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.


List of
attendees


List of
posters


Supplementary
materials


Printed
handout


Local
organizers


Twitter watch

Support for the 2010 SBML-BioModels.net Hackathon is being provided by:

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NIH/NIGMS

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Univ. of Washington,
Dept. of Bioengineering
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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:

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

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This page was last modified 00:47, 26 May 2010.



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