September 2010 GMOD Meeting
September 2010 GMOD Meeting 13-14 September 2010 Cambridge, UK |
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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.
Contents
Agenda
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 | PDF, Summary |
10:30 | Break | ||
11:00 | Help Desk Update | Dave Clements | PDF, PPT, Summary |
11:30 | Keynote: The Open Microscopy Environment: Open Informatics for Biological Imaging | Jason Swedlow | PDF, PPT, Summary |
12:30 | Catered Lunch | ||
13:45 | PSICQUIC: The PSI Common QUery Interface | Bruno Aranda | PDF, Summary |
14:15 | MolGenIS and XGAP | Morris Swertz | PDF, Summary |
14:45 | The GMOD Chado Natural Diversity Module | Bob MacCallum | PDF, PPT, gdoc, Summary |
15:15 | Break | ||
15:45 | Cosmic GBrowse: Visualising cancer mutations in genomic context | David Beare | PDF, PPT, Summary |
16:15 | GMOD Projects at the Center for Genomics and Bioinformatics | Chris Hemmerich | PDF, PPT, Summary |
Tuesday, 14 September
Time | Topic | Presenter(s) | Links |
---|---|---|---|
09:15 | GMOD RPC API: The almost RESTful GMOD API | Josh Goodman | PDF, Summary |
09:45 | Overview of current resources and update on DAS Meeting Cambridge 2010 | Jonathan Warren | PDF, PPT, Summary |
10:15 | InterMine: new Mines and new features | Richard Smith | PDF, Summary |
10:40 | Break | ||
11:00 | Literature Curation in GMOD | Daniel Renfro | PDF, PPT, Summary |
11:30 | Towards a GO Annotation Tool: Curation Accelerator Software | Helen Field | PDF, KEY, Summary |
12:00 | BioPivot: Applying Microsoft Live Labs Pivot to Problems in Bioinformatics | Steve Taylor | PDF, PPT, Summary |
12:30 | Catered Lunch | ||
13:45 | CRAWL (Chado RESTful Access Web-service Layer) | Giles Verlarde | PDF, Summary |
14:15 | Lessons the GMOD community can glean from the Apache Software Foundation | Summary | |
14:45 | Lightning talks | Summary | |
Scott Cain | Summary | ||
Joan Pontius | Summary | ||
Dave Clements | Summary | ||
15:15 | Break |
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:
The State of GMOD
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
- 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
- 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 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 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.
- 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
- 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 is a query-oriented data management system
- Provides a web based query interface
- Strong data federation
- BioMart Workshop on Thursday.
- InterMine is a query-oriented data management system
- Provides a web based query interface
- Very flexible queries and query optimization
- InterMine Workshop on Wednesday
- 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
- 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
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
- Microsoft Live Labs’ Pivot, which what BioPivot uses.
Bioinformatics has very few compelling interfaces. Wouldn't it be cool to use this in bioinformatics. Take thousands of regions of interest of genomes and view and filter seamlessly on metadata.
Steve then did a BioPivot demo showing over 6000 peaks found in a ChIP-Seq experiment. (Editor's note: There aren't any screen shots of the demo in the slides so this is hard to imagine. My notes during the demo simply said "Holy cow.") Facets were shown on the side, and you could filter the peaks based on their facets, or metadata.
Here are a couple of examples that can be viewed and manipulated with the Silverlight plug-in that can be used on Windows PCs and Mac OS X (though not with Chrome just yet). Eventually this will work on Linux in Moonlight.
These facets came from column 9 of the GFF3 files for the genomes. BioPivot includes tools to create Pivot metadata from GFF3, and to add annotation to a GFF3 file for things like nearest gene, exons, introns, intergenic, intragenic, and TSS/TES up and down stream regions.
BioPivot uses Pivot, but other Zoomable User Interfaces (ZUIs) are available. OpenZoom is one such package that includes an SDK for Flash, Flex, and AIR, as well as APIs.
There are a number of ways they would like to extend BioPivot:
- RNA-Seq parsers e.g. cufflinks, DESeq
- Get feedback from the community
- What else can we do with this tech?
See the BioPivot page at CBRG for more.
CRAWL (Chado RESTful Access Web-service Layer)
- A programmatic interface for querying pathogen genomics data
Editor's note: None of these summaries do the talks justice. However, this summary is especially short of the mark. To really appreciate the talk, download the slides.
Caveat: Vaporware Alert! This talk is about work that is currently in the rapid prototypes, proof of concepts, and requirements gathering stage. Terms and conditions apply. This is by no means a standard (yet), but it might be useful to others.
