Difference between revisions of "GMOD News"

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''2009/12/18''
 
''2009/12/18''
 
== BioPerl Podcast ==
 
 
{{ImageRight|BioPerl_logo.jpg|BioPerl Podcast|70|http://twit.tv/floss96}}
 
 
A [http://twit.tv/floss96 podcast on the BioPerl project] is available at [http://twit.tv/FLOSS 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 [[User:Cjfields|Chris Fields]] and [[User:Stajich|Jason Stajich]].
 
 
[[User:Clements|Dave Clements]]<br />
 
''2009/11/23''
 
 
== InterMine 0.92 Released ==
 
 
{{ImageRight|InterMine.png|InterMine Release Notes|180|http://www.intermine.org/wiki/ReleaseNotes}}
 
 
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 [http://www.intermine.org/wiki/ReleaseNotes Release Notes] and [http://www.intermine.org/wiki/UpgradeInterMine 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.
 
 
[mailto:dev@mail.intermine.org Let us know] if you have problems or suggestions for the next releases.
 
 
The InterMine team.
 
 
''2009/11/23''
 
 
== CMap Paper in Bioinformatics ==
 
 
{{ImageRight|BionformaticsCover.gif|Bioinformatics||http://bioinformatics.oxfordjournals.org/cgi/content/full/25/22/3040}}
 
 
A [http://bioinformatics.oxfordjournals.org/cgi/content/full/25/22/3040 paper] describing the [[CMap]] comparative map viewer is in the [http://bioinformatics.oxfordjournals.org/content/vol25/issue22/index.dtl current issue] of ''[http://bioinformatics.oxfordjournals.org/ Bioinformatics]'':
 
 
: [http://bioinformatics.oxfordjournals.org/cgi/content/full/25/22/3040 CMap 1.01: a comparative mapping application for the Internet], by Ken Youens-Clark, [[User:Faga|Ben Faga]], Immanuel V. Yap, [[User:Lstein|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|CMap page]] to learn more.  CMap will also be covered in the [http://www.intl-pag.org/18/18-gramene.html Gramene workshop] and in a poster at [[PAG 2010]].
 
 
[[User:Clements|Dave Clements]]<br />
 
[[GMOD Help Desk]]
 
 
''2009/11/14''
 
 
== January 2010 GMOD Meeting ==
 
 
{{ImageRight|Jan2010MtgLogo170.png|January 2010 GMOD Meeting||January 2010 GMOD Meeting}}
 
 
 
<div style="font-size: 140%; text-align: center">[[January 2010 GMOD Meeting|Register for the January 2010 GMOD Meeting]]</div>
 
 
 
I am pleased to announce that the [[January 2010 GMOD Meeting|January GMOD meeting]] will be taking place on January 14 and 15, 2010 in San Diego at the [[January 2010 GMOD Meeting#Lodging|Best Western Seven Seas]]
 
(the same location as last year).  Please see the [[January 2010 GMOD Meeting|meeting page]] for registration information.
 
 
Please also take a moment to [[January 2010 GMOD Meeting#Agenda Proposals|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 [[January 2010 GMOD Meeting|GMOD meeting]] and the [[PAG 2010|Plant and Animal Genome meeting]] before it may stay at the Best Western the entire time.
 
 
Please direct follow up questions to the [https://lists.sourceforge.net/lists/listinfo/gmod-devel gmod-devel mailing list] ([mailto:gmod-devel@lists.sourceforge.net gmod-devel@lists.sourceforge.net]).
 
 
Thanks and I look forward to seeing you in San Diego!
 
 
[[User:Scott|Scott]]
 
 
''2009/11/13''
 
 
== Long Term Database Funding ==
 
 
You may have heard about [http://www.arabidopsis.org/doc/about/tair_funding/410 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 [http://mailman.tairgroup.org/mailman/listinfo/biocurator Biocurator list]) on October 22.  A day later the paper "[http://database.oxfordjournals.org/cgi/content/full/2009/0/bap017 Models for financial sustainability of biological databases and resources]" appeared in ''[http://database.oxfordjournals.org/ Database: The Journal of Biological Databases and Curation]''.
 
