The 7th SBML Hackathon
European Bioinformatics Institute
March 26–28, 2009
SBML Hackathons are annual meetings of developers of SBML software, tools, and other resources and facilities. The Hackathons are hands-on work sessions providing an opportunity to discuss software interoperability and other practical matters involving SBML.
The 2009 SBML Hackathon was held at the familiar EBI in Hinxton, UK, which was also the site of the 2004 Hackathon. In 2009, the event took place immediately after BioSysBio (March 23–25 in Cambridge, UK) and was itself be followed immediately afterwards by the 2009 BioModels Meeting on March 28–30, also at the EBI. Persons interested in these events may also want to learn about the CellML-SBGN-SBO-MIASE-BioPAX super-workshop, which was held shortly afterwards in Auckland, New Zealand, April 5–9.
In 2009, for the first time in the SBML Hackathon series, we introduced the option for people to bring and display posters about their work. The purpose was to compensate for the fact that the hackathons do not provide opportunities for people to give oral presentations about their software and other projects, yet not everyone at a hackathon is familiar with all the work being done by others. We therefore arranged poster display space near the hackathon rooms, and attendees used the posters to provide information about ongoing projects as well to create opportunities for face-to-face conversations about their work.
Major support for the 2009 SBML Hackathon was provided by the ELIXIR project.
We were also grateful for additional sponsorship from the following organizations:
- The European Molecular Biology Laboratory (EMBL)
- The National Institute of General Medical Sciences (NIGMS), USA
- Caltech Beckman Institute's Biological Network Modeling Center, USA
Agenda
In order to accommodate different people's level of experience and different goals, we went back to using two rooms (something that we did in past SBML Hackathons, though not in the two previous).
Arrival day (Wednesday, March 25)
Arrivals from airports (most people) or from Cambridge (for people who were attending BioSysBio 2009).
Day 1 (Thursday, March 26)
| Time | Activity (Main room) | Activity (2nd room) |
|---|---|---|
| 07:00–08:00 | Breakfast at Arundel Hotel in Cambridge (provided) | |
| 08:00–09:15 | Buses to the EBI + security check-in for Wellcome Trust Genome Campus | |
| 09:15–09:45 | Computer set up & poster mounting | |
| 09:45–09:55 | Introduction by Nicolas Le Novère | |
| 09:55–10:10 | Introduction by Michael Hucka | |
| 10:10–12:00 | Hacking, collaboration, ad hoc discussions | LibSBML 4.0 API tutorial + Q&A session |
| 12:00–14:30 | Lunch (provided) and poster viewing time | |
| 14:30–18:00 | Hacking, collaboration, ad hoc discussions | SBML Test Suite tutorial & discussion |
| 18:00–19:00 | Social time in pub at Hinxton House (self-funded) | |
| 19:00–19:30 | Buses back to the hotel in Cambridge | |
| 19:30– | Dinner (self-organized and self-funded) | |
Day 2 (Friday, March 27)
| Time | Activity (Main room) | Activity (2nd room) |
|---|---|---|
| 07:00–08:00 | Breakfast at Arundel Hotel (provided) | |
| 08:00–08:30 | Buses to the EBI from the hotel in Cambridge | |
| 08:30–12:00 | Hacking, collaboration, ad hoc discussions | SBML Level 3 Core specification hacking |
| 12:00–14:30 | Lunch (provided) and poster viewing time | |
| 14:30–18:00 | Hacking, collaboration, ad hoc discussions | SBML Level 3 Core specification hacking |
| 19:00–22:00 | Buses to Cambridge Dinner at Trinity Hall in Cambridge (provided) | |
Day 2.5 (Saturday, March 28)
| Time | Activity (Main room) | Activity (2nd room) |
|---|---|---|
| 07:00–08:00 | Breakfast at Arundel Hotel (provided) | |
| 08:00–08:30 | Buses to the EBI from the hotel in Cambridge | |
| 09:00–10:00 | Hacking, collaboration, ad hoc discussions | Guidelines for table formats (Liebermeister) |
| 10:00–11:00 | Hacking, collaboration, ad hoc discussions | Using TEDDY (Knüpfer) |
| 11:00–12:00 | Discussions, conclusions & future plans | |
| 12:00–13:30 | Lunch (self-funded) | |
The BioModels Annual Meeting began on the afternoon of March 28 and went through March 30th. More information can be found on the BioModels meeting page.
Location
Most of the activities of the SBML Hackathon took place in the IT training room at the EMBL-EBI. Address and contact details:
EMBL Outstation - Hinxton
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
United Kingdom
Tel: +44 (0)1223 494 444
The EBI is located on the Wellcome Trust Genome Campus, a 55 acre region of landscaped parkland that lies south of Cambridge. The Campus also houses the Wellcome Trust Sanger Institute, making it one of the world's largest concentrations of expertise in genomics and bioinformatics. The EMBL-EBI grew out of EMBL's pioneering work to provide public biological databases (notably EMBL-Bank and what is now known as UniProt) to the research community. Although geographically separated from EMBL's main headquarters and other sites, the EMBL-EBI is an integral part of EMBL.
Poster details
As mentioned above, at the 2009 Hackathon we experimented with having posters as a means for people to inform each other about their software and other projects. The maximum poster size was 1.7 (66 inches) wide by 1 meter (39 inches); posters could be hung in portrait or landscape orientations, though portrait was preferred. We provided poster boards together with tacks/pins to attach posters to the boards. Posters were displayed in the EBI "IT breakout area" during the Hackathon. Posters could be hung at any time following the participant's arrival at the EBI. (See also the agenda above.)
About Cambridge
Cambridge is less than 10 miles away from Hinxton. The city is the home of the University of Cambridge, which in 2009 celebrates its 800th anniversary. For more information about the city and the university, please visit the following websites:
- Cambridge (UK) Web Sites
- General Cambridge information
- The Fitzwilliam museum (very nice!)
- The list of Cambridge colleges (with websites). Colleges are at the heart of Cambridge history, architecture and current student life.
Contacts
| Nick Juty | Nicolas Le Novère | Linda Taddeo | Michael Hucka |
|---|---|---|---|
| juty at ebi.ac.uk | lenov at ebi.ac.uk | ltaddeo at caltech.edu | mhucka at caltech.edu |
| Tel: +44 (0) 1223 494 418 | Tel: +44 (0) 1223 494 521 | Tel: +1 626 395 3375 | Tel: +1 626 395 6911 |
| European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambridge, CB10 1SD UK | Beckman Institute 139-74 California Institute of Technology Pasadena, California 91125 USA | ||