GMOD News Archives

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The GMOD News Archive contains old news items that have been archived off of the GMOD News page/feed.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.

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

2010 Stories

Most of the 2010 stories are still on the GMOD News page. Items are only moved here when they are more than 6 months old.

Load Chado into BioMart

{{#icon: Biomart250.png|Load Chado into BioMart|125|http://gmod.org/wiki/BioMart#How_to_Load_a_Chado_Database_into_BioMart}}

{{#icon: Urgi.png|INRA URGI|105|http://urgi.versailles.inra.fr/}}

A group at INRA URGI have documented "How to load a Chado database into BioMart". This step by step document details what how to configure BioMart for Chado, and includes some specific use cases useful with Chado. This guide is based on experience at INRA URGI, and was written by Aminah Keliet, Joëlle Amselem, Sandra Derozie, and Delphine Steinbach.

If you are interested in loading your Chado data into a BioMart instance then I recommend starting with this guide.

Thanks,

Dave C.
GMOD Help Desk

2010/05/27

June 2010 Calendar

Calendar

The next 5 weeks includes the a MAKER workshop at the Arthropod Genomics Symposium, and deadlines for ISMB (Boston in July), AMATA (Hobart in September), GIW (Hangzhou in December), ECCB (Ghent in September), InCoB (Tokyo in September), and Genome Informatics (Hinxton in September).

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If you know of any other events or deadlines that the GMOD community would be interested in, please send them to me.

Thanks,

Dave Clements
GMOD Help Desk

2010/05/24

gmod (Chado) 1.1 Released

I am pleased to announce that we released gmod-1.1 today. This release has the GMOD database schema, Chado, and a variety of tools for loading and working with the database. The release can be downloaded from the GMOD SourceForge site.

There have been many people who have helped with getting this release done and I would like to thank all of them. I would like to especially thank Rob Buels and Naama Menda and the rest of the people at the Sol Genomics Network (SGN) for their code contributions, including a pub table loader that works with PubMed and an updated version of the script to calculate cvterm closures.

There have been many changes and bug fixes since the 1.0 release just over two years ago, but the schema itself has changed very little. For a SQL summary of the changes, see Changes.sql in the release that contains SQL statements that should take a 1.0 release of the Chado schema to the 1.1 schema. See the Changes file for a full list.

If you have been using Chado from a recent svn checkout, you don't need to modify your schema at all, since the last change to the schema was about a year ago.

Now that this release is out, the plan going forward is for frequent, smaller releases, with an eye on the Natural Diversity schema modifications being worked on now.

Thanks for your continued support of the GMOD project,

Scott

2010/05/24

GMOD in Boston in July?

From Scott on 2010/05/25:

Due to the short notice, I've decided not to have a GMOD meeting before BOSC/ISMB in July. I am hoping to plan an informal "GMOD lunch" sometime during BOSC or ISMB for people who are going to the meetings and would like to get together to chat.

Scott Cain sent this question about the next GMOD meeting out to several mailing lists on May 17:

Since the last GMOD meeting in January, I had been hoping to have a GMOD meeting around the ISMB and BOSC meetings in Boston this July. Until this week, though, I had had a difficult time finding a place where a meeting could be held for a reasonable price. However, a kind soul at The Broad has offered a meeting space that would easily accommodate a GMOD meeting for two days before BOSC (either July 6-7 or July 7-8). The only question I have is this: can people make it to a GMOD meeting with about 2 months notice? Please let me know your thoughts on this. While there would probably be a registration fee, it would be fairly low (I'm guessing in the ballpark of $50).

Thanks,

Scott

Scott hasn't heard back, yea or nay, from very many people so far and we need to make a decision as soon as possible. If you have any thoughts on this, please send them to Scott before 3pm Eastern US time on Monday, May 24. See the GMOD Calendar for a list of what else is going on in July.

Thanks,

Dave C.
GMOD Help Desk

2010/05/21, updated 2010/05/25

Ergatis Update

Ergatis Paper in Bioinformatics

The paper "Ergatis: A web interface and scalable software system for bioinformatics workflows" is now available as an advance access manuscript in the journal Bioinformatics. Ergatis "enables users to build, execute, and monitor pipelines for computational analysis of genomics data."

Ergatis now includes pipeline templates for prokaryotic genome annotation and comparative genome analysis, as well as 174 modular 'components' that can be used to create custom pipelines, all of which can be executed either locally or on large compute clusters.

New tools available that use Ergatis include CloVR, which enables bioinformatic pipeline execution in compute clouds and the recently-awarded Data Intensive Academic Grid (DIAG), which will provide a publicly-accessible Ergatis instance as one of its access methods. At the January 2010 GMOD Meeting Chris Hemmerich presented ISGA, which provides a customized, abstract interface to Ergatis designed for biologists with specific pipeline needs.

Joshua Orvis

2010/05/20

May 2010 Calendar

Calendar

The next 5 weeks includes the 2010 GMOD Summer School - Americas and the first Galaxy Developers Conference. Upcoming deadlines include the ISMB technology track (tomorrow), posters at Arthropod Genomics and ECCB10, and papers for GIW 2010.

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If you know of any other events or deadlines that the GMOD community would be interested in, please send them to me.

Thanks,

Dave Clements
GMOD Help Desk

2010/04/22

MaizeGDB: Choosing GBrowse

Database Paper

A paper, "Choosing a genome browser for a Model Organism Database: surveying the Maize community," by the MaizeGDB team has been published in Database. To prepare for the availability of a reference genome, MaizeGDB surveyed their community to assess genome visualization needs. This paper summarizes the survey and MaizeGDB's review of available browsers, and describes why they chose GBrowse. The paper finishes by describing how they implemented GBrowse, including the locus lookup tool (described here), a MaizeGDB extension that uses maize's extensive physical and genetic mapping data to localize genomic regions in GBrowse. This is a great paper for anyone considering which genome browser to use.


Database Journal

I'd also like to highlight the journal the paper appears in: Database: The Journal of Biological Databases and Curation. "Biological Databases and Curation" are what GMOD is about and many of the papers cover issues and resources that are widely applicable in the GMOD community. The current issue also includes papers on community annotation using wikis, and a report on best practices in genome annotation from the ISB 3rd International Biocuration Conference. Database is an open access publication, making it an even better match for GMOD.

Dave Clements
GMOD Help Desk

2010/04/19

YAPC::NA 2010 is Almost Here!

{{#icon: Yapc2010Logo.png|YAPC::NA 2010|220|http://conferences.mongueurs.net/yn2010/}}

June 21st – 23rd 2010 is quickly approaching and Columbus.PM is getting very excited. Hotel reservation information is available, dorm reservation details are up and ready, the conference is quickly approaching. For everyone still looking for YAPC::NA 2010 (Yet Another Perl Conference North America) details, here is what we have planned. The conference will be held in the brand new beautiful The Ohio State Union.

Larry Wall, Damian Conway, Randal Schwartz, and many others will be in attendance.

The main dorm location is Morrison Tower and the Hotel conference block is in The Blackwell Inn (see Accommodations). Early registration is quickly coming to an end so make sure that you forward this to all of your friends and coworkers and get signed up today!

I hope to see you all at YAPC::NA 2010 in beautiful Columbus, Ohio.

Heath Bair
YAPC::NA 2010 Conference Chairman

2010/04/13

Don Gilbert Nominated for BFA

Don Gilbert Nominated for Benjamin Franklin Award

The Bioinformatics Organization has announced its nominees for the the 2010 Benjamin Franklin Award.

The Benjamin Franklin Award for Open Access in the Life Sciences is a humanitarian/bioethics award presented annually by this organization to an individual who has, in his or her practice, promoted free and open access to the materials and methods used in the life sciences.

This year's nominees include longtime GMOD contributor Don Gilbert, of Indiana University. Other 2010 nominees are Alex Bateman, David J. Lipman, G.P.S. Raghava, and John Quakenbush. Previous winners of the BFA include Jim Kent, Michael Ashburner, and another long-time GMOD contributor Lincoln Stein.

If you want a say on who should receive the 2010 award, please go to Bioinformatics.org and cast your vote. If you are not already a member you will need to join, but basic membership is free.

Dave Clements
GMOD Help Desk

2010/04/01

April 2010 Calendar

Calendar

There's a lot on the calendar in the next 5 weeks, including (among others) registration deadlines for Arthropod Genomics (early) and the Galaxy Developers Conference, and submission deadlines for ECCB, iEvoBio, BOSC, and ISMB.

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If you know of any other events or deadlines that the GMOD community would be interested in, please send them to me.

Thanks,

Dave Clements
GMOD Help Desk

2010/03/25

Google Summer of Code & OBF

OBF in GSoC

Great news: the Open Bioinformatics Foundation (OBF) has been accepted as a mentoring organization for this summer's Google Summer of Code!

