Pedro Mendes (Virginia Bioinformatics Institute), Sven Sahle and Ralph Gauges (EML Research gGmbH)
COPASI (Complex Pathway Simulator) is a software application for simulation and analysis of biochemical networks. It is developed jointly by the groups of Pedro Mendes (Virginia Bioinformatics Institute, USA) and Ursula Kummer (EML Research, Germany), and is freely available for academic use.
Besides doing deterministic and stochastic time course simulation, COPASI has a number of advanced methods for the analysis of biochemical reaction networks.
In this course we will explain how COPASI can be used to do parameter scans and parameter estimation.
Another topic will be how users can use COPASI to optimize certain model aspects as for example the flux through a certain reaction, via the optimization task.
Although COPASI has a large number of predefined output definitions that the user can choose from, it is sometimes desirable to define your own custom output. In this course we will show how the user can define his/her own complex reports with COPASI's powerful report widget.
modelers (computational biologists) and experimentalists that are already familiar with modeling.
Participants are encouraged to bring their own computers.