TY - JOUR AU - Kitano, H. PY - 2002 DA - 2002// TI - Computational systems biology JO - Nature VL - 420 UR - https://doi.org/10.1038/nature01254 DO - 10.1038/nature01254 ID - Kitano2002 ER - TY - JOUR AU - Albert, R. PY - 2007 DA - 2007// TI - Network Inference, Analysis, and Modeling in Systems Biology JO - Plant Cell VL - 19 UR - https://doi.org/10.1105/tpc.107.054700 DO - 10.1105/tpc.107.054700 ID - Albert2007 ER - TY - JOUR AU - Gombert, A. K. AU - Nielsen, J. PY - 2000 DA - 2000// TI - Mathematical modelling of metabolism JO - Current Opinion in Biotechnology VL - 11 UR - https://doi.org/10.1016/S0958-1669(00)00079-3 DO - 10.1016/S0958-1669(00)00079-3 ID - Gombert2000 ER - TY - JOUR AU - Covert, M. W. AU - Schilling, C. H. AU - Famili, I. AU - Edwards, J. S. AU - Goryanin, I. I. AU - Selkov, E. AU - Palsson, B. O. PY - 2001 DA - 2001// TI - Metabolic modeling of microbial strains in silico JO - Trends in Biochemical Sciences VL - 26 UR - https://doi.org/10.1016/S0968-0004(00)01754-0 DO - 10.1016/S0968-0004(00)01754-0 ID - Covert2001 ER - TY - BOOK AU - Heinrich, R. AU - Schuster, S. PY - 1996 DA - 1996// TI - The Regulation of Cellular Systems. 115 Fifth Avenue New York, NY 10003 PB - Chapman and Hall CY - United Kingdom ID - Heinrich1996 ER - TY - JOUR AU - Kanehisa, M. AU - Goto, S. AU - Hattori, M. AU - Aoki-Kinoshita, K. F. AU - Itoh, M. AU - Kawashima, S. AU - Katayama, T. AU - Araki, M. AU - Hirakawa, M. PY - 2006 DA - 2006// TI - From genomics to chemical genomics: new developments in KEGG JO - Nucl Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkj102 DO - 10.1093/nar/gkj102 ID - Kanehisa2006 ER - TY - JOUR AU - Ogata, H. AU - Goto, S. AU - Sato, K. AU - Fujibuchi, W. AU - Bono, H. AU - Kanehisa, M. PY - 2000 DA - 2000// TI - KEGG: Kyoto Encyclopedia of Genes and Genomes JO - Nucleic Acids Research VL - 27 UR - https://doi.org/10.1093/nar/27.1.29 DO - 10.1093/nar/27.1.29 ID - Ogata2000 ER - TY - JOUR AU - Caspi, R. AU - Foerster, H. AU - Fulcher, C. A. AU - Hopkinson, R. AU - Ingraham, J. AU - Kaipa, P. AU - Krummenacker, M. AU - Paley, S. AU - Pick, J. AU - Rhee, S. Y. AU - Tissier, C. AU - Zhang, P. AU - Karp, P. D. PY - 2006 DA - 2006// TI - a multiorganism database of metabolic pathways and enzymes JO - Nucleic Acids Research VL - 34 UR - https://doi.org/10.1093/nar/gkj128 DO - 10.1093/nar/gkj128 ID - Caspi2006 ER - TY - JOUR AU - Bulik, S. AU - Grimbs, S. AU - Selbig, J. AU - Holzhütter, H. G. PY - 2009 DA - 2009// TI - Combining mechanistic and simplified enzymatic rate equations: A promising approach for speeding up the kinetic modeling of complex metabolic networks JO - FEBS Journal VL - 276 UR - https://doi.org/10.1111/j.1742-4658.2008.06784.x DO - 10.1111/j.1742-4658.2008.06784.x ID - Bulik2009 ER - TY - JOUR AU - Gillespie, D. T. PY - 2000 DA - 2000// TI - The chemical Langevin equation JO - Journal of Chemical Physics VL - 113 UR - https://doi.org/10.1063/1.481811 DO - 10.1063/1.481811 ID - Gillespie2000 ER - TY - JOUR AU - Gillespie, D. T. PY - 1976 DA - 1976// TI - A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions JO - Journal of Computational Physics VL - 22 UR - https://doi.org/10.1016/0021-9991(76)90041-3 DO - 10.1016/0021-9991(76)90041-3 ID - Gillespie1976 ER - TY - JOUR AU - Visser, D. AU - Heijnen, J. PY - 2002 DA - 2002// TI - The Mathematics of Metabolic Control Analysis Revisited JO - Metabolic Engineering VL - 4 UR - https://doi.org/10.1006/mben.2001.0216 DO - 10.1006/mben.2001.0216 ID - Visser2002 ER - TY - JOUR AU - Hatzimanikatis, V. AU - Floudas, C. A. AU - Bailey, J. E. PY - 1996 DA - 1996// TI - Analysis and design of metabolic reaction networks via mixed-integer linear optimization JO - AIChE VL - 42 UR - https://doi.org/10.1002/aic.690420509 DO - 10.1002/aic.690420509 ID - Hatzimanikatis1996 ER - TY - JOUR AU - Hatzimanikatis, V. AU - Bailey, J. E. PY - 1997 DA - 1997// TI - Effects of spatiotemporal variations on metabolic control: Approximate analysis using (log)linear kinetic models JO - Biotechnology and Bioengineering VL - 54 UR - https://doi.org/3.0.CO;2-Q DO - 3.0.CO;2-Q ID - Hatzimanikatis1997 ER - TY - JOUR AU - Hatzimanikatis, V. AU - Emmerling, M. AU - Sauer, U. AU - Bailey, J. E. PY - 1998 DA - 1998// TI - Application of mathematical tools for metabolic design of microbial ethanol production JO - Biotechnology and Bioengineering VL - 58 UR - https://doi.org/3.0.CO;2-K DO - 3.0.CO;2-K ID - Hatzimanikatis1998 ER - TY - JOUR AU - Liebermeister, W. AU - Klipp, E. PY - 2006 DA - 2006// TI - Bringing metabolic networks to life: convenience rate law and thermodynamic constraints JO - Theor Biol Med Model VL - 3 UR - https://doi.org/10.1186/1742-4682-3-41 DO - 10.1186/1742-4682-3-41 ID - Liebermeister2006 ER - TY - BOOK AU - Segel, I. H. PY - 1993 DA - 1993// TI - Enzyme Kinetics – Behavior and Analysis of Rapid Equilibrium and Steady-State Enzyme Systems PB - Wiley Classics Library Edition CY - INDIA ID - Segel1993 ER - TY - BOOK AU - Bisswanger, H. PY - 2000 DA - 2000// TI - Enzymkinetik – Theorie und Methoden PB - Wiley-VCH CY - Weinheim, Germany UR - https://doi.org/10.1002/3527603298 DO - 10.1002/3527603298 ID - Bisswanger2000 ER - TY - BOOK AU - Cornish-Bowden, A. PY - 2004 DA - 2004// TI - Fundamentals of Enzyme Kinetics PB - Portland Press Ltd CY - 59 Portland Place, London ID - Cornish-Bowden2004 ER - TY - JOUR AU - Gillespie, D. T. PY - 2007 DA - 2007// TI - Stochastic simulation of chemical kinetics JO - Annu Rev Phys Chem VL - 58 UR - https://doi.org/10.1146/annurev.physchem.58.032806.104637 DO - 10.1146/annurev.physchem.58.032806.104637 ID - Gillespie2007 ER - TY - JOUR AU - Savageau, M. A. PY - 1970 DA - 1970// TI - Biochemical systems analysis. 3. Dynamic solutions using a power-law approximation JO - J Theor Biol VL - 26 UR - https://doi.org/10.1016/S0022-5193(70)80013-3 DO - 10.1016/S0022-5193(70)80013-3 ID - Savageau1970 ER - TY - JOUR AU - Visser, D. AU - Heijnen, J. J. PY - 2003 DA - 2003// TI - Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics JO - Metab Eng VL - 5 UR - https://doi.org/10.1016/S1096-7176(03)00025-9 DO - 10.1016/S1096-7176(03)00025-9 ID - Visser2003 ER - TY - CHAP AU - Hatzimanikatis, V. AU - Bailey, J. PY - 1996 DA - 1996// TI - MCA Has More to Say BT - Journal of theoretical Biology ID - Hatzimanikatis1996 