GSoC is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents). Students are paid a $5000 USD stipend to work as a developer on an open-source project for the summer. For more on GSoC, see the GSoC 2010 FAQ.

Student applications are due April 9, 2010 at 19:00 UTC. Students who are interested in participating should look at the OBF's GSoC page, which lists project ideas, and who to contact about applying.

For current developers on OBF projects, please consider volunteering to be a mentor if you have not already, and contribute project ideas. Just list your name and project ideas on OBF wiki and on the relevant project's GSoC wiki page.

Thanks to all who helped make OBF's application to GSoC a success, and let's have a great, productive summer of code!

Rob Buels

OBF GSoC 2010 Administrator

2010/03/21

InterMine is Hiring

InterMine is hiring

We have four vacancies on InterMine related projects at The University of Cambridge, UK. We are looking for a Web Developer, Bioinformatics Software Developers and a Java Developer. See the position descriptions for more information.

The closing date for applications is 2nd April 2010.

The InterMine Team.

2010/03/19

Internships @ Dow AgroSciences

Dow AgroSciences

Dow AgroSciences has 7 Bioinformatics summer internship positions open, 2 of which are related to GMOD. We are looking for candidates with experience in installing, configuring, and uploading data into GMOD. Experience with the GBrowse source code and modifying it to create new views (e.g creating new glyphs and modifying existing glyphs as per user needs) is highly preferred. We have started the interview process. Please email your resume ASAP to Navin Elango (nelango@dow.com). For more information about Dow AgroSciences, please visit our website

Navin Elango

2010/03/16

Sr. DB Programmer @ FlyBase

FlyBase Opening

FlyBase has a single opening for a developer to join the database team at Harvard University in Cambridge, Mass. The position consists of roles in two model organism database projects, VectorBase and FlyBase, in the development and maintenance of production applications involving Chado, Apollo, Ensembl, and InterMine. For more information, see the job posting.

Dave Emmert

2010/03/09

NGS Analyses in Galaxy

NGS Analyses in Galaxy

The Galaxy team is announcing the launch of the first free public resource for NGS analysis. This service is the beginning of our campaign to provide free web-based utilities for NGS analysis and later in the year will take advantage of the Cloud resources. At present, there are three main groups of tools including:

  1. NGS QC and manipulation - contains a variety of tools for dealing with all flavors of fastq datasets as well as outputs of SOLiD and 454 instruments.
  2. NGS Mapping - currently includes Bowtie (Illumina & SOLiD), BWA (Illumina), and LASTZ (454) mappers. PerM (SOLiD) is on the way and more will be added in the coming months. Transcriptome tools are also in the final stages of development.
  3. NGS SAMTools - includes a variety of utilities for SAM/BAM manipulation. Some are based on SAMtools library, some are written by Galaxy team.

See the announcement page for more information and for links to several Galaxy Quickies (video tutorials) demonstrating the new service.

Anton Nekrutenko

2010/03/08

Openings @ SGD

Scientific Application Programmers at SGD

There are 3 openings for Scientific Application Programmers at the Saccharomyces Genome Database (SGD), the model organism database for yeast. These positions will be involved in enhancing databases and data pipelines for the sharing of genomic data. See the job postings for more information.

SGD is both a GMOD contributor (e.g., BLAST Graphic Viewer) and GMOD user.

2010/03/05

Logo Program Deadline Extended

GMOD Logo Program

The first call to participate in the GMOD Logo Program has been extended to March 19.

We still have some room for additional participants. If you are interested, please submit an application. Participation is limited to non-profits, and costs US$75. Please see the program page for additional details and requirements, and a link to an application form.

Thanks,

Dave Clements
GMOD Help Desk

2010/03/03

March 2010 Calendar

Calendar

There is always a lot going on that is of interest to the GMOD community. Anything that GMOD staff knows about is added to the GMOD Calendar. I'm going to start posting the GMOD calendar here for the upcoming month.

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Please let me know if this is useful, and I'll keep doing it. If not, I'll stop and the GMOD News will be a little less cluttered.

Thanks,

Dave Clements
GMOD Help Desk

2010/02/22

GMOD Logo Program, Spring 2010

{{#icon: Gmod_cog170.png|The GMOD Logo||GMOD Logo Program}}
{{#icon: Lbcclogo.jpg|GMOD Logo Program||GMOD Logo Program}}

I am pleased to announce the first call for participation in the GMOD Logo Program. This program is for GMOD users and developers that would like a custom designed logo for their web site, database or software. This spring we will be working with students in an advanced design class at Linn-Benton Community College. Interested GMOD users and developers will be paired with students and meet several times (remotely) over a 3 week period this spring, with the end result being a new logo.

Participation is limited to non-profits, and costs US$75. If you are interested, please see the program page for additional details and requirements, and an application form. The program is accepting applications until March 1.

Thanks,

Dave Clements
GMOD Help Desk

2010/02/03

GMOD Summer School - Americas

We are now accepting applications for the 2010 GMOD Summer School - Americas. This will be a hands-on multi-day course aimed at teaching new GMOD administrators how to get GMOD Components up and running. The course will introduce participants to the GMOD project and then focus on installation, configuration and integration of popular GMOD Components.

The course will be held May 6-9, at NESCent in Durham, NC. These GMOD Components will be covered:

{{#icon: 2010SummerSchoolAmericas170.png|GMOD Summer School||2010 GMOD Summer School - Americas}}

  

The deadline for applying is the end of Friday, February 22. Admission is competitive and is based on the strength of the application (especially the statement of interest). In 2009 there were over 50 applications for the 25 slots. Any applications received after the deadline will be automatically placed on the waiting list.

Thanks,

Dave Clements
GMOD Help Desk

PS: We are also investigating holding a GMOD course in the Asia/Pacific region, sometime this fall. Watch the GMOD Mailing Lists and the GMOD News for updates.

2010/01/29

GMOD @ February NextGenBUG

NextGenBUG 9 Feb Dundee

If you are anywhere close to Dundee, Scotland on 9 February, consider attending the NextGen Sequencing Bioinformatics User Group (NextGenBUG) meeting being held at the University of Dundee. The program includes two talks with GMOD related content.

There will also be talks by Dan Bolser of Dundee and Darrol Baker of CLCBio. If you are interested in attending, please add your name to the participants list.

Dave Clements
GMOD Help Desk

2010/01/29

GBrowse 2.0

GBrowse2Thumb.png

With thanks to the many people who have worked long and hard on this project, as well as the people who found and reported bugs during the prerelease stage, I am happy I announce that GBrowse 2.00 is now available for downloading from CPAN, and SourceForge.

The following are highlights of the many new features that have been added since the 1.70 release:

  • A completely rewritten internal rearchitecture loads tracks asynchronously, providing a more responsive user experience.
  • Different database backends can be associated with each track, making backend management much simpler.
  • A revamped user interface for a less cluttered and more functional end-user experience.
  • A UI theming system with three predefined themes, including a cool "transparent" theme.
  • A custom track upload and management system gives users much greater control over custom tracks.
  • An optional admin interface allows an authorized user to upload and manage public tracks without editing config files.
  • An optional user registration and login system allows users to register stable GBrowse accounts and to keep their settings and custom tracks when they move from one computer to another.
  • Support for named subtracks (tracks within tracks) and filtering of those subtracks.
  • Support for next generation sequencing data.

There are also a number of features that didn't make it into the 2.00 release, most notably:

  • The internal DAS server does not work, although the DAS client (ability to import DAS tracks) does. This will be added in a 2.01 release.
  • Internationalization has lagged way behind, and so most of the new features will be presented in English rather than in the user's preferred language (volunteers are needed to help with translations).

Please send help queries to the GBrowse mailing list, and file bug reports at SourceForge.

On behalf of the GMOD team,

Lincoln Stein

2010/01/28

WebGBrowse 2.0

WebGBrowse at the Center for Genomics and Bioinformatics

WebGBrowse 2.0 is now available at http://webgbrowse.cgb.indiana.edu. Here is some of what's new in WebGBrowse 2.0:

  • WebGBrowse 2.0 continues to help the inexperienced users of GBrowse with hosting their GFF3 data without worrying about installation or configuration semantics.
  • Users now have a choice of GBrowse display between versions 1.7 and 2.0.
  • The display from one version can be migrated to the other by simple button clicks. This helps the users to compare their data display between the two versions without much hassle. It also helps the WebGBrowse users in upgrading/migrating their existing GBrowse displays to version 2.0 seamlessly.
  • A few bug fixes from the earlier version.
  • For those interested in installing WebGBrowse locally, the current installation package is lot more easier to install and less clumsy than the previous version.

