COPASI's Use In Computational Method

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
Fortuny AF (2017) Chemometric Approaches for Systems Biology. PhD Thesis, Universitat Politècnica de València. Computational Method Link
Stalidzans E, Mozga I, Sulins J, Zikmanis P (2017) Search for a Minimal Set of Parameters by Assessing the Total Optimization Potential for a Dynamic Model of a Biochemical Network. IEEE/ACM transactions on computational biology and bioinformatics 14:978–985 Computational Method Biotechnology Link
Zimmer C, Yaesoubi R, Cohen T (2017) A Likelihood Approach for Real-Time Calibration of Stochastic Compartmental Epidemic Models. PLOS Computational Biology 13:e1005257 Computational Method Link

4 publications
2016
Behinaein B, Rudie K, Sangrar W (2016) Petri net siphon analysis and graph theoretic measures for identifying combination therapies in cancer. IEEE/ACM Transactions on Computational Biology and Bioinformatics doi:10.1109/TCBB.2016.2614301 Computational Method Link
Bergmann FT, Sahle S, Zimmer C (2016) Piecewise parameter estimation for stochastic models in COPASI. Bioinformatics 32:1586–1588 Computational Method Link
Ganesan N, Li J, Sharma V, Jiang H, Compagnoni A (2016) Process Simulation of Complex Biological Pathways in Physical Reactive Space and Reformulated for Massively Parallel Computing Platforms. IEEE/ACM Transactions on Computational Biology and Bioinformatics 13:365–379 Computational Method Link
Hamgini BB (2016) Petri net siphon analysis and network centrality measures for identifying combination therapies in signaling pathways. PhD Thesis, Queen’s University, Kingston, Ontario, Canada Computational Method Link
Henkel R, Hoehndorf R, Kacprowski T, Knüpfer C, Liebermeister W, Waltemath D (2016) Notions of similarity for systems biology models. Briefings in Bioinformatics bbw090 Computational Method Link
Julien-Laferrière A (2016) Models and algorithms applied to metabolism: From revealing the responses to perturbations towards the design of microbial consortia. PhD Thesis, Université Lyon 1-Claude Bernard Computational Method Metabolism Microbiology Link
Mizeranschi AE, Swain MT, Scona R, Fazilleau Q, Bosak B, Piontek T, Kopta P, Thompson P, Dubitzky W (2016) MultiGrain/MAPPER: A distributed multiscale computing approach to modeling and simulating gene regulation networks. Future Generation Computer Systems 63:1–14 Computational Method Link
Panchal C, Azimi S, Petre I (2016) Generating the Logicome of a Biological Network. International Conference on Algorithms for Computational Biology. Springer, 38–49 Computational Method Signaling Link
Scharm M, Waltemath D (2016) A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos. F1000Research 5:2421 Computational Method Link
Stalidzans E, Mozga I, Sulins J, Zikmanis P (2016) Search for a minimal set of parameters by assessing the total optimisation potential for a dynamic model of a biochemical network. IEEE/ACM Transactions on Computational Biology and Bioinformatics 14:978–985 Computational Method Link
Vinciotti V, Augugliaro L, Abbruzzo A, Wit EC (2016) Model selection for factorial Gaussian graphical models with an application to dynamic regulatory networks. Statistical Applications in Genetics and Molecular Biology 15:193–212 Computational Method Link
Walker MA, Madduri R, Rodriguez A, Greenstein JL, Winslow RL (2016) Models and Simulations as a Service: Exploring the Use of Galaxy for Delivering Computational Models. Biophysical Journal 110:1038–1043 Computational Method Link
Zimmer C, Bergmann FT, Sahle S (2016) Reducing local minima in fitness landscapes of parameter estimation by using piecewise evaluation and state estimation. arXiv preprint arXiv:1601.04458 Computational Method Link
Zimmer C, Sahle S (2016) Comparison of approaches for parameter estimation on stochastic models: Generic least squares versus specialized approaches. Computational Biology and Chemistry 61:75–85 Computational Method Link

