics, text mining ([[Textpresso]]) and biological ontology projects. Gramene is a long-time GMOD user and is the home of the [[CMap]] comparative map viewer.
| + | |
− | | + | |
− | See [http://news.gramene.org/?p=392 the position announcement] for full details.
| + | |
− | | + | |
− | ''2009/10/02''
| + | |
− | | + | |
− | == GMOD @ Bioinformatics Australia ==
| + | |
− | | + | |
− | {{ImageRight|BA2009Logo.png|GMOD workshop at Bioinformatics Australia||BA2009}}
| + | |
− | There will be a half-day [[BA2009|pre-conference GMOD workshop]] on 28 October, 2009, at [http://www.ausbiotech2009.com.au/bia/bia-home Bioinformatics Australia (BA2009)]. The workshop will introduce [[GMOD Components]] for [[visualization]], [[annotation]], and data management, and the GMOD project as a whole. The workshop will also include a [[GBrowse]] demonstration with a worked example that includes [[next generation sequencing]] data.
| + | |
− | | + | |
− | Thanks to sponsorship from [http://www.bioplatforms.com/ Bioplatforms Australia] admission to the workshop is included in the conference registration fee.
| + | |
− | | + | |
− | Please see the [[BA2009|workshop page]] or [mailto:help@gmod.org contact the GMOD Help Desk] for more information.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/10/01''
| + | |
− | | + | |
− | == InterMine Data Warehouse Workshop ==
| + | |
− | | + | |
− | {{ImageRight|InterMine.png|InterMine Workshop|180|http://www.biomed.cam.ac.uk/gradschool/skills/intermine.html}}
| + | |
− | | + | |
− | We are running another [http://www.biomed.cam.ac.uk/gradschool/skills/intermine.html InterMine workshop] in Cambridge, UK on November 16th-17th.
| + | |
− | | + | |
− | This is intended for software developers to learn the [[InterMine]] system. The two day course will step through creating a new Mine, integrating real data and deploying and customising the web application.
| + | |
− | | + | |
− | The course is free to attend, more details and sign up information
| + | |
− | are available on the [http://www.biomed.cam.ac.uk/gradschool/skills/intermine.html workshop page].
| + | |
− | | + | |
− | Please get in touch if you have any questions.
| + | |
− | | + | |
− | Regards,
| + | |
− | | + | |
− | [mailto:richard@flymine.org Richard Smith]
| + | |
− | | + | |
− | ''2009/09/29''
| + | |
− | | + | |
− | == Tripal: A Web Front End for Chado ==
| + | |
− | | + | |
− | {{ImageRight|TripalLogo.jpg|Tripal|200|Tripal}}
| + | |
− | [[Tripal]] is a new web front end for [[Chado]] databases and is now a part of GMOD. Tripal is a collection of [http://www.drupal.org Drupal] modules initially developed by the [http://www.genome.clemson.edu/ Clemson University Genomics Institute (CUGI)]. Tripal is already powering several web sites, including the [http://www.marinegenomics.org Marine Genomics Project] and [http://www.fagaceae.org/ Fagaceae Genomics Web].
| + | |
− | | + | |
− | Tripal supports Drupal themes, page content and look and feel customization, materialized views, searching, and job management out of the box.
| + | |
− | | + | |
− | Tripal can be downloaded from the GMOD [[SVN]] repository. Tripal (already!) has an extensive [[Media:TripalUsersGuideJune2009.pdf|User's Guide]] and a [[Tripal Tutorial|tutorial]] to help users install, configure and extend Tripal.
| + | |
− | | + | |
− | If you use or are considering using [[Chado]], please take a look at [[Tripal]].
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/09/28''
| + | |
− | | + | |
− | == Reactome User Survey ==
| + | |
− | | + | |
− | Reactome is committed to providing access to high-quality pathway information and helpful data analysis tools. With this in mind, we are actively soliciting comments from the research community in order to assess community needs. We are interested to hear about your experience with Reactome, and would like to know a bit about your background and research interests so that we can continue to improve the Reactome site and tools.
| + | |
− | | + | |
− | You can access the survey at [http://www.surveymonkey.com/s.aspx?sm=Ph5q56zmGkqVabn9QNfemw_3d_3d SurveyMonkey]
| + | |
− | | + | |
− | Thank you for taking part.
| + | |
− | | + | |
− | Robin Haw
| + | |
− | Manager of Reactome Outreach
| + | |
− | Outreach [at] reactome.org
| + | |
− | http://www.reactome.org
| + | |
− | | + | |
− | Posted by [[User:Scott|Scott Cain]]
| + | |
− | | + | |
− | ''2009/09/28''
| + | |
− | | + | |
− | == DIYA: Do It Yourself Annotator ==
| + | |
− | | + | |
− | {{ImageRight|DIYALogo.png|DIYA|100|DIYA}}
| + | |
− | [[DIYA]], the ''Do It Yourself Annotator'' is now officially a part of GMOD. DIYA is a modular and configurable open source pipeline framework, written in Perl, used (initially) for the rapid [[annotation]] of microbial genome sequences. The software is currently used to take nucleotide sequence contigs as input, either in the form of complete genomes or the result of shotgun sequencing, and produce an annotated sequence in [[GFF]] format. Current development seeks to integrate DIYA with the [http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS AMOS] collection of assembly tools.
| + | |
− | | + | |
− | DIYA [http://sourceforge.net/projects/diyg/ resides in Sourceforge], where it has [http://sourceforge.net/mail/?group_id=205628 mailing lists] and a [http://sourceforge.net/apps/wordpress/diyg/ blog], and uses [http://sourceforge.net/apps/trac/diyg/ Trac] for development tracking. DIYA is stable and version 1.0 has been released.
| + | |
− | | + | |
− | DIYA is part of the ''[http://sourceforge.net/projects/diyg/ Do It Yourself Genomics (DIYG) Project]''. Developers of DIYA (and DIYG) include Andrew Stewart and [[User:Bosborne|Brian Osborne]] (formerly of the [[GMOD Help Desk]]). The DIYA community is looking for interested developers to contribute to DIYA. See the [[DIYA]] page for more.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/09/23''
| + | |
− | | + | |
− | == Chado in RDF: OpenFlyData ==
| + | |
− | | + | |
− | {{ImageRight|RDF_icon_96.gif|RDF||http://gmod.org/wiki/August_2009_GMOD_Meeting#Linked_Data_for_GMOD_Databases}}
| + | |
− | | + | |
− | The [[August 2009 GMOD Meeting#Linked Data for GMOD Databases|OpenFlyData project has ported the FlyBase Chado database]] and several other ''Drosophila'' gene expression databases to the [http://www.w3.org/RDF/ Resource Description Framework (RDF)]. Each source database has a separate [http://en.wikipedia.org/wiki/Triplestore RDF store], and [http://openflydata.org/ OpenFlyData] provides both a browser and a programmatic [http://www.w3.org/TR/rdf-sparql-query/ SPARQL-based] interface to each. Source databases include the [[Chado]] database from [[:Category:FlyBase|FlyBase]], [http://www.fruitfly.org/ BDGP], [http://www.flyatlas.org/ FlyAtlas] and [http://www.fly-ted.org/ FlyTED].
| + | |
− | | + | |
− | Transforming databases into RDF can be an effective way to merge these data, and does not require mapping everything to a central [[Glossary#RDBMS|relational]] [[Glossary#Schema|schema]]. The common graph-based data model facilitates the reuse of RDF data published by other projects, with fewer constraints on the kind of questions you can ask.
| + | |
− | | + | |
− | For more on [http://openflydata.org/OpenFlyData OpenFlyData], see the [[August 2009 GMOD Meeting#Linked Data for GMOD Databases|''Linked Data for GMOD Databases'']] presentation from the [[August 2009 GMOD Meeting]], and the [http://openflydata.org OpenFlyData web site].
| + | |
− | | + | |
− | [[User:JunZhao|Jun Zhou]] and [[User:Clements|Dave Clements]]
| + | |
− | | + | |
− | ''2009/09/23''
| + | |
− | | + | |
− | == Bioinformatics Position at SpBase ==
| + | |
− | | + | |
− | {{ImageRight|SpBaseLogo.png|Position at SpBase||http://www2.recruitingcenter.net/clients/CalTech/publicjobs/controller.cfm?jbaction=JobProfile&Job_Id=15519&esid=az}}
| + | |
− | | + | |
− | The [http://www.spbase.org Sea Urchin Model Organism database (SpBase)] has an opening for a Bioinformatician. From the [http://www2.recruitingcenter.net/clients/CalTech/publicjobs/controller.cfm?jbaction=JobProfile&Job_Id=15519&esid=az position announcement]:
| + | |
− | <div class="indent">The computation group supporting the Sea Urchin Model Organism database, SpBase, is seeking a highly motivated individual to take responsibility for collecting, organizing and displaying gene expression information at all life stages of the purple sea urchin ''Strongylocentrotus purpuratus''. The individual will work with existing computer code as well as develop new software. A particular challenge of the project is to move data from various sourves and of various types to a common framework for presentation and manipulation by the user.</div>
| + | |
− | | + | |
− | See the [http://www2.recruitingcenter.net/clients/CalTech/publicjobs/controller.cfm?jbaction=JobProfile&Job_Id=15519&esid=az job posting] for more on the position. Please contact [mailto:acameron@caltech.edu Andy Cameron] if you have questions about the position.
| + | |
− | | + | |
− | SpBase uses several [[GMOD Components]], including [[GBrowse]], [[Apollo]], [[BioMart]], and [[Chado]].
| + | |
− | | + | |
− | [[User:Clements|Dave C.]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/09/22''
| + | |
− | | + | |
− | == 2009 GMOD Community Survey ==
| + | |
− | <div style="float:right">
| + | |
− | {|
| + | |
− | | {{#icon: GMODMug150x150.jpg|GMOD Mug|100|}}
| + | |
− | | {{#icon: TShirtThumb.jpg|GMOD T Shirt||}}
| + | |
− | |}
| + | |
− | </div>
| + | |
− | Please take a few minutes to fill out the [http://survey.oit.duke.edu/ViewsFlash/servlet/viewsflash?cmd=page&pollid=NESCent!GMODUserSurvey2009 2009 GMOD Community Survey] and your name will be entered to win a free GMOD T-shirt or mug! This year's survey focuses on genome and comparative genomics visualization (and is much shorter than the [[2008 GMOD Community Survey|2008 survey]]). We are asking all GMOD users and developers to provide your feedback.
| + | |
− | | + | |
− | '''Three randomly selected survey participants will receive the [http://www.cafepress.com/GenericMOD/ GMOD T-shirt or mug] of their choice. Names will be drawn from the first 100 responses, so get your response in early.''' The survey closes at the end of the day on September 25.
| + | |
− | | + | |
− | Please contact the [mailto:help@gmod.org GMOD Help Desk] if you have any questions.
| + | |
− | | + | |
− | Thank you,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br>
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/09/16''
| + | |
− | | + | |
− | == CVS to SVN Conversion: Done ==
| + | |
− | <div style="float: right">
| + | |
− | {|
| + | |
− | | {{#icon: Cvs_logo.gif|CVS|70|CVS to Subversion Conversion}}
| + | |
− | | <span style="font-size: 200%; font-weight: bold">⇒</span>
| + | |
− | | {{#icon: Subversion_logo.jpg|Subversion||CVS to Subversion Conversion}}
| + | |
− | |}
| + | |
− | </div>
| + | |
− | GMOD's CVS source code repository was [[CVS to Subversion Conversion|converted to Subversion (SVN)]] on September 15, 2009. Directions on how to use [[SVN]] are explained at [[Version Control System Access]]. Details of the conversion itself are at [[CVS to Subversion Conversion]].
| + | |
− | | + | |
− | Inactive projects were moved out of the main directory and placed in the <tt>{{SF_SVN|Inactive|Inactive}}</tt> directory. The CVS repository is still there and accessible, but it is now ''read-only''. The GMOD web site has been updated to reflect the move to [[Subversion]].
| + | |
− | | + | |
− | We have identified a few outstanding issues and these are [[CVS to Subversion Conversion#Outstanding Issues|listed on the conversion page]]. If you come across any additional issues, please either update [[CVS to Subversion Conversion#Outstanding Issues|that list]] or [mailto:help@gmod.org email] the [[GMOD Help Desk]].
| + | |
− | | + | |
− | Finally, ''many'' thanks to [[User:RobertBuels|Rob Buels]] of Cornell / [[:Category:SGN|SGN]] for doing the work.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]
| + | |
− | | + | |
− | ''2009/09/15''
| + | |
− | | + | |
− | == FlyBase Bioinformatics Engineer ==
| + | |
− | | + | |
− | {{ImageRight|Fly_logo.png|FlyBase Opening|200}}
| + | |
− | | + | |
− | Please see the [http://flybase.org/static_pages/news/positions.html official advert] for full details and application procedure.
| + | |
− | | + | |
− | The [http://iub.edu Indiana University] division of [http://flybase.org FlyBase] in [http://en.wikipedia.org/wiki/Bloomington,_Indiana Bloomington, Indiana] is currently looking for a qualified software engineer to help with deploying the [http://intermine.org InterMine] and [http://biomart.org BioMart] data management systems. The developer will be responsible for the web accessible aspect of these technologies. This includes the initial setup and configuration of these two systems, setting up and automating update cycles in sync with the existing FlyBase release cycle, evaluating the capabilities of each, aiding in the integration of these services with existing FlyBase reports and tools, and coordinating these efforts with other model organism databases (MODs). Loading and preprocessing of data for these systems will be performed at the Harvard University FlyBase site so close coordination with developers there will also be required.
| + | |
− | | + | |
− | [[User:Jogoodma|Josh Goodman]]
| + | |
− | | + | |
− | ''2009/09/14''
| + | |
− | | + | |
− | == Server Maintenance: Sept 9 ==
| + | |
− | | + | |
− | <span style="float: left">{{#icon: WorkInProgressTools.gif|||}} </span>
| + | |
− | The [[Main Page|GMOD website]] and server will be down for maintenance on Wednesday, September 9, 2009 for up to 90 minutes, sometime between 1pm and 5pm Eastern US time. The server is being moved to a new a data center. We apologize for any inconvenience this may cause you.
| + | |
− | | + | |
− | Please let us know if you have any questions.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]
| + | |
− | <br />[[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/09/08''
| + | |
− | | + | |
− | == BioMart Ruby API ==
| + | |
− | {{ImageRight|Biomart250.png|BioMart Ruby API|200|http://github.com/dazoakley/biomart/}}
| + | |
− | | + | |
− | Daz Oakley of the Wellcome Trust Sanger Institute has released a [http://github.com/dazoakley/biomart/ Ruby library/API] for [[BioMart]]. Daz says "It's quite basic for the moment and only does single dataset queries, but it will be quite easy to build upon the base from here."
