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.

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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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 others ...

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

January 2009 GMOD Meeting

{{#icon: SanDiegoConvention.gif|January in San Diego - think about that||}}

Note: Registration is now open for the January 2009 GMOD Meeting. 2008/11/20

The next GMOD community meeting will be held January 15-16, 2009 in sunny San Diego, immediately following the 2009 Plant and Animal Genome Conference (PAG 2009). Early details on the GMOD meeting are now available on the January 2009 GMOD Meeting page. We'll update that page as we have more. If you want to know what happens at a GMOD meeting see the notes from the July 2008 GMOD Meeting or any of the other previous meetings.

It's also worth noting that GMOD will again have a strong presence at the PAG 2009 meeting itself. If you are interested in attending PAG 2009, early registration closes November 1.

And, just in case it slipped your mind, it is still not too late to fill out the GMOD Community Survey and be entered to win GMOD gear!

Thanks,

Dave Clements
GMOD Help Desk

2008/10/23, updated 2008/11/20

2008 GMOD Community Survey

Thanks to everyone who participated in the 2008 GMOD Community Survey. Survey results are now available. The winners are Randall Svancara of Washington State University, Victor Jun M. Ulat of the International Rice Research Institute and Pinglei Zhou of FlyBase. 2008/11/20

Please take a few minutes to fill out the 2008 GMOD Community Survey and your name will be entered to win a free GMOD T-shirt or mug!

We are asking all GMOD users and developers to provide input on how GMOD is doing, and how it can be improved. All questions are optional, but please provide as much information as you can. The survey covers GMOD in general, and any GMOD components that you use (and it only asks about components that you indicate you use).

Three randomly selected survey participants will receive the GMOD T-shirt or mug of their choice. Names will be drawn from the first 100 responses we receive, so get your response in early.

Please contact the GMOD Help Desk at <help@gmod.org> if you have any questions.

Thank you,

The GMOD Team

2008/10/17, updated 2008/11/20

Get GMOD Gear!

{{#icon: GMODMug150x150.jpg|GMOD Mug||http://www.cafepress.com/GenericMOD/}}
{{#icon: TShirtThumb.jpg|GMOD T Shirt||http://www.cafepress.com/GenericMOD/}}


Tired of not having a cool T-shirt to wear at meetings?

Tired of drinking your coffee from a styrofoam cup?

Want to show off your affiliation with GMOD and promote it at the same time?

Be the first person in your lab, community, organization, building, campus or country to be seen with some GMOD gear!


Note: Want to win a shirt of mug for free? Then participate in the 2008 GMOD Community Survey. Three participants will be randomly selected to receive the GMOD item of their choice.

GMOD has a store at CafePress where you can buy GMOD gear. Currently there are two T-shirt styles and a coffee mug. (We also take requests if you want to see additional gear - for example, a long sleeved T shirt or even a GMOD Pet Bowl).

Please note:

  • GMOD gear is offered at cost. GMOD does not make any money from the sale of these items.
  • The GMOD News will return to its usual, somewhat more sedate, style with the next posting.


Dave Clements
GMOD Help Desk

2008/10/09

Updated 2008/10/17

InterMine Data Warehouse Workshop

{{#icon: InterMine.png|InterMine||http://www.biomed.cam.ac.uk/gradschool/current/courses/intermine.html}}

An InterMine Workshop is being offered at the University of Cambridge, 30th-31st October 2008. This workshop is intended for software developers aspiring to build a database and web interface with the InterMine software. An example of such a database is FlyMine but InterMine imposes no restriction on the sort of data it can be used to manage. A reasonable grasp of programming in either Java or PERL is essential. Some experience with relational database would also be very useful.

The workshop will be hands-on, taking you through all the steps of setting up an InterMine data warehouse. We will integrate some real data using existing InterMine parsers then extend the data model and write parsers in Java/Perl to include some custom data. This will include loading data from Chado. On the second day we will deploy and configure the web application, add a new widget for analysing lists and learn how to query with web services and the API. This should provide you with the necessary experience to set up your own InterMine system.

See the workshop announcement for details and registration information. The workshop is free to attend.

