R
Ralph Gauges
Researcher at Heidelberg University
Publications - 17
Citations - 3801
Ralph Gauges is an academic researcher from Heidelberg University. The author has contributed to research in topics: SBML & Software. The author has an hindex of 10, co-authored 16 publications receiving 3478 citations. Previous affiliations of Ralph Gauges include University Hospital Heidelberg.
Papers
More filters
Journal ArticleDOI
COPASI---a COmplex PAthway SImulator
Stefan Hoops,Sven Sahle,Ralph Gauges,Christine Lee,Jürgen Pahle,Natalia Simus,Mudita Singhal,Liang Xu,Pedro Mendes,Ursula Kummer +9 more
TL;DR: COPASI is presented, a platform-independent and user-friendly biochemical simulator that offers several unique features, and numerical issues with these features are discussed; in particular, the criteria to switch between stochastic and deterministic simulation methods, hybrid deterministic-stochastic methods, and the importance of random number generator numerical resolution in Stochastic simulation.
Journal ArticleDOI
The Systems Biology Graphical Notation
Nicolas Le Novère,Michael Hucka,Huaiyu Mi,Stuart L. Moodie,Falk Schreiber,Falk Schreiber,Anatoly Sorokin,Emek Demir,Katja Wegner,Mirit I. Aladjem,Sarala M. Wimalaratne,Frank T Bergman,Ralph Gauges,Peter Ghazal,Hideya Kawaji,Lu Li,Yukiko Matsuoka,Alice Villéger,Sarah Elizabeth Boyd,Laurence Calzone,Mélanie Courtot,Ugur Dogrusoz,Tom C. Freeman,Akira Funahashi,Samik Ghosh,Akiya Jouraku,Sohoung Kim,Fedor A. Kolpakov,Augustin Luna,Sven Sahle,Esther Schmidt,Steven Watterson,Steven Watterson,Guanming Wu,Igor Goryanin,Douglas B. Kell,Chris Sander,Herbert M. Sauro,Jacky L. Snoep,Kurt W. Kohn,Hiroaki Kitano +40 more
TL;DR: The Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists, believes that it will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge.
Book ChapterDOI
Computational modeling of biochemical networks using COPASI.
TL;DR: Practical examples are described for steady-state and time-course simulations, stoichiometric analyses, parameter scanning, sensitivity analysis, global optimization, parameter estimation, and stochastic simulation.
Journal ArticleDOI
Comparison of the dynamics of substrate access channels in three cytochrome P450s reveals different opening mechanisms and a novel functional role for a buried arginine.
TL;DR: The results for these three P450s suggest that the channel opening mechanisms are adjusted to the physico-chemical properties of the substrate and can kinetically modulate protein-substrate specificity.
Proceedings ArticleDOI
Simulation of biochemical networks using COPASI: a complex pathway simulator
Sven Sahle,Ralph Gauges,Jürgen Pahle,Natalia Simus,Ursula Kummer,Stefan Hoops,Christine Lee,Mudita Singhal,Liang Xu,Pedro Mendes +9 more
TL;DR: A new software tool is presented that is platform independent, user friendly and offers several unique features of simulation and modeling software and discusses numerical considerations and support for the switching between simulation methods.