Toward community standards and software for whole-cell modeling

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WALTEMATH, Dagmar, Jonathan KARR, Frank BERGMANN, Vijayalakshmi CHELLIAH, Michael HUCKA, Marcus KRANTZ, Wolfram LIEBERMEISTER, Pedro MENDES, Argyris ZARDILIS, Falk SCHREIBER, 2016. Toward community standards and software for whole-cell modeling. In: IEEE Transactions on Biomedical Engineering. 63(10), pp. 2007-2014. ISSN 0018-9294. eISSN 1558-2531

@article{Waltemath2016-10Towar-34863, title={Toward community standards and software for whole-cell modeling}, year={2016}, doi={10.1109/TBME.2016.2560762}, number={10}, volume={63}, issn={0018-9294}, journal={IEEE Transactions on Biomedical Engineering}, pages={2007--2014}, author={Waltemath, Dagmar and Karr, Jonathan and Bergmann, Frank and Chelliah, Vijayalakshmi and Hucka, Michael and Krantz, Marcus and Liebermeister, Wolfram and Mendes, Pedro and Zardilis, Argyris and Schreiber, Falk} }

<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bibo="http://purl.org/ontology/bibo/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > <rdf:Description rdf:about="https://kops.uni-konstanz.de/rdf/resource/123456789/34863"> <dc:contributor>Hucka, Michael</dc:contributor> <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2016-07-25T13:58:34Z</dcterms:available> <dc:contributor>Chelliah, Vijayalakshmi</dc:contributor> <dc:creator>Hucka, Michael</dc:creator> <dcterms:rights rdf:resource="http://nbn-resolving.de/urn:nbn:de:bsz:352-20150914100631302-4485392-8"/> <dcterms:abstract xml:lang="eng">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.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 SBML. 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.</dcterms:abstract> <dc:contributor>Karr, Jonathan</dc:contributor> <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/34863"/> <dc:contributor>Waltemath, Dagmar</dc:contributor> <dc:contributor>Krantz, Marcus</dc:contributor> <dc:contributor>Bergmann, Frank</dc:contributor> <dc:contributor>Mendes, Pedro</dc:contributor> <dc:creator>Waltemath, Dagmar</dc:creator> <dc:contributor>Zardilis, Argyris</dc:contributor> <dcterms:issued>2016-10</dcterms:issued> <dc:language>eng</dc:language> <dcterms:title>Toward community standards and software for whole-cell modeling</dcterms:title> <dc:creator>Chelliah, Vijayalakshmi</dc:creator> <dc:contributor>Schreiber, Falk</dc:contributor> <dc:creator>Zardilis, Argyris</dc:creator> <dc:creator>Schreiber, Falk</dc:creator> <dc:creator>Karr, Jonathan</dc:creator> <dc:creator>Krantz, Marcus</dc:creator> <dc:creator>Mendes, Pedro</dc:creator> <dc:creator>Liebermeister, Wolfram</dc:creator> <dc:contributor>Liebermeister, Wolfram</dc:contributor> <dc:creator>Bergmann, Frank</dc:creator> <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2016-07-25T13:58:34Z</dc:date> </rdf:Description> </rdf:RDF>

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