Sven Sahle (Heidelberg University), Frank Bergmann (Heidelberg University), Stefan Hoops (University of Virginia), Ursula Kummer (Heidelberg University), Pedro Mendes (University of Connecticut), Jürgen Pahle (Heidelberg University), Egils Stalidzans (University of Latvia) (de.NBI-SysBio / de.NBI-ModSim)
Thursday, October 31st, 2019
Room 3, Okinawa Institute of Science and Technology Graduate University
COPASI is a widely used software tool for creating, simulating and analysing 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, optimisation 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. For experienced users of the software, we will present an overview of new features added in the latest releases, such as stochastic differential equation models. A special session will demonstrate an optimisation workflow, highlighting how COPASI can be integrated in third party software projects. The developers of COPASI will also be available for the discussion of individual questions from the participants.
systems biology, software tools, quantitative models, parameter estimation, model simulation, metabolic networks, model databases, community standards
Frank T. Bergmann,