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Volumn 2, Issue DEC, 2014, Pages

Improving collaboration by standardization efforts in systems biology

Author keywords

Model databases; Model formats; Modeling guidelines; Network visualization; Ontologies; Software support

Indexed keywords

BIOINFORMATICS; BIOLOGY; COMPUTER SOFTWARE; KNOWLEDGE REPRESENTATION; ONTOLOGY; OPEN SOURCE SOFTWARE; SOFTWARE ENGINEERING; STANDARDIZATION;

EID: 84991905414     PISSN: None     EISSN: 22964185     Source Type: Journal    
DOI: 10.3389/fbioe.2014.00061     Document Type: Review
Times cited : (54)

References (169)
  • 1
    • 84859738427 scopus 로고    scopus 로고
    • SED-ED, a workflow editor for computational biology experiments written in SED-ML
    • Adams, R. R. (2012). SED-ED, a workflow editor for computational biology experiments written in SED-ML. Bioinformatics 28, 1180-1181. doi: 10.1093/bioinformatics/bts101
    • (2012) Bioinformatics , vol.28 , pp. 1180-1181
    • Adams, R.R.1
  • 2
    • 84923692507 scopus 로고    scopus 로고
    • A versatile platform for multilevel modeling of physiological systems: SBML-PHML hybrid modeling and simulation
    • Asai, Y., Abe, T., Oka, H., Okita, M., Hagihara, K.-I., Ghosh, S., et al. (2014). A versatile platform for multilevel modeling of physiological systems: SBML-PHML hybrid modeling and simulation. Adv Biomed Eng 3, 50-58. doi:10.1109/EMBC.2013.6610802
    • (2014) Adv Biomed Eng , vol.3 , pp. 50-58
    • Asai, Y.1    Abe, T.2    Oka, H.3    Okita, M.4    Hagihara, K.-I.5    Ghosh, S.6
  • 5
    • 58149310478 scopus 로고    scopus 로고
    • Specifications of insilicoML 1.0: a multilevel biophysical model description language
    • Asai, Y., Suzuki, Y., Kido, Y., Oka, H., Heien, E., Nakanishi, M., et al. (2008). Specifications of insilicoML 1.0: a multilevel biophysical model description language. J. Physiol. Sci. 58, 447-458. doi:10.2170/physiolsci.RP013308
    • (2008) J. Physiol. Sci , vol.58 , pp. 447-458
    • Asai, Y.1    Suzuki, Y.2    Kido, Y.3    Oka, H.4    Heien, E.5    Nakanishi, M.6
  • 8
    • 34347258175 scopus 로고    scopus 로고
    • Quantitative prediction of cellular metabolism with constraint-based models: the COBRA toolbox
    • Becker, S. A., Feist, A. M., Mo, M. L., Hannum, G., Palsson, B. Ø., and Herrgård, M. J. (2007). Quantitative prediction of cellular metabolism with constraint-based models: the COBRA toolbox. Nat. Protoc. 2, 727-738. doi:10.1038/nprot.2007.99
    • (2007) Nat. Protoc , vol.2 , pp. 727-738
    • Becker, S.A.1    Feist, A.M.2    Mo, M.L.3    Hannum, G.4    Palsson, B.Ø.5    Herrgård, M.J.6
  • 9
    • 84991302069 scopus 로고    scopus 로고
    • 'History of neural simulation software,'
    • eds J. M. Bower (New York: Springer)
    • Beeman, D. (2013). "History of neural simulation software," in Years of Computational Neuroscience, Vol. 9, ed. J. M. Bower (New York: Springer), 33-71.
    • (2013) Years of Computational Neuroscience , vol.9 , pp. 33-71
    • Beeman, D.1
  • 12
    • 50549101468 scopus 로고    scopus 로고
    • Comparing simulation results of SBML capable simulators
    • Bergmann, F. T., and Sauro, H. M. (2008). Comparing simulation results of SBML capable simulators. Bioinformatics 24, 1963-1965. doi:10.1093/bioinformatics/btn319
    • (2008) Bioinformatics , vol.24 , pp. 1963-1965
    • Bergmann, F.T.1    Sauro, H.M.2
  • 13
    • 34447513053 scopus 로고    scopus 로고
    • Sysmo: back to the future
    • Booth, I. R. (2007). Sysmo: back to the future. Nat. Rev. Microbiol. 5, 566-566. doi:10.1038/nrmicro1719
    • (2007) Nat. Rev. Microbiol , vol.5 , pp. 566-566
    • Booth, I.R.1
  • 14
    • 84892788440 scopus 로고    scopus 로고
    • Constraint-based models predict metabolic and associated cellular functions
    • Bordbar, A., Monk, J. M., King, Z. A., and Palsson, B. Ø. (2014). Constraint-based models predict metabolic and associated cellular functions. Nat. Rev. Gen. 15, 107-120. doi:10.1038/nrg3643
    • (2014) Nat. Rev. Gen , vol.15 , pp. 107-120
    • Bordbar, A.1    Monk, J.M.2    King, Z.A.3    Palsson, B.Ø.4
  • 16
  • 17
    • 84896691944 scopus 로고    scopus 로고
    • FieldML, a proposed open standard for the physiome project for mathematical model representation
    • Britten, R. D., Christie, G. R., Little, C., Miller, A. K., Bradley, C., Wu, A., et al. (2013). FieldML, a proposed open standard for the physiome project for mathematical model representation. Med. Biol. Eng. Comput. 51, 1191-1207. doi:10.1007/s11517-013-1097-7
    • (2013) Med. Biol. Eng. Comput , vol.51 , pp. 1191-1207
    • Britten, R.D.1    Christie, G.R.2    Little, C.3    Miller, A.K.4    Bradley, C.5    Wu, A.6
  • 19
    • 84886740491 scopus 로고    scopus 로고
    • Large-scale generation of computational models from biochemical pathway maps
    • Büchel, F., Rodriguez, N., Swainston, N., Wrzodek, C., Czauderna, T., Keller, R., et al. (2013a). Large-scale generation of computational models from biochemical pathway maps. BMC Syst. Biol. 7:116. doi:10.1186/1752-0509-7-116
    • (2013) BMC Syst. Biol , vol.7 , pp. 116
    • Büchel, F.1    Rodriguez, N.2    Swainston, N.3    Wrzodek, C.4    Czauderna, T.5    Keller, R.6
  • 20
    • 84888239359 scopus 로고    scopus 로고
    • Parkinson's disease: dopaminergic nerve cell model is consistent with experimental finding of increased extracellular transport of a-synuclein
    • Büchel, F., Saliger, S., Dräger, A., Hoffman, S., Wrzodek, C., Zell, A., et al. (2013b). Parkinson's disease: dopaminergic nerve cell model is consistent with experimental finding of increased extracellular transport of a-synuclein. BMC Neurosci. 14:136. doi:10.1186/1471-2202-14-136
    • (2013) BMC Neurosci , vol.14 , pp. 136
    • Büchel, F.1    Saliger, S.2    Dräger, A.3    Hoffman, S.4    Wrzodek, C.5    Zell, A.6
  • 21
    • 84870474617 scopus 로고    scopus 로고
    • Qualitative translation of relations from BioPAX to SBML qual
    • Büchel, F., Wrzodek, C., Mittag, F., Dräger, A., Eichner, J., Rodriguez, N., et al. (2012). Qualitative translation of relations from BioPAX to SBML qual. Bioinformatics 28, 2648-2653. doi:10.1093/bioinformatics/bts508
    • (2012) Bioinformatics , vol.28 , pp. 2648-2653
    • Büchel, F.1    Wrzodek, C.2    Mittag, F.3    Dräger, A.4    Eichner, J.5    Rodriguez, N.6
  • 23
    • 84907584117 scopus 로고    scopus 로고
    • LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2
    • Cannon, R. C., Gleeson, P., Crook, S., Ganapathy, G., Marin, B., Piasini, E., et al. (2014). LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2. Front. Neuroinform. 8:79. doi:10.3389/fninf.2014.00079
    • (2014) Front. Neuroinform , vol.8 , pp. 79
