Authors and Contributors

Current Developers

See github for currently active developers.

Original Developers

Rainer Machné, Christoph Flamm, Andrew Finney, Stefan Müller, James Lu, Akira Funahashi and the CellDesigner team.


Colin Gillespie, Eryk Wolski, Nicolas Le Novère, Tommi Aho and W. Eryk Wolski have reported bugs and/or made great suggestions for new functionalities.


Initial work

In the early 90ies Walter Fontana started to apply Scott Cohen's and Alan Hindmarsh's CVODE (a solver for stiff and non-stiff ODEs) to chemical kinetics problems arising from the (`RNA world') theory of early bio/chemical evolution, as studied at Peter Schuster's group at the TBI. Stefanie Widder and Christoph Flamm took up this work to create a generic reaction network solver for models of evolving gene regulatory networks. SBML's official library libSBML enabled Rainer Machné to adapt this work and tie up both to the institute's tradition of providing interfaces to efficient algorithms (see the Vienna RNA Package) and to SBML's and libSBML's spirit of providing application developers and researchers in Systems Biology with a community standard of well-defined methods. SCAMP and libSBML, and email discussions with their authors Herbert Sauro and Ben Bornstein, respectively, were an inspiring motivation for finally starting the SOSlib project. Stefan Müller has greatly improved the mathematical backend for symbolic operations such as formula differentiation and simplification which started to open SOSlib usage for symbolic analysis.

The Tokyo Release Series

The CellDesigner team was the first group to implement the SOSlib as a library, and Akira Funahashi provided the first pre-compiled Windows version. Their experience and suggestions have greatly contributed to the high level API interfaces to SOSlib. In May 2005 Christoph Flamm and Rainer Machné attended the Third SBML Hackathon in Tokyo, a meeting which shaped the current state of the library and therefore provided the name of this release series. Andrew Finney has joined the team and started the work on an official API interface, consistent error management and performance optimization of integration routines. Andrew is also responsible for a full implementation for Windows, including pre-compiled applications and a MSVC developer framework. Finally, James Lu and Stefan Müller from Heinz Engl's Inverse Problems group at the RICAM helped to incorporate CVODES' sensitivity analysis features, which will start off a larger attempt to comprehensively utilize the SUNDIALS package's powerful algorithms and input settings.


SBML Compliance Logo SourceForge.net Logo OpenSource.org Logo GNU Logo


Please email to admins to report problems or questions with this website.
Last modified: 2006-08-31 13:43:26 raim raim