Difference between revisions of "GMOD News Archives"

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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 />
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[[GMOD News|Recent News Only]]<br />
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The GMOD News Archive contains old news items that have been archived off of the [[GMOD News]] page/feed.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The GMOD News Archive contains old news items that have been archived off of the [[GMOD News]] page/feed.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.
  
 
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.
  
= 2009 Stories =
+
= All News Items =
 
+
Most news items from 2009 are still on the [[GMOD News]] page.  They only show up here once they are more than 6 months old.
+
 
+
== Aug 2009 GMOD Meeting Report ==
+
 
+
{{ImageRight|Aug2009MeetingPhoto.JPG|August 2009 GMOD Meeting||August 2009 GMOD Meeting}}
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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:
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* [[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.
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* 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]]
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* 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]]
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<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)
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+
''2009/08/29''
+
 
+
== InterMine 0.91 Released ==
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{{ImageRight|InterMine.png|InterMine|200|InterMine}}
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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 ==
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<div style="float: right">
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{|
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| {{#icon: Cvs_logo.gif|CVS|70|CVS to Subversion Conversion}}
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| <span style="font-size: 200%; font-weight: bold">&rArr;</span>
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| {{#icon: Subversion_logo.jpg|Subversion||CVS to Subversion Conversion}}
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|}
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</div>
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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.
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<div class="emphasisbox">
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'''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.'''
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</div>
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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.
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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.
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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.
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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.
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+
Thanks,
+
 
+
[[User:Clements|Dave Clements]] and [[User:RobertBuels|Rob Buels]]
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+
''2009/08/26''
+
 
+
== GBrowse 1.70 Released ==
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+
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:
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* 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.
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* Fixed problem with feature highlighting which caused highlighting to get "stuck"on beige.
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* Removed annoying debugging statements from log files
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* Fixed character encoding issues for onClick popup balloons
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* Killed annoying "missing path" warning on windows systems
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* Fixed issue in which the selected region shown in the overview is offset from true region.
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* Silenced log file warnings when inkscape isn't present.
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* Added "merge searches" option to turn merging of similarly-named features on and off.
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* 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
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* Fixed encoding of version number at the bottom of the page.
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* Made the [[DAS]] script compatible with DAS Registry
+
 
+
[[User:Scott|Scott]]
+
 
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''2009/08/24''
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== Lepidoptera Bioinformatics ==
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{{ImageRight|Butterfly1.jpg|International Workshop on Molecular Biology and Genetics of Lepidoptera||http://bio.demokritos.gr/leps/leps.htm}}
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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.
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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''
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== Ant Genomics Bioinformatician ==
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{{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.''
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+
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 ==
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<div style="text-align: center">
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{{#icon: InformationSystemsForInsectPests.gif|Information Systems for Insect Pests|400|http://colloque.inra.fr/isyip}}
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<div style="font-size: 120%">[http://colloque.inra.fr/isyip 1st International Workshop]</div>
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<div style="font-size: 110%">16-17th November 2009<br />INRIA Rennes-Bretagne-Atlantique</div>
+
</div>
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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.
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+
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
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* 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''
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== August 2009 GMOD Meeting ==
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{{ImageRight|GMOD2009Europe170.png|August 2009 GMOD Meeting||August 2009 GMOD Meeting}}
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<div style="font-size: 140%; text-align: center">[[August 2009 GMOD Meeting|Register for the August 2009 GMOD Meeting]]</div>
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+
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 &pound;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.
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Please join us in Oxford this August,
+
 
+
[[User:Clements|Dave Clements]]<br />
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[[GMOD Help Desk]]
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+
''2009/07/01''
+
 
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'''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.
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== Join ISB ==
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{{ImageRight|ISB_logo.gif‎|International Society for Biocuration||http://colleagues.biocurator.org/join}}
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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.
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+
Please consider this investment,
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
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+
''2009/06/25''
+
 
+
== Apollo 1.11.0 Released ==
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+
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|||}}&nbsp;</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||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&rarr;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.
+
# '''[[Calendar]]''' - Calendar of events of interest to the GMOD project.
+
# '''[[Glossary]]''' - Short definitions of non-biological terms used in GMOD.
+
# '''[[GMOD Mailing Lists]]''' - Shows more lists, and sorts them into Overview, Component, and Inactive lists. If your list isn't here, please add it.
+
# '''[[Site Guidelines]]''' - Guidelines for creating and editing content on the GMOD web site.
+
# '''[[GMOD Help Desk]]''' - Explains services offered by the help desk.
+
# '''[[Computing Requirements]]''' - Description of expertise and computing systems you'll need to set up a GMOD installation.
+
# '''[[Databases and GMOD]]''' - An overview of database concepts and how databases are used in GMOD.
+
 
+
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.
+
 
+
Our next big goal for the web site is to reorganize the [[:Category:Chado|Chado documentation]].  Watch the web site for details on this.
+
 
+
As always, please let us know if you have any questions or comments.
+
 
+
Thanks,
+
 
+
Dave Clements, [[GMOD Help Desk]]<br />
+
[mailto:help@gmod.org help@gmod.org]
+
 
+
''2008/02/13''
+
 
+
== Pathway Tools Workshop ==
+
 
+
''2008/01/28''
+
 
+
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:
+
* [[:Category:MGI|Mouse]]
+
* [[:Category:DictyBase|dictyBase]]
+
* [[:Category:SGD|SGD]]
+
* [[:Category:SGN|Solanaceae Genomics Network]]
+
 
+
Early registration is available until February 22, 2008
+
 
+
== GMOD at Arthropod Genomics ==
+
 
+
''2008/01/21''
+
 
+
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.
+
* ''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.
+
* ''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]].
+
 
+
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.
+
 
+
[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.
+
 
+
 
+
== Apollo 1.7.0 Released ==
+
 
+
''2008/01/11''
+
 
+
Version 1.7.0 of [[Apollo]] has just been released.  You can access the updated Apollo page at http://www.fruitfly.org/annot/apollo
+
 
+
Changes in this version include
+
* Added [[Glossary#GFF|GFF3]] support
+
* Added program source filtering for reading off [[Chado]] databases
+
* 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
+
* 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.
+
* 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.
+
* 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)
+
* 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.
+
* 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.
+
* Uses of Log4J for generating log files.
+
 
+
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.
+
 
+
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.
+
 
+
= 2007 Stories =
+
 
+
== GBrowse Tutorial at PAG XVI ==
+
 
+
''2007/12/27''
+
 
+
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.
+
 
+
See the [http://www.intl-pag.org/16/16-gbrowse.html PAG tutorial page] for additional information.
+
 
+
== Modware Feedback Wanted ==
+
 
+
''2007/12/11''
+
 
+
[[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.
+
 
+
Recently, a VMware Virutal Machine was released to make download and
+
testing of a fully configured and installed version of Modware
+
available.  Modware developers continue to add new features, including
+
representation of BLAST hits (currently on CVS HEAD).
+
 
+
One critical piece of the project that is missing is feedback from the
+
community.  If you are interested in a Chado API, please download the
+
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].
+
 
+
== November 2007 GMOD Meeting ==
+
 
+
''2007/11/08''
+
 
+
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.
+
 
+
== GMODTools 1.1 Released ==
+
 
+
''2007/10/16''
+
 
+
Version 1.1 of [[GMODTools]] has been released.  Version 1.1 adds these features and corrections:
+
 
+
* 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).
+
* Gene Ontology association file, see go_association tags in configurations
+
* 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.
+
* Miscellany bugs cured and configuration updates, e.g., tables/overview now again active.
+
 
+
[[GMODTools]] is a Perl package that generates Fasta, [[GFF]], DNA and other bulk genome annotation files from Chado databases.
+
 
+
== GMOD Help Desk is Back ==
+
 
+
''2007/10/01''
+
 
+
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.
+
 
+
== FlyBase Converts to Chado ==
+
 
+
''2007/09/01''
+
 
+
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
+
in collaboration with GMOD and several GMOD-affiliated database
+
projects.  The FlyBase implementation of Chado integrates over 100
+
years of ''Drosophila'' genetic and genomic research data.  In addition to
+
supporting the ongoing genome annotation and scientific literature
+
curation for ''D. melanogaster'', the main Drosophilid model organism,
+
FlyBase is currently working to incorporate  the new genome sequences,
+
annotations, and cross-species comparative data for eleven additional
+
Drosophila species into the single production instance of Chado.
+
 
+
PostgreSQL dumps of FlyBase-chado are available at ftp://ftp.flybase.net/releases/current/psql/
+
 
+
== Pathway Tools 11.5 Released ==
+
 
+
''2007/08/15''
+
 
+
Version 11.5 of Pathway Tools has been [http://bioinformatics.ai.sri.com/ptools/release-notes.html released].  Version 11.5 includes
+
* Support for cellular regulation.
+
* Electron transport information
+
* Zooming in genome view
+
* Stricter  pruning to eliminate pathway predictions that are likely to be false-positive predictions
+
 
+
See the [http://bioinformatics.ai.sri.com/ptools/release-notes.html Pathway Tools release notes] for details.
+
 
+
[[Pathway Tools]] is a comprehensive symbolic systems biology software package that supports several use cases in bioinformatics and systems biology.
+
 
+
== ISMB/Bioinformatics Chado Paper ==
+
 
+
''2007/07/13''
+
 
+
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].
+
 
+
The paper describes the overall [[Chado]] philosophy and the 5 core Chado modules.
+
 
+
== BioMart 0.6 Released ==
+
 
+
''2007/06/15''
+
 
+
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.
+
 
+
[[BioMart]] is a query oriented database management system for biological data.
+
 
+
== GBrowse 1.68 Released ==
+
 
+
''2007/04/17''
+
  
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.
+
<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>
  
 
= The Really Old News Archive =
 
= The Really Old News Archive =
Line 1,349: Line 32:
  
 
[[Category:GMOD Community]]
 
[[Category:GMOD Community]]
 +
[[Category:!FixAfterUpgrade]]

Latest revision as of 11:12, 22 August 2013

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.

