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== Software Requirements V2.0 ==
{{ImageRight|Gmod-gears.png|Software Requirements, Ver 2 Proposal||http://gmod.org/wiki/GMOD_Membership#Software}}
The [[#Software Requirement V2.0?|proposed revisions]] to GMOD's [[GMOD Membership#Software|software membership requirements]] have been approved.
The ''Version 2'' requirements are:
* Meets a common need
* Useful over time
* Configurable and Extensible
* Open source license for all users
* Interoperable with existing GMOD Components
* Commitment of support
* Publicly archived mailing list (new)
* Publicly accessible code repository (new)
The revised requirements were discussed at the [[September 2010 GMOD Meeting#GMOD Membership Requirements|September 2010 GMOD Meeting]], and on [[GMOD Mailing Lists]]. Not surprisingly, these uncontroversial revisions were approved in both forums (and even [http://twitter.com/OpenHelix/status/12248306868551680 on Twitter]).
Thanks for your help and input,
[[User:Clements|Dave Clements]]<br />
[[GMOD Help Desk]]
== GMOD Evo Hackathon Report ==
== GMOD Evo Hackathon Report ==

Revision as of 13:44, 21 December 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 />

Software Requirements V2.0

Software Requirements, Ver 2 Proposal

The proposed revisions to GMOD's software membership requirements have been approved.

The Version 2 requirements are:

  • Meets a common need
  • Useful over time
  • Configurable and Extensible
  • Open source license for all users
  • Interoperable with existing GMOD Components
  • Commitment of support
  • Publicly archived mailing list (new)
  • Publicly accessible code repository (new)

The revised requirements were discussed at the September 2010 GMOD Meeting, and on GMOD Mailing Lists. Not surprisingly, these uncontroversial revisions were approved in both forums (and even on Twitter).

Thanks for your help and input,

Dave Clements
GMOD Help Desk


GMOD Evo Hackathon Report

GMOD Evo Hackathon

The GMOD Evo Hackathon was held November 8-12 at NESCent. The 30 participants self-organized into eight groups with at least one group addressing each of the event's three objectives. The outcomes for each group are summarized below.

Worked on establishing a common database backend and JSON-based API for comparative genomics data, using several visualization tools (including JBrowse and GBrowse_syn) as targets. Will enable sharing of comparative data in multiple tools from multiple sources.
GBrowse_syn is built on and takes advantage of the GBrowse genome browser code and config files. However, it did not work well with GBrowse2, due to significant architectural changes. This group refactored GBrowse2 to naturally support GBrowse_syn. This work will also enable several other GBrowse1-only applications (SynView, Primer Designer, ...) to be ported to GBrowse2 as well. Two participants also became core GBrowse_syn developers.
This group set out to extend JBrowse to be a comparative genomics browser. The group removed the existing "single genome" assumption from the code and successfully displayed several genomes in parallel. Several participants also became familiar with JBrowse code and architecture.
PhyloBox is a flexible and fast web based tree visualization program. At the hackathon the PhyloBox team extended PhyloBox in numerous ways to make it a "widget" that can interact with other widgets. PhyloBox documentation was also created.
Integration PhyloBox JBrowse Integration
The group is the perfect example of the interaction that can happen at a hackathon. They worked with the JBrowse_syn, PhyloBox and GMatchbox groups to enable integration of these three technologies. This group was very helpful at getting teams to work together.
Natural Diversity and Phenotypes in Chado
This group focused on two outcomes, both relating to Chado. The first was a prototype Rails application that provided a web interface to the new Natural Diversity module in Chado. This was built on top of the emerging Chado on Rails project. The second was a better understanding, slight refactoring, and updated documentation for Chado's phenotype module.
Galaxy + HyPhy
Galaxy is both a workflow system and a means of persisting computational pipelines and results. This group worked on improving Galaxy's ability to integrate interactive tools, using HyPhy as the prototype application. The Galaxy and HyPhy code bases were modified to support this.
This subgroup worked on improving tree handling in BioPerl. Specifically, they addressed the handling of very large trees or large numbers of small trees. BioPerl now supports storing such trees in a lightweight database instead of in memory.

Dave Clements
GMOD Help Desk


GMOD Project Statistics Page

GMOD Project Statistics Page

A GMOD Project Statistics page has been created as a place to find and record information about interest in and adoption of GMOD. This includes info on downloads, source code repository updates, mailing list traffic and membership, web site traffic, event attendance, and course applications. The numbers are pretty impressive, and the most impressive graphs (growth in mailing list volume) aren't even there yet.

If you have any statistics related to the project or GMOD Components, please add them to the Project Statistics page.

Dave Clements
GMOD Help Desk


Opening @ Cancer Research UK

Bioinformatician and Pancreatic Expression Database

The BioMart-related position that was advertised in October has been reopened.

There is an opening for a bioinformatician at the Barts Cancer Centre 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. The new application deadline is January 17.