Thanks,

Ram Podicheti
Center for Genomics and Bioinformatics
Indiana University

2010/01/25

Tripal v0.2 Released

Triapl

I’d like to announce the release of the second version of Tripal, v0.2. This version provides new support for controlled vocabularies, databases and several analysis types. This includes better support and visualizations for GO, new KEGG pathways and BRITE hierarchies, InterProScan results and improved BLAST results.

Tripal has been freely and publicly available since May of 2009 and provides a PHP-based Drupal front-end for the Chado database schema. It his highly customizable and is extendable by anyone with Drupal and PHP experience. We encourage end-users to develop new or improved modules that can be shared back with the community. We can offer assistance when needed in the development of new modules.

An updated user’s manual is available, but not quite complete. An update to the manual will be added soon. If you have any questions please feel free to email the Tripal mailing list for assistance.

Tripal can be downloaded from the CUGI website as a compressed package, or developers can retrieve the most up-to-date code from the GMOD SVN.

Best Regards,

Stephen Ficklin
Clemson University Genomics Institute

2010/01/23

CMap3D

CMap3D

CMap3D is a 3D visualisation tool for comparative genetic maps that runs on top of a CMap database. CMap, a GMOD component, is a common tool for the storage, comparison and visualisation of genetic maps. However, current map visualisation in CMap is limited to the comparison of adjacent aligned maps. CMap3D overcomes this limitation. Multiple genetic maps can now be compared in three-dimensional space. The CMap3D visualisation tool is based on a client server model ensuring operability with current CMap data repositories.

CMap3D can be applied to any species where genetic map information is available and enables rapid, direct comparison between multiple aligned maps. For more on CMap3D see the CMap3D page at the Australian Centre for Plant Functional Genomics (ACPFG), the PAG 2010 presentation on CMap3D (and other tools), and the CMap3D paper in Bioinformatics.

Chris Duran

2010/01/21

DAS Workshop 7-9 April 2010

DAS Workshop

There will be a Distributed Annotation System (DAS) Workshop at EBI, 7-9 April 2010. In GMOD, DAS is supported by GBrowse, and Chado (and DAS support in Apollo is in the works).

If you don't know about DAS and wish to know how to distribute your latest biological annotation to the world then the upcoming DAS workshop may be for you.

If you know about DAS and are maybe a DAS client developer then the upcoming DAS workshop is for you (as you will need to know about the upcoming DAS 1.6 Specification and how it may affect your software).

See the workshop page for more information and registration details.

Jonathan Warren

2010/01/21


GBrowse.org

GBrowse.org|80|http://www.gbrowse.org/}}
GBrowse.org

GBrowse.org is a resource for using and setting up GBrowse genome browsers. The site provides one location where biologists and bioinformaticians can find:

  1. Genome browser web sites for any organism that has them. If a species has a genome browser anywhere on the web, then we aim to link to it.
  2. Links to sequence and annotation files that are available online.
  3. Links to genome browser configuration files, when available
  4. An FTP site containing genome annotation and configuration files for each annotated genome that does not have its own web site.

GBrowse.org emphasizes the GBrowse genome browser in its organization, but also links to sites that use other browser packages such as UCSC, Ensembl, and JBrowse.

Also, we are currently conducting a survey seeking input on future project direction. Please take a few minutes now to provide your feedback.

GBrowse.org was first introduced at the August 2009 GMOD Meeting.

Ciao,

Alessandra Bilardi
CRIBI Genomics, University of Padua

2010/01/11

Bio::Chado::Schema 0.05 Released

I'd like to announce a new Schema release, version 0.05. Changes in this release:

  • Got POD generation working, now all classes and methods have POD, including the embedded table and column comments! Thanks to the wonderful DBIx::Class::Schema::Loader folks.
  • Turned off DBIC's cascade_delete and cascade_copy on all relations (thanks to Siddhartha Basu for troubleshooting). Deletes break if these are on and you don't have every part of the schema installed.

I uploaded it to CPAN a week ago, so it should have propagated by now to almost all of the CPAN mirrors.

See the Schema wiki page for more on what Schema is and what it's for.

Rob Buels
SGN

2010/01/08

GMOD at PAG 2010

GMOD will once again have a strong presence at the Plant and Animal Genome Conference (PAG 2010), being held January 9-13 in San Diego. There will be over 45 talks, workshops, demonstrations and posters about GMOD Components and projects that use them. See the PAG 2010 page for a full listing and a flier showing highlights. Highlights at PAG 2010 include:


GMOD @ PAG

Many GMOD staff and developers (Scott Cain, Dave Clements, Stephen Ficklin, Carson Holt, Sheldon McKay, Anton Nekrutenko, Mitch Skinner, Ken Youens-Clark) and even more GMOD users will be at PAG. If you are attending please keep an eye open for us.

Finally, the January 2010 GMOD Meeting is being held immediately after PAG. The meeting is full (you are encouraged to add your name to the short waiting list), but there will be several Satellite Meetings, held during PAG, that you can attend even if you don't go to the main GMOD Meeting.

See you in San Diego,

Dave Clements
GMOD Help Desk

2010/01/05

2009 Stories

Galaxy Developer Conference

http://meetings.cshl.edu/meetings/meetingsregistration_galaxy10.asp


Galaxy Developer Conference

The First Galaxy Developer Conference will be held at Cold Spring Harbor Laboratory May 15-17, 2010, immediately after the Biology of Genomes conference. Registration is now open.

This meeting is aimed at developers of analysis tools, bioinformatics staff, and IT managers of sequencing facilities. The meeting will focus on these features of the Galaxy framework:

  • tool integration and distributed job management
  • deployment of private Galaxy instances on local resources and on the cloud
  • management of large datasets with the Galaxy Library System
  • using the Galaxy LIMS functionality for managing sample submission at NGS sequencing facilities.

Please register now if you are interested in using and extending Galaxy.

Dave Clements
GMOD Help Desk

2009/12/28

Arthropod Genomics Consortium

Arthropod Genomics Consortium

The Arthropod Genomics Consortium encourages collaboration and information exchange amongst arthropod researchers. The consortium, launched at the 2009 Arthropod Genomics Symposium, has now started a wiki to enable this community to self-organize:

Our goal is to provide a central location for information about arthropod genomics projects, bioinformatics tools, and people interested in arthropod genomics. We think this is a great way to "identify the community"; information from the wiki can be used to support white papers and grant proposals. It will also serve as a central location for links to arthropod genomics resources, news releases and meeting announcements.
Sue Brown, Director, K-State Arthropod Genomics Center

If you are an arthropod researcher, please consider joining this growing consortium.

Dave Clements
GMOD Help Desk

2009/12/18

BioPerl Podcast

BioPerl Podcast

A podcast on the BioPerl project is available at FLOSS Weekly. It's about an hour long and it's a good introduction to BioPerl, a set of libraries that many popular GMOD Components are built upon. The podcast is an interview with BioPerl heavy hitters Chris Fields and Jason Stajich.

Dave Clements
2009/11/23

InterMine 0.92 Released

InterMine Release Notes

We have released version 0.92 of InterMine.

The main changes are some improvements to the way integration keys and priorities are configured and validated, a BioPax parser, performance enhancements and some webapp fixes.

Version 0.92 has Release Notes and upgrade information.

Upgrade should be quite straightforward from either 0.9 or 0.91. The only issue is compatibility of the GO enrichment widget with old databases built before 0.91.

Let us know if you have problems or suggestions for the next releases.

The InterMine team.

2009/11/23

CMap Paper in Bioinformatics

Bioinformatics

A paper describing the CMap comparative map viewer is in the current issue of Bioinformatics:

CMap 1.01: a comparative mapping application for the Internet, by Ken Youens-Clark, Ben Faga, Immanuel V. Yap, Lincoln Stein and Doreen Ware.

CMap is a web-based tool for displaying and comparing maps of any type and from any species. Users can compare an arbitrary number of maps, view pair-wise comparisons of known correspondences, and search for maps or for features by name, species, type and accession.

See the CMap page to learn more. CMap will also be covered in the Gramene workshop and in a poster at PAG 2010.

Dave Clements
GMOD Help Desk

2009/11/14

January 2010 GMOD Meeting

January 2010 GMOD Meeting


Register for the January 2010 GMOD Meeting


I am pleased to announce that the January GMOD meeting will be taking place on January 14 and 15, 2010 in San Diego at the Best Western Seven Seas (the same location as last year). Please see the meeting page for registration information.

Please also take a moment to add suggestions for the agenda. There is no registration fee for this meeting. However, there is limited space, so please register early.

The proprietors of the Best Western have given us an excellent room rate, and extended it to the previous week, so that people attending the GMOD meeting and the Plant and Animal Genome meeting before it may stay at the Best Western the entire time.

Please direct follow up questions to the gmod-devel mailing list (gmod-devel@lists.sourceforge.net).

Thanks and I look forward to seeing you in San Diego!