    • Cannon, R.C.1    Gleeson, P.2    Crook, S.3    Ganapathy, G.4    Marin, B.5    Piasini, E.6
  • 24
    • 84891774001 scopus 로고    scopus 로고
    • The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
    • Caspi, R., Altman, T., Billington, R., Dreher, K., Foerster, H., Fulcher, C. A., et al. (2014). The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 42, D459-D471. doi:10.1093/nar/gkt1103
    • (2014) Nucleic Acids Res , vol.42 , pp. D459-D471
    • Caspi, R.1    Altman, T.2    Billington, R.3    Dreher, K.4    Foerster, H.5    Fulcher, C.A.6
  • 25
    • 71849095864 scopus 로고    scopus 로고
    • TinkerCell: modular CAD tool for synthetic biology
    • Chandran, D., Bergmann, F. T., and Sauro, H. M. (2009). TinkerCell: modular CAD tool for synthetic biology. J. Biol. Eng. 3, 19. doi:10.1186/1754-1611-3-19
    • (2009) J. Biol. Eng , vol.3 , pp. 19
    • Chandran, D.1    Bergmann, F.T.2    Sauro, H.M.3
  • 26
    • 84889794047 scopus 로고    scopus 로고
    • SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
    • Chaouiya, C., Berenguier, D., Keating, S. M., Naldi, A., van Iersel, M. P., Rodriguez, N., et al. (2013). SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst. Biol. 7:135. doi:10.1186/1752-0509-7-135
    • (2013) BMC Syst. Biol , vol.7 , pp. 135
    • Chaouiya, C.1    Berenguier, D.2    Keating, S.M.3    Naldi, A.4    van Iersel, M.P.5    Rodriguez, N.6
  • 27
  • 29
    • 77951969603 scopus 로고    scopus 로고
    • Standard virtual biological parts: a repository of modular modeling components for synthetic biology
    • Cooling, M. T., Rouilly, V., Misirli, G., Lawson, J., Yu, T., Hallinan, J., et al. (2010). Standard virtual biological parts: a repository of modular modeling components for synthetic biology. Bioinformatics 26, 925-931. doi:10.1093/bioinformatics/btq063
    • (2010) Bioinformatics , vol.26 , pp. 925-931
    • Cooling, M.T.1    Rouilly, V.2    Misirli, G.3    Lawson, J.4    Yu, T.5    Hallinan, J.6
  • 33
    • 77956549590 scopus 로고    scopus 로고
    • Editing, validating and translating of SBGN maps
    • Czauderna, T., Klukas, C., and Schreiber, F. (2010). Editing, validating and translating of SBGN maps. Bioinformatics 26, 2340-2341. doi:10.1093/bioinformatics/btq407
    • (2010) Bioinformatics , vol.26 , pp. 2340-2341
    • Czauderna, T.1    Klukas, C.2    Schreiber, F.3
  • 34
    • 84881540711 scopus 로고    scopus 로고
    • Conversion of KEGG metabolic pathways to SBGN maps including automatic layout
    • Czauderna, T., Wybrow, M., Marriott, K., and Schreiber, F. (2013). Conversion of KEGG metabolic pathways to SBGN maps including automatic layout. BMC Bioinformatics 14:250. doi:10.1186/1471-2105-14-250
    • (2013) BMC Bioinformatics , vol.14 , pp. 250
    • Czauderna, T.1    Wybrow, M.2    Marriott, K.3    Schreiber, F.4
  • 35
    • 77951953604 scopus 로고    scopus 로고
    • SBRML: a markup language for associating systems biology data with models
    • Dada, J. O., Spasic, I., Paton, N. W., and Mendes, P. (2010). SBRML: a markup language for associating systems biology data with models. Bioinformatics 26, 932-938. doi:10.1093/bioinformatics/btq069
    • (2010) Bioinformatics , vol.26 , pp. 932-938
    • Dada, J.O.1    Spasic, I.2    Paton, N.W.3    Mendes, P.4
  • 36
    • 84892965416 scopus 로고    scopus 로고
    • Software applications toward quantitative metabolic flux analysis and modeling
    • Dandekar, T., Fieselmann, A., Majeed, S., and Ahmed, Z. (2012). Software applications toward quantitative metabolic flux analysis and modeling. Brief. Bioinformatics 15, 91-107. doi:10.1093/bib/bbs065
    • (2012) Brief. Bioinformatics , vol.15 , pp. 91-107
    • Dandekar, T.1    Fieselmann, A.2    Majeed, S.3    Ahmed, Z.4
  • 37
    • 33751376743 scopus 로고    scopus 로고
    • Supporting the SBML layout extension
    • Deckard, A., Bergmann, F. T., and Sauro, H. M. (2006). Supporting the SBML layout extension. Bioinformatics 22, 2966-2967. doi:10.1093/bioinformatics/btl520
    • (2006) Bioinformatics , vol.22 , pp. 2966-2967
    • Deckard, A.1    Bergmann, F.T.2    Sauro, H.M.3
  • 39
    • 77956664073 scopus 로고    scopus 로고
    • The BioPAX community standard for pathway data sharing
    • Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., et al. (2010). The BioPAX community standard for pathway data sharing. Nat. Biotechnol. 28, 935-942. doi:10.1038/nbt.1666
    • (2010) Nat. Biotechnol , vol.28 , pp. 935-942
    • Demir, E.1    Cary, M.P.2    Paley, S.3    Fukuda, K.4    Lemer, C.5    Vastrik, I.6
  • 41
    • 44949099336 scopus 로고    scopus 로고
    • SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks
    • Dräger, A., Hassis, N., Supper, J., Schröder, A., and Zell, A. (2008). SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks. BMC Syst. Biol. 2:39. doi:10.1186/1752-0509-2-39
    • (2008) BMC Syst. Biol , vol.2 , pp. 39
    • Dräger, A.1    Hassis, N.2    Supper, J.3    Schröder, A.4    Zell, A.5
  • 42
    • 63649141014 scopus 로고    scopus 로고
    • Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies
    • Dräger, A., Kronfeld, M., Ziller, M. J., Supper, J., Planatscher, H., Magnus, J. B., et al. (2009a). Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies. BMC Syst. Biol. 3:5. doi:10.1186/1752-0509-3-5
    • (2009) BMC Syst. Biol , vol.3 , pp. 5
    • Dräger, A.1    Kronfeld, M.2    Ziller, M.J.3    Supper, J.4    Planatscher, H.5    Magnus, J.B.6
  • 43
    • 65649112429 scopus 로고    scopus 로고
    • SBML2LATEX: conversion of SBML files into human-readable reports
    • Dräger, A., Planatscher, H., Wouamba, D. M., Schröder, A., Hucka, M., Endler, L., et al. (2009b). SBML2LATEX: conversion of SBML files into human-readable reports. Bioinformatics 25, 1455-1456. doi:10.1093/bioinformatics/btp170
    • (2009) Bioinformatics , vol.25 , pp. 1455-1456
    • Dräger, A.1    Planatscher, H.2    Wouamba, D.M.3    Schröder, A.4    Hucka, M.5    Endler, L.6
  • 48
    • 33846910173 scopus 로고    scopus 로고
    • Global reconstruction of the human metabolic network based on genomic and bibliomic data
    • Duarte, N. C., Becker, S. A., Jamshidi, N., Thiele, I., Mo, M. L., Vo, T. D., et al. (2007). Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc. Natl. Acad. Sci. U. S. A. 104, 1777-1782. doi:10.1073/pnas.0610772104
    • (2007) Proc. Natl. Acad. Sci. U. S. A , vol.104 , pp. 1777-1782
    • Duarte, N.C.1    Becker, S.A.2    Jamshidi, N.3    Thiele, I.4    Mo, M.L.5    Vo, T.D.6
  • 50
    • 84881152495 scopus 로고    scopus 로고
    • COBRApy: constraints-based reconstruction and analysis for python
    • Ebrahim, A., Lerman, J. A., Palsson, B. Ø., and Hyduke, D. R. (2013). COBRApy: constraints-based reconstruction and analysis for python. BMC Syst. Biol. 7:74. doi:10.1186/1752-0509-7-74
