COPASI's Use In Software

2017
Dalle Pezze P, Le Novère N (2017) SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks. BMC Systems Biology, 11:46 Computational Method Software Link

1 publication
2016
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
Troják M, Šafránek D, Hrabec J, Šalagovič J, Romanovská F, Červenỳ J (2016) E-Cyanobacterium. org: A Web-Based Platform for Systems Biology of Cyanobacteria. International Conference on Computational Methods in Systems Biology. Springer, 316–322. Software Link

2 publications
2015
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

4 publications
2014
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
Boba P, Gries S, Hamacher K (2014) R as an Integration Tool in High Performance Computing - Lessons Learned. GI-Jahrestagung. Lecture Notes in Informatics 232:138–148 Computational Method 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. 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), IEEE, 391–396 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
Palmisano A, Hoops S, Watson LT, Jones Jr TC, Tyson JJ, Shaffer CA (2014) Multistate Model Builder (MSMB): a flexible editor for compact biochemical models. BMC Systems Biology 8:42 Software Computational Method 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. Biomededical Health Informatics 18:824-31 Software Link

8 publications
2013
Chelliah V, Laibe C, Le Novere N (2013) BioModels database: a repository of mathematical models of biological processes. Methods in Molecular Biology 1021:189–199 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

4 publications
2012
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

7 publications
2011
Chandran D (2011) TinkerCell: Computer-Aided Design for Synthetic Biology. PhD Thesis, University of Washington, Seattle. Software Synthetic Biology Link
Gauges R (2011) Standards and Tools for Model Exchange and Analysis in Systems Biology. PhD Thesis, Heidelberg University Software Computational Method Link

2 publications
2010

0 publication
2009
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 Method Software Link

2 publications
2008
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

1 publication
2007

0 publication
2006

0 publication