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Oberwolfach Seminar

19 – 25 November 2017

The seminar will include tutorial courses and modeling exercises focusing on the following topics:

  • different modeling paradigms for biological systems on the cellular level (ODEs, discrete dynamical systems, stochastic models), their advantages and disadvantages, challenges, and potential applications

  • property conservation across formalisms

  • parameter estimation and uncertainty quantification

The seminar takes place at the Mathematisches Forschungsinstitut Oberwolfach. The Institute covers board and lodging. By the support of the Carl Friedrich von Siemens Foundation travel expenses can be reimbursed up to 150 EUR in average per person (against copies of travel receipts). The number of participants is restricted to 25.

For organizational information see:

Applications should include

  • full name and university/institute address, e-mail address
  • short CV, present position, university
  • name of supervisor of Ph.D. thesis
  • a short summary of previous work and interest
  • title, ID and date of the intended seminar

and should be sent preferably by e-mail (with attachments in pdf format) to:

Prof. Dr. Dietmar Kröner
Mathematisches Forschungsinstitut Oberwolfach Schwarzwaldstr. 9 – 11
77709 Oberwolfach

Preliminary Program

The Seminar will start on Sunday with a poster session, on Wednesday an excursion is planned. Departure is on Saturday. It is obligatory for all participants to attend the full program, a partial participation is not possible!

Monday: Discrete modelling

9:00-9:30       Introduction

9:30-11:00     Discrete modeling I: Basics Boolean modeling - mathematics and application

11:30-12:30   Discrete modeling II: Advanced analysis 

13:30-14:30   Software Introduction, application example

15:00-17:00   Group work

  • Study of application problems from scientific publications and model repositories

  • Testing mathematical hypotheses

  • Additional methods and theoretical results 

17:00-17:30   Results preparation in the groups

17:30-18:15   Presentation and discussion

Tuesday: Metabolic networks

9:00  - 10:30    Biochemical reaction networks and mass balancing, stoichiometric analysis, quasi-steady state assumption

11:00 - 12:30   Constrained based models: Optimization principle, flux balance analysis, dynamic flux balance analysis

13:30 - 14:30   Matlab toolboxes for metabolic network analysis

15:00 - 17:00   Group work:

  • Analysis and simulation of models from public repositories

  • Discussion / presentation of own research for attendants already working in this field

17:00 - 17:30   Results preparation in the groups

17:30 - 18:15   Presentation and discussion of group work results

Wednesday: Regulatory and signaling pathways

9:00 - 10:30     Dynamics of regulatory and signaling pathways (stability, oscillations, bifurcations, sensitivity)

11:00 - 12:30   Stochastic chemical kinetics (Markov jump processes and the CME, rare events)

14:00 - 18:00   Excursion

Thursday: Parameter estimation

9:00 - 10:30    Parameter optimization:

  • Local and global search methods

  • Analysis of goodness-of-fit

11:00 - 12:30   Identifiability and uncertainty analysis:

  • Asymptotic methods

  • Profile likelihood

  • Markov-chain Monte-Carlo methods

13:30 - 14:30   Toolboxes for analysis, simulation and parameter estimation for ODEs and/or stochastics models (e.g. Copasi, AMICI, Data2Dynamics)

15:00 - 17:00   Group work: Analysis, simulation and parameter estimation for models and datasets from public repositories

17:00 - 17:30   Results preparation in the groups

17:30 - 18:15   Presentation and discussion

Friday: Hybrid modeling approaches and open problems

9:00 - 10:30     Hybrid discrete/continuous modelling, property conservation across formalisms

11:00 - 12:30   Further modeling approaches: semi-quantitative, agent-based, spatio-temporal

13:30 - 14:30   Open problems

15:00 - 17:00   Current plan: each group chooses a different formalism, explains the mathematical background, and presents an example (from literature) with emphasis on the question why a particular formalism is particularly useful for the specific example system

17:00 - 18:00   Presentation and discussion of results

18:00 - 18:15   Wrap-up




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