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News 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.

If you have a news item you want added here, please send it to the GMOD Help Desk or add it to this page directly.

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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.

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.


Ben Faga,


GMOD Summer School

SummerSchoolSmall.png 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.


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 (this page) - 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.


Dave Clements, GMOD Help Desk


Pathway Tools at Pathway Analysis


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


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


Version 1.7.0 of Apollo has just been released. You can access the updated Apollo page at

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.

GBrowse Tutorial at PAG XVI


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


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

November 2007 GMOD Meeting


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


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


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


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

Pathway Tools 11.5 Released


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


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


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


Version 1.68 of GBrowse is a stability release which improves the documentation and installation process. It includes a new script called, which will semi-automatically install GBrowse across the Internet on Windows, Mac OSX and Linux platforms.

News Archive

Earlier news items are available at SourceForge.

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