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Volumn 7, Issue , 2013, Pages

The systems biology simulation core algorithm

Author keywords

Algorithms; Biological networks; Mathematical modeling; Numerical integration; Ordinary differential equation systems; Simulation; Software engineering; Systems biology

Indexed keywords

ALGORITHM; ARTICLE; METHODOLOGY; STATISTICAL MODEL; SYSTEMS BIOLOGY;

EID: 84879801381     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-7-55     Document Type: Article
Times cited : (30)

References (60)
  • 1
    • 79952676360 scopus 로고    scopus 로고
    • Systems biology: evolving into the mainstream
    • 10.1016/j.cell.2011.02.044, 21414474
    • Macilwain C. Systems biology: evolving into the mainstream. Cell 2011, 144(6):839-841. [http://dx.doi.org/10.1016/j.cell.2011.02.044], 10.1016/j.cell.2011.02.044, 21414474.
    • (2011) Cell , vol.144 , Issue.6 , pp. 839-841
    • Macilwain, C.1
  • 2
    • 84859840179 scopus 로고    scopus 로고
    • The virtual liver: a multidisciplinary, multilevel challenge for systems biology
    • 10.1002/wsbm.1158, 22246674
    • Holzhutter HG, Drasdo D, Preusser T, Lippert J, Henney AM. The virtual liver: a multidisciplinary, multilevel challenge for systems biology. Wiley Interdiscip Rev Syst Biol Med 2012, 4(3):221-235. [http://dx.doi.org/10.1002/wsbm.1158], 10.1002/wsbm.1158, 22246674.
    • (2012) Wiley Interdiscip Rev Syst Biol Med , vol.4 , Issue.3 , pp. 221-235
    • Holzhutter, H.G.1    Drasdo, D.2    Preusser, T.3    Lippert, J.4    Henney, A.M.5
  • 4
    • 34147189103 scopus 로고    scopus 로고
    • Systems biology standards-the community speaks
    • 10.1038/nbt0407-390, 17420739
    • Klipp E, Liebermeister W, Helbig A, Kowald A, Schaber J. Systems biology standards-the community speaks. Nat Biotechnol 2007, 25(4):390-391. [http://dx.doi.org/10.1038/nbt0407-390], 10.1038/nbt0407-390, 17420739.
    • (2007) Nat Biotechnol , vol.25 , Issue.4 , pp. 390-391
    • Klipp, E.1    Liebermeister, W.2    Helbig, A.3    Kowald, A.4    Schaber, J.5
  • 6
    • 85017132128 scopus 로고    scopus 로고
    • SemanticSBML: a tool for annotating, checking, and merging of biochemical models in SBML format
    • Nature Publishing Group
    • Liebermeister W, Krause F, Uhlendorf J, Lubitz T, Klipp E. SemanticSBML: a tool for annotating, checking, and merging of biochemical models in SBML format. 3rd International Biocuration Conference 2009, Nature Publishing Group, [http://dx.doi.org/10.1038/npre.2009.3093.1].
    • (2009) 3rd International Biocuration Conference
    • Liebermeister, W.1    Krause, F.2    Uhlendorf, J.3    Lubitz, T.4    Klipp, E.5
  • 8
    • 84872261630 scopus 로고    scopus 로고
    • The Systems Biology Markup Language
    • The Systems Biology Markup Language. [http://sbml.org].
  • 9
    • 2442595958 scopus 로고    scopus 로고
    • CellML: its future, present and past
    • Lloyd CM, Halstead MDB, Nielsen PF. CellML: its future, present and past. Prog Biophys Mol Bio 2004, 85(2-3):433-450. [http://dx.doi.org/10.1016/j.pbiomolbio.2004.01.004].
    • (2004) Prog Biophys Mol Bio , vol.85 , Issue.2-3 , pp. 433-450
    • Lloyd, C.M.1    Halstead, M.D.B.2    Nielsen, P.F.3
  • 10
    • 84880136618 scopus 로고    scopus 로고
    • The CellML project
    • The CellML project. [http://cellml.org].
  • 12
    • 51749096446 scopus 로고    scopus 로고
    • The CellML Model Repository
    • 10.1093/bioinformatics/btn390, 18658182
    • Lloyd CM, Lawson JR, Hunter PJ, Nielsen PF. The CellML Model Repository. Bioinformatics 2008, 24(18):2122-2123. [http://dx.doi.org/10.1093/bioinformatics/btn390], 10.1093/bioinformatics/btn390, 18658182.
