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. This year's event is a back-to-back combination of SBML and BioModels.net (BioModels Database, SBO, MIRIAM, SED-ML) hackathons, and is being hosted by the Sauro Group in the University of Washington Department of Bioengineering. It will run for 4 days in Seattle, Washington, USA.
As with last year's event, attendees have the option of bringing and displaying posters about their work. The purpose is 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 will therefore arrange poster display space near the hackathon rooms, and attendees can use the posters to provide information about ongoing projects as well as opportunities for face-to-face conversations about their work. The poster dimension requirements are discussed in a separate section below.
New this year: we will attempt to provide a live video/audio streaming feed for the break-out discussions, for the benefit of people who cannot travel to the event.
Support for the 2010 SBML-BioModels.net Hackathon is being provided by:
| | Univ. of Washington, Dept. of Bioengineering | Biotechnology and Biological Sciences Research Council |
We anticipate being able to provide local accommodations for 5 nights for attendees, and to organize two group dinners. We regret that we do not anticipate having funding for people's flights or other expenses.
Agenda (Final)
In order to accommodate different people's level of experience and different goals, we will use one main room, and provide nearby meeting rooms for break-out discussions. The following agenda may still change somewhat as we get closer to the actual event.
Arrival day (Friday, April 30)
Arrivals from the airport or other sources. (See the transportation information page for 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)
Departure 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 will take 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
Accommodations
As noted above, we anticipate being able to arrange and pay for local accommodations for 5 nights for attendees from academic and nonprofit institutions. We will be housing people at one or both of the following hotels (most likely the first, but possibly also the second if we have a lot of people):
Watertown Hotel
4242 Roosevelt Way NE
Seattle, WA 98105
University Inn
4140 Roosevelt Way NE
Seattle, WA 98105
Transportation
Ground transportation options include taxi, shuttle, light rail and bus. The following page includes detailed information, airport maps, and photos showing your route to to taxis, trains and buses, as well as site views of the two hotels.
Ground Transportation Information
Other notes
The following sections provide some additional general information about this year's hackathon.
Poster details
As mentioned above, attendees will have the opportunity to display posters. This is a means for people to inform each other about their software and other projects in a setting that offers the opportunity for interaction and in-depth discussion.
The maximum poster dimensions are 36 in (91 cm) wide by up to 48 in (122 cm) tall. Note that the posters are in a portrait orientation. Posters can be taller than 48 in, but cannot be wider than 36 in.
We anticipate putting the posters in a separate conference room. Poster sessions will be held semi-concurrently with lunch breaks. The basic approach will be to make the lunch breaks be extra long, so that people can get some food & beverages, then come back and discuss their work in the poster room.
Electrical supply
If you are traveling from outside of the USA, be sure to bring an appropriate power plug converter for your laptop and all other electrical devices you're bringing. Electric current in the USA is 60 Hz, 120 V. The plug types are the types "A" and "B" described at this website.
You may be able to find an appropriate converter once you get to Seattle, but it's best not to count on it, and to bring your own before you leave your home country.
Internet networking
Both hotels have wireless networking available. We do not yet know whether they have wired ethernet ports in the rooms; often hotels do, but we do not have specific confirmation at this time about either the Watertown or University Inn.
Wireless and wired network access will be available in the meeting rooms, which are located on the campus of the University of Washington. Everyone will be provided with a group wireless account name and password when you get to the venue.
Weather
Travelers will probably want to bring an umbrella. With an average of 37 inches of rain a year, Seattle has a justified reputation for wet weather. However, the precipitation generally falls as a misty drizzle rather than in hard rain, and the average for May 1-4 is only .07 inches (1.78 mm) per day. Temperatures are moderate, with an early May average high of 62°F (17°C) and low of 45°F (7°C). The hilly terrain does create convergence zones, which can result in exciting and rapid changes in weather, and many locals adopt layering as a clothing strategy to deal with these changes. For the period of the Hackathon, sunrise will be about 4:45 am and sunset about 7:20 pm.
The widget on the right shows the current weather in Seattle.
For a longer range forecast with more detail, you may want to visit the Weather Underground's site for zip code 98195.
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.
Other activities to be found in Seattle
Here are some sources of information for activities happening in the area, if people want to look for a break and some fun in the evenings:
- National Film Festival for Talented Youth: Best of NFFTY 2007-2010
- Seattle events calendar
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 | ||