    • (2013) BMC Syst. Biol , vol.7 , pp. 74
    • Ebrahim, A.1    Lerman, J.A.2    Palsson, B.Ø.3    Hyduke, D.R.4
  • 51
    • 67650674074 scopus 로고    scopus 로고
    • Designing and encoding models for synthetic biology
    • Endler, L., Rodriguez, N., Juty, N., Chelliah, V., Laibe, C., Li, C., et al. (2009). Designing and encoding models for synthetic biology. J. R. Soc. Interface 6(Suppl. 4), S405-S417. doi:10.1098/rsif.2009.0035.focus
    • (2009) J. R. Soc. Interface , vol.6 , pp. S405-S417
    • Endler, L.1    Rodriguez, N.2    Juty, N.3    Chelliah, V.4    Laibe, C.5    Li, C.6
  • 52
    • 34347332311 scopus 로고    scopus 로고
    • A genome-scale metabolic reconstruction for escherichia coli k-12 mg1655 that accounts for 1260 orfs and thermodynamic information
    • Feist, A. M., Henry, C. S., Reed, J. L., Krummenacker, M., Joyce, A. R., Karp, P. D., et al. (2007). A genome-scale metabolic reconstruction for escherichia coli k-12 mg1655 that accounts for 1260 orfs and thermodynamic information. Mol. Syst. Biol. 3, 121. doi:10.1038/msb4100155
    • (2007) Mol. Syst. Biol , vol.3 , pp. 121
    • Feist, A.M.1    Henry, C.S.2    Reed, J.L.3    Krummenacker, M.4    Joyce, A.R.5    Karp, P.D.6
  • 54
    • 0348049802 scopus 로고    scopus 로고
    • Systems biology markup language: level 2 and beyond
    • Finney, A., and Hucka, M. (2003). Systems biology markup language: level 2 and beyond. Biochem. Soc. Trans. 31(Pt 6), 1472-1473. doi:10.1042/BST0311472
    • (2003) Biochem. Soc. Trans , vol.31 , pp. 1472-1473
    • Finney, A.1    Hucka, M.2
  • 56
    • 84902159136 scopus 로고    scopus 로고
    • The synthetic biology open language (SBOL) provides a community standard for communicating designs in synthetic biology
    • Galdzicki, M., Clancy, K. P., Oberortner, E., Pocock, M., Quinn, J. Y., Rodriguez, C. A., et al. (2014). The synthetic biology open language (SBOL) provides a community standard for communicating designs in synthetic biology. Nat. Biotechnol. 32, 545-550. doi:10.1038/nbt.2891
    • (2014) Nat. Biotechnol , vol.32 , pp. 545-550
    • Galdzicki, M.1    Clancy, K.P.2    Oberortner, E.3    Pocock, M.4    Quinn, J.Y.5    Rodriguez, C.A.6
  • 58
    • 33747825750 scopus 로고    scopus 로고
    • A model diagram layout extension for SBML
    • Gauges, R., Rost, U., Sahle, S., and Wegner, K. (2006). A model diagram layout extension for SBML. Bioinformatics 22, 1879-1885. doi:10.1093/bioinformatics/btl195
    • (2006) Bioinformatics , vol.22 , pp. 1879-1885
    • Gauges, R.1    Rost, U.2    Sahle, S.3    Wegner, K.4
  • 60
    • 81355123249 scopus 로고    scopus 로고
    • Software for systems biology: from tools to integrated platforms
    • Ghosh, S., Matsuoka, Y., Asai, Y., Hsin, K.-Y., and Kitano, H. (2011). Software for systems biology: from tools to integrated platforms. Nat Rev Genet 12, 821-832. doi:10.1038/nrg3096
    • (2011) Nat Rev Genet , vol.12 , pp. 821-832
    • Ghosh, S.1    Matsuoka, Y.2    Asai, Y.3    Hsin, K.-Y.4    Kitano, H.5
  • 61
    • 85021374853 scopus 로고    scopus 로고
    • 'Software tools for modelling in computational neuroscience: overview,'
    • eds D. Jaeger and R. Jung (New York: Springer)
    • Gleeson, P. (2013). "Software tools for modelling in computational neuroscience: overview," in Encyclopedia of Computational Neuroscience, eds D. Jaeger and R. Jung (New York: Springer), 1-4. doi:10.1007/978-1-4614-7320-6_93-1
    • (2013) Encyclopedia of Computational Neuroscience , pp. 1-4
    • Gleeson, P.1
  • 62
    • 77955483472 scopus 로고    scopus 로고
    • NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail
    • Gleeson, P., Crook, S., Cannon, R. C., Hines, M. L., Billings, G. O., Farinella, M., et al. (2010). NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS Comput. Biol. 6:e1000815. doi:10.1371/journal.pcbi.1000815
    • (2010) PLoS Comput. Biol , vol.6
    • Gleeson, P.1    Crook, S.2    Cannon, R.C.3    Hines, M.L.4    Billings, G.O.5    Farinella, M.6
  • 65
    • 84872199382 scopus 로고    scopus 로고
    • CySBGN: a cytoscape plug-in to integrate SBGN maps
    • Gonçalves, E., van Iersel, M., and Saez-Rodriguez, J. (2013). CySBGN: a cytoscape plug-in to integrate SBGN maps. BMC Bioinformatics 14:17. doi:10.1186/1471-2105-14-17
    • (2013) BMC Bioinformatics , vol.14 , pp. 17
    • Gonçalves, E.1    van Iersel, M.2    Saez-Rodriguez, J.3
  • 66
    • 33646352954 scopus 로고    scopus 로고
    • GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks
    • Gonzalez Gonzalez, A., Naldi, A., Sánchez, L., Thieffry, D., and Chaouiya, C. (2006). GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks. BioSystems 84, 91-100. doi:10.1016/j.biosystems.2005.10.003
    • (2006) BioSystems , vol.84 , pp. 91-100
    • Gonzalez Gonzalez, A.1    Naldi, A.2    Sánchez, L.3    Thieffry, D.4    Chaouiya, C.5
  • 67
    • 84907911242 scopus 로고    scopus 로고
    • Graphical modeling tools for systems biology
    • Gostner, R., Baldacci, B., Morine, M. J., and Priami, C. (2014). Graphical modeling tools for systems biology. ACM Comput. Surv. 47, 1-21. doi:10.1145/2633461
    • (2014) ACM Comput. Surv , vol.47 , pp. 1-21
    • Gostner, R.1    Baldacci, B.2    Morine, M.J.3    Priami, C.4
  • 68
    • 70350029519 scopus 로고    scopus 로고
    • FBA-SimVis: interactive visualization of constraint-based metabolic models
    • Grafahrend-Belau, E., Klukas, C., Junker, B. H., and Schreiber, F. (2009). FBA-SimVis: interactive visualization of constraint-based metabolic models. Bioinformatics 25, 2755-2757. doi:10.1093/bioinformatics/btp408
    • (2009) Bioinformatics , vol.25 , pp. 2755-2757
    • Grafahrend-Belau, E.1    Klukas, C.2    Junker, B.H.3    Schreiber, F.4
  • 69
    • 84902438421 scopus 로고    scopus 로고
    • Megascience efforts and the brain
    • Grillner, S. (2014). Megascience efforts and the brain. Neuron 82, 1209-1211. doi:10.1016/j.neuron.2014.05.045
    • (2014) Neuron , vol.82 , pp. 1209-1211
    • Grillner, S.1
  • 70
    • 84891635463 scopus 로고    scopus 로고
    • Software platforms to facilitate reconstructing genome-scale metabolic networks
    • Hamilton, J. J., and Reed, J. L. (2013). Software platforms to facilitate reconstructing genome-scale metabolic networks. Environ. Microbiol. 16, 49-59. doi:10.1111/1462-2920.12312
    • (2013) Environ. Microbiol , vol.16 , pp. 49-59
    • Hamilton, J.J.1    Reed, J.L.2
  • 71
    • 84876560358 scopus 로고    scopus 로고
    • The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013
    • Hastings, J., de Matos, P., Dekker, A., Ennis, M., Harsha, B., Kale, N., et al. (2013). The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res. 41, D456-D463. doi:10.1093/nar/gks1146
