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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.


List of
attendees


List of
posters


Supplementary
materials


Printed
handout


Local
organizers


Travel
information

Support for the 2010 SBML-BioModels.net Hackathon was 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


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

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