14 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
Bodei C, Bortolussi L, Chiarugi D, Guerriero ML, Policriti A, Romanel A (2015) On the impact of discreteness and abstractions on modelling noise in gene regulatory networks. Comput. Biol Chem. 56:98-1089 Computational Method Link
Dromms RA, Styczynski MP (2015) Improved metabolite profile smoothing for flux estimation. Molecular BioSystems 11:2394-2405 Computational Method Laboratory Method Link
Hinze T, Kirkici K, Sauer P, Sauer P, Behre J (2015) Membrane Computing Meets Temperature: A Thermoreceptor Model as Molecular Slide Rule with Evolutionary Potential. Lecture Notes Comp. Sci. 9504:215-235 Computational Method Link
Koutsouradis E, Provelengios G, Kouskoumvekakis E, Manolakos ES (2015) Scalable FPGA Accelerator of the NRM Algorithm for Efficient Stochastic Simulation of Large-Scale Biochemical Reaction Networks. in 2015 Euromicro Conference on Digital System Design (DSD) pp.583-590 Computational Method Link
Lu P, Abedi V, Mei Y, Hontecillas R, Hoops S, Carbo A, Bassaganya-Riera J (2015) Supervised learning methods in modeling of CD4+ T cell heterogeneity. BioData Mining 8:1-21 Computational Method Immunology Link
Madsen C, Shmarov F, Zuliani P (2015) BioPSy: An SMT-based Tool for Guaranteed Parameter Set Synthesis of Biological Models. Proceedings 13th International Conference, CMSB 2015 (Roux O, Bourdon J, Eds.), Springer pp182-94 Computational Method Link
Phelix CF, Feltus FA (2015) Plant stress biomarkers from biosimulations: the Transcriptome-To-Metabolome(TTM) technology-effects of drought stress on rice. Plant Biol. 17:63-73 Computational Method Link
Rezgui A, Madec M, Lallement C, Haiech J (2015) Integration of SBML models for the description of biological system in a lab-on-chip. Proceedings of the 22nd International Conference Mixed Design of Integrated Circuits & Systems 165-70 Computational Method Laboratory Method Link
Samal SS, Grigoriev D, Fröhlich H, Weber A, Radulescu O (2015) A Geometric Method for Model Reduction of Biochemical Networks with Polynomial Rate Functions. Bull. Math. Biol. 77:2180-211. Computational Method Theory Link
Tummler K, Kühn C, Klipp E (2015) Dynamic metabolic models in context: biomass backtracking. Integr. Biol.7:940-51 Computational Method Link
Villaverde AF, Henriques D, Smallbone K; Bongard S, Schmid J, Cicin-Sain D, Crombach A, Saez-Rodriguez J, Mauch K, Balsa-Canto E, Mendes P, Jaeger J, Banga JR (2015) BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. BMC Systems Biol. 9:8 Computational Method Link
Zimmer C (2015) Reconstructing the hidden states in time course data of stochastic models. Math. Biosci. 269:117-29 Computational Method Link
Zimmer C, Sahle S. (2015) A termination criterion for parameter estimation in stochastic models in systems biology. Biosystems 9:181-92 Computational Method Link

