Simulation of biochemical networks using COPASI: a complex pathway simulator

Authors:
Sven Sahle;Ralph Gauges;Jürgen Pahle;Natalia Simus;Ursula Kummer;Stefan Hoops;Christine Lee;Mudita Singhal;Liang Xu;Pedro Mendes
Affiliations:
EML Research, Schloss-Wolfsbrunnenweg, Heidelberg, Germany;EML Research, Schloss-Wolfsbrunnenweg, Heidelberg, Germany;EML Research, Schloss-Wolfsbrunnenweg, Heidelberg, Germany;EML Research, Schloss-Wolfsbrunnenweg, Heidelberg, Germany;EML Research, Schloss-Wolfsbrunnenweg, Heidelberg, Germany;Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA;Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA;Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA;Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA;Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA
Venue:
Proceedings of the 38th conference on Winter simulation
Year:
2006

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Abstract

Simulation and modeling is becoming one of the standard approaches to understand complex biochemical processes. Therefore, there is a big need for software tools that allow access to diverse simulation and modeling methods as well as support for the use of these methods. Here, we present a new software tool that is platform independent, user friendly and offers several unique features. In addition, we discuss numerical considerations and support for the switching between simulation methods.