Modelling, parameter identification, and simulation play an important role in Systems Biology. In recent years, various software packages have been established for scientific use in both licencing types, open source as well as commercial.  Many of these codes are based on inefficient and mathematically outdated algorithms. By introducing the package BioPARKIN, we want to improve this situation. The development of the software BioPARKIN involves long standing mathematical ideas that, however, have not yet entered the field of Systems Biology, as well as new ideas and tools that are particularly important for the analysis of the dynamics of biological networks.

Developed as part of the project POEM.

BioPARKIN is open-source software under the LGPL.

The source code can be downloaded at github.com. Currently, the user manual and an executable BioPARKIN for Windows can be found in our download section at github.

T. Dierkes, M. Wade, U. Nowak, S. Röblitz: BioPARKIN: Biology-related Parameter Identification in Large Kinetic Networks, ZIB-report 11-15.