ER - TY - JOUR AU - Barthelmes, J. AU - Ebeling, C. AU - Chang, A. AU - Schomburg, I. AU - Schomburg, D. PY - 2007 DA - 2007// TI - BRENDA, AMENDA and FRENDA: the enzyme information system in 2007 JO - Nucl Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkl972 DO - 10.1093/nar/gkl972 ID - Barthelmes2007 ER - TY - JOUR AU - Schomburg, I. AU - Chang, A. AU - Schomburg, D. PY - 2002 DA - 2002// TI - BRENDA, enzyme data and metabolic information JO - Nucl Acids Res VL - 30 UR - https://doi.org/10.1093/nar/30.1.47 DO - 10.1093/nar/30.1.47 ID - Schomburg2002 ER - TY - JOUR AU - Schomburg, I. AU - Chang, A. AU - Ebeling, C. AU - Gremse, M. AU - Heldt, C. AU - Huhn, G. AU - Schomburg, D. PY - 2004 DA - 2004// TI - BRENDA, the enzyme database: updates and major new developments JO - Nucleic Acids Research VL - 32 UR - https://doi.org/10.1093/nar/gkh081 DO - 10.1093/nar/gkh081 ID - Schomburg2004 ER - TY - BOOK AU - Metzler, D. E. PY - 2001 DA - 2001// TI - Biochemistry PB - Harcourt/Academic Press CY - USA ID - Metzler2001 ER - TY - JOUR AU - Banga, J. R. PY - 2008 DA - 2008// TI - Optimization in computational systems biology JO - BMC Systems Biology VL - 2 UR - https://doi.org/10.1186/1752-0509-2-47 DO - 10.1186/1752-0509-2-47 ID - Banga2008 ER - TY - JOUR AU - Rodriguez-Fernandez, M. R. AU - Mendes, P. AU - Banga, J. R. PY - 2006 DA - 2006// TI - A hybrid approach for efficient and robust parameter estimation in biochemical pathways JO - Biosystems VL - 83 UR - https://doi.org/10.1016/j.biosystems.2005.06.016 DO - 10.1016/j.biosystems.2005.06.016 ID - Rodriguez-Fernandez2006 ER - TY - JOUR AU - Rodriguez-Fernandez, M. AU - Egea, J. A. AU - Banga, J. R. PY - 2006 DA - 2006// TI - Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-483 DO - 10.1186/1471-2105-7-483 ID - Rodriguez-Fernandez2006 ER - TY - JOUR AU - Balsa-Canto, E. AU - Peifer, M. AU - Banga, J. R. AU - Timmer, J. AU - Fleck, C. PY - 2008 DA - 2008// TI - Hybrid optimization method with general switching strategy for parameter estimation JO - BMC Systems Biology VL - 2 UR - https://doi.org/10.1186/1752-0509-2-26 DO - 10.1186/1752-0509-2-26 ID - Balsa-Canto2008 ER - TY - JOUR AU - Spieth, C. AU - Streichert, F. AU - Speer, N. AU - Zell, A. PY - 2004 DA - 2004// TI - Optimizing Topology and Parameters of Gene Regulatory Network Models from Time-Series Experiments JO - Proceedings of the Genetic and Evolutionary Computation Conference (GECCO 2004), (Part I) of LNCS VL - 3102 UR - https://doi.org/10.1007/978-3-540-24854-5_46 DO - 10.1007/978-3-540-24854-5_46 ID - Spieth2004 ER - TY - CHAP AU - Spieth, C. AU - Worzischek, R. AU - Streichert, F. AU - Supper, J. AU - Speer, N. AU - Zell, A. PY - 2006 DA - 2006// TI - Comparing Evolutionary Algorithms on the Problem of Network Inference BT - Proceedings of the Genetic and Evolutionary Computation Conference (GECCO 2006) ID - Spieth2006 ER - TY - CHAP AU - Spieth, C. AU - Hassis, N. AU - Streichert, F. AU - Supper, J. AU - Beyreuther, K. AU - Zell, A. PY - 2006 DA - 2006// TI - Comparing Mathematical Models on the Problem of Network Inference BT - Proceedings of the Genetic and Evolutionary