Giles works at GeneDB, a pathogen database with 45 organisms as of a couple months ago, and getting new ones all the time. GeneDB has a focus on web services and includes a lot of Chado related code. It also include cross-organism computed data such as orthologues and domains.
Chado is a relational database schema that underlies many GMOD installations. It is capable of representing many of the general classes of data frequently encountered in modern biology such as sequence, sequence comparisons, phenotypes, genotypes, ontologies, publications, and phylogeny. It has been designed to handle complex representations of biological knowledge and should be considered one of the most sophisticated relational schemas currently available in molecular biology. The price of this capability is that the new user must spend some time becoming familiar with its fundamentals.
- A database for very deep curation
- An integrated database
- A database that is generic enough to use for any organism
GeneDB's web front end uses Hibernate mappings to Chado, DAO caches, and Lucene search. It has weekly data updates (that take over a day to run). The code is quite meaty.
GeneDB collaborates with EupathDB an umbrella functional genomics integrative resource. It's annotation team is at Sanger, SBRI, and the University of Georgia. GeneDB also integrates and shares data from TriTrypDB and PlasmoDB.
Challenges
There are several challenges here:
- EupathDB
- Need to know what has changed
- Need to be able to get the data
- Remote annotation
- DB-Artemis via VPN
- Consistency
- Current setup works for power users, but need to build Rich Internet Applications to broadly enable this.
- Sanger
- Need to exploit our own data as well!
- Chado-complexity - SQL is hard.
The solutions to these challenges must all support rapid prototyping where it is quick to implement new queries, and it runs directly on top of the database (pure SQL), and there is no time to rebuild caches. Solutions also need to be lightweight and not tax the existing website.
Solutions
CRAWL uses Python, Jython, CherryPy, and Ropy to address these challenges. CherryPy is a multi-threaded web app server in which it is simple to reuse controller classes in different contexts. Code is built as a library first, implementing the model and controller parts of the MVC architecture. There is a conscious choice to ignore the view part of MVC early on. This enforced a decoupling of the data layer from the view. It also lends itself to building a command line wrapper application, and to supporting unit testing.
The essential purpose of CRAWL is mask the complexity of the SQL as much as possible, and allow you to get on with data analysis development.
EupathDB queries GeneDB daily using a "what's new" web service implemented with CRAWL. This gathers recent annotation changes which result in links back to GeneDB in EupathDB web sites.
The command line wrapper is used locally at Sanger to extract all sorts of information. This capability could be used by non-local bioinformaticians as well.
Collaborative Interfaces and Rich Internet Applications
Rich Internet Applications (RIAs) use AJAX techniques such as data refreshing without page reloads, and autocompletes of text boxes. Google Maps and Flickr are well known examples of RIAs. These fundamentally depend on web services.
Giles then showed several screenshots from what some folks call Web-Artemis, a genome annotation editor implemented in a web browser. This has several potential uses. Genomics visualisation and community annotation are two of them. Since it's web based, annotators won’t have to use a desktop application via a VPN. This is the kind of application we are moving towards. Whole point is that people can build applications without having to use Giles. It is possible (and Giles showed an example, SNP-Mashup) to use things like Web-Artemis in a mashup, embedding it as widget with other independently written widgets, integrating software that integrates data.
The way of CRAWL
- Built as a library first
- Deployed as
- Standalone Web services app
- Command line app
- Deployed as
- Used for
- Collaborating with EupathDB
- Query multi-organism data sets in house without going through WS
- Building RIAs and (s)mashups
GMOD Rest
CRAWL currently use the Ropy Python REST framework. It speaks Chado. Is it time to implement the GMOD REST interface? GeneDB’s Chado may have little differences. Any work must be tested on other databases.
Lessons from the Apache Community
There was a thought-provoking talk by Ross Gardler at BOSC this year on "Community Development at the Apache Software Foundation". There might be some lessons we can apply to the GMOD community.
- All technical discussions are made in public.
- You have to have a community before a project.
- If you contribute to a project, you get a vote.
- You can approve new projects, and volunteer to work on it.
- You can veto, but you have to say why.
- Make components generic enough so they could be used outside their domain.
- Jakarta managed all the Java projects under Apache. Switched to flat model. Jakarta no longer exists. Every project is now at the same organizational level.
Lightning Talks
GBrowse 2 and JBrowse Features
Scott talked about new features in GBrowse 2 and JBrowse. Some topics covered:
- Really fine grained control of downloads.
- Early uploading of files and sharing.
- Can have user accounts.
- Chado GBrowse now supports full text searching.
- feature table gets a new column, other tables get a new column, and there's a new materialized view, with a new column.