Dave Clements
GMOD Help Desk


Searchable GMOD Mail Archive

GMOD Archive at Nabble http://gmod.827538.n3.nabble.com/}}

I am pleased to announce that a searchable archive of all GMOD mailing lists is now available at Nabble. This archive has all GMOD Mailing Lists, no matter where they are hosted. You can search all lists at once, or just a particular list.

The archive contains all email posted since May and June of 2010, depending on list. (We are investigating options for loading email from before then as well.)

Happy searching,

Dave Clements
GMOD Help Desk


WebGBrowse Joins GMOD

WebGBrowse now a part of GMOD

WebGBrowse, a web interface for setting up GBrowse instances, is now a part of GMOD. WebGBrowse enables biologists and bioinformaticians to

  1. upload genome annotation information in GFF3 format,
  2. configure display of each genomic feature through simple mouse clicks on a web browser,
  3. visualize the configured genome with the integrated GBrowse software.

There is no manual editing of GBrowse configuration files with WebGBrowse. WebGBrowse relieves both the burden of installing GBrowse and the need to learn the configuration semantics. It is also a good way to learn the many GBrowse glyphs and how to configure them.

WebGBrowse is a good match for any organization that has users who want to create their own GBrowse instances, but lack enough computing resources and expertise to do so. WebGBrowse was developed at Indiana University's Center for Genomics and Bioinformatics.

WebGBrowse can be downloaded and installed locally, or you can use the WebGBrowse at CGB. The source is available at SourceForge. WebGBrowse comes with a tutorial, FAQ, and a user and support mailing list.

Ram Podicheti
Center for Genomics and Bioinformatics


New Topic-Based Mailing Lists

Two new GMOD mailing lists have been created as a result of the GMOD Evo Hackathon and subsequent feedback from the community. The two lists are both based on research topics, rather than on specific components:

Name List Link Topics Archive(s)
CoGePhy gmod-cogephy Discussion of comparative genomics, phylogeny, and related topics. Nabble, SourceForge
PhenDiver gmod-phendiver Discussion of phenotype, natural diversity, population genetics and related topics. Nabble, SourceForge

If you are interested in these topics, please subscribe to the lists and post any comments or questions that you just didn't know where to post before!


Dave Clements
GMOD Help Desk


PS: Also, while not (yet!) a part of GMOD, if you are interested in tree visualization, you are also encouraged to join the PhyloBox Google Group. The PhyloBox group was well represented at the hackathon.

Sr. DB Programmer @ FlyBase

Senior Database Programmer at FlyBase

The FlyBase genome database project group at Harvard University is looking for a new software developer to work on Chado related activities. See the job posting for details.


Software Requirements V2.0?

Software Requirements, Ver 2 Proposal

GMOD's procedures and requirements for software to become a part of GMOD were codified in February 2010, following the January 2010 GMOD Meeting. These requirements were in use before February, but were not documented or consistently applied.

These Version 1 requirements are:

  • Meets a common need
  • Useful over time
  • Configurable and Extensible
  • Open source license for all users
  • Interoperable with existing GMOD Components
  • Commitment of support

We'd now like to add two new requirements that probably should have been there in the first version:

  1. Component has a support mailing list that is publicly archived
  2. Publicly accessible code repository

We discussed these changes at the September 2010 GMOD Meeting , and attendees recommended they be implemented. We are now contacting the community at large (you!) to solicit feedback on the proposal.

If you have any comments, please post them to the membership requirements thread on the gmod-devel list in the next two weeks. If we reach consensus and approval, we'll update the requirements.

Dave Clements
GMOD Help Desk


GMOD Spring Training: Apply Now

Applications are now being accepted for the 2011 GMOD Spring Training course, a five-day hands-on school aimed at teaching new GMOD administrators how to install, configure and integrate popular GMOD Components. The course will be held March 8-12 at the US National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, as part of GMOD Americas 2011.

These components will be covered at the school:

{{#icon: GMODAmericas2011Logo.jpg|2011 GMOD Spring Training|170|2011 GMOD Spring Training}}
Apply Now
  • Apollo - genome annotation editor
  • Chado - biological database schema
  • Galaxy - workflow system
  • GBrowse - genome viewer
  • GBrowse_syn - synteny viewer
  • GFF3 - genome annotation file format and tools
  • InterMine - biological data mining system
  • JBrowse - next generation genome browser
  • MAKER - genome annotation pipeline
  • Tripal - web front end to Chado databases

The deadline for applying is the end of Friday, January 7, 2011. Admission is competitive and is based on the strength of the application, especially the statement of interest. The 2010 school had over 60 applicants for the 25 slots. Any application received after deadline will be automatically placed on the waiting list.

The course requires some knowledge of Linux as a prerequisite. The registration fee will be $265 (only $53 per day). There will be a limited number of scholarships available.

This may be the only GMOD School offered in 2011. If you are interested, you are strongly encouraged to apply by January 7.


