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.

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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

July 2008 GMOD Meeting Report

The July 2008 GMOD Meeting was held on July 16-17, 2008 at the University of Toronto. The meeting was attended by over 30 people representing more than 20 different organizations. The meeting report and links to presentations are now available on the July 2008 GMOD Meeting page. Several GMOD Components were covered, including Chado, the Community Annotation System, and Table Editor (plus several more). We also heard reports from many GMOD users, including SGN, WikiMods, and Xenbase (plus several more).

Dave Clements
GMOD Help Desk

2008/07/28

GMOD2008Discussion.JPG

cas-utils-0.1 Released

In the wake of the GMOD Summer School a little over a week ago, I decided that I should create a release that has the tools that I used to tie together GBrowse, Apollo and Chado. It can be downloaded at:

http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=284978

These utilities consist of 4 main tools:

  • A CGI for selecting a region in GBrowse, extracting the data for

that region from Apollo and creating an XML file and a jnlp (webstart) file for Apollo.

  • A CGI for accepting uploads of edited XML files to either be

immediately loaded into Chado or to be held for validation.

  • A configuration perl module to make modifying the CGI's behavior easy.
  • A Module::Build based installer that queries the user for needed setup data.

While this release of cas-utils assumes that the port for connecting to the database is blocked for outside users, future releases of these tools could be configured to assume the reverse. Another item planned for a future release is tools for integrating Chado with a MediaWiki site for more text-based annotation. Of course, because of the nature of these tools, it is assumed that several things are already in place and working:

  • Chado with computational analysis and annotation data already loaded.
  • GBrowse (either 1.69 (to be released soon) or from the stable cvs branch).
  • Apollo, both as an installed application (like in /usr/bin), and as

source that has been built into a webstart application and installed for the web server to use.

If you have questions about either cas-utils or any of the prerequisites, please send questions to the most appropriate mailing list:

  • Chado: gmod-schema@lists.sourceforge.net
  • GBrowse: gmod-gbrowse@lists.sourceforge.net
  • Apollo: apollo@fruitfly.org

I've only tested this application on CentOS 4.6 and Ubuntu 8.04, though there is no reason to believe that this wouldn't work on any Linux and probably on MacOS as well. I am considerably less sure that this would work out of the box on Windows, but support for that could probably be in a future release if the demand is there.

Thanks and happy curating! Scott Cain

07/22/2008


Job Openings with GnpAnnot

GnpAnnot, an INRA project, is offering 2 positions for programmers to implement and/or improve GMOD interfaces for Chado databases.


1st Position: IRISA

IRISALogo.jpg 18 month position for a Java programmer

Environment:

The job opportunity will be located at IRISA, in Rennes France.

Description:

The engineer will write specifications, design, develop, test and deploy diverse applications and web interfaces dedicated to genomics analyses and comparative genomics.

The applications will use a 3-tiered architecture based on J2EE technology.

Skills:

  • experience in Java development
  • good knowledge of J2EE technologies (Hibernate, Spring, Struts et JSP) - experience with BioPerl or Perl objects

The job should start on the first of September 2008

Contact: Fabrice Legeai fabrice.legeai@rennes.inra.fr


2nd Position: INRA-URGI

Urgi.png

One year object-oriented programmer (Java, Perl Object)

Environment:

The job opportunity will be located at INRA-URGI in Versailles (Near Paris), France.

Description:

The applicant will write specifications and develop/improve, databases and interfaces from the GMOD project (Chado, Apollo, GBrowse).

Skills

  • Good experience in Java and Perl programming
  • Knowledge of GMOD tools will be appreciated

Answers expected before September the 5th. The job should start on the 1st of October.

Contacts:


Stéphanie Sidibe-Bocs, the PI of GnpAnnot, will be at BOSC and ISMB this week and is available to discuss the project and these openings. You can e-mail Stéphanie at stephanie.sidibe-bocs@cirad.fr, or just introduce yourself when you see her.

2008/07/17

GMOD @ ISMB and BOSC

GMOD has a strong presence at the ISMB 2008 and BOSC 2008 meetings, getting under way this week in Toronto. There are over a dozen talks and posters at the BOSC and ISMB conferences about GMOD Components, or that feature research that using GMOD components. See ISMB 2008 for a complete list and for a flier we'll be distributing at the conference.