CpG Island and STR Annotator Plugins
Joan Pontius
Two GBrowse plugins were presented that were designed by Joey Bullard, an undergraduate student at RIT, and a summer student at the Laboratory of Genomic Diversity in Frederick Maryland under the direction of Joan Pontius. CpG islands in mammalian genomes are often an indication of a well conserved region, such as those of genes and promoter regions. ShortTandemRepeats are useful in experiments for mapping phenotypes to a genetic locus.
- CpGIslandAnnotator.pm
- Finds total number of CG dimers in a window (default size of 400 bp) and also calculates the expected number of CG dimers based on the basepair composition of the window. A "segments" glyph is used to display the CpG islands, with the height of the glyph representing the number of CG dimers, and the color representing the ratio of observed counts to expected.
- STRAnnotator.pm
- A plugin that uses the segments glyph to show Short Tandem Repeats, 2mer-5mers occurring in tandem a minimum of 5 times. The user can configure the number of tandem repeats.
Also presented was a CGI script that generates and displays in real time, the scatterplot of a GWA study SNP. The CGI script uses an offset file, that has, for each SNP, the offset in the Affymetrix or Illumina file of the genotype calls and fluorescence values of the SNPs. The CGI takes as an argument the SNP id, it then looks up the offset, retrieves the data and generates the scatterplot as a png file.
The CGI can be used in GBrowse to display the scatterplots for individual SNPs as a mouseover. By embedding the call to the CGI inside image tags (<img>), and having the <img> tags inside a balloon click, the scatterplot can be displayed to the GBrowse display instantly (less than a second) and without generating a temporary flat file.
GMOD Sustainability and Organization
The GMOD project has no central organization per se, and has no legal status whatsoever. The GMOD core, such as it is, is not particularly well funded. It currently consists of Scott Cain, the GMOD Project Coordinator, and Dave Clements, the GMOD Help Desk. Scott's funding comes entirely from WormBase, while Dave is only 60% funded (via the JBrowse/GBrowse grant) to work on the Help Desk. This is not particularly good ground to stand on for the long term.
NSF is moving towards funding software infrastructure projects such as GMOD:
- Software Infrastructure for Sustained Innovation (SI2), specifically the Scientific Software Integration (SSI) and Scientific Software Innovation Institutes (S2I2) awards.
What can we do to take advantage of these opportunities, and what other opportunities are there?
Anup Mahurkar suggested also pursuing funding from NIGMS. Joan Pontius wondered if there might be support for a Google Genomes project?
Steve Taylor pointed out that In Britain, the BBSRC has a program for funding this sort of thing. Being the BBSRC, it must have some sort of British focus. (Subsequent followup also identified BILAT-USA and Link2US as a possible sources of general European funding.)
Josh Goodman suggested having a hosted GMOD service as a possible way to support this. This comes up every year and would be a possible way to initially get funding and then generate revenue from support fees.
We also discussed if GMOD events should strive to become larger, and if the GMOD organization should aim to become more "official". Daniel Renfro stressed that going for larger events should not be done at the expense of the relatively small (~40-60 people), informal and networking-intensive GMOD Meetings that we currently have. Scott Cain posed the question of becoming a sister organization to the International Society for Biocuration. That organization is the natural complement to GMOD, and they have (larger) annual meetings and are a legal entity.
Chris Hemmerich raised the possibility of having more frequent hackathons. This question was spawned by the upcoming GMOD Evo Hackathon (November 2010). That hackathon is unique event, given its extensive organizational and financial support from NESCent. The 2007 Hackathon and future hackathons are unlikely to have that degree of support. That said, GMOD is quite willing to organize future hackathons on particular topics, given that they need to be done with probably minimal organizational support and no financial support.
Jerven Bolleman suggested teaming up with user interface specialists and setting up testing suites and doing integration testing. Giles Velarde suggested education and training as a core deliverable. These are all areas that span GMOD and would benefit from more central support, and the need for for training funds is increasing, given that funds for this were greatly reduced in the upcoming Help Desk grant.
Finally, Jerven suggested extending GMOD past its core genomic strength as another growth area.
