GMOD News

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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. See Adding a News Item for how to do this.

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News Items

Want to add your news item here? See Adding a News Item below for how to do just that.

<startFeed />

Bio::Chado::Schema 0.03 Released

The first official release of Schema is now on the CPAN. This project establishes a standard set of base modules for building Chado middleware in Perl. The project is looking for development help, and discussion is on the GMOD Schema mailing list.

--RobertBuels 22:10, 29 August 2009 (UTC)

2009/08/27

InterMine 0.91 Released

InterMine

We've released InterMine 0.91 and there is a new subversion branch and tar.gz for download. The main changes are fixes to some QueryBuilder features, occasional export issues and improved password security. There is a new TreeFam parser and an improvement to ontology querying.

This update shouldn't require any changes to Mines and sources you have created. See details on upgrading and the release notes.

Please let us know if you have any bug reports or feature requests.

The InterMine team

2009/08/27

CVS to SVN Conversion: Sept 15

CVS|70|CVS to Subversion Conversion}} Subversion CVS to Subversion Conversion}}

GMOD's CVS source code repository will be converted to Subversion (SVN) on September 15, 2009. Rob Buels of Cornell / SGN has generously offered to to do this. Notes on the conversion are described on the CVS to Subversion Conversion page. The discussion leading up to this decision on the GMOD Developers mailing list.

If you are not a GMOD developer then this will, at most, change how you get pre-release copies of GMOD components. In the future you will do SVN checkouts instead of CVS checkouts. The doc on this web site will be updated to describe how to do this.

If you are a GMOD developer and your project is in GMOD's CVS repository then this move will significantly affect you.

See SourceForge for a complete list of projects in GMOD CVS. This list is reproduced on the CVS to Subversion Conversion page. Between now and September 15, we will contact project developers to confirm what projects are still active. All projects will be moved to SVN, but any projects that are no longer active will be placed in a separate archive directory. This will significantly clean up the repository. See the CVS to Subversion Conversion page for the current status of each project.

Rob has created a preview version of the repository. Feel free to poke around. This version does not have any projects archived.

Rob will move the projects on September 15. Before then everyone with uncommitted code changes should commit them to CVS. After September 15, all CVS checkouts you have should be removed and new checkouts made with SVN. We'll provide doc on how to do this. We will send out exact details on the move a few days before it happens.


Please let Rob and Dave know if you have any questions. We'll send out a reminder and additional info a few days before the conversion.

Thanks,

Dave Clements and Rob Buels

2009/08/26

GBrowse 1.70 Released

Hello,

I am pleased to announce the official release of GBrowse 1.70. This is a bug fix release for GBrowse 1.69. It introduces no new functionality to the GBrowse portion of the application, however, GBrowse_syn is considerably improved along with documentation and a tutorial.

There will likely be one more release in the GBrowse 1 development path, which will introduce improved support for circular genomes. After that, development on this path will end and further development will focus on GBrowse 2.

GBrowse can be installed with the GBrowse netinstaller.

GBrowse 1.70 can be downloaded directly from SourceForge.

A big thanks to Lincoln Stein, the lead developer of GBrowse, Sheldon McKay, the developer of GBrowse_syn, and all of the GBrowse users who debug and provide help on the GBrowse mailing list.

Changes from 1.69 to 1.70:

  • Bug fixes for the Chado adapter, including improving wildcard searching and fixing a bug that caused ALL features on a reference sequence to be returned when the segment was at the beginning of the reference sequence.
  • Fixed Galaxy support bug which caused prevented features from multiple tracks being selected.
  • Fixed problem with feature highlighting which caused highlighting to get "stuck"on beige.
  • Removed annoying debugging statements from log files
  • Fixed character encoding issues for onClick popup balloons
  • Killed annoying "missing path" warning on windows systems
  • Fixed issue in which the selected region shown in the overview is offset from true region.
  • Silenced log file warnings when inkscape isn't present.
  • Added "merge searches" option to turn merging of similarly-named features on and off.
  • Moved Bio::DB::Das::Chado and Bio::DB::BioSQL to their own packages and out of the GBrowse distribution so they can be updated independently via CPAN
  • Fixed encoding of version number at the bottom of the page.
  • Made the DAS script compatible with DAS Registry

Scott

2009/08/24

Lepidoptera Bioinformatics Workshop

International Workshop on Molecular Biology and Genetics of Lepidoptera

A session on data analysis, mining, general bioinformatics support, and related topics will be held on Friday, August 28th 2009, at the International Workshop on Molecular Biology and Genetics of Lepidoptera in Crete. The aim is to find solutions to common problems of annotation, curation and comparative analysis of the growing body of transcript and genomic sequences for lepidopteran species. Several databases, including InsectaCentral and LepidoDB, both of which use GMOD Components, will be discussed in the workshop.

