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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.


List of attendees


Abstracts


Printed handout


Supplementary Materials


Photos


Travel
information


Major support for the 2009 SBML Hackathon was provided by the ELIXIR project.


We were also grateful for additional sponsorship from the following organizations:

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


View Larger Map

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:

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

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