Modular modeling of cellular systems with ProMoT/Diva.

@article{GinkelM_Bioinformatics_03, abstract = {MOTIVATION: Need for software to setup and analyze complex mathematical models for cellular systems in a modular way, that also integrates the experimental environment of the cells. RESULTS: A computer framework is described which allows the building of modularly structured models using an abstract, modular and general modeling methodology. With this methodology, reusable modeling entities are introduced which lead to the development of a modeling library within the modeling tool ProMot. The simulation environment Diva is used for numerical analysis and parameter identification of the models. The simulation environment provides a number of tools and algorithms to simulate and analyze complex biochemical networks. The described tools are the first steps towards an integrated computer-based modeling, simulation and visualization environment Availability: Available on request to the authors. The software itself is free for scientific purposes but requires commercial libraries. SUPPLEMENTARY INFORMATION: http://www.mpi-magdeburg.mpg.de/projects/promot}, address = {Max-Planck-Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, D-39106 Magdeburg, Germany. ginkel@mpi-magdeburg.mpg.de}, author = {Ginkel, M. and Kremling, A. and Nutsch, T. and Rehner, R. and Gilles, E. D. }, citeulike-article-id = {326281}, issn = {1367-4803}, journal = {Bioinformatics}, keywords = {mpicompnotes, mpipubs}, month = {June}, number = {9}, pages = {1169--1176}, posted-at = {2006-06-26 10:35:20}, priority = {2}, title = {Modular modeling of cellular systems with ProMoT/Diva.}, url = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/9/1169}, volume = {19}, year = {2003} }

TY - JOUR ID - GinkelM_Bioinformatics_03 L3 - citeulike-article-id:326281 TI - Modular modeling of cellular systems with ProMoT/Diva. JF - Bioinformatics VL - 19 IS - 9 SP - 1169 EP - 1176 AD - Max-Planck-Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, D-39106 Magdeburg, Germany. ginkel@mpi-magdeburg.mpg.de SN - 1367-4803 N2 - MOTIVATION: Need for software to setup and analyze complex mathematical models for cellular systems in a modular way, that also integrates the experimental environment of the cells. RESULTS: A computer framework is described which allows the building of modularly structured models using an abstract, modular and general modeling methodology. With this methodology, reusable modeling entities are introduced which lead to the development of a modeling library within the modeling tool ProMot. The simulation environment Diva is used for numerical analysis and parameter identification of the models. The simulation environment provides a number of tools and algorithms to simulate and analyze complex biochemical networks. The described tools are the first steps towards an integrated computer-based modeling, simulation and visualization environment Availability: Available on request to the authors. The software itself is free for scientific purposes but requires commercial libraries. SUPPLEMENTARY INFORMATION: http://www.mpi-magdeburg.mpg.de/projects/promot KW - mpicompnotes KW - mpipubs AU - Ginkel, M AU - Kremling, A AU - Nutsch, T AU - Rehner, R AU - Gilles, ED PY - 2003/06/12/ UR - http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/9/1169 ER -