Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/22718
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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.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.authorPinto Burke, Paulo E.-
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.authorKAZAKEVICH, Dzianis-
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.date.accessioned2016-11-23T10:43:01Z-
dc.date.available2016-11-23T10:43:01Z-
dc.date.issued2016-
dc.identifier.citationIEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING, 63(10), p. 2007-2014-
dc.identifier.issn0018-9294-
dc.identifier.urihttp://hdl.handle.net/1942/22718-
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.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.language.isoen-
dc.publisherIEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC-
dc.rightsThis work is licensed under a Creative Commons Attribution 3.0 License. For more information, see http://creativecommons.org/licenses/by/3.0/-
dc.subject.otherComputational biology; education; simulation; standards; systems biology; whole-cell (WC) modeling-
dc.subject.othercomputational biology; education; simulation; standards; systems biology; whole-cell (WC) modeling-
dc.titleToward Community Standards and Software for Whole-Cell Modeling-
dc.typeJournal Contribution-
dc.identifier.epage2014-
dc.identifier.issue10-
dc.identifier.spage2007-
dc.identifier.volume63-
local.format.pages8-
local.bibliographicCitation.jcatA1-
dc.description.notes[Waltemath, Dagmar; Bittig, Arne T.; Scharm, Martin; Theile, Tom; Toure, Vasundra; Wendland, Florian; Wolfien, Markus] Univ Rostock, Inst Comp Sci, D-18051 Rostock, Germany. [Karr, Jonathan R.; Chew, Yin Hoon; Goldberg, Arthur P.] Icahn Sch Med Mt Sinai, Dept Genet & Genom Sci, New York, NY 10029 USA. [Bergmann, Frank T.] Heidelberg Univ, BioQuant, Bergheimer Str 58, D-69115 Heidelberg, Germany. [Chelliah, Vijayalakshmi; Aranganathan, Naveen K.; Lloret-Villas, Audald] European Mol Biol Lab, European Bioinformat Inst EMBL EBI, Heidelberg, Germany. [Hucka, Michael] CALTECH, Dept Comp & Math Sci, Pasadena, CA 91125 USA. [Krantz, Marcus; Hahn, Jens; Uhlendorf, Jannis] Humboldt Univ, Dept Biol, Berlin, Germany. [Liebermeister, Wolfram] Univ Med Charite Berlin, Inst Biochem, Berlin, Germany. [Mendes, Pedro] Univ Manchester, Manchester Inst Biotechnol, Manchester M13 9PL, Lancs, England. [Mendes, Pedro] Univ Manchester, Sch Comp Sci, Manchester M13 9PL, Lancs, England. [Mendes, Pedro] Univ Connecticut, Ctr Hlth, Ctr Quantitat Med, Storrs, CT USA. [Mendes, Pedro] Univ Connecticut, Ctr Hlth, Dept Cell Biol, Storrs, CT USA. [Myers, Chris J.; Watanabe, Leandro H.] Univ Utah, Dept Elect & Comp Engn, Salt Lake City, UT 84112 USA. [Pir, Pinar] Gebze Tech Univ, Gebze, Turkey. [Alaybeyoglu, Begum] Bogazici Univ, Dept Chem Engn, TR-80815 Bebek, Turkey. [Baghalian, Kambiz] Univ Oxford, Dept Plant Sci, Oxford OX1 2JD, England. [Pinto Burke, Paulo E.] Univ Fed Sao Paulo, Inst Sci & Technol, Sao Paulo, Brazil. [Chew, Yin