| + | |
− | | + | |
− | The source is [http://github.com/dazoakley/biomart available from GitHub], and the documentation is at [http://rdoc.info/projects/dazoakley/biomart rdoc.info].
| + | |
− | | + | |
− | The Ruby API is the latest addition to a growing list of third party software that supports [[BioMart]]. This list includes [[Galaxy]], [http://www.bioclipse.net/ Bioclipse], [http://bioconductor.org/packages/release/bioc/html/biomaRt.html biomaRt-BioConductor], [http://www.cytoscape.org/ Cytoscape], [http://www.mygrid.org.uk/ Taverna], and
| + | |
− | [http://weblab.cbi.pku.edu.cn/ WebLab]
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]
| + | |
− | <br />[[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/09/08''
| + | |
− | | + | |
− | == JBrowse paper ==
| + | |
− | A [http://genome.cshlp.org/content/19/9/1630.full paper] on the [[JBrowse]] genome browser is in [http://genome.cshlp.org/content/19/9 this month's issue] of [http://genome.cshlp.org/ Genome Research]. If you haven't looked at [[JBrowse]] before, ''it feels both very familiar and radically different at the same time.''
| + | |
− | | + | |
− | JBrowse is a Web 2.0 genome browser that features:
| + | |
− | * Client side rendering, and very fast rendering at that.
| + | |
− | * As a consequence it has very low server disk space, server CPU, security and network bandwidth requirements.
| + | |
− | * An interface that is entirely [[Glossary#AJAX|AJAX]] based. ''Everything'' is done with AJAX.
| + | |
− | * [[GFF3]], [[Chado]] and/or [https://cgwb.nci.nih.gov/goldenPath/help/wiggle.html Wiggle track] compatibility
| + | |
− | * [[Glossary#JSON|JSON]] based configuration files (very similar to GBrowse config files in their content)
| + | |
− | * Easy embedding in other web applications (an example of embedding a genome browser in a wiki is provided)
| + | |
− | | + | |
− | JBrowse features smooth panning, zooming, navigation, and track selection and sets a new standard for the genome browser interface.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]
| + | |
− | <br />[[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/09/01''
| + | |
− | | + | |
− | == Aug 2009 GMOD Meeting Report ==
| + | |
− | | + | |
− | {{ImageRight|Aug2009MeetingPhoto.JPG|August 2009 GMOD Meeting||August 2009 GMOD Meeting}}
| + | |
− | The [[August 2009 GMOD Meeting]] was held 6-7 August, 2009 in Oxford, UK, immediately following the [[2009 GMOD Summer School - Europe]]. It was the first [[Meetings|GMOD meeting]] outside North America and it was an excellent way to finish [[GMOD Europe 2009]]. The meeting was attended by ~45 people representing almost 30 different organizations. The meeting report and links to presentations are now available on the [[August 2009 GMOD Meeting]] page. There were [[August 2009 GMOD Meeting#Presentations|17 presentations]] by GMOD users, developers, and project staff.
| + | |
− | | + | |
− | Some highlights:
| + | |
− | * [[August 2009 GMOD Meeting#Quest for Standard: Sequence alignment/map format (SAM) and SAMtools|SAM and SAMtools]]: file formats and programs for compact representation of [[Next Generation Sequencing]] data, and a talk on [[August 2009 GMOD Meeting#Visualising NGS Data in GBrowse 2|using SAM/SAMtools in GBrowse]].
| + | |
− | * An [[August 2009 GMOD Meeting#Linked Data for GMOD Databases|RDF implementation]] of data from a Chado database.
| + | |
− | * Reports from 2 power GBrowse users, [[August 2009 GMOD Meeting#GMOD in the Trenches|the CBRG at Oxford]], and [[August 2009 GMOD Meeting#GBrowse: Lessons Learned and Statement of Interest|Bayer CropScience]]
| + | |
− | * New [[August 2009 GMOD Meeting#A DBIx::Class layer for Chado|Perl]] and [[August 2009 GMOD Meeting#GMOD Biological Object Layer|Java]] [[:Category:Middleware|middleware]] packages for [[Chado]].
| + | |
− | Plus many other excellent presentations on topics ranging from [[August 2009 GMOD Meeting#DAS update|DAS]] to [[August 2009 GMOD Meeting#GBrowse.org|GBrowse.org]].
| + | |
− | | + | |
− | Please take a look at the [[August 2009 GMOD Meeting|meeting report]] for an update on what's going on in the GMOD community.
| + | |
− | | + | |
− | Finally, I'd like to thank the [http://www.molbiol.ox.ac.uk/ Computational Biology Research Group (CBRG) at the University of Oxford] for hosting and financially supporting [[GMOD Europe 2009]]. We could not have done this without you.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]
| + | |
− | <br />[[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/08/29''
| + | |
− | | + | |
− | == Bio::Chado::Schema 0.03 Released ==
| + | |
− | The first official release of [[Bio::Chado::Schema]] is now on the [http://search.cpan.org/~rbuels/Bio-Chado-Schema/ CPAN]. This project establishes a standard set of base modules for building Chado middleware in Perl. The project is looking for development help, and discussion is on the [https://lists.sourceforge.net/lists/listinfo/gmod-schema GMOD Schema mailing list].
| + | |
− | | + | |
− | --[[User:RobertBuels|RobertBuels]] 22:10, 29 August 2009 (UTC)
| + | |
− | | + | |
− | ''2009/08/29''
| + | |
− | | + | |
− | == InterMine 0.91 Released ==
| + | |
− | {{ImageRight|InterMine.png|InterMine|200|InterMine}}
| + | |
− | We've released [[InterMine]] 0.91 and there is a new subversion branch and tar.gz for download. The main changes are fixes to some [http://www.intermine.org/wiki/GettingStartedAdvanced QueryBuilder] features, occasional export issues and improved password security. There is a new [http://www.treefam.org/ TreeFam] parser and an improvement to ontology querying.
| + | |
− | | + | |
− | This update shouldn't require any changes to Mines and sources you have created. See [http://www.intermine.org/wiki/UpgradeInterMine details on upgrading] and the [http://www.intermine.org/wiki/ReleaseNotes release notes].
| + | |
− | | + | |
− | Please [mailto:dev@intermine.org let us know] if you have any bug reports or feature requests.
| + | |
− | | + | |
− | The [[InterMine]] team
| + | |
− | | + | |
− | ''2009/08/27''
| + | |
− | | + | |
− | == CVS to SVN Conversion: Sept 15 ==
| + | |
− | <div style="float: right">
| + | |
− | {|
| + | |
− | | {{#icon: Cvs_logo.gif|CVS|70|CVS to Subversion Conversion}}
| + | |
− | | <span style="font-size: 200%; font-weight: bold">⇒</span>
| + | |
− | | {{#icon: Subversion_logo.jpg|Subversion||CVS to Subversion Conversion}}
| + | |
− | |}
| + | |
− | </div>
| + | |
− | GMOD's CVS source code repository will be [[CVS to Subversion Conversion|converted to Subversion (SVN)]] on September 15, 2009. [[User:RobertBuels|Rob Buels]] of Cornell / [[:Category:SGN|SGN]] has generously offered to to do this. Notes on the conversion are described on the [[CVS to Subversion Conversion]] page. The discussion leading up to this decision on the [http://comments.gmane.org/gmane.science.biology.gmod.devel/364 GMOD Developers mailing list].
| + | |
− | | + | |
− | '''If you are not a GMOD developer then this will, at most, change how you get pre-release copies of GMOD components.''' In the future you will do SVN checkouts instead of CVS checkouts. The doc on this web site will be updated to describe how to do this.
| + | |
− | | + | |
− | <div class="emphasisbox">
| + | |
− | '''If you are a GMOD developer and your project is in GMOD's [http://gmod.cvs.sourceforge.net/gmod/ CVS repository] then this move will significantly affect you.'''
| + | |
− | </div>
| + | |
− | | + | |
− | See [http://gmod.cvs.sourceforge.net/gmod/ SourceForge] for a complete list of projects in GMOD CVS. This list is reproduced on the [[CVS to Subversion Conversion]] page. Between now and September 15, we will contact project developers to confirm what projects are still active. All projects will be moved to SVN, but any projects that are no longer active will be placed in a separate archive directory. This will significantly clean up the repository. See the [[CVS to Subversion Conversion]] page for the current status of each project.
| + | |
− | | + | |
− | Rob has created a [http://bugs.sgn.cornell.edu/trac/gmod_test_svn/browser/ preview version of the repository]. Feel free to poke around. This version does not have any projects archived.
| + | |
− | | + | |
− | Rob will move the projects on September 15. '''Before then everyone with uncommitted code changes should commit them to CVS.''' After September 15, all CVS checkouts you have should be removed and new checkouts made with SVN. We'll provide doc on how to do this. We will send out exact details on the move a few days before it happens.
| + | |
− | | + | |
− | | + | |
− | Please let Rob and Dave know if you have any questions. We'll send out a reminder and additional info a few days before the conversion.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]] and [[User:RobertBuels|Rob Buels]]
| + | |
− | | + | |
− | ''2009/08/26''
| + | |
− | | + | |
− | == GBrowse 1.70 Released ==
| + | |
− | | + | |
− | Hello,
| + | |
− | | + | |
− | I am pleased to announce the official release of [[GBrowse]] 1.70. This is a bug fix release for GBrowse 1.69. It introduces no new functionality to the GBrowse portion of the application, however, [[GBrowse_syn]] is considerably improved along with [[GBrowse_syn|documentation]] and a [[GBrowse_syn Tutorial|tutorial]].
| + | |
− | | + | |
− | There will likely be one more release in the GBrowse 1 development path, which will introduce improved support for circular genomes. After that, development on this path will end and further development will focus on [[:Category:GBrowse 2|GBrowse 2]].
| + | |
− | | + | |
− | GBrowse can be installed with the [[GBrowse Install HOWTO|GBrowse netinstaller]].
| + | |
− | | + | |
− | GBrowse 1.70 can be [http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/GBrowse-1.70/Generic-Genome-Browser-1.70.tar.gz/download downloaded directly from SourceForge].
| + | |
− | | + | |
− | A big thanks to [[User:Lstein|Lincoln Stein]], the lead developer of GBrowse, [[User:Mckays|Sheldon McKay]], the developer of GBrowse_syn, and all of the GBrowse users who debug and provide help on the [[GMOD Mailing Lists|GBrowse mailing list]].
| + | |
− | | + | |
− | Changes from 1.69 to 1.70:
| + | |
− | * Bug fixes for the Chado adapter, including improving wildcard searching and fixing a bug that caused ALL features on a reference sequence to be returned when the segment was at the beginning of the reference sequence.
| + | |
− | * Fixed [[Galaxy]] support bug which caused prevented features from multiple tracks being selected.
| + | |
− | * Fixed problem with feature highlighting which caused highlighting to get "stuck"on beige.
| + | |
− | * Removed annoying debugging statements from log files
| + | |
− | * Fixed character encoding issues for onClick popup balloons
| + | |
− | * Killed annoying "missing path" warning on windows systems
| + | |
− | * Fixed issue in which the selected region shown in the overview is offset from true region.
| + | |
− | * Silenced log file warnings when inkscape isn't present.
| + | |
− | * Added "merge searches" option to turn merging of similarly-named features on and off.
| + | |
− | * Moved Bio::DB::Das::Chado and Bio::DB::BioSQL to their own packages and out of the GBrowse distribution so they can be updated independently via CPAN
| + | |
− | * Fixed encoding of version number at the bottom of the page.
| + | |
− | * Made the [[DAS]] script compatible with DAS Registry
| + | |
− | | + | |
− | [[User:Scott|Scott]]
| + | |
− | | + | |
− | ''2009/08/24''
| + | |
− | == Lepidoptera Bioinformatics ==
| + | |
− | | + | |
− | {{ImageRight|Butterfly1.jpg|International Workshop on Molecular Biology and Genetics of Lepidoptera||http://bio.demokritos.gr/leps/leps.htm}}
| + | |
− | A session on data analysis, mining, general bioinformatics support, and related topics will be held on Friday, August 28th 2009, at the [http://bio.demokritos.gr/leps/leps.htm International Workshop on Molecular Biology and Genetics of Lepidoptera] in Crete. The aim is to find solutions to common problems of annotation, curation and comparative analysis of the growing body of transcript and genomic sequences for lepidopteran species. Several databases, including [http://insectacentral.org InsectaCentral] and [http://www.inra.fr/lepidodb LepidoDB], both of which use [[GMOD Components]], will be discussed in the workshop.
| + | |
− | | + | |
− | The session is held during the last conference day and is one hour long; we encourage Crete participants to talk to us during the week and point out related problems you are facing in your own work. We will then produce a list to be discussed during the session and focus on soliciting ideas on how to organize collaborative and centralized efforts to everyone's benefit. We would especially like to identify potential funding sources, groups willing to help write consultation papers and grant proposals and individuals willing to contribute to realistic solutions.
| + | |
− | | + | |
− | We would like to encourage those of you who are not planning to attend the Crete workshop to contact us with your thoughts and ideas on these and related subjects.
| + | |
− | | + | |
− | [mailto:mki101@uri.edu Marian Goldsmith], [mailto:a.papanicolaou@ex.ac.uk Alexie Papanicolaou], and [mailto:flegeai@rennes.inra.fr Fabrice Legeai].
| + | |
− | | + | |
− | ''2009/08/18''
| + | |
− | | + | |
− | == Ant Genomics Bioinformatician ==
| + | |
− | {{ImageRight|sib_logo.gif|Fourmidable opening||http://www.isb-sib.ch/about-sib/jobs/details/91-sib-bioinformatician-at-sib--unil.html}}
| + | |
− | ''The deadline for this position has now passed.''
| + | |
− | | + | |
− | The [http://www.isb-sib.ch/ Swiss Institute of Bioinformatics] and the [http://www.unil.ch/dee/page6763.html Keller lab] in Lausanne have an opening for a full-time bioinformatician.
| + | |
− | In brief, this position will focus on the assembly and annotation of genomic sequence from ants, as well as sharing the results with molecular myrmecologists via a GMOD database.
| + | |
− | | + | |
− | Closing date: 15 September 2009
| + | |
− | | + | |
− | See the [http://www.isb-sib.ch/about-sib/jobs/details/91-sib-bioinformatician-at-sib--unil.html official ad] for full details and application procedure
| + | |
− | | + | |
− | Informal enquiries to yannick.wurm \at\ unil.ch or laurent.falquet \at\ isb-sib.ch
| + | |
− | | + | |
− | ''2009/08/15, updated 2009/09/27''
| + | |
− | | + | |
− | == FlyBase Sys Admin/Developer ==
| + | |
− | | + | |
− | {{ImageRight|Fly_logo.png|FlyBase Opening|200|http://www.admin.cam.ac.uk/offices/hr/jobs/vacancies.cgi?job=5487}}
| + | |
− | The [http://www.gen.cam.ac.uk/Research/flybase.htm Cambridge (UK) division] of [http://flybase.org FlyBase] currently seeks a [http://www.admin.cam.ac.uk/offices/hr/jobs/vacancies.cgi?job=5487 Systems Administrator/Software Developer], working either full or part-time to support its team of genetic literature curators.