14 publications
2014
Bellini M, Besozzi D, Cazzaniga P, Mauri G, Nobile MS (2014) Simulation and analysis of the blood coagulation cascade accelerated on GPU. 2014 22nd Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP), IEEE, 590–593 Computational Method 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
Castaldi DF (2014) Network Based Simulation on HPC for Translational Medicine: an Application to Anticoagulation. PhD Thesis, University of Milano-Bicocca, Milan, Italy. Computational Method Link
Cazzaniga P, Nobile MS, Besozzi D, Bellini M, Mauri G (2014) Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization. BioMed Res. Int. 2014:863298 Computational Method Link
Ivan ANY (2014) Assisted Design of DNA Computing Systems: the DNA Toolbox and Beyond. PhD Thesis, University of Tokyo. Synthetic Biology Computational Method Link
Liao C, Cai Y (2014) Towards Modeling Automation for Synthetic Biology. In: Kulkarni V., Stan GB., Raman K. (eds) A Systems Theoretic Approach to Systems and Synthetic Biology II: Analysis and Design of Cellular Systems. Springer, Dordrecht, 201–217 Synthetic Biology Computational Method Link
Mozga I, Stalidzans E (2014) Reduction of Combinatorial Space of Adjustable Kinetic Parameters of Biochemical Network Models in Optimisation Task. Baltic Journal of Modern Computing 150:150–159 Computational Method Link
Nobile MS, Cazzaniga P, Besozzi D, Mauri G (2014) GPU-accelerated simulations of mass-action kinetics models with cupSODA. J. Supercomputing 69:17-24 Computational Method Link
Nobile MS, Cazzaniga P, Besozzi D, Pescini D, Mauri G (2014) cuTauLeaping: A GPU-Powered Tau-Leaping Stochastic Simulator for Massive Parallel Analyses of Biological Systems. PLoS ONE 9:e91963. Computational Method 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
Phelix CF, Villareal G, LeBaron RG, Roberson DJ (2014) Biomarkers from biosimulations: Transcriptome-to-reactome™ Technology for individualized medicine. 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 3452–3455 Computational Method Link
Rao S, van der Schaft A, van Eunen K, Bakker BM, Jayawardhana B (2014) A model reduction method for biochemical reaction networks. BMC systems biology 8:52 Computational Method Link
Schmitz U, Lai X, Winter F, Wolkenhauer O, Vera J, Gupta SK (2014) Cooperative gene regulation by microRNA pairs and their identification using a computational workflow. Nucleic Acids Res. 42:7539-7552 Computational Method Link
Zimmer C, Sahle S, Pahle J (2014) Exploiting intrinsic fluctuations to identify model parameters. IET Systems Biology 9:64-73 Computational Method Link

14 publications
2013
Berestovsky N, Nakhleh L (2013) An Evaluation of Methods for Inferring Boolean Networks from Time-Series Data. PLoS ONE 8:e66031 Computational Method Link
Bulipopa N, Sulins J (2013) Automatic termination of parallel optimization runs of global stochastic optimization methods by upper limit criterion. Biosystems and Information Technol. 2:15-18 Computational Method Link
Coskun SA, Cicek AE, Lai N, Dash RK, Ozsoyoglu ZM, Ozsoyoglu G (2013) An online model composition tool for system biology models. BMC Systems Biol. 7:88 Computational Method Link
Jensen MV, Hay JO (2013) Systems Biology Markup Language formulation of a dynamic kinetic model and its uses in quantitative and computational metabolic modeling. A Compilation of Internship Reports. Brookhaven National Laboratory, Office of Educational Programs. pp. 108–112 Computational Method Link
Kennedy N, Mizeranschi A, Thompson P, Zheng H, Dubitzky W (2013) Reverse engineering of gene regulation models from multi-condition experiments. Proceedings of the 2013 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), pp.112-119 Computational Method Link
Kent E, Neumann S, Kummer U, Mendes P (2013) What Can We Learn from Global Sensitivity Analysis of Biochemical Systems? PLoS ONE 8:e79244 Computational Method Link
Mednis M, Vigants A (2013) Automatic comparison of metabolites names: impact of criteria thresholds. Biosystems and Information Technol. 2:1-5 Computational Method 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
Mei Y, Hontecillas R, Zhang X; Carbo A, Bassaganya-Riera J (2013) Neural network models for classifying immune cell subsets. 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 18-21 Dec. 2013, pp.5-11 Computational Method Link
Mozga I (2013) Determinition of best set of adjustable parameters with full search and limited search methods. Biosystems and Information Technology 2:11–14 Computational Method Link
Nobile MS , Besozzi D, Cazzaniga P, Mauri G, Pescini D (2013) cupSODA: a CUDA-powered simulator of mass-action kinetics. Parallel Computing Technologies Proceedings of the 12th International Conference, PaCT 2013, St. Petersburg, pp.344-357 Computational Method Link
Palaniappan SK (2013) Probabilistic verification and analysis of biopathway dynamics. Ph.D. Thesis School of Computing, National University of Singapore Computational Method Link
Roberts E, Stone JE, Luthey-Schulten Z (2013) Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation. J. Comput. Chem. 34:245-255 Computational Method Link
Sharma V, Compagnoni A (2013) Computational and mathematical models of the JAK-STAT signal transduction pathway. Proceedings of the 2013 Summer Computer Simulation Conference 15 Computational Method Signaling Link
Stanford NJ, Lubitz T, Smallbone K, Klipp E, Mendes P, Liebermeister W (2013) Systematic construction of kinetic models from genome-scale metabolic networks. PloS One 8:e79195 Computational Method Whole-Cell Models Link
Tapinos A, Mendes P (2013) A Method for Comparing Multivariate Time Series with Different Dimensions. PLoS ONE 8:e54201 Computational Method Theory Link

