메뉴 건너뛰기




Volumn 3, Issue FEB, 2015, Pages

Promoting coordinated development of community-based information standards for modeling in biology: The COMBINE initiative

(12)  Hucka, Michael a   Nickerson, David P b   Bader, Gary D c   Bergmann, Frank T a,d   Cooper, Jonathan e   Demir, Emek f   Garny, Alan b   Golebiewski, Martin g   Myers, Chris J h   Schreiber, Falk i,j   Waltemath, Dagmar k   Le Novère, Nicolas l,m  


Author keywords

Biology; Computational modeling; Data sharing; File formats; Reproducible science; Standardization

Indexed keywords


EID: 84938816567     PISSN: None     EISSN: 22964185     Source Type: Journal    
DOI: 10.3389/fbioe.2015.00019     Document Type: Article
Times cited : (63)

References (35)
  • 2
    • 33644873677 scopus 로고    scopus 로고
    • Pathguide: a pathway resource list
    • Bader, G. D., Cary, M. P., and Sander, C. (2006). Pathguide: a pathway resource list. Nucleic Acids Res. 34, D504-D506. doi: 10.1093/nar/gkj126
    • (2006) Nucleic Acids Res , vol.34 , pp. D504-D506
    • Bader, G.D.1    Cary, M.P.2    Sander, C.3
  • 3
    • 84923910740 scopus 로고    scopus 로고
    • One file to share them all: using the COMBINE archive and the OMEX format to share all information about a modeling project
    • Bergmann, F. T., Adams, R., Moodie, S., Cooper, J., Glont, M., Golebiewski, M., et al. (2014). One file to share them all: using the COMBINE archive and the OMEX format to share all information about a modeling project. BMC Bioinformatics 15:369. doi:10.1186/s12859-014-0369-z
    • (2014) BMC Bioinformatics , vol.15 , pp. 369
    • Bergmann, F.T.1    Adams, R.2    Moodie, S.3    Cooper, J.4    Glont, M.5    Golebiewski, M.6
  • 4
    • 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
  • 5
    • 84886740491 scopus 로고    scopus 로고
    • Path2Models: large-scale generation of computational models from biochemical pathway maps
    • Büchel, F., Rodriguez, N., Swainston, N., Wrzodek, C., Czauderna, T., Keller, R., et al. (2013). Path2Models: 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
  • 8
    • 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
  • 9
    • 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
  • 10
    • 22044443709 scopus 로고    scopus 로고
    • The sequence ontology: a tool for the unification of genome annotations
    • Eilbeck, K., Lewis, S. E., Mungall, C. J., Yandell, M., Stein, L., Durbin, R., et al. (2005). The sequence ontology: a tool for the unification of genome annotations. Genome Biol. 6, R44. doi:10.1186/gb-2005-6-5-r44
    • (2005) Genome Biol , vol.6
    • Eilbeck, K.1    Lewis, S.E.2    Mungall, C.J.3    Yandell, M.4    Stein, L.5    Durbin, R.6
  • 11
    • 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. doi:10.1038/nbt.2891
    • (2014) Nat. Biotechnol , vol.32 , pp. 545
    • Galdzicki, M.1    Clancy, K.P.2    Oberortner, E.3    Pocock, M.4    Quinn, J.Y.5    Rodriguez, C.A.6
  • 12
    • 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
  • 13
    • 85042577287 scopus 로고    scopus 로고
    • Combining computational models, semantic annotations, and associated simulation experiments in a graph database
    • Henkel, R., Wolkenhauer, O., and Walthemath, D. (2015). Combining computational models, semantic annotations, and associated simulation experiments in a graph database. Database 2015. doi:10.7287/peerj.preprints.376v2
    • (2015) Database , vol.2015
    • Henkel, R.1    Wolkenhauer, O.2    Walthemath, D.3
  • 14
    • 0742323374 scopus 로고    scopus 로고
    • The HUPO PSI's molecular interaction format-a community standard for the representation of protein interaction data
    • Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, J., Salwinski, L., Ceol, A., et al. (2004a). The HUPO PSI's molecular interaction format-a community standard for the representation of protein interaction data. Nat. Biotechnol. 22, 177-183. doi:10.1038/nbt926
    • (2004) Nat. Biotechnol , vol.22 , pp. 177-183
    • Hermjakob, H.1    Montecchi-Palazzi, L.2    Bader, G.3    Wojcik, J.4    Salwinski, L.5    Ceol, A.6
  • 15
    • 0742323374 scopus 로고    scopus 로고
    • The HUPO PSI's molecular interaction format-a community standard for the representation of protein interaction data
    • Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, R., Salwinski, L., Ceol, A., et al. (2004b). The HUPO PSI's molecular interaction format-a community standard for the representation of protein interaction data. Nat. Biotechnol. 22, 177-183. doi:10.1038/nbt926
    • (2004) Nat. Biotechnol , vol.22 , pp. 177-183