See the GMOD News page for instruction on how to post a news item.

All News Items

Prospecting for Proposals for GSoC 2024

The Open Genome Informatics group and GMOD has submitted an application for Google Summer of Code (GSoC) this year, and we are soliciting project ideas from people and groups involved in the GMOD project.

GSoC is a global program run by Google to encourage students to get real-world experience of participating in a software project; students work on a project over the summer months and receive a stipend from Google for participating. Thousands of organizations of different sizes participate in GSoC, with the common factor being that they must produce open-source code.

Please take a look at the GSoC wiki page and think about any projects that might work well for a GSoC student, and add them to the wiki. If you are interested in being a mentor, don't hesitate to get in touch with us at robin.haw@oicr.on.ca help@gmod.org.

If you have any questions--e.g. what constitutes an appropriate project; whether your idea is sufficiently GMOD-related--please feel free to email rhaw@oicr.on.ca and help@gmod.org for advice!


Posted to the GMOD News on 2024/02/12

JBrowse2 v1.1.0 Released

We're pleased to announce a new release of JBrowse Web!

(Reposted by permission from https://jbrowse.org/jb2/blog/2021/03/29/v1.1.0-release

Changed callbacks language from JavaScript to Jexl

To allow users to safely and seamlessly share advanced configurations in sessions, we now use Jexl to express configuration callbacks. Note that this is a breaking change, function()-style callbacks will no longer work.

For details, see the callbacks section of our configuration guide.

Fetch intron and upstream/downstream sequences

We also have several other improvements including the ability to get intron and upstream/downstream sequence in the feature details

<img alt="Upstream downstream.png" src="http://gmod.org/mediawiki/images/thumb/7/76/Upstream_downstream.png/700px-Upstream_downstream.png" width="700" height="248" srcset="/mediawiki/images/thumb/7/76/Upstream_downstream.png/1050px-Upstream_downstream.png 1.5x, /mediawiki/images/thumb/7/76/Upstream_downstream.png/1400px-Upstream_downstream.png 2x" />

Interactive documentation using Storybook

Another new update is the first release of our interactive Storybook docs for the embeddable React Linear Genome View. The docs contain live examples of how the LGV component can be used, along with source-code examples. The site can be found here.

Enhanced navigation to drawer widget stack

We have added a dropdown to enhance navigation between stack of active widgets. The update also adds a minimize button to allow quick access to full screen JBrowse web.

See below for demos of the new navigation UI.

<img alt="Minimize button demo.gif" src="http://gmod.org/mediawiki/images/0/0f/Minimize_button_demo.gif" width="480" height="414" />

Demo of using the minimize button in the drawer

Downloads

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

1.1.0 (2021-03-29)

🚀 Enhancement

core

  1. 1846 Improve copy+paste in the data grids for feature details (@cmdcolin)
  2. 1814 Add ability to get promoter sequence and intron sequence for genes from the feature details panel (@cmdcolin)
  3. 1816 Remove some animation effects (@cmdcolin)
  4. 1778 Adds dropdown to show drawer widget stack (@teresam856)
  5. 1685 Change callbacks language from JavaScript to Jexl (@peterkxie)

Other

  1. 1831 Add dialog for launching breakpoint split view from variant feature details (@cmdcolin)
  2. 1803 Transcript and gene glyphs can now display implied UTRs, active by default (@cmdcolin)
  3. 1808 Add another heuristic for returning gene features from BigBed (@cmdcolin)
  4. 1774 Add warning dialog in LGV before returning to import form to prevent accidentally losing the current view (@cmdcolin)

🐛 Bug Fix

core

  1. 1811 Check for existence of window more robustly to allow in SSR or node applications (@elliothershberg)
  2. 1793 Fix dotplot rendering outside it's allowed bounds (@cmdcolin)
  3. 1783 Add hic aborting and fix remoteAbort signal propagation (@cmdcolin)
  4. 1723 A few bugfixes (@garrettjstevens)

Other

  1. 1815 Clear tracks when using "Return to import form" (@cmdcolin)
  2. 1819 Standardized sentence casing on drawer widget titles (@cmdcolin)
  3. 1796 Bump generic-filehandle for fixing CORS errors from Chrome cache pollution (@cmdcolin)

📝 Documentation

  1. 1824 Add storybook docs page for nextjs usage (@elliothershberg)
  2. 1770 1469 storybook deploy (@elliothershberg)
  3. 1807 Update developer guide to cover displays, and highlight working external plugins (@cmdcolin)
  4. 1779 Collaborative release announcement editing (@rbuels)
  5. 1791 Add a couple more demos for our live version with MDX (@cmdcolin)

🏠 Internal

Other

  1. 1820 Create v1.1.0.md, draft of release announcements (@garrettjstevens)
  2. 1823 Add note about previewing changelog to CONTRIBUTING.md (@garrettjstevens)

core

  1. 1834 Change jbrowse-components monorepo default branch from 'master' to 'main' (@rbuels)

Committers: 6

  • Colin Diesh (@cmdcolin)
  • Elliot Hershberg (@elliothershberg)
  • Garrett Stevens (@garrettjstevens)
  • Peter Xie (@peterkxie)
  • Robert Buels (@rbuels)
  • Teresa Martinez (@teresam856)


Posted to the GMOD News on 2021/03/30

Prospecting for Proposals for GSoC 2021

The Genome Informatics group and GMOD will be submitting an application for Google Summer of Code (GSoC) this year, and we are soliciting project ideas from people and groups involved in the GMOD project.

GSoC is a global program run by Google to encourage students to get real-world experience of participating in a software project; students work on a project over the summer months and receive a stipend from Google for participating. Thousands of organizations of many different sizes take part in GSoC, with the common factor being that they must produce open-source code.

Please take a look at the GSoC wiki page and think about any projects that might work well for a GSoC student, and add them to the wiki. If you are interested in being a mentor, please contact us at robin.haw@oicr.on.ca help@gmod.org.

If you have any questions--e.g. what constitutes an appropriate project; whether your idea is sufficiently GMOD-related--please feel free to email robin.haw@oicr.on.ca and help@gmod.org for advice!


Posted to the GMOD News on 2021/02/16

Codefest 2020


Handlery Hotel in the Balboa room
(down the street from the Town and Country Hotel)
San Diego, California
January 9-10, 2020 </strong>

Immediately before Plant and Animal Genome XXVIII (PAG 2020)

</center>

Participant list now available


There will be a GMOD codefest occurring before the Plant and Animal Genomes meeting in San Diego. The codefest will be at the Town and Country hotel on January 9 and 10. If you would like to suggest a problem or project to address, add it to this Google Doc. The codefest is open to anyone who'd like to work on any GMOD project (or, better yet, any combination of GMOD projects), including but not limited to

We already know that there will be Tripal, Chado, Apollo and JBrowse developers present.

Agenda

Thursday:

9:00-10:00 Introduction and working group organization
10:00-12:00 Working groups
12:00-1:30 Lunch (on your own)
1:30-4:00 Working groups
4:00-5:00 Report on progress

Friday:

9:00-12:00 Working groups
12:00-1:30 Lunch (on your own)
1:30-3:00 Working groups
3:00-3:45 Report on progress
  • Note: the Tripal steering committee will meet on Friday from 12:00 - 3:00 pm at the Postcard Bistro in the Handlery.


Posted to the GMOD News on 2020/01/08

Tripal 3.5 Released

This Tripal release includes major performance improvements including an improved and blazing fast GFF3 loader. Follow standard Drupal updating procedures to update. Changes in this version:

  1. Performance improvements to the Cross References, Relationships, and References.
  2. A rewritten GFF3 loader that is extremely fast, even with a fully populated Tripal site.
  3. A new Sequences fields that combines reference-dervied sequences with primary sequences, and CDS/proteins for mRNA features and sequences now have more informative definition lines for FASTA sequences.
  4. Updates to the online documentation
  5. Bug fixes in web services
  6. Bug fixes in the OBO loader for ontologies that won't import.


Posted to the GMOD News on 2021/02/08

JBrowse 2 release

We are pleased to announce the first public release of JBrowse 2!

JBrowse 2 is the successor to JBrowse, but is a completely new application written with modern web standards and frameworks.

Some of the features new to JBrowse 2 include:

  • New types of views, including circular, synteny, and dotplot views
  • Graphical configuration editing
  • Connections to resources such as UCSC Track Hubs

You can see some demos of JBrowse 2 in action here. To get started using JBrowse 2, visit our quickstart guide here.

We'd love to hear what you think! You can find information about how to contact us here.

The JBrowse Team

Posted to the GMOD News on 2020/11/09

Prospecting for Proposals for GSoC 2020

The Genome Informatics group and GMOD will be submitting an application for Google Summer of Code (GSoC) this year, and we are soliciting project ideas from people and groups involved in the GMOD project.