    • (2008) Bioinformatics , vol.24 , Issue.18 , pp. 2122-2123
    • Lloyd, C.M.1    Lawson, J.R.2    Hunter, P.J.3    Nielsen, P.F.4
  • 13
    • 40749162829 scopus 로고    scopus 로고
    • LibSBML: an API library for SBML
    • 10.1093/bioinformatics/btn051, 2517632, 18252737
    • Bornstein BJ, Keating SM, Jouraku A, Hucka M. LibSBML: an API library for SBML. Bioinformatics 2008, 24(6):880-881. [http://dx.doi.org/10.1093/bioinformatics/btn051], 10.1093/bioinformatics/btn051, 2517632, 18252737.
    • (2008) Bioinformatics , vol.24 , Issue.6 , pp. 880-881
    • Bornstein, B.J.1    Keating, S.M.2    Jouraku, A.3    Hucka, M.4
  • 15
    • 79960423002 scopus 로고    scopus 로고
    • JSBML: a flexible Java library for working with SBML
    • 10.1093/bioinformatics/btr361, 3137227, 21697129
    • Drager A, Rodriguez N, Dumousseau M, Dorr A, Wrzodek C, Le Novere N, Zell A, Hucka M. JSBML: a flexible Java library for working with SBML. Bioinformatics 2011, 27(15):2167-2168. [http://bioinformatics.oxfordjournals.org/content/27/15/2167], 10.1093/bioinformatics/btr361, 3137227, 21697129.
    • (2011) Bioinformatics , vol.27 , Issue.15 , pp. 2167-2168
    • Drager, A.1    Rodriguez, N.2    Dumousseau, M.3    Dorr, A.4    Wrzodek, C.5    Le Novere, N.6    Zell, A.7    Hucka, M.8
  • 19
    • 0038745251 scopus 로고    scopus 로고
    • Systems Biology Markup Language (SBML) level 2: structures and facilities for model definitions.
    • Finney A, Hucka M, Le Novere N. Systems Biology Markup Language (SBML) level 2: structures and facilities for model definitions. Tech. rep 2006,
    • (2006) Tech. rep
    • Finney, A.1    Hucka, M.2    Le Novere, N.3
  • 20
    • 0038745251 scopus 로고    scopus 로고
    • Systems Biology Markup Language (SBML) level 2: structures and facilities for model definitions
    • Hucka M, Finney AM, Hoops S, Keating SM, Le Novere N. Systems Biology Markup Language (SBML) level 2: structures and facilities for model definitions. Tech. rep 2007,
    • (2007) Tech. rep
    • Hucka, M.1    Finney, A.M.2    Hoops, S.3    Keating, S.M.4    Le Novere, N.5
  • 21
    • 0038745251 scopus 로고    scopus 로고
    • Systems biology markup language (SBML) Level 2: structures and facilities for model definitions
    • Hucka M, Finney A, Hoops S, Keating SM, Le Novere N. Systems biology markup language (SBML) Level 2: structures and facilities for model definitions. Tech. rep. Nature Precedings 2008, [http://dx.doi.org/10.1038/npre.2008.2715.1].
    • (2008) Tech. rep. Nature Precedings
    • Hucka, M.1    Finney, A.2    Hoops, S.3    Keating, S.M.4    Le Novere, N.5
  • 24
    • 84880132218 scopus 로고    scopus 로고
    • SBML Test Suite
    • SBML Test Suite. [http://sbml.org/Software/SBML_Test_Suite].
  • 25
    • 50549101468 scopus 로고    scopus 로고
    • Comparing simulation results of SBML capable simulators
    • 10.1093/bioinformatics/btn319, 2732216, 18579569
    • Bergmann FT, Sauro HM. Comparing simulation results of SBML capable simulators. Bioinformatics 2008, 24(17):1963-1965. [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/17/1963], 10.1093/bioinformatics/btn319, 2732216, 18579569.
    • (2008) Bioinformatics , vol.24 , Issue.17 , pp. 1963-1965
    • Bergmann, F.T.1    Sauro, H.M.2
  • 27
    • 33846617808 scopus 로고    scopus 로고
    • Bringing metabolic networks to life: convenience rate law and thermodynamic constraints
    • 1781438, 17173669
    • Liebermeister W, Klipp E. Bringing metabolic networks to life: convenience rate law and thermodynamic constraints. Theor Biol Med Model 2006, 3(42):41. [http://dx.doi.org/10.1186/1742-4682-3-41], 1781438, 17173669.
