Publications of Martin Ginkel

Saez-Rodriguez, J.; Gayer, S.; Ginkel, M.; Gilles, E. D.: Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules. Bioinformatics 24 (16), pp. i213 - i219 (2008)

Krasnyk, M.; Ginkel, M.; Mangold, M.; Kienle, A.: Numerical analysis of higher order singularities in chemical process models. Computers and Chemical Engineering 31 (9), pp. 1100 - 1110 (2007)

Saez-Rodriguez, J.; Mirschel, S.; Hemenway, R.; Klamt, S.; Gilles, E. D.; Ginkel, M.: Visual set-up of logical models of signaling and regulatory networks with ProMoT. BMC Bioinformatics 7, 506 (2006)

Waschler, R.; Angeles-Palacios, O.; Ginkel, M.; Kienle, A.: Object-oriented modelling of large scale chemical engineering processes with ProMoT. Mathematical and Computer Modelling of Dynamical Systems 12 (1), pp. 5 - 18 (2006)

Mangold, M.; Angeles-Palacios, O.; Ginkel, M.; Kremling, A.; Waschler, R.; Kienle, A.; Gilles, E. D.: Computer Aided Modeling of Chemical and Biological Systems: Methods, Tools, and Applications. Industrial and Engineering Chemistry Research 44 (8), pp. 2579 - 2591 (2005)

Kremling, A.; Ginkel, M.; Klamt, S.; Gilles, E. D.: Workbench zur Modellbildung, Simulation und Analyse zellulärer Systeme. it - Information Technology 46, pp. 12 - 19 (2004)

Mangold, M.; Ginkel, M.; Gilles, E. D.: A model library for membrane reactors implemented in the process modelling tool ProMoT. Computers and Chemical Engineering 28 (3), pp. 319 - 332 (2004)

Ginkel, M.; Kremling, A.; Nutsch, T.; Rehner, R.; Gilles, E. D.: Modular modeling of cellular systems with ProMoT/Diva. Bioinformatics 19, pp. 1169 - 1176 (2003)

Hucka, M.; Finney, A.; Sauro, H. M.; Bolouri, H.; Doyle, J. C.; Kitano, H.; Arkin, A. P.; Bornstein, B. J.; Bray, D.; Cornish-Bowden, A. et al.; Cuellar, A. A.; Dronov, S.; Gilles, E. D.; Ginkel, M.; Gor, V.; Goryanin, I. I.; Hedley, W. J.; Hodgman, T. C.; Hofmeyr, J. H.; Hunter, P. J.; Juty, N. S.; Kasberger, J. L.; Kremling, A.; Kummer, U.; Le Novere, N.; Loew, L. M.; Lucio, D.; Mendes, P.; Minch, E.; Mjolsness, E. D.; Nakayama, Y.; Nelson, M. R.; Nielsen, P. F.; Sakurada, T.; Schaff, J. C.; Shapiro, B. E.; Shimizu, T. S.; Spence, H. D.; Stelling, J.; Takahashi, K.; Tomita, M.; Wagner, J.; Wang, J.: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19 (4), pp. 524 - 531 (2003)

Klamt, S.; Stelling, J.; Ginkel, M.; Gilles, E. D.: FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics 19 (2), pp. 261 - 269 (2003)

Sundmacher, K.; Schultz, T.; Zhou, S.; Scott, K.; Ginkel, M.; Gilles, E. D.: Dynamics of the direct methanol fuel cell (DMFC): experiments and model-based analysis. Chemical Engineering Science 56 (2), pp. 333 - 341 (2001)

Tränkle, F.; Zeitz, M.; Ginkel, M.; Gilles, E. D.: PROMOT: A modeling tool for chemical processes. Mathematical and Computer Modelling of Dynamical Systems 6 (3), pp. 283 - 307 (2000)

Eils, J.; Lawerenz, C.; Astrahantseff, K.; Ginkel, M.; Eils, R.: Databases for Systems Biology. In: Computational Systems Biology, pp. 15 - 38 (Eds. Kriete, A.; Eils, R.). Elsevier, Amsterdam [u.a.] (2005)

Schoeberl, B.; Ginkel, M.; Gilles, E. D.; Müller, G.: Mathematical modeling of signaling cascades: principles and future prospects. In: Function and Regulation of Cellular Systems: Experiments and Models, pp. 73 - 87 (Eds. Deutsch, A.; Howard, J.; Falcke, M.; Zimmermann, W.). Birkhäuser, Basel [u.a.] (2004)

Stelling, J.; Kremling, A.; Ginkel, M.; Bettenbrock, K.; Gilles, E. D.: Towards a Virtual Biological Laboratory. In: Foundations of systems biology, pp. 189 - 212 (Ed. Kitano, H.). MIT Press, Cambridge/Massachusetts (2001)

Krasnyk, M.; Bondareva, K.; Milokhov, O.; Teplinskiy, K.; Ginkel, M.; Kienle, A.: The ProMoT/Diana Simulation Environment. In: 16th European Symposium on Computer Aided Process Engineering and 9th International Symposium on Process Systems Engineering, pp. 445 - 450 (Eds. Marquardt, M.; Pantelides, C.). 16th European Symposium on Computer Aided Process Engineering and 9th International Symposium on Process Systems Engineering, Garmisch-Partenkirchen, Germany, July 09, 2006 - July 13, 2006. Elsevier, Amsterdam (2006)

Krasnyk, M.; Ginkel, M.; Mangold, M.; Kienle, A.: Numerical Analysis of Higher-Order Singularities in Complex Chemical Process Models in ProMoT. In: European Symposium on Computer Aided Process Engineering - 15, pp. 223 - 228 (Eds. Puigjaner, L.; Espuña, A.). 15th European Symposium on Computer Aided Process Engineering , Barcelona, Spain, May 29, 2005 - June 01, 2005. Elsevier, Amsterdam (2005)

Chebotarov, M.; Ginkel, M.; Häfele, M.; Mangold, M.; Gilles, E. D.; Kienle, A.; Svjatnyj, V.: DIVAGUI: the graphical user interface for the simulation environment DIVA. In: Simulationstechnik: 17. Symposium in Magdeburg, pp. 155 - 160 (Ed. Hohmann, R.). ASIM 2003 : 17. Symposium Simulationstechnik, Magdeburg, Germany, May 16, 2003 - May 19, 2003. (2003)

Kremling, A.; Bettenbrock, K.; Fischer, S.; Ginkel, M.; Sauter, T.; Gilles, E. D.: Towards whole cell in silico models for cellular systems: model set-up and model validation. In: Positive systems: proceedings of the First Multidisciplinary International Symposium on Positive Systems (POST 2003), pp. 92 - 102 (Eds. Benvenuti, L.; de Santis, A.; Farina, L.). First Multidisciplinary International Symposium on Positive Systems (POST 2003), Rome, Italy, August 28, 2003 - August 30, 2003. (2003)

Mangold, M.; Ginkel, M.; Gilles, E. D.: Entwicklung einer Bibliothek dynamischer Membranreaktormodelle mit Hilfe des Modellierungswerkzeugs ProMoT. In: Simulationstechnik: 17. Symposium in Magdeburg, pp. 161 - 166 (Ed. Hohmann, R.). ASIM 2003 - 17. Symposium Simulationstechnik, Magdeburg, Germany, September 16, 2003 - September 19, 2003. (2003)