GSoC is a global program run by Google to encourage students to get real-world experience of participating in a software project; students work on a project over the summer months and receive a stipend from Google for participating. Thousands of organizations of many different sizes take part in GSoC, with the common factor being that they must produce open-source code.

Please take a look at the GSoC wiki page and think about any projects that might work well for a GSoC student, and add them to the wiki. If you are interested in being a mentor, please contact us at robin.haw@oicr.on.ca help@gmod.org.

If you have any questions--e.g. what constitutes an appropriate project; whether your idea is sufficiently GMOD-related--please feel free to email robin.haw@oicr.on.ca and help@gmod.org for advice!


Posted to the GMOD News on 2020/02/03

Call for PAG Abstracts

Call for PAG Abstracts

Time is short!

If you want to attend PAG and would like to present on a topic that would be of interest to the GMOD community, please send an abstract or at least a descriptive title to help@gmod.org. Types of talks typically include updates on GMOD software projects, usage stories for successful sites, proposals for new GMOD projects and descriptions of plugins for existing GMOD software projects like Tripal, JBrowse and Galaxy.

Please consider giving a talk and sharing your experience and ideas!


Posted to the GMOD News on 2016/11/04

New GMOD Server

GMOD.org has a new home

Due to a old server being retired, gmod.org has a new home. In the course of migrating the server, we also had to update the version of MediaWiki that is powering the site. If you notice any problems with gmod.org, please send an email to help at gmod dot org to let us know what's going on.


Posted to the GMOD News on 2016/09/29

GMOD-JBrowse 2016 Survey

Hello Genome Informaticians,

The following survey is aimed at users (and potential users) of GMOD genome databases, especially the JBrowse genome browser. It will directly inform the priorities for renewal of the R01 that funds JBrowse software development and the GMOD helpdesk.

We know surveys are thankless and dull. Your time in filling out this one is GREATLY appreciated.

https://goo.gl/forms/1bKIuAMjGKrS0hUi1

Thanks & best wishes,

The JBrowse team


Posted to the GMOD News on 2016/09/23

GCC2016

The 2016 Galaxy Community Conference (GCC2016) will be held June 25-29, at Indiana University in Bloomington, Indiana, United states, immediately before the June 2016 GMOD Meeting, also in Bloomington. Galaxy is a GMOD Component which interacts with many other GMOD Components, including:

  • Tripal: A web front end for Chado databases. Galaxy is working with the Tripal project to make Galaxy be Tripal's analysis engine.
  • JBrowse: A client-side genome browser and successor to the venerable GBrowse. JBrowse as a Galaxy Tool was presented by Eric Rasche at GCC2015. Ian Holmes, the JBrowse PI, has put JBrowse-Galaxy integration at "top of the list" for JBrowse's infrastructure upcoming infrastructure work.
  • MAKER: A genome annotation pipeline that integrates several gene annotation engines, and combines them to produce annotation that is better than any individual tool produces. A MAKER-Galaxy by Agriculture and Agri-Food Canada was presented at ISMB 2014.
  • InterMine and BioMart: These are both popular data sources that are integrated with Galaxy.

Galaxy Community Conferences are an opportunity to participate in presentations, discussions, poster sessions, lightning talks and breakouts, all about high-throughput biology and the tools that support it.  The conference also includes two days of training offering in-depth topic coverage across several concurrent sessions, and two days of hackathons.

Oral presentation abstract submission closes April 8; poster and demo abstract submission close May 20; and scholarship applications close May 1.


Posted to the GMOD News on 2016/04/04

2016 GMOD Meeting

The next GMOD Community Meeting will be held at Indiana University in Bloomington, Indiana, United States, June 30-July 1, directly after the 2016 Galaxy Community Conference (GCC2016). GMOD Meetings are a mix of user and developer presentations, and are a great place to find out what is happening in the project, what's coming up, and what others are doing.


Please register online at Eventbrite by June 20th 2016. Early bird registration ends May 21.

For those who would like to present a talk or poster, the meeting registration form includes a section for submitting the presentation title and abstract.

If you have any suggestions or requests for the meeting, please contact the GMOD help desk.


Posted to the GMOD News on 2016/04/04

Please Support EcoCyc

EcoCyc, the E. coli information resource and one of the resources offered by the Pathway Tools group, is in need of letters of support from the community after receiving a poor grant review, which could result in a complete loss of funding on July 1st, 2014. If you are a user of EcoCyc, please consider writing a short letter in support of this vital resource. The deadline for letters is May 26th, 2014.

From the Pathway Tools website

ECOCYC FUNDING CRISIS -- DEADLINE MAY 26

EcoCyc received a very unfavorable grant review in February 2014. We are in discussions with the NIH to resolve this situation.

EcoCyc's usage has steadily increased. We made very strong progress on our challenging aims from the current grant period, and the project has produced many publications. EcoCyc received excellent reviews on previous grant applications. Furthermore, the needs of the prokaryotic research community for the content and software tools offered by EcoCyc have never been higher.

In the worst case, we will lose all funding on July 1, 2014 and be forced to re-apply. Even in the best case, we may receive a crippling funding cut that causes us to fall behind in its manual literature curation effort, and requires us to lay off experienced curation staff until funding can be obtained.

These events could seriously undermine EcoCyc, end the project altogether, or force us to begin charging usage fees.

To maintain EcoCyc as the free, up to date, and high-quality resource that you depend on, please tell the NIH what EcoCyc means to your research. Please click the button below to submit a PDF letter of support on institutional letterhead, or a short support statement, explaining the importance of EcoCyc.

We ask all regular users to submit; a short statement will take less than two minutes of your time. Students and post-docs, please ask your lab head to submit in addition to your submission.

More information on what to write and where to submit letters is available at the Pathway Tools website.


Posted to the GMOD News on 2014/05/21

June 2014 WebApollo Hackathon

Berkeley Bioinformatics Open-Source Projects (BBOP) invites you to join us this summer for a WebApollo Hackathon at Lawrence Berkeley National Laboratory, California.

When: Monday, June 2 - 6, 2014

Where: Lawrence Berkeley National Laboratory. Building 74 (B74), Room 104. 1 Cyclotron Rd, Berkeley, CA 94720

What: five days of intensive, collaborative WebApollo development!

For five days developers will work on new features of interest to their research communities, improve existing features, and collaborate on developing features of interest to other colleagues.

Participants should:

  • be able to set up their own WebApollo server before arriving in Berkeley, including Postgres, Tomcat, etc.
  • code comfortably in JavaScript (client) and Java (server).

What will we do while we are there? You tell us! Send your suggestions for feature development, your questions, and any additional comments to apollo [dash] dev [at] lists [dot] lbl [dot] gov

Registration is free of charge, but tickets are required. Register online!

Participants are responsible for arranging travel and accommodation on their own.

More details: WebApollo Hackathon information

via Monica Munoz-Torres


Posted to the GMOD News on 2014-04-22

Applications Open for GMOD Online Training

GMOD will be holding its first online training course for those interested in the set up and use of GMOD components.

The course will be held from Monday 19th May to Friday 23rd May 2014, and will cover core GMOD software, including GBrowse and JBrowse, Galaxy, MAKER, Tripal, WebApollo, Canto, and the Chado database.

If you are interested in attending, please see GMOD Online Training 2014 for more information and to submit your application.


Posted to the GMOD News on 2014-03-31

Canto Workshop at Biocuration 2014

GMOD will be running a workshop at Biocuration 2014 to demonstrate the use of Canto, on Wednesday 9th April in the afternoon. Canto is a literature curation tool that allows users to create functional annotations for genes and gene products using OBO (ontology) terms. Canto will soon be added to GMOD in the Cloud, and this workshop will show participants how to get a GMOD in the Cloud instance up and running--it takes less than ten minutes!--and how to use Canto for literature curation.

We will have more information closer to the time.


Posted to the GMOD News on 2014/03/25

Tripal 2.0a released

The Tripal Development Team is pleased to announce an alpha release of Tripal 2.0 for Drupal 7. This release is expected to have bugs and there is some functionality still under development. However, this release is made to help early adopters of Tripal for Drupal 7. Reports of bugs or other issues are highly welcomed. Below are available resources for Tripal 2.0a

   Download Instructions
   New Functionality
   Installation and Tutorial
   Tripal 2.0 API site
   Tripal Mailing List
   Tripal Developer's Mailing List

The Installation tutorial is still under development but should have enough information for complete installation of Tripal v2.0a as well as loading of organisms and features.


Posted to the GMOD News on 2014/02/27

Precompiled Ontologies in Chado

Eric Rasche and the Center for Phage Technology at Texas A&M University are making Chado database dumps of precompiled ontologies publicly available to save other Chado users the time and hassle of downloading and compiling the ontologies themselves.

Go to the download site.

The ontologies currently available are:

  • Chado Feature Properties
  • Gene Ontology
  • Plant Ontology
  • Relationship Ontology
  • Sequence Ontology

These are updated weekly; the workflow is as follows:

  • clone Chado from SVN
  • build
  • load ontologies
  • dump database as SQL
  • upload to a publicly accessible webserver

Please contact Eric if you are interested in having other ontologies added to the dumps, other builds with different (sub)sets of ontologies, or archived copies of schemas over time.

Note that none of the Chado-related scripts are installed, and the GMOD conf files are not created in GMOD_ROOT. For remote access (e.g., via Artemis), and tools that do not make use of GMOD_ROOT locally, this is not a problem.