| + | |
− | | + | |
− | The core tasks of this role include systems administration and the maintenance of Perl scripts and files required by the curators in their work. These tasks will occupy approximately 50% of a full-time position, and we are happy to consider applicants who only wish to work part-time (50%) to perform these essential tasks. However, we would like to enhance the current scripts/files and develop additional software to aid curators, and the remaining 50% of the full-time position would be spent on these areas.
| + | |
− | | + | |
− | Closing date: 24 August 2009.
| + | |
− | | + | |
− | See the [http://www.admin.cam.ac.uk/offices/hr/jobs/vacancies.cgi?job=5487 official advert] for full details and application procedure.
| + | |
− | | + | |
− | Informal enquiries to Steven Marygold ([mailto:sjm41@gen.cam.ac.uk sjm41@gen.cam.ac.uk]).
| + | |
− | | + | |
− | ''2009/07/31''
| + | |
− | | + | |
− | == Insect Pest Workshop, 16-17 Nov ==
| + | |
− | | + | |
− | <div style="text-align: center">
| + | |
− | {{#icon: InformationSystemsForInsectPests.gif|Information Systems for Insect Pests|400|http://colloque.inra.fr/isyip}}
| + | |
− | <div style="font-size: 120%">[http://colloque.inra.fr/isyip 1st International Workshop]</div>
| + | |
− | <div style="font-size: 110%">16-17th November 2009<br />INRIA Rennes-Bretagne-Atlantique</div>
| + | |
− | </div>
| + | |
− | | + | |
− | Given the development of cheaper high throughput sequencing technologies, it is easy to predict that in the very near future, new genomes of insects relevant to agriculture will be available. This opens several other challenges such as the bioinformatics treatment of the raw data (handling of billions of sequences, assembly of short reads…) and the development of databases opened to biologists for an easy, friendly and efficient extraction of information. With access to several insect species genomes, one will not only work on their favourite insect, but will take advantage of the increasing knowledge from genomic comparison analyses. This compels the community to develop standards for different tasks towards the exploitation of genome sequences: annotation, cross-species comparisons, interoperability between databases, ... Several tools and databases already exist and are used for genome browsing and annotation.
| + | |
− | | + | |
− | In that context, the purpose of this workshop will be:
| + | |
− | * To exchange within an international panel of attendants our views on the present and future of insect genome databases
| + | |
− | * To settle an international community that will form a functional network for insect genome and database development
| + | |
− | * To discuss strategies to meet the demand of increasing number of new insect genomes
| + | |
− | * To prepare a new road map for integration of genomes databases for insects relevant to agriculture
| + | |
− | | + | |
− | The perimeter of that discussion encompasses insect species related to agriculture, either harmful (pests) or beneficial as controllers of pest populations or as producers of plant by-products (such as silk, honey, ...).
| + | |
− | | + | |
− | Registration for the meeting is free and has to be done online on [https://colloque.inra.fr/isyip/Registration/Symposium/Symposium-registration this website] and will be limited to 40 participants. A statement of interest is needed. A 10 minute presentation may be asked.
| + | |
− | | + | |
− | ''2009/07/20''
| + | |
− | | + | |
− | == August 2009 GMOD Meeting ==
| + | |
− | | + | |
− | {{ImageRight|GMOD2009Europe170.png|August 2009 GMOD Meeting||August 2009 GMOD Meeting}}
| + | |
− | | + | |
− | | + | |
− | <div style="font-size: 140%; text-align: center">[[August 2009 GMOD Meeting|Register for the August 2009 GMOD Meeting]]</div>
| + | |
− | | + | |
− | | + | |
− | The [[August 2009 GMOD Meeting|next GMOD meeting]] will be held 6-7 August, at the University of Oxford, in Oxford, United Kingdom. [[August 2009 GMOD Meeting#Cost and Registration|Registration is now open]]. Space is available on a first come, first served basis and there is room for 55 attendees. The meeting cost is £50.
| + | |
− | | + | |
− | As with [[Meetings|previous GMOD meetings]], the meeting will have a mixture of project talks, [[GMOD Components|component]] talks, and user talks. The agenda is driven by attendee suggestions, and you are encouraged to [[August 2009 GMOD Meeting#Agenda Suggestions|add your suggestions]] now. For examples of what happens at a GMOD meeting, see the writeups of the [[January 2009 GMOD Meeting|January 2009]], [[July 2008 GMOD Meeting|July 2008]], or any [[Meetings|other previous meeting]]. GMOD meetings are an excellent way to meet GMOD developers and users and to learn (and affect) what's coming in the project.
| + | |
− | | + | |
− | Details on transportation, suggested lodging, and other logistics are on the [[August 2009 GMOD Meeting]] page.
| + | |
− | | + | |
− | Please join us in Oxford this August,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/07/01''
| + | |
− | | + | |
− | '''Note:''' Unless you have applied to and been admitted to the [[2009 GMOD Summer School - Europe]], don't you dare register for it. The registration web site will let you do this, but bureaucratic hellishness will ensue.
| + | |
− | | + | |
− | == Join ISB ==
| + | |
− | | + | |
− | {{ImageRight|ISB_logo.gif|International Society for Biocuration||http://colleagues.biocurator.org/join}}
| + | |
− | | + | |
− | The [http://biocurator.org/ International Society for Biocuration (ISB)] is now accepting [http://colleagues.biocurator.org/join member registrations]. I strongly encourage GMOD community members to think about joining ISB. GMOD and ISB have [http://www.biocurator.org/mission.shtml many shared and complementary interests].
| + | |
− | | + | |
− | Membership rates start at less than US$20 for students to a little over US$100 for principal investigators from industry.
| + | |
− | | + | |
− | Please consider this investment,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/06/25''
| + | |
− | | + | |
− | == Apollo 1.11.0 Released ==
| + | |
− | | + | |
− | A new version of [[Apollo]] has been released. Highlights for this release include:
| + | |
− | | + | |
− | * The "Sequence Aligner" ("Exon Detail Editor" with alignment viewing) is now public
| + | |
− | * Brought back the "Types panel" which works in conjunction with the the "Preferences editor"
| + | |
− | * Various bug fixes
| + | |
− | | + | |
− | As always, you can download the current version at:
| + | |
− | :http://apollo.berkeleybop.org/current/install.html
| + | |
− | | + | |
− | Ed Lee
| + | |
− | | + | |
− | ''2009/06/05''
| + | |
− | | + | |
− | == NextGen Sequence in GBrowse ==
| + | |
− | | + | |
− | {{ImageRight|Aga_logo.png|Next Generation Genome Analysis in Non-Model Organisms--An American Genetic Association Special Event||http://www.regonline.com/Nextgeneration}}
| + | |
− | | + | |
− | There will be a [[Media:AGA_NGS_2009.pdf|talk]] on visualizing [[Next Generation Sequencing|next generation sequence]] data in [[GBrowse]] at [http://www.regonline.com/Nextgeneration Next Generation Genome Analysis in Non-Model Organisms], an [http://www.theaga.org American Genetic Association] Special Event held June 11-13, 2009 at the University of Connecticut. The talk will demonstrate how GBrowse can visualize both individual reads and summary and derived data. This talk will become a wiki page after the meeting.
| + | |
− | | + | |
− | June will be a busy month for [[Training and Outreach|GMOD outreach]]. If you can't make it to this meeting, there will also be [[#GMOD Workshops at SMBE, AGS|GMOD workshops]] at [http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27 SMBE] and the [http://www.k-state.edu/agc/symp2009/seminar.html Arthropod Genomics Symposium].
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/05/19''
| + | |
− | | + | |
− | == WebGBrowse Has Arrived ==
| + | |
− | {|
| + | |
− | ! <div class="quotebox" style="font-size: 130%">[http://webgbrowse.cgb.indiana.edu/ WebGBrowse] - A Web Server for [[GBrowse]] Configuration Made Easy</div>
| + | |
− | ! {{#icon: cgb_logo.png|WebGBrowse at the Center for Genomics and Bioinformatics||http://webgbrowse.cgb.indiana.edu/}}
| + | |
− | |}
| + | |
− | [http://webgbrowse.cgb.indiana.edu/ WebGBrowse] is a web site that guides users through the process of creating a [[GBrowse]] configuration file and then shows them how their data renders with that configuration. Users can [[GBrowse Configuration HOWTO|configure]] GBrowse, either from scratch, or by uploading a preexisting GBrowse configuration file. Tracks are defined using a graphical user interface where users first select the glyph to use ([http://webgbrowse.cgb.indiana.edu/webgbrowse/glyphdoc.html over 40 glyphs are currently supported]), and are then prompted for that glyph's settings. Data is provided by uploading a [[GFF3]] file.
| + | |
− | | + | |
− | WebGBrowse has an extensive [http://webgbrowse.cgb.indiana.edu/webgbrowse/tutorial.html tutorial] and [http://webgbrowse.cgb.indiana.edu/webgbrowse/faq.html FAQ], and was just [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp239v1?papetoc published in Bioinformatics]. WebGBrowse is open source and can also be [http://webgbrowse.cgb.indiana.edu/webgbrowse/software.html installed locally].
| + | |
− | | + | |
− | WebGBrowse was created by Ram Podicheti, Rajesh Gollapudi, and Qunfeng Dong, all of the [http://cgb.indiana.edu/ The Center for Genomics and Bioinformatics (CGB)] at [http://www.indaina.edu Indiana University - Bloomington]. WebGBrowse was first presented by Ram Podicheti at the [[January 2009 GMOD Meeting#WebGBrowse: GBrowse Configuration Management|January 2009 GMOD Meeting]].
| + | |
− | | + | |
− | WebGBrowse is an excellent way to get started with GBrowse, and to learn what glyphs are available, and what options each glyph supports. Please [mailto:biohelp@cgb.indiana.edu contact the CGB] if you have any questions.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/04/22''
| + | |
− | | + | |
− | == GMOD Workshops at SMBE, AGS ==
| + | |
− | | + | |
− | There will be GMOD workshops at two major conferences in June 2009:
| + | |
− | | + | |
− | {|
| + | |
− | | {{#icon: SMBE2009Corn.png|SMBE 2009|120|http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27}}
| + | |
− | | <center>'''[http://ccg.biology.uiowa.edu/smbe/ Annual Meeting of the Society for Molecular Biology and Evolution (SMBE 2009)]'''<br />
| + | |
− | June 3-7, 2009<br />Iowa City, Iowa</center>
| + | |
− | | '''[http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27 Database Tools for Evolutionary Genomics: An introduction to GMOD software for managing, annotating and visualizing genomic data]'''<br />
| + | |
− | Saturday, June 6, 2:30-5:00pm<br />
| + | |
− | This workshop will cover some of the most widely used GMOD software components, including the [[Chado]] database, the [[GBrowse]] genome browser, the [[CMap]] comparative map browser, and the [[Apollo]] genome curation tool. The workshop will also cover, in some depth, the [[GBrowse_syn]] comparative genomics viewer, and the [[MAKER]] genome annotation pipeline for eukaryotes. Speakers ([[User:Faga|Ben Faga]], [[User:Mckays|Sheldon McKay]], Mark Yandell, and [[User:Clements|Dave Clements]]) will address both existing functionality and ongoing developments specifically targeted at better supporting evolutionary data and research. No knowledge of programming is necessary.
| + | |
− | |-
| + | |
− | ! {{#icon: AGSBug170.png|Arthropod Genomics Symposium|100|http://www.k-state.edu/agc/symp2009/seminar.html}}
| + | |
− | | <center>'''[http://www.k-state.edu/agc/symp2009/ 3rd Annual Arthropod Genomics Symposium]'''<br />
| + | |
− | June 11 - 14, 2009<br />Kansas City, Missouri</center>
| + | |
− | | '''[http://www.k-state.edu/agc/symp2009/seminar.html Chado Databases and Integration with GMOD Tools]'''<br />
| + | |
− | Pre-Symposium Workshop - Thursday, June 11, 4:30-6:30 p.m.<br />
| + | |
− | [[User:Scott|Scott Cain]], Ontario Institute for Cancer Research, will provide training on [[Chado]] database design, data loading and exporting, and integration with other GMOD tools such as [[Apollo]] and [[GBrowse]]. Particular emphasis will be given to comparative genomics tools. There is no cost to attend this optional workshop, but registration is requested.
| + | |
− | |}
| + | |
− | | + | |
− | Please let [[User:Clements|Dave]] (SMBE) or [[User:Scott|Scott]] (AGS) know if you have any questions about the workshops.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/04/09''
| + | |
− | | + | |
− | == Pathway Tools Workshop, August ==
| + | |
− | <div class="emphasisbox">''[http://brg.ai.sri.com/ptools09/reg.html Registration] is now open for this workshop. 2009/04/24''</div>
| + | |
− | {{ImageRight|SRILogo.png|Pathway Tools Workshop||http://brg.ai.sri.com/ptools09/}}
| + | |
− | | + | |
− | There will be a [http://brg.ai.sri.com/ptools09/ Pathway Tools Workshop], August 19-28, 2009 at [http://www.sri.com SRI International]. This two-part workshop covers [[Pathway Tools]] and the BioCyc Database Collection.
| + | |
− | | + | |
− | '''Part 1: Tutorial, August 19-21'''
| + | |
− | | + | |
− | This introductory tutorial will educate the new user on aspects of [[Pathway Tools]] including basic use of the Pathway/Genome Navigator, Editors, and PathoLogic. Students can bring a genome and leave with a draft Pathway/Genome Database.
| + | |
− | | + | |
− | Tutorial space is limited.
| + | |
− | | + | |
− | '''Part 2: Workshop August 24-28'''
| + | |
− | | + | |
− | The workshop will combine formal presentations by groups outside SRI International (invited speakers and speakers selected through an abstract-submission process), tutorials by SRI International staff, and a hackathon. Suggested topics include but are not limited to:
| + | |
− | | + | |
− | * Share expertise on how to develop new organism-specific databases with [[Pathway Tools]]
| + | |
− | * Present new scientific results achieved with Pathway Tools and BioCyc
| + | |
− | * Share experiences on how to make the most of Pathway Tools
| + | |
− | * Presentations by users on extensions they have developed to Pathway Tools
| + | |
− | * Presentations by SRI International on recent and planned developments to the software, and on software APIs and the database schema, to educate users on how to compute with PGDBs
| + | |
− | * Discussions of requested future enhancements to Pathway Tools and BioCyc
| + | |
− | * Ideas for other software tools to integrate with Pathway Tools
| + | |
− | * Group development of new Pathway Tools enhancements
| + | |
− | | + | |
− | Should you wish to make a presentation at the meeting, please submit a proposed title and abstract to [mailto:ptools-info@ai.sri.com ptools-info@ai.sri.com].