 
All GMOD users need to give at least some thought to long term funding issues.  A [http://biocurator.proboards.com/index.cgi?board=fundingissues discussion thread on long term database funding] has now been started on the [http://biocurator.org International Society for Biocuration]'s (ISB) [http://biocurator.proboards.com/ forum site].
 
 
{{ImageRight|TAIR_logo.gif|TAIR Funding Update and Discussion Forum||http://www.arabidopsis.org/doc/about/tair_funding/410}}
 
[http://www.arabidopsis.org/ TAIR] asked people to do a couple things:
 
# Cite TAIR in publications: as a reference, as a source of data in methods sections, and under acknowledgments.
 
# Contribute to a [http://www.arabidopsis.org/doc/about/tair_funding/410 discussion on the TAIR web site] about
 
## the bioinformatics needs of the ''Arabidopsis'' and wider plant biology communities and
 
## how resources like TAIR should be funded.
 
 
The [http://www.arabidopsis.org/doc/about/tair_funding/410 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 ''[http://database.oxfordjournals.org/cgi/content/full/2009/0/bap017 Database]'' paper discusses similar proposals, plus some others.
 
 
If you are interested in long-term funding issues, I encourage you to participate in the [http://biocurator.proboards.com/index.cgi?board=fundingissues discussion at ISB].  If you use TAIR and want to see it funded, please [http://www.arabidopsis.org/doc/about/tair_funding/410 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.
 
 
[[User:Clements|Dave Clements]]
 
 
''2009/11/06''
 
 
== Two Openings at Bayer CropScience ==
 
{{ImageRight|Logo_BayerCropScience.gif|Open positions at Bayer CropScience||http://www.mybayerjob.com/en}}
 
'''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: [https://mybayerjob.bayerbbs.com/sap(bD1lbiZjPTAwNQ==)/bc/bsp/sap/hrrcf_pinst_pbl/application.do?PARAM=UElOU1RfR1VJRD00QUE2NjQ4RkNFNjUwMDlBRTEwMDgwMDAwQUJGRDkwRQ%3d%3d 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. [[Glossary#Perl|perl]] and/or python). The candidate should have a good background in (plant) genetics and/or genomics and/or molecular biology.
 
 
More information: [https://mybayerjob.bayerbbs.com/sap(bD1lbiZjPTAwNQ==)/bc/bsp/sap/hrrcf_pinst_pbl/application.do?PARAM=UElOU1RfR1VJRD00QUI3NUU2MzIzRDcwMTEyRTEwMDgwMDAwQUJGRDkwRQ%3d%3d BioAnalyst Researcher]
 
 
Operating language in the company is English.
 
 
'''Interested in any of these positions?''' You can apply [http://www.mybayerjob.com/en here] or send your CV to [mailto:Laurent.viau@bayercropscience.com Laurent Viau]
 
 
[[User:ErickAntezana|Erick Antezana]]
 
 
''2009/11/06''
 
 
== GBrowse NGS Tutorial & Poster==
 
 
{{ImageRight|BA2009Logo.png|GBrowse NGS Tutorial|100|GBrowse NGS Tutorial}}
 
A tutorial on using [[GBrowse NGS Tutorial|GBrowse 2 to visualize next generation sequencing (NGS) data]] is now available.  The [[:Category:Tutorials|tutorial]] walks through how to configure the [[GBrowse]] 2 genome browser to display [[next generation sequencing]] (NGS) data using the [http://samtools.sourceforge.net SAMtools] GBrowse adaptor, Bio::DB::Sam. This tutorial was originally taught at the [[BA2009|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 [[:Image:GBrowse_nextgen_poster.pdf|poster]] (by [[User:Scott|Scott Cain]]) demonstrating how to use the adaptor with ''GBrowse 1 and GBrowse 2'' is also available.
 
