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Toward community standards and software for whole-cell modeling

Waltemath, Dagmar and Karr, Jonathan R. and Bergmann, Frank T. and Chelliah, Vijayalakshmi and Hucka, Michael and Krantz, Marcus and Liebermeister, Wolfram and Mendes, Pedro and Myers, Chris J. and Pir, Pinar and Alaybeyoglu, Begum and Aranganathan, Naveen K. and Baghalian, Kambiz and Bittig, Arne T. and Burke, Paulo E. Pinto and Cantarelli, Matteo and Chew, Yin Hoon and Costa, Rafael S. and Cursons, Joseph and Czauderna, Tobias and Goldberg, Arthur P. and Gómez, Harold F. and Hahn, Jens and Hameri, Tuure and Gardiol, Daniel F. Hernandez and Kazakiewicz, Denis and Kiselev, Ilya and Knight-Schrijver, Vincent and Knuepfer, Christian and Koenig, Matthias and Lee, Daewon and Lloret-Villas, Audald and Mandrik, Nikita and Medley, J. Kyle and Moreau, Bertrand and Naderi-Meshkin, Hojjat and Palaniappan, Sucheendra K. and Priego-Espinosa, Daniel and Scharm, Martin and Sharma, Mahesh and Smallbone, Kieran and Stanford, Natalie J. and Song, Je-Hoon and Theile, Tom and Tokic, Milenko and Tomar, Namrata and Toure, Vasundra and Uhlendorf, Jannis and Varusai, Thawfeek M. and Watanabe, Leandro H. and Wendland, Florian and Wolfien, Markus and Yurkovich, James T. and Zhu, Yan and Zardilis, Argyris and Zhukova, Anna and Schreiber, Falk (2016) Toward community standards and software for whole-cell modeling. IEEE Transactions on Biomedical Engineering, 63 (10). pp. 2007-2014. ISSN 0018-9294. PMCID PMC5451320. https://resolver.caltech.edu/CaltechAUTHORS:20160714-164837343

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Abstract

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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1109/TBME.2016.2560762DOIArticle
http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=7489010PublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451320/PubMed CentralArticle
ORCID:
AuthorORCID
Waltemath, Dagmar0000-0002-5886-5563
Hucka, Michael0000-0001-9105-5960
Additional Information:© 2016 IEEE. This work is licensed under a Creative Commons Attribution 3.0 License. Manuscript received August 3, 2015; accepted April 18, 2016. Date of publication June 10, 2016; date of current version September 16, 2016. The 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.
Funders:
Funding AgencyGrant Number
Volkswagon Foundation88495
James S. McDonnell FoundationUNSPECIFIED
NSFMCB-1548123
Australian Research CouncilCE140100036
Subject Keywords:Whole-cell modeling, Systems biology, Computational biology, Simulation, Standards, Education
Issue or Number:10
PubMed Central ID:PMC5451320
Record Number:CaltechAUTHORS:20160714-164837343
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20160714-164837343
Official Citation:D. Waltemath et al., "Toward Community Standards and Software for Whole-Cell Modeling," in IEEE Transactions on Biomedical Engineering, vol. 63, no. 10, pp. 2007-2014, Oct. 2016. doi: 10.1109/TBME.2016.2560762
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:69034
Collection:CaltechAUTHORS
Deposited By: Linda Taddeo
Deposited On:15 Jul 2016 17:00
Last Modified:03 Oct 2019 10:18

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