    • (2006) Theor Biol Med Model , vol.3 , Issue.42 , pp. 41
    • Liebermeister, W.1    Klipp, E.2
  • 28
    • 77954196484 scopus 로고    scopus 로고
    • Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation
    • 10.1093/bioinformatics/btq141, 20385728
    • Liebermeister W, Uhlendorf J, Klipp E. Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation. Bioinformatics 2010, 26(12):1528-1534. [http://dx.doi.org/10.1093/bioinformatics/btq141], 10.1093/bioinformatics/btq141, 20385728.
    • (2010) Bioinformatics , vol.26 , Issue.12 , pp. 1528-1534
    • Liebermeister, W.1    Uhlendorf, J.2    Klipp, E.3
  • 29
    • 0001009871 scopus 로고
    • An n5/2 algorithm for maximum matchings in bipartite graphs
    • Hopcroft JE, Karp RM. An n5/2 algorithm for maximum matchings in bipartite graphs. SIAM J Comput 1973, 2(4):225-231. [http://dx.doi.org/10.1137/0202019].
    • (1973) SIAM J Comput , vol.2 , Issue.4 , pp. 225-231
    • Hopcroft, J.E.1    Karp, R.M.2
  • 31
    • 44949099336 scopus 로고    scopus 로고
    • SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks
    • 10.1186/1752-0509-2-39, 2412839, 18447902
    • Drager A, Hassis N, Supper J, Schroder A, Zell A. SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks. BMC Syst Biol 2008, 2:39. [http://www.biomedcentral.com/1752-0509/2/39], 10.1186/1752-0509-2-39, 2412839, 18447902.
    • (2008) BMC Syst Biol , vol.2 , pp. 39
    • Drager, A.1    Hassis, N.2    Supper, J.3    Schroder, A.4    Zell, A.5
  • 32
    • 84880132452 scopus 로고    scopus 로고
    • Commons Math: The Apache Commons Mathematics Library
    • Commons Math: The Apache Commons Mathematics Library. [http://commons.apache.org/proper/commons-math/].
  • 35
    • 0034088868 scopus 로고    scopus 로고
    • Transduction of intracellular and intercellular dynamics in yeast glycolytic oscillations
    • 10.1016/S0006-3495(00)76672-0, 1300717, 10692304
    • Wolf J, Passarge J, Somsen OJG, Snoep JL, Heinrich R, Westerhoff HV. Transduction of intracellular and intercellular dynamics in yeast glycolytic oscillations. Biophys J 2000, 78(3):1145-1153. [http://dx.doi.org/10.1016/S0006-3495(00)76672-0], 10.1016/S0006-3495(00)76672-0, 1300717, 10692304.
    • (2000) Biophys J , vol.78 , Issue.3 , pp. 1145-1153
    • Wolf, J.1    Passarge, J.2    Somsen, O.J.G.3    Snoep, J.L.4    Heinrich, R.5    Westerhoff, H.V.6
  • 36
    • 83055187942 scopus 로고    scopus 로고
    • A quantitative comparison of Calvin-Benson cycle models
    • 10.1016/j.tplants.2011.09.004, 22001849
    • Arnold A, Nikoloski Z. A quantitative comparison of Calvin-Benson cycle models. Trends Plant Sci 2011, 16(12):676-683. [http://dx.doi.org/10.1016/j.tplants.2011.09.004], 10.1016/j.tplants.2011.09.004, 22001849.
    • (2011) Trends Plant Sci , vol.16 , Issue.12 , pp. 676-683
    • Arnold, A.1    Nikoloski, Z.2
  • 37
    • 33644877164 scopus 로고    scopus 로고
    • BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
    • 10.1093/nar/gkj092, 1347454, 16381960
    • Le Novere N, Bornsteinm BJ, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B, Snoep JL, Hucka M. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res 2006, 34:D689-D691. [http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D689], 10.1093/nar/gkj092, 1347454, 16381960.
