Over the years, we have been involved in the development of two software packages in close collaboration with Dr Brett Olivier (Systems Bioinformatics, VU University) and Timo Maarleveld (Systems Bioinformatics, VU University & Life Science, CWI):
- Pysces. This package was developed by Dr Brett Olivier while he was in Stellenbosch (South Afrika) and extended with constraint-based stoichiometric modeling of metabolism in Amsterdam.
- StochPy. This package is an extension of Pysces and has been developed by Timo Maarleveld under supervision of Dr Brett Olivier and Dr Frank Bruggeman with help of two master students, Maxime Moinat & Katy Wei, and Anne Schwabe (a PhD student). It allows for stochastic simulation of molecular systems inside living cells.