Scott

2009/11/13

Long Term Database Funding

You may have heard about TAIR's funding situation. Basically, their funding is being cut by 25% per year, starting in September 2010, and NSF is encouraging them to find alternative funding sources. This news was sent to the TAIR community (and posted on the Biocurator list) on October 22. A day later the paper "Models for financial sustainability of biological databases and resources" appeared in Database: The Journal of Biological Databases and Curation.

All GMOD users need to give at least some thought to long term funding issues. A discussion thread on long term database funding has now been started on the International Society for Biocuration's (ISB) forum site.


TAIR Funding Update and Discussion Forum

TAIR asked people to do a couple things:

  1. Cite TAIR in publications: as a reference, as a source of data in methods sections, and under acknowledgments.
  2. Contribute to a discussion on the TAIR web site about
    1. the bioinformatics needs of the Arabidopsis and wider plant biology communities and
    2. how resources like TAIR should be funded.

The discussion at TAIR is now 19 pages long and contains mountains of praise for TAIR, and a few suggestions on alternative funding, including subscriptions, international and industrial support, and advertising. It also contains many statements that none of those options will work. The Database paper discusses similar proposals, plus some others.

If you are interested in long-term funding issues, I encourage you to participate in the discussion at ISB. If you use TAIR and want to see it funded, please post a comment at the TAIR web site. And, if you aren't already doing so, make it easy for your users to cite your database by including an easy to find "Citing this resource" link on your site.

Dave Clements

2009/11/06

Two Openings at Bayer CropScience

Open positions at Bayer CropScience

1. BioAnalyst Scientist:

You will provide support in various activities: Next Generation Sequencing (NGS) data analysis, expression data (microarrays) analysis, genomics and biological networks. The successful applicant should have a PhD or equivalent experience in (plant) genetics and/or genomics. Computer skills are not mandatory but knowledge of bioinformatics applications is required. Excellent communication skills and the ability to support and train researchers with genomics data analysis is essential.

More information: BioAnalyst Scientist

2. BioAnalyst Researcher:

You will support and foster the data management and analysis of Next Generation Sequencing (NGS) data (assembly, processing, development of analysis methods, pipelines, etc.). Candidates must be highly motivated to work on biological questions and flexible to interact with the various groups of the research center. They should have a degree (MSc or PhD) in computational biology, boinformatics, statistics or equivalent level of knowledge and possess some programming skills (e.g. perl and/or python). The candidate should have a good background in (plant) genetics and/or genomics and/or molecular biology.

More information: BioAnalyst Researcher

Operating language in the company is English.

Interested in any of these positions? You can apply here or send your CV to Laurent Viau

Erick Antezana

2009/11/06

GBrowse NGS Tutorial & Poster

GBrowse NGS Tutorial

A tutorial on using GBrowse 2 to visualize next generation sequencing (NGS) data is now available. The tutorial walks through how to configure the GBrowse 2 genome browser to display next generation sequencing (NGS) data using the SAMtools GBrowse adaptor, Bio::DB::Sam. This tutorial was originally taught at the Bioinformatics Australia 2009 (BA2009) GMOD Workshop. The tutorial includes a VMware image to work with and step-by-step instructions for visualizing the example human data that comes with the SAMtools package.

The tutorial includes examples showing read depth coverage, individual reads - including mismatches, using color to show alignment quality, and read-pairs.

A poster (by Scott Cain) demonstrating how to use the adaptor with GBrowse 1 and GBrowse 2 is also available.

Dave Clements
GMOD Help Desk

2009/11/04

Galaxy Project Hiring

Galaxy Project Hiring

There are several open software engineer and postdoc positions with the Galaxy project. Galaxy is looking for engineers with with experience in distributed computing, visualization, and usability. The positions will initially focus on making next generation sequencing (NGS) data analysis more widely accessible, transparent, and reproducible, as well as development of bioinformatic tools in areas enabled by NGS: re-sequencing, de novo assembly, metagenomics, transcriptome analysis and epigenetics. Postdoc positions will address biological questions (e.g., mutagenesis and sex chromosome evolution from NGS data) using Galaxy tools.

See the official posting for full details and contact information.

2009/11/02

Visualizing Biological Data Workshop

Visualizing Biological Data (VizBi)

The first EMBO Workshop on Visualizing Biological Data (VizBi) will be held 3-5 March 2010, at the EMBL Advanced Training Centre in Heidelberg, Germany.

The goal of the workshop is to bring together researchers developing and using visualization systems across all areas of biology, including genomics, sequence analysis, macromolecular structures, systems biology, and imaging (including microscopy and magnetic resonance imaging). The primary focus will be on visualizing processed and annotated data in their biological context, rather than on processing of raw data.

The workshop is limited in the total number participants, and each participant is normally required to present a poster and to give a fastforward presentation about their work (limited to 30 seconds and 1 slide). To apply to join the workshop, please submit an abstract and image related to your work. Submissions close on 16 November 2009.

2009/10/21

Openings at Syngenta

Openings at Syngenta

There are two openings at Syngenta, recently named one of the top biotechnology employers by Science, in Research Triangle Park, NC.

Genomic Database Specialist (#1435): We are currently using the Chado schema, and this individual will be responsible for maintaining and optimizing database systems for genome annotation and related information. Experience overseeing database systems is required and experience with Oracle and PostgreSQL is desirable. The ideal candidate will have a solid understanding of genomics and a background in a life sciences setting. Strong competency with Unix and Perl is required.

Genome Annotation Specialist (#1434): This individual will be responsible for implementing automated annotation pipelines for genome, transcript, and proteins sequences. Advanced knowledge of sequence analysis tools is required. Experience with modern high throughput sequencing analytics is desirable. A strong competency with Unix and scripting in a language such as Perl is required.

Both positions will work with Chado and GBrowse, and will help evaluate the adoption of additional GMOD tools. See the links for more details.

Eric Ganko

2009/10/21

Opening at SGD

There is an opening for a Bioinformatics Analyst at the Saccharomyces Genome Database (SGD), the model organism database for yeast.


Bioinformatics Analyst at SGD

The position includes interacting with international research laboratories, working with genomic data, evaluating new technologies, analysis via computational methods created by others but integrated at SGD, knowledge of new experimental methodology, large genomic datasets and their computational analysis, and bioinformatic analysis of data types such as RNA transcription and second-generation sequencing. Experience with comparative genomics is also desirable.

SGD is both a GMOD contributor (e.g., BLAST Graphic Viewer) and GMOD user, and this position will work with the GBrowse genome viewer as well as other GMOD tools.

See the Stanford jobs site (search for posting 36125) for more.

2009/10/20

Apollo 1.11.2 Released

I've just cut a new Apollo release that fixes some GFF3 and Chado writeback issues. As usual, you can get the most current version of Apollo at:

http://apollo.berkeleybop.org/current/

Cheers,

Ed Lee

2009/10/07

2009 GMOD Survey Results

The results of the 2009 GMOD Community Survey are now available online. This year's survey focused on genomic and comparative genomics visualization was taken by 45 respondents. The survey includes:

The survey results will be used to improve GMOD and guide its future direction. This year's survey complements the 2008 GMOD Community Survey, which covered all of GMOD.


GMOD Mug

And, finally, we have our 3 winners of GMOD Gear:

Thanks to everyone who took the time to participate in the survey.

Dave Clements
GMOD Help Desk

2009/10/05

GMOD Tutorials! GMOD Training!

Summer School - Europe


Summer School - Americas

Detailed and hands-on online tutorials are now available for the GMOD Components that were covered at the 2009 GMOD Summer Schools. Each tutorial includes a VMware system image to work with, and detailed instructions on how to setup the component on that image.

The tutorials are:


There is also a plethora of GMOD related training and outreach going on in the next few months. Here's what I know about:

Date Topic Conference / Location
October 12-27 Programming for Biology
This includes a session on GBrowse.
Cold Spring Harbor Laboratory, Cold Spring Harobr, NY, USA
October 21-22 Interactive Workshops on the UCSC Genome Browser and Galaxy Framework The American Society of Human Genetics (AHSG), Honolulu, Hawaii, USA
October 27-30 GBrowse and Next Generation Sequencing Data Genome Informatics, Cold Spring Harbor, New York, USA
October 28-30 Database Tools for Biologists: A Half-Day GMOD Workshop Bioinformatics Australia 2009 (BA2009), Melbourne, Australia
Visualizing Next Generation Sequence Data with GBrowse and SAMtools (poster)
November 16-17 InterMine Data Warehouse Workshop Cambridge, UK
Comparative Genomics with GMOD Information Systems for Insect Pests, Rennes, France
January 9-13 The Generic Genome Browser: A Hands on Workshop for Installing, Configuring and Using Your Own GBrowse Plant and Animal Genome XVII Conference (PAG 2010), San Diego, CA, USA
See PAG 2010 for links to many talks and presentations.
Comparative Genomics with GBrowse_syn: A hands on workshop for visualizing your comparative genomics data with GBrowse_syn
MAKER: An easy to use genome annotation pipeline

Dave Clements
GMOD Help Desk

2009/10/02

modENCODE & Gramene Openings

The modENCODE and Gramene projects are both hiring.

modENCODE


modENCODE Project Openings

modENCODE is looking for a few consultants. The project's aim is to discover and explore the genomes of C. elegans and D. melanogaster, using new scientific strategies and new technologies for discovery.