Computation Conference (GECCO 2006) ID - Spieth2006 ER - TY - BOOK AU - Weise, T. PY - 2008 DA - 2008// TI - Global Optimization Algorithms – Theory and Application ID - Weise2008 ER - TY - BOOK AU - Charbonneau, P. AU - Knapp, B. PY - 1995 DA - 1995// TI - A User's Guide to PIKAIA 1.0 ID - Charbonneau1995 ER - TY - CHAP AU - Streichert, F. AU - Ulmer, H. PY - 2005 DA - 2005// TI - JavaEvA – A Java Framework for Evolutionary Algorithms BT - Technical Report WSI-2005–06, Center for Bioinformatics Tübingen PB - University of Tübingen CY - Germany ID - Streichert2005 ER - TY - BOOK AU - Kronfeld, M. PY - 2008 DA - 2008// TI - EvA2 Short Documentation PB - University of Tübingen, Dept. of Computer Architecture, Sand 1, 72076 Tübingen CY - Germany ID - Kronfeld2008 ER - TY - STD TI - Mathtools.net : MATLAB/Optimization.http://www.mathtools.net/MATLAB/Optimization UR - http://www.mathtools.net/MATLAB/Optimization ID - ref39 ER - TY - BOOK AU - Holland, J. H. PY - 1975 DA - 1975// TI - Adaptation in Natural and Artificial Systems PB - The University of Michigan Press CY - USA ID - Holland1975 ER - TY - BOOK AU - Rechenberg, I. PY - 1973 DA - 1973// TI - Evolutionsstrategie: Optimierung technischer Systeme nach Prinzipien der biologischen Evolution PB - Fromman-Holzboog CY - Stuttgart ID - Rechenberg1973 ER - TY - CHAP AU - Storn, R. PY - 1996 DA - 1996// TI - On the Usage of Differential Evolution for Function Optimization BT - 1996 Biennial Conference of the North American Fuzzy Information Processing Society PB - IEEE, New York, USA CY - Berkeley ID - Storn1996 ER - TY - JOUR AU - Tovey, C. A. PY - 1985 DA - 1985// TI - Hill climbing with multiple local optima JO - Alg Disc Meth VL - 6 UR - https://doi.org/10.1137/0606040 DO - 10.1137/0606040 ID - Tovey1985 ER - TY - JOUR AU - Kirkpatrick, S. AU - Gelatt, C. D. AU - Vecchi, M. P. PY - 1983 DA - 1983// TI - Optimization by Simulated Annealing JO - Science VL - 220 UR - https://doi.org/10.1126/science.220.4598.671 DO - 10.1126/science.220.4598.671 ID - Kirkpatrick1983 ER - TY - JOUR AU - Clerc, M. AU - Kennedy, J. PY - 2002 DA - 2002// TI - The Particle Swarm – Explosion, Stability, and Convergence in a Multidimensional Complex Space JO - IEEE Transactions on Evolutionary Computation VL - 6 UR - https://doi.org/10.1109/4235.985692 DO - 10.1109/4235.985692 ID - Clerc2002 ER - TY - BOOK AU - Clerc, M. PY - 2005 DA - 2005// TI - Particle Swarm Optimization ID - Clerc2005 ER - TY - CHAP AU - Dräger, A. AU - Supper, J. AU - Planatscher, H. AU - Magnus, J. B. AU - Oldiges, M. AU - Zell, A. ED - Srinivasan, D. ED - Wang, L. PY - 2007 DA - 2007// TI - Comparing Various Evolutionary Algorithms on the Parameter Optimization of the Valine and Leucine Biosynthesis in Corynebacterium glutamicum BT - 2007 IEEE Congress on Evolutionary Computation PB - IEEE Press CY - IEEE Computational Intelligence Society, Singapore UR - https://doi.org/10.1109/CEC.2007.4424528 DO - 10.1109/CEC.2007.4424528 ID - Dräger2007 ER - TY - CHAP AU - Dräger, A. AU - Kronfeld, M. AU - Supper, J. AU - Planatscher, H. AU - Magnus, J. B. AU - Oldiges, M. AU - Zell, A. ED - Srinivasan, D. ED - Wang, L. PY - 