Posted to the GMOD News on 2014/02/20

GCC2014 Registration is Open

We are pleased to announce that Early Registration and Talk and Poster Abstract Submission are now open for the 2014 Galaxy Community Conference (GCC2014).

GCC2014 will be held at the Homewood Campus of Johns Hopkins University, in Baltimore, Maryland, United States, from June 30 through July 2, 2014. GCC2014 starts with a Training Day featuring five parallel tracks, each with three, two and half hour long workshops. There are 13 different topics spanning the full Galactic spectrum of topics. Take a look!

Early registration is now open. Register early and avoid paying 70% more for regular registration costs.  Early registration is very affordable, with combined registration (Training Day + main meeting) starting at $140 for post-docs and students. Registration is capped this year at 250 participants, and we expect to hit that limit. Registering early assures you a place at the conference and also a spot in the Training Day workshops you want to attend.

You can also book affordable conference housing at the same time you register. See the conference Logistics page for details on this and other housing options.

Abstract submission for both oral presentations and posters is also open.  Abstract submission for oral presentations closes April 4, while poster submission closes April 25. Poster authors will be notified of acceptance status within two weeks of submission, while presentation authors will be notified no later than May2.  Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about your work.

The GigaScience "Galaxy: Data Intensive and Reproducible Research" series announced for the last conference has published its first papers, and is continuing to take submissions for this year's meeting and beyond. BGI is also continuing to cover the article processing charges until the end of the year, and for more information see their latest update.

Thanks, and hope to see you in Baltimore!

The http:GCC2014 Organizing Committee


Posted to the GMOD News on 2014/02/14

GMOD Paper Cuts, Feb 10th, 2014

__NOFACTBOX__

GMOD Paper Cuts is a periodic selection of choice cuts from the scientific literature featuring interesting, exciting, or otherwise eye-catching GMOD-related work.

If you would like a paper to appear in GMOD Paper Cuts, please email the details to the GMOD helpdesk. Ideally the paper should be in an open-access publication so that anyone can read it.

For more GMOD and GMOD-related papers, and to contribute your own GMOD-related publications, join our Mendeley group.


Finding the missing honey bee genes: lessons learned from a genome upgrade [1]

The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes.

Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data.

Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.

Interesting findings from the new assembly of the honey bee genome, including many more genes than were found in the initial assembly. The Hymenoptera Genome Database uses numerous GMOD resources, including MAKER for automated genome annotation, JBrowse and GBrowse for sequence browsing, and WebApollo for community genome annotation.


Highly Specific and Efficient CRISPR/Cas9-Catalyzed Homology-Directed Repair in Drosophila [2]

We and others recently demonstrated that the readily programmable CRISPR/Cas9 system can be used to edit the Drosophila genome. However, most applications to date have relied on aberrant DNA repair to stochastically generate frame-shifting indels and adoption has been limited by a lack of tools for efficient identification of targeted events. Here we report optimized tools and techniques for expanded application of the CRISPR/Cas9 system in Drosophila through homology-directed repair (HDR) with double-stranded DNA (dsDNA) donor templates that facilitate complex genome engineering through the precise incorporation of large DNA sequences including screenable markers. Using these donors, we demonstrate the replacement of a gene with exogenous sequences and the generation of a conditional allele. To optimize efficiency and specificity, we generated transgenic flies that express Cas9 in the germline, and directly compared HDR and off-target cleavage rates of different approaches for delivering CRISPR components. We also investigated HDR efficiency in a mutant background previously demonstrated to bias DNA repair towards HDR. Finally, we developed a web-based tool that identifies CRISPR target sites and evaluates their potential for off-target cleavage using empirically rooted rules. Overall, we have found that injection of a dsDNA donor and guide RNA-encoding plasmids into vasa-Cas9 flies yields the highest efficiency HDR, and that target sites can be selected to avoid off-target mutations. Efficient and specific CRISPR/Cas9-mediated HDR opens the door to a broad array of complex genome modifications and greatly expands the utility of CRISPR technology for Drosophila research.

CRISPR is one of the most exciting recent technological advancements of the past couple of years. This paper reports new techniques and tools for using the CRISPR/Cas9 system for complex genome engineering. For more information, see the flyCRISPR website.


Analysis of Global Gene Expression in Brachypodium distachyon Reveals Extensive Network Plasticity in Response to Abiotic Stress [3]

Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

Check out the JBrowse-powered Brachypodium web genome browser and other resources on the new Brachypodium website!


Analyses of Hypomethylated Oil Palm Gene Space[4]

Demand for palm oil has been increasing by an average of ~8% the past decade and currently accounts for about 59% of the world's vegetable oil market. This drives the need to increase palm oil production. Nevertheless, due to the increasing need for sustainable production, it is imperative to increase productivity rather than the area cultivated. Studies on the oil palm genome are essential to help identify genes or markers that are associated with important processes or traits, such as flowering, yield and disease resistance. To achieve this, 294,115 and 150,744 sequences from the hypomethylated or gene-rich regions of Elaeis guineensis and E. oleifera genome were sequenced and assembled into contigs. An additional 16,427 shot-gun sequences and 176 bacterial artificial chromosomes (BAC) were also generated to check the quality of libraries constructed. Comparison of these sequences revealed that although the methylation-filtered libraries were sequenced at low coverage, they still tagged at least 66% of the RefSeq supported genes in the BAC and had a filtration power of at least 2.0. A total 33,752 microsatellites and 40,820 high-quality single nucleotide polymorphism (SNP) markers were identified. These represent the most comprehensive collection of microsatellites and SNPs to date and would be an important resource for genetic mapping and association studies. The gene models predicted from the assembled contigs were mined for genes of interest, and 242, 65 and 14 oil palm transcription factors, resistance genes and miRNAs were identified respectively. Examples of the transcriptional factors tagged include those associated with floral development and tissue culture, such as homeodomain proteins, MADS, Squamosa and Apetala2. The E. guineensis and E. oleifera hypomethylated sequences provide an important resource to understand the molecular mechanisms associated with important agronomic traits in oil palm.

The newly-sequenced oil palm genome used the MAKER automated annotation pipeline. The oil palm is one of a number of genomics projects taking off in Malaysia at the moment. Perfect timing for a GMOD workshop!


Production of a reference transcriptome and transcriptomic database (EdwardsiellaBase) for the lined sea anemone, Edwardsiella lineata, a parasitic cnidarian [5]

The lined sea anemone Edwardsiella lineata is an informative model system for evolutionary-developmental studies of parasitism. In this species, it is possible to compare alternate developmental pathways leading from a larva to either a free-living polyp or a vermiform parasite that inhabits the mesoglea of a ctenophore host. Additionally, E. lineata is confamilial with the model cnidarian Nematostella vectensis, providing an opportunity for comparative genomic, molecular and organismal studies.

[...]

The transcriptomic data and database described here provide a platform for studying the evolutionary developmental genomics of a derived parasitic life cycle. In addition, these data from E. lineata will aid in the interpretation of evolutionary novelties in gene sequence or structure that have been reported for the model cnidarian N. vectensis (e.g., the split NF-κB locus). Finally, we include custom computational tools to facilitate the annotation of a transcriptome based on high-throughput sequencing data obtained from a “non-model system.”

Information and resources for the newly-sequenced cnidarian E. lineata; all genomic data is publicly available at EdwardsiellaBase, and can be searched according to contig ID, gene ontology, protein family motif (Pfam), enzyme commission number, and BLAST. The alignment of the raw reads to the contigs can also be visualized via JBrowse.


Happy reading!


  1. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1186.2F1471-2164-15-86
  2. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1534.2Fgenetics.113.160713
  3. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1371.2Fjournal.pone.0087499
  4. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1371.2Fjournal.pone.0086728
  5. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1186.2F1471-2164-15-71
Disclaimer: the papers included in this feature are for your entertainment and edification only. Inclusion does not imply an endorsement of the material or any association between the authors and the GMOD project.


Posted to the GMOD News on 2014/02/10

Galaxy Australasia Workshop 2014

The 1st Galaxy Australasia Workshop 2014 (GAW 2014) will be held in Melbourne, Australia on 24 and 25th March 2014.

The Galaxy Australasia Workshop is a great opportunity to participate in two full days of presentations, discussions, poster sessions, keynotes and lightning talks, all about ways of using Galaxy for high-throughput biology, imaging and other scientific applications. The workshop will also include Training Sessions taught by Galaxy developers and master users. GAW 2014 will run 24 and 25th March, immediately preceding Computational and Simulation Sciences and eResearch in Melbourne.

GAW 2014 will also include poster session, keynote speakers.

You should attend to:

  • Present your work!
  • Learn best practices for deploying Galaxy, defining and installing resources, and managing and moving large datasets.
  • Network with others in the Galaxy community who are facing similar challenges and using Galaxy and other tools to address them.
  • Learn what the Galaxy Project's plans are, and contribute to Galaxy's future direction.
  • Learn
    • how to visualize your data in Galaxy and use visualization to guide your analysis (visual analytics)
    • how to share, publish, and reuse your analyses with Galaxy
    • how to perform and enable your users to perform common, yet complex, analyses using Galaxy
    • when and how to use Galaxy on the Cloud

Topics will potentially include:

  • Image analysis and processing using Galaxy.
  • RNAseq/ChIPseq/Variant Calling/RNA Quality Control.
  • Galaxy on the Research Cloud.
  • CSIRO galaxy service - partnership between science and IT.
  • Identifying proteins from mass spec data with Galaxy.