Consultants will be responsible for interacting with several external research labs, as well as with internal software developers, to collect and collate experimental data of many different types. In addition to a strong background in biology, candidates must be knowledgeable in programming and/or software development. Candidates must also possess verbal and written communication skills, particularly for understanding requirements from biologists, and to productively work in a collaborative environment.

Please see the complete job description for details.

modENCODE is a power GMOD user. The project uses GBrowse, Chado, InterMine, JBrowse, and GBrowse_syn. (See Nicole Washington's talk at the January 2009 GMOD Meeting for some details on how they are used.)


Gramene


Grameene Project Opening

Gramene has several bioinformatics openings in the Jaiswal lab at Oregon State University.

The positions involve development and maintenance of the databases, software and analysis pipelines necessary for development of the Plant Gene Expression, biochemical and regulatory pathway networks, comparative genomics, text mining (Textpresso) and biological ontology projects. Gramene is a long-time GMOD user and is the home of the CMap comparative map viewer.

See the position announcement for full details.

2009/10/02

GMOD @ Bioinformatics Australia

GMOD workshop at Bioinformatics Australia

There will be a half-day pre-conference GMOD workshop on 28 October, 2009, at Bioinformatics Australia (BA2009). The workshop will introduce GMOD Components for visualization, annotation, and data management, and the GMOD project as a whole. The workshop will also include a GBrowse demonstration with a worked example that includes next generation sequencing data.

Thanks to sponsorship from Bioplatforms Australia admission to the workshop is included in the conference registration fee.

Please see the workshop page or contact the GMOD Help Desk for more information.

Dave Clements
GMOD Help Desk

2009/10/01

InterMine Data Warehouse Workshop

InterMine Workshop

We are running another InterMine workshop in Cambridge, UK on November 16th-17th.

This is intended for software developers to learn the InterMine system. The two day course will step through creating a new Mine, integrating real data and deploying and customising the web application.

The course is free to attend, more details and sign up information are available on the workshop page.

Please get in touch if you have any questions.

Regards,

Richard Smith

2009/09/29

Tripal: A Web Front End for Chado

Tripal

Tripal is a new web front end for Chado databases and is now a part of GMOD. Tripal is a collection of Drupal modules initially developed by the Clemson University Genomics Institute (CUGI). Tripal is already powering several web sites, including the Marine Genomics Project and Fagaceae Genomics Web.

Tripal supports Drupal themes, page content and look and feel customization, materialized views, searching, and job management out of the box.

Tripal can be downloaded from the GMOD SVN repository. Tripal (already!) has an extensive User's Guide and a tutorial to help users install, configure and extend Tripal.

If you use or are considering using Chado, please take a look at Tripal.

Dave Clements
GMOD Help Desk

2009/09/28

Reactome User Survey

Reactome is committed to providing access to high-quality pathway information and helpful data analysis tools. With this in mind, we are actively soliciting comments from the research community in order to assess community needs. We are interested to hear about your experience with Reactome, and would like to know a bit about your background and research interests so that we can continue to improve the Reactome site and tools.

You can access the survey at SurveyMonkey

Thank you for taking part.

Robin Haw Manager of Reactome Outreach Outreach [at] reactome.org http://www.reactome.org

Posted by Scott Cain

2009/9/28

DIYA: Do It Yourself Annotator

DIYA

DIYA, the Do It Yourself Annotator is now officially a part of GMOD. DIYA is a modular and configurable open source pipeline framework, written in Perl, used (initially) for the rapid annotation of microbial genome sequences. The software is currently used to take nucleotide sequence contigs as input, either in the form of complete genomes or the result of shotgun sequencing, and produce an annotated sequence in GFF format. Current development seeks to integrate DIYA with the AMOS collection of assembly tools.

DIYA resides in Sourceforge, where it has mailing lists and a blog, and uses Trac for development tracking. DIYA is stable and version 1.0 has been released.

DIYA is part of the Do It Yourself Genomics (DIYG) Project. Developers of DIYA (and DIYG) include Andrew Stewart and Brian Osborne (formerly of the GMOD Help Desk). The DIYA community is looking for interested developers to contribute to DIYA. See the DIYA page for more.

Dave Clements
GMOD Help Desk

2009/09/23

Chado in RDF: OpenFlyData

RDF

The OpenFlyData project has ported the FlyBase Chado database and several other Drosophila gene expression databases to the Resource Description Framework (RDF). Each source database has a separate RDF store, and OpenFlyData provides both a browser and a programmatic SPARQL-based interface to each. Source databases include the Chado database from FlyBase, BDGP, FlyAtlas and FlyTED.

Transforming databases into RDF can be an effective way to merge these data, and does not require mapping everything to a central relational schema. The common graph-based data model facilitates the reuse of RDF data published by other projects, with fewer constraints on the kind of questions you can ask.

For more on OpenFlyData, see the Linked Data for GMOD Databases presentation from the August 2009 GMOD Meeting, and the OpenFlyData web site.

Jun Zhou and Dave Clements

2009/09/23

Bioinformatics Position at SpBase

Position at SpBase

The Sea Urchin Model Organism database (SpBase) has an opening for a Bioinformatician. From the position announcement:

The computation group supporting the Sea Urchin Model Organism database, SpBase, is seeking a highly motivated individual to take responsibility for collecting, organizing and displaying gene expression information at all life stages of the purple sea urchin Strongylocentrotus purpuratus. The individual will work with existing computer code as well as develop new software. A particular challenge of the project is to move data from various sourves and of various types to a common framework for presentation and manipulation by the user.

See the job posting for more on the position. Please contact Andy Cameron if you have questions about the position.

SpBase uses several GMOD Components, including GBrowse, Apollo, BioMart, and Chado.

Dave C.
GMOD Help Desk

2009/09/22

2009 GMOD Community Survey

GMOD Mug|100|}} GMOD T Shirt }}

Please take a few minutes to fill out the 2009 GMOD Community Survey and your name will be entered to win a free GMOD T-shirt or mug! This year's survey focuses on genome and comparative genomics visualization (and is much shorter than the 2008 survey). We are asking all GMOD users and developers to provide your feedback.

Three randomly selected survey participants will receive the GMOD T-shirt or mug of their choice. Names will be drawn from the first 100 responses, so get your response in early. The survey closes at the end of the day on September 25.

Please contact the GMOD Help Desk if you have any questions.

Thank you,

Dave Clements
GMOD Help Desk

2009/09/16

CVS to SVN Conversion: Done

CVS|70|CVS to Subversion Conversion}} Subversion CVS to Subversion Conversion}}

GMOD's CVS source code repository was converted to Subversion (SVN) on September 15, 2009. Directions on how to use SVN are explained at Version Control System Access. Details of the conversion itself are at CVS to Subversion Conversion.

Inactive projects were moved out of the main directory and placed in the Inactive directory. The CVS repository is still there and accessible, but it is now read-only. The GMOD web site has been updated to reflect the move to Subversion.

We have identified a few outstanding issues and these are listed on the conversion page. If you come across any additional issues, please either update that list or email the GMOD Help Desk.

Finally, many thanks to Rob Buels of Cornell / SGN for doing the work.

Dave Clements

2009/09/15

FlyBase Bioinformatics Engineer

FlyBase Opening

Please see the official advert for full details and application procedure.

The Indiana University division of FlyBase in Bloomington, Indiana is currently looking for a qualified software engineer to help with deploying the InterMine and BioMart data management systems. The developer will be responsible for the web accessible aspect of these technologies. This includes the initial setup and configuration of these two systems, setting up and automating update cycles in sync with the existing FlyBase release cycle, evaluating the capabilities of each, aiding in the integration of these services with existing FlyBase reports and tools, and coordinating these efforts with other model organism databases (MODs). Loading and preprocessing of data for these systems will be performed at the Harvard University FlyBase site so close coordination with developers there will also be required.

Josh Goodman

2009/09/14

Server Maintenance: Sept 9

{{#icon: WorkInProgressTools.gif|||}}  The GMOD website and server will be down for maintenance on Wednesday, September 9, 2009 for up to 90 minutes, sometime between 1pm and 5pm Eastern US time. The server is being moved to a new a data center. We apologize for any inconvenience this may cause you.

Please let us know if you have any questions.