 
[[User:Clements|Dave Clements]]<br />
 
[[GMOD Help Desk]]
 
 
''2009/11/04''
 
 
== Galaxy Project Hiring ==
 
 
{{ImageRight|GalaxyLogoSmall.png‎|Galaxy Project Hiring||http://bitbucket.org/galaxy/galaxy-central/wiki/job_rc2}}
 
There are several open [http://bitbucket.org/galaxy/galaxy-central/wiki/job_rc2 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 [http://bitbucket.org/galaxy/galaxy-central/wiki/job_rc2 official posting] for full details and contact information.
 
 
''2009/11/02''
 
  
 
<endFeed />
 
<endFeed />

Revision as of 23:38, 24 May 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 />

June 2010 Calendar

Calendar

The next 5 weeks includes the a MAKER workshop at the Arthropod Genomics Symposium, and deadlines for ISMB (Boston in July), AMATA (Hobart in September), GIW (Hangzhou in December), ECCB (Ghent in September), InCoB (Tokyo in September), and Genome Informatics (Hinxton in September).

<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=20100601%2F20100601</embedurl>

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

Thanks,

Dave Clements
GMOD Help Desk

2010/05/24

gmod (Chado) 1.1 Released

I am pleased to announce that we released gmod-1.1 today. This release has the GMOD database schema, Chado, and a variety of tools for loading and working with the database. The release can be downloaded from the GMOD SourceForge site.

There have been many people who have helped with getting this release done and I would like to thank all of them. I would like to especially thank Rob Buels and Naama Menda and the rest of the people at the Sol Genomics Network (SGN) for their code contributions, including a pub table loader that works with PubMed and an updated version of the script to calculate cvterm closures.

There have been many changes and bug fixes since the 1.0 release just over two years ago, but the schema itself has changed very little. For a SQL summary of the changes, see Changes.sql in the release that contains SQL statements that should take a 1.0 release of the Chado schema to the 1.1 schema. See the Changes file for a full list.

If you have been using Chado from a recent svn checkout, you don't need to modify your schema at all, since the last change to the schema was about a year ago.

Now that this release is out, the plan going forward is for frequent, smaller releases, with an eye on the Natural Diversity schema modifications being worked on now.

Thanks for your continued support of the GMOD project,

Scott

2010/05/24

GMOD in Boston in July?

Scott Cain sent this question about the next GMOD meeting out to several mailing lists on May 17:

Since the last GMOD meeting in January, I had been hoping to have a GMOD meeting around the ISMB and BOSC meetings in Boston this July. Until this week, though, I had had a difficult time finding a place where a meeting could be held for a reasonable price. However, a kind soul at The Broad has offered a meeting space that would easily accommodate a GMOD meeting for two days before BOSC (either July 6-7 or July 7-8). The only question I have is this: can people make it to a GMOD meeting with about 2 months notice? Please let me know your thoughts on this. While there would probably be a registration fee, it would be fairly low (I'm guessing in the ballpark of $50).

Thanks,

Scott

Scott hasn't heard back, yea or nay, from very many people so far and we need to make a decision as soon as possible. If you have any thoughts on this, please send them to Scott before 3pm Eastern US time on Monday, May 24. See the GMOD Calendar for a list of what else is going on in July.

Thanks,

Dave C.
GMOD Help Desk

2010/05/21

Ergatis Update

Ergatis Paper in Bioinformatics

The paper "Ergatis: A web interface and scalable software system for bioinformatics workflows" is now available as an advance access manuscript in the journal Bioinformatics. Ergatis "enables users to build, execute, and monitor pipelines for computational analysis of genomics data."

Ergatis now includes pipeline templates for prokaryotic genome annotation and comparative genome analysis, as well as 174 modular 'components' that can be used to create custom pipelines, all of which can be executed either locally or on large compute clusters.

