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== Positions @ JCVI ==
From the Galaxy mailing list:
<div class="indent">
We have a few open [https://careers.jcvi.org/careers/Careers.aspx?adata=Q%2fhMgU9ioOU2Q2IBMeDlPzojZaM309CBtHV%2b%2bLtKWW0PRb6H39%2fWK4hiwgS3QLR6dvwqIVTrFzs%3d Bioinformatics/Software Engineers positions] at the [http://www.jcvi.org/ J.Craig  Venter Institute], {{ImageRight|JCVILogo.jpg|Galaxy/Python and Bioinformatics Engineers positions at the J.Craig Venter Institute||https://careers.jcvi.org/careers/Careers.aspx?adata=Q%2fhMgU9ioOU2Q2IBMeDlPzojZaM309CBtHV%2b%2bLtKWW0PRb6H39%2fWK4hiwgS3QLR6dvwqIVTrFzs%3d}} one of which involves largely developing further the [[Galaxy]] platform for use in-house (writing additional Galaxy wrappers for internal pipelines / tools, integrating Galaxy with existing cluster systems, SGE etc.)
Besides working with Galaxy, these positions involve quite a broad range of software development opportunities (languages ranging from Perl to Java), while at the same time they offer great learning opportunities for working with next-generation sequencing datasets, and learning fundamental techniques related to bioinformatic analysis of these types of data.
Please pass the word, feel free to [mailto:kkrampis@jcvi.org email me] for additional information, or
even go to the [https://careers.jcvi.org/careers/Careers.aspx?adata=Q%2fhMgU9ioOU2Q2IBMeDlPzojZaM309CBtHV%2b%2bLtKWW0PRb6H39%2fWK4hiwgS3QLR6dvwqIVTrFzs%3d careers page] to apply.
many thanks !
Konstantinos (Ntino) Krampis, Ph.D.<br />
Bioinformatics Engineer<br />
[http://www/jcvi.org J.Craig Venter Institute]
== Comparative Genomics Workshop ==
== Comparative Genomics Workshop ==

Revision as of 18:26, 18 November 2010

News that is relevant to the GMOD user and developer communities. News items more than 6 months old are listed in the GMOD News Archives. If you have a news item you want added here, please see Adding a News Item below. Also see the GMOD Calendar and Events List.

This GMOD News is also available as an RSS feed. {{#icon: RSSIcon16x16.gif|RSS feed||http://gmod.org/w/index.php?title=GMOD_News&action=feed&feed=rss}}

News Items

Want to add your news item here? See Adding a News Item below.

<startFeed />

Positions @ JCVI

From the Galaxy mailing list:

We have a few open Bioinformatics/Software Engineers positions at the J.Craig Venter Institute,

Galaxy/Python and Bioinformatics Engineers positions at the J.Craig Venter Institute
one of which involves largely developing further the Galaxy platform for use in-house (writing additional Galaxy wrappers for internal pipelines / tools, integrating Galaxy with existing cluster systems, SGE etc.)

Besides working with Galaxy, these positions involve quite a broad range of software development opportunities (languages ranging from Perl to Java), while at the same time they offer great learning opportunities for working with next-generation sequencing datasets, and learning fundamental techniques related to bioinformatic analysis of these types of data.

Please pass the word, feel free to email me for additional information, or even go to the careers page to apply.

many thanks !

Konstantinos (Ntino) Krampis, Ph.D.
Bioinformatics Engineer
J.Craig Venter Institute


Comparative Genomics Workshop

Workshop on Comparative Genomics

The Workshop on Comparative Genomics is being held in Český Krumlov, Czech Republic, 9-21 January 2011. The workshop consists of a series of lectures, demonstrations and computer laboratories that cover various aspects of comparative genomics. Faculty include Anton Nekrutenko leading a session on Galaxy and Sheldon McKay leading a session on GBrowse_syn.

The course is designed for established investigators, postdoctoral scholars, and advanced graduate students. Scientists with strong interests in the uses of short-read sequence data, analytical methods, comparative structure of genomes, SNP detection and analysis, CNV, genome visualization tools and related areas are encouraged to apply for admission. Lectures and computer laboratories total ~90 hours of scheduled instruction. No programming experience is required.

The official application deadline has passed, but there are still a few openings for qualified candidates. There are also some openings in the Workshop on Molecular Evolution, being held immediately after.