    • (2013) Nucleic Acids Res , vol.41 , pp. D456-D463
    • Hastings, J.1    de Matos, P.2    Dekker, A.3    Ennis, M.4    Harsha, B.5    Kale, N.6
  • 73
    • 53749085229 scopus 로고    scopus 로고
    • A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
    • Herrgård, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., et al. (2008). A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat. Biotechnol. 26, 1155-1160. doi:10.1038/nbt1492
    • (2008) Nat. Biotechnol , vol.26 , pp. 1155-1160
    • Herrgård, M.J.1    Swainston, N.2    Dobson, P.3    Dunn, W.B.4    Arga, K.Y.5    Arvas, M.6
  • 74
    • 33745217791 scopus 로고    scopus 로고
    • SUNDIALS: suite of nonlinear and differential/algebraic equation solvers
    • Hindmarsh, A. C., Brown, P. N., Grant, K. E., Lee, S. L., Serban, R., Shumaker, D. E., et al. (2005). SUNDIALS: suite of nonlinear and differential/algebraic equation solvers. ACM T Math Software 31, 363-396. doi:10.1145/1089014.1089020
    • (2005) ACM T Math Software , vol.31 , pp. 363-396
    • Hindmarsh, A.C.1    Brown, P.N.2    Grant, K.E.3    Lee, S.L.4    Serban, R.5    Shumaker, D.E.6
  • 75
    • 3342941917 scopus 로고    scopus 로고
    • ModelDB: a database to support computational neuroscience
    • Hines, M. L., Morse, T., Migliore, M., Carnevale, N. T., and Hines, M. L. (2004). ModelDB: a database to support computational neuroscience. J. Comput. Neurosci. 17, 7-11. doi:10.1023/B:JCNS.0000023869.22017.2e
    • (2004) J. Comput. Neurosci , vol.17 , pp. 7-11
    • Hines, M.L.1    Morse, T.2    Migliore, M.3    Carnevale, N.T.4    Hines, M.L.5
  • 78
    • 78651553577 scopus 로고    scopus 로고
    • FASIMU: flexible software for flux-balance computation series in large metabolic networks
    • Hoppe, A., Hoffmann, S., Gerasch, A., Gille, C., and Holzhütter, H.-G. (2011). FASIMU: flexible software for flux-balance computation series in large metabolic networks. BMC Bioinformatics 12:28. doi:10.1186/1471-2105-12-28
    • (2011) BMC Bioinformatics , vol.12 , pp. 28
    • Hoppe, A.1    Hoffmann, S.2    Gerasch, A.3    Gille, C.4    Holzhütter, H.-G.5
  • 79
    • 10644250404 scopus 로고    scopus 로고
    • Evolving a lingua franca and associated software infrastructure for computational systems biology: the systems biology markup language (SBML) project
    • Hucka, M., Finney, A., Bornstein, B. J., Keating, S. M., Shapiro, B. E., Matthews, J., et al. (2004). Evolving a lingua franca and associated software infrastructure for computational systems biology: the systems biology markup language (SBML) project. Syst Biol (Stevenage) 1, 41-53. doi:10.1049/sb:20045008
    • (2004) Syst Biol (Stevenage) , vol.1 , pp. 41-53
    • Hucka, M.1    Finney, A.2    Bornstein, B.J.3    Keating, S.M.4    Shapiro, B.E.5    Matthews, J.6
  • 80
    • 0037342537 scopus 로고    scopus 로고
    • The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
    • Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., et al. (2003). The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19, 524-531. doi:10.1093/bioinformatics/btg015
    • (2003) Bioinformatics , vol.19 , pp. 524-531
    • Hucka, M.1    Finney, A.2    Sauro, H.M.3    Bolouri, H.4    Doyle, J.C.5    Kitano, H.6
  • 81
    • 0037336350 scopus 로고    scopus 로고
    • Integration from proteins to organs: the physiome project
    • Hunter, P. J., and Borg, T. K. (2003). Integration from proteins to organs: the physiome project. Nat. Rev. Mol. Cell Biol. 4, 237-243. doi:10.1038/nrm1054
    • (2003) Nat. Rev. Mol. Cell Biol , vol.4 , pp. 237-243
    • Hunter, P.J.1    Borg, T.K.2
  • 82
    • 33746674977 scopus 로고    scopus 로고
    • VANTED: a system for advanced data analysis and visualization in the context of biological networks
    • Junker, B. H., Klukas, C., and Schreiber, F. (2006). VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics 7:219. doi:10.1186/1471-2105-7-219
    • (2006) BMC Bioinformatics , vol.7 , pp. 219
    • Junker, B.H.1    Klukas, C.2    Schreiber, F.3
  • 83
    • 84883258975 scopus 로고    scopus 로고
    • 'Controlled annotations for systems biology,'
    • eds M. V. Schneider (New York: Springer)
    • Juty, N., Laibe, C., and Le Novère, N. (2013). "Controlled annotations for systems biology," in In silico Systems Biology, Vol. 1021, ed. M. V. Schneider (New York: Springer), 227-245.
    • (2013) In silico Systems Biology , vol.1021 , pp. 227-245
    • Juty, N.1    Laibe, C.2    Le Novère, N.3
  • 84
    • 84862156032 scopus 로고    scopus 로고
    • Identifiers.org and MIRIAM registry: community resources to provide persistent identification
    • Juty, N., Le Novère, N., and Laibe, C. (2012). Identifiers.org and MIRIAM registry: community resources to provide persistent identification. Nucleic Acids Res. 40, D580-D586. doi:10.1093/nar/gkr1097
    • (2012) Nucleic Acids Res , vol.40 , pp. D580-D586
    • Juty, N.1    Le Novère, N.2    Laibe, C.3
  • 86
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: kyoto encyclopedia of genes and genomes
    • Kanehisa, M., and Goto, S. (2000). KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27-30. doi:10.1093/nar/28.1.27
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 87
    • 33646884848 scopus 로고    scopus 로고
    • SBMLToolbox: an SBML toolbox for MATLAB users
    • Keating, S. M., Bornstein, B. J., Finney, A., and Hucka, M. (2006). SBMLToolbox: an SBML toolbox for MATLAB users. Bioinformatics 22, 1275-1277. doi:10.1093/bioinformatics/btl111
    • (2006) Bioinformatics , vol.22 , pp. 1275-1277
    • Keating, S.M.1    Bornstein, B.J.2    Finney, A.3    Hucka, M.4
  • 90
    • 23444439817 scopus 로고    scopus 로고
    • Using process diagrams for the graphical representation of biological networks
    • Kitano, H., Funahashi, A., Matsuoka, Y., and Oda, K. (2005). Using process diagrams for the graphical representation of biological networks. Nat. Biotechnol. 23, 961-966. doi:10.1038/nbt1111
    • (2005) Nat. Biotechnol , vol.23 , pp. 961-966
    • Kitano, H.1    Funahashi, A.2    Matsuoka, Y.3    Oda, K.4
  • 91
    • 77956514437 scopus 로고    scopus 로고
    • 'Towards a semantic description of biomodels: meaning facets-a case study,'
    • eds S. Ananiadou, S. Pyysalo, D. Rebholz-Schuhmann, F. Rinaldi, and T. Salakoski (Jena: CEUR-WS)
    • Knüpfer, C., Beckstein, C., and Dittrich, P. (2006). "Towards a semantic description of biomodels: meaning facets-a case study," in Proceedings of the Second International Symposium on Semantic Mining in Biomedicine (SMBM 2006), eds S. Ananiadou, S. Pyysalo, D. Rebholz-Schuhmann, F. Rinaldi, and T. Salakoski (Jena: CEUR-WS), 97-100.