2007 DA - 2007// TI - Benchmarking Evolutionary Algorithms on Convenience Kinetics Models of the Valine and Leucine Biosynthesis in C. glutamicum BT - 2007 IEEE Congress on Evolutionary Computation PB - IEEE Press CY - IEEE Computational Intelligence Society, Singapore UR - https://doi.org/10.1109/CEC.2007.4424565 DO - 10.1109/CEC.2007.4424565 ID - Dräger2007 ER - TY - CHAP AU - Chassagnole, C. AU - Noisommit-Rizzi, N. AU - Schmid, J. W. AU - Mauch, K. AU - Reuss, M. PY - 2002 DA - 2002// BT - Dynamic Modeling of the Central Carbon Metabolism of Escherichia coli PB - Wiley Periodicals CY - Inc ID - Chassagnole2002 ER - TY - JOUR AU - Klipp, E. AU - Nordlander, B. AU - Kruger, R. AU - Gennemark, P. AU - Hohmann, S. PY - 2005 DA - 2005// TI - Integrative model of the response of yeast to osmotic shock JO - Nature Biotechnology VL - 23 UR - https://doi.org/10.1038/nbt1114 DO - 10.1038/nbt1114 ID - Klipp2005 ER - TY - CHAP AU - Guthke, R. AU - Schmidt-Heck, W. AU - Pless, G. AU - Gebhardt, R. AU - Pfaff, M. AU - Gerlach, J. C. AU - Zeilinger, K. PY - 2006 DA - 2006// TI - Dynamic Model of Amino Acid and Carbohydrate Metabolism in Primary Human Liver Cells BT - VII International Symposium on Biological and Medical Data Analysis ID - Guthke2006 ER - TY - JOUR AU - Magnus, J. B. AU - Hollwedel, D. AU - Oldiges, M. AU - Takors, R. PY - 2006 DA - 2006// TI - Monitoring and Modeling of the Reaction Dynamics in the Valine/Leucine Synthesis Pathway in Corynebacterium glutamicum JO - Biotechnology Progress VL - 22 UR - https://doi.org/10.1021/bp060072f DO - 10.1021/bp060072f ID - Magnus2006 ER - TY - JOUR AU - Guthke, R. AU - Zeilinger, K. AU - Sickinger, S. AU - Schmidt-Heck, W. AU - Buentemeyer, H. AU - Iding, K. AU - Lehmann, J. AU - Pfaff, M. AU - Pless, G. AU - Gerlach, J. C. PY - 2006 DA - 2006// TI - Dynamics of amino acid metabolism of primary human liver cells in 3D bioreactors JO - Bioprocess Biosystem Engineering VL - 28 UR - https://doi.org/10.1007/s00449-005-0040-1 DO - 10.1007/s00449-005-0040-1 ID - Guthke2006 ER - TY - JOUR AU - Savageau, M. A. PY - 1969 DA - 1969// TI - Biochemical systems analysis. I. Some mathematical properties of the rate law for the component enzymatic reactions JO - J Theor Biol VL - 25 UR - https://doi.org/10.1016/S0022-5193(69)80026-3 DO - 10.1016/S0022-5193(69)80026-3 ID - Savageau1969 ER - TY - JOUR AU - Savageau, M. A. PY - 1969 DA - 1969// TI - Biochemical systems analysis. II. The steady-state solutions for an n-pool system using a power-law approximation JO - J Theor Biol VL - 25 UR - https://doi.org/10.1016/S0022-5193(69)80027-5 DO - 10.1016/S0022-5193(69)80027-5 ID - Savageau1969 ER - TY - JOUR AU - Liu, P. K. AU - Wang, F. S. PY - 2008 DA - 2008// TI - Inference of Biochemical Network Models in S-System Using Multi-Objective Optimization Approach JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn075 DO - 10.1093/bioinformatics/btn075 ID - Liu2008 ER - TY - JOUR AU - Vera, J. AU - Sun, C. AU - Oertel, Y. AU - Wolkenhauer, O. PY - 2007 DA - 2007// TI - PLMaddon: a power-law module for the Matlab™ SBToolbox JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm245 