| + | |
− | | + | |
− | Please check the following [http://brg.ai.sri.com/ptools09/ website] for updates.
| + | |
− | | + | |
− | ''2009/04/07, updated 2009/04/24''
| + | |
− | | + | |
− | == 2009 GMOD Summer Schools ==
| + | |
− | | + | |
− | {{Template:2009SummerSchoolApplicationBlurb}}
| + | |
− | | + | |
− | We are now accepting applications for the [[GMOD Summer School|2009 GMOD Summer Schools]]. GMOD Summer Schools are hands-on multi-day courses aimed at teaching new GMOD users how to get up and running with GMOD. Summer schools introduce participants to the GMOD project and focus on installation, configuration and integration of popular [[GMOD Components]]. In 2009 we are proud to offer two schools, one on each side of the Atlantic:
| + | |
− | {| style="vertical-align: middle; width=80%" cellpadding="10"
| + | |
− | | align="center" | {{#icon: 2009SummerSchoolAmericas170.png|Americas||2009 GMOD Summer School - Americas}}
| + | |
− | | <span style="font-size: 160%; line-height: 120%"><b>[[2009 GMOD Summer School - Americas|Americas]]</b></span><span style="font-size: 140%; line-height: 120%"><br />16-19 July<br />NESCent<br />Durham NC</span>
| + | |
− | | rowspan="2" bgcolor="#eeeeee" width="2px" |
| + | |
− | | rowspan="2" |
| + | |
− | The courses include sessions on these popular GMOD components:
| + | |
− | * [[GBrowse]] - the Generic Genome Browser
| + | |
− | * [[Chado]] - a modular and extensible database schema
| + | |
− | * [[Apollo]] - genome annotation editor
| + | |
− | * [[BioMart]] - biological data warehouse system
| + | |
− | * [[GBrowse_syn]] - a GBrowse based synteny viewer
| + | |
− | * [[JBrowse]] - a brand new Web 2.0 genome browser
| + | |
− | * [[Artemis]] - [[Chado]] Integration ([[2009 GMOD Summer School - Europe|Europe]] only)
| + | |
− | * [[MAKER]] - Genome annotation pipeline ([[2009 GMOD Summer School - Americas|Americas]] only)
| + | |
− | * [[Tripal]] - Web front end for Chado ([[2009 GMOD Summer School - Americas|Americas]] only)
| + | |
− | |-
| + | |
− | | align="center" | {{#icon: GMOD2009Europe170.png|Europe||2009 GMOD Summer School - Europe}}
| + | |
− | | <span style="font-size: 160%; line-height: 120%"><b>[[2009 GMOD Summer School - Europe|Europe]]</b></span><span style="font-size: 140%; line-height: 120%"><br />3-6 August<br />Oxford University<br />Oxford UK</span>
| + | |
− | |}
| + | |
− | The [[2009 GMOD Summer School - Europe|European summer school]] is part of [[GMOD Europe 2009]], a week long event which also includes the [[August 2009 GMOD Meeting]]. This is the first time a [[GMOD Summer School]] or [[Meetings|GMOD meeting]] will be held outside of North America.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/03/15, updated 2009/04/06, 2008/04/27''
| + | |
− | | + | |
− | == Apollo 1.10 Released ==
| + | |
− | | + | |
− | A new version of [[Apollo]] has been released. Highlights for this release include:
| + | |
− | | + | |
− | * Support for remote NCBI BLAST (blastn, blastx, tblastx)
| + | |
− | * Support for remote NCBI Primer BLAST (primer identification tool)
| + | |
− | * Numerous bug fixes
| + | |
− | | + | |
− | The nice thing about the remote analysis support is that now users do not have to install those tools locally (which can be a pain) and don't need to download the very large NCBI databases. These requests are handled in the background, so you can keep on working as usual and once the analysis is complete, the results will be automatically incorporated into the results track.
| + | |
− | | + | |
− | We're very interested in getting [mailto:apollo@fruitfly.org feedback from users] who may use the primer identification functionality. If you could provide information on how you'd use such a tool and possibly what kind of filtering criteria you might need, it would be great so that we may incorporate these changes in future releases.
| + | |
− | | + | |
− | As always, you can download the current version at:
| + | |
− | :http://apollo.berkeleybop.org/current/install.html
| + | |
− | | + | |
− | [[User:Elee|Ed Lee]]
| + | |
− | | + | |
− | ''2009/03/02''
| + | |
− | | + | |
− | == Biocuration Conference, April ==
| + | |
− | | + | |
− | {{ImageRight|2009BiocurationLogo.jpg|3rd International Biocuration Conference|400|http://projects.eml.org/sdbv/events/BiocurationMeeting/index.html}}
| + | |
− | | + | |
− | The [http://projects.eml.org/sdbv/events/BiocurationMeeting/index.html 3rd International Biocuration Conference] will be held in Berlin, Germany, April 16-19, 2009. This conference is a forum for curators and developers of biological databases to discuss their work, promote collaboration, and foster a sense of community in this active and growing area of research. I don't think GMOD community members will find a higher concentration of people working on biological databases at any other conference. Anyone interested in the methods and tools employed in biocuration is encouraged to attend.
| + | |
− | | + | |
− | Early [http://projects.eml.org/sdbv/events/BiocurationMeeting/registration.html registration] '''ends in two days''' (on 20 February, 2009).
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]
| + | |
− | <br />[[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/02/18''
| + | |
− | | + | |
− | == Biomedical Ontology Conference ==
| + | |
− | | + | |
− | The [http://icbo.buffalo.edu/ International Conference on Biomedical Ontologies (ICBO)], will be held in Buffalo, New York from July 23-26, 2009. Ontologies are widely used in GMOD for annotation, controlled vocabularies, reasoning, and data sharing. [http://icbo.buffalo.edu/Call_for_Papers.pdf Paper submissions] are due March 1, and [http://icbo.buffalo.edu/Poster.pdf posters] are due April 10. [http://icbo.buffalo.edu/ ICBO] will be held in conjunction with [http://www.bioontology.org/wiki/index.php/Tutorials_and_Classes four days of tutorials and classes] from July 20-23, 2009.
| + | |
− | | + | |
− | See the [http://icbo.buffalo.edu/ ICBO conference web site] for details.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]
| + | |
− | <br />[[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/02/17''
| + | |
− | | + | |
− | == January 2009 Meeting Report ==
| + | |
− | | + | |
− | {{ImageRight|Jan2009Meeting.JPG|January 2009 GMOD Meeting||January 2009 GMOD Meeting}}
| + | |
− | The [[January 2009 GMOD Meeting]] was held January 15-16, 2009 in San Diego, immediately following the [[PAG 2009|Plant and Animal Genome (PAG)]] conference. The meeting was attended by over 50 people representing about 35 different organizations. The meeting report and links to presentations are now available on the [[January 2009 GMOD Meeting]] page. There were [[January 2009 GMOD Meeting#Presentations|19 presentations]] by GMOD users and developers.
| + | |
− | | + | |
− | Some highlights:
| + | |
− | * How best to [[January 2009 GMOD Meeting#Data Sharing|share data]]?
| + | |
− | * [[January 2009 GMOD Meeting#BioMart|BioMart]] integration with other GMOD Components.
| + | |
− | * [[January 2009 GMOD Meeting#JBrowse|JBroswe]] update
| + | |
− | * [[January 2009 GMOD Meeting#WebGBrowse: GBrowse Configuration Management|WebGBrowse]] - [[GBrowse]] configuration on the web.
| + | |
− | * A [[January 2009 GMOD Meeting#Drupal and MarineGenomics.org|Drupal interface to Chado]].
| + | |
− | Plus 14 other excellent user and developer presentations.
| + | |
− | | + | |
− | Please take a look at the [[January 2009 GMOD Meeting|meeting report]] for an update on what's going on in the GMOD community.
| + | |
− | | + | |
− | We hope to see you at the upcoming [[August 2009 GMOD Meeting]], in Oxford UK (and our first meeting in Europe).
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]
| + | |
− | <br />[[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/02/09''
| + | |
− | | + | |
− | == GBrowse User Tutorial ==
| + | |
− | | + | |
− | {{ImageRight|OpenHelixLogosmaller.jpg|OpenHelix||http://www.openhelix.com/gbrowse}}
| + | |
− | | + | |
− | A comprehensive [http://www.openhelix.com/gbrowse GBrowse User Tutorial] was released by [http://www.openhelix.com OpenHelix] this week. The narrated tutorial covers:
| + | |
− | * the basic layout and search methods in [[GBrowse]]
| + | |
− | * how to access detailed annotation data tied to genomic sequences
| + | |
− | * how to select and customize annotations using tracks
| + | |
− | * how to upload and incorporate your own data or other external data sources
| + | |
− | * take a tour of different GBrowse installations at model organism databases
| + | |
− | | + | |
− | The tutorial also includes [http://www.openhelix.com/downloads/gbrowse/gbrowseslidesDL.shtml PowerPoint slides], [http://www.openhelix.com/downloads/gbrowse/gbrowsehandoutsDL.shtml handouts], and [http://www.openhelix.com/downloads/gbrowse/gbrowseexercisesDL.shtml exercises] that can be used for reference or for training others. The narration is reproduced in the notes area on the slides.
| + | |
− | | + | |
− | The [http://www.openhelix.com/gbrowse GBrowse User Tutorial] is part of a [http://www.openhelix.com/model_organisms.shtml set of model organism resource tutorials] funded in a large part by [http://www.genome.gov/ NHGRI]. The set includes tutorials on how to navigate and use [http://www.openhelix.com/rgd RGD], [http://www.openhelix.com/mgi MGI], and [http://www.openhelix.com/wormbase WormBase], and in the future for [http://zfin.org ZFIN], [[:Category:FlyBase|FlyBase]], and [[:Category:SGD|SGD]] (''all'' of which are GMOD users and/or contributors).
| + | |
− | | + | |
− | This tutorial focuses on ''using'' GBrowse and complements the {{GBrowseAdminTutorialLink|GBrowse Administration Tutorial}}. It is an excellent resource for any organization that wants to help its users use GBrowse better.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]
| + | |
− | | + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/02/05''
| + | |
− | | + | |
− | == Opening at Dow AgroSciences ==
| + | |
− | | + | |
− | {{ImageRight|Dow_AgroSciences_logo.gif|Dow AgroSciences||http://www.dowagro.com/}}
| + | |
− | | + | |
− | [http://www.dowagro.com/ Dow AgroSciences] has a short term contract position available for someone with GMOD experience. The candidate proposed here will be responsible for three main tasks and several secondary ones:
| + | |
− | | + | |
− | # Install the open source software components for the [[Chado]] database, data loaders, and genome browser.
| + | |
− | # Deploy the [[GBrowse]] genome browser in a centralized location in our intranet, which can be used by Dow AgroSciences scientists across functions.
| + | |
− | # Test the system by performing preprocess (e.g annotate, perform alignments) and upload whole-genome data from Arabidopsis.
| + | |
− | # Link the genome browser to Dow AgroSciences major internal databases, such as Variety, markerDB, QTL locate, and microarray database.
| + | |
− | # Provide integration tests to ensure the transparency of the data among the different systems.
| + | |
− | # Present to other Dow AgroSciences scientists to raise awareness of capability.
| + | |
− | # Complete written documentation of project development, implementation, and continued maintenance.
| + | |
− | | + | |
− | Interested candidates please send a resume to Mindi Dippold at [mailto:mdippold@dow.com mdippold@dow.com].
| + | |
− | | + | |
− | ''2009/02/03''
| + | |
− | | + | |
− | == New Ergatis Release ==
| + | |
− | | + | |
− | A new version of [[Ergatis]], a web-based utility for creating, running and reusing computational analysis pipelines, is now [https://sourceforge.net/project/showfiles.php?group_id=148765 available for download].
| + | |
− | | + | |
− | This version includes
| + | |
− | * Interface improvements
| + | |
− | * New components, notably:
| + | |
− | ** RNAmmer - RNA identification on genomic sequence
| + | |
− | ** p_func - Derives gene function assertions based on tiers of provided evidence, such as BLAST, HMM, etc..
| + | |
− | ** 454_mplex_seq_bin_trim - A binning and trimming script for multiplex 454 sequence data
| + | |
− | ** phylip_dnadist - A wrapper for a parallelized version of PHYLIP's dnadist
| + | |
− | * New pipeline templates
| + | |
− | * Bug fixes
| + | |
− | | + | |
− | A new version of the automated Prokaryotic Annotation Pipeline is also included, as well as a pipeline creation tutorial. For a full list of the changes, see the [http://ergatis.svn.sourceforge.net/viewvc/ergatis/tags/ergatis-v2r10b1/doc/CHANGELOG?revision=5828&view=markup&sortby=date CHANGELOG file].
| + | |
− | | + | |
− | As always, installation instructions can be found within each package and in [http://ergatis.sourceforge.net/documentation/install_guide.html web form].
| + | |
− | | + | |
− | ''2009/01/27''
| + | |
− | | + | |
− | == Job Openings at Georgetown ==
| + | |
− | | + | |
− | Two Positions Immediately Available at Georgetown University in Washington, DC
| + | |
− | | + | |
− | '''Bioinformatics Engineer'''
| + | |
− | | + | |
− | This position is part of the USDA-funded [http://genomes.arc.georgetown.edu/hymenoptera/ Hymenoptera Genome Database] project, which includes [http://www.beebase.org/ BeeBase] (honey bee genome) and [http://genomes.arc.georgetown.edu/nasonia/ NasoniaBase] (wasp genome). This person will implement GMOD software and develop new query interfaces; develop scripts for automated data retrieval and database loading; develop computational pipelines for updating homology, functional annotation data and [[GBrowse]] tracks. Requires MS degree in bioinformatics or related field, and demonstration of programming experience. Experience with Perl, HTML, CGI, Java, [[MySQL]] and [[PostgreSQL]] is preferred.
| + | |
− | | + | |
− | '''Bioinformatics Systems Analyst'''
| + | |
− | | + | |
− | Duties include system administration, bioinformatics database maintenance, system backup management, problem diagnosis, and creation of system documentation. Must have experience in Linux system administration Perl, Java, Apache PostgreSQL, and MySQL. Experience with GMOD and [[BioPerl]] is highly desired.
