HARMONY 2013: The Hackathon on Resources for Modeling in Biology

Center for Cell Analysis and Modeling
University of Connecticut Health Center
Farmington, CT, USA
May 20–23, 2013
Phone: +1-860-679-6103
Fax: +1-860-679-1039

In 2010, the systems biology standards communities inaugurated a new, broader series of meetings to replace, among other events, the individual SBML and SBGN workshops and BioPAX meetings.

HARMONY is a hackathon-type meeting, with a focus on development of the standards, interoperability and infrastructure. There are generally not many general discussions or oral presentations during HARMONY; instead, the time is devoted to allowing hands-on hacking and interaction between people focused on practical development of software and standards. The HARMONY 2013 meeting will be hosted by the Richard D. Berlin Center for Cell Analysis and Modeling of the University of Connecticut Health Center Farmington, CT, USA.

List of attendees


Agenda days 2-5




Online self-registration is now closed. If you want to register, please contact the organizers directly. Thanks to our sponsors, there is no conference fee for HARMONY 2013.


HARMONY 2013 would not have been possible without funding from the following organizations:






The detailed agenda for the full group sessions on Days 1 and 2 is shown below. The agenda for the parallel track sessions ond Days 2-4 is dynamic - check this GoogleDoc spreadsheet for the latest updates.

Contacts: Ion Moraru (general topics, session proposals), Lucian Smith (SBML), Stuart Moodie (SBGN), David Nickerson (SED-ML), Igor Rodchenkov (BioPAX).

Monday, May 20, 2013

The morning session will be devoted to check-in, poster and A/V setup, and tutorials.
Posters will be on display for the entire 4 days.

Tutorials - Demo Lab, 9:00 - 12:00

Time Topic Presenter
09:00 - 09:30 Semantic integration using BioPAX Martijn van Iersel, General Bioinformatics Ltd.
09:30 - 10:00 BudHat: version control for computational models Martin Scharm, U of Rostock
10:00 - 10:30 The Physiome model repository David Nickerson, U of Auckland
10:30 - 11:00 Coffee break
11:00 - 11:30 Pharmacogenomics knowledge management Oliver Ruebenacker, PanGenX
11:30 - 12:00 Model builiding with Paxtools and Groovy Emek Demir, Memorial Sloan-Kettering Cancer Center

NOTE: The SBML Team are not providing formal tutorials but will be available during this time to discuss libSBML, JSBML, SBML Test-Suite, SBFC and any other SBML Team software. Please feel free to approach us (Frank Bergmann, Sarah Keating, Nicolas Rodriguez, Lucian Smith and Mike Hucka).

Lunch - Commons, 12:00 - 1:00

The afternoon session will be an open symposium on computational biology applications, followed by a reception.

SYMPOSIUM - Edmund and Arlene Grossman Auditorium, 1:00 - 4:45

Time Topic Speaker Affiliation
1:00 - 1:10 Welcome Marc Lalande Associate Dean for Research, UCHC
1:10 - 1:50 Biophysical modeling; e-publishing Leslie Loew Center for Cell Analysis and Modeling, UCHC
Editor-in-Chief, Biophysical Journal
1:50 - 2:30 Large scale networks Pedro Mendes Centre for Integrative Systems Biology, Manchester Univ
Virginia Bioinformatics Institute, Virginia Tech
2:30 - 2:40 Coffee break
2:40 - 3:20 Synthetic biology Herbert Sauro Dept of Bioengineering, U of Washington
3:20 - 4:00 Genetic circuits Chris Myers Dept of Electrical and Computer Engineering, U of Utah
4:00 - 4:45 Genomic medicine Edison Liu CEO, The Jackson Laboratory
President, Human Genome Organization

Reception - Commons 4:45 - 6:00

Tuesday, May 21, 2013

The morning session will be devoted to brief presentations by workshop participants on various projects and computational/bioinformatics tools. The afternoon session will be composed by two parallel tracks, followed by a full group round-up session.

Project Updates - Edmund and Arlene Grossman Auditorium, 9:00 - 12:30

Time Topic Presenter
09:00 - 10:30 BioPAX layout Martijn van Iersel, General Bioinformatics Ltd.
Pathway Commons 2 (PC2) Igor Rodchenkov, U of Toronto
BioPAX validator Emek Demir, Memorial Sloan-Kettering Cancer Center
SBGN-9 Stuart Moodie, European Bioinformatics Institute
Pathways@VCell Michael Blinov, UCHC
TBA Thomas Kepler, Boston University
10:30 - 10:45 Coffee break
10:45 - 12:30 Multistate models Alida Palmisano, Virginia Tech
SABIO-RK, Virtual Liver SEEK Martin Golebiweski, Heidelberg Institute for Theoretical Studies
COPASI Pedro Mendes, Manchester University
Hybrid spatial solver James Schaff, UCHC
Chaste Jonathan Cooper, Oxford University
JDesigner, Jarnac Herbert Sauro, U of Washington
Antimony Lucian Smith, Caltech

Lunch - Commons, 12:30 - 1:30

Two parallel tracks, 1:30 - 5:00

Track 1 (SBML) - Demo Lab
Track 2 (Other) - Conference Room 1673

Round-up session - Grossman Auditorium, 5:00-5:30

Wednesday, May 22, 2013

Three parallel tracks, 9:30 - 5:00

Track 1 (SBML) - Demo Lab
Track 2 (Other) - Conference Room 1673
Track 3 (BioPAX) - Conference Room 1390

Round-up session - Grossman Auditorium, 5:00 - 5:30
Conference dinner, 7:30 - 11:00

Thursday, May 23, 2013

Two parallel tracks, 9:30 - 3:00

Track 1 (SBML) - Demo Lab
Track 2 (Other) - Conference Room 1673


New: Funding is now available to support lodging costs for a limited number of attendees. If you require assistance, please send an application letter requesting a travel award in PDF format to Tiffany Gough. Please state your current position, funding situation, and areas of interest related to HARMONY.

We have made special arrangements with the Homewood Suites by Hilton hotel that is located across the street from the meeting venue. It is a 4-star hotel with excellent amenities for business travelers.

A block of rooms has been reserved for HARMONY 2013 attendees.

  • Accommodations: all rooms are suites with bedroom, living room with sleeper sofa, and fully-equipped kitchenette
  • Rate: $125 per night, tax free (see below)
  • Breakfast: full breakfast included every day
  • Internet: complimentary, both in-room and in common areas
  • Dinner: complimentary dinner and drinks on four days, May 20-23

Guests can make reservations at the special rate by referencing Harmony 2013 via phone reservations (+1-860-321-0000) or using Group Code HR3 via on-line reservations. Please note that on-line reservations will show that there is applicable state tax, however the group is tax exempt and when reservations are made it will change them to tax exempt (the online booking code has expired; please call the hotel directly).

Travel Information

Farmington is served by Hartford's Bradley International Airport (BDL) located about 30 min driving distance away.

Boston's Logan International Airport (BOS) and two of New York's airports (JFK and LGA) are ~2.5 hrs away and bus service from these airports may sometimes be a better alterantive, if flying into BDL would connect through these airports.

CTLimo bus lines provide direct service from JFK and LGA to Farmington; Peter Pan and Greyhound bus lines provide service from the city of Boston to Hartford/Farmington.

More details on travel options


The meeting will be held in the:

Cell and Genome Sciences Building
400 Farmington Ave
Farmington, CT 06030

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