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Add STEPS to the list of "Actively Supported Open-Source Software Applications"
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| SpringSaLaD
| SpringSaLaD
| Particle-based spatial simulator in which molecules are spheres that are linked by springs<ref>{{cite journal |last1=Michalski |first1=P.J. |last2=Loew |first2=L.M. |date=2016 |title=SpringSaLaD: a spatial, particle-based biochemical simulation platform with excluded volume |journal=Biophys. J. |volume=110 |pages=523–529}}</ref> || multiplatform || Unknown || [https://vcell.org/ssalad]|| Not applicable
| Particle-based spatial simulator in which molecules are spheres that are linked by springs<ref>{{cite journal |last1=Michalski |first1=P.J. |last2=Loew |first2=L.M. |date=2016 |title=SpringSaLaD: a spatial, particle-based biochemical simulation platform with excluded volume |journal=Biophys. J. |volume=110 |pages=523–529}}</ref> || multiplatform || Unknown || [https://vcell.org/ssalad]|| Not applicable
|-
|STEPS
|STochastic Engine for Pathway Simulation<ref>{{cite journal |last1=Hepburn |first1=Iain |last2=Chen |first2=Weiliang |last3=Wils |first3=Stefan |last4=De Schutter |first4=Erik |title=STEPS: efficient simulation of stochastic reaction–diffusion models in realistic morphologies |journal=BMC Systems Biology |date=May 2012 |volume=7 |issue=1 |pages=36 |doi=10.1186/1752-0509-6-36}}</ref><ref>{{cite journal |last1=Chen |first1=Weiliang |last2=De Schutter |first2=Erik |title=Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers |journal=Frontiers in Neuroinformatics |date=February 2017 |volume=11 |issue=1 |pages=13 |doi=10.3389/fninf.2017.00013}}</ref><ref>{{cite journal |last1=Hepburn |first1=Iain |last2=Chen |first2=Weiliang |last3=De Schutter |first3=Erik |title=Accurate reaction-diffusion operator splitting on tetrahedral meshes for parallel stochastic molecular simulations |journal=The Journal of Chemical Physics |date=August 2016 |volume=145 |issue=5 |pages=054118 |doi=10.1063/1.4960034}}</ref><ref>{{cite journal |last1=Chen |first1=Weiliang |last2=Carel |first2=Tristan |last3=Awile |first3=Omar |last4=Cantarutti |first4=Nicola |last5=Castiglioni |first5=Giacomo |last6=Cattabiani |first6=Alessandro |last7=Del Marmol |first7=Baudouin |last8=Hepburn |first8=Iain |last9=King |first9=James G. |last10=Kotsalos |first10=Christos |last11=Kumbhar |first11=Pramod |last12=Lallouette |first12=Jules |last13=Melchior |first13=Samuel |last14=Schürmann |first14=Felix |last15=De Schutter |first15=Erik |title=STEPS 4.0: Fast and memory-efficient molecular simulations of neurons at the nanoscale |journal=Frontiers in Neuroinformatics |date=October 2022 |volume=16 |doi=10.3389/fninf.2022.883742 |ISSN=1662-5196}}</ref>
|multiplatform (C++/Python)
|[[GPLv2]]
|[https://steps.sourceforge.net]
|Partial [https://steps.sourceforge.net/manual/sbml_importer.html#Level-of-support]
|-
|-
| [[Tellurium (software)|Tellurium]]
| [[Tellurium (software)|Tellurium]]

Revision as of 10:38, 2 November 2022

Systems biology relies heavily on building mathematical models to help understand and make predictions of biological processes. Specialized software to assist in building models has been developed since the arrival of the first digital computers.[1][2][3][4] The following list gives the currently supported software applications available to researchers.

The vast majority of modern systems biology modeling software support SBML, which is the de facto standard for exchanging models of biological cellular processes. Some tools also support CellML, a standard used for representing physiological processes. The advantage of using standard formats is that even though a particular software application may eventually become unsupported and even unusable, the models developed by that application can be easily transferred to more modern equivalents. This allows scientific research to be reproducible long after the original publication of the work.