| + | |
− | | + | |
− | Contact Chris Elsik: [mailto:chris.elsik@gmail.com chris.elsik@gmail.com]
| + | |
− | | + | |
− | ''2009/01/15''
| + | |
− | | + | |
− | == BioGraphics now at gmod.org ==
| + | |
− | | + | |
− | The Bio::Graphics modules which have long been a core part of [[BioPerl]] have been separated out and the code base is now housed in the [[CVS|cvs repository at SourceForge]]. This action has been taken to give the authors more flexibility over releases, particularly so that frequent updates can occur as needed around new [[GBrowse]] releases. Releases of Bio::Graphics are already on CPAN, so it can be installed in the cpan shell. Additionally, the [[GBrowse_Install_HOWTO#The_NetInstaller|gbrowse_netinstall.pl]] script for installing GBrowse automatically has been updated to install Bio::Graphics before installing GBrowse.
| + | |
− | | + | |
− | ''2009/1/6''
| + | |
− | | + | |
− | = 2008 Stories =
| + | |
− | | + | |
− | == GMOD at PAG 2009 ==
| + | |
− | | + | |
− | <div style="float: right; padding: 0.5em">{{#icon: Paglogo.gif|GMOD @ PAG||PAG 2009}}</div>
| + | |
− | GMOD will once again have a strong presence at the [[PAG 2009|Plant and Animal Genome Conference (PAG 2009)]]. There will be [[PAG 2009|'''over 35''' talks, workshops, demonstrations and posters]] about [[GMOD Components]] and projects that use them. See the [[PAG 2009]] page for a printable listing of GMOD related events.
| + | |
− | | + | |
− | The [[January 2009 GMOD Meeting]] is immediately after PAG, and many GMOD developers and users will likely attend both meetings.
| + | |
− | | + | |
− | If you haven't registered yet for either or the [[January 2009 GMOD Meeting|GMOD meeting]], you are encouraged to do so.
| + | |
− | | + | |
− | ''2009/01/03''
| + | |
− | | + | |
− | == GMOD Meeting Registration Open ==
| + | |
− | | + | |
− | <div style="float: right; padding: 0.5em">
| + | |
− | {|
| + | |
− | |{{#icon: Jan2009MtgLogoNoText.png|January in San Diego - think about that||January 2009 GMOD Meeting}}
| + | |
− | |-
| + | |
− | | '''[[January 2009 GMOD Meeting]]'''
| + | |
− | |}
| + | |
− | </div>
| + | |
− | Registration is now open for the [[January 2009 GMOD Meeting]]. The meeting will be held January 15-16, 2009 in sunny [http://www.sandiego.org/nav/Visitors San Diego], immediately following the [[PAG 2009|2009 Plant and Animal Genome Conference (PAG 2009)]].
| + | |
− | | + | |
− | '''Registration is free.'''
| + | |
− | | + | |
− | If you haven't attended a [[:Category:Meetings|GMOD Meeting]] before then you are encouraged to find out why the [[2008 GMOD Community Survey#GMOD Meetings|overwhelming majority of past attendees]] have found meetings to be useful and well organized. See the [[July 2008 GMOD Meeting]] report (or any of the other [[:Category:Meetings|previous report]]) for an idea of what goes on at GMOD Meetings.
| + | |
− | | + | |
− | Finally, if you have items that you would like on the agenda, please add them to the [[January 2009 GMOD Meeting|meeting page]].
| + | |
− | | + | |
− | As always, please let the [mailto:help@gmod.org GMOD Help Desk] know if you have any questions.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2008/11/20''
| + | |
− | | + | |
− | == GMOD Community Survey Results ==
| + | |
− | | + | |
− | The [[2008 GMOD Community Survey|results of the 2008 GMOD Community Survey]] are now available online. The survey was taken by 89 respondents. The survey includes questions on:
| + | |
− | * What GMOD Components they use
| + | |
− | * Feedback on the specific components they use.
| + | |
− | * The servers that GMOD runs on.
| + | |
− | * GMOD Meetings
| + | |
− | * GMOD Project overall (What is being done well, what needs improvement, what should be our focus for the next 12-18 months)
| + | |
− | * GMOD Help Desk
| + | |
− | * GMOD course in Europe and Asia/Pacific
| + | |
− | * Organisms studied
| + | |
− | * Biological areas of interest
| + | |
− | | + | |
− | Your responses will be used to improve GMOD and guide its future direction.
| + | |
− | | + | |
− | And finally, we have our 3 winners of [[#Get GMOD Gear!|GMOD Gear]]:
| + | |
− | | + | |
− | * Randall Svancara of [http://www.bioinfo.wsu.edu Washington State University]
| + | |
− | * Victor Jun M. Ulat of the [http://www.irri.org International Rice Research Institute]
| + | |
− | * Pinglei Zhou of [http://flybase.org FlyBase].
| + | |
− | | + | |
− | Please let the [mailto:help@gmod.org GMOD Help Desk] know if you have any questions about the survey.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave C]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2008/11/20''
| + | |
− | | + | |
− | == January 2009 GMOD Meeting ==
| + | |
− | | + | |
− | <div style="float: right; padding: 0.5em">{{#icon: SanDiegoConvention.gif|January in San Diego - think about that||}}</div>
| + | |
− | | + | |
− | ''Note: Registration is now open for the [[January 2009 GMOD Meeting]]. 2008/11/20''
| + | |
− | | + | |
− | The next GMOD community meeting will be held [[January 2009 GMOD Meeting|January 15-16, 2009]] in sunny [http://www.sandiego.org/nav/Visitors San Diego], immediately following the [[PAG 2009|2009 Plant and Animal Genome Conference (PAG 2009)]]. Early details on the GMOD meeting are now available on the [[January 2009 GMOD Meeting]] page. We'll update that page as we have more. If you want to know what happens at a GMOD meeting see the notes from the [[July 2008 GMOD Meeting]] or any of the other [[:Category:Meetings|previous meetings]].
| + | |
− | | + | |
− | It's also worth noting that GMOD will again have a [[PAG 2009|strong presence]] at the PAG 2009 meeting itself. If you are interested in attending [http://www.intl-pag.org/ PAG 2009], early registration closes November 1.
| + | |
− | | + | |
− | And, ''just in case it slipped your mind,'' it is still not too late to fill out the [[2008 GMOD Community Survey|GMOD Community Survey]] and be entered to win [[#Get GMOD Gear!|GMOD gear]]!
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2008/10/23, updated 2008/11/20''
| + | |
− | | + | |
− | == 2008 GMOD Community Survey ==
| + | |
− | | + | |
− | {| class="wikitable"
| + | |
− | | ''Thanks to everyone who participated in the [[2008 GMOD Community Survey]]. Survey results are [[2008 GMOD Community Survey|now available]]. The winners are Randall Svancara of [http://www.bioinfo.wsu.edu Washington State University], Victor Jun M. Ulat of the [http://www.irri.org International Rice Research Institute] and Pinglei Zhou of [http://flybase.org FlyBase]. 2008/11/20''
| + | |
− | |}
| + | |
− | Please take a few minutes to fill out the [[2008 GMOD Community Survey]] and your name will be entered to win a free [[#Get GMOD Gear!|GMOD T-shirt or mug]]!
| + | |
− | | + | |
− | We are asking all GMOD users and developers to provide input on how GMOD is doing, and how it can be improved. All questions are optional, but please provide as much information as you can. The survey covers GMOD in general, and any GMOD components that you use (and it only asks about components that you indicate you use).
| + | |
− | | + | |
− | '''Three randomly selected survey participants will receive the [http://www.cafepress.com/GenericMOD/ GMOD T-shirt or mug] of their choice. Names will be drawn from the first 100 responses we receive, so get your response in early.'''
| + | |
− | | + | |
− | Please contact the [[GMOD Help Desk]] at [mailto:help@gmod.org|<help@gmod.org>] if you have any questions.
| + | |
− | | + | |
− | Thank you,
| + | |
− | | + | |
− | ''The GMOD Team''
| + | |
− | | + | |
− | ''2008/10/17'', updated ''2008/11/20''
| + | |
− | | + | |
− | == Get GMOD Gear! ==
| + | |
− | | + | |
− | <div style="float:left; padding:0.5em">{{#icon: GMODMug150x150.jpg|GMOD Mug||http://www.cafepress.com/GenericMOD/}}</div>
| + | |
− | <div style="float:right; padding:0.5em">{{#icon: TShirtThumb.jpg|GMOD T Shirt||http://www.cafepress.com/GenericMOD/}}</div>
| + | |
− | | + | |
− | | + | |
− | <div style="text-align: center">
| + | |
− | <div style="font-size: 135%">
| + | |
− | Tired of not having a cool T-shirt to wear at meetings?
| + | |
− | </div><div style="font-size: 135%">
| + | |
− | Tired of drinking your coffee from a ''styrofoam'' cup?
| + | |
− | </div><div style="font-size: 135%">
| + | |
− | Want to show off your affiliation with GMOD and promote it at the same time?
| + | |
− | </div><div style="font-size: 150%;">[http://www.cafepress.com/GenericMOD/ '''Be the first person in your lab, community, organization, building, campus or country to be seen with some GMOD gear!''']
| + | |
− | </div>
| + | |
− | </div>
| + | |
− | | + | |
− | | + | |
− | '''Note:''' Want to win a shirt of mug for free? Then participate in the [[#2008 GMOD Community Survey|2008 GMOD Community Survey]]. Three participants will be randomly selected to receive the GMOD item of their choice.
| + | |
− | | + | |
− | GMOD has a [http://www.cafepress.com/GenericMOD/ store] at CafePress where you can buy GMOD gear. Currently there are two T-shirt styles and a coffee mug. (We also take requests if you want to see additional gear - for example, a long sleeved T shirt or even a ''GMOD Pet Bowl'').
| + | |
− | | + | |
− | Please note:
| + | |
− | * GMOD gear is offered at cost. GMOD does not make any money from the sale of these items.
| + | |
− | * The ''GMOD News'' will return to its usual, somewhat more sedate, style with the next posting.
| + | |
− | | + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br>
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2008/10/09''
| + | |
− | | + | |
− | ''Updated 2008/10/17''
| + | |
− | | + | |
− | == InterMine Workshop ==
| + | |
− | | + | |
− | {{ImageRight|InterMine.png|InterMine||http://www.biomed.cam.ac.uk/gradschool/current/courses/intermine.html}}
| + | |
− | An [http://www.biomed.cam.ac.uk/gradschool/current/courses/intermine.html InterMine Workshop] is being offered at the University of Cambridge, 30th-31st October 2008. This workshop is intended for software developers aspiring to build a database and web interface with the [[InterMine]] software. An example of such a database is [http://flymine.org FlyMine] but InterMine imposes no restriction on the sort of data it can be used to manage. A reasonable grasp of programming in either Java or PERL is essential. Some experience with relational database would also be very useful.
| + | |
− | | + | |
− | The workshop will be hands-on, taking you through all the steps of setting up an InterMine data warehouse. We will integrate some real data using existing InterMine parsers then extend the data model and write parsers in Java/Perl to include some custom data. This will include loading data from [[Chado]]. On the second day we will deploy and configure the web application, add a new widget for analysing lists and learn how to query with web services and the API. This should provide you with the necessary experience to set up your own InterMine system.
| + | |
− | | + | |
− | See the [http://www.biomed.cam.ac.uk/gradschool/current/courses/intermine.html workshop announcement] for details and registration information. The workshop is free to attend.
| + | |
− | | + | |
− | Richard Smith
| + | |
− | | + | |
− | ''2008/09/11''
| + | |
− | | + | |
− | == Pathway Tools Tutorial in London ==
| + | |
− | | + | |
− | A [[Pathway Tools]] and BioCyc [http://brg.ai.sri.com/ptools/tutorial/2008-09-London.html tutorial] well be held September 22-23, 2008 at Kings College London. This tutorial is kindly hosted by the [http://www.kcl.ac.uk/schools/pse/bioinform/ Centre for Bioinformatics at King's College London (KCBI)].
| + | |
− | | + | |
− | Day 1 is intended to teach users of Pathway Tools databases such as [http://biocyc.org/ BioCyc], [http://pathway.yeastgenome.org/biocyc/ YeastCyc], [http://mousecyc.jax.org/ MouseCyc], and [http://www.arabidopsis.org/biocyc/index.jsp AraCyc] how to make the most of these resources.
| + | |
− | | + | |
− | Day 2 will address creation of new Pathway/Genome Databases (PGDBs) with Pathway Tools,
| + | |
− | and how to query PGDBs programmatically.
| + | |
− | | + | |
− | [[Pathway Tools]] includes a unique combination of bioinformatics algorithms including a
| + | |
− | predictor of metabolic pathways, an operon predictor, and an algorithm for predicting
| + | |
− | which genes in a genome code for missing enzymes in predicted metabolic pathways
| + | |
− | ("pathway holes"). It also contains tools for painting omics data onto genome-scale
| + | |
− | visualizations of metabolic networks and regulatory networks.
| + | |
− | | + | |
− | The tutorial is free of charge.
| + | |
− | | + | |
− | For more information see the [http://brg.ai.sri.com/ptools/tutorial/2008-09-London.html tutorial page at SRI].
| + | |
− | | + | |
− | Peter Karp
| + | |
− | | + | |
− | ''2008/08/28''
| + | |
− | | + | |
− | == GBrowse 1.69 Released ==
| + | |
− | | + | |
− | I am very happy to announce that [[GBrowse]] 1.69 was released today. This release of GBrowse comes with a variety of user interface enhancements, performance improvements, bug fixes and a security fix. This release come courtesy of considerable work from the GBrowse developers, most notably [[User:Lstein|Lincoln Stein]], the lead developer and [[User:Mckays|Sheldon McKay]] who did much of the JavaScript work. The release can be
| + | |
− | obtained from [http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=34513&release_id=621342 SourceForge], or, you can use the [http://gmod.cvs.sourceforge.net/*checkout*/gmod/Generic-Genome-Browser/bin/gbrowse_netinstall.pl GBrowse net installer].
| + | |
− | | + | |
− | More information about GBrowse, including platform specific installation instructions, can be found on the [[GBrowse]] page.
| + | |
− | | + | |
− | You can try out the new version on the [http://gmod.org/cgi-bin/gbrowse/yeast/ GMOD website] as well.
| + | |
− | | + | |
− | Finally, here is a list of the major changes since the 1.68 release:
| + | |
− | | + | |
− | * Draggable tracks; use "drag and drop" option to activate.
| + | |
− | * Collapsible tracks - comes for free with "drag and drop"
| + | |
− | * [[GBrowse Popup Balloons|Popup balloons]] w/ Ajax content; use "balloon tips" option to activate.
| + | |
− | * Caching of individual tracks for better performance; use "cache time" option to control.
| + | |
− | * Changed licensing model to dual license under Perl Artistic 2.0 and GPL.
| + | |
− | * Fix duplicated tracks during dragging.
| + | |
− | * Features with same name are now found, not merged.
| + | |
− | * [[Galaxy]] support, courtesy Greg Von Kuster
| + | |
− | * Can change fill and outline color of selected regions on overview & regionview.
| + | |
− | * Various bugs [http://sourceforge.net/tracker/?group_id=27707&atid=391291 squashed].
| + | |
− | * When updating settings or searching, the browser scrolls to the top of the overview section as a convenience.
| + | |
− | * Fixed cross-site scripting vulnerability.
| + | |
− | | + | |
− | Thank you and happy GBrowsing,
| + | |
− | | + | |
− | [[User:Scott|Scott Cain]]
| + | |
− | | + | |
− | GMOD Project Coordinator
| + | |
− | | + | |
− | ''2008/08/22''
| + | |
− | | + | |
− | == Web Site Changes ==
| + | |
− | | + | |
− | The [[Main Page|GMOD web site]] doesn't look very different, but it was updated on Monday, August 11,2008. Here's what changed:
| + | |
− | * The site was upgraded from [http://mediawiki.org Mediawiki] 1.9.3 to [http://mediawiki.org/wiki/Manual:Upgrading_to_1.12 MediaWiki 1.12.0].
| + | |
− | * Replaced the default MediaWiki site search mechanism with Google.
| + | |
− | * URLs have been rationalized. Previously, there were many different URL to get to each wiki page. Now all URLs are redirected to <nowiki>http://gmod.org/wiki/Page_Name</nowiki>
| + | |
− | | + | |
− | We have done our best to make this upgrade as smooth and transparent as possible. However, if you do notice anything unusual, please notify the [mailto:help@gmod.org GMOD Help Desk].
