메뉴 건너뛰기




Volumn 29, Issue 6, 2013, Pages 742-748

Improving the reuse of computational models through version control

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; COMPUTER PROGRAM; COMPUTER SIMULATION; SYSTEMS BIOLOGY;

EID: 84875175386     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt018     Document Type: Article
Times cited : (21)

References (31)
  • 1
    • 67149131701 scopus 로고    scopus 로고
    • CellML metadata standards, associated tools and repositories
    • Beard,D.A. et al. (2009) CellML metadata standards, associated tools and repositories. Philos. Transact. A Math. Phys. Eng. Sci., 367, 1845-1867.
    • (2009) Philos. Transact. A Math. Phys. Eng. Sci. , vol.367 , pp. 1845-1867
    • Beard, D.A.1
  • 2
    • 0030157266 scopus 로고    scopus 로고
    • Change detection in hierarchically structured information
    • Chawathe,S. et al. (1996) Change detection in hierarchically structured information. ACM SIGMOD Rec, 25, 493-504.
    • (1996) ACM SIGMOD Rec , vol.25 , pp. 493-504
    • Chawathe, S.1
  • 3
    • 80053605881 scopus 로고    scopus 로고
    • High-throughput functional curation of cellular electrophysiology models
    • Cooper,J. et al. (2011) High-throughput functional curation of cellular electrophysiology models. Prog. Biophys. Mol. Biol, 107, 11-20.
    • (2011) Prog. Biophys. Mol. Biol , vol.107 , pp. 11-20
    • Cooper, J.1
  • 4
    • 2442498807 scopus 로고    scopus 로고
    • (30 January 2013, date last accessed)
    • Cuellar,A. et al. (2006) The CellML metadata 1.0 specification. http://www.cellml. org/specifications/metadata/cellml-metadata-1.0 (30 January 2013, date last accessed).
    • (2006) The CellML Metadata 1.0 Specification.
    • Cuellar, A.1
  • 5
    • 1342329447 scopus 로고    scopus 로고
    • An overview of CellML 1.1, a biological model description language
    • Cuellar,A.A. et al. (2003) An overview of CellML 1.1, a biological model description language. Simulation, 79, 740-747.
    • (2003) Simulation , vol.79 , pp. 740-747
    • Cuellar, A.A.1
  • 6
    • 3042678959 scopus 로고    scopus 로고
    • Computational challenges of systems biology
    • Finkelstein,A. et al. (2004) Computational challenges of systems biology. IEEE Comp., 37, 26-33.
    • (2004) IEEE Comp. , vol.37 , pp. 26-33
    • Finkelstein, A.1
  • 7
    • 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. 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.
    • (2010) PLoS Comput. Biol. , vol.6
    • Gleeson, P.1
  • 8
    • 77955385319 scopus 로고    scopus 로고
    • Ranked retrieval of computational biology models
    • Henkel,R. et al. (2010) Ranked retrieval of computational biology models. BMC Bioinformatics, 11. 423.
    • (2010) BMC Bioinformatics , vol.11 , pp. 423
    • Henkel, R.1
  • 9
    • 84904718597 scopus 로고    scopus 로고
    • Considerations of graph-based concepts to manage computational biology models and associated simulations
    • In: Goltz,U. et al. (ed.) Workshop on data in the life sciences. ''INFORMATIK 2012''
    • Henkel,R. et al. (2012) Considerations of graph-based concepts to manage computational biology models and associated simulations. In: Goltz,U. et al. (ed.) Workshop on data in the life sciences. ''INFORMATIK 2012'', Lecture Notes in Informatics 208, 1545-1551.
    • (2012) Lecture Notes in Informatics , vol.208 , pp. 1545-1551
    • Henkel, R.1
  • 10
    • 53749085229 scopus 로고    scopus 로고
    • A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
    • Herrga?rd,M. et al. (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat. Biotechnol., 26, 1155-1160.
    • (2008) Nat. Biotechnol. , vol.26 , pp. 1155-1160
    • Herrgard, M.1
  • 11
    • 3342941917 scopus 로고    scopus 로고
    • ModelDB: A database to support computational neuroscience
    • Hines,M.L. et al. (2004) ModelDB: a database to support computational neuroscience. J. Comput. Neurosci., 17, 7-11-11.
    • (2004) J. Comput. Neurosci. , vol.17 , pp. 71111
    • Hines, M.L.1
  • 12
    • 84976825385 scopus 로고
    • Algorithms for the longest common subsequence problem
    • Hirschberg,D. (1977) Algorithms for the longest common subsequence problem. J. ACM, 24, 664-675.
    • (1977) J. ACM , vol.24 , pp. 664-675
    • Hirschberg, D.1
  • 13
    • 80051514749 scopus 로고    scopus 로고
    • Integrating systems biology models and biomedical ontologies
    • Hoehndorf,R. et al. (2011) Integrating systems biology models and biomedical ontologies. BMC Syst. Biol., 5, 124.
    • (2011) BMC Syst. Biol. , vol.5 , pp. 124
    • Hoehndorf, R.1
  • 14
    • 0037342537 scopus 로고    scopus 로고
    • The systems biology markup language (sbml): A medium for representation and exchange of biochemical network models
    • Hucka,M. et al. (2003) The systems biology markup language (sbml): a medium for representation and exchange of biochemical network models. Bioinformatics, 19, 524-531.