Participants
Participant | Affilliation(s) | URL |
---|---|---|
Scott Cain | OICR | http://gmod.org/ |
Dave Clements | NESCent, GMOD | http://nescent.org http://gmod.org |
Josh Goodman | FlyBase - Indiana University | http://flybase.org |
Richard Smith | Cambridge University | http://www.intermine.org |
Anup Mahurkar | Institute for Genome Sciences University of Maryland School of Medicine | |
joan pontius | SAIC-NCI-FREDERICK Laboratory of Genomic Diversity | http://lgd.abcc.ncifcrf.gov/cgi-bin/gbrowse/cat/ |
Christelle Robert | The Roslin Institute The University of Edinburgh | |
Matthew Eldridge | Cancer Research UK - Cambridge Research Institute | |
Fengyuan Hu | Department of Genetics, University of Cambridge | |
Daniel Renfro | EcoliWiki, SubtilisWiki, Hu lab - Texas A&M University | EcoliWiki, SubtilisWiki, GONUTS |
Ellen Adlem | Cambridge University Cambridge Institue of Medical Research | http://www.t1dbase.org |
Kerstin Koch | KWS Saat AG Bioinformatics Grimsehlstr. | |
Oliver Burren | Cambridge University | http://www.t1dbase.org |
Chris Jiggins | University of Cambridge | http://heliconius.zoo.cam.ac.uk/ |
Jason Swedlow | Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, The Open Microscopy Environment (OME) | http://gre.lifesci.dundee.ac.uk/staff/jason_swedlow.html, http://www.openmicroscopy.org/ |
Dave Beare | Cancer Genome Project, Wellcome Trust Sanger Institute | http://www.sanger.ac.uk/research/projects/cancergenome.html |
seth redmond | Imperial College / Vectorbase | |
Chris Hemmerich | http://cgb.indiana.edu | |
Emmanuel Quevillon | Institut Pasteur | http://www.pasteur.fr/ip/easysite/go/03b-00000m-0q8/recherche/logiciels-et-banques-de-donnees |
Bob MacCallum | VectorBase Imperial College London | http://www.vectorbase.org |
Ewan Mollison | Tun Abdul Razak Research Centre, Hertford | http://www.tarrc.co.uk |
Jen Harrow | Wellcome Trust Sanger Institute | |
Gos Micklem | University of Cambridge | http://www.sysbiol.cam.ac.uk/index.php?page=dr-gos-micklem |
Malcolm Hinsley | Wellcome Trust Sanger Institute | |
Gemma Barson | Wellcome Trust Sanger Institute | http://www.sanger.ac.uk/ |
Brett Whitty | Michigan State University | http://buell-lab.plantbiology.msu.edu, http://solanaceae.plantbiology.msu.edu, http://potatogenome.net |
Morris Swertz | Genomics Coordination Center, University Medical Center Groningen EMBL - European Bioinformatics Institute | http://www.molgenis.org |
Jerven Bolleman | UniProt Swiss-Prot | |
Alex Kalderimis | InterMine, Cambridge University | http://www.intermine.org, http://www.flymine.org |
Oksana Riba Grognuz | Swiss Institute of Bioinformatics (SIB) Department of Ecology and Evolution, University of Lausanne | |
Dr Helen Imogen Field | FlyBase Dept Genetics University of Cambridge | http://www.gen.cam.ac.uk/research/flybase.html |
Kim Rutherford | Cambridge Systems Biology Centre | http://www.pombase.org/ |
Robert Wilson | National Institute for Medical Research, London | |
Gerd Anders | Public research institute: Max-Delbrueck-Centrum Berlin (MDC), Researcher and database developer | http://www.mdc-berlin.de/en/research/core_facilities/cf_massspectromety_bimsb/teammember/index.html http://www.mdc-berlin.de/en/research/core_facilities/cf_bioinformatic/teammember/index.html |
Joeri van der Velde | University of Groningen, GBIC UMGC, dept. of Genetics Genomics Coordination Center | |
Jonathan Warren | The Sanger Institute | http://www.dasregistry.org |
Stephen Taylor | CBRG, Oxford University | http://www.cbrg.ox.ac.uk/ |
Bruno Aranda | EMBL-EBI | http://www.ebi.ac.uk/intact, http://psicquic.googlecode.com |
Mahmut Uludag | European Bioinformatics Institute | |
Giles Velarde | The Sanger Centre | http://www.genedb.org, http://www.sanger.ac.uk |
Andy Jenkinson | European Bioinformatics Institute | |
Kevin Howe | Wellcome Trust Sanger Institute |
Logistics
This meeting was held in the Biffen Lecture Theatre, in the Department of Genetics on the University of Cambridge campus.
- Wireless
Thanks to Ian Clark, the Biffen Lecture Theatre had wireless. Dave Judge requested accounts for all attendees for the duration of GMOD Europe 2010.
- Power
The Biffen Lecture Theatre did not have power outlets throughout the room. To help us through the days, Gos Micklem secured a 15-socket extension strip which was placed at the back of the room.
- Transportation and Lodging
See the Transportation and Lodging sections on the GMOD Europe 2010 pages for details.