Registration

Registration is open. Registration is also free, but space is limited.

Call For Abstracts

Participants who wish to give presentations or present posters (potentially with technical demonstrations) that showcase use of Galaxy should submit an abstract and brief one-paragraph bio by February 15th, 2014. Submitters will be notified by February 28th. Speakers, panelists, and poster presenters will be selected by the program committee based on relevance to symposium objectives and workshop balance.

Looking forward to seeing you all in Melbourne!

Committee GAW 2014 Organising Committee


Posted to the GMOD News on yyyy/mm/dd

GMOD Paper Cuts, Jan 24th, 2014

After a break for the festive season, PAG XXII, and the GMOD community meeting in San Diego, GMOD Paper Cuts is back with a selection of scholarly publications for your reading pleasure.

__NOFACTBOX__

GMOD Paper Cuts is a periodic selection of choice cuts from the scientific literature featuring interesting, exciting, or otherwise eye-catching GMOD-related work.

If you would like a paper to appear in GMOD Paper Cuts, please email the details to the GMOD helpdesk. Ideally the paper should be in an open-access publication so that anyone can read it.

For more GMOD and GMOD-related papers, and to contribute your own GMOD-related publications, join our Mendeley group.


CoryneBase: Corynebacterium Genomic Resources and Analysis Tools at Your Fingertips [1]

Corynebacteria are used for a wide variety of industrial purposes but some species are associated with human diseases. With increasing number of corynebacterial genomes having been sequenced, comparative analysis of these strains may provide better understanding of their biology, phylogeny, virulence and taxonomy that may lead to the discoveries of beneficial industrial strains or contribute to better management of diseases. [...] CoryneBase offers the access of a range of Corynebacterium genomic resources as well as analysis tools for comparative genomics and pathogenomics.

A new bacterial resource that uses JBrowse for genome visualization. The justification for using JBrowse is interesting:

We chose JBrowse for CoryneBase for the following main reasons: (1) most of the traditional genome browsers, e.g., GBrowse, are implemented using the Common Gateway Interface (CGI) protocol—the use of CGI-based genome browsers will inadvertently incurs unnecessary delays since the whole-genome browser page need to be reloaded when users change how the data are displayed; and (2) with the advances in next-generation sequencing technologies and bioinformatic tools, we would expect more corynebacterial genomes will be sequenced and annotated. Therefore a user-friendly genome browser that allows rapid and seamless browsing of the huge genomic data will be a major advantage to the research communities.


The Genome Sequence of the Fungal Pathogen Fusarium virguliforme That Causes Sudden Death Syndrome in Soybean [2]

Fusarium virguliforme causes sudden death syndrome (SDS) of soybean, a disease of serious concern throughout most of the soybean producing regions of the world. Despite the global importance, little is known about the pathogenesis mechanisms of F. virguliforme. Thus, we applied Next-Generation DNA Sequencing to reveal the draft F. virguliforme genome sequence and identified putative pathogenicity genes to facilitate discovering the mechanisms used by the pathogen to cause this disease.

A new draft sequence of the fungal disease Fusarium virguliforme. The genome sequence can be browsed online using GBrowse.


Palaeosymbiosis revealed by genomic fossils of Wolbachia in a strongyloidean nematode

Georgios Koutsovoulos, Benjamin Makepeace, Vincent N. Tanya, Mark Blaxter; published on arxiv.org

Wolbachia are common endosymbionts of terrestrial arthropods, and are also found in nematodes, the animal-parasitic filaria, and the plant-parasite Radopholus similis. Lateral transfer of Wolbachia

DNA to the host genome is common. We generated a draft genome sequence for the strongyloidean nematode parasite Dictyocaulus viviparus, the cattle lungworm. In the assembly, we identified nearly 1 Mb of sequence with similarity to Wolbachia. The fragments were unlikely to derive from a live Wolbachia infection: most were short, and the genes were disabled through inactivating mutations. Many fragments were co-assembled with definitively nematode-derived sequence. We found limited evidence of expression of the Wolbachia-derived genes. The D. viviparus Wolbachia genes were most similar to filarial strains, and strains from the host-promiscuous clade F. We conclude that D. viviparus was infected by Wolbachia in the past. Genome sequence based surveys are a powerful tool for revealing the genome archaeology of infection and symbiosis.

A fascinating study that uses genetic techniques to dig into the history of a host-parasite relationship. The D. viviparus genome was annotated using the MAKER pipeline.


Genome of the human hookworm Necator americanus [3]

The hookworm Necator americanus is the predominant soil-transmitted human parasite. Adult worms feed on blood in the small intestine, causing iron-deficiency anemia, malnutrition, growth and development stunting in children, and severe morbidity and mortality during pregnancy in women. We report sequencing and assembly of the N. americanus genome (244 Mb, 19,151 genes). Characterization of this first hookworm genome sequence identified genes orchestrating the hookworm's invasion of the human host, genes involved in blood feeding and development, and genes encoding proteins that represent new potential drug targets against hookworms. N. americanus has undergone a considerable and unique expansion of immunomodulator proteins, some of which we highlight as potential treatments against inflammatory diseases. We also used a protein microarray to demonstrate a postgenomic application of the hookworm genome sequence. This genome provides an invaluable resource to boost ongoing efforts toward fundamental and applied postgenomic research, including the development of new methods to control hookworm and human immunological diseases.

Another somewhat gruesome parasite, the human hookworm, which is responsible for causing more disease than any other soil-based helminth. The genome was annotated using MAKER and can be viewed online at Nematode.net and Wormbase.


Happy reading!


  1. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1371.2Fjournal.pone.0086318
  2. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1371.2Fjournal.pone.0081832
  3. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1038.2Fng.2875
Disclaimer: the papers included in this feature are for your entertainment and edification only. Inclusion does not imply an endorsement of the material or any association between the authors and the GMOD project.


Posted to the GMOD News on 2014/01/24

Postdoc Position in Computational and Plant Evolutionary Biology

The project involves construction and analysis of plant gene families and phylogenies, particularly focusing on the large legume family, and development of a corresponding database and on-line tools for accessing and exploring gene families and associated annotations. Analysis of gene families and genes with known functions for better understanding of key events in evolution of selected plants and agronomic traits.

The primary research groups are located at Iowa State University (Ames, IA) and at National Center for Genome Resources (Santa Fe, NM). Remote work may be considered. This is a two-year position, with possibility for extension. Salary will be at competitive federal rates (>$50k). U.S. citizenship will not be a requirement for the position.

Applicants must have received Ph.D. in computational biology, bioinformatics, computer science, plant biology, genetics, or related discipline involving significant computational experience, statistics, and genetics.

If interested, please contact Steven Cannon.


Posted to the GMOD News on 2014/1/24

Prospecting for Proposals for GSoC 2014

GMOD is participating in Google Summer of Code (GSoC) this year, and we are soliciting project ideas from people and groups involved in the GMOD project.

GSoC is a global program run by Google to encourage students to get real-world experience of participating in a software project; students work on a project over the summer months and receive a stipend from Google for participating. Thousands of organizations of many different sizes take part in GSoC, with the common factor being that they must produce open-source code.

Please take a look at the GSoC wiki page and think about any projects that might work well for a GSoC student, and add them to the wiki. If you are interested in being a mentor, please contact us at help@gmod.org.

If you have any questions--e.g. what constitutes an appropriate project; whether your idea is sufficiently GMOD-related--please feel free to email help@gmod.org for advice!


Posted to the GMOD News on 2014/01/22

Biocuration 2014

7th International Biocuration Conference

April 6-9, 2014 -- Toronto, Canada

Abstracts Due: February 10, 2014

Biocuration 2014 will provide a forum for trainees, biocurators, investigators, clinicians and developers of biological databases to discuss their work, promote collaboration and foster a sense of community in this very active and growing area of research. Participants from academia, government and industry interested in the methods and tools employed in curation of biological and medical data are encouraged to attend. While a number of speakers have been invited, please note that the majority of oral presentations will be drawn from openly submitted abstracts.

SCOPE:

The proposed 2014 conference sessions and workshops will address the following challenges in biocuration:

  • Automated Function Prediction (workshop)
  • Big Data Curation: Dealing with supplementary data (workshop)
  • Biocreative Text Mining (workshop)
  • Biological and Clinical Ontologies (session)
  • Clinical Annotations (session)
  • Data Integration and Data Sharing (session)
  • Functional Annotations (session)
  • Microbial Informatics (session)
  • Phenotype (workshop)
  • Social Tools for publishing and curation (workshop)

INVITED SPEAKERS:

  • Dr. Tim Hubbard, Wellcome Trust Sanger Institute
  • Dr. Suzanna Lewis, Lawrence Berkeley National Laboratory
  • Dr. Patricia Babbitt, California Institute for Quantitative Biosciences (QB3)
  • Dr. Lincoln Stein, Ontario Institute for Cancer Research

WEBSITE:

7th International Biocuration Conference


REGISTRATION:

Online registration is now open


ABSTRACT SUBMISSION:

Submit your abstract for presentation (poster or talks only)


Posted to the GMOD News on 2014/01/17

Announcing GMOD Malaysia 2014

We are pleased to announce that GMOD will be running a three day training course in Kuala Lumpur, Malaysia, on 26-28 February 2014. The course will be run by experienced GMOD developers and tutors, and will cover the following tools:

Date: February 26-28, 2014

Venue: Kuala Lumpur, Malaysia.