    • (2003) Bioinformatics , vol.19 , pp. 524-531
    • Hucka, M.1
  • 16
    • 84862156032 scopus 로고    scopus 로고
    • Identifiers.org andMIRIAMRegistry: Community resources to provide persistent identification
    • Juty,N. et al. (2012) Identifiers.org andMIRIAMRegistry: community resources to provide persistent identification. Nucleic Acids Res., 40 (D1), D580-D586.
    • (2012) Nucleic Acids Res. , vol.40 , Issue.1
    • Juty, N.1
  • 17
    • 85044709890 scopus 로고    scopus 로고
    • Annotation and merging of SBML models with semanticSBML
    • Krause,F. et al. (2010) Annotation and merging of SBML models with semanticSBML. Bioinformatics, 2, 421.
    • (2010) Bioinformatics , vol.2 , pp. 421
    • Krause, F.1
  • 18
    • 0003449831 scopus 로고    scopus 로고
    • Resource description framework (RDF) model and syntax specification
    • (30 January 2013, date last accessed)
    • Lassila,O. et al. (1998) Resource description framework (RDF) model and syntax specification. W3C Recommendation. http://www.w3.org/TR/REC-rdf-syntax/ (30 January 2013, date last accessed).
    • (1998) W3C Recommendation.
    • Lassila, O.1
  • 19
    • 28644433993 scopus 로고    scopus 로고
    • Minimum Information Requested in the Annotation of biochemical Models (MIRIAM)
    • Le Novere et al. (2005) Minimum Information Requested In the Annotation of biochemical Models (MIRIAM). Nature Biotechnol., 23, 1509-1515.
    • (2005) Nature Biotechnol. , vol.23 , pp. 1509-1515
    • Novere, L.1
  • 20
    • 68449103579 scopus 로고    scopus 로고
    • The systems biology graphical notation
    • Le Novere,N. et al. (2009) The systems biology graphical notation. Nature Biotechnol., 27, 735-741.
    • (2009) Nature Biotechnol. , vol.27 , pp. 735-741
    • Le Novere, N.1
  • 21
    • 77953934646 scopus 로고    scopus 로고
    • Biomodels database: An enhanced, curated and annotated resource for published quantitative kinetic models
    • Li,C. et al. (2010) Biomodels database: an enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst. Biol., 4, 92.
    • (2010) BMC Syst. Biol. , vol.4 , pp. 92
    • Li, C.1
  • 22
    • 84874661973 scopus 로고    scopus 로고
    • An overview of the cellml api and its implementation
    • Miller,A. et al. (2010) An overview of the cellml api and its implementation. BMC Bioinformatics, 11, 178.
    • (2010) BMC Bioinformatics , vol.11 , pp. 178
    • Miller, A.1
  • 23
    • 78651371376 scopus 로고    scopus 로고
    • Revision history aware repositories of computational models of biological systems
    • Miller,A. et al. (2011) Revision history aware repositories of computational models of biological systems. BMC Bioinformatics., 12, 22.
    • (2011) BMC Bioinformatics. , vol.12 , pp. 22
    • Miller, A.1
  • 26
    • 77950956660 scopus 로고    scopus 로고
    • An XQuery-based version extension of an XML Native Database
    • ACM, New York, NY, USA
    • Rosado,A.L. et al. (2009) An XQuery-based version extension of an XML Native Database. In: Proceedings of the 2009 EDBT/ICDT Workshops. ACM, New York, NY, USA, pp. 99-106.
    • (2009) Proceedings of the 2009 EDBT/ICDT Workshops , pp. 99-106
    • Rosado, A.L.1
  • 27
    • 65149101663 scopus 로고    scopus 로고
    • Version control of pathway models using xml patches
    • Saffrey,P. and Owen,R. (2009) Version control of pathway models using xml patches. BMC Syst. Biol., 3, 34.
    • (2009) BMC Syst. Biol. , vol.3 , pp. 34
    • Saffrey, P.1    Owen, R.2
  • 28
    • 0025826876 scopus 로고
    • Modeling the cell division cycle: Cdc2 and cyclin interactions
    • Tyson,J.J. (1991) Modeling the cell division cycle: cdc2 and cyclin interactions. Proc. Natl Acad. Sci. USA, 88, 7328-7332.
    • (1991) Proc. Natl Acad. Sci. USA , vol.88 , pp. 7328-7332
    • Tyson, J.J.1
  • 29
    • 83455162737 scopus 로고    scopus 로고
    • Reproducible computational biology experiments with SED-ML-The simulation experiment description markup language
    • Waltemath,D. et al. (2011) Reproducible computational biology experiments with SED-ML-the simulation experiment description markup language. BMC Syst. Biol., 5, 198.
    • (2011) BMC Syst. Biol. , vol.5 , pp. 198
    • Waltemath, D.1
  • 30
    • 33746675631 scopus 로고    scopus 로고
    • Sabio-rk: Integration and curation of reaction kinetics data
    • Springer, Berlin Heidelberg
    • Wittig,U. et al. (2006) Sabio-rk: integration and curation of reaction kinetics data. In: Data Integration in the Life Sciences. Springer, Berlin Heidelberg, pp. 94-103.
    • (2006) Data Integration in the Life Sciences , pp. 94-103
    • Wittig, U.1
  • 31
    • 79951986255 scopus 로고    scopus 로고
    • The physiome model repository 2
    • Yu,T. et al. (2011) The physiome model repository 2. Bioinformatics, 27, 743-744.
    • (2011) Bioinformatics , vol.27 , pp. 743-744
    • Yu, T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.