COPASI's Use In Software


Coakley S, Richmond P, Gheorghe M, Chin S, Worth D, Holcombe M, Greenough C (2016) Large-Scale Simulations with FLAME. In Intelligent Agents in Data-intensive Computing (Kolodziej J, Correia L, Molina JM eds.), Springer pp.123-142 Software Link

Azimi S, Czeizler E, Gratie C, Gratie D, Iancu B, Ibssa N, Petre I, Rogojin V, Shadbahr T, Shokri F (2015) An Excursion Through Quantitative Model Refinement. Lecture Notes in Computer Science 9504:25-47 Computational Method Software Link
Juty N, Ali R, Glont M, Keating S, Rodriguez N, Swat MJ, Wimalaratne SM, Hermjakob H, Le Novère N, Laibe C, Chelliah V (2015) BioModels: Content, Features, Functionality, and Use. CPT:Pharmacometrics & Systems Pharmacology 4:1-14 Software Link
Mei Y, Carbo A, Hoops S, Hontecillas R, Bassaganya-Riera J (2015) ENISI SDE: A New Web-Based Tool for Modeling Stochastic Processes. IEEE/ACM Trans. Comput. Biol. Bioinformatics 12:289-97 Software Link
Palmisano A, Hoops S, Watson LT, Jones TC Jr, Tyson JJ, Shaffer CA (2015) JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations. BMC Systems Biol. 9:95 Software Link

Aubert N, Mosca C, Fujii T, Hagiya M, Rondelez Y (2014) Computer-assisted design for scaling up systems based on DNA reaction networks J. Royal Soc. Interface 11:20131167 Software Link
Le Muzic M, Parulek J, Stavrum A-K, Viola I (2014) Illustrative visualization of molecular reactions using omniscient intelligence and passive agents. Computer Graphics Forum 33:141-150 Software Link
Matsuoka Y, Funahashi A, Ghosh S, Kitano H (2014) Modeling and simulation using CellDesigner. Methods Mol. Biol. 1164:121-145 Software Link
Mei Y, Carbo A, Hontecillas R, Hoops S, Liles N, Lu P, Philipson C, Bassaganya-Riera J (2014) ENISI MSM: A novel multi-scale modeling platform for computational immunology. Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 391-396 Software Link
Sakkalis V, Sfakianakis S, Tzamali E, Marias K, Stamatakos G, Misichroni F, Ouzounoglou E, Kolokotroni E, Dionysiou D, Johnson D, McKeever S, Graf N (2014) Web-based workflow planning platform supporting the design and execution of complex multiscale cancer models. IEEE J. Biomed. Health Informatics 18:824-31 Software Link

Klement M, Safránek D, Ded T, Pejznoch A, Nedbal L, Steuer R, Cerveny J, Müller S (2013) A comprehensive web-based platform for domain-specific biological models. Electronic Notes in Theoretical Computer Science 299:61-67 Software Link
Mei Y, Carbo A, Hontecillas R, Bassaganya-Riera J (2013) ENISI SDE: a novel web-based stochastic modeling tool for computational biology. 2013 Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 392-397 Computational Method Software Link
Sütterlin T, Kolb C, Dickhaus H, Jäger D, Grabe N (2013) Bridging the scales: semantic integration of quantitative SBML in graphical multi-cellular models and simulations with EPISIM and COPASI. Bioinformatics 29:223-9 Software Link

Dada JO, Mendes P (2012) ManyCell: A Multiscale Simulator for Cellular Systems. (Gilbert D and Heiner M eds) Computational Methods in Systems Biology. Berlin, Heidelberg: Springer Berlin Heidelberg, 366-369. Software Link
Kent E, Hoops S, Mendes P (2012) Condor-COPASI: high-throughput computing for biochemical networks. BMC Systems Biology 6:91 Software Link
Kostromins A, Mozga I, Stalidzans E (2012) ConvAn: A convergence analyzing tool for optimization of biochemical networks. Biosystems 108:73-77 Software Computational Method Link
Pahle J, Challenger JD, Mendes P, McKane AJ (2012) Biochemical fluctuations, optimisation and the linear noise approximation. BMC Systems Biology 6:86 Computational Method Software Link
Sulins J, Mednis M (2012) Automatic termination of parallel optimization runs of stochastic global optimization methods in consensus or stagnation cases. Biosystems and Information technology 1:1-5 Software Computational Method Link
Surovtsova I, Simus N, Hübner K, Sahle S, Kummer U (2012) Simplification of biochemical models: a general approach based on the analysis of the impact of individual species and reactions on the systems dynamics. BMC Systems Biology 6:14 Software Computational Method Link
Tagore S, De RK (2012) SAGPAR: Structural Grammar-based automated pathway reconstruction. Interdisciplinary Sciences: Computational Life Sciences 4:116-127 Software Computational Method Link



Schulz M, Bakker BM, Klipp E (2009) TIde: a software for the systematic scanning of drug targets in kinetic network models. BMC Bioinformatics 10:344 Software Link
Sun T, Adra S, Smallwood R, Holcombe M, MacNeil S (2009) Exploring Hypotheses of the Actions of TGF-β1 in Epidermal Wound Healing Using a 3D Computational Multiscale Model of the Human Epidermis. PLoS ONE 4:e8515 Immunology Computational Methods Software Link

Roy S, Werner-Washburne M, Lane T (2008) A system for generating transcription regulatory networks with combinatorial control of transcription. Bioinformatics 24:1318-1320 Software Link