The 2010 SBML-BioModels.net Hackathon
University of Washington Dept. of Bioengineering
May 1–4, 2010
Hackathons are annual meetings of developers of software and other resources and facilities. The SBML Hackathons are hands-on work sessions providing an opportunity to discuss software interoperability and other practical matters involving SBML. The 2010 event was a back-to-back combination of SBML and BioModels.net (BioModels Database, SBO, MIRIAM, SED-ML) hackathons, and was hosted by the Sauro Group in the University of Washington Department of Bioengineering. It ran for 4 days in Seattle, Washington, USA.
As with the 2009 event, attendees had the option of bringing and displaying 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 going on by other people. We therefore arranged poster display space near the hackathon rooms, and attendees were able to use the posters to provide information about ongoing projects as well as have face-to-face conversations about their work. The dimensions that were required for these posters are described in a separate section below.
New in 2010: we provided a live Twitter watch and video/audio streaming feed for the break-out discussions, for the benefit of people who could not travel to the event.
Support for the 2010 SBML-BioModels.net Hackathon was provided by:
 |  Univ. of Washington, Dept. of Bioengineering |  Biotechnology and Biological Sciences Research Council |
Agenda (Final)
In order to accommodate different people's level of experience and different goals, we used one main room, and provided nearby meeting rooms for break-out discussions.
Arrival day (Friday, April 30)
People arrived from the airport or other sources. (The transportation information page provided information about how to get from the airport to your hotel.)
Day 1 (Saturday, May 1)
| Time | Activity (Main room) | Activity (Break-out rooms) | Files | Audio (MP3) |
|---|---|---|---|---|
| –08:30 | Eat breakfast at hotel | |||
| 08:30–09:00 | Walk from hotel to venue | |||
| 09:00–09:20 | Poster set up, computer hook-ups, etc. | |||
| 09:20–09:40 | • Introduction and welcome (Herbert Sauro) • General logistics info (Lucian Smith) • Goals & info about the hackathon (Mike Hucka) • Vision of standards interoperability (Nicolas Le Novère) | none none Slides Slides | n/a n/a n/a Audio | |
| 09:40–12:30 | • SBML Level 3 Core differences from Level 2 (Mike Hucka) • libSBML 4 & 5 plug-in architecture explanations, part 1 (Sarah Keating) • jSBML short status updated & roadmap (Nicolas Rodriguez) • SED-ML status update (Frank Bergmann) • libSBML 4 & 5 plug-in architecture explanations, part 2 (Sarah Keating) | Slides Slides Slides Slides Slides | Audio Audio Audio Audio Audio | |
| 12:30–14:30 | Lunch + poster viewing | |||
| 14:45–15:35 | • SBML L3 "Multi*" package (Nicolas Le Novère — see also proposal, diagram & SBML) • BioNetGen, GetBonNie and SBML Multi* (Bin Hu) | Slides Slides | Audio Audio | |
| 15:35–16:00 | Break | |||
| 16:00–16:15 | • BioModels Database search demo (Camille Laibe) and new annotation-based search system (Ron Henkel) — combined presentation | Slides | Audio | |
| 16:15–18:00 | • Hacking with ad-hoc breaks | (#1) SBML L3 "Multi*" package (Nicolas Le Novère) (#2) BioModels Database search system hacking | none none | Audio none |
| 18:00–19:00 | Free time | |||
| 19:00–21:30 | Group dinner at restaurant Mamma Melina Ristorante (find it on a map) | |||
Day 2 (Sunday, May 2)
| Time | Activity (Main room) | Activity (Break-out rooms) | Files | Audio (MP3) |
|---|---|---|---|---|
| –08:30 | Eat breakfast at hotel | |||
| 08:30–09:00 | Walk from hotel to venue | |||
| 09:00–12:00 | Hacking with ad-hoc breaks | SBML L3 "spatial" package discussion (Jim Schaff) | Fig.1 Fig.2 Fig.3 | Audio 1 Audio 2 |
| 12:00–14:00 | Lunch + poster viewing | |||
| 14:00–18:00 | Hacking with ad-hoc breaks | SED-ML implementation (see latest spec) | Slides | Audio 1 Audio 2 |
| 18:00– | Free time | |||
Day 3 (Monday, May 3)
| Time | Activity (Main room) | Activity (Break-out rooms) | Files | Audio (MP3) |
|---|---|---|---|---|
| –08:30 | Eat breakfast at hotel | |||
| 08:30–09:00 | Walk from hotel to venue | |||
| 09:15–12:00 | Hacking with ad-hoc breaks | SBML hierarchical model composition proposal | Slides | Audio |
| 12:00–14:00 | Lunch + poster viewing | |||
| 14:00–14:30 | More discussion about spatial models (Jim Bassingthwaite, Jim Schaff) | none | Audio | |
| 14:30–18:00 | Hacking with ad-hoc breaks | (#1) On the semantics of SBML Events (Chris Myers) (#2) BioModels.net web services training | Slides none | Audio none |
| 18:00–19:00 | Free time | |||
| 19:00–21:30 | Group dinner at restaurant Shalimar (find it on a map) | |||
Day 4 (Tuesday, May 4)
| Time | Activity (Main room) | Activity (Break-out rooms) | Files | Audio (MP3) |
|---|---|---|---|---|
| –08:30 | Eat breakfast at hotel | |||
| 08:30–09:00 | Walk from hotel to venue | |||
| 09:15–12:00 | Hacking with ad-hoc breaks | (#1) SBML L3 "distributions & ranges" (Darren Wilkinson) (#2) BioModels Database community dev. | Slides none | Audio none |
| 12:00–14:00 | Lunch + poster viewing | |||
| 14:00–18:00 | Hacking with ad-hoc breaks | SBML annotations (both current SBML and new SBML L3 "annot" package) | Slides | Audio |
| 18:00– | Free time | |||
Departure day (Wednesday, May 5)
Attendees departed to airport or other places.
Location
View 2010 SBML-BioModels.net Hackathon in a larger map
Most of the activities of the 2010 SBML-BioModels.net Hackathon took place in a room in the William H. Foege building on the UW campus. The physical address is
UW Department of Bioengineering
N107 William H. Foege Building
1705 NE Pacific Street
Seattle, WA 98195-5061
About the University of Washington
The University of Washington (UW, and commonly called "U-Dub") was founded in 1861. It is one of the oldest universities on the west coast of the United States. Its main campus is in Seattle.
Poster details
As mentioned above, attendees had the opportunity to display posters. This served as a means for people to inform each other about their software and other projects in a setting that offered the opportunity for interaction and in-depth discussion.
The maximum poster dimensions were 36 in (91 cm) wide by up to 48 in (122 cm) tall. Note that the posters were in a portrait orientation. Posters could be taller than 48 in, but not wider than 36 in.
Poster sessions were held semi-concurrently with lunch breaks. The basic approach was to make the lunch breaks be extra long, so that people were able to get food & beverages, then come back and discuss their work in the poster room.
Contacts
| Lucian Smith | Frank Bergmann | Linda Taddeo | Michael Hucka |
|---|---|---|---|
| lpsmith at u.washington.edu | fbergmann at u.washington.edu | ltaddeo at caltech.edu | mhucka at caltech.edu |
| Tel: +1 206 543 4791 | Tel: +1 206 543 4791 | Tel: +1 626 395 3375 | Tel: +1 626 395 6911 |
| Dept. of Bioengineering University of Washington Seattle, Washington 98195 USA | Beckman Institute 139-74 California Institute of Technology Pasadena, California 91125 USA | ||