Modware Status Update

Modwware Middleware

Good news and update on the current status of Modware development. Modware is getting back on track and is currently being actively developed at dictyBase since last few months. It is being written using Moose and DBIx::Class (more precisely Schema or BCS) ORM. This part of development is done in sync with dictyBase's major data migration project which includes literature and gene ontology annotations. So, the first release of this new version is expected to deal with publication and ontology datasets in Chado. Handling of feature module will be added after the first release gets settled down. Like any other standard Perl module Modware's public release will be available from CPAN and the bleeding edge can be grabbed from github.

Relevant documentations and guidelines will also be added to the GMOD wiki. The first CPAN release is expected to be early next year.


Siddhartha Basu
Modware developer, dictyBase


Opening @ Cancer Research UK

Bioinformatician and Pancreatic Expression Database

There is an opening for a bioinformatician at the Centre Barts Cancer Research UK for Molecular Oncology and Imaging working on the Pancreas Expression Database:

... contribute to the development of the pancreatic cancer bioinformatics platform and tools. Working mainly with BioMart, the successful candidate will be expected to address bioinformatics needs related to the update, maintenance and expansion of the pancreatic expression database (www.pancreasexpression.org) to set up the Bioinformatics Infrastructure. The successful candidate will additionally be responsible for pancreatic cancer literature data curation, release cycles as well as the wider development and extension of the analytical side of this platform.

See the full announcement for details. A related position in the same group is also open. Applications close 12 November.

Dave Clements
GMOD Help Desk


Pathway Tools 2010: Virtual, Now

Attend the Pathway Tools Workshop Remotely

We are offering individuals the ability to attend presentations at the Pathway Tools Workshop remotely. We will be broadcasting the presentation slides via WebEx, and you can hear the voice of the presenter by calling in to a conference call. Please see the workshop teleconference page for information on how to connect via WebEx and how to call into the conference call. See the Workshop agenda, for complete talk titles and times.

Feel free to forward this announcement to interested colleagues.

If you experience any difficulties with connecting, please contact PTools Support <ptools-support@ai.sri.com>

Best regards,

Tomer Altman
Pathway Tools Workshop Coordinator


November 2010 Calendar

GMOD Calendar

November has a number of deadlines and meetings:

  • PAG 2011 abstract deadline for posters and demos - November 1
  • SWAT4LS: Semantic Web Applications for Life Sciences posters and demos
  • Rocky '10 early registration
Conferences, Meetings, and Courses


If you know of any upcoming events that are not on the calendar, please send them to me.


Dave Clements
GMOD Help Desk


Pathway Tools 2010 Deadline!

Pathway Tools Workshop 2010

Registration for the Pathway Tools Workshop 2010 closes in two days, on Thursday, October 21. The workshop is being held next week in Menlo Park, CA. This workshop is oriented around SRI's Pathway Tools software and BioCyc Database Collection and will explore pathway bioinformatics and Pathway/Genome Databases.

It will combine presentations by groups outside SRI, tutorials by SRI staff, and a hackathon. See the workshop website for more information and registration link.

Dave Clements
GMOD Help Desk


InterMine 0.94.1 Release

InterMine 0.94.1 release

InterMine 0.94.1 is now released, and available as a subversion branch and zip file.

0.94.1 contains fixes for bugs discovered by users when upgrading to 0.94 and a number of minor enhancements.

InterMine 0.94 is a major release with many new features, including:

  • a new full text search over the entire database
  • template queries with optional constraints
  • selection of multiple values in template query constraints
  • layout improvements to the template query form
  • drag/drop selection of constraint order when creating templates
  • better automatic data model generation from the Sequence Ontology
  • sequences stored as CLOBs in the database
  • major data loading and query/export performance improvements
  • export of query results direct to Galaxy

See the full release notes for 0.94 and 0.94.1, and the upgrade instructions if you are migrating from an earlier release.

As always, let us know if you have any problems or questions.


The InterMine developers


GMOD Europe 2010 Report

{{#icon: Sept2010MtgLogo300.png|September 2010 GMOD Meeting|150|September 2010 GMOD Meeting}}

{{#icon: InterMineLogo.png|InterMine Workshop|150|http://gmod.org/wiki/InterMine_Workshop_-_GMOD_Europe_2010}}
{{#icon:Biomart250.png|BioMart Workshop|170|http://gmod.org/wiki/BioMart_Workshop_-_GMOD_Europe_2010}}
{{#icon: GMOD2010Europe300.png|GMOD Europe 2010|160|GMOD Europe 2010}}

GMOD Europe 2010 was held 13-16 September, 2010 in Cambridge, UK. More than 60 people attended one or more of the events during the week. The September 2010 GMOD Meeting kicked off GMOD Europe 2010. Summaries of all 19 talks are now available on the September 2010 GMOD Meeting page. Talks were given by GMOD users, developers and staff, including:

Plus many other excellent presentations on topics ranging from Cosmic GBrowse to GMOD Sustainability and Organization.