Please check the GMOD Malaysia 2014 wiki page for updates, or email the GMOD help desk for more information.


Posted to the GMOD News on 2013/12/28

MAKER-P: an annotation pipeline for plants

The popular MAKER annotation pipeline has been extended and optimised to allow the annotation of plant species:

Sequencing diverse plant species of evolutionary, agricultural, and medicinal interest is becoming routine for even small groups; genome annotation and analysis is much less so. The MAKER-P pipeline is designed to make the annotation of novel plant genomes tractable for small groups with limited bioinformatics experience and resources, and faster and more transparent for large groups with more experience and resources. The MAKER-P pipeline generates species-specific repeat libraries, as well as structural annotations of protein coding genes, non-coding RNAs, and pseudogenes.

—Michael Campbell, MAKER development team


Posted to the GMOD News on 2013/12/16

GMOD Paper Cuts, Dec 6th, 2013

__NOFACTBOX__

GMOD Paper Cuts is a periodic selection of choice cuts from the scientific literature featuring interesting, exciting, or otherwise eye-catching GMOD-related work.

If you would like a paper to appear in GMOD Paper Cuts, please email the details to the GMOD helpdesk. Ideally the paper should be in an open-access publication so that anyone can read it.

For more GMOD and GMOD-related papers, and to contribute your own GMOD-related publications, join our Mendeley group.


The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system [1]

Snakes are limbless predators, and many species use venom to help overpower relatively large, agile prey. Snake venoms are complex protein mixtures encoded by several multilocus gene families that function synergistically to cause incapacitation. To examine venom evolution, we sequenced and interrogated the genome of a venomous snake, the king cobra (Ophiophagus hannah), and compared it, together with our unique transcriptome, microRNA, and proteome datasets from this species, with data from other vertebrates.

A fascinating insight into the biology and genome of the king cobra; the Burmese python has also been recently been sequenced [2], with both projects using MAKER for automated annotation.


PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools [3]

PortEco aims to collect, curate and provide data and analysis tools to support basic biological research in Escherichia coli (and eventually other bacterial systems). PortEco is implemented as a 'virtual' model organism database that provides a single unified interface to the user, while integrating information from a variety of sources.

PortEco integrates E. coli data from numerous sources and uses a wiki-based system to enable collaborative knowledge management. PortEco is currently testing a JBrowse installation with the view to migrating over to JBrowse from their current GBrowse sequence browser.


The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse [4]

The Mouse Genome Database (MGD) is the community model organism database resource for the laboratory mouse, a premier animal model for the study of genetic and genomic systems relevant to human biology and disease. MGD maintains a comprehensive catalog of genes, functional RNAs and other genome features as well as heritable phenotypes and quantitative trait loci.

An update on the resources available at Mouse Genome Database (MGD), one of the groups involved in GMOD since the very beginning of the project.


NECTAR: a database of codon-centric missense variant annotations [5]

NECTAR (Non-synonymous Enriched Coding muTation ARchive) is a database and web application to annotate disease-related and functionally important amino acids in human proteins.

This stylishly-designed website draws data on disease mutations from numerous sources, including Ensembl, HGMD-PUBLIC, UniProt, COSMIC, and ClinVar, and includes GBrowse-able disease variants, function annotations, and paralogue annotations and a DAS server. Sweet!


Identification of a 31-bp Deletion in the RELN Gene Causing Lissencephaly with Cerebellar Hypoplasia in Sheep [6]

Lissencephaly is an inherited developmental disorder in which neuronal migration is impaired. A type of lissencephaly associated with cerebellar hypoplasia (LCH) was diagnosed in a commercial flock of Spanish Churra sheep. The genotyping of 7 affected animals and 33 controls with the OvineSNP50 BeadChip enabled the localization of the causative mutation for ovine LCH to a 4.8-Mb interval on sheep chromosome 4 using genome-wide association and homozygosity mapping.

Tracking down a sequence variation that causes developmental problems in sheep: a nice combination of classical genetics (studying families trees and examining phenotypes) and modern techniques, using resources provided at CSIRO's Livestock Genomics website.


Happy reading!


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Disclaimer: the papers included in this feature are for your entertainment and edification only. Inclusion does not imply an endorsement of the material or any association between the authors and the GMOD project.


Posted to the GMOD News on 2013/12/06

Canto, a GMOD tool for functional annotation

We are pleased to announce that Canto, the PomBase community curation tool, is now a GMOD component.

Canto is an online tool that supports functional gene annotation by community researchers as well as by professional curators. It provides a simple interface to gather genetic and molecular data from publications for inclusion in public biological databases.

Curation in Canto uses OBO ontologies, and the specific set of ontologies is configurable upon setup. The PomBase Canto instance currently uses GO, PSI-MOD and FYPO.

Genetic and physical interaction annotation is also supported. Canto captures all necessary information about each interaction for submission to BioGRID.

Canto currently supports annotation export in JSON format, either by individual paper or in bulk (see some example data from PomBase Chado loading tests).

The JSON data from Canto can be loaded into a relational database using the Chado schema (as at PomBase) or alternative schemas.

Basic gene association file (GAF) export is also supported for GO annotations.

More information about Canto:


Posted to the GMOD News on 2013/12/02

New WebApollo Release (2013/11/22)

There is a new release of WebApollo available from the WebApollo release website. The updated server setup instructions are available on the WebApollo Installation page, and the WebApollo user guide has been updated accordingly.

If you currently have WebApollo instances up, please make sure to read the updated server setup instructions as some of the configuration files have changed. Since we now support multiple annotation types, you might want to upgrade your existing data stores to change transcripts to mRNAs (the only supported transcript type in previous versions). See the instructions on upgrading your data store.

You can try the public demo at http://genomearchitect.org/WebApolloDemo.

Summary of changes:

  • using JBrowse 1.10.9 release
  • new hybrid store (memory/disk) should use much less memory than the pure memory store (with a small degrade in performance) - useful for genomes with many annotations (you can configure which one to use as best fits your needs)
  • viewing of annotation info editor for users without write privilege (cannot modify the data)
  • FASTA data adapter
  • different annotation info editor configurations for different annotation types
  • database/history merger tool (command line)
  • data adapters now use iterators when exporting data (improves memory footprint)
  • add a configurable option for dumping owner and other meta-data to the GFF3 adapter
  • undoing an "add_feature/add_transcript" operation will now warn the user that proceed will delete the feature
  • data adapter grouping (see FASTA adapter)
  • adding/updating PubMed ID will now show the publication title for confirmation
  • improved add_transcripts_from_gff3_to_annotations.pl
  • adding of different annotation types (gene, pseudogene, tRNA, snRNA, snoRNA, ncRNA, rRNA, miRNA, repeat_region, transposable_element)
  • adding GO terms now supports searching/autocompletion
  • annotation info editor now requests data from the server in batch mode (should improve speed)

Fixes:

  • Chado featureprop writeback for generic attributes
  • add_transcripts_from_gff3_to_annotations.pl now properly loads status attributes
  • attributes being lost after undo/redo
  • redo of a merge_transcript operation after deleting one of the transcripts *should* work now
  • properly handle dragged transcripts that contain UTR elements
  • compressed data sent to the client no longer causes the client to hang when there are too many annotations
  • rewrote much of the split_transcript operation to better handle gene splitting

(via Ed Lee on the WebApollo mailing list)


Posted to the GMOD News on 2013/11/22

GMOD Paper Cuts, Nov 22nd, 2013

__NOFACTBOX__

GMOD Paper Cuts is a periodic selection of choice cuts from the scientific literature featuring interesting, exciting, or otherwise eye-catching GMOD-related work.

If you would like a paper to appear in GMOD Paper Cuts, please email the details to the GMOD helpdesk. Ideally the paper should be in an open-access publication so that anyone can read it.

For more GMOD and GMOD-related papers, and to contribute your own GMOD-related publications, join our Mendeley group.


The Genome Database for Rosaceae (GDR): year 10 update [1]

The Genome Database for Rosaceae (GDR), the long-standing central repository and data mining resource for Rosaceae research, has been enhanced with new genomic, genetic and breeding data, and improved functionality.

Lots of GMOD goodness in the Genome Database for Rosaceae, which is built using Tripal, includes Pathway Tools data, and has integrated GBrowse and GBrowse syn instances for sequence and synteny viewing respectively.


FlyBase 102—advanced approaches to interrogating FlyBase [2]

FlyBase is the leading website and database of Drosophila genes and genomes. Whether you are using the fruit fly Drosophila melanogaster as an experimental system or wish to understand Drosophila biological knowledge in relation to human disease or to other model systems, FlyBase can help you successfully find the information you are looking for.

A followup to the FlyBase 101 paper [3] with updates on new features and functionality at FlyBase. FlyBase use the Chado database schema and users can query the database directly.


PATRIC, the bacterial bioinformatics database and analysis resource [4]

The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC). [...] PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein–protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata.

PATRIC provides an immense data bank on bacteria: over 10,000 bacterial genomes as of Sept. 2013, projections of 15,000 by 2014. This paper details the resources provided, including their JBrowse-based genome browser, and Disease View, which integrates data on pathogens, genes, diseases, and geolocation of disease reports. Very cool!


