GMOD

September 2010 GMOD Meeting

September 2010 GMOD Meeting
13-14 September 2010
Cambridge, UK

Part of GMOD Europe 2010

This GMOD community meeting was held 13-14 September 2010, in Cambridge, UK, as part of GMOD Europe 2010, which also included Satellite Meetings, an InterMine Workshop, and a BioMart Workshop. The meeting was sponsored and hosted by the Cambridge Computational Biology Institute at the University of Cambridge.

GMOD Meetings are a mix of user and developer presentations, and are a great place to find out what is happening in the project, what’s coming up, and what others are doing. The January 2010 GMOD Meeting was the previous event. The next meeting is likely to be held in spring 2011.

1 Agenda
2 Presentations
3 Participants
4 Logistics
5 Sponsor: Cambridge Computational Biology Institute
6 Feedback
7 The Next Meeting

Agenda

Professor Jason Swedlow

The Open Microscopy Environment: Open Informatics for Biological Imaging

Professor, Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee
Principal Investigator, Open Microscopy Environment (OME)

The meeting’s guest speaker was Prof Jason Swedlow, who discussed his work with with the Open Microscopy Environment (OME), an open international consortium that develops and releases data specifications and management tools for biological imaging. OME metadata enables image sharing, analysis, and integration with other data types.

Dr Swedlow is a Professor at the Wellcome Trust Centre for Gene Regulation and Expression and the University of Dundee. Jason’s research focuses on mechanisms and regulation of chromosome segregation during mitotic cell division.

Monday, 13 September

Time	Topic	Presenter(s)	Links
09:15	Introductions	Scott Cain
10:00	The State of GMOD	Scott Cain	<a href=”https://raw.githubusercontent.com/GMOD/gmod.github.io/main/mediawiki/images/7/78/TheStateofGMODSept2010.pdf”
class=”internal” title=”TheStateofGMODSept2010.pdf”>PDF</a>, Summary
10:30	Break
11:00	Help Desk Update	Dave Clements	<a href=”https://raw.githubusercontent.com/GMOD/gmod.github.io/main/mediawiki/images/b/bf/HelpDeskSept2010.pdf” class=”internal”

Tuesday, 14 September

Time	Topic	Presenter(s)	Links
09:15	GMOD RPC API: The almost RESTful GMOD API	Josh Goodman	<a href=”https://raw.githubusercontent.com/GMOD/gmod.github.io/main/mediawiki/images/e/ee/GMOD_RPC_Sept_2010.pdf”
class=”internal” title=”GMOD RPC Sept 2010.pdf”>PDF</a>, Summary
09:45	Overview of current resources and update on DAS Meeting Cambridge 2010	Jonathan Warren	<a href=”https://raw.githubusercontent.com/GMOD/gmod.github.io/main/mediawiki/images/e/e6/DAS_Sept2010.pdf” class=”internal”

Wednesday & Thursday, 15-16 September

GMOD Europe 2010 continued after the GMOD meeting, starting with the Satellite Meetings (topics were Post Reference Genome Tools and Community Annotation) and the InterMine Workshop, and finishing with the BioMart Workshop. See GMOD Europe 2010 for a complete schedule.

Presentations

Presentations spanned two days and covered a wide variety of topics.

By Topic

The talks can be roughly categorized:

GMOD Project The State of GMOD Help Desk Update Lessons from the Apache Community GMOD Sustainability and Organization
Components What's New JBrowse Development and JBrowse Grant Proposal New Components The GMOD Chado Natural Diversity Module Cosmic GBrowse: Visualising cancer mutations in genomic context GMOD Projects at the Center for Genomics and Bioinformatics GMOD RPC API: The almost RESTful GMOD API InterMine: new Mines and new features GBrowse 2 and JBrowse Features
Extending GMOD New Components PSICQUIC: The PSI Common QUery Interface MolGenIS and XGAP The GMOD Chado Natural Diversity Module GMOD Projects at the Center for Genomics and Bioinformatics GMOD RPC API: The almost RESTful GMOD API Towards a GO Annotation Tool: Curation Accelerator Software BioPivot CRAWL (Chado RESTful Access Web-service Layer) CpG Island and STR Annotator Plugins Also see the Post Reference Genome Tools Satellite Meeting.