The session is held during the last conference day and is one hour long; we encourage Crete participants to talk to us during the week and point out related problems you are facing in your own work. We will then produce a list to be discussed during the session and focus on soliciting ideas on how to organize collaborative and centralized efforts to everyone's benefit. We would especially like to identify potential funding sources, groups willing to help write consultation papers and grant proposals and individuals willing to contribute to realistic solutions.

We would like to encourage those of you who are not planning to attend the Crete workshop to contact us with your thoughts and ideas on these and related subjects.

Marian Goldsmith, Alexie Papanicolaou, and Fabrice Legeai.

2009/08/18

Ant Genomics Assembly and Database Sysadmin position

Fourmidable opening

The Swiss Institute of Bioinformatics and the Keller lab in Lausanne have an opening for a full-time bioinformatician. In brief, this position will focus on the assembly and annotation of genomic sequence from ants, as well as sharing the results with molecular myrmecologists via a GMOD database.

Closing date: 15 September 2009

See the official ad for full details and application procedure

Informal enquiries to yannick.wurm \at\ unil.ch or laurent.falquet \at\ isb-sib.ch

2009/08/15

FlyBase Sys Admin/Developer position

FlyBase Opening

The Cambridge (UK) division of FlyBase currently seeks a Systems Administrator/Software Developer, working either full or part-time to support its team of genetic literature curators.

The core tasks of this role include systems administration and the maintenance of Perl scripts and files required by the curators in their work. These tasks will occupy approximately 50% of a full-time position, and we are happy to consider applicants who only wish to work part-time (50%) to perform these essential tasks. However, we would like to enhance the current scripts/files and develop additional software to aid curators, and the remaining 50% of the full-time position would be spent on these areas.

Closing date: 24 August 2009.

See the official advert for full details and application procedure.

Informal enquiries to Steven Marygold (sjm41@gen.cam.ac.uk).

2009/07/31

Insect Pest Workshop, 16-17 Nov

{{#icon: InformationSystemsForInsectPests.gif|Information Systems for Insect Pests|400|http://colloque.inra.fr/isyip}}

1st International Workshop
16-17th November 2009
INRIA Rennes-Bretagne-Atlantique

Given the development of cheaper high throughput sequencing technologies, it is easy to predict that in the very near future, new genomes of insects relevant to agriculture will be available. This opens several other challenges such as the bioinformatics treatment of the raw data (handling of billions of sequences, assembly of short reads…) and the development of databases opened to biologists for an easy, friendly and efficient extraction of information. With access to several insect species genomes, one will not only work on their favourite insect, but will take advantage of the increasing knowledge from genomic comparison analyses. This compels the community to develop standards for different tasks towards the exploitation of genome sequences: annotation, cross-species comparisons, interoperability between databases, ... Several tools and databases already exist and are used for genome browsing and annotation.

In that context, the purpose of this workshop will be:

  • To exchange within an international panel of attendants our views on the present and future of insect genome databases
  • To settle an international community that will form a functional network for insect genome and database development
  • To discuss strategies to meet the demand of increasing number of new insect genomes
  • To prepare a new road map for integration of genomes databases for insects relevant to agriculture

The perimeter of that discussion encompasses insect species related to agriculture, either harmful (pests) or beneficial as controllers of pest populations or as producers of plant by-products (such as silk, honey, ...).

Registration for the meeting is free and has to be done online on this website and will be limited to 40 participants. A statement of interest is needed. A 10 minute presentation may be asked.

2009/07/20

August 2009 GMOD Meeting

August 2009 GMOD Meeting


Register for the August 2009 GMOD Meeting


The next GMOD meeting will be held 6-7 August, at the University of Oxford, in Oxford, United Kingdom. Registration is now open. Space is available on a first come, first served basis and there is room for 55 attendees. The meeting cost is £50.

