Difference between revisions of "GMOD News"

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== GBrowse Tutorial at PAG XVI ==
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''2007/12/27''
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Scott Cain will present a [http://www.intl-pag.org/16/16-gbrowse.html GBrowse tutorial] at the [http://www.intl-pag.org/ Plant and Animal Genome XVI Conference (PAG-XVI)], January 12-16, 2008, in San Diego.  This will be a hands-on tutorial on how to install and use the [[GBrowse]] genome browser.  If you are attending PAG and you are interested in GBrowse then please consider attending.
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See the [http://www.intl-pag.org/16/16-gbrowse.html PAG tutorial page] for additional information.
  
 
== Modware Feedback Wanted ==
 
== Modware Feedback Wanted ==
  
2007/12/11
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''2007/12/11''
  
 
[[Modware]] provides an object-oriented Perl API for [[Chado]] suitable for use by any application based on GMOD.  This Chado API supports creating, retrieving and updating objects in a Chado database. Modware makes heavy use of [[bp:Main Page|BioPerl]] to provide a familiar and intuitive interface for objects stored inside of a Chado database.
 
[[Modware]] provides an object-oriented Perl API for [[Chado]] suitable for use by any application based on GMOD.  This Chado API supports creating, retrieving and updating objects in a Chado database. Modware makes heavy use of [[bp:Main Page|BioPerl]] to provide a familiar and intuitive interface for objects stored inside of a Chado database.

Revision as of 17:50, 27 December 2007

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.

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.

This page is also available as an RSS feed. RSSIcon16x16.gif

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GBrowse Tutorial at PAG XVI

2007/12/27

Scott Cain will present a GBrowse tutorial at the Plant and Animal Genome XVI Conference (PAG-XVI), January 12-16, 2008, in San Diego. This will be a hands-on tutorial on how to install and use the GBrowse genome browser. If you are attending PAG and you are interested in GBrowse then please consider attending.

See the PAG tutorial page for additional information.

Modware Feedback Wanted

2007/12/11

Modware provides an object-oriented Perl API for Chado suitable for use by any application based on GMOD. This Chado API supports creating, retrieving and updating objects in a Chado database. Modware makes heavy use of BioPerl to provide a familiar and intuitive interface for objects stored inside of a Chado database.

Recently, a VMware Virutal Machine was released to make download and testing of a fully configured and installed version of Modware available. Modware developers continue to add new features, including representation of BLAST hits (currently on CVS HEAD).

One critical piece of the project that is missing is feedback from the community. If you are interested in a Chado API, please download the Modware Virtual Machine found on the Modware home page and give it a try. Email all feature requests, questions, and comments to gmod-ware-users@sourceforge.net.


November 2007 GMOD Meeting

2007/11/08

The November 2007 GMOD Meeting was attended by nearly 40 people from across the GMOD community. Community annotation and comparative genomics were two popular topics at this meeting. See November 2007 GMOD Meeting for a list of presentations and a summary of the meeting.



GMODTools 1.1 Released

2007/10/16

Version 1.1 of GMODTools has been released. Version 1.1 adds these features and corrections:

  • No chromosome/scaffold/golden_path files. This change is needed to handle partially assembled genomes with many (1000s to 100,000s) of scaffolds. Flag no_csomesplit=1 to use this (should become default).
  • Gene Ontology association file, see go_association tags in configurations
  • Validate main variables in chado database: ${golden_path}, ${seq_ontology}. This step, on now by default, checks that database contains configured values. If failed, db is inspected for real values.
  • Miscellany bugs cured and configuration updates, e.g., tables/overview now again active.

GMODTools is a Perl package that generates Fasta, GFF, DNA and other bulk genome annotation files from Chado databases.

GMOD Help Desk is Back

2007/10/01

After a several month hiatus, the GMOD Help Desk is back. Dave Clements has taken the role created by Brian Osborne earlier this year. Dave will work on the same sorts of things that Brian did: Maintaining and improving the GMOD web site and documentation, and supporting the GMOD user community. See GMOD Help Desk for more.

FlyBase Converts to Chado

2007/09/01

This summer, FlyBase finished its reimplementation using Chado, the modular GMOD database schema which FlyBase originated and continues to develop in collaboration with GMOD and several GMOD-affiliated database projects. The FlyBase implementation of Chado integrates over 100 years of Drosophila genetic and genomic research data. In addition to supporting the ongoing genome annotation and scientific literature curation for D. melanogaster, the main Drosophilid model organism, FlyBase is currently working to incorporate the new genome sequences, annotations, and cross-species comparative data for eleven additional Drosophila species into the single production instance of Chado.

PostgreSQL dumps of FlyBase-chado are available at ftp://ftp.flybase.net/releases/current/psql/



Pathway Tools 11.5 Released

2007/08/15

Version 11.5 of Pathway Tools has been released. Version 11.5 includes

  • Support for cellular regulation.
  • Electron transport information
  • Zooming in genome view
  • Stricter pruning to eliminate pathway predictions that are likely to be false-positive predictions

See the Pathway Tools release notes for details.

Pathway Tools is a comprehensive symbolic systems biology software package that supports several use cases in bioinformatics and systems biology.

ISMB/Bioinformatics Chado Paper

2007/07/13

The paper 'A Chado case study: an ontology-based modular schema for representing genome-associated biological information' by Chris Mungall, Dave Emmert, and The FlyBase Consortium, was presented at ISMB/ECCB 2007, and is now available in the journal Bioinformatics.

The paper describes the overall Chado philosophy and the 5 core Chado modules.


BioMart 0.6 Released

2007/06/15


Version 0.6 of the BioMart has been released. Version 0.6 includes support for a 1.5 DAS server, and improvements to MartView and MartBuilder. See BioMart News for more.

BioMart is a query oriented database management system for biological data.

GBrowse 1.68 Released

2007/04/17

Version 1.68 of GBrowse is a stability release which improves the documentation and installation process. It includes a new script called gbrowse_netinstall.pl, which will semi-automatically install GBrowse across the Internet on Windows, Mac OSX and Linux platforms.


News Archive

Earlier news items are available at SourceForge.

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