COMBINE & de.NBI Tutorial: Modelling and Simulation Tools in Systems Biology



Dates: Saturday, October 27th, 2018 (9:00 - 18:00)
Location: Lyon, France

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 19th 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, and multicellular modelling • Constraint-based and logical modeling of metabolic and signaling networks • Database supported modelling: integrated data management and model databases • Community standards and formats for systems and synthetic 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

Travel Information and Accommodation

Additional Information

Organization

Tutors



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. It is planned to have joint demo and hands-on sessions in the afternoon with the FAIRDOM workshop (FAIR Data Management in Life-Sciences), that will be running in parallel at the same venue: https://fair-dom.org/2018/05/30/join-us-at-fair-data-management-in-life-sciences-a-workshop-and-user-meeting-in-lyon-france-sat-27th-oct/

Agenda outline:

09.00-12.30 Introduction lessons
09.00-10.30 Tools and Data Resources for Modeling and Simulation
10.30-11.00 Coffee break
11.00-12.30 Tools and Data Resources for Modeling and Simulation

12.30-14.00 Lunch break

The afternoon session will be a joint session with the Workshop FAIR Data Management in Life-Sciences. There are 4 different tracks, with sessions to choose from. You can swap tracks through the afternoon.

14.00-18.00 COMBINE & de.NBI Hands-on Track 1
14.00-16.00 SABIO-RK (30 min demo/hands-on) and COPASI (1.5 h hands-on)
16.00-16.30 Coffee break
16.30-18.00 SEEK/FAIRDOMhub (30 min demo) and JWS online (1 h hands-on)

14.00-18.00 COMBINE & de.NBI Hands-on Track 2
14.00-16.00 CellDesigner (1 h hands-on) and CellNetAnalyzer (1 h hands-on)
16.00-16.30 Coffee break
16.30-18.00 BioModels (30 min demo) and Morpheus (1 h hands-on)

14.00-18.00 FAIRDOM Track 1 (shared with Workshop FAIR Data Management in Life-Sciences)
14.00-16.00 SEEK advanced training
16.00-16.30 Coffee break
16.30-18.00 openBIS advanced training

14.00-18.00 FAIRDOM Track 2 (shared with Workshop FAIR Data Management in Life-Sciences)
14.00-16.00 Metadata integration between platforms
16.00-16.30 Coffee break
16.30-18.00 Attendee guided breakouts


Detailed agenda: ...Coming soon...

Covered tools, platforms and databases

Introduced standard formats

Some commonly used community standards for model and modelling data exchange, as well as for model visualization will be introduced (SBGN, SBML and SED-ML) in practical examples using the covered tools. More information about the standards can be found on the COMBINE (Computational Modeling in Biology Network) website: http://co.mbine.org

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Registration

The participation in the tutorial is free of charge, but please register by September 15th, 2018

TUTORIAL REGISTRATION:
https://docs.google.com/forms/d/e/1FAIpQLSfoKANWs9rUI7ZI_3iXp6F6X59U4iKr6vE5Q-CM0E0sHg01RQ/viewform


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Location

Ecole Normale Supérieure de Lyon
Site Monod
Main reception desk is at 46 Allée d'Italie, 69007 Lyon.
Entrance for the workshop building (MGN2) is just opposite.
http://international.ens-lyon.fr/how-to-get-to-the-ens-de-lyon--106627.kjsp

Beware that ENS de Lyon has 2 locations in the same area so that some of the street signs leads to the wrong location. The map at http://international.ens-lyon.fr/plan-d-acces-aux-sites-de-l-ens-de-lyon-147995.kjsp?RH=1436533833707
clearly illustrates the situation.


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Travel Information and Accommodation

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.


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




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Funding Acknowledgements

Support for this COMBINE tutorial is provided by the following organisations:


HITS

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