Hoon; Zardilis, Argyris] Univ Edinburgh, Ctr Synthet & Syst Biol, Edinburgh EH8 9YL, Midlothian, Scotland. [Costa, Rafael S.] Univ Lisbon, Inst Super Tecn, Ctr Intelligent Syst IDMEC, P-1699 Lisbon, Portugal. [Cursons, Joseph] Univ Melbourne, Syst Biol Lab, Melbourne Sch Engn, Melbourne, Vic 3010, Australia. [Cursons, Joseph] Univ Melbourne, ARC Ctr Excellence Convergent Bionano Sci & Techn, Melbourne Sch Engn, Melbourne, Vic 3010, Australia. [Czauderna, Tobias; Schreiber, Falk] Monash Univ, Fac Informat Technol, Clayton, Vic 3800, Australia. [Gomez, Harold F.] Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Zurich, Switzerland. [Hameri, Tuure; Gardiol, Daniel F. Hernandez; Tokic, Milenko] Swiss Fed Inst Technol, Lab Computat Syst Biotechnol, Zurich, Switzerland. [Kazakiewicz, Denis] Univ Hasselt, Ctr Stat, Hasselt, Belgium. [Kazakiewicz, Denis] Med Univ Bialystok, Ctr Innovat Res, Bialystok, Poland. [Kiselev, Ilya] Russian Acad Sci, Design Technol Inst Digital Tech, Siberian Branch, Moscow 117901, Russia. [Knight-Schrijver, Vincent] Babraham Inst, Babraham, England. [Koenig, Matthias] Humboldt Univ, Inst Biochem, Berlin, Germany. [Lee, Daewon; Song, Je-Hoon] Korea Adv Inst Sci & Technol, Dept Bio & Brain Engn, Daejeon, South Korea. [Mandrik, Nikita] Russian Acad Sci, Sobolev Inst Math, Siberian Branch, Moscow 117901, Russia. [Medley, J. Kyle] Univ Washington, Dept Bioengn, Seattle, WA 98195 USA. [Naderi-Meshkin, Hojjat] Iranian Acad Ctr Educ Culture Res ACECR, Stem Cell & Regenerat Med Res Dept, Tehran, Iran. [Palaniappan, Sucheendra K.] Rennes Bretagne Atlantique Res Ctr, Inst Res Comp Sci & Automat, Rennes, France. [Priego-Espinosa, Daniel] Univ Nacl Autonoma Mexico, Inst Ciencias Fis, Mexico City 04510, DF, Mexico. [Sharma, Mahesh] Natl Inst Pharmaceut Educ & Res, Dept Pharmacoinformat, Sahibzada Ajit Singh Nag, Punjab, India. [Smallbone, Kieran; Stanford, Natalie J.] Univ Manchester, Manchester Ctr Integrat Syst Biol, Manchester M13 9PL, Lancs, England. [Tokic, Milenko] Swiss Inst Bioinformat, Geneva, Switzerland. [Tomar, Namrata] Univ Erlangen Nurnberg, Univ Med, Dept Dermatol, Erlangen, Germany. [Varusai, Thawfeek M.] Univ Coll Dublin, Dept Syst Biol Ireland, Dublin, Ireland. [Zhu, Yan] Monash Univ, Monash Inst Pharmaceut Sci, Clayton, Vic 3800, Australia. [Zhukova, Anna] Natl Ctr Sci Res, Inst Biochim & Genet Cellulaires, Paris, France. [Zhukova, Anna] Univ Bordeaux, Bordeaux, France. [Schreiber, Falk] Univ Konstanz, Dept Comp & Informat Sci, Constance, Germany.-
local.publisher.placePISCATAWAY-
local.type.refereedRefereed-
local.type.specifiedArticle-
dc.identifier.doi10.1109/TBME.2016.2560762-
dc.identifier.isi000384570200004-
item.contributorWaltemath, Dagmar-
item.contributorKarr, Jonathan R.-
item.contributorBergmann, Frank T.-
item.contributorChelliah, Vijayalakshmi-
item.contributorHucka, Michael-
item.contributorKrantz, Marcus-
item.contributorLiebermeister, Wolfram-
item.contributorMendes, Pedro-
item.contributorMyers, Chris J.-
item.contributorPir, Pinar-
item.contributorAlaybeyoglu, Begum-