Identical sets of methylated and nonmethylated genes in Ciona intestinalis sperm and muscle cells [5]

The discovery of gene body methylation, which refers to DNA methylation within gene coding region, suggests an as yet unknown role of DNA methylation at actively transcribed genes. In invertebrates, gene bodies are the primary targets of DNA methylation, and only a subset of expressed genes is modified.

Some interesting results from studies of gene body methylation in the sea squirt Ciona intestinalis during development.


Large-Scale Collection and Analysis of Full-Length cDNAs from Brachypodium distachyon and Integration with Pooideae Sequence Resources [6]

A comprehensive collection of full-length cDNAs is essential for correct structural gene annotation and functional analyses of genes. [...] The [RIKEN Brachypodium FL cDNA] database represents a “one-stop” information resource for all genomic information in the Pooideae, facilitating functional analysis of genes in this model grass plant and seamless knowledge transfer to the Triticeae crops.

TriFLDB, or the Triticeae full-length CDS database, is a new resource of Brachypodium full length cDNA clones and other resources; it includes GBrowse for exploring the B. distachyon genome and its annotations further.


Happy reading!


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Disclaimer: the papers included in this feature are for your entertainment and edification only. Inclusion does not imply an endorsement of the material or any association between the authors and the GMOD project.


Posted to the GMOD News on 2013/11/22

GMOD Paper Cuts, Nov 15th, 2013

__NOFACTBOX__

GMOD Paper Cuts is a periodic selection of choice cuts from the scientific literature featuring interesting, exciting, or otherwise eye-catching GMOD-related work.

If you would like a paper to appear in GMOD Paper Cuts, please email the details to the GMOD helpdesk. Ideally the paper should be in an open-access publication so that anyone can read it.

For more GMOD and GMOD-related papers, and to contribute your own GMOD-related publications, join our Mendeley group.


The Aspergillus genome database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations [1]

The Aspergillus Genome Database (AspGD) is a freely available web-based resource that was designed for Aspergillus researchers and is also a valuable source of information for the entire fungal research community.

A redesigned website and expanded resources for AspGD, which is now using JBrowse as primary genome browser.


CottonGen: a genomics, genetics and breeding database for cotton research [2]

CottonGen is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton.

An update on the CottonGen database, which uses the Tripal framework to make available data from a Chado database, and to integrate the GMOD tools GBrowse and CMap.


WormBase 2014: new views of curated biology [3]

WormBase is a highly curated resource dedicated to supporting research using the model organism Caenorhabditis elegans.

Updates and expansions on the WormBase website, which is notable not only for developing and using a number of GMOD tools, including GBrowse and Textpresso, but also for being hosted entirely in the cloud.


Gleaning evolutionary insights from the genome sequence of a probiotic yeast Saccharomyces boulardii. [4]

The yeast Saccharomyces boulardii is used worldwide as a probiotic to alleviate the effects of several gastrointestinal diseases and control antibiotics-associated diarrhea. While many studies report the probiotic effects of S. boulardii, no genome information for this yeast is currently available in the public domain. We report the 11.4 Mbp draft genome of this probiotic yeast.

The newly-sequenced Saccharomyces boulardii genome, which was annotated with using MAKER.


DOOR 2.0: presenting operons and their functions through dynamic and integrated views [5]

We have recently developed a new version of the DOOR operon database, DOOR 2.0, which is available online at http://csbl.bmb.uga.edu/DOOR/ and will be updated on a regular basis. DOOR 2.0 contains genome-scale operons for 2072 prokaryotes with complete genomes, three times the number of genomes covered in the previous version published in 2009.

A bright, lively update to the Database of prokaryotic operons, which uses JBrowse for sequence visualization.


And finally, if you have access to the Wiley Online Library through your institution, you may like to check out [http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi0915s43/abstract Cloud Computing with iPlant Atmosphere], from Current Protocols in Bioinformatics, which details the resources available on the [www.iplantcollaborative.org/‎ iPlant website] and how to get started with tools such as GBrowse.


Happy reading!


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Disclaimer: the papers included in this feature are for your entertainment and edification only. Inclusion does not imply an endorsement of the material or any association between the authors and the GMOD project.


Posted to the GMOD News on 2013/11/15

GMOD Job At QMUL

There is a position as a sysadmin/computing officer open at the School of Biological & Chemical Sciences at Queen Mary University of London (QMUL), with duties including setting up Galaxy and GMOD servers. The closing date for applications is 21st November 2013; for more details, see the job description.


Posted to the GMOD News on 2013/11/12

GMOD Paper Cuts, Nov 8th, 2013

__NOFACTBOX__

GMOD Paper Cuts is a periodic selection of choice cuts from the scientific literature featuring interesting, exciting, or otherwise eye-catching GMOD-related work.

If you would like a paper to appear in GMOD Paper Cuts, please email the details to the GMOD helpdesk. Ideally the paper should be in an open-access publication so that anyone can read it.

For more GMOD and GMOD-related papers, and to contribute your own GMOD-related publications, join our Mendeley group.


mRNA-Seq and microarray development for the Grooved carpet shell clam, Ruditapes decussatus: a functional approach to unravel host-parasite interaction [1]
The first characterization of the Ruditapes decussatus transcriptome; the team responsible have also set up Rdecusdb, the Ruditapes decussatus database, built with Tripal
The database of genomic variants: a curated collection of structural variation in the human genome [2]
An update on the Database of Genomic Variants (DGV), which provides a publicly accessible, comprehensive curated catalogue of structural variation (SV) found in the genomes of control individuals from worldwide populations. The core visualization tool, GBrowse, has been upgraded with additional functions to facilitate data analysis and comparison.
Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease [3]
A genome-wide association study on humans of European ancestry that identifies new loci associated with Alzheimer's disease.
Crossover Heterogeneity in the Absence of Hotspots in Caenorhabditis elegans [4]
Computational framework to support integration of biomolecular and clinical data within a translational approach [5]
This article was published earlier this year, and is a good example of extending the Chado schema to fit the needs of the project.


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Posted to the GMOD News on 2013/11/08

Open Position At dictyBase

dictyBase is hiring. We have an open position for a Bioinformatics Software Engineer at dictyBase.
See the official posting for full details.


Posted to the GMOD News on 2013/11/04

Tripal 1.1 Publication

The Tripal team have put out a publication on the 1.1 version of the software. Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases. can be read for free at PubMedCentral or at the Database journal.

Here is the abstract:

Tripal is an open-source freely available toolkit for construction of online genomic and genetic databases. It aims to facilitate development of community-driven biological websites by integrating the GMOD Chado database schema with Drupal, a popular website creation and content management software. Tripal provides a suite of tools for interaction with a Chado database and display of content therein. The tools are designed to be generic to support the various ways in which data may be stored in Chado. Previous releases of Tripal have supported organisms, genomic libraries, biological stocks, stock collections and genomic features, their alignments and annotations. Also, Tripal and its extension modules provided loaders for commonly used file formats such as FASTA, GFF, OBO, GAF, BLAST XML, KEGG heir files and InterProScan XML. Default generic templates were provided for common views of biological data, which could be customized using an open Application Programming Interface to change the way data are displayed. Here, we report additional tools and functionality that are part of release v1.1 of Tripal. These include

  1. a new bulk loader that allows a site curator to import data stored in a custom tab delimited format;
  2. full support of every Chado table for Drupal Views (a powerful tool allowing site developers to construct novel displays and search pages);
  3. new modules including 'Feature Map', 'Genetic', 'Publication', 'Project', 'Contact' and the 'Natural Diversity' modules.

Tutorials, mailing lists, download and set-up instructions, extension modules and other documentation can be found at the Tripal website located at http://tripal.info.


Posted to the GMOD News on 2013/10/31

San Diego 2014 Registration Open

Registration is now open for the upcoming GMOD community meeting, to be held at the Best Western Seven Seas, San Diego, CA, on January 16th and 17th 2014.

Register online at Eventbrite now!

Early birds can catch the $50 registration worm, which is available until mid-December; after this, the registration fee will rise to $70.

If you would like to give a presentation at the meeting, please submit your abstract with your meeting registration form.

A block of rooms is being held for attendees of the GMOD meeting at a very good rate; to make reservations in this block, you must call (800) 328-1618 and ask for the GMOD rate. The GMOD rate is not available through online bookings.

If you have any questions or comments, please feel free to contact the GMOD helpdesk on help@gmod.org!


Posted to the GMOD News on 2013/10/25

GCC2014: June 30 - July 2

The 2014 Galaxy Community Conference (GCC2013) will be held June 30 through July 2, at the Homewood Campus of Johns Hopkins University], in Baltimore, Maryland, United States.

Galaxy Community Conferences are an opportunity to participate in presentations, discussions, poster sessions, lightning talks and breakouts, all about high-throughput biology and the tools that support it.  The conference will also includes a Training Day offering in-depth topic coverage, across several concurrent sessions.  See the GCC2013 web site for an idea of what happens at a Galaxy Community Conference. The GCC2013 site includes links to slides and videos for all accepted talks.


Posted to the GMOD News on 2014/10/02

Get the Full ImpactStory

The GMOD wiki now includes ImpactStory altmetrics for publications cited in the page text. See the Publications page for an example of ImpactStory altmetrics.