BoscPear.png

ISMB2008Skyline.png

Dave Clements
GMOD Help Desk

2008/07/16

2008 GMOD Summer School Report

SummerSchoolSmall.png

Or, what 29 people did with their summer vacation.

The first annual GMOD Summer Schoolsummer was held July 11-13, 2008 at NESCent in Durham, NC. It was attended by 25 students and 4 instructors from 19 different states plus France and The Netherlands. Researchers came from the arthropod, vertebrate, prokaryote, plant, fungus, and virus communities. The questions and discussions were lively and participants were fully involved in the hands-on class. Students started the class with a minimal install of Linux and finished 2 1/2 (sometimes bumpy) days later with a system that was running Chado, GBrowse, Apollo, and CMap.

I would like to thank the participants, the instructors (Scott, Ben and Ed) and the folks at NESCent for getting the GMOD Summer School off to a fabulous start.

We will be having a Second Annual Summer School in 2009 at NESCent. We will use what we learned at this year's course to make next year's even better. Watch this space for information on that course as next summer gets closer.

There has also been some discussion of holding the course in Europe. If you would be interested in attending a several day course on GMOD in Europe please send me an e-mail. If we get enough interest, we might try and pull it off.

Thanks,

Dave Clements
GMOD Help Desk

2008/07/15

CMap 1.01 Released

Version 1.01 of CMap has been released.

I'm quite excited about using GFF3 for data import/export which is possible with this release.

You can get the new version from SourceForge, http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=55129

Highlights of this release are:

  • Added a GFF3 parser and producer for easier and more complete data import and export (requires latest version of bioperl-live to import GFF).
  • Added a module to serve data to CMap3D, a 3D viewer being developed by Chris Duran and Dave Edwards.

If you have any questions, please let me know.

This is only an incremental update. For anyone who installed version 1.0, simply download the new release and run

perl Build.PL; ./Build; sudo ./Build install

No updates to the database or config files are needed.

If you are updating from an older version, see the documentation in the upgrade/ directory included in the package.

Ben

2008/07/01

GMOD Meeting Registration Open

July2008LogoSmaller.png Registration is now open for the July 2008 GMOD Meeting. The meeting is scheduled for July 16-17, 2008 at the University of Toronto, immediately before ISMB 2008 (also in Toronto), and just a few days after the 2008 GMOD Summer School.

Watch the July 2008 GMOD Meeting page for more information as the meeting draws nearer. If you have any questions or requests about the July 2008 meeting, please contact the GMOD Help Desk at help@gmod.org. See the notes from previous meetings for an idea of what is discussed at GMOD meetings.

2008/06/09

MAKER Joins GMOD

MAKER is a portable and easy to configure genome annotation pipeline that has just become a part of GMOD. It's purpose is to allow smaller eukaryotic genome projects to annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on subsequent runs. MAKER's inputs are minimal. It outputs are in GFF3 or FASTA format, and can be directly loaded into Chado, GBrowse, and Apollo.

MAKER was created and is maintained by the Mark Yandell Lab at the University of Utah.

See MAKER for more on how you can use it to automatically annotate your genomic data.

2008/05/16

Apollo 1.9 Released

Apollo 1.9.0 has been released. This release includes a number of bug fixes and some additions. The biggest new feature for this release is the Preferences Editor, which gives a graphical way to edit style/tiers files. This is aimed towards the non-power users and as such, it only supports a small subset (the ones we figured would be most useful) of the many options for those files. Power users might still want to manually edit the style/tiers files if they want to change something not supported through the GUI. Note that with this addition, the old Types Panel and Style Editor (which was basically just a text editor) have been retired.

You can get the new release of Apollo at:

http://apollo.berkeleybop.org

Ed Lee

2008/05/12

GMOD Summer School Update

SummerSchoolSmall.png July 11-13, 2008
National Evolutionary Synthesis Center (NESCent)
Durham, North Carolina, USA

GMOD Summer School is a 2 1/2 day hands-on workshop aimed at teaching new GMOD users how to get up and running with popular GMOD components. The summer school was announced on March 7, 2008.

