Instructors:
Frank Bergmann (Heidelberg University), Ursula Kummer (Heidelberg University), Jürgen Pahle (Heidelberg University), Sven Sahle (Heidelberg University), (de.NBI-SysBio), Stefan Hoops (Virginia Tech), Pedro Mendes (University of Connecticut)
Date:
27th Oct 2018 1:00 pm - 6:00pm
Location:
Amphitheater F, Ecole Normale Supérieure de Lyon, 46 Allée d’Italie, 69007 Lyon.
Content:
COPASI is a widely used software tool for creating, simulating and analyzing models of biochemical reaction networks. It is open source free software and available for all major operating systems. Its features include deterministic and stochastic simulation, steady state analysis, stoichiometric analysis, optimization and parameter estimation, time scale analysis, sensitivities and metabolic control analysis, Lyapunov exponents, linear noise approximation, etc. In the workshop we will demonstrate the use of advanced features of COPASI, focusing on parameter estimation and parameter identifiability analysis, and the use of COPASI from scripting languages. The developers of COPASI will also be available for the discussion of individual questions from the participants.
Motivation:
COPASI is one of the most widely used tools for kinetic modelling of biochemical reaction networks. It is used in hundreds of (published) research projects for many years (see http://copasi.org/Research/), and for teaching at numerous universities. It aims at providing scientists with a professional tool that can be used by biologists with modelling expertise but does not require expert knowledge in numerical mathematics or computer programming. The target user base of COPASI therefore overlaps very well with the audience of the ICSB (which is why we have offered similar workshops at almost every ICSB in the past). While many scientists in the field already know about COPASI (or use it), we think it will be beneficial for many participants of the ICBS to have the possibility to learn about new and advanced features of COPASI, and to be able to directly discuss with the developers. As the focus of the workshop we chose parameter estimation and parameter identifiability analysis since these are very central techniques in computational systems biology.
Tools:
COPASI
Prerequisites:
The participants should bring their own laptop computers.
Contact:
Name: Frank T. Bergmann
Email:
Website & Registration: http://denbi-modsim.de/icsb_copasi_2018/