COPASI

COPASI's Use In Software

2025

0 publication
2024
Durmaz MG, Tulluk N, Aksoy RD, Yilmaz HB, Yang B, Wipat A, Pusane AE, Mısırlı G, Tugcu T (2024) BioRxToolbox: a computational framework to streamline genetic circuit design in molecular data communications. Synthetic Biology 9:ysae015 Synthetic Biology Computational Method Software Link
Jacopin E (2024) Model-Based Biology Using Soft Real-Time Systems. Ph.D. Thesis, Osaka University, Japan Computational Method Software Link
Matzko RO, Konur S (2024) BioNexusSentinel: a visual tool for bioregulatory network and cytohistological RNA-seq genetic expression profiling within the context of multicellular simulation research using ChatGPT-augmented software engineering. Bioinformatics Advances 4:vbae046 Computational Method Software Link
McCloskey NS, Mammedova A, Liberles DA (2024) PEMPS: a phylogenetic software tool to model the evolution of metabolic pathways. BMC Bioinformatics 25:244 Computational Method Software Link
Mutsuddy A (2024) Single Cell Pharmacodynamic Modeling of Cancer Cell Lines. Ph.D. Thesis, Clemson University, Clemson, SC, USA Software Computational Method Link
Ospina De Los Ríos S, Bastian P, Keegan L, Sahle S, Vermoortele D, Wehling L (2024) DuneCopasi: A multi-compartment reaction-diffusion simulator for systems biology. Journal of Open Source Software 9:6836 Software Link
Silberberg M, Hermjakob H, Malik-Sheriff RS, Grecco HE (2024) Poincaré and SimBio: a versatile and extensible Python ecosystem for modeling systems. Bioinformatics 40:btae465 Software Computational Method Link

7 publications
2023
Bergmann FT (2023) BASICO: A simplified Python interface to COPASI. Journal of Open Source Software 8:5553 Software Link
Cruz E, Montoya A, Ágreda J (2023) Linear stability analysis of chemical mechanism, Listanalchem: A tool for the search of spontaneous mirror symmetry breaking. MethodsX 11:102307 Chemistry Software Link
Kaya HE, Naidoo KJ (2023) CytoCopasi: A Chemical Systems Biology Target and Drug Discovery Visual Data Analytics Platform. Bioinformatics 39:btad745 Software Link
Loman TE, Ma Y, Ilin V, Gowda S, Korsbo N, Yewale N, Rackauckas C, Isaacson SA (2023) Catalyst: Fast and flexible modeling of reaction networks. PLOS Computational Biology 19:e1011530 Software Link
Medasani B, Kasiraju S, Vlachos DG (2023) OpenMKM: An Open-Source C++ Multiscale Modeling Simulator for Homogeneous and Heterogeneous Catalytic Reactions. Journal of Chemical Information and Modeling 63:3377–3391 Software Chemistry Link

5 publications
2022
Garay-Ruiz D, Bo C (2022) Chemical reaction network knowledge graphs: the OntoRXN ontology. Journal of Cheminformatics 14:29 Software Computational Method Link
Schälte Y, Klinger E, Alamoudi E, Hasenauer J (2022) pyABC: Efficient and robust easy-to-use approximate Bayesian computation. Journal of Open Source Software 7:4304 Software Link
Yuan L, Wu C, Guo X, Yang C (2022) ParaCopasi: A package for parallel biochemical simulation and analysis. Journal of Computational Chemistry 43:144–154 Computational Method Software Link

3 publications
2021
Förster J, Bergmann FT, Pahle J (2021) CoRC - the COPASI R Connector. Bioinformatics 37:2778–2779 Software Link
Gupta A, Mendes P (2021) ShinyCOPASI: a web-based exploratory interface for COPASI models. arXiv:2110.03796. Software Link
Shaikh B, Marupilla G, Wilson M, Blinov ML, Moraru II, Karr JR (2021) RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats. Nucleic Acids Research 49:W597–W602 Software Link
Tomasoni D, Paris A, Giampiccolo S, Reali F, Simoni G, Marchetti L, Kaddi C, Neves-Zaph S, Priami C, Azer K, Lombardo R (2021) QSPcc reduces bottlenecks in computational model simulations. Communications Biology 4:1022 Computational Method Software Link
Yamada TG, Ii K, König M, Feierabend M, Dräger A, Funahashi A (2021) SBMLWebApp: Web-Based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models. Processes 9:1830 Software Link

