Toward Community Standards and Software for Whole-Cell Modeling

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dc.citation.issue10
dc.citation.volume63
dc.contributor.authorWaltemath, Dagmar
dc.contributor.authorKarr, Jonathan R.
dc.contributor.authorBergmann, Frank T.
dc.contributor.authorChelliah, Vijayalakshmi
dc.contributor.authorHucka, Michael
dc.contributor.authorKrantz, Marcus
dc.contributor.authorLiebermeister, Wolfram
dc.contributor.authorMendes, Pedro
dc.contributor.authorMyers, Chris J.
dc.contributor.authorPir, Pinar
dc.contributor.authorAlaybeyoglu, Begum
dc.contributor.authorAranganathan, Naveen K.
dc.contributor.authorBaghalian, Kambiz
dc.contributor.authorBittig, Arne T.
dc.contributor.authorBurke, Paulo Eduardo Pinto [UNIFESP]
dc.contributor.authorCantarelli, Matteo
dc.contributor.authorChew, Yin Hoon
dc.contributor.authorCosta, Rafael S.
dc.contributor.authorCursons, Joseph
dc.contributor.authorCzauderna, Tobias
dc.contributor.authorGoldberg, Arthur P.
dc.contributor.authorGomez, Harold F.
dc.contributor.authorHahn, Jens
dc.contributor.authorHameri, Tuure
dc.contributor.authorGardiol, Daniel F. Hernandez
dc.contributor.authorKazakiewicz, Denis
dc.contributor.authorKiselev, Ilya
dc.contributor.authorKnight-Schrijver, Vincent
dc.contributor.authorKnuepfer, Christian
dc.contributor.authorKoenig, Matthias
dc.contributor.authorLee, Daewon
dc.contributor.authorLloret-Villas, Audald
dc.contributor.authorMandrik, Nikita
dc.contributor.authorMedley, J. Kyle
dc.contributor.authorMoreau, Bertrand
dc.contributor.authorNaderi-Meshkin, Hojjat
dc.contributor.authorPalaniappan, Sucheendra K.
dc.contributor.authorPriego-Espinosa, Daniel
dc.contributor.authorScharm, Martin
dc.contributor.authorSharma, Mahesh
dc.contributor.authorSmallbone, Kieran
dc.contributor.authorStanford, Natalie J.
dc.contributor.authorSong, Je-Hoon
dc.contributor.authorTheile, Tom
dc.contributor.authorTokic, Milenko
dc.contributor.authorTomar, Namrata
dc.contributor.authorToure, Vasundra
dc.contributor.authorUhlendorf, Jannis
dc.contributor.authorVarusai, Thawfeek M.
dc.contributor.authorWatanabe, Leandro H.
dc.contributor.authorWendland, Florian
dc.contributor.authorWolfien, Markus
dc.contributor.authorYurkovich, James T.
dc.contributor.authorZhu, Yan
dc.contributor.authorZardilis, Argyris
dc.contributor.authorZhukova, Anna
dc.contributor.authorSchreiber, Falk
dc.coveragePiscataway
dc.date.accessioned2020-07-31T12:47:42Z
dc.date.available2020-07-31T12:47:42Z
dc.date.issued2016
dc.description.abstractObjective: Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate comprehensive models of complex cells. Methods: We organized the 2015 Whole-Cell Modeling Summer School to teach WC modeling and evaluate the need for new WC modeling standards and software by recoding a recently published WC model in the Systems Biology Markup Language. Results: Our analysis revealed several challenges to representing WC models using the current standards. Conclusion: We, therefore, propose several new WC modeling standards, software, and databases. Significance: We anticipate that these new standards and software will enable more comprehensive models.en
dc.description.affiliationUniv Rostock, Inst Comp Sci, D-18051 Rostock, Germany
dc.description.affiliationIcahn Sch Med Mt Sinai, Dept Genet & Genom Sci, New York, NY 10029 USA
dc.description.affiliationHeidelberg Univ, BioQuant, Bergheimer Str 58, D-69115 Heidelberg, Germany
dc.description.affiliationEuropean Mol Biol Lab, European Bioinformat Inst EMBL EBI, Heidelberg, Germany
dc.description.affiliationCALTECH, Dept Comp & Math Sci, Pasadena, CA 91125 USA
dc.description.affiliationHumboldt Univ, Dept Biol, Berlin, Germany
dc.description.affiliationUniv Med Charite Berlin, Inst Biochem, Berlin, Germany
dc.description.affiliationUniv Manchester, Manchester Inst Biotechnol, Manchester M13 9PL, Lancs, England
dc.description.affiliationUniv Manchester, Sch Comp Sci, Manchester M13 9PL, Lancs, England
dc.description.affiliationUniv Connecticut, Ctr Hlth, Ctr Quantitat Med, Storrs, CT USA
dc.description.affiliationUniv Connecticut, Ctr Hlth, Dept Cell Biol, Storrs, CT USA
dc.description.affiliationUniv Utah, Dept Elect & Comp Engn, Salt Lake City, UT 84112 USA
dc.description.affiliationGebze Tech Univ, Gebze, Turkey