Two Satellite Meetings followed the GMOD meeting. These were lively discussions with ~10 participants on two topics of interest to the GMOD community:

There is also a writeup of the satellites by Mary Mangan on the OpenHelix blog.

The week finished with a BioMart Workshop, which was full, and a InterMine Workshop that was nearly sold out as well.

Finally, I'd like to thank the Cambridge Computational Biology Institute and the School of Biological Sciences Bioinformatics Training Facility for sponsoring and hosting the GMOD Europe 2010 events. I would also like to heap copious gratitude on Gos Micklem, Shelley Lawson, Dave Judge, Xose Fernandez, Syed Haider, and Richard Smith for their work on making this event happen.

Dave Clements
GMOD Help Desk


InterMine Workshop 15-16 Nov

InterMine Workshop

There will be an InterMine workshop in Cambridge, UK on November 15th-16th. You can register for both days or just attend either one.

Day One - InterMine Developers
Building an InterMine data warehouse and deploying the web application. This will use the new MineManager GUI to set up an example InterMine, load data and write a new parser to add custom data, deploy and configure the webapp including the new full text search.
Day Two (morning only) - InterMine Users
Advanced querying. A brief tour of creating custom queries, creating your own templates and using the web service API to build and run queries from Perl or Java code.

InterMine is an open source system for building biological data warehouses with a powerful web interface and query API. See FlyMine or modMine for examples. InterMine can integrate data from many common biological formats and is easy to extend to include your own data. Parsers are included to load data from Chado, Ensembl, UniProt, KEGG, PubMed, TreeFam, GFF3, FASTA, BioPax and many others.

The web application works out of the box for querying any data is easily customisable. It provides a custom query builder, template queries for creating simple 'canned queries', upload and operations on lists, graphical and statistical widgets for analysing lists of data and MyMine accounts for saving user data.

Richard Smith


Community Annotation Satellite

Community Annotation Satellite Meeting Report

The report from the GMOD Europe 2010 Community Annotation Satellite Meeting is now available. Nine participants from a range of research communities gathered for several hours to discuss their experiences with and thoughts on community annotation. The report covers what has worked and what hasn't, as well as some analysis of why. It also discusses possible models for doing successful community annotation in the future. If you are interested in engaging your community to help you do annotation then I recommend reviewing this.

Many, many thanks to all who participated in this discussion and helped compile the report.

Dave Clements
GMOD Help Desk


October 2010 Calendar

GMOD Calendar

October is calmer than September, but is still relatively full:

  • SWAT4LS: Semantic Web Applications for Life Sciences abstracts
  • Rocky '10 Bionformatics Conference abstracts
  • Plant and Animal Genome (PAG) early registration
  • EMBO Global Exchange Lecture Course on Bioinformatics and Comparative Genome Analysis registration
Conferences, Meetings, and Courses
  • Biocuration 2010
  • Pathway Tools Workshop
  • Programming for Biology course
  • Next Generation Sequencing Workshop
  • RECOMB Comparative Genomics Satellite
  • Automated Functional Annotation and Data Mining course
  • VisWeek 2010


If you know of any upcoming events that are not on the calendar, please send them to me.


Dave Clements
GMOD Help Desk


InterMine Java / DB Developer

InterMine Java Developer

We are looking for a software developer to work with Java and PostgreSQL as part of the Wellcome Trust funded InterMine project here in the Department of Genetics. InterMine is an open source software system for building data warehouses of biological data. It can integrate data from many different formats into a central database and makes the data available to query via a flexible web application and web services. InterMine is used at several high profile genomics databases around the world including databases that we build and maintain in Cambridge. See InterMine.org for more information. Core InterMine development is carried out by a team of developers at Cambridge University. We need a developer to work on all aspects of the server side InterMine code, in particular taking responsibility for the database access and performance of the system.

See the position announcement for full details. The closing date for applications is 24 September 2010.