Dave Clements
GMOD Help Desk

2009/09/08

BioMart Ruby API

BioMart Ruby API

Daz Oakley of the Wellcome Trust Sanger Institute has released a Ruby library/API for BioMart. Daz says "It's quite basic for the moment and only does single dataset queries, but it will be quite easy to build upon the base from here."

The source is available from GitHub, and the documentation is at rdoc.info.

The Ruby API is the latest addition to a growing list of third party software that supports BioMart. This list includes Galaxy, Bioclipse, biomaRt-BioConductor, Cytoscape, Taverna, and WebLab

Dave Clements
GMOD Help Desk

2009/09/08

JBrowse paper

A paper on the JBrowse genome browser is in this month's issue of Genome Research. If you haven't looked at JBrowse before, it feels both very familiar and radically different at the same time.

JBrowse is a Web 2.0 genome browser that features:

  • Client side rendering, and very fast rendering at that.
  • As a consequence it has very low server disk space, server CPU, security and network bandwidth requirements.
  • An interface that is entirely AJAX based. Everything is done with AJAX.
  • GFF3, Chado and/or Wiggle track compatibility
  • JSON based configuration files (very similar to GBrowse config files in their content)
  • Easy embedding in other web applications (an example of embedding a genome browser in a wiki is provided)

JBrowse features smooth panning, zooming, navigation, and track selection and sets a new standard for the genome browser interface.

Dave Clements
GMOD Help Desk

2009/09/01

Aug 2009 GMOD Meeting Report

August 2009 GMOD Meeting

The August 2009 GMOD Meeting was held 6-7 August, 2009 in Oxford, UK, immediately following the 2009 GMOD Summer School - Europe. It was the first 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 17 presentations by GMOD users, developers, and project staff.

Some highlights:

Plus many other excellent presentations on topics ranging from DAS to GBrowse.org.

Please take a look at the meeting report for an update on what's going on in the GMOD community.

Finally, I'd like to thank the 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.

Dave Clements
GMOD Help Desk

2009/08/29

Bio::Chado::Schema 0.03 Released

The first official release of Schema is now on the 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 GMOD Schema mailing list.

--RobertBuels 22:10, 29 August 2009 (UTC)

2009/08/29

InterMine 0.91 Released

InterMine

We've released InterMine 0.91 and there is a new subversion branch and tar.gz for download. The main changes are fixes to some QueryBuilder features, occasional export issues and improved password security. There is a new TreeFam parser and an improvement to ontology querying.

This update shouldn't require any changes to Mines and sources you have created. See details on upgrading and the release notes.

Please let us know if you have any bug reports or feature requests.

The InterMine team

2009/08/27

CVS to SVN Conversion: Sept 15

CVS|70|CVS to Subversion Conversion}} Subversion CVS to Subversion Conversion}}

GMOD's CVS source code repository will be converted to Subversion (SVN) on September 15, 2009. Rob Buels of Cornell / 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 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.

If you are a GMOD developer and your project is in GMOD's CVS repository then this move will significantly affect you.

See SourceForge for a complete list of projects in GMOD CVS. This list is reproduced on the CVS to Subversion Conversion page. Between now and September 15, we will contact project developers to confirm what projects are still active. All projects will be moved to SVN, but any projects that are no longer active will be placed in a separate archive directory. This will significantly clean up the repository. See the CVS to Subversion Conversion page for the current status of each project.

Rob has created a preview version of the repository. Feel free to poke around. This version does not have any projects archived.

Rob will move the projects on September 15. Before then everyone with uncommitted code changes should commit them to CVS. After September 15, all CVS checkouts you have should be removed and new checkouts made with SVN. We'll provide doc on how to do this. We will send out exact details on the move a few days before it happens.


Please let Rob and Dave know if you have any questions. We'll send out a reminder and additional info a few days before the conversion.

Thanks,

Dave Clements and Rob Buels

2009/08/26

GBrowse 1.70 Released

Hello,

I am pleased to announce the official release of GBrowse 1.70. This is a bug fix release for GBrowse 1.69. It introduces no new functionality to the GBrowse portion of the application, however, GBrowse_syn is considerably improved along with documentation and a 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 GBrowse 2.

GBrowse can be installed with the GBrowse netinstaller.

GBrowse 1.70 can be downloaded directly from SourceForge.

A big thanks to Lincoln Stein, the lead developer of GBrowse, Sheldon McKay, the developer of GBrowse_syn, and all of the GBrowse users who debug and provide help on the GBrowse mailing list.

Changes from 1.69 to 1.70:

  • Bug fixes for the Chado adapter, including improving wildcard searching and fixing a bug that caused ALL features on a reference sequence to be returned when the segment was at the beginning of the reference sequence.
  • Fixed Galaxy support bug which caused prevented features from multiple tracks being selected.
  • Fixed problem with feature highlighting which caused highlighting to get "stuck"on beige.
  • Removed annoying debugging statements from log files
  • Fixed character encoding issues for onClick popup balloons
  • Killed annoying "missing path" warning on windows systems
  • Fixed issue in which the selected region shown in the overview is offset from true region.
  • Silenced log file warnings when inkscape isn't present.
  • Added "merge searches" option to turn merging of similarly-named features on and off.
  • Moved Bio::DB::Das::Chado and Bio::DB::BioSQL to their own packages and out of the GBrowse distribution so they can be updated independently via CPAN
  • Fixed encoding of version number at the bottom of the page.
  • Made the DAS script compatible with DAS Registry

Scott

2009/08/24

Lepidoptera Bioinformatics

International Workshop on Molecular Biology and Genetics of Lepidoptera

A session on data analysis, mining, general bioinformatics support, and related topics will be held on Friday, August 28th 2009, at the 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 InsectaCentral and LepidoDB, both of which use GMOD Components, will be discussed in the workshop.

The session is held during the last conference day and is one hour long; we encourage Crete participants to talk to us during the week and point out related problems you are facing in your own work. We will then produce a list to be discussed during the session and focus on soliciting ideas on how to organize collaborative and centralized efforts to everyone's benefit. We would especially like to identify potential funding sources, groups willing to help write consultation papers and grant proposals and individuals willing to contribute to realistic solutions.

We would like to encourage those of you who are not planning to attend the Crete workshop to contact us with your thoughts and ideas on these and related subjects.

Marian Goldsmith, Alexie Papanicolaou, and Fabrice Legeai.

2009/08/18

Ant Genomics Bioinformatician

Fourmidable opening

The deadline for this position has now passed.

The Swiss Institute of Bioinformatics and the 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 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

FlyBase Opening

The Cambridge (UK) division of FlyBase currently seeks a 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 official advert for full details and application procedure.

Informal enquiries to Steven Marygold (sjm41@gen.cam.ac.uk).

2009/07/31

Insect Pest Workshop, 16-17 Nov

{{#icon: InformationSystemsForInsectPests.gif|Information Systems for Insect Pests|400|http://colloque.inra.fr/isyip}}

1st International Workshop
16-17th November 2009
INRIA Rennes-Bretagne-Atlantique

Given the development of cheaper high throughput sequencing technologies, it is easy to predict that in the very near future, new genomes of insects relevant to agriculture will be available. This opens several other challenges such as the bioinformatics treatment of the raw data (handling of billions of sequences, assembly of short reads…) and the development of databases opened to biologists for an easy, friendly and efficient extraction of information. With access to several insect species genomes, one will not only work on their favourite insect, but will take advantage of the increasing knowledge from genomic comparison analyses. This compels the community to develop standards for different tasks towards the exploitation of genome sequences: annotation, cross-species comparisons, interoperability between databases, ... Several tools and databases already exist and are used for genome browsing and annotation.

In that context, the purpose of this workshop will be:

  • To exchange within an international panel of attendants our views on the present and future of insect genome databases
  • To settle an international community that will form a functional network for insect genome and database development
  • To discuss strategies to meet the demand of increasing number of new insect genomes
  • To prepare a new road map for integration of genomes databases for insects relevant to agriculture

The perimeter of that discussion encompasses insect species related to agriculture, either harmful (pests) or beneficial as controllers of pest populations or as producers of plant by-products (such as silk, honey, ...).

Registration for the meeting is free and has to be done online on this website and will be limited to 40 participants. A statement of interest is needed. A 10 minute presentation may be asked.

2009/07/20

August 2009 GMOD Meeting

August 2009 GMOD Meeting


Register for the August 2009 GMOD Meeting


The next GMOD meeting will be held 6-7 August, at the University of Oxford, in Oxford, United Kingdom. Registration is now open. Space is available on a first come, first served basis and there is room for 55 attendees. The meeting cost is £50.

