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Title: Toward Community Standards and Software for Whole-Cell Modeling
Authors: Waltemath, 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
Kazakiewicz, Denis 
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
Issue Date: 2016
Abstract: Objective: 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.
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.
Keywords: computational biology; education; simulation; standards; systems biology; whole-cell (WC) modeling;Computational biology; education; simulation; standards; systems biology; whole-cell (WC) modeling
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ISSN: 0018-9294
e-ISSN: 1558-2531
DOI: 10.1109/TBME.2016.2560762
ISI #: 000384570200004
Rights: This work is licensed under a Creative Commons Attribution 3.0 License. For more information, see
Category: A1
Type: Journal Contribution
Validations: ecoom 2017
Appears in Collections:Research publications

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