Toward Community Standards and Software for Whole-Cell Modeling | Zendy

Dagmar Waltemath | Zendy; Jonathan R. Karr | Zendy; Frank T. Bergmann | Zendy; Vijayalakshmi Chelliah | Zendy; Michael Hucka | Zendy; Marcus Krantz | Zendy; Wolfram Liebermeister | Zendy; Pedro Mendes | Zendy; Chris J. Myers | Zendy; Pinar Pir | Zendy; Begum Alaybeyoglu | Zendy; Naveen K Aranganathan | Zendy; Kambiz Baghalian | Zendy; Arne T. Bittig | Zendy; Paulo E. Pinto Burke | Zendy; Matteo Cantarelli | Zendy; Yin Hoon Chew | Zendy; Rafael S. Costa | Zendy; Joseph Cursons | Zendy; Tobias Czauderna | Zendy; Arthur P. Goldberg | Zendy; Harold F. Gomez | Zendy; Jens Hahn | Zendy; Tuure Hameri | Zendy; Daniel F. Hernandez Gardiol | Zendy; Denis Kazakiewicz | Zendy; Ilya Kiselev | Zendy; Vincent Knight-Schrijver | Zendy; Christian Knupfer | Zendy; Matthias Konig | Zendy; Daewon Lee | Zendy; Audald Lloret-Villas | Zendy; Nikita Mandrik | Zendy; J. Kyle Medley | Zendy; Bertrand Moreau | Zendy; Hojjat Naderi-Meshkin | Zendy; Sucheendra K. Palaniappan | Zendy; Daniel Priego-Espinosa | Zendy; Martin Scharm | Zendy; Mahesh Sharma | Zendy; Kieran Smallbone | Zendy; Natalie J. Stanford | Zendy; Je-Hoon Song | Zendy; Tom Theile | Zendy; Milenko Tokic | Zendy; Namrata Tomar | Zendy; Vasundra Toure | Zendy; Jannis Uhlendorf | Zendy; Thawfeek M Varusai | Zendy; Leandro H. Watanabe | Zendy; Florian Wendland | Zendy; Markus Wolfien | Zendy; James T. Yurkovich | Zendy; Yan Zhu | Zendy; Argyris Zardilis | Zendy; Anna Zhukova | Zendy; Falk Schreiber | Zendy

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Toward Community Standards and Software for Whole-Cell Modeling

Author(s) -

Dagmar Waltemath,

Jonathan R. Karr,

Frank T. Bergmann,

Vijayalakshmi Chelliah,

Michael Hucka,

Marcus Krantz,

Wolfram Liebermeister,

Pedro Mendes,

Chris J. Myers,

Pinar Pir,

Begum Alaybeyoglu,

Naveen K Aranganathan,

Kambiz Baghalian,

Arne T. Bittig,

Paulo E. Pinto Burke,

Matteo Cantarelli,

Yin Hoon Chew,

Rafael S. Costa,

Joseph Cursons,

Tobias Czauderna,

Arthur P. Goldberg,

Harold F. Gomez,

Jens Hahn,

Tuure Hameri,

Daniel F. Hernandez Gardiol,

Denis Kazakiewicz,

Ilya Kiselev,

Vincent Knight-Schrijver,

Christian Knupfer,

Matthias Konig,

Daewon Lee,

Audald Lloret-Villas,

Nikita Mandrik,

J. Kyle Medley,

Bertrand Moreau,

Hojjat Naderi-Meshkin,

Sucheendra K. Palaniappan,

Daniel Priego-Espinosa,

Martin Scharm,

Mahesh Sharma,

Kieran Smallbone,

Natalie J. Stanford,

Je-Hoon Song,

Tom Theile,

Milenko Tokic,

Namrata Tomar,

Vasundra Toure,

Jannis Uhlendorf,

Thawfeek M Varusai,

Leandro H. Watanabe,

Florian Wendland,

Markus Wolfien,

James T. Yurkovich,

Yan Zhu,

Argyris Zardilis,

Anna Zhukova,

Falk Schreiber

Publication year - 2016

Publication title -

ieee transactions on biomedical engineering

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 1.148

H-Index - 200

eISSN - 1558-2531

pISSN - 0018-9294

DOI - 10.1109/tbme.2016.2560762

Subject(s) - bioengineering , computing and processing , components, circuits, devices and systems , communication, networking and broadcast technologies

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.

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