Richard Smith


BioMart Openings @ OICR

4 openings at OICR


The Ontario Institute for Cancer Research (OICR) has four BioMart or BioMart-related openings:

The BioMart biological data warehouse system is developed at OICR. Please see the job postings for additional details.

Dave Clements
GMOD Help Desk


JBrowse 1.1 Released

JBrowse 1.1 Released

JBrowse version 1.1 is released! You can find the code here.

What's new:

  • Scalability: JBrowse can now handle very large data tracks, including human EST/SNP tracks, or tracks of next-gen sequence reads. Large datasets are broken into smaller chunks, so there is no loading delay for big tracks.
  • Extensibility: A Perl module (ImageTrackRenderer.pm) for creating user-drawn image tracks is now available, based on the CPAN GD.pm module. An example program is provided, draw-basepair-track.pl, that uses this module to draw arcs over a sequence representing the base-pairing interactions of RNA secondary structure.
  • Bug fixes: Numerous display glitches have been fixed, including issues with wide-screen monitors and long mostly-offscreen features.

Note: The JSON format used by 1.1 is not backward compatible with previous releases. If you are upgrading from an older version of JBrowse, you will have to regenerate all the JSON files on your server.

See the release notes for full details.

Mitch Skinner


The TopoView Glyph Needs You!

TopoView from FlyBase

TopoView is a GBrowse glyph created by Victor Strelets at FlyBase to show large amounts of quantitative data in limited screen space. TopoView does this with a 3D plot, showing each new set of data just below and offset from the previous data set. It was developed to display RNA-Seq data.

Josh Goodman presented TopoView at the January 2010 GMOD Meeting, and also discussed it with many attendees at ISMB 2010 (and I'm sure will be willing to discuss it at GMOD Europe 2010 next week). There is a lot of interest in TopoView becoming a standard GBrowse glyph. However, as Victor explains in this posting, TopoView is not yet ready for general release It needs some more work before it is ready for production.

If you are interested in helping get this glyph production ready and in the released glyph set, then please contact Victor. He is looking for folks to help get this out there.


Dave Clements
GMOD Help Desk


InterMine/BioMart Job @ FlyBase

{{#icon: Fly_logo.png|Open position at FlyBase|220|http://www.bioinformatics.org/forums/forum.php?forum_id=8313}}
{{#icon: InterMineLogo.png|InterMine|100|InterMine}} {{#icon:Biomart250.png|BioMart|100|BioMart}}

FlyBase is looking for a qualified software engineer to undertake a project to deploy the InterMine and BioMart data management systems. The developer will be responsible for the web and database aspects of these technologies, which will be hosted at the Indiana University FlyBase site in Bloomington, IN. 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. See the position announcement for details.


GMOD Europe 2010 Update

GMOD Europe 2010

GMOD Europe 2010 starts in less than two weeks. If you are planning on attending and haven't yet registered, then please do so in the next few days. The BioMart Workshop has only a few slots left, and the registration fee for the GMOD Meeting goes from £50 to £65 on 6 September. We are encouraging people to submit topic suggestions for the GMOD Meeting and the GMOD Satellite Meetings.

We are also pleased to announce that Jason Swedlow of the University of Dundee will be the guest speaker at the GMOD Meeting. Jason will speak on The Open Microscopy Environment: Open Informatics for Biological Imaging, a particularly timely topic as many researchers move into image intensive areas such as phenotypes and gene expression, and as high-throughput imaging platforms become available.

There is still space available at all 4 events, and registration for the GMOD Satellite Meetings, InterMine Workshop and BioMart Workshop are free.

Scott Cain and Dave Clements


Biocuration 2010

Biocuration 2010

I would like to encourage the GMOD community to consider attending Biocuration 2010, being held October 11-14 in Tokyo, Japan. Biocuration is one of the most directly relevant conferences to research communtities working with biological databases. It is sponsored by the International Society for Biocuration (an organization which I strongly encourage GMOD members to join).

Biocuration 2010 "aims to invite all biocurators and their colleagues, providing them with a platform where all the participants including speakers and chairpersons can have intimate discussion and exchange of information under superb environments."

The ISB would particularly like to encourage students and new curators (with less than 5 years of experience) to attend. The ISB is sponsoring the registration fees for 5 students and 5 curators. To apply, please send a request to the ISB before September 6, including the abstract of your presentation. Note that you must be an ISB member to apply for sponsorship. If you are not already a member, you can sign up here. Early bird registration also closes September 6.

The abstract submission deadline has been extended to August 31.