    • (2006) Nucleic Acids Res , vol.34
    • Le Novere, N.1    Bornsteinm, B.J.2    Broicher, A.3    Courtot, M.4    Donizelli, M.5    Dharuri, H.6    Li, L.7    Sauro, H.8    Schilstra, M.9    Shapiro, B.10    Snoep, J.L.11    Hucka, M.12
  • 38
    • 0004317158 scopus 로고    scopus 로고
    • Solving Ordinary Differential Equations. 1 Nonstiff Problems
    • Berlin: Springer
    • Hairer E, Norsett SP, Wanner G. Solving Ordinary Differential Equations. 1 Nonstiff Problems. 2000, Berlin: Springer.
    • (2000)
    • Hairer, E.1    Norsett, S.P.2    Wanner, G.3
  • 39
    • 84880131906 scopus 로고    scopus 로고
    • SBML Software Matrix (October 8th 2012)
    • SBML Software Matrix (October 8th 2012). [http://sbml.org/SBML_Software_Guide/SBML_Software_Matrix].
  • 40
    • 84880135888 scopus 로고    scopus 로고
    • BioUML-open source plug-in based platform for bioinformatics: invitation to collaboration
    • Department of Bioengineering and Bioinformatics of MV Lomonosov Moscow State University
    • Kolpakov FA, Tolstykh NI, Valeev TF, Kiselev IN, Kutumova EO, Ryabova A, Yevshin IS, Kel AE. BioUML-open source plug-in based platform for bioinformatics: invitation to collaboration. Moscow Conference on Computational Molecular Biology 2011, 172-173. Department of Bioengineering and Bioinformatics of MV Lomonosov Moscow State University, [http://mccmb.genebee.msu.ru/2011/mccmb11.pdf].
    • (2011) Moscow Conference on Computational Molecular Biology , pp. 172-173
    • Kolpakov, F.A.1    Tolstykh, N.I.2    Valeev, T.F.3    Kiselev, I.N.4    Kutumova, E.O.5    Ryabova, A.6    Yevshin, I.S.7    Kel, A.E.8
  • 42
    • 70350669878 scopus 로고    scopus 로고
    • IBioSim: a tool for the analysis and design of genetic circuits
    • 10.1093/bioinformatics/btp457, 19628507
    • Myers CJ, Barker N, Jones K, Kuwahara H, Madsen C, Nguyen NPD. iBioSim: a tool for the analysis and design of genetic circuits. Bioinformatics 2009, 25(21):2848-2849. [http://dx.doi.org/10.1093/bioinformatics/btp457], 10.1093/bioinformatics/btp457, 19628507.
    • (2009) Bioinformatics , vol.25 , Issue.21 , pp. 2848-2849
    • Myers, C.J.1    Barker, N.2    Jones, K.3    Kuwahara, H.4    Madsen, C.5    Nguyen, N.P.D.6
  • 43
    • 33845387962 scopus 로고    scopus 로고
    • JSIM: Free software package for teaching physiological modeling and research
    • Raymond GM, Butterworth E, Bassingthwaighte JB. JSIM: Free software package for teaching physiological modeling and research. Exp Biol 2003, 280:102-107.
    • (2003) Exp Biol , vol.280 , pp. 102-107
    • Raymond, G.M.1    Butterworth, E.2    Bassingthwaighte, J.B.3
  • 47
    • 84880135183 scopus 로고    scopus 로고
    • SBML Test Suite Database-Test results for SBML-compatible software systems
    • SBML Test Suite Database-Test results for SBML-compatible software systems. [http://sbml.org/Facilities/Database/Simulator].
  • 48
    • 80052337295 scopus 로고    scopus 로고
    • JHGM: Analyzing the functional properties of the creatine kinase system with multiscale 'sloppy' modeling
    • 10.1371/journal.pcbi.1002130, 3166207, 21912519
    • Hettling H, van B. JHGM: Analyzing the functional properties of the creatine kinase system with multiscale 'sloppy' modeling. PLoS Comput Biol 2011, 7(8):e1002130. [http://dx.doi.org/10.1371/journal.pcbi.1002130], 10.1371/journal.pcbi.1002130, 3166207, 21912519.
    • (2011) PLoS Comput Biol , vol.7 , Issue.8
    • Hettling, H.1    van, B.2
  • 49
    • 70349574614 scopus 로고    scopus 로고
    • Monte Carlo analysis of an ODE model of the Sea Urchin Endomesoderm network
    • 2739852, 19698179
    • Kuhn C, Wierling C, Kühn A, Klipp E, Panopoulou G, Lehrach H, Poustka AJ. Monte Carlo analysis of an ODE model of the Sea Urchin Endomesoderm network. BMC Syst Biol 2009, 3(3):83. [http://dx.doi.org/10.1186/1752-0509-3-83], 2739852, 19698179.