item.contributorAranganathan, Naveen K.-
item.contributorBaghalian, Kambiz-
item.contributorBittig, Arne T.-
item.contributorPinto Burke, Paulo E.-
item.contributorCantarelli, Matteo-
item.contributorChew, Yin Hoon-
item.contributorCosta, Rafael S.-
item.contributorCursons, Joseph-
item.contributorCzauderna, Tobias-
item.contributorGoldberg, Arthur P.-
item.contributorGomez, Harold F.-
item.contributorHahn, Jens-
item.contributorHameri, Tuure-
item.contributorGardiol, Daniel F. Hernandez-
item.contributorKAZAKEVICH, Dzianis-
item.contributorKiselev, Ilya-
item.contributorKnight-Schrijver, Vincent-
item.contributorKnuepfer, Christian-
item.contributorKoenig, Matthias-
item.contributorLee, Daewon-
item.contributorLloret-Villas, Audald-
item.contributorMandrik, Nikita-
item.contributorMedley, J. Kyle-
item.contributorMoreau, Bertrand-
item.contributorNaderi-Meshkin, Hojjat-
item.contributorPalaniappan, Sucheendra K.-
item.contributorPriego-Espinosa, Daniel-
item.contributorScharm, Martin-
item.contributorSharma, Mahesh-
item.contributorSmallbone, Kieran-
item.contributorStanford, Natalie J.-
item.contributorSong, Je-Hoon-
item.contributorTheile, Tom-
item.contributorTokic, Milenko-
item.contributorTomar, Namrata-
item.contributorToure, Vasundra-
item.contributorUhlendorf, Jannis-
item.contributorVarusai, Thawfeek M.-
item.contributorWatanabe, Leandro H.-
item.contributorWendland, Florian-
item.contributorWolfien, Markus-
item.contributorYurkovich, James T.-
item.contributorZhu, Yan-
item.contributorZardilis, Argyris-
item.contributorZhukova, Anna-
item.contributorSchreiber, Falk-
item.accessRightsOpen Access-
item.fullcitationWaltemath, Dagmar; Karr, Jonathan R.; Bergmann, Frank T.; Chelliah, Vijayalakshmi; Hucka, Michael; Krantz, Marcus; Liebermeister, Wolfram; Mendes, Pedro; Myers, Chris J.; Pir, Pinar; Alaybeyoglu, Begum; Aranganathan, Naveen K.; Baghalian, Kambiz; Bittig, Arne T.; Pinto Burke, Paulo E.; Cantarelli, Matteo; Chew, Yin Hoon; Costa, Rafael S.; Cursons, Joseph; Czauderna, Tobias; Goldberg, Arthur P.; Gomez, Harold F.; Hahn, Jens; Hameri, Tuure; Gardiol, Daniel F. Hernandez; KAZAKEVICH, Dzianis; Kiselev, Ilya; Knight-Schrijver, Vincent; Knuepfer, Christian; Koenig, Matthias; Lee, Daewon; Lloret-Villas, Audald; Mandrik, Nikita; Medley, J. Kyle; Moreau, Bertrand; Naderi-Meshkin, Hojjat; Palaniappan, Sucheendra K.; Priego-Espinosa, Daniel; Scharm, Martin; Sharma, Mahesh; Smallbone, Kieran; Stanford, Natalie J.; Song, Je-Hoon; Theile, Tom; Tokic, Milenko; Tomar, Namrata; Toure, Vasundra; Uhlendorf, Jannis; Varusai, Thawfeek M.; Watanabe, Leandro H.; Wendland, Florian; Wolfien, Markus; Yurkovich, James T.; Zhu, Yan; Zardilis, Argyris; Zhukova, Anna & Schreiber, Falk (2016) Toward Community Standards and Software for Whole-Cell Modeling. In: IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING, 63(10), p. 2007-2014.-
item.fulltextWith Fulltext-
item.validationecoom 2017-
crisitem.journal.issn0018-9294-
crisitem.journal.eissn1558-2531-
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