As with previous GMOD meetings, the meeting will have a mixture of project talks, component talks, and user talks. The agenda is driven by attendee suggestions, and you are encouraged to add your suggestions now. For examples of what happens at a GMOD meeting, see the writeups of the January 2009, July 2008, or any other previous meeting. GMOD meetings are an excellent way to meet GMOD developers and users and to learn (and affect) what's coming in the project.

Details on transportation, suggested lodging, and other logistics are on the August 2009 GMOD Meeting page.

Please join us in Oxford this August,

Dave Clements
GMOD Help Desk

2009/07/01

Note: Unless you have applied to and been admitted to the 2009 GMOD Summer School - Europe, don't you dare register for it. The registration web site will let you do this, but bureaucratic hellishness will ensue.

Join the Int'l Society for Biocuration

International Society for Biocuration

The International Society for Biocuration (ISB) is now accepting member registrations. I strongly encourage GMOD community members to think about joining ISB. GMOD and ISB have many shared and complementary interests.

Membership rates start at less than US$20 for students to a little over US$100 for principal investigators from industry.

Please consider this investment,

Dave Clements
GMOD Help Desk

2009/06/25

Apollo 1.11.0 Released

A new version of Apollo has been released. Highlights for this release include:

  • The "Sequence Aligner" ("Exon Detail Editor" with alignment viewing) is now public
  • Brought back the "Types panel" which works in conjunction with the the "Preferences editor"
  • Various bug fixes

As always, you can download the current version at:

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

Ed Lee

2009/06/05

NextGen Sequence in GBrowse

Next Generation Genome Analysis in Non-Model Organisms--An American Genetic Association Special Event

There will be a talk on visualizing next generation sequence data in GBrowse at Next Generation Genome Analysis in Non-Model Organisms, an American Genetic Association Special Event held June 11-13, 2009 at the University of Connecticut. The talk will demonstrate how GBrowse can visualize both individual reads and summary and derived data. This talk will become a wiki page after the meeting.

June will be a busy month for GMOD outreach. If you can't make it to this meeting, there will also be GMOD workshops at SMBE and the Arthropod Genomics Symposium.

Dave Clements
GMOD Help Desk

2009/05/19

WebGBrowse Has Arrived

WebGBrowse - A Web Server for GBrowse Configuration Made Easy
WebGBrowse at the Center for Genomics and Bioinformatics http://webgbrowse.cgb.indiana.edu/}}

WebGBrowse is a web site that guides users through the process of creating a GBrowse configuration file and then shows them how their data renders with that configuration. Users can configure GBrowse, either from scratch, or by uploading a preexisting GBrowse configuration file. Tracks are defined using a graphical user interface where users first select the glyph to use (over 40 glyphs are currently supported), and are then prompted for that glyph's settings. Data is provided by uploading a GFF3 file.

WebGBrowse has an extensive tutorial and FAQ, and was just published in Bioinformatics. WebGBrowse is open source and can also be installed locally.

WebGBrowse was created by Ram Podicheti, Rajesh Gollapudi, and Qunfeng Dong, all of the The Center for Genomics and Bioinformatics (CGB) at Indiana University - Bloomington. WebGBrowse was first presented by Ram Podicheti at the January 2009 GMOD Meeting.

WebGBrowse is an excellent way to get started with GBrowse, and to learn what glyphs are available, and what options each glyph supports. Please contact the CGB if you have any questions.

Dave Clements
GMOD Help Desk

2009/04/22

GMOD Workshops at SMBE, AGS

There will be GMOD workshops at two major conferences in June 2009:

SMBE 2009|120|http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27}}
Annual Meeting of the Society for Molecular Biology and Evolution (SMBE 2009)
June 3-7, 2009
Iowa City, Iowa
Database Tools for Evolutionary Genomics: An introduction to GMOD software for managing, annotating and visualizing genomic data

Saturday, June 6, 2:30-5:00pm
This workshop will cover some of the most widely used GMOD software components, including the Chado database, the GBrowse genome browser, the CMap comparative map browser, and the Apollo genome curation tool. The workshop will also cover, in some depth, the GBrowse_syn comparative genomics viewer, and the MAKER genome annotation pipeline for eukaryotes. Speakers (Ben Faga, Sheldon McKay, Mark Yandell, and Dave Clements) will address both existing functionality and ongoing developments specifically targeted at better supporting evolutionary data and research. No knowledge of programming is necessary.

