HARMONY 2011: The Hackathon on Resources for Modeling in Biology
Computational Biology, Memorial Sloan-Kettering Cancer Center
New York City, USA
April 18–22, 2011
In 2010, the systems biology standards community inaugurated a new, broader series of meetings to replace, among other events, the individual SBML and SBGN workshops and BioPAX meetings. The new meetings, COMBINE (Computational Modeling in Biology Network) and HARMONY are a recognition of the fact that there are multiple allied standardization efforts that should work more closely together to ensure smooth interoperability.
The two meetings address different needs and community emphases. COMBINE is a workshop-style event with oral presentation, posters and breakout sessions. The first annual COMBINE meeting took place in Edinburgh from Oct 6th to 9th, 2010.
HARMONY was a hackathon-type meeting, with a focus on development of the standards, interoperability and infrastructure. Unlike what happens at COMBINE meetings, there were not general discussions or oral presentations during HARMONY; instead, the time was devoted to allowing hands-on hacking and interaction between people focused on practical development of software and standards. The 2011 HARMONY meeting was hosted by the Computational Biology group at the Memorial Sloan-Kettering Cancer Center.
 List of attendees |  Poster List |  Supplementary materials |  Photos |  Organizers |  Travel Information |  Exit Survey |
Agenda
Day 1 (Monday, April 18)
| Time | Topic | Materials | Slides | Recordings |
|---|---|---|---|---|
| 09:00-09:05 | Day's Introduction | Slides | ||
| 09:05-09:25 | SBML Overview | Slides | ||
| 09:25-09:45 | BioPAX Overview | Slides | ||
| 09:45-10:05 | SBGN Overview | |||
| 10:05-10:30 | break | |||
| 10:30-11:30 | Tutorial 1: Paxtools | Slides | ||
| 11:30-12:30 | Tutorial 2: SPARQL/OWL | Materials | Slides | |
| 12:30-14:00 | lunch | |||
| 14:00-15:10 | Tutorial 3: libSBGN | Slides | ||
| 15:10-15:25 | break | |||
| 15:25-16:35 | Tutorial 4: libSBML | Slides | Slides | |
| 16:35-16:50 | break | |||
| 16:50-18:00 | Tutorial 5: JSBML | Slides | ||
| 18:00 | Poster Session | Poster List |
Day 2 (Tuesday, April 19)
| Time | Topic | Materials | Slides | Recordings |
|---|---|---|---|---|
| 08:30-09:00 | Introduction | Slides | <html><a href="/sites/combine/files/2011-04-19-harmony-lenovere-intro.mp3">Audio</a></html> | |
| 09:00-09:15 | SBGN status update | Slides | <html><a href="/sites/combine/files/2011-04-19-harmony-lenovere-sbgn.mp3">Audio</a></html> | |
| 09:15-10:15 | Update on SBGN-PD & pending issues | Slides | <html><a href="/sites/combine/files/2011-04-19-harmony-moodie-sbgn-pd.mp3">Audio</a></html> | |
| 10:15-10:30 | break | |||
| 10:30-11:35 | Update on SBGN-ER and pending issues | Slides | <html><a href="/sites/combine/files/2011-04-19-harmony-lenovere-sbgn-er.mp3">Audio</a></html> | |
| 11:35-11:50 | Update on SBGN-AF and pending issues | Slides | <html><a href="/sites/combine/files/2011-04-19-harmony-mi-sbgn-af.mp3">Audio</a></html> | |
| 11:50-12:00 | libSBGN roadmap & future plans | Slides | ||
| 12:00-12:30 | Update on libSBGN | <html><a href="/sites/combine/files/2011-04-19-harmony-vaniersel-libsbgn.mp3">Audio</a></html> | ||
| 12:30-14:00 | lunch | |||
| 14:00-15:00 | SBGN quiz | Example | ||
| 14:00-15:00 | Directed practical work (2 rooms available) |
Day 3 (Wednesday, April 20)
