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Modelling Workshop

 

ODE Modelling in Systems Biology


- Current Methodology
and Solutions of Application Issues -

 

FRIAS Junior Researcher Conference

Uni Freiburg, Germany

 

Sep 19th – Sep 22th, 2017
(Tuesday evening - Friday noon)

 

https://www.frias.uni-freiburg.de/de/startseite/carousel/forschungsthemen-1/image

 

Invited Speakers

 

·         Dr. Andreas Raue, Merrimack Pharmaceutical, Boston, USA

·         Dr. Jan Hasenauer, Group Leader Data-driven Computational Modeling, Helmholtz-Center, Munich

·         Prof. Jörg Stelling, Head of Computational Systems Biology Group, ETH Zürich, Switzerland

·         Dr. Alejandro Villaverde, Bioprocess Engineering Group, Vigo, Spain.

Workshop Summary


Workshop summary as Flyer (pdf).

Topic

 

The focus of the workshop is

(1)    methodology for establishing ODE models, especially recent developments in optimization, parameter estimation and uncertainty quantification

(2)    discussing and solving application show cases and issues

Focus (1) covers the following aspects:

·         Parameter estimation

·         Network reconstruction/model discrimination

·         L1 penalization

·         Uncertainty analysis (parameters and predictions)

·         Concepts of identifiability and observability analyses

·         Optimization issues

·         Numerical aspects

·         Appropriate handling of replicates, detection limits and saturation

·         Error models

·         Benchmarking and performance improvement

·         Overcoming of limitations and bottlenecks

Focus (2): For discussing and illustrating implementation issues, we request problems and questions from the workshop participants as they occur in applications (guidelines and an example are provided here). They are called “application issues” in the following.
These problems are presented at the workshop, discussed by the audience with the ultimate goal to suggest and demonstrate a solution using one of the modelling toolboxes applied in Systems Biology (e.g. D2D, dmod, PESTO, Copasi, …). In an ideal case, there are experts/developers for these toolboxes in the audience.

The workshop is intended for researchers at the PhD/PostDoc level. Everybody is invited.

It is NOT intended to give general introductions (like in summer/winter schools) for people who are new in this field. Instead, the focus is on advanced methodological questions for researchers which already have some experience.

Program

 

The preliminary program:

 

Registration

 

Registration and abstract submission for posters, talks and “application issues” are done here.  Alternatively, send an email to ckreutz@fdm.uni-freiburg.de.

In the registration form, you can specify whether you want to present a poster and/or talk or an “application issue”. Talks should have a focus on methodology.

 

Important dates and conference fee

 

The conference fee is 130€ and includes catering as well as bus transfer to the social events.

Please register as early as possible. The number of participants is limited to 50.

 

If there are more requests for talks than time slots, then the organizers will decide based on the topic and submission date (early submission are preferred).

·         Registration deadline for talks: June 30th, 2017.

·         Registration deadline for “application issues”: July 31st, 2017.

Please register as early as possible. An example for an application issue is shown here. The number of application issues is limited to 10.

·         The final registration deadline for participation and posters is July 31th, 2017.

 

Venue

 

The workshop takes place at the

Freiburg Institute for Advanced Studies (FRIAS)

University of Freiburg

Albertstraße 19
79104 Freiburg
Germany


Phone: +49 761 203 97404
Fax: +49 761 203 97450
Mail: info@frias.uni-freiburg.de

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Accommodation

Please book accommodation by yourself.

Acknowledgement

The workshop is supported by funding provided by the Freiburg Institute for Advanced Studies (FRIAS).

The scientific work behind this workshop is funded by the German Ministry of Education and Research (BMBF) via e:Bio Grant No. 031L0080.

 

Contact

 

Major Organizer:

Dr. Clemens Kreutz

Center for Biosystems Analysis (ZBSA)
Center for Data Analysis and Modelling (FDM)
Habsburger Str. 49
79104 Freiburg, Germany

Office 1: +49 761 203 97207
Office 2: +49 761 203 8533

If there are any issues, please contact me.

 

2nd Organizer:

Prof. Jens Timmer

Institute of Physics
Hermann Herder Str. 3
79104 Freiburg, Germany

Office +49 761 203 5829

 

 

FRIAS-Hörsaal

Workshop Lecture Hall in the FRIAS.