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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.

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News Items

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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.


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:

Ed Lee


GMOD Summer School Update

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

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 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:

but rather:

Please update your bookmarks accordingly.

Ed Lee


Sea Urchin Genome Database

SpBaseLogo.png 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


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.


Dave Clements
GMOD Help Desk


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.


GMOD 1.0 Released

I am very pleased to announce the release of GMOD 1.0. The file can be downloaded from SourceForge at:

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,

Scott Cain


CMap 1.0 Released

Version 1.0 of CMap has been released.

You can get the new version from SourceForge,

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.



GMOD Meeting July 16-17, Toronto

July2008LogoSmall.png 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 See the notes from previous meetings for an idea of what is discussed at GMOD meetings.

Dave Clements
GMOD Help Desk


SynBrowse Developers Needed

SynBrowse_logoNoText.png 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


Dave Clements
GMOD Help Desk


GMOD at ParameciumDB

ParameciumDBIcon133x42.png 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 <> 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.


Dave Clements
GMOD Help Desk


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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Adding a News Item

This page generates both an RSS feed and updates the GMOD News list on the home page. Therefore please follow these guidelines when adding a news item.

  1. Edit the News Items section of this page. This will allow you to see how big your news item title is, compared to existing news items.
  2. Add your news item immediately after the <startFeed /> tag.
  3. Title
    • Use a short title. Titles should be small enough to fit on a single line in the GMOD News list on the home page.
    • Place the title in a second level heading: == Your Title ==
  4. News Text
    • Make the news item succinct.
    • The first link in the news item should point to the page/URL you want the RSS feed to link to. For example, the first link in a news item about Chado could point to the Chado page.
    • End the news item with your name and the date in the format YYYY/MM/DD.
  5. Preview your changes
    • Check the table of contents. Is the title no longer than any previous title? Is the title at the same depth as the other news item titles?
    • Check the news item. Does the text look good, does it look like the other news items, and does the first link point to where you want it to?
    • Revise until you like it and then save it.

Once you have saved the page, a link to the new item will show up on the home page in about an hour.

Note: If you don't want to do this on your own, please send the item to the GMOD Help Desk and we will post it.