Data Types The Open Microscopy Environment: Open Informatics for Biological Imaging (Images) PSICQUIC: The PSI Common QUery Interface (Molecular Interactions) Cosmic GBrowse: Visualising cancer mutations in genomic context (Mutations) Literature Curation in GMOD (Literature) Towards a GO Annotation Tool: Curation Accelerator Software (GO) CpG Island and STR Annotator Plugins (CpG islands and short tandem repeats)
Community Annotation Literature Curation in GMOD Towards a GO Annotation Tool: Curation Accelerator Software CRAWL (Chado RESTful Access Web-service Layer) See also the Community Annotation Satellite Meeting.
Visualization Cosmic GBrowse: Visualising cancer mutations in genomic context BioPivot GBrowse 2 and JBrowse Features Some Interesting Documents CpG Island and STR Annotator Plugins
Web Services and Distributed Resources PSICQUIC: The PSI Common QUery Interface GMOD RPC API: The almost RESTful GMOD API Overview of current resources and update on DAS Meeting Cambridge 2010 CRAWL (Chado RESTful Access Web-service Layer)

The State of GMOD

Scott Cain, PDF

GMOD is:

A set of interoperable open-source software components for visualizing, annotating, and managing biological data.
An active community of developers and users asking diverse questions, and facing common challenges, with their biological data.

These two things are equally important.

GMOD is used by

hundreds of organizations
large and small
corporate and academic
all over the world
across the tree of life

What’s New

GBrowse

Releases
- 1.70, 2.14
Features
- Rubberband region selection
- Drag and drop track ordering
- Collapsible tracks
- Popup balloons
- Allele/gentotype frequency
- Geolocation popups
- Circular genome support (1.71)
- Asynchronous updates (2.0)
- User authentication
- Multiple server support (2.0)
- SQLite, SAMtools (NGS) adaptors

JBrowse

GMOD’s 2nd Generation Genome Browser
It’s fast
Completely new genome browser implementation:
- Client side rendering
- Heavy use of AJAX
- Uses JSON and Nested Containment Lists

GBrowse_syn

GBrowse based comparative genomics viewer
Shows a reference sequence compared to 2+ others
Can also show any GBrowse-based annotations
Syntenic blocks do not have to be colinear
Can also show duplications

Chado

Chado is the GMOD schema; it is modular and extensible, allowing the addition of new data types “easily.” Covered data types in ontologies, organisms, sequence features, genotypes, phenotypes, libraries, stocks, microarrays, with natural diversity recently being rolled into the schema (but not yet released).
1.0 Release solidified the Chado that most people were already using from source.
1.1 Introduced support for GBrowse to use full text searching and “summary statistics” (i.e., feature density plots). Version 0.30 of Bio::DB::Das::Chado is needed for these functions.

Tripal

New (2009) web front end for Chado databases
Set of Drupal modules
Modules approximately correspond to Chado modules
Easy to create new modules
Includes user authentication, job management, curation support

TableEdit

A MediaWiki extension (MediaWiki software used at Wikipedia, GMOD.org)
Provides graphical user interface (GUI) to wiki tables
Can also provide GUI to database tables
Work in progress to use this with Chado
Potential to give wiki access to a Chado database
See http://ecoliwiki.net

BioMart

BioMart is a query-oriented data management system
Provides a web based query interface
Strong data federation
BioMart Workshop on Thursday.

InterMine

InterMine is a query-oriented data management system
Provides a web based query interface
Very flexible queries and query optimization
InterMine Workshop on Wednesday

MAKER

Genome annotation pipeline for creating gene models
Output can be loaded into GBrowse, Apollo, Chado, …
Incorporates
- SNAP, RepeatMasker, exonerate, BLAST, Augustus, FGENESH, GeneMark, MPI
Other capabilities
Map existing annotation onto new assemblies
Merge multiple legacy annotation sets into a consensus set
Update existing annotations with new evidence
Integrate raw InterProScan results
MAKER Online in beta

Apollo

Java-based GUI application for browsing and annotating genomic sequences
Can be installed via WebStart (i.e., by clicking on a link)
Can read/write to Chado, GFF3, GenBank, GAME XML

Next GMOD Meeting?