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]
| + | |
− | <br />[[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2008/08/11''
| + | |
− | | + | |
− | == Website Down: Aug 11 2008 ==
| + | |
− | | + | |
− | <span style="float: left">{{#icon: WorkInProgressTools.gif|||}} </span>
| + | |
− | The [[Main Page|GMOD website]] will be down for maintenance on Monday, August 11, 2008 starting at 8pm Eastern / 5pm Pacific (both US). We expect it to be down for about an hour. We apologize for any inconvenience this may cause you.
| + | |
− | | + | |
− | Please let us know if you have any questions.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]
| + | |
− | <br />[[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2008/08/08''
| + | |
− | | + | |
− | == Upcoming Pathway Tools Tutorial ==
| + | |
− | | + | |
− | SRI's Bioinformatics Research Group will hold a [http://bioinformatics.ai.sri.com/ptools/tutorial/ Pathway Tools tutorial session] from September 2-5, 2008, at SRI International in Menlo Park, CA. Each day will combine lectures with lab sessions in which students apply the software to a sample genome. No programming experience is required.
| + | |
− | | + | |
− | [[Pathway Tools]] includes a unique combination of bioinformatics algorithms including a predictor of metabolic pathways, an operon predictor, and an algorithm for predicting which genes in a genome code for missing enzymes in predicted metabolic pathways ("pathway holes").
| + | |
− | | + | |
− | Please see the [http://bioinformatics.ai.sri.com/ptools/tutorial/ Pathway Tools Tutorial page] for a detailed schedule, registration information, and other details.
| + | |
− | | + | |
− | Peter Karp<br />
| + | |
− | ''2008/08/07''
| + | |
− | | + | |
− | | + | |
− | == July 2008 GMOD Meeting Report ==
| + | |
− | | + | |
− | {{ImageRight|GMOD2008Discussion.JPG|July 2008 GMOD Meeting||July 2008 GMOD Meeting}}
| + | |
− | The [[July 2008 GMOD Meeting]] was held on July 16-17, 2008 at the University of Toronto. The meeting was attended by over 30 people representing more than 20 different organizations. The meeting report and links to presentations are now available on the [[July 2008 GMOD Meeting]] page. Several [[GMOD Components]] were covered, including [[July 2008 GMOD Meeting#Chado|Chado]], the [[July 2008 GMOD Meeting#Community Annotation System|Community Annotation System]], and [[July 2008 GMOD Meeting#Table Editor|Table Editor]] (plus several more). We also heard reports from many [[July 2008 GMOD Meeting#GMOD User Community|GMOD users]], including [[July 2008 GMOD Meeting#SGN|SGN]], [[July 2008 GMOD Meeting#WikiMods.org|WikiMods]], and [[July 2008 GMOD Meeting#Xenbase|Xenbase]] (plus several more).
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]
| + | |
− | <br />[[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2008/07/28''
| + | |
− | | + | |
− | == cas-utils-0.1 Released ==
| + | |
− | | + | |
− | In the wake of the [[GMOD Summer School]] a little over a week ago, I
| + | |
− | decided that I should create a release that has the tools that I used
| + | |
− | to tie together [[GBrowse]], [[Apollo]] and [[Chado]]. It can be downloaded at:
| + | |
− | | + | |
− | http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=284978
| + | |
− | | + | |
− | These utilities consist of 4 main tools:
| + | |
− | | + | |
− | * A CGI for selecting a region in GBrowse, extracting the data for
| + | |
− | that region from Apollo and creating an [[Glossary#XML|XML]] file and a Java Webstart (.jnlp)
| + | |
− | file for Apollo.
| + | |
− | * A CGI for accepting uploads of edited XML files to either be
| + | |
− | immediately loaded into Chado or to be held for validation.
| + | |
− | * A configuration perl module to make modifying the CGI's behavior easy.
| + | |
− | * A Module::Build based installer that queries the user for needed setup data.
| + | |
− | | + | |
− | While this release of cas-utils assumes that the port for connecting
| + | |
− | to the database is blocked for outside users, future releases of these
| + | |
− | tools could be configured to assume the reverse. Another item planned
| + | |
− | for a future release is tools for integrating Chado with a MediaWiki
| + | |
− | site for more text-based annotation. Of course, because of the nature
| + | |
− | of these tools, it is assumed that several things are already in place
| + | |
− | and working:
| + | |
− | | + | |
− | * Chado with computational analysis and annotation data already loaded.
| + | |
− | * GBrowse (either 1.69 (to be released soon) or from the stable cvs branch).
| + | |
− | * Apollo, both as an installed application (like in /usr/bin), and as
| + | |
− | source that has been built into a webstart application and installed
| + | |
− | for the web server to use.
| + | |
− | | + | |
− | If you have questions about either cas-utils or any of the
| + | |
− | prerequisites, please send questions to the most appropriate mailing
| + | |
− | list:
| + | |
− | | + | |
− | * Chado: [mailto:gmod-schema@lists.sourceforge.net gmod-schema@lists.sourceforge.net]
| + | |
− | * GBrowse: [mailto:gmod-gbrowse@lists.sourceforge.net gmod-gbrowse@lists.sourceforge.net]
| + | |
− | * Apollo: [mailto:apollo@fruitfly.org apollo@fruitfly.org]
| + | |
− | | + | |
− | I've only tested this application on CentOS 4.6 and Ubuntu 8.04,
| + | |
− | though there is no reason to believe that this wouldn't work on any
| + | |
− | Linux and probably on MacOS as well. I am considerably less sure that
| + | |
− | this would work out of the box on Windows, but support for that could
| + | |
− | probably be in a future release if the demand is there.
| + | |
− | | + | |
− | Thanks and happy curating!
| + | |
− | [[User:Scott|Scott Cain]]
| + | |
− | | + | |
− | ''07/22/2008''
| + | |
− | | + | |
− | | + | |
− | == Job Openings with GnpAnnot ==
| + | |
− | | + | |
− | [http://urgi.versailles.inra.fr/projects/GnpAnnot/ GnpAnnot], an [http://www.inra.fr/ INRA] project, is offering 2 positions for programmers to implement and/or improve GMOD interfaces for [[Chado]] databases.
| + | |
− | | + | |
− | | + | |
− | <div style="font-size: 140%">1st Position: IRISA</div>
| + | |
− | {{ImageRight|IRISALogo.jpg|IRISA||http://www.irisa.fr/home_html-en?set_language=en}}
| + | |
− | 18 month position for a Java programmer
| + | |
− | | + | |
− | '''Environment:'''
| + | |
− | | + | |
− | The job opportunity will be located at [http://www.irisa.fr/home_html-en?set_language=en IRISA], in Rennes France.
| + | |
− | | + | |
− | '''Description:'''
| + | |
− | | + | |
− | The engineer will write specifications, design, develop, test and deploy diverse applications and web interfaces dedicated to genomics analyses and comparative genomics.
| + | |
− | | + | |
− | The applications will use a 3-tiered architecture based on J2EE technology.
| + | |
− | | + | |
− | '''Skills:'''
| + | |
− | * experience in Java development
| + | |
− | * good knowledge of J2EE technologies (Hibernate, Spring, Struts et JSP) - experience with [[BioPerl]] or Perl objects
| + | |
− | | + | |
− | The job should start on the first of September 2008
| + | |
− | | + | |
− | '''Contact:'''
| + | |
− | Fabrice Legeai [mailto:fabrice.legeai@rennes.inra.fr fabrice.legeai@rennes.inra.fr]
| + | |
− | | + | |
− | | + | |
− | <div style="font-size: 140%">2nd Position: INRA-URGI</div>
| + | |
− | {{ImageRight|Urgi.png|URGI|170|http://urgi.versailles.inra.fr/}}
| + | |
− | | + | |
− | One year object-oriented programmer (Java, Perl Object)
| + | |
− | | + | |
− | '''Environment:'''
| + | |
− | | + | |
− | The job opportunity will be located at [http://urgi.versailles.inra.fr/ INRA-URGI] in Versailles (Near Paris), France.
| + | |
− | | + | |
− | '''Description:'''
| + | |
− | | + | |
− | The applicant will write specifications and develop/improve, databases and interfaces from the GMOD project ([[Chado]], [[Apollo]], [[GBrowse]]).
| + | |
− | | + | |
− | '''Skills'''
| + | |
− | * Good experience in Java and Perl programming
| + | |
− | * Knowledge of GMOD tools will be appreciated
| + | |
− | | + | |
− | Answers expected before September the 5th. The job should start on the 1st of October.
| + | |
− | | + | |
− | '''Contacts:'''
| + | |
− | * Joelle Amselem: [mailto:joelle.amselem@versailles.inra.fr joelle.amselem((at))versailles.inra.fr]
| + | |
− | * Michael Alaux: [mailto:michael.alaux@versailles.inra.fr michael.alaux((at))versailles.inra.fr]
| + | |
− | '''
| + | |
− | ''update october 2008: position for the first year now assigned.'''''
| + | |
− | | + | |
− | | + | |
− | Stéphanie Sidibe-Bocs, the PI of GnpAnnot, will be at BOSC and ISMB this week and is available to discuss the project and these openings. You can e-mail Stéphanie at [mailto:stephanie.sidibe-bocs@cirad.fr stephanie.sidibe-bocs@cirad.fr], or just introduce yourself when you see her.
| + | |
− | | + | |
− | ''2008/07/17''
| + | |
− | | + | |
− | == GMOD @ ISMB and BOSC ==
| + | |
− | | + | |
− | {{ImageRight|ISMB2008Skyline.png|ISMB 2008||http://www.iscb.org/ismb2008/}} {{ImageRight|BoscPear.png|BOSC 2008||http://open-bio.org/wiki/BOSC_2008}}
| + | |
− | GMOD has a [[ISMB 2008|strong presence]] at the [http://www.iscb.org/ismb2008/ ISMB 2008] and [http://open-bio.org/wiki/BOSC_2008 BOSC 2008] meetings, getting under way this week in Toronto. There are over a dozen talks and posters at the BOSC and ISMB conferences about [[GMOD Components]], or that feature research that using GMOD components. See [[ISMB 2008]] for a complete list and for a [[Media:GMODatISMB2008.pdf|flier we'll be distributing at the conference]].
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]
| + | |
− | <br />[[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2008/07/16''
| + | |
− | | + | |
− | == 2008 Summer School Report ==
| + | |
− | | + | |
− | {{ImageRight|SummerSchoolSmall.png|2008 GMOD Summer School||2008 GMOD Summer School}}
| + | |
− | | + | |
− | Or, ''what 29 people did with their summer vacation.''
| + | |
− | | + | |
− | The first annual [[GMOD Summer School]]summer was held July 11-13, 2008 at NESCent in Durham, NC. It was attended by 25 students and 4 instructors from 19 different states plus France and The Netherlands. Researchers came from the arthropod, vertebrate, prokaryote, plant, fungus, and virus communities. The questions and discussions were lively and participants were fully involved in the hands-on class. Students started the class with a minimal install of Linux and finished 2 1/2 (sometimes bumpy) days later with a system that was running [[Chado]], [[GBrowse]], [[Apollo]], and [[CMap]].
| + | |
− | | + | |
− | I would like to thank the participants, the instructors ([[User:Scott|Scott]], [[User:Faga|Ben]] and Ed) and the folks at NESCent for getting the GMOD Summer School off to a fabulous start.
| + | |
− | | + | |
− | We will be having a Second Annual Summer School in 2009 at NESCent. We will use what we learned at this year's course to make next year's even better. Watch this space for information on that course as next summer gets closer.
| + | |
− | | + | |
− | There has also been some discussion of holding the course in Europe. If you would be interested in attending a several day course on GMOD in Europe please send me an e-mail. If we get enough interest, we might try and pull it off.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2008/07/15''
| + | |
− | | + | |
− | == CMap 1.01 Released ==
| + | |
− | | + | |
− | Version 1.01 of [[CMap]] has been released.
| + | |
− | | + | |
− | I'm quite excited about using [[GFF3]] for data import/export which is possible with this release.
| + | |
− | | + | |
− | You can get the new version from SourceForge, http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=55129
| + | |
− | | + | |
− | Highlights of this release are:
| + | |
− | * Added a GFF3 parser and producer for easier and more complete data import and export (requires latest version of [[BioPerl|bioperl-live]] to import GFF).
| + | |
− | * Added a module to serve data to [http://acpfg.imb.uq.edu.au/cmap3d.php CMap3D], a 3D viewer being developed by Chris Duran and Dave Edwards.
| + | |
− | | + | |
− | If you have any questions, please [mailto:faga@cshl.edu let me know].
| + | |
− | | + | |
− | This is only an incremental update. For anyone who installed [[#CMap 1.0 Released|version 1.0]], simply download the new release and run
| + | |
− | | + | |
− | perl Build.PL; ./Build; sudo ./Build install
| + | |
− | | + | |
− | No updates to the database or config files are needed.
| + | |
− | | + | |
− | If you are updating from an older version, see the documentation in the <tt>upgrade/</tt> directory included in the package.
| + | |
− | | + | |
− | [[User:Faga|Ben]]
| + | |
− | | + | |
− | ''2008/07/01''
| + | |
− | | + | |
− | == GMOD Meeting Registration ==
| + | |
− | | + | |
− | {{ImageRight|July2008LogoSmaller.png|July 2008 GMOD Meeting||July 2008 GMOD Meeting}}
| + | |
− | [[July 2008 GMOD Meeting Registration|Registration]] is now open for the [[July 2008 GMOD Meeting]]. The meeting is scheduled for July 16-17, 2008 at the University of Toronto, immediately before [http://www.iscb.org/ismb2008/ ISMB 2008] (also in Toronto), and just a few days after the 2008 [[GMOD Summer School]].