    • (2006) Proceedings of the Second International Symposium on Semantic Mining in Biomedicine (SMBM 2006) , pp. 97-100
    • Knüpfer, C.1    Beckstein, C.2    Dittrich, P.3
  • 92
    • 30044440098 scopus 로고    scopus 로고
    • Molecular interaction maps of bioregulatory networks: a general rubric for systems biology
    • Kohn, K. W., Aladjem, M. I., Weinstein, J. N., and Pommier, Y. (2006). Molecular interaction maps of bioregulatory networks: a general rubric for systems biology. Mol. Biol. Cell 17, 1-13. doi:10.1091/mbc.E05-09-0824
    • (2006) Mol. Biol. Cell , vol.17 , pp. 1-13
    • Kohn, K.W.1    Aladjem, M.I.2    Weinstein, J.N.3    Pommier, Y.4
  • 93
    • 84880135888 scopus 로고    scopus 로고
    • 'BioUML-open source plug-in based platform for bioinformatics: invitation to collaboration,'
    • (Moskow: Department of Bioengineering and Bioinformatics of MV Lomonosov Moscow State University)
    • Kolpakov, F. A., Tolstykh, N. I., Valeev, T. F., Kiselev, I. N., Kutumova, E. O., Ryabova, A., et al. (2011). "BioUML-open source plug-in based platform for bioinformatics: invitation to collaboration," in Moscow Conference on Computational Molecular Biology (Moskow: Department of Bioengineering and Bioinformatics of MV Lomonosov Moscow State University), 172-173.
    • (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
  • 94
    • 84866459866 scopus 로고    scopus 로고
    • CySBML: a cytoscape plugin for SBML
    • König, M., Dräger, A., and Holzhütter, H.-G. (2012). CySBML: a cytoscape plugin for SBML. Bioinformatics 28, 2402-2403. doi:10.1093/bioinformatics/bts432
    • (2012) Bioinformatics , vol.28 , pp. 2402-2403
    • König, M.1    Dräger, A.2    Holzhütter, H.-G.3
  • 95
    • 84912544153 scopus 로고    scopus 로고
    • Computational approaches for microalgal biofuel optimization: a review
    • Koussa, J., Chaiboonchoe, A., and Salehi-Ashtiani, K. (2014). Computational approaches for microalgal biofuel optimization: a review. Biomed Res. Int. 2014, 1-12. doi:10.1155/2014/649453
    • (2014) Biomed Res. Int , vol.2014 , pp. 1-12
    • Koussa, J.1    Chaiboonchoe, A.2    Salehi-Ashtiani, K.3
  • 96
    • 84901335842 scopus 로고    scopus 로고
    • R-based software for the integration of pathway data into bioinformatic algorithms
    • Kramer, F., Bayerlová, M., and Beißbarth, T. (2014). R-based software for the integration of pathway data into bioinformatic algorithms. Biology 3, 85-100. doi:10.3390/biology3010085
    • (2014) Biology , vol.3 , pp. 85-100
    • Kramer, F.1    Bayerlová, M.2    Beißbarth, T.3
  • 97
    • 84878336037 scopus 로고    scopus 로고
    • Biographer: web-based editing and rendering of SBGN compliant biochemical networks
    • Krause, F., Schulz, M., Ripkens, B., Flöttmann, M., Krantz, M., Klipp, E., et al. (2013). Biographer: web-based editing and rendering of SBGN compliant biochemical networks. Bioinformatics 29, 1467-1468. doi:10.1093/bioinformatics/btt159
    • (2013) Bioinformatics , vol.29 , pp. 1467-1468
    • Krause, F.1    Schulz, M.2    Ripkens, B.3    Flöttmann, M.4    Krantz, M.5    Klipp, E.6
  • 98
    • 63649101029 scopus 로고    scopus 로고
    • Tübingen: University of Tübingen, Department of Computer Architecture
    • Kronfeld, M. (2008). EvA2 Short Documentation. Tübingen: University of Tübingen, Department of Computer Architecture.
    • (2008) EvA2 Short Documentation
    • Kronfeld, M.1
  • 99
    • 84871222795 scopus 로고    scopus 로고
    • 'On the benefits of multimodal optimization for metabolic network modeling,'
    • eds I. Grosse, S. Neumann, S. Posch, F. Schreiber, and P. Stadler (Halle: German Informatics society)
    • Kronfeld, M., Dräger, A., Aschoff, M., and Zell, A. (2009). "On the benefits of multimodal optimization for metabolic network modeling," in German Conference on Bioinformatics (GCB 2009), Volume P-157 of Lecture Notes in Informatics, eds I. Grosse, S. Neumann, S. Posch, F. Schreiber, and P. Stadler (Halle: German Informatics society), 191-200.
    • (2009) German Conference on Bioinformatics (GCB 2009), Volume P-157 of Lecture Notes in Informatics , pp. 191-200
    • Kronfeld, M.1    Dräger, A.2    Aschoff, M.3    Zell, A.4
  • 101
    • 40349100409 scopus 로고    scopus 로고
    • MIRIAM resources: tools to generate and resolve robust cross-references in systems biology
    • Laible, C., and Le Novère, N. (2007). MIRIAM resources: tools to generate and resolve robust cross-references in systems biology. BMC Syst. Biol. 13:58. doi:10.1186/1752-0509-1-58
    • (2007) BMC Syst. Biol , vol.13 , pp. 58
    • Laible, C.1    Le Novère, N.2
  • 102
    • 85051910653 scopus 로고    scopus 로고
    • 'Network inference by considering multiple objectives: insights from in vivo transcriptomic data generated by a synthetic network,'
    • eds H. R. Arabnia, Q.-N. Tran, R. Chang, M. He, A. Marsh, A. M. G. Solo, (Las Vegas, NV: CSREA Press)
    • Lambeck, S., Dräger, A., and Guthke, R. (2010). "Network inference by considering multiple objectives: insights from in vivo transcriptomic data generated by a synthetic network," in International Conference on Bioinformatics and Computational Biology, BIOCOMP 2010, Vol. 2, eds H. R. Arabnia, Q.-N. Tran, R. Chang, M. He, A. Marsh, A. M. G. Solo, (Las Vegas, NV: CSREA Press), 734-742.