16 publications
2012
Adams RR, Tsorman N, Stratford K, Akman OE, Gilmore S, Juty N, Le Novère N, Millar AJ, Millar AJ (2012) The Input Signal Step Function (ISSF), a standard method to encode input signals in SBML models with software support, applied to circadian clock models. Journal of Biological Rhythms 27:328–332 Computational Method Link
Challenger JD, McKane AJ, Pahle J (2012) Multi-compartment linear noise approximation. Journal of Statistical Mechanics: Theory and Experiment 2012:P11010 Computational Method Link
Chua HE, Bhowmick SS, Tucker-Kellogg L, Forbes Dewey, Jr C (2012) STEROID: in silico heuristic target combination identification for disease-related signaling networks. Proceedings of the 2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine BCB'12 pp. 4-11 Computational Method Link
Georgoulas A, Clark A, Ocone A, Gilmore S, Sanguinetti G (2012) A subsystems approach for parameter estimation of ODE models of hybrid systems. Electronic Proceedings in Theoretical Computer Science 92:30-41 Computational Method Link
Holcombe M, Adra S, Bicak M, Chin S, Coakley S, I. Graham A, Green J, Greenough C, Jackson D, Kiran M, MacNeil S, Maleki-Dizaji A, McMinn P, Pogson M, Poole R, Qwarnstrom E, Ratnieks F, D. Rolfe M, Smallwood R, Sun T, Worth D (2012) Modelling complex biological systems using an agent-based approach. Integrative Biology 4:53–64 Computational Method 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
Schaber J (2012) Easy parameter identifiability analysis with COPASI. Biosystems 110:183-185 Computational Method Link
Stalidzans E, Kostromins A, Sulins J (2012) Two stage optimization of biochemical pathways using parallel runs of global stochastic optimization methods. 13th IEEE International Symposium on Computational Intelligence and Informatics (CINTI 2012), IEEE, 365–369 Computational Method 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
Warren PB, Allen RJ (2012) Steady-state parameter sensitivity in stochastic modeling via trajectory reweighting. The Journal of Chemical Physics 136:104106 Computational Method Link
Zimmer C (2012) Parameter estimation for stochastic models of biochemical reactions. PhD Thesis, Heidelberg University. Computational Method Link

14 publications
2011
Bandaru P, Bansal M, Nemenman I (2011) Mass Conservation and Inference of Metabolic Networks from High-Throughput Mass Spectrometry Data. J. Comput. Biol. 18:147-154 Laboratory Method Computational Method Link
Berestovsky N (2011) On the modeling of signaling networks with petri nets. MS Thesis, Rice University, Houston, Texas, USA. Computational Method Link
DasGupta B, Vera-Licona P, Sontag E (2011) Reverse engineering of molecular networks from a common combinatorial approach. In Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, M. Elloumi and A. Zomaya (editors). John Wiley & Sons, Inc. Computational Method Link
Gauges R (2011) Standards and Tools for Model Exchange and Analysis in Systems Biology. PhD Thesis, Heidelberg University Software Computational Method Link
Mauch S, Stalzer M (2011) Efficient formulations for exact stochastic simulation of chemical systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics 8:27-35 Computational Method Link
Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, Laibe C, Miller AK, Moraru I, Nickerson D, Nielsen P, Nikolski M, Sahle S, Sauro HM, Schmidt H, Snoep JL, Tolle D, Wolkenhauer O, Novère NL (2011) Minimum Information About a Simulation Experiment (MIASE). PLOS Computational Biology 7:e1001122 Computational Method Link