New tools available that use Ergatis include CloVR, which enables bioinformatic pipeline execution in compute clouds and the recently-awarded Data Intensive Academic Grid (DIAG), which will provide a publicly-accessible Ergatis instance as one of its access methods. At the January 2010 GMOD Meeting Chris Hemmerich presented ISGA, which provides a customized, abstract interface to Ergatis designed for biologists with specific pipeline needs.

Joshua Orvis

2010/05/20


May 2010 Calendar

Calendar

The next 5 weeks includes the 2010 GMOD Summer School - Americas and the first Galaxy Developers Conference. Upcoming deadlines include the ISMB technology track (tomorrow), posters at Arthropod Genomics and ECCB10, and papers for GIW 2010.

<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=20100501%2F20100501</embedurl>

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

Thanks,

Dave Clements
GMOD Help Desk

2010/04/22

MaizeGDB: Choosing GBrowse

Database Paper

A paper, "Choosing a genome browser for a Model Organism Database: surveying the Maize community," by the MaizeGDB team has been published in Database. To prepare for the availability of a reference genome, MaizeGDB surveyed their community to assess genome visualization needs. This paper summarizes the survey and MaizeGDB's review of available browsers, and describes why they chose GBrowse. The paper finishes by describing how they implemented GBrowse, including the locus lookup tool (described here), a MaizeGDB extension that uses maize's extensive physical and genetic mapping data to localize genomic regions in GBrowse. This is a great paper for anyone considering which genome browser to use.


Database Journal

I'd also like to highlight the journal the paper appears in: Database: The Journal of Biological Databases and Curation. "Biological Databases and Curation" are what GMOD is about and many of the papers cover issues and resources that are widely applicable in the GMOD community. The current issue also includes papers on community annotation using wikis, and a report on best practices in genome annotation from the ISB 3rd International Biocuration Conference. Database is an open access publication, making it an even better match for GMOD.

Dave Clements
GMOD Help Desk

2010/04/19

YAPC::NA 2010 is Almost Here!

{{#icon: Yapc2010Logo.png|YAPC::NA 2010|220|http://conferences.mongueurs.net/yn2010/}}

June 21st – 23rd 2010 is quickly approaching and Columbus.PM is getting very excited. Hotel reservation information is available, dorm reservation details are up and ready, the conference is quickly approaching. For everyone still looking for YAPC::NA 2010 (Yet Another Perl Conference North America) details, here is what we have planned. The conference will be held in the brand new beautiful The Ohio State Union.

Larry Wall, Damian Conway, Randal Schwartz, and many others will be in attendance.

The main dorm location is Morrison Tower and the Hotel conference block is in The Blackwell Inn (see Accommodations). Early registration is quickly coming to an end so make sure that you forward this to all of your friends and coworkers and get signed up today!

I hope to see you all at YAPC::NA 2010 in beautiful Columbus, Ohio.

Heath Bair
YAPC::NA 2010 Conference Chairman

2010/04/13

Don Gilbert Nominated for BFA

Don Gilbert Nominated for Benjamin Franklin Award

The Bioinformatics Organization has announced its nominees for the the 2010 Benjamin Franklin Award.

The Benjamin Franklin Award for Open Access in the Life Sciences is a humanitarian/bioethics award presented annually by this organization to an individual who has, in his or her practice, promoted free and open access to the materials and methods used in the life sciences.

This year's nominees include longtime GMOD contributor Don Gilbert, of Indiana University. Other 2010 nominees are Alex Bateman, David J. Lipman, G.P.S. Raghava, and John Quakenbush. Previous winners of the BFA include Jim Kent, Michael Ashburner, and another long-time GMOD contributor Lincoln Stein.

If you want a say on who should receive the 2010 award, please go to Bioinformatics.org and cast your vote. If you are not already a member you will need to join, but basic membership is free.

