Toward Community Standards and Software for Whole-Cell Modeling.
Toward Community Standards and Software for Whole-Cell Modeling.
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DOI：
10.1109/tbme.2016.2560762
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发表时间：
2016-10
期刊：
影响因子：
--
通讯作者：
Schreiber F
中科院分区：
文献类型：
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作者：
Waltemath D;Karr JR;Bergmann FT;Chelliah V;Hucka M;Krantz M;Liebermeister W;Mendes P;Myers CJ;Pir P;Alaybeyoglu B;Aranganathan NK;Baghalian K;Bittig AT;Burke PE;Cantarelli M;Chew YH;Costa RS;Cursons J;Czauderna T;Goldberg AP;Gomez HF;Hahn J;Hameri T;Gardiol DF;Kazakiewicz D;Kiselev I;Knight-Schrijver V;Knupfer C;Konig M;Lee D;Lloret-Villas A;Mandrik N;Medley JK;Moreau B;Naderi-Meshkin H;Palaniappan SK;Priego-Espinosa D;Scharm M;Sharma M;Smallbone K;Stanford NJ;Song JH;Theile T;Tokic M;Tomar N;Toure V;Uhlendorf J;Varusai TM;Watanabe LH;Wendland F;Wolfien M;Yurkovich JT;Zhu Y;Zardilis A;Zhukova A;Schreiber F
全细胞（WC）建模在生物研究、生物工程和医学领域是一种很有前途的工具。然而，要建立精确、全面的复杂细胞模型，还有大量的工作要做。我们组织了2015年全细胞建模暑期学校，通过在SBML中重新编码最近发布的WC模型，教授WC建模，并评估新的WC建模标准和软件的需求。我们的分析揭示了使用当前标准表示WC模型的几个挑战。因此，我们提出了几个新的WC建模标准、软件和数据库。我们预计这些新的标准和软件将使更全面的模型成为可能。
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. 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. Our analysis revealed several challenges to representing WC models using the current standards. We, therefore, propose several new WC modeling standards, software, and databases. We anticipate that these new standards and software will enable more comprehensive models.