| Time | Topic | Materials | Slides | Recordings | |
|---|---|---|---|---|---|
| 09:00-09:10 | BioPAX day overview/org | Slides | |||
| 09:10-10:10 | Specification/data overview | Slides | |||
| 10:10-10:30 | Work in progress/proposal overview | ||||
| 10:30-10:45 | break | ||||
| 10:45-11:15 | Software/tools overview | Slides | |||
| 11:15-11:45 | Interoperability overview | ||||
| 11:45-12:15 | CV requirements overview | ||||
| 12:15-12:45 | Additional projects | ||||
| 12:45-14:00 | lunch | ||||
| 14:00-15:00 | Directed practical work (2 rooms available) | ||||
| 15:00 | Talk by Chris Sander | ||||
| 17:00 | Group dinner @ Fatty Fish, a fusion Japanese restaurant located a few blocks from MSKCC. | ||||
Day 4 (Thursday, April 21)
| Time | Topic | Materials | Slides | Recordings |
|---|---|---|---|---|
| 08:30-09:00 | Introduction | Slides | ||
| 09:00-09:30 | SBML status overview, including Level 3 development | Slides | ||
| 09:30-09:45 | libSBML status update | Slides | ||
| 09:45-10:15 | Other software updates | |||
| 10:15-10:30 | break | |||
| 10:30-11:30 | Emerging SBML areas/requests: (1) multicellular models, (2) SBML-BioPAX | Slides | ||
| 11:30-12:30 | Elaborations on certain current Level 3 packages: (1) spatial, (2) flux balance constraints/analysis, (3) hierarchical composition, (4) annotation | Slides Slides | ||
| 12:30-14:00 | lunch | |||
| 14:00 | BioPAX working group | Slides | ||
| 14:00 | Continuing discussions on SBML Level 3 packages | |||
| 15:00 | Other SBML discussions | |||
| 16:30- | Interoperability talks |
Day 5 (Friday, April 22)
| Time | Topic | Materials | Slides | Recordings |
|---|---|---|---|---|
| 08:30-09:00 | Introduction | SED-ML website | ||
| 09:00-09:20 | SED-ML specification | <html><a href="/sites/combine/files/2011-04-22-harmony-sedml-l1v1.pdf">SED-ML spec</a>, <a href="http://precedings.nature.com/documents/4257/version/1">Proposal on nested simulations</a></html> | Slides | |
| 09:20-9:30 | JlibSED-ML and CSBE tools | JlibSEDML site validator | Slides | |
| 09:30-9:40 | libSedML | libSedML | Slides | |
| 09:40-10:00 | SEDML and CellML | Discussion on the list SProS | ||
| 10:00-10:10 | Update on KiSAO | new OWL KiSAO | Slides | |
| 10:10-10:30 | Discussion | |||
| 10:30-10:45 | break | |||
| 10:45-11:35 | Coordinating outreach | Slides | ||
| 11:35-12:30 | Coordinating governance and process | SBML SBGN BioPAX | ||
| 12:30-14:00 | lunch | |||
| 14:00-15:00 | BioPAX activities | |||
| 14:00-15:00 | Continuation of morning | |||
| 15:00 | MIRIAM |
Location
<html>The meeting was held in the Rockefeller Research Laboratories of the Memorial Sloan-Kettering Cancer Center. MSKCC is located in the Upper East Side of Manhattan and is within walking distance of major subway lines.
RRL - Rockefeller Research Laboratories, MSKCC
430 East 67th Street
New York, New York 10065
We put together a comprehensive Google map, showing the meeting location, the hotel, various restaurants and subway entrances.
Funding acknowledgments
Major funding for HARMONY 2011 was provided by:
 Biotechnology and Biological Sciences Research Council |
Additional funding was provided by:
| | | |
Contact
Computational Biology Center
Memorial Sloan-Kettering Cancer Center
1275 York Avenue, Box #460
New York, NY 10065
USA
Phone: +1 646 888 2624 or +1 646 888 2602
Fax: +1 646 422 0717
Email: harmony2011@biopax.org