| + | |
− | | + | |
− | Watch the [[July 2008 GMOD Meeting]] page for more information as the meeting draws nearer. If you have any questions or requests about the July 2008 meeting, please contact the [[GMOD Help Desk]] at [mailto:help@gmod.org help@gmod.org]. See the [[:Category:Meetings|notes from previous meetings]] for an idea of what is discussed at GMOD meetings.
| + | |
− | | + | |
− | ''2008/06/09''
| + | |
− | | + | |
− | == MAKER Joins GMOD ==
| + | |
− | | + | |
− | [[MAKER]] is a portable and easy to configure genome [[:Category:Annotation|annotation]] pipeline that has just become a part of GMOD. It's purpose is to allow smaller ''eukaryotic'' genome projects to annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ''ab initio'' gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on subsequent runs. MAKER's inputs are minimal. It outputs are in GFF3 or FASTA format, and can be directly loaded into [[Chado]], [[GBrowse]], and [[Apollo]].
| + | |
− | | + | |
− | MAKER was created and is maintained by the [http://www.yandell-lab.org/ Mark Yandell Lab] at the [http://www.utah.edu University of Utah].
| + | |
− | | + | |
− | See [[MAKER]] for more on how you can use it to automatically annotate your genomic data.
| + | |
− | | + | |
− | ''2008/05/16''
| + | |
− | | + | |
− | == Apollo 1.9 Released ==
| + | |
− | | + | |
− | [[Apollo]] 1.9.0 has been released. This release includes a number of bug fixes and some additions. The biggest new feature for this release is the Preferences Editor, which gives a graphical way to edit style/tiers files. This is aimed towards the non-power users and as such, it only supports a small subset (the ones we figured would be most useful) of the many options for those files. Power users might still want to manually edit the style/tiers files if they want to change something not supported through the GUI. Note that with this addition, the old Types Panel and Style Editor (which was basically just a text editor) have been retired.
| + | |
− | | + | |
− | You can get the new release of Apollo at:
| + | |
− | | + | |
− | http://apollo.berkeleybop.org
| + | |
− | | + | |
− | Ed Lee
| + | |
− | | + | |
− | ''2008/05/12''
| + | |
− | | + | |
− | == GMOD Summer School Update ==
| + | |
− | | + | |
− | {{ImageRight|SummerSchoolSmall.png|2008 GMOD Summer School||2008 GMOD Summer School}}
| + | |
− | <span style="font-size: 120%; font-weight: bold">July 11-13, 2008<br />National Evolutionary Synthesis Center (NESCent)<br />Durham, North Carolina, USA</span>
| + | |
− | | + | |
− | The [[2008 GMOD Summer School]] is a 2 1/2 day hands-on workshop aimed at teaching new GMOD users how to get up and running with popular GMOD components. The summer school was [[#GMOD Summer School|announced]] on March 7, 2008.
| + | |
− | | + | |
− | '''The [[2008 GMOD Summer School]] is now full.''' However, the waiting list is still small and if you are interested then you are encouraged to [[GMOD Summer School Statement of Interest|submit an application]].'''
| + | |
− | | + | |
− | If you have already applied for the GMOD Summer School you should have received an e-mail from the [[GMOD Help Desk|Help Desk]] informing you of your admission status.
| + | |
− | | + | |
− | ''2008/04/24, last updated 2008/05/16''
| + | |
− | | + | |
− | == Apollo 1.8 Released ==
| + | |
− | | + | |
− | I'm excited to let everyone know that we're releasing a new version of
| + | |
− | [[Apollo]] (1.8.0) today. There are many additions/bug fixes with this
| + | |
− | release. Most notably, due to popular demand, an 'undo' system. You
| + | |
− | can now access the 'undo' function through 'Edit→Undo' (or ctrl-u).
| + | |
− | For more information on the changes, check out the [http://gmod.cvs.sourceforge.net/gmod/apollo/doc/release-notes/release-1.8.0-notes?view=markup release doc].
| + | |
− | | + | |
− | On another note, the official Apollo URL has changed. It's no longer:
| + | |
− | | + | |
− | http://www.fruitfly.org/annot/apollo
| + | |
− | | + | |
− | but rather:
| + | |
− | | + | |
− | http://apollo.berkeleybop.org
| + | |
− | | + | |
− | Please update your bookmarks accordingly.
| + | |
− | | + | |
− | Ed Lee
| + | |
− | | + | |
− | ''2008/04/10''
| + | |
− | | + | |
− | == Sea Urchin Genome Database ==
| + | |
− | | + | |
− | {{ImageRight|SpBaseLogo.png|Sea Urchin Genome Database||http://spbase.org/}}
| + | |
− | Today, Tuesday April 4th, the [http://spbase.org Sea Urchin Genome Database] went public. Based on the GMOD tools and applications the site organizes and displays the genome sequence and annotations produced by the [http://www.hgsc.bcm.tmc.edu/ Baylor College of Medicine Human Genome Sequencing Center] and the sea urchin research community. This site housed at the Center for Computational Regulatory Genomics, the [http://www.its.caltech.edu/~bi/ Beckman Institute] at [http://www.caltech.edu/ California Institute of Technology] plans to enrich and extend the sea urchin sequence and annotations.
| + | |
− | | + | |
− | Visit us at [http://spbase.org SpBase].
| + | |
− | | + | |
− | [[User:Acameron|Andy Cameron]]<br />
| + | |
− | | + | |
− | ''2008/04/08''
| + | |
− | | + | |
− | | + | |
− | == Chado Doc Reorganization ==
| + | |
− | | + | |
− | Chado is the database schema of GMOD and it has quite a bit of documentation in this web site. However, this documentation could be better organized and integrated. We are launching the [[Chado Documentation Reorganization]] effort to do just that.
| + | |
− | | + | |
− | During this effort the existing [[:Category:Chado|Chado documentation]] may be unstable. We will do our best to make this reorganization be as painless as possible.
| + | |
− | | + | |
− | The [[Chado Documentation Reorganization]] page summarizes our existing documentation and then [[Chado Documentation Reorganization#Plan|proposes a plan]] for restructuring it. If you have any suggestions or comments on this then please send us your [[Chado Documentation Reorganization#Feedback|feedback]].
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2008/04/04''
| + | |
− | | + | |
− | == iPlant Collaborative Job Openings ==
| + | |
− | | + | |
− | Cold Spring Harbor Laboratory is seeking experienced software developers/bioinformaticians to join the [http://www.iplantcollaborative.org/ iPlant Collaborative], a new NSF-funded initiative which seeks to develop a comprehensive national cyberinfrastructure which will unite researchers in every plant biology discipline.
| + | |
− | | + | |
− | See the [http://www.iplantcollaborative.org/resources/job-postings/45-professional iPlant job board] for job descriptions.
| + | |
− | | + | |
− | ''2008/04/01''
| + | |
− | | + | |
− | | + | |
− | | + | |
− | == GMOD 1.0 Released ==
| + | |
− | | + | |
− | I am very pleased to announce the release of GMOD 1.0. The file can be
| + | |
− | downloaded from SourceForge at:
| + | |
− | | + | |
− | http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=19511
| + | |
− | | + | |
− | This release comes at a time when both the [[Chado]] schema and its
| + | |
− | associated tools have matured and are now quite stable. The plan going
| + | |
− | forward is to have more frequent releases with schema changes between
| + | |
− | versions clearly delineated.
| + | |
− | | + | |
− | In addition to the Chado schema, this release includes:
| + | |
− | | + | |
− | * Tools for creating a new database.
| + | |
− | * Tools for populating it with [[:Category:Ontologies|ontology]] data (using go-perl).
| + | |
− | * A fairly new tool for updating ontologies contributed by the developers of [[:Category:SGN|SGN]], the Sol Genomics Network.
| + | |
− | * Tools for loading sequence feature (i.e. [[GFF3]]) data.
| + | |
− | * GMODTools for creating bulk download files like GFF and Fasta (See [[GMODTools]] for more information).
| + | |
− | | + | |
− | Other data can be loaded using [[XORT]].
| + | |
− | This release of Chado works well with the upcoming release of [[GBrowse]],
| + | |
− | as well as with the current versions of [[Apollo]] and [[CMap]]. It should also
| + | |
− | work well with [[GMODWeb]]/[[Turnkey]].
| + | |
− | | + | |
− | With this release, there are so many people in the GMOD community that I
| + | |
− | would like to thank that I couldn't possibly list them all, but at a
| + | |
− | bare minimum, I would like to thank the developers at [[:Category:FlyBase|FlyBase]] and the
| + | |
− | Berkeley Drosophila Genome Project, especially Chris Mungall and Dave
| + | |
− | Emmert, as well as others who have contributed code to the GMOD project
| + | |
− | over the past several years.
| + | |
− | | + | |
− | Please direct any questions about using this release to the GMOD schema mailing list, [mailto:gmod-schema@lists.sourceforge.net gmod-schema@lists.sourceforge.net].
| + | |
− | | + | |
− | [[User:Scott|Scott Cain]]
| + | |
− | | + | |
− | ''2008/03/31''
| + | |
− | | + | |
− | == CMap 1.0 Released ==
| + | |
− | | + | |
− | Version 1.0 of CMap has been released.
| + | |
− | | + | |
− | You can get the new version from SourceForge, http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=55129
| + | |
− | | + | |
− | Highlights of this release are:
| + | |
− | * Ribbon option for correspondences
| + | |
− | * New Feature Glyphs
| + | |
− | * A dot-plot view
| + | |
− | * An image_only URL parameter allowing a CMap image to be embedded in another page
| + | |
− | * Easier install with directory guessing
| + | |
− | * API better documented for writing custom scripts to load data
| + | |
− | | + | |
− | If you have any questions, please email the [mailto:gmod-cmap@lists.sourceforge.net CMap mailing list].
| + | |
− | | + | |
− | Ben
| + | |
− | | + | |
− | ''2008/03/28''
| + | |
− | | + | |
− | == July 2008 GMOD Meeting ==
| + | |
− | | + | |
− | <div style="float: right; padding: 0.5em">{{#icon: July2008LogoSmaller.png|July 2008 GMOD Meeting||July 2008 GMOD Meeting}}</div>
| + | |
− | The next [[July 2008 GMOD Meeting|GMOD community meeting]] has been scheduled for July 16-17, 2008 at the University of Toronto, immediately before [http://www.iscb.org/ismb2008/ ISMB 2008] (also in Toronto), and just a few days after the 2008 [[GMOD Summer School]].
| + | |
− | | + | |
− | Watch the [[July 2008 GMOD Meeting]] page for more information as the meeting gets nearer. If you have any questions or requests about the July 2008 meeting, please contact the [[GMOD Help Desk]] at [mailto:help@gmod.org help@gmod.org]. See the [[Meetings|notes from previous meetings]] for an idea of what is discussed at GMOD meetings.
| + | |
− | | + | |
− | Thanks, <br />
| + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2008/03/25''
| + | |
− | | + | |
− | | + | |
− | == SynBrowse Developers Needed ==
| + | |
− | | + | |
− | <div style="float: right; padding: 0.5em">{{#icon: SynBrowse_logoNoText.png|SynBrowse||SynBrowse}}</div>
| + | |
− | The [[SynBrowse]] [[synteny]] viewer, a GMOD component, is moving towards its second major release. Xiaokang Pan, the project's lead developer, is looking for volunteer developers to help get this release out sooner.
| + | |
− | | + | |
− | SynBrowse2 is written in Perl, and is built on several open source components, including parts of [[GBrowse]]. SynBrowse2 need particular improvements in run-time performance and its alignment parsing tools. Ideally, programmers will develop SynBrowse2 using a set of animal or microbial genomes (Xiaokang is already working with several plant genomes). Programmers can improve the alignment parsing tools, fix potential bugs and hopefully improve other parts of SynBrowse as well.
| + | |
− | | + | |
− | If you have any interest in and/or experience with multiple alignment or synteny visualization tools please considering contributing to the SynBrowse project. Xiaokang can be reached at [mailto:xiaokangpan@gmail.com xiaokangpan@gmail.com].
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2008/03/21''
| + | |
− | | + | |
− | == GMOD at ParameciumDB ==
| + | |
− | | + | |
− | <div style="float: right; padding: 0.5em">{{#icon: ParameciumDBIcon133x42.png|ParameciumDB||ParameciumDB}}</div>
| + | |
− | Curious to know what is involved in becoming a GMOD user and creating a GMOD based web site? You can now read the GMOD User Story, an article about [[ParameciumDB]]'s experience with implementing GMOD. The article describes what GMOD components ParameciumDB uses and how they connect them together. [[ParameciumDB]] uses several GMOD components, including [[Chado]], [[GMODWeb]], [[Apollo]], and [[GBrowse]]. Please contact [[User:Sperling|Linda Sperling]] <[mailto:linda.sperling@cgm.cnrs-gif.fr linda.sperling@cgm.cnrs-gif.fr]> if you have questions about GMOD at ParameciumDB.
| + | |
− | | + | |
− | This is the first of a series of articles on how different organizations use GMOD components to achieve their goals. User stories will give readers a feel for what implementation choices are involved and which ones each organization made. If you are interested in describing your experience with GMOD, please consider creating a user story page for your project. You can just start writing (this is a wiki!) or contact the [[GMOD Help Desk]] for assistance. If we aren't swamped with volunteers, then I will be asking (cajoling?) several not-so-randomly picked projects to write user stories describing their experiences. I'm hoping to have a new story every other month or so.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2008/03/18''
| + | |
− | | + | |
− | == Beta Test CMap: Win a T-Shirt! ==
| + | |
− | UPDATE: We have our winners. Even still, please feel free to give the release candidate a try and let us know how it goes.
| + | |
− | | + | |
− | We need beta testers for the [[CMap]] 1.0 release candidate.
| + | |
− | | + | |
− | <div style="float: right; border: 1px solid blue; margin: 0.5em">{{#icon: TShirtThumb.jpg|GMOD T Shirt||
| + | |
− | http://www.cafepress.com/genericmod.238973590}}<br /><center>Win this shirt!</center></div>
| + | |
− | | + | |
− | If I get four (or more) people who let me know that they will try out the release candidate, I will draw two of their names (or email addresses) and buy them each a GMOD T-shirt (based on random drawing, void where prohibited, etc). Testers from around the world are welcome (and eligible for the shirts as long as Cafe Press ships there and it isn't prohibited by law).
| + | |
− | | + | |
− | You can get the release candidate from [http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=55129&release_id=583120 SourceForge].
| + | |
− | | + | |
− | To view the T-shirt or get one for yourself visit
| + | |
− | [http://www.cafepress.com/genericmod.238973590 Cafe Press]. Note: There is no price markup for GMOD. The only one making money on the shirts is Cafe Press.
| + | |
− | | + | |
− | If the threshold is broken, I will hold the drawing on Friday the 15th at 1pm CST (2pm Eastern) and email the winners for their addresses and shirt sizes. If you don't want to be entered in the drawing just let me know. There is already one beta tester, so only three to go.
| + | |
− | | + | |
− | Remember: ''If no one beta tests, everyone beta tests.''