6 publications
2010
Baker, S.M., Schallau, K., Junker, B.H. (2010). Comparison of different algorithms for simultaneous estimation of multiple parameters in kinetic metabolic models. Journal of Integrative Bioinformatics 7(3):519-520 Computational Method Link
Dada JO, Spasic I, Paton NW, Mendes P (2010) SBRML: a markup language for associating systems biology data with models. Bioinformatics 26:932–938 Computational Method Link
Dimitrova ES, Vera Licona MP, McGee J, Laubenbacher R. (2010) Discretization of Time Series Data. J. Comput. Biol. J17:853-68. Computational Method Link
Escuela G, Hinze T, Dittrich P, Schuster S, Moreno-Alvarez M (2010) Modelling Modified Atmosphere Packaging for Fruits and Vegetables using Membrane Systems. BIOSIGNALS, 306–311 Computational Method Biotechnology Link
Li P, Dada JO, Jameson D, Spasic I, Swainston N, Carroll K, Dunn W, Khan F, Malys N, Messiha HL, Simeonidis E, Weichart D, Winder C, Wishart J, Broomhead DS, Goble CA, Gaskell SJ, Kell DB, Westerhoff HV, Mendes P, Paton NW (2010) Systematic integration of experimental data and models in systems biology. BMC Bioinformatics 11:582 Computational Method Metabolism Link
Morrissey ER, Juarez MA, Denby KJ, Burroughs NJ (2010) On reverse engineering of gene interaction networks using time course data with repeated measurements. Bioinformatics 26:2305–2312 Computational Method Link
Swainston N, Jameson D, Li P, Spasic I, Mendes P, Paton N (2010) Integrative information management for systems biology. Data Integration in the Life Sciences, DILS2010 (Lambrix P, Kemp G, eds.), Lecture Notes in Computer Science, 6254:164–178 Computational Method Link

7 publications
2009
Baralla A, Mentzen WI, De La Fuente A (2009) Inferring Gene Networks: Dream or Nightmare?: Part 1: Challenges 1 and 3. Annals of the New York Academy of Sciences 1158:246-256 Computational Method Link
Cai Y, Lux MW, Adam L, Peccoud J (2009) Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars. PLoS Computational Biology 5:e1000529 Synthetic Biology Computational Method Laboratory Method Link
Mendes P, Messiha H, Malys N, Hoops S (2009) Enzyme Kinetics and Computational Modeling for Systems Biology. Methods in Enzymology 467:583–599 Enzymology Computational Method Link
Pokrzywa RM (2009) Systems Biology in an Imperfect World: Modeling Biological Systems with Incomplete Information. PhD Thesis, Virginia Tech Computational Method 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

5 publications
2008
Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kırdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology 26:1155–1160 Microbiology Computational Method Link
Long J, Roth M (2008) Synthetic microarray data generation with RANGE and NEMO. Bioinformatics 24:132–134 Computational Method Genomics Link
Sahle S, Mendes P, Hoops S, Kummer U (2008) A new strategy for assessing sensitivities in biochemical models. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 366:3619-3631 Computational Method Link
Wilkinson SJ, Benson N, Kell DB (2008) Proximate parameter tuning for biochemical networks with uncertain kinetic parameters. Molecular BioSystems 4:74–97 Computational Method Link

4 publications
2007
Camacho, D, Vera-Licona P, Mendes P, Laubenbacher R (2007) Comparison of reverse-engineering methods using an in silico network. Ann. N.Y. Acad. Sci. 1115:73-89. Computational Method Link

1 publication
2006

0 publication