COMBINE & de.NBI Tutorial: Modelling and Simulation Tools in Systems Biology
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Dates: Sunday, August 6th, 2017 (9:00 - 18:00)
Location: Blacksburg, Virginia (USA)
Hosted by: HITS - Heidelberg Institute for Theoretical Studies
The participation in the tutorial is free of charge.
This tutorial workshop is a satellite of the 18th International Conference on Systems Biology (ICSB).
Participants will learn how to set up computer models of biological systems (e.g. metabolic or signalling networks) using experimental kinetic data and how to simulate them in different systems biology platforms. Hands-on sessions, lectures and software demonstrations will be included, providing attendees with the necessary skills to access experimental kinetics data from available resources, to assemble computer models with these data, and finally to simulate the generated models using simulation tools. Also handling and exchange of biological models based on existing community standards will be demonstrated along with the basic principles of the underlying standard formats.
The topics will include:
- Model setup using different software tools and systems biology platforms
- Using experimental data for setting up quantitative models
- Parameter estimation, optimization and model fitting
- Simulation, analysis and visualization of biochemical models
- Database supported modelling: integrated data management and model databases
- Community standards and formats for systems biology models
Target audience
Experimentalists and modellers with some very basic experience in modelling and simulation of biological networks and everybody who would like to learn more about the tools and standards. Attendees are expected to bring their own computer.
 Tutors |  Agenda |  Registration |  Location |  Accommodation |  Travel |  Additional Information | Organization |
Tutors
- Akira Funahashi and Noriko Hiroi: Keio University (Yokohama, Japan)
- Martin Golebiewski, Ron Henkel and Andreas Weidemann: HITS, Heidelberg (Germany)
- Stefan Hoops: Biocomplexity Institute of Virginia Tech (Blacksburg, Virginia, USA)
- Ursula Kummer, Frank Bergmann, Jürgen Pahle and Sven Sahle: University of Heidelberg (Germany)
- Leslie M. Loew: UConn Health - Richard D. Berlin Center for Cell Analysis and Modeling (Farmington, CT, USA)
- Pedro Mendes: UConn Health - Center for Quantitative Medicine (Farmington, CT, USA)
Agenda
There will be short presentations about the covered tools, databases and modeling standards, as well as hands-on sessions and software demonstrations for practical training. It will be demonstrated how the different tools can be used in concerted modeling workflows.
Detailed agenda: Download HERE
Full Agenda (including presentation slides)
Covered tools, platforms and databases
- CellDesigner: http://www.celldesigner.org/
- COPASI: http://www.copasi.org
- JWS Online: http://jjj.biochem.sun.ac.za/
- SABIO-RK: http://sabio.h-its.org/
- SEEK: http://fair-dom.org/platform/seek/
- Virtual Cell (VCell): http://vcell.org
Covered standards
- SBGN: http://www.sbgn.org
- SBML: http://sbml.org
- SED-ML: http://sed-ml.org/
- and more...
Registration
The participation in the tutorial is free of charge.
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Location
Squires student center
290 College Avenue
Blacksburg, Virginia 24061
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Accommodation
Please refer to the ICSB accommodation website to book your hotel:
Accommodation
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Travel Information
Please refer to the ICSB website for travel details:
Travel
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Additional Information
Internet Access
The meeting rooms have wireless internet access. More information will be provided on-site.
Electrical Supply
If you are travelling from abroad, make sure to bring an appropriate travel adapter for your laptop and all other electrical devices you are bringing. The mains supply in the US works with 110-120 V at 60 Hz. The plug types are Type A or B.
Organization
| Martin Golebiewski |
| Phone: +49-6221-533-281 |
| FAX: +49-6221-533-298 |
| HITS gGmbH |
| Schloss-Wolfsbrunnenweg 35 |
| D-69118 Heidelberg |
| Germany |
| http://www.h-its.org |
Funding Acknowledgements
Support for this COMBINE tutorial is provided by the following organisations:
| HITS |