DO - 10.1093/bioinformatics/btm245 ID - Vera2007 ER - TY - JOUR AU - Shapiro, B. E. AU - Levchenko, A. AU - Meyerowitz, E. M. AU - Wold, B. J. AU - Mjolsness, E. D. PY - 2002 DA - 2002// TI - Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg042 DO - 10.1093/bioinformatics/btg042 ID - Shapiro2002 ER - TY - JOUR AU - Hoops, S. AU - Sahle, S. AU - Gauges, R. AU - Lee, C. AU - Pahle, J. AU - Simus, N. AU - Singhal, M. AU - Xu, L. AU - Mendes, P. AU - Kummer, U. PY - 2006 DA - 2006// TI - COPASI-a COmplex PAthway SImulator JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl485 DO - 10.1093/bioinformatics/btl485 ID - Hoops2006 ER - TY - JOUR AU - Dräger, A. AU - Hassis, N. AU - Supper, J. AU - Schröder, A. AU - Zell, A. PY - 2008 DA - 2008// TI - SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks JO - BMC Systems Biology VL - 2 UR - https://doi.org/10.1186/1752-0509-2-39 DO - 10.1186/1752-0509-2-39 ID - Dräger2008 ER - TY - JOUR AU - Yang, C. R. AU - Shapiro, B. E. AU - Mjolsness, E. D. AU - Hatfield, G. W. PY - 2004 DA - 2004// TI - An enzyme mechanism language for the mathematical modeling of metabolic pathways JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti068 DO - 10.1093/bioinformatics/bti068 ID - Yang2004 ER - TY - JOUR AU - Borger, S. AU - Liebermeister, W. AU - Uhlendorf, J. AU - Klipp, E. PY - 2007 DA - 2007// TI - Automatically generated model of a metabolic network JO - International Conference on Genome Informatics VL - 18 ID - Borger2007 ER - TY - CHAP AU - Jamshidi, N. AU - Palsson, B. O. PY - 2008 DA - 2008// TI - Formulating genome-scale kinetic models in the post-genome era BT - Molecular Systems Biology ID - Jamshidi2008 ER - TY - JOUR AU - Voss, H. U. AU - Timmer, J. AU - Kurths, J. PY - 2004 DA - 2004// TI - Nonlinear Dynamical System Identification from Uncertain and Indirect Measurements JO - International Journal of Bifurcation and Chaos VL - 14 UR - https://doi.org/10.1142/S0218127404010345 DO - 10.1142/S0218127404010345 ID - Voss2004 ER - TY - BOOK AU - Eggeling, L. AU - Bott, M. PY - 2005 DA - 2005// TI - Handbook of Corynebacterium glutamicum PB - Francis CY - Boca Raton UR - https://doi.org/10.1201/9781420039696 DO - 10.1201/9781420039696 ID - Eggeling2005 ER - TY - JOUR AU - Hansen, N. AU - Ostermeier, A. PY - 2001 DA - 2001// TI - Completely Derandomized Self-Adaptation in Evolution Strategies JO - Evolutionary Computation VL - 9 UR - https://doi.org/10.1162/106365601750190398 DO - 10.1162/106365601750190398 ID - Hansen2001 ER - TY - JOUR AU - Gillespie, D. PY - 1992 DA - 1992// TI - A rigorous derivation of the chemical master equation JO - Physica A VL - 188 UR - https://doi.org/10.1016/0378-4371(92)90283-V DO - 10.1016/0378-4371(92)90283-V ID - Gillespie1992 ER - TY - JOUR AU - Kitano, H. AU - Funahashi, A. AU - Matsuoka, Y. AU - Oda, K. PY - 2005 DA - 2005// TI - Using process diagrams for the graphical representation of biological networks JO - Nature Biotechnology VL - 23 UR - https://doi.org/10.1038/nbt1111 DO - 10.1038/nbt1111 ID - Kitano2005 ER - TY - JOUR AU - Funahashi, A. AU - Tanimura, N. AU - Morohashi, M. AU - Kitano, H. PY - 2003 DA - 2003// TI - CellDesigner: a process diagram editor for gene-regulatory and biochemical networks JO - BioSilico VL - 1 UR - https://doi.org/10.1016/S1478-5382(03)02370-9 DO - 10.1016/S1478-5382(03)02370-9 ID - Funahashi2003 ER - TY - JOUR AU - Spieth, C. AU - Supper, J. AU - Streichert, F. AU - Speer, N. AU - Zell, A. PY - 2006 DA - 2006// TI - JCell – a Java-based framework for inferring regulatory networks from time series data JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl322 DO - 10.1093/bioinformatics/btl322 ID - Spieth2006 ER - TY - CHAP AU - Shampine, L. F. AU - Reichelt, M. W. PY - 2007 DA - 2007// TI - The MATLAB ODE Suite BT - Tech rep ID - Shampine2007 ER - TY - JOUR AU - Shampine, L. F. AU - Reichelt, M. W. AU - Kierzenka, J. A. PY - 1999 DA - 1999// TI - Solving Index-1 DAEs in MATLAB and Simulink JO - SIAM Rev VL - 41 UR - https://doi.org/10.1137/S003614459933425X DO - 10.1137/S003614459933425X ID - Shampine1999 ER - TY - JOUR AU - Schauer, M. AU - Heinrich, R. PY - 1983 DA - 1983// TI - Quasi-steady-state approximation in the mathematical modeling of biochemical reaction networks JO - Mathematical Bioscience VL - 65 UR - https://doi.org/10.1016/0025-5564(83)90058-5 DO - 10.1016/0025-5564(83)90058-5 ID - Schauer1983 ER - TY - BOOK AU - Kloeden, P. E. AU - Platen, E. PY - 1992 DA - 1992// TI - Numerical Solution of Stochastic Differential Equations PB - Springer-Verlag CY - Applications of Mathematics, Berlin UR - https://doi.org/10.1007/978-3-662-12616-5 DO - 10.1007/978-3-662-12616-5 ID - Kloeden1992 ER - TY - CHAP AU - Bentele, M. PY - 2004 DA - 2004// TI - Stochastic Simulation and System Identification of large Signal Transduction Networks in Cells BT - PhD thesis PB - Combined Faculties for the Natural Sciences and for Mathematics of the Ruperto-Carola University Heidelberg CY - Germany ID - Bentele2004 ER - TY - CHAP AU - Kennedy, J. AU - Eberhart, R. PY - 1995 DA - 1995// TI - Particle Swarm Optimization BT - IEEE Int Conf on Neural Networks, Perth, Australia ID - Kennedy1995 ER - TY - CHAP AU - Carlisle, A. AU - Dozier, G. PY - 2001 DA - 2001// TI - An off-the-shelf PSO BT - Proceedings of the Workshop on Particle Swarm Optimization PB - Purdue School of Engineering and Technology, Indianapolis CY - Indianapolis ID - Carlisle2001 ER - TY - BOOK AU - Kaufman, L. AU - Rousseeuv, P. J. PY - 1990 DA - 1990// TI - Finding Groups in Data: An Introduction to Cluster Analysis PB - John Wiley and Sons, Inc CY - Probability and Mathematical Statistics, New York UR - https://doi.org/10.1002/9780470316801 DO - 10.1002/9780470316801 ID - Kaufman1990 ER - TY - CHAP AU - Maechler, M. AU - Rousseeuw, P. AU - Struyf, A. AU - Hubert, M. PY - 2005 DA - 2005// BT - Cluster Analysis Basics and Extensions ID - Maechler2005 ER - TY - BOOK PY - 2007 DA - 2007// TI - R: A Language and Environment for Statistical Computing PB - R Foundation for Statistical Computing CY - Vienna, Austria ID - ref80 ER - TY - BOOK AU - Hartung, J. PY - 2002 DA - 2002// TI - Statistik PB - Oldenburg Wissenschaftsverlag GmbH CY - München UR - https://doi.org/10.1515/9783486810585 DO - 10.1515/9783486810585 ID - Hartung2002 ER -