Arthropod Genomics Symposium|100|http://www.k-state.edu/agc/symp2009/seminar.html}}
3rd Annual Arthropod Genomics Symposium
June 11 - 14, 2009
Kansas City, Missouri
Chado Databases and Integration with GMOD Tools

Pre-Symposium Workshop - Thursday, June 11, 4:30-6:30 p.m.
Scott Cain, Ontario Institute for Cancer Research, will provide training on Chado database design, data loading and exporting, and integration with other GMOD tools such as Apollo and GBrowse. Particular emphasis will be given to comparative genomics tools. There is no cost to attend this optional workshop, but registration is requested.

Please let Dave (SMBE) or Scott (AGS) know if you have any questions about the workshops.

Thanks,

Dave Clements
GMOD Help Desk

2009/04/09

Pathway Tools Workshop in August

Registration is now open for this workshop. 2009/04/24


Pathway Tools Workshop

There will be a Pathway Tools Workshop, August 19-28, 2009 at SRI International. This two-part workshop covers Pathway Tools and the BioCyc Database Collection.

Part 1: Tutorial, August 19-21

This introductory tutorial will educate the new user on aspects of Pathway Tools including basic use of the Pathway/Genome Navigator, Editors, and PathoLogic. Students can bring a genome and leave with a draft Pathway/Genome Database.

Tutorial space is limited.

Part 2: Workshop August 24-28

The workshop will combine formal presentations by groups outside SRI International (invited speakers and speakers selected through an abstract-submission process), tutorials by SRI International staff, and a hackathon. Suggested topics include but are not limited to:

  • Share expertise on how to develop new organism-specific databases with Pathway Tools
  • Present new scientific results achieved with Pathway Tools and BioCyc
  • Share experiences on how to make the most of Pathway Tools
  • Presentations by users on extensions they have developed to Pathway Tools
  • Presentations by SRI International on recent and planned developments to the software, and on software APIs and the database schema, to educate users on how to compute with PGDBs
  • Discussions of requested future enhancements to Pathway Tools and BioCyc
  • Ideas for other software tools to integrate with Pathway Tools
  • Group development of new Pathway Tools enhancements

Should you wish to make a presentation at the meeting, please submit a proposed title and abstract to ptools-info@ai.sri.com.

Please check the following website for updates.

2009/04/07, updated 2009/04/24

2009 GMOD Summer Schools

Template:2009SummerSchoolApplicationBlurb

We are now accepting applications for the 2009 GMOD Summer Schools. GMOD Summer Schools are hands-on multi-day courses aimed at teaching new GMOD users how to get up and running with GMOD. Summer schools introduce participants to the GMOD project and focus on installation, configuration and integration of popular GMOD Components. In 2009 we are proud to offer two schools, one on each side of the Atlantic:

{{#icon: 2009SummerSchoolAmericas170.png|Americas 2009 GMOD Summer School - Americas}} Americas
16-19 July
NESCent
Durham NC

The courses include sessions on these popular GMOD components:

{{#icon: GMOD2009Europe170.png|Europe 2009 GMOD Summer School - Europe}} Europe
3-6 August
Oxford University
Oxford UK

The European summer school is part of GMOD Europe 2009, a week long event which also includes the August 2009 GMOD Meeting. This is the first time a GMOD Summer School or GMOD meeting will be held outside of North America.

Thanks,

Dave Clements
GMOD Help Desk

2009/03/15, updated 2009/04/06, 2008/04/27

Apollo 1.10 Released

A new version of Apollo has been released. Highlights for this release include:

  • Support for remote NCBI BLAST (blastn, blastx, tblastx)
  • Support for remote NCBI Primer BLAST (primer identification tool)
  • Numerous bug fixes

The nice thing about the remote analysis support is that now users do not have to install those tools locally (which can be a pain) and don't need to download the very large NCBI databases. These requests are handled in the background, so you can keep on working as usual and once the analysis is complete, the results will be automatically incorporated into the results track.

