Difference between revisions of "GMOD News"

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== Logo Program Deadline Extended ==
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{{ImageRight|Lbcclogo.jpg|GMOD Logo Program||GMOD Logo Program}}
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'''The first call to participate in the [[GMOD Logo Program]] has been extended to March 19.''' 
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We still have some room for additional participants. If you are interested, please [[GMOD Logo Program|submit an application]].  '''Participation is limited to non-profits, and costs US$75.'''  Please see the [[GMOD Logo Program|program page]] for additional details and requirements, and a link to an application form.
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Thanks,
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[[User:Clements|Dave Clements]]<br />
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[[GMOD Help Desk]]
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''2010/03/03''
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== March 2010 Calendar ==
 
== March 2010 Calendar ==
  

Revision as of 19:15, 3 March 2010

News that is relevant to the GMOD user and developer communities. This includes a wide range of topics, from GMOD meetings and releases to user success stories and GMOD related publications. 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 send it to the GMOD Help Desk or add it to this page directly. See Adding a News Item for how to do this.

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 for how to do just that.

<startFeed />

Logo Program Deadline Extended

GMOD Logo Program

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

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

Thanks,

Dave Clements
GMOD Help Desk

2010/03/03

March 2010 Calendar

Calendar

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

<embedurl>http://www.google.com/calendar/embed?src=0ajv0bm32ue3c2o2v1c8i889hk%40group.calendar.google.com&showTitle=0&showCalendars=0&height=350&mode=AGENDA&ctz=America/NewYork&dates=20100301%2F20100301</embedurl>

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

Thanks,

Dave Clements
GMOD Help Desk

2010/02/22

GMOD Logo Program, Spring 2010

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

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

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

Thanks,

Dave Clements
GMOD Help Desk

2010/02/03

GMOD Summer School - Americas

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

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

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

  

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

Thanks,

Dave Clements
GMOD Help Desk

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

2010/01/29

GMOD @ February NextGenBUG

NextGenBUG 9 Feb Dundee

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

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

Dave Clements
GMOD Help Desk

2010/01/29

GBrowse 2.0

GBrowse2Thumb.png

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

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

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

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

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

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

On behalf of the GMOD team,

Lincoln Stein

2010/01/28

WebGBrowse 2.0

WebGBrowse at the Center for Genomics and Bioinformatics

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

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

Thanks,

Ram Podicheti
Center for Genomics and Bioinformatics
Indiana University

2010/01/25

Tripal v0.2 Released

Triapl

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

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

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

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

Best Regards,

Stephen Ficklin
Clemson University Genomics Institute

2010/01/23

CMap3D

CMap3D

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

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

Chris Duran

2010/01/21

DAS Workshop 7-9 April 2010

DAS Workshop

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

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

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

See the workshop page for more information and registration details.

Jonathan Warren

2010/01/21


GBrowse.org

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

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

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

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

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

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

Ciao,

Alessandra Bilardi
CRIBI Genomics, University of Padua

2010/01/11

Bio::Chado::Schema 0.05 Released

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

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

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

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

Rob Buels
SGN

2010/01/08

GMOD at PAG 2010

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


GMOD @ PAG

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

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

See you in San Diego,

Dave Clements
GMOD Help Desk

2010/01/05

Galaxy Developer Conference

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


Galaxy Developer Conference

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

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

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

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

Dave Clements
GMOD Help Desk

2009/12/28

Arthropod Genomics Consortium

Arthropod Genomics Consortium

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

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

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

Dave Clements
GMOD Help Desk

2009/12/18

BioPerl Podcast

BioPerl Podcast

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

Dave Clements
2009/11/23

InterMine 0.92 Released

InterMine Release Notes

We have released version 0.92 of InterMine.

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

Version 0.92 has Release Notes and upgrade information.

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

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

The InterMine team.

2009/11/23

CMap Paper in Bioinformatics

Bioinformatics

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

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

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

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

Dave Clements
GMOD Help Desk

2009/11/14

January 2010 GMOD Meeting

January 2010 GMOD Meeting


Register for the January 2010 GMOD Meeting


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

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

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

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

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

Scott

2009/11/13

Long Term Database Funding

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

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


TAIR Funding Update and Discussion Forum

TAIR asked people to do a couple things:

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

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

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

Dave Clements

2009/11/06

Two Openings at Bayer CropScience

Open positions at Bayer CropScience

1. BioAnalyst Scientist:

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

More information: BioAnalyst Scientist

2. BioAnalyst Researcher:

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

More information: BioAnalyst Researcher

Operating language in the company is English.

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

Erick Antezana

2009/11/06

GBrowse NGS Tutorial & Poster

GBrowse NGS Tutorial

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

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

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

Dave Clements
GMOD Help Desk

2009/11/04

Galaxy Project Hiring

Galaxy Project Hiring

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

See the official posting for full details and contact information.

2009/11/02

Visualizing Biological Data Workshop

Visualizing Biological Data (VizBi)

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

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

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

2009/10/21

Openings at Syngenta

Openings at Syngenta

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

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

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

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

Eric Ganko

2009/10/21

Opening at SGD

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


Bioinformatics Analyst at SGD

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

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

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

2009/10/20

Apollo 1.11.2 Released

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

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

Cheers,

Ed Lee

2009/10/07

2009 GMOD Survey Results

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

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


GMOD Mug

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

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

Dave Clements
GMOD Help Desk

2009/10/05

GMOD Tutorials! GMOD Training!

Summer School - Europe


Summer School - Americas

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

The tutorials are:


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

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

Dave Clements
GMOD Help Desk

2009/10/02


modENCODE & Gramene Openings

The modENCODE and Gramene projects are both hiring.

modENCODE


modENCODE Project Openings

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

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

Please see the complete job description for details.

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


Gramene


Grameene Project Opening

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

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

See the position announcement for full details.

2009/10/02

GMOD @ Bioinformatics Australia

GMOD workshop at Bioinformatics Australia

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

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

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

Dave Clements
GMOD Help Desk

2009/10/01

InterMine Data Warehouse Workshop

InterMine Workshop

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

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

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

Please get in touch if you have any questions.

Regards,

Richard Smith

2009/09/29

Tripal: A Web Front End for Chado

Tripal

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

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

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

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

Dave Clements
GMOD Help Desk

2009/09/28

Reactome User Survey

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

You can access the survey at SurveyMonkey

Thank you for taking part.

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

Posted by Scott Cain

2009/9/28

DIYA: Do It Yourself Annotator

DIYA

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

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

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

Dave Clements
GMOD Help Desk

2009/09/23

Chado in RDF: OpenFlyData

RDF

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

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

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

Jun Zhou and Dave Clements

2009/09/23

Bioinformatics Position at SpBase

Position at SpBase

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

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

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

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

Dave C.
GMOD Help Desk

2009/09/22

2009 GMOD Community Survey

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

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

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

Thank you,

Dave Clements
GMOD Help Desk

2009/09/16

CVS to SVN Conversion: Done

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

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

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

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

Dave Clements

2009/09/15

FlyBase Bioinformatics Engineer position

FlyBase Opening

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

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

Josh Goodman

2009/09/14

Server Maintenance: Sept 9

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

Please let us know if you have any questions.

Dave Clements
GMOD Help Desk

2009/09/08

BioMart Ruby API

BioMart Ruby API

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

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

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

Dave Clements
GMOD Help Desk

2009/09/08

JBrowse paper

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

JBrowse is a Web 2.0 genome browser that features:

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

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

Dave Clements
GMOD Help Desk

2009/09/01

<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.
  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.

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 +