    • (2010) International Conference on Bioinformatics and Computational Biology, BIOCOMP 2010 , vol.2 , pp. 734-742
    • Lambeck, S.1    Dräger, A.2    Guthke, R.3
  • 103
    • 28644433993 scopus 로고    scopus 로고
    • Minimum information requested in the annotation of biochemical models (MIRIAM)
    • Le Novère, N., Finney, A., Hucka, M., Bhalla, U. S., Campagne, F., Collado-Vides, J., et al. (2005). Minimum information requested in the annotation of biochemical models (MIRIAM). Nat. Biotechnol. 23, 1509-1515. doi:10.1038/nbt1156
    • (2005) Nat. Biotechnol , vol.23 , pp. 1509-1515
    • Le Novère, N.1    Finney, A.2    Hucka, M.3    Bhalla, U.S.4    Campagne, F.5    Collado-Vides, J.6
  • 104
    • 83255181846 scopus 로고    scopus 로고
    • Meeting report from the first meetings of the computational modeling in biology network (combine)
    • Le Novère, N., Hucka, M., Anwar, N., Bader, G. D., Demir, E., Moodie, S., et al. (2011). Meeting report from the first meetings of the computational modeling in biology network (combine). Stand. Genomic Sci. 5, 230-242. doi:10.4056/sigs.2034671
    • (2011) Stand. Genomic Sci , vol.5 , pp. 230-242
    • Le Novère, N.1    Hucka, M.2    Anwar, N.3    Bader, G.D.4    Demir, E.5    Moodie, S.6
  • 106
    • 84875378445 scopus 로고    scopus 로고
    • Systems biology graphical notation: entity relationship language level 1 (version 1.2)
    • Le Novere, N., Le Novere, N., Demir, E., Mi, H., Moodie, S., and Villeger, A. (2011). Systems biology graphical notation: entity relationship language level 1 (version 1.2). Nature Precedings doi:10.1038/npre.2011.5902.1
    • (2011) Nature Precedings
    • Le Novere, N.1    Le Novere, N.2    Demir, E.3    Mi, H.4    Moodie, S.5    Villeger, A.6
  • 107
    • 84864843180 scopus 로고    scopus 로고
    • In silico method for modelling metabolism and gene product expression at genome scale
    • Lerman, J. A., Hyduke, D. R., Latif, H., Portnoy, V. A., Lewis, N. E., Orth, J. D., et al. (2012). In silico method for modelling metabolism and gene product expression at genome scale. Nat. Commun. 3, 929. doi:10.1038/ncomms1928
    • (2012) Nat. Commun , vol.3 , pp. 929
    • Lerman, J.A.1    Hyduke, D.R.2    Latif, H.3    Portnoy, V.A.4    Lewis, N.E.5    Orth, J.D.6
  • 109
    • 2442595958 scopus 로고    scopus 로고
    • CellML: its future, present and past
    • Lloyd, C. M., Halstead, M. D. B., and Nielsen, P. F. (2004). CellML: its future, present and past. Prog Biophys Mol Biol 85, 433-450. doi:10.1016/j.pbiomolbio.2004.01.004
    • (2004) Prog Biophys Mol Biol , vol.85 , pp. 433-450
    • Lloyd, C.M.1    Halstead, M.D.B.2    Nielsen, P.F.3
  • 110
    • 33745631242 scopus 로고    scopus 로고
    • The SBML ODE solver library: a native API for symbolic and fast numerical analysis of reaction networks
    • Machné, R., Finney, A., Müller, S., Lu, J., Widder, S., and Flamm, C. (2006). The SBML ODE solver library: a native API for symbolic and fast numerical analysis of reaction networks. Bioinformatics 22, 1406-1407. doi:10.1093/bioinformatics/btl086
    • (2006) Bioinformatics , vol.22 , pp. 1406-1407
    • Machné, R.1    Finney, A.2    Müller, S.3    Lu, J.4    Widder, S.5    Flamm, C.6
  • 111
    • 79952676360 scopus 로고    scopus 로고
    • Systems biology: evolving into the mainstream
    • Macilwain, C. (2011). Systems biology: evolving into the mainstream. Cell 144, 839-841. doi:10.1016/j.cell.2011.02.044
    • (2011) Cell , vol.144 , pp. 839-841
    • Macilwain, C.1
  • 113
    • 84922481872 scopus 로고    scopus 로고
    • Modeling and simulation using CellDesigner
    • Matsuoka, Y., Funahashi, A., Ghosh, S., and Kitano, H. (2014). Modeling and simulation using CellDesigner. Methods Mol. Biol. 1164, 121-145. doi:10.1007/978-1-4939-0805-9_11
    • (2014) Methods Mol. Biol , vol.1164 , pp. 121-145
    • Matsuoka, Y.1    Funahashi, A.2    Ghosh, S.3    Kitano, H.4
  • 115
    • 0038226460 scopus 로고    scopus 로고
    • ModelDB: making models publicly accessible to support computational neuroscience
    • Migliore, M., Morse, T. M., Davison, A. P., Marenco, L., Shepherd, G. M., and Hines, M. L. (2003). ModelDB: making models publicly accessible to support computational neuroscience. Neuroinformatics 1, 135-140. doi:10.1385/NI:1:1:135
    • (2003) Neuroinformatics , vol.1 , pp. 135-140
    • Migliore, M.1    Morse, T.M.2    Davison, A.P.3    Marenco, L.4    Shepherd, G.M.5    Hines, M.L.6
  • 116
    • 84863614163 scopus 로고    scopus 로고
    • Declarative representation of uncertainty in mathematical models
    • Miller, A. K., Britten, R. D., and Nielsen, P. M. F. (2012). Declarative representation of uncertainty in mathematical models. PLoS ONE 7:e39721. doi:10.1371/journal.pone.0039721
    • (2012) PLoS ONE , vol.7
    • Miller, A.K.1    Britten, R.D.2    Nielsen, P.M.F.3
  • 120
    • 82355181974 scopus 로고    scopus 로고
    • 'Standardization in synthetic biology,'
    • eds W. Weber and M. Fussenegger (New York: Springer)
    • Müller, K. M., and Arndt, K. M. (2012). "Standardization in synthetic biology," in Synthetic Gene Networks, eds W. Weber and M. Fussenegger (New York: Springer), 23-43.
    • (2012) Synthetic Gene Networks , pp. 23-43
    • Müller, K.M.1    Arndt, K.M.2
  • 121
    • 70350669878 scopus 로고    scopus 로고
    • ibiosim: A tool for the analysis and design of genetic circuits
    • Myers, C. J., Barker, N., Jones, K., Kuwahara, H., Madsen, C., and Nguyen, N.-P. D. (2009). ibiosim: A tool for the analysis and design of genetic circuits. Bioinformatics 25, 2848-2849. doi:10.1093/bioinformatics/btp457
    • (2009) Bioinformatics , vol.25 , pp. 2848-2849
    • Myers, C.J.1    Barker, N.2    Jones, K.3    Kuwahara, H.4    Madsen, C.5    Nguyen, N.-P.D.6
  • 122
    • 84886494826 scopus 로고    scopus 로고
    • 'Standards and tools supporting collaborative development of the virtual physiological human,'
    • (EMBC) 2013 35th Annual International Conference of the IEEE (Osaka: IEEE)
    • Nickerson, D. P., Garny, A., Nielsen, P. M. F., and Hunter, P. J. (2013). "Standards and tools supporting collaborative development of the virtual physiological human," in Engineering in Medicine and Biology Society (EMBC), 2013 35th Annual International Conference of the IEEE (Osaka: IEEE), 5541-5544.
    • (2013) Engineering in Medicine and Biology Society , pp. 5541-5544
    • Nickerson, D.P.1    Garny, A.2    Nielsen, P.M.F.3    Hunter, P.J.4
  • 123
    • 84885367114 scopus 로고    scopus 로고
    • Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction
    • O'Brien, E. J., Lerman, J. A., Chang, R. L., Hyduke, D. R., and Palsson, B. Ø. (2013). Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction. Mol. Syst. Biol. 9, 693. doi:10.1038/msb.2013.52
    • (2013) Mol. Syst. Biol , vol.9 , pp. 693
    • O'Brien, E.J.1    Lerman, J.A.2    Chang, R.L.3    Hyduke, D.R.4    Palsson, B.Ø.5
  • 124
    • 14644422159 scopus 로고    scopus 로고
    • Modelling cellular systems with PySCeS
    • Olivier, B. G., Rohwer, J. M., and Hofmeyr, J.-H. S. (2005). Modelling cellular systems with PySCeS. Bioinformatics 21, 560-561. doi:10.1093/bioinformatics/bti046
    • (2005) Bioinformatics , vol.21 , pp. 560-561
    • Olivier, B.G.1    Rohwer, J.M.2    Hofmeyr, J.-H.S.3
  • 125
    • 4544344218 scopus 로고    scopus 로고
    • Web-based kinetic modelling using JWS Online
    • Olivier, B. G., and Snoep, J. L. (2004). Web-based kinetic modelling using JWS Online. Bioinformatics 20, 2143-2144. doi:10.1093/bioinformatics/bth200
    • (2004) Bioinformatics , vol.20 , pp. 2143-2144
    • Olivier, B.G.1    Snoep, J.L.2
  • 126
    • 77749320898 scopus 로고    scopus 로고
    • What is flux balance analysis?
