Toward Community Standards and Software for Whole-Cell Modeling

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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.date.accessioned2025-10-29T11:13:59Z
dc.date.issued2016
dc.departmentGebze Teknik Üniversitesi
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.
dc.description.sponsorshipVolkswagen Foundation [88495]
dc.description.sponsorshipJames S. McDonnell Foundation
dc.description.sponsorshipNational Science Foundation [1548123]
dc.description.sponsorshipAustralian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology [CE140100036]
dc.description.sponsorshipBiotechnology and Biological Sciences Research Council [1443802] Funding Source: researchfish
dc.description.sponsorshipDirect For Biological Sciences
dc.description.sponsorshipDiv Of Molecular and Cellular Bioscience [1548123] Funding Source: National Science Foundation
dc.description.sponsorshipThe Rostock and Utah meetings were supported by the Volkswagen Foundation (Grant 88495 to D. Waltemath and F. Schreiber). The work of J. R. Karr was supported by the James S. McDonnell Foundation Postdoctoral Fellowship Award in Studying Complex Systems and the National Science Foundation under Grant 1548123. The work of J. Cursons was supported by the Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology through Project CE140100036. Asterisk indicates corresponding authors.
dc.identifier.doi10.1109/TBME.2016.2560762
dc.identifier.endpage2014
dc.identifier.issn0018-9294
dc.identifier.issn1558-2531
dc.identifier.issue10
dc.identifier.orcid0000-0002-9307-3254
dc.identifier.orcid0000-0002-2605-5080
dc.identifier.orcid0000-0003-4519-7030
dc.identifier.orcid0000-0003-4933-1145
dc.identifier.orcid0000-0002-1887-4772
dc.identifier.orcid0000-0003-2200-7935
dc.identifier.orcid0000-0003-1725-179X
dc.identifier.pmid27305665
dc.identifier.scopus2-s2.0-84993897548
dc.identifier.scopusqualityQ1
dc.identifier.startpage2007
dc.identifier.urihttps://doi.org/10.1109/TBME.2016.2560762
dc.identifier.urihttps://hdl.handle.net/20.500.14854/7021
dc.identifier.volume63
dc.identifier.wosWOS:000384570200004
dc.identifier.wosqualityQ1
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.language.isoen
dc.publisherIEEE-Inst Electrical Electronics Engineers Inc
dc.relation.ispartofIEEE Transactions on Biomedical Engineering
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/openAccess
dc.snmzKA_WOS_20251020
dc.subjectComputational biology
dc.subjecteducation
dc.subjectsimulation
dc.subjectstandards
dc.subjectsystems biology
dc.subjectwhole-cell (WC) modeling
dc.titleToward Community Standards and Software for Whole-Cell Modeling
dc.typeArticle

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