Dave Clements
GMOD Help Desk

2010/04/01

April 2010 Calendar

Calendar

There's a lot on the calendar in the next 5 weeks, including (among others) registration deadlines for Arthropod Genomics (early) and the Galaxy Developers Conference, and submission deadlines for ECCB, iEvoBio, BOSC, and ISMB.

<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=20100401%2F20100401</embedurl>

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

Thanks,

Dave Clements
GMOD Help Desk

2010/03/25

Google Summer of Code & OBF

OBF in GSoC

Great news: the Open Bioinformatics Foundation (OBF) has been accepted as a mentoring organization for this summer's Google Summer of Code!

GSoC is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents). Students are paid a $5000 USD stipend to work as a developer on an open-source project for the summer. For more on GSoC, see the GSoC 2010 FAQ.

Student applications are due April 9, 2010 at 19:00 UTC. Students who are interested in participating should look at the OBF's GSoC page, which lists project ideas, and who to contact about applying.

For current developers on OBF projects, please consider volunteering to be a mentor if you have not already, and contribute project ideas. Just list your name and project ideas on OBF wiki and on the relevant project's GSoC wiki page.

Thanks to all who helped make OBF's application to GSoC a success, and let's have a great, productive summer of code!

Rob Buels

OBF GSoC 2010 Administrator

2010/03/21

InterMine is Hiring

InterMine is hiring

We have four vacancies on InterMine related projects at The University of Cambridge, UK. We are looking for a Web Developer, Bioinformatics Software Developers and a Java Developer. See the position descriptions for more information.

The closing date for applications is 2nd April 2010.

The InterMine Team.

2010/03/19

Internships @ Dow AgroSciences

Dow AgroSciences

Dow AgroSciences has 7 Bioinformatics summer internship positions open, 2 of which are related to GMOD. We are looking for candidates with experience in installing, configuring, and uploading data into GMOD. Experience with the GBrowse source code and modifying it to create new views (e.g creating new glyphs and modifying existing glyphs as per user needs) is highly preferred. We have started the interview process. Please email your resume ASAP to Navin Elango (nelango@dow.com). For more information about Dow AgroSciences, please visit our website

Navin Elango

2010/03/16

Sr. DB Programmer @ FlyBase

FlyBase Opening

FlyBase has a single opening for a developer to join the database team at Harvard University in Cambridge, Mass. The position consists of roles in two model organism database projects, VectorBase and FlyBase, in the development and maintenance of production applications involving Chado, Apollo, Ensembl, and InterMine. For more information, see the job posting.

Dave Emmert

2010/03/09

NGS Analyses in Galaxy

NGS Analyses in Galaxy

The Galaxy team is announcing the launch of the first free public resource for NGS analysis. This service is the beginning of our campaign to provide free web-based utilities for NGS analysis and later in the year will take advantage of the Cloud resources. At present, there are three main groups of tools including:

  1. NGS QC and manipulation - contains a variety of tools for dealing with all flavors of fastq datasets as well as outputs of SOLiD and 454 instruments.
  2. NGS Mapping - currently includes Bowtie (Illumina & SOLiD), BWA (Illumina), and LASTZ (454) mappers. PerM (SOLiD) is on the way and more will be added in the coming months. Transcriptome tools are also in the final stages of development.
  3. NGS SAMTools - includes a variety of utilities for SAM/BAM manipulation. Some are based on SAMtools library, some are written by Galaxy team.

See the announcement page for more information and for links to several Galaxy Quickies (video tutorials) demonstrating the new service.

Anton Nekrutenko

2010/03/08

Openings @ SGD

Scientific Application Programmers at SGD

There are 3 openings for Scientific Application Programmers at the Saccharomyces Genome Database (SGD), the model organism database for yeast. These positions will be involved in enhancing databases and data pipelines for the sharing of genomic data. See the job postings for more information.

SGD is both a GMOD contributor (e.g., BLAST Graphic Viewer) and GMOD user.

2010/03/05

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

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