Actively Supported Open-Source Software Applications

Name Description/Notability OS License Site SBML Support
iBioSim iBioSim[5][6] is a computer-aided design (CAD) tool for the modeling, analysis, and design of genetic circuits. multiplatform (Java/C++) Apache [1] Yes
CompuCell3D GUI/Scripting tool[7] for building and simulating multicellular models. multiplatform (C++/Python) MIT [2] Yes, but only for reactions.
COPASI GUI tool[8][9] for analyzing and simulating SBML models. multiplatform (C++) Artistic License [3] Yes
Cytosim Spatial simulator for flexible cytoskeletal filaments and motor proteins[10] Mac, Linux, Cygwin (C++) GPL3 [4] Not applicable
libroadrunner High-performance software library for simulation and analysis of SBML models[11][12] multiplatform (C/C++) Apache License [5] Yes
massPy Simulation tool [13][14] that can work with COBRApy[15] multiplatform (Python) MIT [6] Yes
MCell GUI tool for particle-based spatial stochastic simulation with individual molecules[16][17][18] multiplatform MIT and GPLv2 [7] Not applicable
OpenCOR A cross-platform modelling environment, which is aimed at organizing, editing, simulating, and analysing CellML files on Windows, Linux and macOS. multiplatform (C++/Python) GPLv3 [8] Uses CellML
PhysiBoSS A specialized form of the PhysiCell agent-based modeling platform that directly integrates Boolean signaling networks into cell Agents[19] multiplatform (C++) BSD-3 [9] Yes, but only for reactions
PhysiCell A agent-based[20] modeling framework for multicellular systems biology. multiplatform (C++) BSD-3 [10] Yes, but only for reactions
PySCeS Python tool for modeling and analyzing SBML models[21][22][23] multiplatform (Python) BSD-3 [11] Yes
pySB Python-based[24] platform with specialization in rule-based models. multiplatform (Python) BSD-3 [12] Partial
ReaDDy Particle-based spatial simulator with intermolecular potentials[25] Linux and Mac Custom [13] Not applicable
SBSCL Java library[26][27] with efficient and exhaustive support for SBML multiplatform (Java) LGPL [14] Yes
SBW A distributed workbench[28][29] that includes many modeling tools multiplatform (C/C++) BSD-3 [15] Yes
Smoldyn Particle-based simulator for spatial stochastic simulations with individual molecules[30][31][32][33] multiplatform (C/C++/Python) LGPL [16] Not applicable
Spatiocyte Spatial modeling software that uses a fine lattice with up to one molecule per site[34][35] multiplatform Unknown [17] Not applicable
SpringSaLaD Particle-based spatial simulator in which molecules are spheres that are linked by springs[36] multiplatform Unknown [18] Not applicable
STEPS STochastic Engine for Pathway Simulation[37][38][39][40] multiplatform (C++/Python) GPLv2 [19] Partial [20]
Tellurium Simulation environment,[41][42] that packages multiple libraries into one platform. multiplatform (Python) Apache License [21] Yes
URDME Stochastic reaction-diffusion simulation on unstructured meshes[43] MatLab on Mac, Linux GPL3 [22] Not applicable
VCell Comprehensive modeling platform[44][45] for non-spatial, spatial, deterministic and stochastic simulations, including both reaction networks and reaction rules. multiplatform (Java) MIT [23] Yes

Legacy Open-Source Software Applications

The following list shows some of the software modeling applications that were developed in the 1980s and 1990s. There are listed for historical interest.

Name Description/Notability Language SBML Support Terminus ante quem[46]
COR[47] First public CellML-based environment. Object Pascal Uses CellML 2010
DBsolve[48] Early GUI based simulation platform. C/C++ No 1999
E-Cell[49] One of the earliest attempts at a whole-cell modeling platform. C/C++ No 1999
Gepasi[50] First GUI application that supported metabolic control analysis and parameter estimation. C/C++ Yes 1993
Jarnac[51] First GUI based application to support scripting in systems biology modeling. Object Pascal Yes 2000
JSim[52][53] First Java-based systems biology modeling platform Java Yes 2003
MetaModel[54] One of the first PC-based systems biology simulators Turbo Pascal 5.0 No 1991
MIST[55] GUI based simulator Borland Pascal 7.0 No 1995
SCAMP[56] First application to support metabolic control analysis and simulation on a PC Pascal, later in C No 1991