    • Orth, J. D., Thiele, I., and Palsson, B. Ø. (2010). What is flux balance analysis? Nat. Biotechnol. 28, 245-248. doi:10.1038/nbt.1614
    • (2010) Nat. Biotechnol , vol.28 , pp. 245-248
    • Orth, J.D.1    Thiele, I.2    Palsson, B.Ø.3
  • 129
    • 80053375237 scopus 로고    scopus 로고
    • The human metabolic reconstruction recon 1 directs hypotheses of novel human metabolic functions
    • Rolfsson, O., Palsson, B. Ø., and Thiele, I. (2011). The human metabolic reconstruction recon 1 directs hypotheses of novel human metabolic functions. BMC Syst. Biol. 5:155. doi:10.1186/1752-0509-5-155
    • (2011) BMC Syst. Biol , vol.5 , pp. 155
    • Rolfsson, O.1    Palsson, B.Ø.2    Thiele, I.3
  • 130
    • 0347511691 scopus 로고    scopus 로고
    • Next generation simulation tools: the systems biology workbench and BioSPICE integration
    • Sauro, H. M., Hucka, M., Finney, A., Wellock, C., Bolouri, H., Doyle, J., et al. (2003). Next generation simulation tools: the systems biology workbench and BioSPICE integration. OMICS 7, 355-372. doi:10.1089/153623103322637670
    • (2003) OMICS , vol.7 , pp. 355-372
    • Sauro, H.M.1    Hucka, M.2    Finney, A.3    Wellock, C.4    Bolouri, H.5    Doyle, J.6
  • 133
    • 85043546925 scopus 로고    scopus 로고
    • Technical Report. Pasadena, CA: Caltech
    • Schaff, J. C., Lakshminarayana, A., and Smith, L. P. (2013). "Spatial processes," in Technical Report. Pasadena, CA: Caltech. Available from: http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/spatial
    • (2013) "Spatial processes,"
    • Schaff, J.C.1    Lakshminarayana, A.2    Smith, L.P.3
  • 134
    • 77951612556 scopus 로고    scopus 로고
    • Bigg: a biochemical genetic and genomic knowledgebase of large scale metabolic reconstructions
    • Schellenberger, J., Park, J. O., Conrad, T. M., and Palsson, B. Ø. (2010). Bigg: a biochemical genetic and genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics 11:213. doi:10.1186/1471-2105-11-213
    • (2010) BMC Bioinformatics , vol.11 , pp. 213
    • Schellenberger, J.1    Park, J.O.2    Conrad, T.M.3    Palsson, B.Ø.4
  • 135
    • 79551662521 scopus 로고    scopus 로고
    • Quantitative prediction of cellular metabolism with constraint-based models: the cobra toolbox v2.0
    • Schellenberger, J., Que, R., Fleming, R. M. T., Thiele, I., Orth, J. D., Feist, A. M., et al. (2011). Quantitative prediction of cellular metabolism with constraint-based models: the cobra toolbox v2.0. Nat. Protoc. 6, 1290-1307. doi:10.1038/nprot.2011.308
    • (2011) Nat. Protoc , vol.6 , pp. 1290-1307
    • Schellenberger, J.1    Que, R.2    Fleming, R.M.T.3    Thiele, I.4    Orth, J.D.5    Feist, A.M.6
  • 137
    • 34047103529 scopus 로고    scopus 로고
    • SBaddon: high performance simulation for the systems biology toolbox for MATLAB
    • Schmidt, H. (2007). SBaddon: high performance simulation for the systems biology toolbox for MATLAB. Bioinformatics 23, 646-647. doi:10.1093/bioinformatics/btl668
    • (2007) Bioinformatics , vol.23 , pp. 646-647
    • Schmidt, H.1
  • 138
    • 32544443964 scopus 로고    scopus 로고
    • Systems biology toolbox for MATLAB: a computational platform for research in systems biology
    • Schmidt, H., and Jirstrand, M. (2006). Systems biology toolbox for MATLAB: a computational platform for research in systems biology. Bioinformatics 22, 514-515. doi:10.1093/bioinformatics/bti799
    • (2006) Bioinformatics , vol.22 , pp. 514-515
    • Schmidt, H.1    Jirstrand, M.2
  • 139
    • 79960596028 scopus 로고    scopus 로고
    • Retrieval, alignment, and clustering of computational models based on semantic annotations
    • Schulz, M., Krause, F., Le Novère, N., Klipp, E., and Liebermeister, W. (2011). Retrieval, alignment, and clustering of computational models based on semantic annotations. Mol. Syst. Biol. 7, 512. doi:10.1038/msb.2011.41
    • (2011) Mol. Syst. Biol , vol.7 , pp. 512
    • Schulz, M.1    Krause, F.2    Le Novère, N.3    Klipp, E.4    Liebermeister, W.5
  • 140
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: a software environment for integrated models of biomolecular interaction networks
    • Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., et al. (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504. doi:10.1101/gr.1239303
    • (2003) Genome Res , vol.13 , pp. 2498-2504
    • Shannon, P.1    Markiel, A.2    Ozier, O.3    Baliga, N.S.4    Wang, J.T.5    Ramage, D.6
  • 142
    • 8844269072 scopus 로고    scopus 로고
    • MathSBML: a package for manipulating SBML-based biological models
    • Shapiro, B. E., Hucka, M., Finney, A., and Doyle, J. (2004). MathSBML: a package for manipulating SBML-based biological models. Bioinformatics 20, 2829-2831. doi:10.1093/bioinformatics/bth271
    • (2004) Bioinformatics , vol.20 , pp. 2829-2831
    • Shapiro, B.E.1    Hucka, M.2    Finney, A.3    Doyle, J.4
  • 144
    • 0032212617 scopus 로고    scopus 로고
    • The human brain project: neuroinformatics tools for integrating, searching and modeling multidisciplinary neuroscience data
    • Shepherd, G. M., Mirsky, J. S., Healy, M. D., Singer, M. S., Skoufos, E., Hines, M. S., et al. (1998). The human brain project: neuroinformatics tools for integrating, searching and modeling multidisciplinary neuroscience data. Trends Neurosci. 21, 460-468. doi:10.1016/S0166-2236(98)01300-9
    • (1998) Trends Neurosci , vol.21 , pp. 460-468
    • Shepherd, G.M.1    Mirsky, J.S.2    Healy, M.D.3    Singer, M.S.4    Skoufos, E.5    Hines, M.S.6
  • 145
    • 69849093395 scopus 로고    scopus 로고
    • Antimony: a modular model definition language
    • Smith, L. P., Bergmann, F. T., Chandran, D., and Sauro, H. M. (2009). Antimony: a modular model definition language. Bioinformatics 25, 2452-2454. doi:10.1093/bioinformatics/btp401
    • (2009) Bioinformatics , vol.25 , pp. 2452-2454
    • Smith, L.P.1    Bergmann, F.T.2    Chandran, D.3    Sauro, H.M.4
  • 148
    • 0345306191 scopus 로고    scopus 로고
    • JWS online cellular systems modelling and microbiology
    • Snoep, J. L., and Olivier, B. G. (2003). JWS online cellular systems modelling and microbiology. Microbiology 149, 3045-3047. doi:10.1099/mic.0.C0124-0
    • (2003) Microbiology , vol.149 , pp. 3045-3047
    • Snoep, J.L.1    Olivier, B.G.2
  • 150
    • 84856038703 scopus 로고    scopus 로고
    • The SuBliMinaL toolbox: automating steps in the reconstruction of metabolic networks