Dave Clements
GMOD Help Desk


Phenotype RCN Launched


We are pleased to inform you that NSF has recently funded the Phenotype Research Coordination Network (RCN) for researchers who are interested in searching and comparing phenotypes across species and in developing the tools and methods needed in making this possible. The representation of morphology, behavior and other phenotypic features using computational methods such as ontologies and controlled vocabularies is in its infancy. Integrating phenotypes with data across all levels of the biological hierarchy, however, is possible if standards are co-developed and coordinated.

This RCN envisions building a broad base of community knowledge and resources so as to maximize the research potential of web-based data. Funding for participation in meetings, presentations and laboratory exchanges for students, postdocs and faculty from ontology and taxonomic domains (initially plants, arthropods, and vertebrates) is available through the RCN.

We are eager to have you join us! Please sign up for our participant and mailing lists for further information and feel free to contact one of the PIs: Paula Mabee, Andy Deans, Eva Huala, and Suzanna Lewis.

Hope to hear from you soon,

Paula, Andy, Eva, and Suzanna


Help Desk Transition

Help Desk Transition

After three years at the GMOD Help Desk I have decided to take a similar position with the Galaxy project, starting on January 1. I'll still be a part of the GMOD community (and I will still be involved in planning GMOD Americas 2011), but I will no longer be GMOD project staff. I have enormously enjoyed my time on this project and I have learned a lot from working on the project and with the community.

This transition make this an ideal time to reconsider and reconfigure what the GMOD Help Desk does. The Help Desk's current core tasks will continue, including:

What should the balance be between these tasks? What additional tasks should be added to the mix? If you have any suggestions on how the position should evolve, please send them to the Help Desk. We'll compile your ideas and use them to guide the next incarnation of the help desk.

We are also looking for someone to fill the updated position. If you know of anyone, or are interested yourself, then please contact us as well. It's a great job and there is no better community to work with.

Thanks for everything. It's been a great three years.

Dave Clements
GMOD Help Desk (for one more month)


Virtual Issue in Journal Database

Database: The Journal of Biological Databases and Curation

I recently had a chat with one of the editors of the journal Database, an open access journal whose aim for publications lines up very nicely with the goals of GMOD. During this discussion, the idea of a GMOD virtual issue came up, and it is one that I am very excited about. Therefore, I'm reaching out to you (the GMOD community) for ideas as well as commitments to write peer reviewed articles for this publication. Articles can be about theory, tutorial or community. I expect we'll have papers covering many components and for some components we will have multiple papers with different emphases (for example, Chado theory, Chado tutorial, and Chado community papers). Please contact me if you'd like to discuss this further.

The virtual issue approach that Database takes is very appealing, in that the submitted papers do not need to be in by a certain cutoff date, as this is not going to put into a "dead tree" form :-) So, the virtual issue can be created at any point, either when there is just one paper, or when there is a critical mass (which we would have control over), and more papers can be added to it at any time. An example of a Database virtual issue is the one they created for the Biocurator meeting last year.

I look forward to your ideas and commitments!

Scott Cain
GMOD Project Coordinator


December 2010 Calendar

GMOD Calendar

There are almost no submission deadlines in December. (However, to buck the trend, the deadline for applying to the 2011 GMOD Spring Training School will probably be in December.) There are a number of interesting events though:

  • BioInfoSummer 2010 and the NETTAB Workshop on Bio-wikis (these both start in November and end in December)
  • Automated Imaging and High-Throughput Phenotyping
  • International Digital Curation Conference
  • Australasian Ontology Workshop
  • EMBO Course o Bioinformatics and Comparative Genome Analysis
  • International Conference on Genome Informatics


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

Happy holidays,

Dave Clements
GMOD Help Desk


GMOD Americas: March 2011

GMOD Americas 2011

GMOD Americas 2011 has been scheduled for March 5-12 at the National Evolutionary Synthesis Center (NESCent), in Durham, North Carolina. GMOD Americas 2011 will include:

The next GMOD Community Meeting will be held March 5-6. For the first time, it will be preceded by an Introduction to GMOD session on the evening of March 4. This session will be targeted at GMOD newcomers.
GMOD community members gather to discuss and work on common topics of interest.
A 5 day GMOD Course covering installation, configuration and integration of GMOD Components.

The details for each of these will be filled in shortly. In particular, we expect to start taking applications for the course in December. Registration for the meetings will likely open in January.

In the meantime, if you have any topics you want to discuss at the Community Meeting or the Satellite Meetings, please add your idea to the meeting page, or contact the GMOD Help Desk.

Mark your calendars!

Dave Clements
GMOD Help Desk


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


<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
    • 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''. The two apostrophes will cause the date to be italicized: 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?
    • Make sure that your MediaWiki markup (links, italics, etc.) is correct. The MediaWiki extension that lists news items on the home page is temperamental. Incorrect markup can lead to garbage on the home page.
    • Revise until you like it and then save it. Try not to revise and save repeatedly. Each saved revision has the potential to send a new item to the RSS feed. People will be watching you edit in real time. You don't want that.

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
BioSchema +
ChadoSchema +