Publications of Martin Ginkel

Saez-Rodriguez, J., Gayer, S., Ginkel, M., & Gilles, E. D. (2008)Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modulesBioinformatics, 24 (16), i213–i219doi: 10.1093/bioinformatics/btn289.

Krasnyk, M., Ginkel, M., Mangold, M., & Kienle, A. (2007)Numerical analysis of higher order singularities in chemical process modelsComputers and Chemical Engineering, 31 (9), 1100–1110doi: 10.1016/j.compchemeng.2006.09.010.

Saez-Rodriguez, J., Mirschel, S., Hemenway, R., Klamt, S., Gilles, E. D., & Ginkel, M. (2006)Visual set-up of logical models of signaling and regulatory networks with ProMoTBMC Bioinformatics, 7, 506doi: 10.1186/1471-2105-7-506.

Waschler, R., Angeles-Palacios, O., Ginkel, M., & Kienle, A. (2006)Object-oriented modelling of large scale chemical engineering processes with ProMoTMathematical and Computer Modelling of Dynamical Systems, 12 (1), 5–18doi: 10.1080/13873950500071017.

Mangold, M., Angeles-Palacios, O., Ginkel, M., Kremling, A., Waschler, R., Kienle, A., & Gilles, E. D. (2005)Computer Aided Modeling of Chemical and Biological Systems: Methods, Tools, and ApplicationsIndustrial and Engineering Chemistry Research, 44 (8), 2579–2591doi: 10.1021/ie0496434.

Kremling, A., Ginkel, M., Klamt, S., & Gilles, E. D. (2004)Workbench zur Modellbildung, Simulation und Analyse zellulärer Systemeit - Information Technology, 46, 12–19doi: 10.1524/itit.46.1.12.26503 .

Mangold, M., Ginkel, M., & Gilles, E. D. (2004)A model library for membrane reactors implemented in the process modelling tool ProMoTComputers and Chemical Engineering, 28 (3), 319–332doi: 10.1016/S0098-1354(03)00189-3.

Ginkel, M., Kremling, A., Nutsch, T., Rehner, R., & Gilles, E. D. (2003)Modular modeling of cellular systems with ProMoT/DivaBioinformatics, 19, 1169–1176doi: 10.1093/bioinformatics/btg128.

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., 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. (2003)The systems biology markup language (SBML): a medium for representation and exchange of biochemical network modelsBioinformatics, 19 (4), 524–531doi: 10.1093/bioinformatics/btg015.

Klamt, S., Stelling, J., Ginkel, M., & Gilles, E. D. (2003)FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux mapsBioinformatics, 19 (2), 261–269doi: 10.1093/bioinformatics/19.2.261.

Sundmacher, K., Schultz, T., Zhou, S., Scott, K., Ginkel, M., & Gilles, E. D. (2001)Dynamics of the direct methanol fuel cell (DMFC): experiments and model-based analysisChemical Engineering Science, 56 (2), 333–341doi: 10.1016/S0009-2509(00)00233-5.

Tränkle, F., Zeitz, M., Ginkel, M., & Gilles, E. D. (2000)PROMOT: A modeling tool for chemical processesMathematical and Computer Modelling of Dynamical Systems, 6 (3), 283–307doi: 10.1076/1387-3954(200009)6:3;1-I;FT283.

Eils, J., Lawerenz, C., Astrahantseff, K., Ginkel, M., & Eils, R. (2005)Databases for Systems BiologyComputational Systems Biology15–38Amsterdam [u.a.]: Elsevierdoi: 10.1016/B978-012088786-6/50021-6.

Schoeberl, B., Ginkel, M., Gilles, E. D., & Müller, G. (2004)Mathematical modeling of signaling cascades: principles and future prospectsFunction and Regulation of Cellular Systems: Experiments and Models73–87Basel [u.a.]: Birkhäuserdoi: 10.1007/978-3-0348-7895-1_8.

Stelling, J., Kremling, A., Ginkel, M., Bettenbrock, K., & Gilles, E. D. (2001)Towards a Virtual Biological LaboratoryFoundations of systems biology189–212.

Krasnyk, M., Bondareva, K., Milokhov, O., Teplinskiy, K., Ginkel, M., & Kienle, A. (2006)The ProMoT/Diana Simulation EnvironmentIn: 16th European Symposium on Computer Aided Process Engineering and 9th International Symposium on Process Systems Engineering, 445–450doi: 10.1016/S1570-7946(06)80086-6.

Krasnyk, M., Ginkel, M., Mangold, M., & Kienle, A. (2005)Numerical Analysis of Higher-Order Singularities in Complex Chemical Process Models in ProMoTIn: European Symposium on Computer Aided Process Engineering - 15, 223–228doi: 10.1016/S1570-7946(05)80159-2.

Chebotarov, M., Ginkel, M., Häfele, M., Mangold, M., Gilles, E. D., Kienle, A., & Svjatnyj, V. (2003)DIVAGUI: the graphical user interface for the simulation environment DIVAIn: Simulationstechnik: 17. Symposium in Magdeburg, 155–160.

Kremling, A., Bettenbrock, K., Fischer, S., Ginkel, M., Sauter, T., & Gilles, E. D. (2003)Towards whole cell in silico models for cellular systems: model set-up and model validationIn: Positive systems: proceedings of the First Multidisciplinary International Symposium on Positive Systems (POST 2003), 92–102.

Mangold, M., Ginkel, M., & Gilles, E. D. (2003)Entwicklung einer Bibliothek dynamischer Membranreaktormodelle mit Hilfe des Modellierungswerkzeugs ProMoTIn: Simulationstechnik: 17. Symposium in Magdeburg, 161–166.