Next Spring Sometime:
ABRF: Association of Biomolecular Resource Facilities
- Feb. 19-22, San Antonio, TX
Biology of Genomes
- May 10-14, Cold Spring Harbor Lab, NY
Suggestions?

Note: The next meeting is the March 2011 GMOD Meeting being held at NESCent, in Durham, North Carolina, United States, as part of GMOD Americas 2011.

Help Desk Update

Dave Clements, PDF, PPT

Mailing List Archives

GMOD Mailing Lists are all over. Many are hosted at SourceForge, but several are elsewhere (EBI, Bluehost, Berkeley, …). Some don’t have public archives and those that do are spread around The lists at SourceForge have searchable archives but the search interface is frustrating.

Since May/June 2010, all emails to GMOD mailing lists have been archived in a single searchable hierarchy at Nabble. Nabble has a functional search capability and you can now search all lists, or just a single list.

GMOD Membership Requirements

GMOD’s requirements for software to join GMOD were codified in February 2010, following the January 2010 GMOD Meeting. These requirements were in use before February, but were inconsistently applied.

Version 1 Requirements:

Meets a common need
Useful over time
Configurable and Extensible
Open source license for all users
Interoperable with existing GMOD Components
Commitment of support

For next version, want to add:

Support mailing list that is publicly archived
Publicly accessible code repository

Discussion favored these additions. The issue of incompatible open source licenses also came up. GMOD currently requires any OSI approved license. However, some of those licenses are not compatible with each other, meaning they such components can’t be bundled together.

GMOD Promotion

Help spread the word about GMOD components and the GMOD project.

Why?

Increased visibility leads to → Increased adoption, which leads to → more projects contributing back
Increased adoption & development leads to → increased funding

How?

Cite GMOD, GMOD Components in your papers, presentations, grants
Powered by GMOD icons
Speakers at your event; not just Scott and Dave. PIs and developers are also available.
Graphics & slides for your presentations, posters
Presentation and event promotion
Brochures (GMOD project, events)
Bling!

The GMOD Promotion page launched in July 2010.

GMOD Logo Program

| | | | | | | | | | | — | — | — | — | — | — | — | — | — |

| | | | | | | | | |

Nine projects got new logos in the Spring 2010 Logo Program. Logos were done by John Aikman’s Spring 2010 Advanced Design class at Linn-Benton Community College, Albany, Oregon, United States. Each project worked with 2-3 students during the quarter to produce the selected logos.

We might do this again in 2011.

2010 GMOD Community Survey

The 2008 GMOD Community Survey covered components and project wide topics. The 2009 GMOD Community Survey focused on genome and comparative genomics browsing. The 2010 GMOD Community Survey will cover components and project wide topics. We may use it to produce a GMOD Project publication.

These surveys help guide the project and also show potential and current GMOD users what the larger community is doing.

Look for the 2010 survey in October.

Events

Satellite Meetings!

The satellites at the January 2010 GMOD Meeting were such a success that we decided to do them again. Satellites are birds of a feather discussions where participants with a common interest discuss that topic. The satellites at this meeting were:

See the satellite meeting pages for summaries of the discussion.

GMOD Summer School

In 2010 we held our 4th summer school in May at NESCent, in Durham, North Carolina, US. We had 62 applicants for 25 slots.

The 2011 course will likely be at NESCent again. However, starting in 2011, summer school expenses will no longer be covered by a grant (see below). This means that we will start charging tuition, and that we will also start seeking sponsors.

Summer school sessions become online tutorials that include starting and ending VMware images, step by step instructions, and example datasets.

Other Upcoming Events of Note

Documentation

Community

Tools

Browse properties
Last updated at 17:31 on 30 November 2012.
Content is available under a GNU Free Documentation License unless otherwise noted.