dc.description.affiliationBogazici Univ, Dept Chem Engn, TR-80815 Bebek, Turkey
dc.description.affiliationUniv Oxford, Dept Plant Sci, Oxford OX1 2JD, England
dc.description.affiliationUniv Fed Sao Paulo, Inst Sci & Technol, Sao Paulo, Brazil
dc.description.affiliationUniv Edinburgh, Ctr Synthet & Syst Biol, Edinburgh EH8 9YL, Midlothian, Scotland
dc.description.affiliationUniv Lisbon, Inst Super Tecn, Ctr Intelligent Syst IDMEC, P-1699 Lisbon, Portugal
dc.description.affiliationUniv Melbourne, Syst Biol Lab, Melbourne Sch Engn, Melbourne, Vic 3010, Australia
dc.description.affiliationUniv Melbourne, ARC Ctr Excellence Convergent Bionano Sci & Techn, Melbourne Sch Engn, Melbourne, Vic 3010, Australia
dc.description.affiliationMonash Univ, Fac Informat Technol, Clayton, Vic 3800, Australia
dc.description.affiliationSwiss Fed Inst Technol, Dept Biosyst Sci & Engn, Zurich, Switzerland
dc.description.affiliationSwiss Fed Inst Technol, Lab Computat Syst Biotechnol, Zurich, Switzerland
dc.description.affiliationUniv Hasselt, Ctr Stat, Hasselt, Belgium
dc.description.affiliationMed Univ Bialystok, Ctr Innovat Res, Bialystok, Poland
dc.description.affiliationRussian Acad Sci, Design Technol Inst Digital Tech, Siberian Branch, Moscow 117901, Russia
dc.description.affiliationBabraham Inst, Babraham, England
dc.description.affiliationHumboldt Univ, Inst Biochem, Berlin, Germany
dc.description.affiliationKorea Adv Inst Sci & Technol, Dept Bio & Brain Engn, Daejeon, South Korea
dc.description.affiliationRussian Acad Sci, Sobolev Inst Math, Siberian Branch, Moscow 117901, Russia
dc.description.affiliationUniv Washington, Dept Bioengn, Seattle, WA 98195 USA
dc.description.affiliationIranian Acad Ctr Educ Culture Res ACECR, Stem Cell & Regenerat Med Res Dept, Tehran, Iran
dc.description.affiliationRennes Bretagne Atlantique Res Ctr, Inst Res Comp Sci & Automat, Rennes, France
dc.description.affiliationUniv Nacl Autonoma Mexico, Inst Ciencias Fis, Mexico City 04510, DF, Mexico
dc.description.affiliationNatl Inst Pharmaceut Educ & Res, Dept Pharmacoinformat, Sahibzada Ajit Singh Nag, Punjab, India
dc.description.affiliationUniv Manchester, Manchester Ctr Integrat Syst Biol, Manchester M13 9PL, Lancs, England
dc.description.affiliationSwiss Inst Bioinformat, Geneva, Switzerland
dc.description.affiliationUniv Erlangen Nurnberg, Univ Med, Dept Dermatol, Erlangen, Germany
dc.description.affiliationUniv Coll Dublin, Dept Syst Biol Ireland, Dublin, Ireland
dc.description.affiliationMonash Univ, Monash Inst Pharmaceut Sci, Clayton, Vic 3800, Australia
dc.description.affiliationNatl Ctr Sci Res, Inst Biochim & Genet Cellulaires, Paris, France
dc.description.affiliationUniv Bordeaux, Bordeaux, France
dc.description.affiliationUniv Konstanz, Dept Comp & Informat Sci, Constance, Germany
dc.description.affiliationUnifespInstitute of Science and Technology, Universidade Federal de São Paulo (UNIFESP), São José dos Campos, Brasil
dc.description.sourceWeb of Science
dc.description.sponsorshipVolkswagen Foundation
dc.description.sponsorshipJames S. McDonnell Foundation
dc.description.sponsorshipNational Science Foundation (NSF)
dc.description.sponsorshipAustralian Research Council (ARC) Centre of Excellence in Convergent Bio-Nano Science and Technology
dc.description.sponsorshipIDVolkswagen Foundation: 88495
dc.description.sponsorshipIDNSF: 1548123
dc.description.sponsorshipIDACR Centre of Excellence in Convergent Bio-Nano Science and Technology: CE140100036
dc.format.extent2007-2014
dc.identifierhttp://dx.doi.org/10.1109/TBME.2016.2560762
dc.identifier.citationIeee Transactions On Biomedical Engineering. Piscataway, v. 63, n. 10, p. 2007-2014, 2016.
dc.identifier.doi10.1109/TBME.2016.2560762
dc.identifier.issn0018-9294
dc.identifier.urihttps://repositorio.unifesp.br/handle/11600/57018
dc.identifier.wosWOS:000384570200004
dc.language.isoeng
dc.publisherIeee-Inst Electrical Electronics Engineers Inc
dc.relation.ispartofIeee Transactions On Biomedical Engineering
dc.rightsinfo:eu-repo/semantics/openAccess
dc.subjectComputational biologyen
dc.subjecteducationen
dc.subjectsimulationen
dc.subjectstandardsen
dc.subjectsystems biologyen
dc.subjectwhole-cell (WC) modelingen
dc.titleToward Community Standards and Software for Whole-Cell Modelingen
dc.typeinfo:eu-repo/semantics/article
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