Dave Clements
GMOD Help Desk

2010/08/24, updated 2010/08/25



ISGA, Integrative Services for Genomic Analysis, is now a part of GMOD. ISGA is a biologist-friendly web interface for running and customizing Ergatis bioinformaitics pipelines with integrated tools for visualizing and searching results. ISGA was originally built for prokaryotic genome annotation and we have added a prokaryotic assembly pipeline, and transcriptome annotation and functional genomics pipelines are under development.

A public instance of ISGA is available at http://isga.cgb.indiana.edu. ISGA is also available for download and has a mailing list and development blog. You can read the ISGA manuscript in Bioinformatics

ISGA is currently under active development at the Center for Genomics and Bioinformatics at Indiana University, and developers or other community members interested in contributing should join the mailing list.

Chris Hemmerich


September 2010 Calendar

GMOD Calendar

There's a lot going on in the next 5 weeks that is of interest to the GMOD community. September will be one of our busier months. Upcoming events include:

GMOD Europe 2010
Lots of relevant conferences
  • IWGD, HIBB, Personal Genomes, BioCreative, AMATA, Genome Informatics, BioImage Informatics, Data Sharing International, PRIB, InCoB, ECCB, and Computational Biology
  • Bioinformatics Short Course, Ensembl Developers Workshop


If you aren't going to something in September, then you aren't trying!


Dave Clements
GMOD Help Desk


Opening @ Phytozome (JGI)

Opening at Phytozome

Phytozome has an opening for a web developer. Phytozome is the public portal to JGI's extensive plant genome data and analysis. The developer in this position will be responsible for creating web interfaces using PHP, CSS, and advanced Javascript. Both the absolute quantity and diversity of plant genomic data produced and integrated by the JGI will be increasing dramatically over the next few years. This is an opportunity to apply your web design and coding skills to an area of biological research undergoing explosive growth and change, working with the JGI's scientists, computational biologists, and developers in a state-of-the-art computational environment.

Phytozome currently incorporates GBrowse and Biomart, as well as Jalview, Lucene, and MView, and will be integrating Galaxy and Chado over the next 12 months.

Please see the job posting for more information on this position.


Chado 1.11 Release

I am pleased to announce the 1.11 release of Chado, the GMOD schema and related tools. The file can be downloaded from SourceForge

In this release, the schema itself has not changed since the 1.1 release in May of this year, but there have been bug fixes (see release notes; thanks to Naama Menda for those fixes) and one added functionality to the materialized view tool. This functionality was required to support full text searching that will be included in the up coming release of the Chado GBrowse adaptor, Bio::DB::Das::Chado.

Also note that the name of the release has changed: previously, releases of the Chado schema were called "gmod" (gmod-0.003, gmod-1.0, and gmod-1.1), but that led to a couple of different kinds of confusion, so with this release going forward, the releases will be called "chado-*".

Since the schema didn't change, if you already have a 1.1 schema and want the bug fixes and added functionality, all you need to do for installation is to go up to the install step and stop there, i.e.:

perl Makefile.PL
sudo make install

Happy GMODing and please direct questions about this release to the schema mailing list,

Scott Cain


GMOD Europe 2010

{{#icon: GMOD2010Europe300.png|GMOD Europe 2010|160|GMOD Europe 2010}}

{{#icon: InterMineLogo.png|InterMine Workshop|150|http://gmod.org/wiki/InterMine_Workshop_-_GMOD_Europe_2010}}
{{#icon:Biomart250.png|BioMart Workshop|170|http://gmod.org/wiki/BioMart_Workshop_-_GMOD_Europe_2010}}
{{#icon: Sept2010MtgLogo300.png|September 2010 GMOD Meeting|150|September 2010 GMOD Meeting}}

We are pleased to announce GMOD Europe 2010, four days of GMOD events being held 13-16 September 2010, at the University of Cambridge. GMOD Europe 2010 includes:

Event Date Description
September 2010 GMOD Meeting Mon-Tues
13-14 Sept
A two day community meeting featuring project updates, developer and user presentations and best practices, and project planning. See the January 2010 GMOD Meeting for an idea of what goes on at GMOD meetings.
Satellite Meetings Wednesday
15 Sept
Special interest groups where GMOD community members meet to discuss specific topics of interest. If you have topics you want covered please add them.
InterMine Workshop A one day workshop on installing, configuring and using the InterMine biological data warehouse system.
BioMart Workshop Thursday
16 Sept
A one day workshop on using the BioMart biological data warehouse system, including accessing data through APIs.

