HARMONY 2012: The Hackathon on Resources for Modeling in Biology

Department of Bioinformatics - BiGCaT
Maastricht, The Netherlands
May 21–25, 2012

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 is 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 2012 meeting will be hosted by the Department of Bioinformatics from Maastricht University.

There is no conference fee, thanks to all the sponsors.

List of attendees

Poster List



Travel Information


Agenda days 2-5

Google+ Page

SBML Competitions

SBML T-Shirts

Exit Survey



Registration for HARMONY 2012 is closed.

We are trying to get more funding to support the accommodation costs of the participants. We have agreed to special room rates with the Apart Hotel Randwyck and the NH hotel. The participants have to book the hotel rooms themselves. For further information please have a look at the different room rates.

The conference dinner will take place on the evening of Wednesday 23rd May at Ipanema. On the first meeting day (Monday 21st May) there will be an open symposium with tutorials, talks and a reception/poster session in the evening.
A full schedule and further information will be provided on this meeting website.

We look forward to welcoming you all in Maastricht.

If you have any questions, please contact us (harmony2012@maastrichtuniversity.nl).


Preliminary agenda:

Day 1 (May 21, 2012)

Time Topic Presenter Slides
09:00 - 09:15 Welcome Slides
09:15 - 10:00 SBGN-ED Tutorial Falk Schreiber & Tobias Czauderna Slides
10:00 - 10:45 BioModels Database Tutorial Camille Laibe Slides
11:15 - 11:25 Introduction libSBML Sarah Keating Slides
11:25 - 11:35 Introduction jSBML Nicolas Rodriguez Slides
11:35 - 11:45 Introduction libSBGN Tobias Czauderna Slides
11:45 - 11:55 Introduction libSedML Frank Bergmann Slides
12:00 - 12:30 SBML Test Suite Tutorial Lucian Smith Slides
12:30 - 13:30 Lunch
13:30 - 13:50 Welcome Lecture Chris Evelo Slides
13:50 - 14:10 BioPAX, Pathway Commons, Cytoscape and the future of scientific publishing Gary Bader Slides
14:15 - 14:35 Software for SBML today Michael Hucka Slides
14:40 - 15:00 Moving on with standard interoperability Nicolas Le Novere Slides
15:30 - 15:45 SBFC - Format Converter Framework Nicolas Rodriguez Slides
15:45 - 16:00 Paxtools Gary Bader Slides
16:00 - 16:15 MIRIAM Registry / Identifiers.org Nicolas Le Novere
16:15 - 16:30 RepoSE Michael Guravage Slides
16:30 - 16:45 Linked Open Data Egon Willighagen Slides
17:00 - 19:00 Reception and Poster Session

Day 2-5 (May 22-25, 2012)

The editors of the different standards have setting up a preliminary session schedule for day 2-5. It's still possible to suggest sessions during the hackathon! Please have a look at the google document to get the most up-to-date schedule.

Time Topic
08:30 - 18:00 Hackathon - three parallel sessions, see here

Social Events

  • Reception on Monday evening (17:00 - 19:30)
  • Dinner on Wednesday evening at Ipanema (19:30 - 23:00)


  • Coffee/tea/mineral water will be provided
  • Lunch will be provided with a variety of sandwiches, mixed salad and fresh fruits.


The meeting will be held in the Maastricht School of Management (http://www.msm.nl/).

Endepolsdomein 150
6229 EP Maastricht
The Netherlands

The map below will be evolving, and we will provide more information about the location.

<html><iframe width="748" height="400" frameborder="0" scrolling="no" marginheight="0" marginwidth="0" src="http://maps.google.com/maps/ms?msa=0&msid=214327796040446067872.0004bcb95d6ff6bc10cb6&gl=us&ie=UTF8&t=m&ll=50.840067,5.711088&spn=0.01084,0.032144&z=15&output=embed"></iframe>
<a href="http://maps.google.com/maps/ms?msa=0&msid=214327796040446067872.0004bcb95d6ff6bc10cb6&gl=us&ie=UTF8&t=m&ll=50.840067,5.711088&spn=0.01084,0.032144&z=15&source=embed" style="color:#0000FF;text-align:left" target="_blank">View a larger version of this HARMONY 2012 map</a> </html>


After registering for HARMONY 2012, please have a look at our arrangements with the two hotels that are located at the meeting location, the Apart Hotel Randwyck and the NH hotel. Both are in walking distance (3-5 min) from the Maastricht School of Management. Prices are per room per night.

Apart Hotel Randwyck:
Modern 4-star hotel

  • Single room: 77 EUR - excl. breakfast - incl. internet
  • Double room: 77 EUR - excl. breakfast - incl. internet
  • Breakfast: 13 EUR per person
  • Contact details: send reservation to info@aparthotelrandwyck.nl and mention the booking code HARMONY 2012

NH Hotel:
Luxurious 4-star hotel with bar, restaurant, health club and parking

  • Single room: 79 EUR - excl. breakfast - excl. internet
  • Double room: 79 EUR - excl. breakfast - excl. internet
  • Breakfast: 15 EUR per person
  • Internet: Bar and lobby have free internet - internet in the room costs 10.75 EUR per 24 hours
  • Contact details: send reservation to n.collard@nh-hotels.com and mention the booking code HARMONY 2012

Please be aware that we are still trying to get funding to support the accommodation costs of the participants.

Travel Information

International airports

Smaller airports (flights within Europe)

How to get to Maastricht from the different airports?

  • Duesseldorf: check the German train company's website (http://www.deutschebahn.com/en/start.html) and search for trains from Duesseldorf Airport to Aachen. From Aachen you can take the bus line 50 to Maastricht (takes around 1hr).

Tip for travelers coming from Germany
If you are coming by train, there is direct bus connection (bus 50) from Aachen train station to Maastricht Station (1 hr trip). Please check the bus information here (in German).


Thanks to all the sponsors, there is no conference fee for HARMONY 2012. We are still trying to get additional funding to support the accommodation costs of the participants.

The sponsors of HARMONY 2012 are:

  • Maastricht University
  • Department of Bioinformatics and the research school NUTRIM of Maastricht University
  • Limburg University Fund/SWOL
  • Netherlands Consortium for Systems Biology (NCSB)
  • Netherlands Bioinformatics Centre (NBIC)
  • City of Maastricht


Department of Bioinformatics
Maastricht University
P.O. Box 616, UNS 50 Box19
6200 MD Maastricht
The Netherlands

Phone: + or +
Fax: +
Email: harmony2012@maastrichtuniversity.nl