    • (2009) BMC Syst Biol , vol.3 , Issue.3 , pp. 83
    • Kuhn, C.1    Wierling, C.2    Kühn, A.3    Klipp, E.4    Panopoulou, G.5    Lehrach, H.6    Poustka, A.J.7
  • 50
    • 34250486951 scopus 로고
    • Klassische Runge-Kutta-Formeln vierter und niedrigerer Ordnung mit Schrittweiten-Kontrolle und ihre Anwendung auf Wärmeleitungsprobleme
    • Fehlberg E. Klassische Runge-Kutta-Formeln vierter und niedrigerer Ordnung mit Schrittweiten-Kontrolle und ihre Anwendung auf Wärmeleitungsprobleme. Computing 1970, 6(1-2):61-71. [http://dx.doi.org/10.1007/BF02241732].
    • (1970) Computing , vol.6 , Issue.1-2 , pp. 61-71
    • Fehlberg, E.1
  • 53
    • 33747825750 scopus 로고    scopus 로고
    • A model diagram layout extension for SBML
    • 10.1093/bioinformatics/btl195, 16709586
    • Gauges R, Rost U, Sahle S, Wegner K. A model diagram layout extension for SBML. Bioinformatics 2006, 22(15):1879-1885. [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/15/1879], 10.1093/bioinformatics/btl195, 16709586.
    • (2006) Bioinformatics , vol.22 , Issue.15 , pp. 1879-1885
    • Gauges, R.1    Rost, U.2    Sahle, S.3    Wegner, K.4
  • 55
    • 9444266171 scopus 로고    scopus 로고
    • CellDesigner: a process diagram editor for gene-regulatory and biochemical networks
    • Funahashi A, Tanimura N, Morohashi M, Kitano H. CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. BioSilico 2003, 1(5):159-162. [http://www.sciencedirect.com/science/article/B75GS-4BS08JD-5/2/5531c80ca62a425f55d224b8a0d3f702].
    • (2003) BioSilico , vol.1 , Issue.5 , pp. 159-162
    • Funahashi, A.1    Tanimura, N.2    Morohashi, M.3    Kitano, H.4
  • 56
    • 84880131259 scopus 로고    scopus 로고
    • SBMLsimulator-An efficient Java solver implementation for SBML
    • SBMLsimulator-An efficient Java solver implementation for SBML. [http://www.cogsys.cs.uni-tuebingen.de/software/SBMLsimulator].
  • 58
    • 84880133960 scopus 로고    scopus 로고
    • Java Resources for SED-ML
    • Java Resources for SED-ML. [http://jlibsedml.sourceforge.net].
  • 59
    • 48249084994 scopus 로고    scopus 로고
    • A pharmacodynamic model for the time course of tumor shrinkage by gemcitabine + carboplatin in non-small cell lung cancer patients
    • 10.1158/1078-0432.CCR-07-4754, 18594002
    • Tham LS, Wang L, Soo RA, Lee SC, Lee HS, Yong WP, Goh BC, Holford NHG. A pharmacodynamic model for the time course of tumor shrinkage by gemcitabine + carboplatin in non-small cell lung cancer patients. Clin Cancer Res 2008, 14(13):4213-4218. [http://dx.doi.org/10.1158/1078-0432.CCR-07-4754], 10.1158/1078-0432.CCR-07-4754, 18594002.
    • (2008) Clin Cancer Res , vol.14 , Issue.13 , pp. 4213-4218
    • Tham, L.S.1    Wang, L.2    Soo, R.A.3    Lee, S.C.4    Lee, H.S.5    Yong, W.P.6    Goh, B.C.7    Holford, N.H.G.8
  • 60
    • 69449108221 scopus 로고    scopus 로고
    • A comprehensive model for the humoral coagulation network in humans
    • 10.1038/clpt.2009.87, 19516255
    • Wajima T, Isbister GK, Duffull SB. A comprehensive model for the humoral coagulation network in humans. Clin Pharmacol Ther 2009, 86(3):290-298. [http://dx.doi.org/10.1038/clpt.2009.87], 10.1038/clpt.2009.87, 19516255.
    • (2009) Clin Pharmacol Ther , vol.86 , Issue.3 , pp. 290-298
    • Wajima, T.1    Isbister, G.K.2    Duffull, S.B.3


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