As with previous GMOD meetings, the meeting will have a mixture of project talks, component talks, and user talks. The agenda is driven by attendee suggestions, and you are encouraged to add your suggestions now. For examples of what happens at a GMOD meeting, see the writeups of the January 2009, July 2008, or any other previous meeting. GMOD meetings are an excellent way to meet GMOD developers and users and to learn (and affect) what's coming in the project.

Details on transportation, suggested lodging, and other logistics are on the August 2009 GMOD Meeting page.

Please join us in Oxford this August,

Dave Clements
GMOD Help Desk

2009/07/01

Note: Unless you have applied to and been admitted to the 2009 GMOD Summer School - Europe, don't you dare register for it. The registration web site will let you do this, but bureaucratic hellishness will ensue.

Join ISB

International Society for Biocuration

The International Society for Biocuration (ISB) is now accepting member registrations. I strongly encourage GMOD community members to think about joining ISB. GMOD and ISB have many shared and complementary interests.

Membership rates start at less than US$20 for students to a little over US$100 for principal investigators from industry.

Please consider this investment,

Dave Clements
GMOD Help Desk

2009/06/25

Apollo 1.11.0 Released

A new version of Apollo has been released. Highlights for this release include:

  • The "Sequence Aligner" ("Exon Detail Editor" with alignment viewing) is now public
  • Brought back the "Types panel" which works in conjunction with the the "Preferences editor"
  • Various bug fixes

As always, you can download the current version at:

http://apollo.berkeleybop.org/current/install.html

Ed Lee

2009/06/05

NextGen Sequence in GBrowse

Next Generation Genome Analysis in Non-Model Organisms--An American Genetic Association Special Event

There will be a talk on visualizing next generation sequence data in GBrowse at Next Generation Genome Analysis in Non-Model Organisms, an 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 GMOD outreach. If you can't make it to this meeting, there will also be GMOD workshops at SMBE and the Arthropod Genomics Symposium.

Dave Clements
GMOD Help Desk

2009/05/19

WebGBrowse Has Arrived

WebGBrowse - A Web Server for GBrowse Configuration Made Easy
WebGBrowse at the Center for Genomics and Bioinformatics 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 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 (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 tutorial and FAQ, and was just published in Bioinformatics. WebGBrowse is open source and can also be installed locally.

WebGBrowse was created by Ram Podicheti, Rajesh Gollapudi, and Qunfeng Dong, all of the The Center for Genomics and Bioinformatics (CGB) at Indiana University - Bloomington. WebGBrowse was first presented by Ram Podicheti at the 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 contact the CGB if you have any questions.

Dave Clements
GMOD Help Desk

2009/04/22

GMOD Workshops at SMBE, AGS

There will be GMOD workshops at two major conferences in June 2009:

SMBE 2009|120|http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27}}
Annual Meeting of the Society for Molecular Biology and Evolution (SMBE 2009)
June 3-7, 2009
Iowa City, Iowa
Database Tools for Evolutionary Genomics: An introduction to GMOD software for managing, annotating and visualizing genomic data

Saturday, June 6, 2:30-5:00pm
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 (Ben Faga, Sheldon McKay, Mark Yandell, and 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.

Arthropod Genomics Symposium|100|http://www.k-state.edu/agc/symp2009/seminar.html}}
3rd Annual Arthropod Genomics Symposium
June 11 - 14, 2009
Kansas City, Missouri
Chado Databases and Integration with GMOD Tools

Pre-Symposium Workshop - Thursday, June 11, 4:30-6:30 p.m.
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 Dave (SMBE) or Scott (AGS) know if you have any questions about the workshops.

Thanks,

Dave Clements
GMOD Help Desk

2009/04/09

Pathway Tools Workshop, August

Registration is now open for this workshop. 2009/04/24


Pathway Tools Workshop

There will be a Pathway Tools Workshop, August 19-28, 2009 at 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 ptools-info@ai.sri.com.

Please check the following website for updates.

2009/04/07, updated 2009/04/24

2009 GMOD Summer Schools

Template:2009SummerSchoolApplicationBlurb

We are now accepting applications for the 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:

{{#icon: 2009SummerSchoolAmericas170.png|Americas 2009 GMOD Summer School - Americas}} Americas
16-19 July
NESCent
Durham NC

The courses include sessions on these popular GMOD components:

{{#icon: GMOD2009Europe170.png|Europe 2009 GMOD Summer School - Europe}} Europe
3-6 August
Oxford University
Oxford UK

The 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 GMOD meeting will be held outside of North America.

Thanks,

Dave Clements
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 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

Ed Lee

2009/03/02

Biocuration Conference, April

3rd International Biocuration Conference

The 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 registration ends in two days (on 20 February, 2009).

Dave Clements
GMOD Help Desk

2009/02/18

Biomedical Ontology Conference

The 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. Paper submissions are due March 1, and posters are due April 10. ICBO will be held in conjunction with four days of tutorials and classes from July 20-23, 2009.

See the ICBO conference web site for details.

Dave Clements
GMOD Help Desk

2009/02/17

January 2009 Meeting Report

January 2009 GMOD Meeting

The January 2009 GMOD Meeting was held January 15-16, 2009 in San Diego, immediately following the 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 19 presentations by GMOD users and developers.

Some highlights:

Plus 14 other excellent user and developer presentations.

Please take a look at the 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).

Dave Clements
GMOD Help Desk

2009/02/09

GBrowse User Tutorial

OpenHelix

A comprehensive GBrowse User Tutorial was released by 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 PowerPoint slides, handouts, and exercises that can be used for reference or for training others. The narration is reproduced in the notes area on the slides.

The GBrowse User Tutorial is part of a set of model organism resource tutorials funded in a large part by NHGRI. The set includes tutorials on how to navigate and use RGD, MGI, and WormBase, and in the future for ZFIN, FlyBase, and SGD (all of which are GMOD users and/or contributors).

This tutorial focuses on using GBrowse and complements the GBrowse2 Admin Tutorial. It is an excellent resource for any organization that wants to help its users use GBrowse better.

Dave Clements

GMOD Help Desk

2009/02/05

Opening at Dow AgroSciences

Dow AgroSciences

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:

  1. Install the open source software components for the Chado database, data loaders, and genome browser.
  2. Deploy the GBrowse genome browser in a centralized location in our intranet, which can be used by Dow AgroSciences scientists across functions.
  3. Test the system by performing preprocess (e.g annotate, perform alignments) and upload whole-genome data from Arabidopsis.
  4. Link the genome browser to Dow AgroSciences major internal databases, such as Variety, markerDB, QTL locate, and microarray database.
  5. Provide integration tests to ensure the transparency of the data among the different systems.
  6. Present to other Dow AgroSciences scientists to raise awareness of capability.
  7. Complete written documentation of project development, implementation, and continued maintenance.

Interested candidates please send a resume to Mindi Dippold at 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 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 CHANGELOG file.

As always, installation instructions can be found within each package and in 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 Hymenoptera Genome Database project, which includes BeeBase (honey bee genome) and 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: 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 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_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

{{#icon: Paglogo.gif|GMOD @ PAG||PAG 2009}}

GMOD will once again have a strong presence at the Plant and Animal Genome Conference (PAG 2009). There will be 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 GMOD meeting, you are encouraged to do so.

2009/01/03

GMOD Meeting Registration Open

January in San Diego - think about that January 2009 GMOD Meeting}}
January 2009 GMOD Meeting

Registration is now open for the January 2009 GMOD Meeting. The meeting will be held January 15-16, 2009 in sunny San Diego, immediately following the 2009 Plant and Animal Genome Conference (PAG 2009).

Registration is free.

If you haven't attended a GMOD Meeting before then you are encouraged to find out why the 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 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 meeting page.

As always, please let the GMOD Help Desk know if you have any questions.

Thanks,

Dave Clements
GMOD Help Desk

2008/11/20

GMOD Community Survey Results

The 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 GMOD Gear:

Please let the GMOD Help Desk know if you have any questions about the survey.

Thanks,

Dave C
GMOD Help Desk

2008/11/20

January 2009 GMOD Meeting

{{#icon: SanDiegoConvention.gif|January in San Diego - think about that||}}

Note: Registration is now open for the January 2009 GMOD Meeting. 2008/11/20

The next GMOD community meeting will be held January 15-16, 2009 in sunny San Diego, immediately following the 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 previous meetings.

It's also worth noting that GMOD will again have a strong presence at the PAG 2009 meeting itself. If you are interested in attending 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 GMOD Community Survey and be entered to win GMOD gear!

Thanks,

Dave Clements
GMOD Help Desk

2008/10/23, updated 2008/11/20

2008 GMOD Community Survey

Thanks to everyone who participated in the 2008 GMOD Community Survey. Survey results are now available. The winners are Randall Svancara of Washington State University, Victor Jun M. Ulat of the International Rice Research Institute and Pinglei Zhou of 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 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 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 <help@gmod.org> if you have any questions.