Registration is now open for these events. There is a £50 registration fee for the GMOD Meeting to cover catered lunches, coffee/tee breaks, and other expenses. Registration for all other events is free. Please register soon, as space is limited.

See you in Cambridge!

Scott Cain and Dave Clements

PS: If you have topics you want to have covered (or you want to cover) at the GMOD Meeting, or at the Satellite Meetings, please add them to the meeting page, or to the Satellite Meetings list, or contact us. We are also looking for guest speaker nominations for the meeting.


GMOD Evo Hackathon Open Call

GMOD Evo Hackathon Open Call for Participation

We are seeking participants for the GMOD Tools for Evolutionary Biology Hackathon, being held November 8-12, 2010 at the US National Evolutionary Synthesis Center (NESCent) in Durham, NC.

This hackathon targets three critical gaps in the capabilities of the GMOD toolbox that currently limit its utility for evolutionary research:

  1. Visualization of comparative genomics data
  2. Visualization of phylogenetic data and trees
  3. Support for population diversity and phenotype data

If you are interested in these areas and have relevant expertise, you are strongly encouraged to apply. Relevant areas of expertise include more than just software development: if you are a GMOD power user, visualization guru, domain expert (comparative, phylogenetics, population, ...), or documentation wizard, then your skills are needed!

See the GMOD Evo Hackathon Open Call for details, and for a link to the application form. Applications are due August 25.

The GMOD Evo Hackathon Organizing Committee:

Nicole Washington, Robert Buels, Scott Cain, Dave Clements, Hilmar Lapp, and Sheldon McKay


GMOD Nomination: ISGA


I would like to nominate ISGA for GMOD Membership. ISGA is a bioinformatics pipeline service based on the Ergatis workflow system. ISGA comes with prokaryotic annotation and assembly pipelines and offers an intuitive interface for biologists to run and customize pipelines. ISGA also integrates tools such as GBrowse and BLAST for visualizing and analyzing pipeline results. Since ISGA utilizes Ergatis, ISGA pipelines can be submitted back to the Ergatis community and Ergatis pipelines can be adapted to use ISGA.

ISGA (pronounced "I-S-G-A") was created at Indiana University's Center for Genomics and Bioinformatics (CGB) by Chris Hemmerich, Aaron Buechlein, Ram Podicheti, Kashi Revanna, and Qunfeng Dong. CGB also hosts a public installation of ISGA.

I believe that ISGA meets all of GMOD's membership requirements. The CGB is willing to support ISGA for at least 2 years. ISGA could be useful to anyone working with complex pipelines and is directly applicable to existing and potential Ergatis users. Please see the ISGA page for more information.

If you have any feedback or comments on ISGA becoming a part of GMOD, please send send it to the help desk by August 6.


Dave Clements
GMOD Help Desk


August 2010 Calendar


There's not a lot going on in August but what is going on is significant. First there are submission deadlines for the International Digital Curation Conference (IDCC), and Data Integration in the Life Sciences (DILS 2010). Several noteworthy conferences are also happening:

  • ACM International Conference on Bioinformatics and Computational Biology
  • YAPC::Europe 2010
  • DILS 2010
  • International Workshop on Genomics Databases (IWGD)
  • High Performance Bioinformatics and Biomedicine (HiBB)

And, sometime in the next month GMOD will


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


Dave Clements
GMOD Help Desk


GMOD: Spread the Word!

Help spread the word about GMOD

Do you use GMOD tools in your research? If so, then you can help others and GMOD by getting the word out about GMOD and its tools.

There are many ways to do this: cite GMOD in publications, put a Powered by GMOD icon on your web pages, invite a GMOD speaker to your institution or event, include information on GMOD in your presentations. See the GMOD Promotion page for these and other ideas.

Increasing GMOD's visibility has many benefits:

  • It introduces biologists to tools that can help them learn from and exploit their data.
  • Increased visibility will lead to increased adoption of GMOD tools.
  • Increased adoption leads to more people contributing back to the project.
  • Increased adoption and development helps GMOD and GMOD components get grant funding.

Finally, GMOD can also help raise the profile of your GMOD-related talk or event by advertising it on GMOD resources.

Please let me know if you have any questions or requests, and please help get the word out.


Dave Clements
GMOD Help Desk


ISMB 2010 Talks & Posters

GMOD @ ISMB 2010

You can now view most of the GMOD-related presentations and posters from ISMB 2010. This includes

Plus additional talks and posters on GBrowse, DIYA, Pathway Tools, and Galaxy.