References

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  2. ^ Change, Britton; Higgins, Joseph; Garfinkel, David (1962). Analogue and digital computer representations of biochemical processes. Federation of American Societies for Experimental Biology..: Federation Proceedings, Vol 12. No. 1-2. p. 75.
  3. ^ Burns, Jim (1 March 1973). "Metabolic Control Analysis". Thesis. doi:10.5281/zenodo.7240738.
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  5. ^ Watanabe, Leandro; Nguyen, Tramy; Zhang, Michael; Zundel, Zach; Zhang, Zhen; Madsen, Curtis; Roehner, Nicholas; Myers, Chris (19 July 2019). "iBioSim3: A Tool for Model-Based Genetic Circuit Design". ACS Synthetic Biology. 8 (7): 1560–1563. doi:10.1021/acssynbio.8b00078.
  6. ^ Martínez-García, Esteban; Goñi-Moreno, Angel; Bartley, Bryan; McLaughlin, James; Sánchez-Sampedro, Lucas; Pascual del Pozo, Héctor; Prieto Hernández, Clara; Marletta, Ada Serena; De Lucrezia, Davide; Sánchez-Fernández, Guzmán; Fraile, Sofía; de Lorenzo, Víctor (8 January 2020). "SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts". Nucleic Acids Research. 48 (D1): D1164–D1170. doi:10.1093/nar/gkz1024.
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  11. ^ Somogyi, Endre T.; Bouteiller, Jean-Marie; Glazier, James A.; König, Matthias; Medley, J. Kyle; Swat, Maciej H.; Sauro, Herbert M. (15 October 2015). "libRoadRunner: a high performance SBML simulation and analysis library: Table 1". Bioinformatics. 31 (20): 3315–3321. doi:10.1093/bioinformatics/btv363.
  12. ^ Ghaffarizadeh, Ahmadreza; Heiland, Randy; Friedman, Samuel H.; Mumenthaler, Shannon M.; Macklin, Paul (23 February 2018). "PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems". PLOS Computational Biology. 14 (2): e1005991. doi:10.1371/journal.pcbi.1005991.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  13. ^ Haiman, Zachary B.; Zielinski, Daniel C.; Koike, Yuko; Yurkovich, James T.; Palsson, Bernhard O. (28 January 2021). "MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics". PLOS Computational Biology. 17 (1): e1008208. doi:10.1371/journal.pcbi.1008208.{{cite journal}}: CS1 maint: unflagged free DOI (link)
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  15. ^ Ebrahim, Ali; Lerman, Joshua A; Palsson, Bernhard O; Hyduke, Daniel R (December 2013). "COBRApy: COnstraints-Based Reconstruction and Analysis for Python". BMC Systems Biology. 7 (1): 74. doi:10.1186/1752-0509-7-74.{{cite journal}}: CS1 maint: unflagged free DOI (link)
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  18. ^ Kerr, R; Bartol, TM; Kaminsky, B; Dittrich, M; Chang, JCJ; Baden, S; Sejnowski, TJ; Stiles, JR (2008). "Fast Monte Carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces". SIAM J. Sci. Comput. 30: 3126–3149.
  19. ^ Letort, Gaelle; Montagud, Arnau; Stoll, Gautier; Heiland, Randy; Barillot, Emmanuel; Macklin, Paul; Zinovyev, Andrei; Calzone, Laurence (1 April 2019). "PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling". Bioinformatics. 35 (7): 1188–1196. doi:10.1093/bioinformatics/bty766.
  20. ^ Ghaffarizadeh, Ahmadreza; Heiland, Randy; Friedman, Samuel H.; Mumenthaler, Shannon M.; Macklin, Paul (23 February 2018). "PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems". PLOS Computational Biology. 14 (2): e1005991. doi:10.1371/journal.pcbi.1005991.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  21. ^ Olivier, B. G.; Rohwer, J. M.; Hofmeyr, J.-H. S. (15 February 2005). "Modelling cellular systems with PySCeS". Bioinformatics. 21 (4): 560–561. doi:10.1093/bioinformatics/bti046.