- Registration
The GMOD Meeting had a registration fee (£50 early, £65 late) to cover catered lunches, coffee/tea breaks, and other expenses.
Sponsor: Cambridge Computational Biology Institute
The September 2010 GMOD Meeting was sponsored by the Cambridge Computational Biology Institute, which is hosting the meeting and is also the home of InterMine. The CCBI is "set up to bring together the unique strengths of Cambridge in medicine, biology, mathematics and the physical sciences. Its aim is to create a centre of excellence in research and teaching and to promote collaborations both within the Cambridge area and beyond."
Please thank Gos Miclem, Shelley Lawson, and Richard Smith for hosting the event. We could not have done this without their support, effort and time.
Feedback
Attendees were asked to provide feedback at the end of the meeting.
Q: Would you recommend GMOD meetings to others
Yes | Maybe | No |
---|---|---|
94% | 6% | 0% |
"Maybe" Response:
- if they are already aware of most of the tools out there - or if more introductory sessions are to be provided.
Q: Please rate the meeting(s) using the following scale: 1 (not at all) to 3 (reasonably) to 5 (exceptionally).
1 | 2 | 3 | 4 | 5 | |
---|---|---|---|---|---|
How useful was the meeting? | 0% | 6% | 13% | 63% | 19% |
Was the meeting well run and organized? | 0% | 0% | 25% | 25% | 50% |
Q: Was the meeting what you expected?
No | Somewhat | Yes | Other |
---|---|---|---|
13% | 20% | 60% | 7% |
Longer responses:
- Smaller and less formal than expected - but have usually attended biology meetings.
- More or less. I was expecting a bigger turnout from experienced UK GMOD developers. This group was mostly fairly new to GMOD, which is good to see from another point of view.
- Almost yes, was attended more around gmod tools dev and future dev
- No, better more interesting
- Every GMOD meeting is different. It was very useful to talk with the attendees from the big European facilities.
- The meeting was not quite what I was expecting in that I would have liked more introductory sessions before the specific jargons of each talk - but having said that I learnt a lot, so I'm not complaining ;-)
Q: Which presentations and sessions at this meeting were the most useful or interesting?
- All were informative
- Jason Swedlow was an inspiration! it is good to learn about collaborative (successful) efforts.
- DAS, all the web service talks, GBrowse updates and InterMine.
- GMOD and PSICQUIC GMOD RPC (aka REST API) CRAWL
- The State of GMOD, GMOD RPC (aka REST API), BioPivot: Applying Microsoft Live Labs Pivot to Problems in Bioinformatics
- Keynote: The Open Microscopy Environment
- They were all pretty good.
- GMOD RPC, InterMine, Literature Curation in GMOD, Update from the Help Desk, The State of GMOD
- DAS, InterMine
- the presentations that included demo's and code
- Update from the Help Desk
- The keynote was extremely interesting. The presentations on web services were useful and I hope to see work continue on this. Finally, the talks on visualization and web interfaces were useful.
- the keynote speakers
- GBrowse talks + BioPivot + InterMine
Q: Do you have suggestions for improving GMOD meetings in the future?
- Cambridgshire is a good location for these due to the large bioinformatics community - lecture theatre was ok - food not so good.
- It's not your fault, but the savoury food was a bit nasty - it had been out of the fridge for an hour, but it would have been better if the 'hot' items had been out of the oven for an hour (or less).
- I liked the idea of engaging in a community. It would be good to have a central location, publication as it took this meeting to get my head around what GMOD was about (it is not really obvious from the website). It would be a nice service for GMOD to use BioPivot to create an OSI bioinformatics 'one-stop-shop': using as images the output screen shots. Sorting perhaps by data type (stuff for microarrays, stuff to annotate genomes, stuff to integrate annotation).
- Great job as always!
- I liked the open discussion format of the satellite meetings.
- It's a very friendly and open forum for discussing work.
- Thanks for the meeting.
- As always, the mix of GMOD developers and users as well as prospective users and external developers makes for a lot of interesting discussion.
- Please can you have at least the next meeting venue decided each time: this will determine who can come. If you had this decided before the meeting you might then also be able to set the agenda - and encourage the right audience to show up. eg [a GMOD veteran] felt things were too low-level this time, but for me as a newbie the agenda was a brilliant introduction to the community and the tools that are around, and how they can enhance bioinformatics services... So advance planning would really keep the ship steering well. Thanks, I enjoyed meeting everyone and learned a lot - and hope to contribute
The Next Meeting
The next GMOD Meeting will be held in March 2011 in Durham, North Carolina at NESCent, as part of GMOD Americas 2011. This event will also include Satellite Meetings and the 2011 GMOD Spring Training GMOD School.