5 publications
2020

0 publication
2019
Malik-Sheriff RS, Glont M, Nguyen TVN, Tiwari K, Roberts MG, Xavier A, Vu MT, Men J, Maire M, Kananathan S, Fairbanks EL, Meyer JP, Arankalle C, Varusai TM, Knight-Schrijver V, Li L, Dueñas-Roca C, Dass G, Keating SM, Park YM, Buso N, Rodriguez N, Hucka M, Hermjakob H (2020) BioModels—15 years of sharing computational models in life science. Nucleic Acids Research 48:D407–D415 Software Computational Method Link

1 publication
2018
Jones Jr TC, Hoops S, Watson LT, Palmisano A, Tyson JJ, Shaffer CA (2018) JigCell Model Connector: building large molecular network models from components. SIMULATION 94:993–1008 Computational Method Software Link
Welsh CM, Fullard N, Proctor CJ, Martinez-Guimera A, Isfort RJ, Bascom CC, Tasseff R, Przyborski SA, Shanley DP (2018) PyCoTools: A Python Toolbox for COPASI. Bioinformatics 34:3702–3710 Computational Method Software Link

2 publications
2017
Bergmann FT, Hoops S, Klahn B, Kummer U, Mendes P, Pahle J, Sahle S (2017) COPASI and its applications in biotechnology. Journal of Biotechnology 261:215–220 Software Link
Chua HE, Bhowmick SS, Tucker-Kellogg L (2017) Synergistic target combination prediction from curated signaling networks: Machine learning meets systems biology and pharmacology. Methods 129:60–80 Computational Method Software Link
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
Elsts A, Pentjuss A, Stalidzans E (2017) SpaceScanner: COPASI wrapper for automated management of global stochastic optimization experiments. Bioinformatics 33:2966–2967 Software Computational Method Link
Madec M, Lallement C, Haiech J (2017) Modeling and simulation of biological systems using SPICE language. PLoS One 12:e0182385 Software Link
Schäuble S, Stavrum A-K, Bockwoldt M, Puntervoll P, Heiland I (2017) SBMLmod: a Python-based web application and web service for efficient data integration and model simulation. BMC Bioinformatics 18:314 Software Link

6 publications
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
Hoops S, Hontecillas R, Abedi V, Leber A, Philipson CW, Carbo A, Bassaganya-Riera J (2016) Chapter 5 - Ordinary Differential Equations (ODEs) Based Modeling. In: Bassaganya-Riera J (ed) Computational Immunology. Academic Press, 63–78. Computational Method 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

3 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 SM, 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 Transactions on Computational Biology and Bioinformatics 12:289-97 Software Link
Palmisano A, Hoops S, Watson LT, Jones TC, Tyson JJ, Shaffer CA (2015) JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations. BMC Systems Biology 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. Journal of the Royal Society 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 in Molecular Biology 1164:121-145 Software Link
Mei Y, Carbo A, Hontecillas R, Hoops S, Liles N, Lu P, Philipson CW, 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 Journal of Biomededical Health Informatics 18:824-31 Software Link

7 publications
2013
Chelliah V, Laibe C, Le Novère N (2013) BioModels database: a repository of mathematical models of biological processes. Methods in Molecular Biology 1021:189–199 Software Link
Klement M, Šafránek 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
Nim TH, White JK, Tucker-Kellogg L (2013) SPEDRE: a web server for estimating rate parameters for cell signaling dynamics in data-rich environments. Nucleic Acids Research 41:W187-191 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

5 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. Ph.D. Thesis, University of Washington, Seattle, USA. Software Synthetic Biology Link
Gauges R (2011) Standards and Tools for Model Exchange and Analysis in Systems Biology. Ph.D. Thesis, Heidelberg University, Germany Software Computational Method Link
Schaber J, Flöttmann M, Li J, Tiger C-F, Hohmann S, Klipp E (2011) Automated ensemble modeling with modelMaGe: analyzing feedback mechanisms in the Sho1 branch of the HOG pathway. PLoS One 6:e14791 Signaling Computational Method Software Link

3 publications
2010
Funahashi A, Matsuoka Y, Jouraku A, Takizawa H, Hiroi NF, Ghosh S, Kikuchi N, Kitano H (2010) 細胞シミュレータCellDesignerの設計と実装. Journal of The Society of Instrument and Control Engineers 49:531–536 Software Link
Mazza T, Iaccarino G, Priami C (2010) Snazer: the simulations and networks analyzer. BMC Systems Biology 4:1 Computational Method Software Link

2 publications
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
Mandel JJ, Fuß H, Palfreyman NM, Dubitzky W (2007) Modeling biochemical transformation processes and information processing with Narrator. BMC Bioinformatics 8:103 Computational Method Software Link

1 publication
2006

0 publication
2005

0 publication