Dave Clements
GMOD Help Desk


Hiring @ Dolan DNALC

Opening @ Dolan DNA Learning Center, job ID 934

There's an opening (Job ID 934) at the Dolan DNA Learning Center (DNALC) of Cold Spring Harbor Laboratory for a programmer to develop cyberinfrastructure to support plant biology research. The programmer will work with a multi-disciplinary team to design, develop, and maintain applications for interfacing public APIs, SQL databases, and large data sets.

The successful candidate should come from a bioinformatics background that includes work with BioPerl, genome databases (such as Chado), browsers, and annotation tools. Expertise in Java, SQL and database schema, and Unix/Linux are essential. Experience developing web user interfaces – templating, Javascript/AJAX, DOM, and CSS – is also desirable.

For more information, go to the CSHL jobs site and search for Job ID 934.


GBrowse 2.13 Release

GBrowse 2.13 Released

GBrowse version 2.13 has been released. 2.13 is a maintenance update to 2.12. GBrowse 2.13 and 2.12 include these changes:

New features & enhancements
  • The DAS server and client are now functional. You will need Bio::Das version 1.17 and Bio::Graphics version 2.11 for best results.
  • The "import track" function now allows you to specify the URL of either a BAM or a BigWig file. The track will be displayed without physically copying the file onto the GBrowse server. You will need Bio::DB::Sam and Bio::DB::BigWig for these features to work.
  • Uploading a Wig file now generates a BigWig database for improved performance and scalability. This requires Bio::DB::BigWig to be installed.
  • There is now a Get chromosome sizes entry in the File menu.
  • Calling GBrowse with the CGI argument action=scan will generate a quick summary of track contents.
  • Improved performance when working with truly huge (>1000 track definition) configuration files.
  • Fasta, GFF3, SAM and wiggle dumps now include the genome build ID if that information is provided in the data source "metadata" configuration variable.
Bug fixes
  • When MySQL is used as the back end for user uploads, it will no longer fail on long filenames.
  • Fixed the "eurl" CGI parameter for importing data sets by their URLs.
  • Fasta and GFF3 dumps are now working when invoked from the File menu.
  • Fixed SAM file processing so as not to die when presented with a SAM @SQ header. This requires Bio::DB::Sam 1.20 to work properly.
  • Fixed upload listing table so as not to duplicate track labels.
  • Fixed track importation via the eurl parameter so that it works when the user's uploadid is empty (due to clearing cache of cookies).
  • Fixed DAS server handling of the link option.

Please use the GMOD bug tracking system to report bugs or feature requests.

Lincoln Stein


Pathway Tools Workshop 2010

Pathway Tools Workshop 2010

Registration is now open for the Pathway Tools Workshop 2010, held October 25th - 29th, 2010 in Menlo Park, CA. Early registration ends September 1.

This workshop is oriented around SRI's Pathway Tools software and BioCyc Database Collection and will explore pathway bioinformatics and Pathway/Genome Databases.

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:

  • Advances in pathway bioinformatics, model organism databases, genome annotation, and systems biology
  • Scientific results achieved with Pathway Tools and BioCyc
  • Share expertise on how to develop new organism-specific databases with Pathway Tools
  • 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

Please visit our registration website for details on speakers, fees, travel, and hotels.

Looking forward to seeing you at an upcoming Pathway Tools event.

Best regards,

Tomer Altman


Galaxy Community Tool Sharing

Galaxy Community Tool Sharing

We have introduced a new Galaxy tool sharing community site. The site currently allows you to upload an archive consisting of a single tool, but will soon allow you to upload an archive consisting of a suite of tools. To learn how to use the community site, click on Help → How to upload, download, and install tools.

We hope that you will find this site useful for hosting tools that you would like to contribute and share.

We'll keep you informed as the site's features evolve.

Greg Von Kuster


Logo Program Logos!

{{#icon: ApolloLogo.png|Apollo logo by Audra Radke|150|Spring 2010 Logo Program}}
{{#icon: RedFlyLogo.png|REDFly logo by Alex Read|65|Spring 2010 Logo Program}}   {{#icon: CMapLogo.png|CMap logo by Kathy Bracken|40|Spring 2010 Logo Program}}
Some of the new logos

The Spring 2010 Logo Program was a smashing success and 9 projects now have eye-catching logos that give each resource a strong graphic brand identify. See the Spring 2010 page for a complete list of logos, as well as some of the alternatives that were not chosen.

