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© Research
Publication : IEEE transactions on bio-medical engineering

Toward community standards and software for whole-cell modeling

Team: Bioinformatics and Biostatistics HUB
Member: Anna Zhukova
Scientific Fields
Diseases
Organisms
Applications
Technique

Published in IEEE transactions on bio-medical engineering - 10 Jun 2016

Waltemath D, Karr J, Bergmann F, Chelliah V, Hucka M, Krantz M, Liebermeister W, Mendes P, Myers C, Pir P, Alaybeyoglu B, Aranganathan N, Baghalian K, Bittig A, Burke P, Cantarelli M, Chew Y, Costa R, Cursons J, Czauderna T, Goldberg A, Gomez H, Hahn J, Hameri T, Gardiol D, Kazakiewicz D, Kiselev I, Knight-Schrijver V, Knupfer C, Konig M, Lee D, Lloret-Villas A, Mandrik N, Medley J, Moreau B, Naderi-Meshkin H, Palaniappan S, Priego-Espinosa D, Scharm M, Sharma M, Smallbone K, Stanford N, Song JH, Theile T, Tokic M, Tomar N, Toure V, Uhlendorf J, Varusai T, Watanabe L, Wendland F, Wolfien M, Yurkovich J, Zhu Y, Zardilis A, Zhukova A, Schreiber F

Link to Pubmed [PMID] – 27305665

IEEE Trans Biomed Eng 2016 Jun;

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.