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



Travel Information

Exit Survey


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 Audio
09:00-09:15 SBGN status update Slides Audio
09:15-10:15 Update on SBGN-PD & pending issues Slides Audio
10:15-10:30 break
10:30-11:35 Update on SBGN-ER and pending issues Slides Audio
11:35-11:50 Update on SBGN-AF and pending issues Slides Audio
11:50-12:00 libSBGN roadmap & future plans Slides
12:00-12:30 Update on libSBGN Audio
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
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 SED-ML spec, Proposal on nested simulations 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


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:



Biological Network Modeling Center


Computational Biology Center
Memorial Sloan-Kettering Cancer Center
1275 York Avenue, Box #460
New York, NY 10065

Phone: +1 646 888 2624 or +1 646 888 2602
Fax: +1 646 422 0717
Email: harmony2011@biopax.org