    • Swainston, N., Smallbone, K., Mendes, P., Kell, D., and Paton, N. (2011). The SuBliMinaL toolbox: automating steps in the reconstruction of metabolic networks. J. Integr. Bioinform. 8, 186. doi:10.2390/biecoll-jib-2011-186
    • (2011) J. Integr. Bioinform , vol.8 , pp. 186
    • Swainston, N.1    Smallbone, K.2    Mendes, P.3    Kell, D.4    Paton, N.5
  • 151
    • 84878290340 scopus 로고    scopus 로고
    • LibSBMLSim: a reference implementation of fully functional SBML simulator
    • Takizawa, H., Nakamura, K., Tabira, A., Chikahara, Y., Matsui, T., Hiroi, N., et al. (2013). LibSBMLSim: a reference implementation of fully functional SBML simulator. Bioinformatics 29, 1474-1476. doi:10.1093/bioinformatics/btt157
    • (2013) Bioinformatics , vol.29 , pp. 1474-1476
    • Takizawa, H.1    Nakamura, K.2    Tabira, A.3    Chikahara, Y.4    Matsui, T.5    Hiroi, N.6
  • 152
    • 45749118607 scopus 로고    scopus 로고
    • Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project
    • Taylor, C. F., Field, D., Sansone, S.-A., Aerts, J., Apweiler, R., Ashburner, M., et al. (2008). Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat. Biotechnol. 26, 889-896. doi:10.1038/nbt.1411
    • (2008) Nat. Biotechnol , vol.26 , pp. 889-896
    • Taylor, C.F.1    Field, D.2    Sansone, S.-A.3    Aerts, J.4    Apweiler, R.5    Ashburner, M.6
  • 153
    • 84867537553 scopus 로고    scopus 로고
    • CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms
    • Terfve, C., Cokelaer, T., Henriques, D., MacNamara, A., Goncalves, E., Morris, M. K., et al. (2012). CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. BMC Syst. Biol. 6:133. doi:10.1186/1752-0509-6-133
    • (2012) BMC Syst. Biol , vol.6 , pp. 133
    • Terfve, C.1    Cokelaer, T.2    Henriques, D.3    MacNamara, A.4    Goncalves, E.5    Morris, M.K.6
  • 157
    • 84899133456 scopus 로고    scopus 로고
    • libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience
    • Vella, M., Cannon, R. C., Crook, S., Davison, A. P., Ganapathy, G., Robinson, H. P. C., et al. (2014). libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience. Front. Neuroinform. 8:38. doi:10.3389/fninf.2014.00038
    • (2014) Front. Neuroinform , vol.8 , pp. 38
    • Vella, M.1    Cannon, R.C.2    Crook, S.3    Davison, A.P.4    Ganapathy, G.5    Robinson, H.P.C.6
  • 158
    • 84882677184 scopus 로고    scopus 로고
    • GRN2SBML: automated encoding and annotation of inferred gene regulatory networks complying with SBML
    • Vlaic, S., Hoffmann, B., Kupfer, P., Weber, M., and Dräger, A. (2013). GRN2SBML: automated encoding and annotation of inferred gene regulatory networks complying with SBML. Bioinformatics 29, 2216-2217. doi:10.1093/bioinformatics/btt370
    • (2013) Bioinformatics , vol.29 , pp. 2216-2217
    • Vlaic, S.1    Hoffmann, B.2    Kupfer, P.3    Weber, M.4    Dräger, A.5
  • 160
    • 83455162737 scopus 로고    scopus 로고
    • Reproducible computational biology experiments with SED-ML-the simulation experiment description markup language
    • Waltemath, D., Adams, R., Bergmann, F. T., Hucka, M., Kolpakov, F., Miller, A. K., et al. (2011b). Reproducible computational biology experiments with SED-ML-the simulation experiment description markup language. BMC Syst. Biol. 5:198. doi:10.1186/1752-0509-5-198
    • (2011) BMC Syst. Biol , vol.5 , pp. 198
    • Waltemath, D.1    Adams, R.2    Bergmann, F.T.3    Hucka, M.4    Kolpakov, F.5    Miller, A.K.6
  • 161
    • 84954120958 scopus 로고    scopus 로고
    • Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)
    • Waltemath, D., Bergmann, F. T., Chaouiya, C., Czauderna, T., Gleeson, P., Goble, C., et al. (2014). Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE). Stand. Genomic Sci. 9, 1285-1301, doi:10.4056/sigs.5279417
    • (2014) Stand. Genomic Sci , vol.9 , pp. 1285-1301
    • Waltemath, D.1    Bergmann, F.T.2    Chaouiya, C.3    Czauderna, T.4    Gleeson, P.5    Goble, C.6
  • 162
    • 84928862879 scopus 로고    scopus 로고
    • 'Reproducibility of model-based results in systems biology,'
    • eds A. Prokop and B. Csukás (New York: Springer)
    • Waltemath, D., Henkel, R., Winter, F., and Wolkenhauer, O. (2013). "Reproducibility of model-based results in systems biology," in Systems Biology, eds A. Prokop and B. Csukás (New York: Springer), 301-320.
    • (2013) Systems Biology , pp. 301-320
    • Waltemath, D.1    Henkel, R.2    Winter, F.3    Wolkenhauer, O.4
  • 164
    • 84892792455 scopus 로고    scopus 로고
    • Challenges for an enzymatic reaction kinetics database
    • Wittig, U., Rey, M., Kania, R., Bittkowski, M., Shi, L., Golebiewski, M., et al. (2014). Challenges for an enzymatic reaction kinetics database. FEBS Journal 281, 572-582. doi:10.1111/febs.12562
    • (2014) FEBS Journal , vol.281 , pp. 572-582
    • Wittig, U.1    Rey, M.2    Kania, R.3    Bittkowski, M.4    Shi, L.5    Golebiewski, M.6
  • 166
    • 84874016103 scopus 로고    scopus 로고
    • Precise generation of systems biology models from KEGG pathways
    • Wrzodek, C., Büchel, F., Ruff, M., Dräger, A., and Zell, A. (2013). Precise generation of systems biology models from KEGG pathways. BMC Syst. Biol. 7:15. doi:10.1186/1752-0509-7-15
    • (2013) BMC Syst. Biol , vol.7 , pp. 15
    • Wrzodek, C.1    Büchel, F.2    Ruff, M.3    Dräger, A.4    Zell, A.5
  • 167
    • 79961195281 scopus 로고    scopus 로고
    • KEGG translator: visualizing and converting the KEGG pathway database to various formats
    • Wrzodek, C., Dräger, A., and Zell, A. (2011). KEGG translator: visualizing and converting the KEGG pathway database to various formats. Bioinformatics 27, 2314-2315. doi:10.1093/bioinformatics/btr377
    • (2011) Bioinformatics , vol.27 , pp. 2314-2315
    • Wrzodek, C.1    Dräger, A.2    Zell, A.3
  • 168
    • 70749149335 scopus 로고    scopus 로고
    • Module master: a new tool to decipher transcriptional regulatory networks
    • Wrzodek, C., Schröder, A., Dräger, A., Wanke, D., Berendzen, K. W., Kronfeld, M., et al. (2010). Module master: a new tool to decipher transcriptional regulatory networks. BioSystems 99, 71-81. doi:10.1016/j.biosystems.2009.09.005
    • (2010) BioSystems , vol.99 , pp. 71-81
    • Wrzodek, C.1    Schröder, A.2    Dräger, A.3    Wanke, D.4    Berendzen, K.W.5    Kronfeld, M.6


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