The GMOD Summer School is now full. However, the waiting list is still small and if you are interested then you are encouraged to submit an application.

If you have already applied for the GMOD Summer School you should have received an e-mail from the Help Desk informing you of your admission status.

2008/04/24, last updated 2008/05/16

Apollo 1.8 Released

I'm excited to let everyone know that we're releasing a new version of Apollo (1.8.0) today. There are many additions/bug fixes with this release. Most notably, due to popular demand, an 'undo' system. You can now access the 'undo' function through 'Edit→Undo' (or ctrl-u). For more information on the changes, check out the release doc.

On another note, the official Apollo URL has changed. It's no longer:

http://www.fruitfly.org/annot/apollo

but rather:

http://apollo.berkeleybop.org

Please update your bookmarks accordingly.

Ed Lee

2008/04/10

Sea Urchin Genome Database

SpBaseLogo.png Today, Tuesday April 4th, the Sea Urchin Genome Database went public. Based on the GMOD tools and applications the site organizes and displays the genome sequence and annotations produced by the Baylor College of Medicine Human Genome Sequencing Center and the sea urchin research community. This site housed at the Center for Computational Regulatory Genomics, the Beckman Institute at California Institute of Technology plans to enrich and extend the sea urchin sequence and annotations.

Visit us at SpBase.

Andy Cameron

2008/04/08


Chado Doc Reorganization

Chado is the database schema of GMOD and it has quite a bit of documentation in this web site. However, this documentation could be better organized and integrated. We are launching the Chado Documentation Reorganization effort to do just that.

During this effort the existing Chado documentation may be unstable. We will do our best to make this reorganization be as painless as possible.

The Chado Documentation Reorganization page summarizes our existing documentation and then proposes a plan for restructuring it. If you have any suggestions or comments on this then please send us your feedback.

Thanks,

Dave Clements
GMOD Help Desk

2008/04/04

iPlant Collaborative Job Openings

Cold Spring Harbor Laboratory is seeking experienced software developers/bioinformaticians to join the iPlant Collaborative, a new NSF-funded initiative which seeks to develop a comprehensive national cyberinfrastructure which will unite researchers in every plant biology discipline.

See the iPlant job board for job descriptions.

2008/04/01

GMOD 1.0 Released

I am very pleased to announce the release of GMOD 1.0. The file can be downloaded from SourceForge at:

http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=19511

This release comes at a time when both the Chado schema and its associated tools have matured and are now quite stable. The plan going forward is to have more frequent releases with schema changes between versions clearly delineated.

In addition to the Chado schema, this release includes:

  • Tools for creating a new database.
  • Tools for populating it with ontology data (using go-perl).
  • A fairly new tool for updating ontologies contributed by the developers of SGN, the SOL Genomics Network.
  • Tools for loading sequence feature (i.e. GFF3) data.
  • GMODTools for creating bulk download files like GFF and Fasta (See GMODTools for more information).

Other data can be loaded using XORT. This release of Chado works well with the upcoming release of GBrowse, as well as with the current versions of Apollo and CMap. It should also work well with GMODWeb/Turnkey.

With this release, there are so many people in the GMOD community that I would like to thank that I couldn't possibly list them all, but at a bare minimum, I would like to thank the developers at FlyBase and the Berkeley Drosophila Genome Project, especially Chris Mungall and Dave Emmert, as well as others who have contributed code to the GMOD project over the past several years.

Please direct any questions about using this release to the GMOD schema mailing list, gmod-schema@lists.sourceforge.net.

Scott Cain

2008/03/31

CMap 1.0 Released

Version 1.0 of CMap has been released.

You can get the new version from SourceForge, http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=55129

Highlights of this release are:

  • Ribbon option for correspondences
  • New Feature Glyphs
  • A dot-plot view
  • An image_only URL parameter allowing a CMap image to be embedded in another page
  • Easier install with directory guessing
  • API better documented for writing custom scripts to load data

If you have any questions, please email the CMap mailing list.

Ben

2008/03/28

GMOD Meeting July 16-17, Toronto

July2008LogoSmall.png The next GMOD community meeting has been scheduled for July 16-17, 2008 at the University of Toronto, immediately before ISMB 2008 (also in Toronto), and just a few days after the 2008 GMOD Summer School.