For those unfamiliar with the term altmetrics, these are measures beyond simple paper citations. The Altmetrics Manifesto provides the following clarification:

Altmetrics expand our view of what impact looks like, but also of what’s making the impact. This matters because expressions of scholarship are becoming more diverse. Articles are increasingly joined by:

  • The sharing of “raw science” like datasets, code, and experimental designs
  • Semantic publishing or “nanopublication,” where the citeable unit is an argument or passage rather than entire article.
  • Widespread self-publishing via blogging, microblogging, and comments or annotations on existing work.


ImpactStory collates metrics from numerous online sources to give a more complete picture of how an article, data set, piece of software, or other research product is being used and discussed. More information is available on the ImpactStory website.


We hope to add impact metrics for GMOD software soon.

GMOD 2014 San Diego: Save the Date

The next GMOD Community Meeting will be held in San Diego, CA, on January 16-17, directly after PAG XXII. In addition to the usual talks and updates, we plan to have a poster session, and a workshop on migrating from GBrowse to JBrowse. If you have items or ideas for the agenda, please feel free to contact the GMOD helpdesk.

GMOD will also have a big presence at PAG, with a day-long workshop covering many of the actively-developed GMOD components.

More details on both the GMOD community meeting and GMOD at PAG will be posted on the wiki closer to the time.


Posted to the GMOD News on 2013-09-10

Statistical Genomics PostDoc at PSU

Are you interested in genomics and do you have skills in Bioinformatics, Computational Biology and Statistics? The Makova lab in the Department of Biology at The Pennsylvania State University is looking to hire a postdoctoral researcher for an NSF-funded project examining regional variation in mutation rates (see our recent publication in PNAS: Kuruppumullage Don, Ananda, Chiaromonte, Makova 2013). With new sequencing technologies, multiple human genomes and their detailed annotations (e.g., ENCODE) are suddenly accessible to us. This gives us a terrific opportunity to explore previously inaccessible evolutionary processes (e.g., mutation) and other biological associations (location of genes in certain mutation states, as identified by HMMs). Such knowledge is vital in a clinical setting where disease mutations need to be evaluated. Our resources and links with medical researchers at Hershey Medical School and computational biologists from the Galaxy team put us in a great position to address these questions.

Candidates should have experience in bioinformatics, working knowledge of statistics and should have a broad understanding of molecular biology and genetics. Familiarity with next-generation sequencing data analysis is desirable. A PhD is required. You will be joining an established dynamic group. We are part of the Center for Medical Genomics and of the Center for Comparative Genomics and Bioinformatics. Penn State is a vibrant scientific community with particular strengths in genomics, bioinformatics and molecular evolution. Our location, in State College, Pennsylvania, is known for excellent schools and numerous opportunities for outdoor activities.

The starting date is flexible, with an earlier date preferred. This position is funded for one year from date of hire, with good possibility of refunding. Interested applicants should send a pdf with a CV, a statement of research interests, and contact information for three referees to Kateryna Makova, indicating postdoc in the subject line. Employment will require successful completion of background check(s) in accordance with University policies. Penn State is committed to affirmative action, equal opportunity, and the diversity of its workforce.


Posted to the GMOD News on 2013/09/09

Support Your Friendly Local GMOD

The Generic Model Organism Database project is applying for a community resources for genomics grant from the NIH to continue the work that GMOD does, with a focus on JBrowse and Chado development, and GMOD coordination (standards, meetings, and courses).

We need to demonstrate that we support the community and have the support of the community, and we would like to demonstrate that by submitting many letters of support from users. We would be very grateful if you could take a couple of minutes to write such a letter; it should include information about how you use or plan to use GMOD software. There are some template paragraphs provided for inspiration.

The letters should be on institutional letterhead, signed, and then scanned to a PDF, or you could mail the original to Scott Cain and he will scan them.

The deadline for getting the letters of support is September 3. Please contact the GMOD helpdesk or email Scott directly if you're willing to write a letter or if you need any help.

This grant would help to secure the future of important parts of the GMOD project, so we would be very grateful for your help!

Via Scott Cain


Posted to the GMOD News on 2013/08/20

2013 Summer School Tutorials Available

The tutorials for the material taught at this year's GMOD summer school are now all available on the GMOD website. There are updated tutorials for several components, particularly those where new software releases have occurred since the last summer school; these include:

The full set of GMOD tutorials, featuring all the material from this year's summer school and more, is available from the Tutorials section of the wiki.


Posted to the GMOD News on 2013-08-02

JBrowse 1.10.0 released

I am very pleased to announce the release of JBrowse 1.10.0, a major new JBrowse release with some big new features, and a *huge* number of smaller improvements!

It can be downloaded from http://jbrowse.org/jbrowse-1-10-0/.

As always, see the updated

JBrowse Configuration Guide for documentation on how to use the new features.

RobertBuels (talk)


Posted to the GMOD News on 2013/07/30

OpenID Account Creation Fixed

Update on July 11:

Account creation using OpenID is currently disabled due to problems with the OpenID plugin. New wiki users wishing to create accounts should use the 'Log in / create account' link and request an account; your request should be dealt with within 24-48 hours. Unfortunately, due to spammers and others creating bogus accounts, we have to had to put protective measures in place.

Please email the GMOD helpdesk if you have any problems or want to expedite the creation of your account!


Posted to the GMOD News on 2013/07/10

GMOD's GSoC Going Great Guns!

GMOD is lucky enough to have a Google Summer of Code student working with us through the summer. Flavien Bossiaux is a computer science student from the University of Nice, France, and he is working on a number of improvements to the GMOD website user experience. He has already created two Mediawiki extensions to allow the embedding of external content into the GMOD wiki; visit the GMOD calendar to see one of them, the iAnn calendar plugin, in action.

Flavien is recording his thoughts and progress on his website through the summer; please check it out! You can also follow Flavien on Twitter, and check out his his Github repo.

If you have any thoughts or suggestions on the GSoC project, please send them along to the GMOD helpdesk.


Posted to the GMOD News on 2013/07/09

GMOD in the Cloud 2.0 Released

from Scott Cain:

I am pleased to announce that GMOD in the Cloud 2.0 has finally been released to the public. This Amazon Web Services (AWS) Amazon Machine Image (AMI) is public and can be cloned by anybody with an AWS account. A demo of GMOD in the Cloud is running (though it may take a day or two for DNS to update fully).

This AMI has several GMOD software packages installed and configured, including:

  • Chado 1.23
  • Tripal 1.0 (plus a few bug fixes from dev)
  • GBrowse 2.54 (with samtools, BigWig and fastCGI support)
  • JBrowse 1.9.5
  • WebApollo (most recent release from May, 2013)

For more information about GMOD in the Cloud, visit the Cloud page on the wiki, and post questions about using GMOD in the Cloud to the GMOD developers mailing list, gmod-devel@lists.sourceforge.net.


Posted to the GMOD News on 2013/06/14

Last Call For Summer School Apps

The deadline to apply for the 2013 GMOD Summer School is rapidly approaching! Please submit your application by June 10th to ensure that you are in consideration for a place.

The GMOD Summer School is the best way to get to grips with key components of the GMOD toolkit, including Chado, GBrowse, Galaxy, JBrowse, WebApollo, MAKER, Tripal, and more. Tool developers will be on hand to answer questions and help with troubleshooting.

Applications received after June 10th will be kept in case there are spare places due to accepted applicants not being able to attend.


Posted to the GMOD News on 2013/06/06

GCC2013 Early Reg closes 24 May

Early registration for the 2013 Galaxy Community Conference (GCC2013) ends this Friday, 24 May. Early registration saves up to 75% off regular registration costs, and is downright affordable, with combined registration (Training Day + main meeting) starting at ~ €95 for post-docs and students. Registering early also assures you a spot in the Training Day workshops you want to attend. Once a Training Day session becomes full, it will be closed to new registrations.

GCC2013 is an opportunity to participate in two full days of presentations, discussions, poster sessions, keynote, and lightning talks, all about high-throughput biology and the tools that support it. The conference also includes a Training Day with in-depth topic coverage of twelve different topics in 15 sessions across 5 tracks.

An early program is available featuring 25 oral presentations, lightning talks and poster sessions, and the just added Birds-of-a-Feather gatherings.

If you are a biologist or bioinformatician performing or enabling high-throughput biological research, then this conference is for you.

Thanks,

GCC2013 Organizing Committee

PS: And please help get the word out!


Posted to the GMOD News on 2013/05/20

New WebApollo Release

From Ed Lee on the WebApollo mailing list:

We'd like to announce a new WebApollo release.

Get the newest release -- Public demo -- Server setup instructions -- Updated user guide

Summary of changes:

  • Fully revamped genomic sequence selection screen
    • sorting by name and length (uses customizable JavaScript function)
    • filtering of genomic sequence names
  • Annotation info editor
    • allows editing of symbols, comments, and dbxrefs
  • Script for bulk loading gene/transcript/exons to annotation track
  • Improved login system
    • allows logging in from either genomic region selection screen or editor
  • Configuration for using computed CDS (if available) when first creating a transcript (rather that using the longest ORF)
  • Improved memory management
  • Improved handling of concurrent edits
  • HTTPS support
  • Deletion of transcripts now warn users
  • Accessing editor without logging in hides annotation track
  • Using "[" and "]" to navigate through subfeatures when a feature in the annotation track is selected
  • Improved interface for adding insertions and deletions
  • Option to hide plus and/or minus strand
  • Various bugfixes


Posted to the GMOD News on 2013/05/17

The Really Old News Archive

Even earlier news items are available at SourceForge.