We're very interested in getting feedback from users who may use the primer identification functionality. If you could provide information on how you'd use such a tool and possibly what kind of filtering criteria you might need, it would be great so that we may incorporate these changes in future releases.

As always, you can download the current version at:

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

Ed Lee

2009/03/02

Biocuration Conference, 16-19 April

3rd International Biocuration Conference

The 3rd International Biocuration Conference will be held in Berlin, Germany, April 16-19, 2009. This conference is a forum for curators and developers of biological databases to discuss their work, promote collaboration, and foster a sense of community in this active and growing area of research. I don't think GMOD community members will find a higher concentration of people working on biological databases at any other conference. Anyone interested in the methods and tools employed in biocuration is encouraged to attend.

Early registration ends in two days (on 20 February, 2009).

Dave Clements
GMOD Help Desk

2009/02/18

Biomedical Ontology Conference, July

The International Conference on Biomedical Ontologies (ICBO), will be held in Buffalo, New York from July 23-26, 2009. Ontologies are widely used in GMOD for annotation, controlled vocabularies, reasoning, and data sharing. Paper submissions are due March 1, and posters are due April 10. ICBO will be held in conjunction with four days of tutorials and classes from July 20-23, 2009.

See the ICBO conference web site for details.

Dave Clements
GMOD Help Desk

2009/02/17

January 2009 GMOD Meeting Report

January 2009 GMOD Meeting

The January 2009 GMOD Meeting was held January 15-16, 2009 in San Diego, immediately following the Plant and Animal Genome (PAG) conference. The meeting was attended by over 50 people representing about 35 different organizations. The meeting report and links to presentations are now available on the January 2009 GMOD Meeting page. There were 19 presentations by GMOD users and developers.

Some highlights:

Plus 14 other excellent user and developer presentations.

Please take a look at the meeting report for an update on what's going on in the GMOD community.

We hope to see you at the upcoming August 2009 GMOD Meeting, in Oxford UK (and our first meeting in Europe).

Dave Clements
GMOD Help Desk

2009/02/09

GBrowse User Tutorial

OpenHelix

A comprehensive GBrowse User Tutorial was released by OpenHelix this week. The narrated tutorial covers:

  • the basic layout and search methods in GBrowse
  • how to access detailed annotation data tied to genomic sequences
  • how to select and customize annotations using tracks
  • how to upload and incorporate your own data or other external data sources
  • take a tour of different GBrowse installations at model organism databases

The tutorial also includes PowerPoint slides, handouts, and exercises that can be used for reference or for training others. The narration is reproduced in the notes area on the slides.

The GBrowse User Tutorial is part of a set of model organism resource tutorials funded in a large part by NHGRI. The set includes tutorials on how to navigate and use RGD, MGI, and WormBase, and in the future for ZFIN, FlyBase, and SGD (all of which are GMOD users and/or contributors).

This tutorial focuses on using GBrowse and complements the GBrowse Administration Tutorial. It is an excellent resource for any organization that wants to help its users use GBrowse better.

Dave Clements

GMOD Help Desk

2009/02/05

Opening at Dow AgroSciences

Dow AgroSciences

Dow AgroSciences has a short term contract position available for someone with GMOD experience. The candidate proposed here will be responsible for three main tasks and several secondary ones:

  1. Install the open source software components for the Chado database, data loaders, and genome browser.
  2. Deploy the GBrowse genome browser in a centralized location in our intranet, which can be used by Dow AgroSciences scientists across functions.
  3. Test the system by performing preprocess (e.g annotate, perform alignments) and upload whole-genome data from Arabidopsis.
  4. Link the genome browser to Dow AgroSciences major internal databases, such as Variety, markerDB, QTL locate, and microarray database.
  5. Provide integration tests to ensure the transparency of the data among the different systems.
  6. Present to other Dow AgroSciences scientists to raise awareness of capability.
  7. Complete written documentation of project development, implementation, and continued maintenance.

Interested candidates please send a resume to Mindi Dippold at mdippold@dow.com.

2009/02/03

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Schema release

News Archives

Items more than 6 months old are available in the GMOD News Archives.

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Facts about "GMOD News"RDF feed
BioSchema +
Category:added news item for first official BioSchema release +
ChadoSchema + and Schema release +