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Faga|Ben Faga]],<br />[mailto:faga.cshl@gmail.com faga.cshl@gmail.com]
| + | |
− | | + | |
− | ''2008/03/11''
| + | |
− | | + | |
− | == GMOD Summer School ==
| + | |
− | | + | |
− | <div style="float: right; padding: 0.5em">{{#icon: SummerSchoolSmall.png|Summer School||2008 GMOD Summer School}}</div>
| + | |
− | <span style="font-size: 120%; font-weight: bold">July 11-13, 2008<br />National Evolutionary Synthesis Center (NESCent)<br />Durham, North Carolina, USA</span>
| + | |
− | | + | |
− | The first annual [[GMOD Summer School]] will be held July 11-13, 2008 at the [http://nescent.org National Evolutionary Synthesis Center (NESCent)], in Durham, North Carolina, USA. This is a 2 1/2 day hands-on workshop aimed at teaching new GMOD users how to get up and running with popular GMOD components. There will also be a concurrent 1 day session aimed at principal investigators that will give decision makers an overview of what GMOD can do, how the project operates, and what level of resources are needed to get a GMOD installation up and running. If you are interested in attending please submit a [[GMOD Summer School Statement of Interest|Statement of Interest]] before April 15, 2008. The course is free but class size is limited. See the [[GMOD Summer School]] page for more information and a tentative program.
| + | |
− | | + | |
− | ''2008/03/07''
| + | |
− | | + | |
− | == Ten Recent Web Site Changes ==
| + | |
− | | + | |
− | This entry summarizes several recent changes in the [[Main Page|GMOD web site]]. These changes are designed to make the site more useful, and hopefully will make your GMOD web site experience more pleasant.
| + | |
− | | + | |
− | '''Ten Recent Web Site Changes to Make Your GMOD Life Easier:'''
| + | |
− | | + | |
− | # '''[[Categories]]''' - Most of the pages in the GMOD web site have now been tagged, and those tags can be used as an alternative way to navigate the site. We have also added tools that make it easier to assign tags when creating content. (Note: The category hierarchy is still work in progress. Suggestions are welcome.)
| + | |
− | # '''[[GMOD News]]''' - News items of interest to the GMOD community. This is also available as an RSS feed.
| + | |
− | # '''[[Main Page]]''' - Items from the GMOD News page and recently edited pages (non-minor edits) now show up in the right sidebar.
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− | # '''[[Calendar]]''' - Calendar of events of interest to the GMOD project.
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− | # '''[[Glossary]]''' - Short definitions of non-biological terms used in GMOD.
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− | # '''[[GMOD Mailing Lists]]''' - Shows more lists, and sorts them into Overview, Component, and Inactive lists. If your list isn't here, please add it.
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− | # '''[[Site Guidelines]]''' - Guidelines for creating and editing content on the GMOD web site.
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− | # '''[[GMOD Help Desk]]''' - Explains services offered by the help desk.
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− | # '''[[Computing Requirements]]''' - Description of expertise and computing systems you'll need to set up a GMOD installation.
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− | # '''[[Databases and GMOD]]''' - An overview of database concepts and how databases are used in GMOD.
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− | Note that several of these pages need continuing contributions from the community. '''That means you!''' We particularly encourage you to get in the habit of submitting new [[Calendar]], [[Glossary]], and News items.
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− | Our next big goal for the web site is to reorganize the [[:Category:Chado|Chado documentation]]. Watch the web site for details on this.
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− | As always, please let us know if you have any questions or comments.
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− | Thanks,
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− | Dave Clements, [[GMOD Help Desk]]<br />
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− | [mailto:help@gmod.org help@gmod.org]
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− | ''2008/02/13''
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− | == Pathway Tools Workshop ==
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− | A session at the Cambridge Healthtech [http://www.tri-conference.com/08_gdd.asp Pathway Analysis conference], March 26-28, 2008 in San Francisco, will describe [[Pathway Tools]], a GMOD component for modeling metabolic pathways and regulatory networks. There will also be presentations by these GMOD [[MOD|member databases]] that use [[Pathway Tools]] in their databases:
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− | * [[:Category:MGI|Mouse]]
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− | * [[:Category:DictyBase|dictyBase]]
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− | * [[:Category:SGD|SGD]]
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− | * [[:Category:SGN|Solanaceae Genomics Network]]
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− | Early registration is available until February 22, 2008
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− | ''2008/01/28''
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− | == GMOD at Arthropod Genomics ==
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− | There will be two [http://www.k-state.edu/agc/Workshop.shtml GMOD related workshops] at the [http://www.k-state.edu/agc/symposium.shtml Arthropod Genomics Symposium], April 10-13, 2008, in Kansas City.
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− | * ''Community Contributions to Genome Annotation'' - Christine Elsik of [http://racerx00.tamu.edu/bee_resources.html BeeBase] will discuss how to install and use the [[Apollo]] genome annotation tool.
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− | * ''Chado: A Database Schema for Integrating Biological Data'' - [[User:Scott|Scott Cain]] and [[User:Clements|Dave Clements]] will cover [[Chado]]'s logical concepts, the types of data it can represent, how to import and export data, and how Chado integrates with other GMOD components such as [[Apollo]] and [[GBrowse]].
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− | GMOD has a particularly strong presence in the arthropod community (e.g., [http://bioinformatics.ksu.edu/BeetleBase/ BeetleBase], [http://racerx00.tamu.edu/bee_resources.html BeeBase], [http://flybase.org FlyBase], [http://wfleabase.org/ wFleaBase], ...). If you are an arthropod researcher interested in using [[GMOD Components]] then this meeting will be time well spent.
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− | [http://www.k-state.edu/agc/Register.shtml Early registration] and [http://www.k-state.edu/agc/AbstractGuidelines.shtml poster abstract submissions] are both open until February 29.
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− | ''2008/01/21''
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− | == Apollo 1.7.0 Released ==
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− | Version 1.7.0 of [[Apollo]] has just been released. You can access the updated Apollo page at http://www.fruitfly.org/annot/apollo
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− | Changes in this version include
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− | * Added [[Glossary#GFF|GFF3]] support
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− | * Added program source filtering for reading off [[Chado]] databases
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− | * Lots of work on the ensj adapter to allow it to work better with recent ensembl schemas, handle ditags, give finer control of gene loading, increase speed of gene loading, bug fixes to history, cigar parsing in ensj layer, loading of contig features
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− | * Allow layout of display to be saved to / loaded from a file. Most useful for synteny where initial display set up can take time. The saved layout also includes the current base position and zoom factor, and on loading you can choose to use those.
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− | * Ability to edit settings for a type (new popup menu item in feature popup). The settings which can be edited are the glyph used for drawing the feature and the columns in the table displayed in the evidence panel.
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− | * New drawing glyph which shades exons darker or lighter depending on their phase (DrawablePhaseHighlightGeneFeatureSet). Also a version of that which uses straight lines to join exons rather than 'hats' (DrawablePhaseHighlightNoHatGeneFeatureSet)
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− | * Work on ensembl synteny adapter so it works with latest ensembl compara db schema, and basic support for allowing different alignment sets to be selected.
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− | * PureJDBCTransactionWriter added. This entailed some changes to other classes, but in almost every case the changes are 1. reverse compatible and 2. invisible to the end user.
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− | * Uses of Log4J for generating log files.
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− | Plus many other changes. See the [http://gmod.cvs.sourceforge.net/gmod/apollo/doc/release-notes/release-1.7.0-notes?view=markup release notes] for more.
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− | We are hoping to cut releases on a more regular basis (after the year and a half long hiatus). So please [[Apollo#Contact|let us know]] if you find any bugs and they will be addressed and put into a new release as soon as possible.
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− | ''2008/01/11''
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− | = 2007 Stories =
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− | == GBrowse Tutorial at PAG XVI ==
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− | ''2007/12/27''
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− | Scott Cain will present a [http://www.intl-pag.org/16/16-gbrowse.html GBrowse tutorial] at the [http://www.intl-pag.org/ Plant and Animal Genome XVI Conference (PAG-XVI)], January 12-16, 2008, in San Diego. This will be a hands-on tutorial on how to install and use the [[GBrowse]] genome browser. If you are attending PAG and you are interested in GBrowse then please consider attending.
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− | See the [http://www.intl-pag.org/16/16-gbrowse.html PAG tutorial page] for additional information.
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− | == Modware Feedback Wanted ==
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− | [[Modware]] provides an object-oriented Perl API for [[Chado]] suitable for use by any application based on GMOD. This Chado API supports creating, retrieving and updating objects in a Chado database. Modware makes heavy use of [[bp:Main Page|BioPerl]] to provide a familiar and intuitive interface for objects stored inside of a Chado database.
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− | Recently, a VMware Virutal Machine was released to make download and
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− | testing of a fully configured and installed version of Modware
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− | available. Modware developers continue to add new features, including
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− | representation of BLAST hits (currently on CVS HEAD).
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− | One critical piece of the project that is missing is feedback from the
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− | community. If you are interested in a Chado API, please download the
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− | Modware Virtual Machine found on the [http://gmod-ware.sourceforge.net Modware home page] and give it a try. Email all feature requests, questions, and comments to [mailto:gmod-ware-users@sourceforge.net gmod-ware-users@sourceforge.net].
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− | ''2007/12/11''
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− | == November 2007 GMOD Meeting ==
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− | The [[November 2007 GMOD Meeting]] was attended by nearly 40 people from across the GMOD community. Community annotation and comparative genomics were two popular topics at this meeting. See [[November 2007 GMOD Meeting]] for a list of presentations and a summary of the meeting.
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− | ''2007/11/08''
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− | == GMODTools 1.1 Released ==
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− | Version 1.1 of [[GMODTools]] has been released. Version 1.1 adds these features and corrections:
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− | * No chromosome/scaffold/golden_path files. This change is needed to handle partially assembled genomes with many (1000s to 100,000s) of scaffolds. Flag no_csomesplit=1 to use this (should become default).
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− | * Gene Ontology association file, see go_association tags in configurations
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− | * Validate main variables in chado database: ${golden_path}, ${seq_ontology}. This step, on now by default, checks that database contains configured values. If failed, db is inspected for real values.
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− | * Miscellany bugs cured and configuration updates, e.g., tables/overview now again active.
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− | [[GMODTools]] is a Perl package that generates Fasta, [[GFF]], DNA and other bulk genome annotation files from Chado databases.
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− | ''2007/10/16''
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− | == GMOD Help Desk is Back ==
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− | After a several month hiatus, the [[GMOD Help Desk]] is back. Dave Clements has taken the role created by Brian Osborne earlier this year. Dave will work on the same sorts of things that Brian did: Maintaining and improving the GMOD web site and documentation, and supporting the GMOD user community. See [[GMOD Help Desk]] for more.
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− | ''2007/10/01''
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− | == FlyBase Converts to Chado ==
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− | This summer, FlyBase [[June 2007 Progress Report#Chado/FlyBase|finished its reimplementation]] using [[Chado]], the modular GMOD database schema which [http://flybase.org/ FlyBase] originated and continues to develop
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− | in collaboration with GMOD and several GMOD-affiliated database
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− | projects. The FlyBase implementation of Chado integrates over 100
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− | years of ''Drosophila'' genetic and genomic research data. In addition to
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− | supporting the ongoing genome annotation and scientific literature
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− | curation for ''D. melanogaster'', the main Drosophilid model organism,
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− | FlyBase is currently working to incorporate the new genome sequences,
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− | annotations, and cross-species comparative data for eleven additional
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− | Drosophila species into the single production instance of Chado.
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− | PostgreSQL dumps of FlyBase-chado are available at ftp://ftp.flybase.net/releases/current/psql/
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− | ''2007/09/01''
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− | == Pathway Tools 11.5 Released ==
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− | Version 11.5 of Pathway Tools has been [http://bioinformatics.ai.sri.com/ptools/release-notes.html released]. Version 11.5 includes
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− | * Support for cellular regulation.
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− | * Electron transport information
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− | * Zooming in genome view
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− | * Stricter pruning to eliminate pathway predictions that are likely to be false-positive predictions
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− | See the [http://bioinformatics.ai.sri.com/ptools/release-notes.html Pathway Tools release notes] for details.
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− | [[Pathway Tools]] is a comprehensive symbolic systems biology software package that supports several use cases in bioinformatics and systems biology.
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− | ''2007/08/15''
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− | == ISMB/Bioinformatics Chado Paper ==
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− | The paper '[http://bioinformatics.oxfordjournals.org/cgi/content/full/23/13/i337 A Chado case study: an ontology-based modular schema for representing genome-associated biological information]' by Chris Mungall, Dave Emmert, and The [http://flybase.org/static_pages/docs/consortium.html FlyBase Consortium], was presented at [http://www.iscb.org/ismbeccb2007/ ISMB/ECCB 2007], and is now available in the journal [http://bioinformatics.oxfordjournals.org/ Bioinformatics].
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− | The paper describes the overall [[Chado]] philosophy and the 5 core Chado modules.
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− | ''2007/07/13''
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− | == BioMart 0.6 Released ==
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− | Version 0.6 of the BioMart has been [http://www.biomart.org/news.html released]. Version 0.6 includes support for a 1.5 [[DAS]] server, and improvements to MartView and MartBuilder. See [http://www.biomart.org/news.html BioMart News] for more.
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− | [[BioMart]] is a query oriented database management system for biological data.
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− | ''2007/06/15''
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− | == GBrowse 1.68 Released ==
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− | Version 1.68 of [[GBrowse]] is a stability release which improves the documentation and installation process. It includes a new script called <tt>gbrowse_netinstall.pl</tt>, which will semi-automatically install GBrowse across the Internet on [[GBrowse Windows HOWTO|Windows]], [[GBrowse MacOSX HOWTO|Mac OSX]] and [[GBrowse Linux HOWTO|Linux]] platforms.
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− | ''2007/04/17''
| + | <rss text number="5000" desc="off" title="off">http://gmod.org/mediawiki/index.php?title=Special%3ANewsChannel&format=rss20&limit=5000&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed</rss> |
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| = The Really Old News Archive = | | = The Really Old News Archive = |
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| [[Category:GMOD Community]] | | [[Category:GMOD Community]] |
| + | [[Category:!FixAfterUpgrade]] |
The GMOD News Archive contains old news items that have been archived off of the GMOD News page/feed. The News includes anything that is relevant to the GMOD user and developer communities. This includes a wide range of topics, from GMOD meetings and releases to user success stories and GMOD related publications.