Publikation:

Toward community standards and software for whole-cell modeling

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2016

Autor:innen

Waltemath, Dagmar
Karr, Jonathan
Bergmann, Frank
Chelliah, Vijayalakshmi
Hucka, Michael
Krantz, Marcus
Liebermeister, Wolfram
Mendes, Pedro
Zardilis, Argyris
et al.

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http://nbn-resolving.de/urn:nbn:de:bsz:352-0-346347
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https://doi.org/10.1109/TBME.2016.2560762
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CC BY 4.0

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IEEE Transactions on Biomedical Engineering. 2016, 63(10), pp. 2007-2014. ISSN 0018-9294. eISSN 1558-2531. Available under: doi: 10.1109/TBME.2016.2560762

Zusammenfassung

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.

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ISO 690WALTEMATH, 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. 2016, 63(10), pp. 2007-2014. ISSN 0018-9294. eISSN 1558-2531. Available under: doi: 10.1109/TBME.2016.2560762
BibTex
@article{Waltemath2016-10Towar-34863,
  year={2016},
  doi={10.1109/TBME.2016.2560762},
  title={Toward community standards and software for whole-cell modeling},
  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}
}
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