Prospecting for Proposals for GSoC 2015

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GoogleSummer 2015logo.jpg
The Genome Informatics group and GMOD will be submitting an application for Google Summer of Code (GSoC) this year, and we are soliciting project ideas from people and groups involved in the GMOD project.
GSoC is a global program run b

Hiring Several Positions WSU

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The Bioinformatics lab of Dr. Dorrie Main at Washington State University in Pullman, WA, is looking to recruit in a number of key computational positions. The successful candidates will be joining a well-resourced, dynamic team who enjoy the benefits of a more flexible schedule, including the opportunity to work remotely, within an academic environment. These positions will either be at the level of Scientific Assistant (Bachelors degree) or Associate in Research (Masters Degree).

Now Hiring JBrowse Lead Developer

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1 Description
2 Responsibilities
3 Qualifications
4 Applications

JBrowse is recruiting a new lead developer. If you are excited by the maturation of bioinformatics into a web-based, broad-utility discipline, this is the job for you. Since 2007 JBrowse has been bringing a modern dynamic HTML aesthetic to the “traditional” genome browser, being the first mainstream web-based genome browser with live panning, zooming, interactive track rearrangement and dynamic filtering of track lists.

BBOP Job Openings

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We're casting a wide net to find the right people for these two positions. To formally apply please go to the links below. If you have questions, please send them to Suzanna Lewis (selewis at lbl dot gov) and copy Chris Mungall (cjm at berkeleybop dot org).

Please Support EcoCyc

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EcoCyc website
EcoCyc, the E. coli information resource and one of the resources offered by the Pathway Tools group, is in need of letters of support from the community after receiving a poor grant review, which could result in a complete loss of funding on July 1st, 2014. If you are a user of EcoCyc, please consider writing a short letter in support of this vital resource.

June 2014 WebApollo Hackathon

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Berkeley Bioinformatics Open-Source Projects (BBOP) invites you to join us this summer for a WebApollo Hackathon at Lawrence Berkeley National Laboratory, California.
When: Monday, June 2 - 6, 2014
Where: Lawrence Berkeley National Laboratory. Building 74 (B74), Room 104. 1 Cyclotron Rd, Berkeley, CA 94720
What: five days of intensive, collaborative WebApollo development!
For five days developers will work on new features of interest to their research communities, improve existing features, and collaborate on developing features of interest to other colleagues.

Applications Open for GMOD Online Training

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GMOD will be holding its first online training course for those interested in the set up and use of GMOD components.
The course will be held from Monday 19th May to Friday 23rd May 2014, and will cover core GMOD software, including GBrowse and JBrowse, Galaxy, MAKER, Tripal, WebApollo, Canto, and the Chado database.
If you are interested in attending, please see GMOD Online Training 2014 for more information and to submit your application.

Posted to the GMOD News on 2014-03-31

Canto Workshop at Biocuration 2014

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GMOD will be running a workshop at Biocuration 2014 to demonstrate the use of Canto, on Wednesday 9th April in the afternoon.

Tripal 2.0a released

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The Tripal Development Team is pleased to announce an alpha release of Tripal 2.0 for Drupal 7. This release is expected to have bugs and there is some functionality still under development. However, this release is made to help early adopters of Tripal for Drupal 7. Reports of bugs or other issues are highly welcomed.

Precompiled Ontologies in Chado

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Eric Rasche and the Center for Phage Technology at Texas A&M University are making Chado database dumps of precompiled ontologies publicly available to save other Chado users the time and hassle of downloading and compiling the ontologies themselves.
Go to the download site.
The ontologies currently available are:

Chado Feature Properties

Gene Ontology

Plant Ontology

Relationship Ontology

Sequence Ontology

These are updated weekly; the workflow is as follows:

clone Chado from SVN


load ontologies

dump database as SQL

upload to a publicly accessible webserver

Please co

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