I would like to thank

The GMOD Logo Program might return in the future. Please watch the GMOD News for details, probably later this year. In the mean time, if you would be interested in participating in the next one, please let me know. The more people I hear from, the more likely it is to happen.


Dave Clements
GMOD Help Desk


GMOD @ ISMB 2010

GMOD @ ISMB 2010

ISMB runs July 9-13 this year and GMOD has a strong presence on the program:

See the GMOD @ ISMB 2010 page for a full listing of GMOD related content, including a session listing you can print in advance. See the ISMB 2010 web site for more on the conference.

Dave Clements
GMOD Help Desk


GMOD Meeting: Sept. 13-14

September 2010 GMOD Meeting

Thanks to the prep work by Gos Micklem at Cambridge, I am pleased to announce that there will be a two day GMOD community meeting starting on Monday September 13 in Cambridge, England. This meeting occurs immediately prior to the Genome Informatics meeting in Hinxton (for which the abstract deadline is June 25). Registration information for this meeting will be available in a few weeks. In the mean time, you can post topic suggestions to the meeting page.

Please feel free to tell your colleagues and to post to mailing lists that you think would be interested in this meeting.

I look forward to seeing you in England this Fall.

Scott Cain


New GMOD Tutorials

Summer School - Americas

Detailed and hands-on online tutorials are now available for the GMOD Components that were covered at the 2010 GMOD Summer School - Americas. Each tutorial includes a VMware system image to work with, and detailed instructions on how to setup the component on that image. This year we have a Galaxy Tutorial for the first time.

The tutorials are:

The 2010 GMOD Summer School - Americas got the best reviews of any course GMOD has ever done. I'd like to thank this year's instructors and participants for making it such a success.


Dave Clements
GMOD Help Desk


ISGA Pipeline Service

ISGA at the Center for Genomics and Bioinformatics

Integrated Services for Genomic Analysis (ISGA) is an Ergatis-based bioinformatics pipeline service based at Indiana University's Center for Genomics and Bioinformatics. ISGA is also a free, open-source software package that you can install locally to provide a biologist-friendly web interface to your computational resources. ISGA currently provides prokaryotic annotation and prokaryotic assembly pipelines and offers an intuitive interface for biologists to run and customize pipelines. ISGA also integrates tools such as GBrowse and Blast for visualizing and analyzing pipeline results. Since ISGA utilizes the Ergatis workflow system to execute pipelines, ISGA pipeline can be submitted back to the Ergatis community and other Ergatis pipelines can be adapted to use ISGA. (See Ergatis Update below for what's new with Ergatis.)

For more on ISGA, see the manuscript "An Ergatis-based prokaryotic genome annotation web server" in Bioinformatics, the ISGA pipeline and account tutorials, and the ISGA FAQ page. For help using or installing ISGA, join the isga-users mailing list.

Chris Hemmerich


MAKER 2.0, AGS Workshop

MAKER 2.0 Released

Arthropod Genomics Symposium

MAKER, the easy to use genome annotation pipeline, is now version 2.0.

Some of the current features and other improvements

  • Improved gene model preparation and evidence filtering...
  • mRNAseq data in your annotations (use output from programs like TopHat, CuffLinks, and others in MAKER)...
  • Annotate eukaryotes and prokayotes...
  • Pass through any kind of evidence evidence from any source via GFF3 pass-through...
  • Easy single-command-line dump of MAKER output to a Chado database and to JBrowse...
  • Same directory parallelization - just start MAKER on top of itself, and it will share the workload with the new process...
  • Auto recovery - start, stop, and restart MAKER at any time; MAKER will always just pick up where it left off...
  • optional web base GUI for a local MAKER installation

There will also be a workshop on MAKER on June 12 at the 4th Annual Arthropod Genomics Symposium in Kansas City. If you are attending AGS and are interested in genome annotation, please consider attending.

Carson Holt


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.


Dave C.
GMOD Help Desk


June 2010 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).


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


Dave Clements
GMOD Help Desk


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,



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).



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.


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


<endFeed />

News Archives

Items more than 6 months old are available in the GMOD News Archives.

Adding a News Item

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 for you.

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
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Once you have saved the page, a link to the new item will show up on the home page in about an hour. (Why the delay? It uses an RSS feed of this page and it queries the feed infrequently.)

Facts about "GMOD News"RDF feed
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