Watch the July 2008 GMOD Meeting page for more information as the meeting gets nearer. If you have any questions or requests about the July 2008 meeting, please contact the GMOD Help Desk at help@gmod.org. See the notes from previous meetings for an idea of what is discussed at GMOD meetings.

Thanks,
Dave Clements
GMOD Help Desk

2008/03/25


SynBrowse Developers Needed

SynBrowse_logoNoText.png The SynBrowse synteny viewer, a GMOD component, is moving towards its second major release. Xiaokang Pan, the project's lead developer, is looking for volunteer developers to help get this release out sooner.

SynBrowse2 is written in Perl, and is built on several open source components, including parts of GBrowse. SynBrowse2 need particular improvements in run-time performance and its alignment parsing tools. Ideally, programmers will develop SynBrowse2 using a set of animal or microbial genomes (Xiaokang is already working with several plant genomes). Programmers can improve the alignment parsing tools, fix potential bugs and hopefully improve other parts of SynBrowse as well.

If you have any interest in and/or experience with multiple alignment or synteny visualization tools please considering contributing to the SynBrowse project. Xiaokang can be reached at xiaokangpan@gmail.com.

Thanks,

Dave Clements
GMOD Help Desk

2008/03/21

GMOD at ParameciumDB

ParameciumDBIcon133x42.png Curious to know what is involved in becoming a GMOD user and creating a GMOD based web site? You can now read the GMOD User Story, an article about ParameciumDB's experience with implementing GMOD. The article describes what GMOD components ParameciumDB uses and how they connect them together. ParameciumDB uses several GMOD components, including Chado, GMODWeb, Apollo, and GBrowse. Please contact Linda Sperling <linda.sperling@cgm.cnrs-gif.fr> if you have questions about GMOD at ParameciumDB.

This is the first of a series of articles on how different organizations use GMOD components to achieve their goals. User stories will give readers a feel for what implementation choices are involved and which ones each organization made. If you are interested in describing your experience with GMOD, please consider creating a user story page for your project. You can just start writing (this is a wiki!) or contact the GMOD Help Desk for assistance. If we aren't swamped with volunteers, then I will be asking (cajoling?) several not-so-randomly picked projects to write user stories describing their experiences. I'm hoping to have a new story every other month or so.

Thanks,

Dave Clements
GMOD Help Desk

2008/03/18

Beta Test CMap: Win a T-Shirt!

UPDATE: We have our winners. Even still, please feel free to give the release candidate a try and let us know how it goes.

We need beta testers for the CMap 1.0 release candidate.

If I get four (or more) people who let me know that they will try out the release candidate, I will draw two of their names (or email addresses) and buy them each a GMOD T-shirt (based on random drawing, void where prohibited, etc). Testers from around the world are welcome (and eligible for the shirts as long as Cafe Press ships there and it isn't prohibited by law).

You can get the release candidate from SourceForge.

To view the T-shirt or get one for yourself visit Cafe Press. Note: There is no price markup for GMOD. The only one making money on the shirts is Cafe Press.

If the threshold is broken, I will hold the drawing on Friday the 15th at 1pm CST (2pm Eastern) and email the winners for their addresses and shirt sizes. If you don't want to be entered in the drawing just let me know. There is already one beta tester, so only three to go.

Remember: If no one beta tests, everyone beta tests.

Thanks,

Ben Faga,
faga.cshl@gmail.com

2008/03/11

GMOD Summer School

SummerSchoolSmall.png July 11-13, 2008
National Evolutionary Synthesis Center (NESCent)
Durham, North Carolina, USA

The first annual GMOD Summer School will be held July 11-13, 2008 at the National Evolutionary Synthesis Center (NESCent), in Durham, North Carolina, USA. This is a 2 1/2 day hands-on workshop aimed at teaching new GMOD users how to get up and running with popular GMOD components. There will also be a concurrent 1 day session aimed at principal investigators that will give decision makers an overview of what GMOD can do, how the project operates, and what level of resources are needed to get a GMOD installation up and running. If you are interested in attending please submit a Statement of Interest before April 15, 2008. The course is free but class size is limited. See the GMOD Summer School page for more information and a tentative program.

2008/03/07

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