  22. ^ Mendoza-Cózatl, David G.; Moreno-Sánchez, Rafael (February 2006). "Control of glutathione and phytochelatin synthesis under cadmium stress. Pathway modeling for plants". Journal of Theoretical Biology. 238 (4): 919–936. doi:10.1016/j.jtbi.2005.07.003.
  23. ^ Ghaffarizadeh, Ahmadreza; Heiland, Randy; Friedman, Samuel H.; Mumenthaler, Shannon M.; Macklin, Paul (23 February 2018). "PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems". PLOS Computational Biology. 14 (2): e1005991. doi:10.1371/journal.pcbi.1005991.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  24. ^ Stefan, Melanie I.; Bartol, Thomas M.; Sejnowski, Terrence J.; Kennedy, Mary B. (25 September 2014). "Multi-state Modeling of Biomolecules". PLOS Computational Biology. 10 (9): e1003844. doi:10.1371/journal.pcbi.1003844.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  25. ^ Schöneberg, J.; Ullrich, A.; Noé, F. (2014). "Simulation tools for particle-based reaction-diffusion dynamics in continuous space". BMC Biophys. 7: 1.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  26. ^ Panchiwala, H; Shah, S; Planatscher, H; Zakharchuk, M; König, M; Dräger, A (23 September 2021). "The Systems Biology Simulation Core Library". Bioinformatics (Oxford, England). doi:10.1093/bioinformatics/btab669. PMID 34554191.
  27. ^ Tangherloni, Andrea; Nobile, Marco S.; Cazzaniga, Paolo; Capitoli, Giulia; Spolaor, Simone; Rundo, Leonardo; Mauri, Giancarlo; Besozzi, Daniela (9 September 2021). "FiCoS: A fine-grained and coarse-grained GPU-powered deterministic simulator for biochemical networks". PLOS Computational Biology. 17 (9): e1009410. doi:10.1371/journal.pcbi.1009410.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  28. ^ Hucka, M.; Finney, A.; Sauro, H. M.; Bolouri, H.; Doyle, J.; Kitano, H. (December 2001). "THE ERATO SYSTEMS BIOLOGY WORKBENCH: ENABLING INTERACTION AND EXCHANGE BETWEEN SOFTWARE TOOLS FOR COMPUTATIONAL BIOLOGY". Biocomputing 2002: 450–461. doi:10.1142/9789812799623_0042.
  29. ^ Kawasaki, Regiane; Baraúna, Rafael A.; Silva, Artur; Carepo, Marta S. P.; Oliveira, Rui; Marques, Rodolfo; Ramos, Rommel T. J.; Schneider, Maria P. C. (2016). "Reconstruction of the Fatty Acid Biosynthetic Pathway of Exiguobacterium antarcticum B7 Based on Genomic and Bibliomic Data". BioMed Research International. 2016: 1–9. doi:10.1155/2016/7863706.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  30. ^ Andrews, Steven S.; Bray, Dennis (2004). "Stochastic simulation of chemical reactions with spatial resolution and single molecule detail". Physical Biology. 1: 137.
  31. ^ Andrews, Steven S.; Addy, Nathan J.; Brent, Roger; Arkin, Adam P. (2010). "Detailed simulations of cell biology with Smoldyn 2.1". PLoS Comp. Biol. 6: e1000705.
  32. ^ Andrews, Steven S. (2017). "Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction, and a library interface". Bioinformatics. 33: 710–717.
  33. ^ Singh, Dilawar; Andrews, Steven S. (2022). "Python interfaces for the Smoldyn simulator". Bioinformatics. 38: 291–293.
  34. ^ Arjunan, S.N.V.; Takahashi, K. (2017). "Multi-algorithm particle simulations with Spatiocyte". Methods in Molecular Biology. 1611: 219–236.
  35. ^ Arjunan, S.N.V.; Miyauchi, A.; Iwamoto, K.; Takahashi, K. (2020). "pSpatiocyte: a high-performance simulator for intracellular reaction-diffusion systems". BMC Bioinformatics. 21: 33.