    • Hermjakob, H.1    Montecchi-Palazzi, L.2    Bader, G.3    Wojcik, R.4    Salwinski, L.5    Ceol, A.6
  • 16
    • 35649001607 scopus 로고
    • A quantitative description of membrane current and its application to conduction and excitation in nerve
    • Hodgkin, A. L., and Huxley, A. F. (1952). A quantitative description of membrane current and its application to conduction and excitation in nerve. J. Physiol. 117, 500. doi:10.1113/jphysiol.1952.sp004764
    • (1952) J. Physiol , vol.117 , pp. 500
    • Hodgkin, A.L.1    Huxley, A.F.2
  • 17
    • 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
  • 18
    • 84862156032 scopus 로고    scopus 로고
    • Identifiers.org and MIRIAM registry: community resources to provide persistent identification
    • Juty, N., Novère, N. L., 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    Novère, N.L.2    Laibe, C.3
  • 20
    • 84962741412 scopus 로고    scopus 로고
    • Computational neuroscience ontology: a new tool to provide semantic meaning to your models
    • Le Franc, Y., Davison, A. P., Gleeson, P., Imam, F. T., Kriener, B., Larson, S. D., et al. (2012). Computational neuroscience ontology: a new tool to provide semantic meaning to your models. BMC Neurosci. 13(Suppl. 1):149. doi:10.1186/1471-2202-13-S1-P149
    • (2012) BMC Neurosci , vol.13 , pp. 149
    • Le Franc, Y.1    Davison, A.P.2    Gleeson, P.3    Imam, F.T.4    Kriener, B.5    Larson, S.D.6
  • 21
    • 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. doi:10.4056/sigs.2034671
    • (2011) Stand. Genomic Sci , vol.5 , pp. 230
    • Le Novère, N.1    Hucka, M.2    Anwar, N.3    Bader, G.D.4    Demir, E.5    Moodie, S.6
  • 23
    • 77953934646 scopus 로고    scopus 로고
    • BioModels database: an enhanced, curated and annotated resource for published quantitative kinetic models
    • Li, C., Donizelli, M., Rodriguez, N., Dharuri, H., Endler, L., Chelliah, V., et al. (2010). BioModels database: an enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst. Biol. 4:92. doi:10.1186/1752-0509-4-92
    • (2010) BMC Syst. Biol , vol.4 , pp. 92
    • Li, C.1    Donizelli, M.2    Rodriguez, N.3    Dharuri, H.4    Endler, L.5    Chelliah, V.6
  • 25
    • 84899945140 scopus 로고    scopus 로고
    • From model specification to simulation of biologically constrained networks of spiking neurons
    • Richmond, P., Cope, A., Gurney, K., and Allerton, D. J. (2014). From model specification to simulation of biologically constrained networks of spiking neurons. Neuroinformatics 12, 307-323. doi:10.1007/s12021-013-9208-z
    • (2014) Neuroinformatics , vol.12 , pp. 307-323
    • Richmond, P.1    Cope, A.2    Gurney, K.3    Allerton, D.J.4
  • 26
    • 84912084327 scopus 로고    scopus 로고
    • Computational thinking in life science education
    • Rubinstein, A., and Chor, B. (2014). Computational thinking in life science education. PLoS Comput. Biol. 10:e1003897. doi:10.1371/journal.pcbi.1003897
    • (2014) PLoS Comput. Biol , vol.10
    • Rubinstein, A.1    Chor, B.2
  • 28
    • 84870000190 scopus 로고    scopus 로고
    • 'Genomic standards consortium workshop: metagenomics, metadata and metaanalysis (M3),'
    • eds R. B. Altman, A. K. Dunker, L. Hunter, T. A. Murray, and T. E. Klein (World Scientific Publishing Co.)
    • Sterk, P., Hirschman, L., Field, D., and Wooley, J. C. (2010). "Genomic standards consortium workshop: metagenomics, metadata and metaanalysis (M3)," in Pacific Symposium on Biocomputing, Vol. 15. eds R. B. Altman, A. K. Dunker, L. Hunter, T. A. Murray, and T. E. Klein (World Scientific Publishing Co.), 481-484. doi:10.1142/9789814295291_0050
    • (2010) Pacific Symposium on Biocomputing , vol.15 , pp. 481-484
    • Sterk, P.1    Hirschman, L.2    Field, D.3    Wooley, J.C.4
  • 29
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology
    • The Gene Ontology Consortium. (2000). Gene ontology: tool for the unification of biology. Nat. Genet. 25, 25-29. doi:10.1038/75556
    • (2000) Nat. Genet , vol.25 , pp. 25-29
  • 31
    • 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. (2011). 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
  • 32
    • 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.2034671
    • (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
  • 33
    • 33745217108 scopus 로고    scopus 로고
    • Computational thinking
    • Wing, J. M. (2006). Computational thinking. Commun. ACM 49, 33-35. doi:10.1145/1118178.1118215
    • (2006) Commun. ACM , vol.49 , pp. 33-35
    • Wing, J.M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.