COMBINE 2012

Dates: August 15–19, 2012
Location: Toronto, Canada
Hosted by: The Donnelly Centre, University of Toronto

The "Computational Modeling in Biology" Network (COMBINE) is an initiative to coordinate the development of the various community standards and formats in systems biology and related fields.

COMBINE is a workshop-style event with oral presentation, posters and breakout sessions. The five meeting days included talks about the COMBINE standards and associated or related standardization efforts, as well as presentations of tools using these standards. Oral presentations were selected from the submitted abstracts. In addition to oral presentations, poster sessions allowed people to inform each other about their software and other projects in a setting that allowed interaction and in-depth discussion.

The third annual COMBINE meeting took place at The Donnelly Centre building at the University of Toronto from Wednesday August 15 through Sunday Aug. 19, 2012, immediately preceding the 13th International Conference on Systems Biology (ICSB2012). The COMBINE conference location was a short walk from ICSB events, and COMBINE 2012 was an official satellite meeting of ICSB, so participants could follow the same travel and accommodation instructions for ICSB and use the same hotel discounts. Toronto is a large city and the University of Toronto is in the city centre, so additional hotel options were available close by for those who preferred a wider selection than what ICSB offered.


List of attendees

Abstract Booklet

Photos

Accommodation

Travel Information

Google+ Page


Agenda

COMBINE 2012 was organized into sessions largely built based on the attendees' suggestions. Those sessions were grouped according to overall themes as summarized in the table below.

The detailed agenda is on a separate page.

Wed Aug 15 Thurs Aug 16 Fri Aug 17 Sat Aug 18 Sun Aug19

09:00-10:00 Keynote:
Peter Zandstra
Not your mama's network biology
Biological Models and Simulations Simulation Algorithm, Experiments and Results Model and Pathway Visualization Software Tools and Databases: Reactome ICSB/COMBINE Tutorial
break
10:30 - 11
break break break break break
Biological Models and Simulations Simulation Algorithm, Experiments and Results Model and Pathway Visualization Software Tools and Databases: Reactome ICSB/COMBINE Tutorial
lunch
12:20-1:40
lunch lunch lunch lunch lunch
Biological Models and Simulations Software Tools and Databases Biological Pathways and Networks Interoperability Between Standards ICSB/COMBINE Tutorial
break
2:20-2:50
break break break break break
Simulation Algorithm, Experiments and Results Software Tools and Databases Biological Pathways and Networks Interoperability Between Standards ICSB starts at 3pm

Keynote
16:00-17:00:
Michael Gruninger
How to be an educated ontology consumer
Will Ryu
Comprehensive measure and modeling of C. elegans behavior
Radhakrishnan Mahadevan
Model-based Engineering of Metabolism

Poster:
all day(Red room)
Poster Reception
Poster:
all day (Red room)
Poster:
all day (Red room)
Poster:
all day (Red room)
19:00 - 23:00
Conference dinner


Example of COMBINE standards, associated efforts and related efforts discussed in different sessions:

Simulation and analysis: SED-ML; KiSAO; SBRML
Interoperability: MIRIAM URIs, SBO
Mathematical model semantics: SBML; NineML, CellML, FieldML
Biological pathway semantics: BioPAX
Visual representation: SBGN
Applying Standards - Tools and Databases: all

Conference dinner

There was a conference dinner on Thursday, August 16th at 7:00 at the restaurant Messis.

Welcome get-together

On Tuesday August 14 we had an informal welcome get-together at 5:30 PM at the Bedford Academy.

Funding acknowledgments

Support for COMBINE 2012 was provided by the following organizations:


OICR


OGI


Venue

COMBINE 2012 location was:
Donnelly Centre for Cellular and Biomolecular Research (CCBR)
University of Toronto
160 College Street
Toronto M5S 3E1
Canada


View COMBINE 2012 in a larger map

We used a main room that seated approximately 90 and three break-out rooms that seated between 15 to 25 people.

Places to eat around the Donnelley Centre




View Places to Eat and Drink in Toronto in a larger map

Additional notes

Social Media

Twitter hashtag #COMBINE2012 https://twitter.com/#!/search/%23COMBINE2012

Poster dimensions

All reasonable dimensions were welcome. Posters were set up in the Red Room.

Electrical supply

If you were traveling from abroad, you needed to bring an appropriate power plug converter for your laptop and all other electrical devices you're bringing. The domestic electric system in North America uses 120 V at 60 Hz. The plug type is described at http://en.wikipedia.org/wiki/Electrical_plug#North_American_and_IEC_60906-2.

Internet access

The meeting room had wireless internet access available Tuesday, August 14.2012 - Thursday, August 23.2012.
Eduroam was also available for those whose institutions participate in it: http://eduroam.utoronto.ca/

Organization

COMBINE 2012 was organized by:

Contact:

Gary Bader
160 College Street, Room 602
The Donnelly Centre
University of Toronto
Toronto, Ontario
Canada, M5S 3E1
Phone: 416-978-3935
Fax: 416-978-8287

Thanks for a great conference