  36. ^ Michalski, P.J.; Loew, L.M. (2016). "SpringSaLaD: a spatial, particle-based biochemical simulation platform with excluded volume". Biophys. J. 110: 523–529.
  37. ^ Hepburn, Iain; Chen, Weiliang; Wils, Stefan; De Schutter, Erik (May 2012). "STEPS: efficient simulation of stochastic reaction–diffusion models in realistic morphologies". BMC Systems Biology. 7 (1): 36. doi:10.1186/1752-0509-6-36.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  38. ^ Chen, Weiliang; De Schutter, Erik (February 2017). "Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers". Frontiers in Neuroinformatics. 11 (1): 13. doi:10.3389/fninf.2017.00013.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  39. ^ Hepburn, Iain; Chen, Weiliang; De Schutter, Erik (August 2016). "Accurate reaction-diffusion operator splitting on tetrahedral meshes for parallel stochastic molecular simulations". The Journal of Chemical Physics. 145 (5): 054118. doi:10.1063/1.4960034.
  40. ^ Chen, Weiliang; Carel, Tristan; Awile, Omar; Cantarutti, Nicola; Castiglioni, Giacomo; Cattabiani, Alessandro; Del Marmol, Baudouin; Hepburn, Iain; King, James G.; Kotsalos, Christos; Kumbhar, Pramod; Lallouette, Jules; Melchior, Samuel; Schürmann, Felix; De Schutter, Erik (October 2022). "STEPS 4.0: Fast and memory-efficient molecular simulations of neurons at the nanoscale". Frontiers in Neuroinformatics. 16. doi:10.3389/fninf.2022.883742. ISSN 1662-5196.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  41. ^ Choi, Kiri; Medley, J. Kyle; König, Matthias; Stocking, Kaylene; Smith, Lucian; Gu, Stanley; Sauro, Herbert M. (September 2018). "Tellurium: An extensible python-based modeling environment for systems and synthetic biology". Biosystems. 171: 74–79. doi:10.1016/j.biosystems.2018.07.006.
  42. ^ Pease, Nicholas A.; Nguyen, Phuc H.B.; Woodworth, Marcus A.; Ng, Kenneth K.H.; Irwin, Blythe; Vaughan, Joshua C.; Kueh, Hao Yuan (March 2021). "Tunable, division-independent control of gene activation timing by a polycomb switch". Cell Reports. 34 (12): 108888. doi:10.1016/j.celrep.2021.108888.
  43. ^ Drawert, B.; Engblom, S.; Hellander, A (2012). "URDME: A modular framework for stochastic simulation of reaction-transport processes in complex geometries". BMC Systems Biology. 6: 1–17.
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  46. ^ Based on earliest publication date
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  52. ^ Butterworth, Erik; Jardine, Bartholomew E.; Raymond, Gary M.; Neal, Maxwell L.; Bassingthwaighte, James B. (30 December 2013). "JSim, an open-source modeling system for data analysis". F1000Research. 2: 288. doi:10.12688/f1000research.2-288.v1.{{cite journal}}: CS1 maint: unflagged free DOI (link)
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  54. ^ Cornish-Bowden, Athel; Hofmeyr, Jan-Hendrik S. (1991). "MetaModel: a program for modelling and control analysis of metabolic pathways on the IBM PC and compatibles". Bioinformatics. 7 (1): 89–93. doi:10.1093/bioinformatics/7.1.89.
  55. ^ Ehlde, Magnus; Zacchi, Guido (1995). "MIST: a user-friendly metabolic simulator". Bioinformatics. 11 (2): 201–207. doi:10.1093/bioinformatics/11.2.201.
  56. ^ Sauro, Herbert M.; Fell, David A. (1991). "SCAMP: A metabolic simulator and control analysis program". Mathematical and Computer Modelling. 15 (12): 15–28. doi:10.1016/0895-7177(91)90038-9.
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