Richard Smith

2008/09/11

Pathway Tools Tutorial in London

A Pathway Tools and BioCyc tutorial well be held September 22-23, 2008 at Kings College London. This tutorial is kindly hosted by the Centre for Bioinformatics at King's College London (KCBI).

Day 1 is intended to teach users of Pathway Tools databases such as BioCyc, YeastCyc, MouseCyc, and AraCyc how to make the most of these resources.

Day 2 will address creation of new Pathway/Genome Databases (PGDBs) with Pathway Tools, and how to query PGDBs programmatically.

Pathway Tools includes a unique combination of bioinformatics algorithms including a predictor of metabolic pathways, an operon predictor, and an algorithm for predicting which genes in a genome code for missing enzymes in predicted metabolic pathways ("pathway holes"). It also contains tools for painting omics data onto genome-scale visualizations of metabolic networks and regulatory networks.

The tutorial is free of charge.

For more information see the tutorial page at SRI.

Peter Karp

2008/08/28

GBrowse 1.69 Released

I am very happy to announce that GBrowse 1.69 was released today. This release of GBrowse comes with a variety of user interface enhancements, performance improvements, bug fixes and a security fix. This release come courtesy of considerable work from the GBrowse developers, most notably Lincoln Stein, the lead developer and Sheldon McKay who did much of the JavaScript work. The release can be obtained from SourceForge, or, you can use the GBrowse net installer.

More information about GBrowse, including platform specific installation instructions, can be found on the GBrowse page.

You can try out the new version on the GMOD website as well.

Finally, here is a list of the major changes since the 1.68 release:

  • Draggable tracks; use "drag and drop" option to activate.
  • Collapsible tracks - comes for free with "drag and drop"
  • Popup balloons w/ Ajax content; use "balloon tips" option to activate.
  • Caching of individual tracks for better performance; use "cache time" option to control.
  • Changed licensing model to dual license under Perl Artistic 2.0 and GPL.
  • Fix duplicated tracks during dragging.
  • Features with same name are now found, not merged.
  • Galaxy support, courtesy Greg Von Kuster
  • Can change fill and outline color of selected regions on overview & regionview.
  • Various bugs squashed.
  • When updating settings or searching, the browser scrolls to the top of the overview section as a convenience.
  • Fixed cross-site scripting vulnerability.

Thank you and happy GBrowsing,

Scott Cain

GMOD Project Coordinator

2008/08/22

Web Site Changes

The GMOD web site doesn't look very different, but it was updated on Monday, August 11,2008. Here's what changed:

  • The site was upgraded from Mediawiki 1.9.3 to MediaWiki 1.12.0.
  • Replaced the default MediaWiki site search mechanism with Google.
  • URLs have been rationalized. Previously, there were many different URL to get to each wiki page. Now all URLs are redirected to http://gmod.org/wiki/Page_Name

We have done our best to make this upgrade as smooth and transparent as possible. However, if you do notice anything unusual, please notify the GMOD Help Desk.

Thanks,

Dave Clements
GMOD Help Desk

2008/08/11

Website Maintenance: Aug 11 2008

WorkInProgressTools.gif  The GMOD website will be down for maintenance on Monday, August 11, 2008 starting at 8pm Eastern / 5pm Pacific (both US). We expect it to be down for about an hour. We apologize for any inconvenience this may cause you.

Please let us know if you have any questions.

Dave Clements
GMOD Help Desk

2008/08/08

Upcoming Pathway Tools Tutorial

SRI's Bioinformatics Research Group will hold a Pathway Tools tutorial session from September 2-5, 2008, at SRI International in Menlo Park, CA. Each day will combine lectures with lab sessions in which students apply the software to a sample genome. No programming experience is required.

Pathway Tools includes a unique combination of bioinformatics algorithms including a predictor of metabolic pathways, an operon predictor, and an algorithm for predicting which genes in a genome code for missing enzymes in predicted metabolic pathways ("pathway holes").

Please see the Pathway Tools Tutorial page for a detailed schedule, registration information, and other details.

Peter Karp
2008/08/07

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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.

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