Difference between revisions of "GMOD News"

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== Apollo 1.11 Released ==
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== Apollo 1.11.0 Released ==
  
 
A new version of [[Apollo]] has been released.  Highlights for this release include:
 
A new version of [[Apollo]] has been released.  Highlights for this release include:

Revision as of 18:40, 5 June 2009

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.

This page 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.

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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

New Ergatis Release

A new version of Ergatis, a web-based utility for creating, running and reusing computational analysis pipelines, is now available for download.

This version includes

  • Interface improvements
  • New components, notably:
    • RNAmmer - RNA identification on genomic sequence
    • p_func - Derives gene function assertions based on tiers of provided evidence, such as BLAST, HMM, etc..
    • 454_mplex_seq_bin_trim - A binning and trimming script for multiplex 454 sequence data
    • phylip_dnadist - A wrapper for a parallelized version of PHYLIP's dnadist
  • New pipeline templates
  • Bug fixes

A new version of the automated Prokaryotic Annotation Pipeline is also included, as well as a pipeline creation tutorial. For a full list of the changes, see the CHANGELOG file.

As always, installation instructions can be found within each package and in web form.

2009/01/27

Job Openings at Georgetown University

Two Positions Immediately Available at Georgetown University in Washington, DC

Bioinformatics Engineer

This position is part of the USDA-funded Hymenoptera Genome Database project, which includes BeeBase (honey bee genome) and NasoniaBase (wasp genome). This person will implement GMOD software and develop new query interfaces; develop scripts for automated data retrieval and database loading; develop computational pipelines for updating homology, functional annotation data and GBrowse tracks. Requires MS degree in bioinformatics or related field, and demonstration of programming experience. Experience with Perl, HTML, CGI, Java, MySQL and PostgreSQL is preferred.

Bioinformatics Systems Analyst

Duties include system administration, bioinformatics database maintenance, system backup management, problem diagnosis, and creation of system documentation. Must have experience in Linux system administration Perl, Java, Apache PostgreSQL, and MySQL. Experience with GMOD and BioPerl is highly desired.

Contact Chris Elsik: chris.elsik@gmail.com

2009/01/15

BioGraphics now housed at gmod.org

The Bio::Graphics modules which have long been a core part of BioPerl have been separated out and the code base is now housed in the cvs repository at SourceForge. This action has been taken to give the authors more flexibility over releases, particularly so that frequent updates can occur as needed around new GBrowse releases. Releases of Bio::Graphics are already on CPAN, so it can be installed in the cpan shell. Additionally, the gbrowse_netinstall.pl script for installing GBrowse automatically has been updated to install Bio::Graphics before installing GBrowse.

2009/1/6

GMOD at PAG 2009

{{#icon: Paglogo.gif|GMOD @ PAG||PAG 2009}}

GMOD will once again have a strong presence at the Plant and Animal Genome Conference (PAG 2009). There will be over 35 talks, workshops, demonstrations and posters about GMOD Components and projects that use them. See the PAG 2009 page for a printable listing of GMOD related events.

The January 2009 GMOD Meeting is immediately after PAG, and many GMOD developers and users will likely attend both meetings.

If you haven't registered yet for either or the GMOD meeting, you are encouraged to do so.

2009/01/03

GMOD Meeting Registration Open

January in San Diego - think about that January 2009 GMOD Meeting}}
January 2009 GMOD Meeting

Registration is now open for the January 2009 GMOD Meeting. The meeting will be held January 15-16, 2009 in sunny San Diego, immediately following the 2009 Plant and Animal Genome Conference (PAG 2009).

Registration is free.

If you haven't attended a GMOD Meeting before then you are encouraged to find out why the overwhelming majority of past attendees have found meetings to be useful and well organized. See the July 2008 GMOD Meeting report (or any of the other previous report) for an idea of what goes on at GMOD Meetings.

Finally, if you have items that you would like on the agenda, please add them to the meeting page.

As always, please let the GMOD Help Desk know if you have any questions.

Thanks,

Dave Clements
GMOD Help Desk

2008/11/20

GMOD Community Survey Results

The results of the 2008 GMOD Community Survey are now available online. The survey was taken by 89 respondents. The survey includes questions on:

  • What GMOD Components they use
  • Feedback on the specific components they use.
  • The servers that GMOD runs on.
  • GMOD Meetings
  • GMOD Project overall (What is being done well, what needs improvement, what should be our focus for the next 12-18 months)
  • GMOD Help Desk
  • GMOD course in Europe and Asia/Pacific
  • Organisms studied
  • Biological areas of interest

Your responses will be used to improve GMOD and guide its future direction.

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

Please let the GMOD Help Desk know if you have any questions about the survey.

Thanks,

Dave C
GMOD Help Desk

2008/11/20 <endFeed />

News Archives

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

Adding a News Item

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.)

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.