Thank you,

The GMOD Team

2008/10/17, updated 2008/11/20

Get GMOD Gear!

{{#icon: GMODMug150x150.jpg|GMOD Mug||http://www.cafepress.com/GenericMOD/}}
{{#icon: TShirtThumb.jpg|GMOD T Shirt||http://www.cafepress.com/GenericMOD/}}


Tired of not having a cool T-shirt to wear at meetings?

Tired of drinking your coffee from a styrofoam cup?

Want to show off your affiliation with GMOD and promote it at the same time?

Be the first person in your lab, community, organization, building, campus or country to be seen with some GMOD gear!


Note: Want to win a shirt of mug for free? Then participate in the 2008 GMOD Community Survey. Three participants will be randomly selected to receive the GMOD item of their choice.

GMOD has a 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.


Dave Clements
GMOD Help Desk

2008/10/09

Updated 2008/10/17

InterMine Workshop

InterMine

An 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 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 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 tutorial well be held September 22-23, 2008 at Kings College London. This tutorial is kindly hosted by the Centre for Bioinformatics at King's College London (KCBI).

Day 1 is intended to teach users of Pathway Tools databases such as BioCyc, YeastCyc, MouseCyc, and 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 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 Lincoln Stein, the lead developer and Sheldon McKay who did much of the JavaScript work. The release can be obtained from SourceForge, or, you can use the 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 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"
  • 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 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,

Scott Cain

GMOD Project Coordinator

2008/08/22

Web Site Changes

The 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 Mediawiki 1.9.3 to 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 http://gmod.org/wiki/Page_Name

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 GMOD Help Desk.

Thanks,

Dave Clements
GMOD Help Desk

2008/08/11

Website Down: Aug 11 2008

{{#icon: WorkInProgressTools.gif|||}}  The 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.

Dave Clements
GMOD Help Desk

2008/08/08

Upcoming Pathway Tools Tutorial

SRI's Bioinformatics Research Group will hold a 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 Pathway Tools Tutorial page for a detailed schedule, registration information, and other details.

Peter Karp
2008/08/07


July 2008 GMOD Meeting Report

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 Chado, the Community Annotation System, and Table Editor (plus several more). We also heard reports from many GMOD users, including SGN, WikiMods, and Xenbase (plus several more).

Dave Clements
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 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:

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! Scott Cain

07/22/2008


Job Openings with GnpAnnot

GnpAnnot, an INRA project, is offering 2 positions for programmers to implement and/or improve GMOD interfaces for Chado databases.


1st Position: IRISA


IRISA

18 month position for a Java programmer

Environment:

The job opportunity will be located at 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 fabrice.legeai@rennes.inra.fr


2nd Position: INRA-URGI


URGI

One year object-oriented programmer (Java, Perl Object)

Environment:

The job opportunity will be located at 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:

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 stephanie.sidibe-bocs@cirad.fr, or just introduce yourself when you see her.

2008/07/17

GMOD @ ISMB and BOSC

ISMB 2008
BOSC 2008

GMOD has a strong presence at the ISMB 2008 and 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 flier we'll be distributing at the conference.

Dave Clements
GMOD Help Desk

2008/07/16

2008 Summer School Report

2008 GMOD Summer School

Or, what 29 people did with their summer vacation.

The first annual GMOD Summer Schoolsummer 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 (Scott, 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,

Dave Clements
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-live to import GFF).
  • Added a module to serve data to CMap3D, a 3D viewer being developed by Chris Duran and Dave Edwards.

If you have any questions, please let me know.

This is only an incremental update. For anyone who installed 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 upgrade/ directory included in the package.

Ben

2008/07/01

GMOD Meeting Registration

July 2008 GMOD Meeting

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 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 help@gmod.org. See the 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 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 Mark Yandell Lab at the 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

2008 GMOD Summer School

July 11-13, 2008
National Evolutionary Synthesis Center (NESCent)
Durham, North Carolina, USA

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 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 submit an application.

If you have already applied for the GMOD Summer School you should have received an e-mail from the Help Desk informing you of your admission status.

2008/04/24, last updated 2008/05/16

Apollo 1.8 Released

I'm excited to let everyone know that we're releasing a new version of Apollo (1.8.0) today. There are many additions/bug fixes with this release. Most notably, due to popular demand, an 'undo' system. You can now access the 'undo' function through 'Edit→Undo' (or ctrl-u). For more information on the changes, check out the 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

Sea Urchin Genome Database

Today, Tuesday April 4th, the 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 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 Beckman Institute at California Institute of Technology plans to enrich and extend the sea urchin sequence and annotations.

Visit us at SpBase.

Andy Cameron

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 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 proposes a plan for restructuring it. If you have any suggestions or comments on this then please send us your feedback.

Thanks,

Dave Clements
GMOD Help Desk

2008/04/04

iPlant Collaborative Job Openings

Cold Spring Harbor Laboratory is seeking experienced software developers/bioinformaticians to join the 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 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 ontology data (using go-perl).
  • A fairly new tool for updating ontologies contributed by the developers of 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 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, gmod-schema@lists.sourceforge.net.

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 CMap mailing list.

Ben

2008/03/28

July 2008 GMOD Meeting

{{#icon: July2008LogoSmaller.png|July 2008 GMOD Meeting||July 2008 GMOD Meeting}}

The next GMOD community meeting has been scheduled for July 16-17, 2008 at the University of Toronto, immediately before 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 help@gmod.org. See the notes from previous meetings for an idea of what is discussed at GMOD meetings.

Thanks,
Dave Clements
GMOD Help Desk

2008/03/25


SynBrowse Developers Needed

{{#icon: SynBrowse_logoNoText.png|SynBrowse||SynBrowse}}

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 xiaokangpan@gmail.com.

Thanks,

Dave Clements
GMOD Help Desk

2008/03/21

GMOD at ParameciumDB

{{#icon: ParameciumDBIcon133x42.png|ParameciumDB||ParameciumDB}}

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 Linda Sperling <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,

Dave Clements
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.

{{#icon: TShirtThumb.jpg|GMOD T Shirt|| http://www.cafepress.com/genericmod.238973590}}
Win this shirt!

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 SourceForge.

To view the T-shirt or get one for yourself visit 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,

Ben Faga,
faga.cshl@gmail.com

2008/03/11

GMOD Summer School

{{#icon: SummerSchoolSmall.png|Summer School||2008 GMOD Summer School}}

July 11-13, 2008
National Evolutionary Synthesis Center (NESCent)
Durham, North Carolina, USA

The first annual GMOD Summer School will be held July 11-13, 2008 at the 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 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 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:

  1. 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.)
  2. GMOD News - News items of interest to the GMOD community. This is also available as an RSS feed.
  3. Main Page - Items from the GMOD News page and recently edited pages (non-minor edits) now show up in the right sidebar.
  4. Calendar - Calendar of events of interest to the GMOD project.
  5. Glossary - Short definitions of non-biological terms used in GMOD.
  6. GMOD Mailing Lists - Shows more lists, and sorts them into Overview, Component, and Inactive lists. If your list isn't here, please add it.
  7. Site Guidelines - Guidelines for creating and editing content on the GMOD web site.
  8. GMOD Help Desk - Explains services offered by the help desk.
  9. Computing Requirements - Description of expertise and computing systems you'll need to set up a GMOD installation.
  10. 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 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
help@gmod.org

2008/02/13

Pathway Tools Workshop

2008/01/28

A session at the Cambridge Healthtech 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 member databases that use Pathway Tools in their databases:

Early registration is available until February 22, 2008

GMOD at Arthropod Genomics

2008/01/21

There will be two GMOD related workshops at the Arthropod Genomics Symposium, April 10-13, 2008, in Kansas City.

  • Community Contributions to Genome Annotation - Christine Elsik of BeeBase will discuss how to install and use the Apollo genome annotation tool.
  • Chado: A Database Schema for Integrating Biological Data - Scott Cain and 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., BeetleBase, BeeBase, FlyBase, wFleaBase, ...). If you are an arthropod researcher interested in using GMOD Components then this meeting will be time well spent.

Early registration and 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 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 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 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 GBrowse tutorial at the 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 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 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 Modware home page and give it a try. Email all feature requests, questions, and comments to 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 finished its reimplementation using Chado, the modular GMOD database schema which 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 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 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 'A Chado case study: an ontology-based modular schema for representing genome-associated biological information' by Chris Mungall, Dave Emmert, and The FlyBase Consortium, was presented at ISMB/ECCB 2007, and is now available in the journal 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 released. Version 0.6 includes support for a 1.5 DAS server, and improvements to MartView and MartBuilder. See 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 gbrowse_netinstall.pl, which will semi-automatically install GBrowse across the Internet on Windows, Mac OSX and Linux platforms.

The Really Old News Archive

Even earlier news items are available at SourceForge.

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