SBML Level 3: an extensible format for the exchange and reuse of biological models.
SBML Level 3: an extensible format for the exchange and reuse of biological models.
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DOI：
10.15252/msb.20199110
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发表时间：
2020-08
影响因子：
9.9
通讯作者：
SBML Level 3 Community members
中科院分区：
文献类型：
--
作者：
Keating SM;Waltemath D;König M;Zhang F;Dräger A;Chaouiya C;Bergmann FT;Finney A;Gillespie CS;Helikar T;Hoops S;Malik-Sheriff RS;Moodie SL;Moraru II;Myers CJ;Naldi A;Olivier BG;Sahle S;Schaff JC;Smith LP;Swat MJ;Thieffry D;Watanabe L;Wilkinson DJ;Blinov ML;Begley K;Faeder JR;Gómez HF;Hamm TM;Inagaki Y;Liebermeister W;Lister AL;Lucio D;Mjolsness E;Proctor CJ;Raman K;Rodriguez N;Shaffer CA;Shapiro BE;Stelling J;Swainston N;Tanimura N;Wagner J;Meier-Schellersheim M;Sauro HM;Palsson B;Bolouri H;Kitano H;Funahashi A;Hermjakob H;Doyle JC;Hucka M;SBML Level 3 Community members
系统生物学在计算模型的数量、规模和复杂性方面经历了戏剧性的增长。为了重现仿真结果和重用模型，研究人员必须交换明确的模型描述。我们回顾了最新版本的系统生物学标记语言（SBML），为此目的而设计的格式。在过去的十年中，建模者和软件作者社区开发了SBML Level 3。它的模块化形式包括一个适合表示基于反应的模型的核心和一个扩展核心的软件包，这些软件包具有适合其他模型类型的功能，包括基于约束的模型，反应扩散模型，逻辑网络模型和基于规则的模型。该格式利用了20年的SBML和丰富的软件生态系统，改变了系统生物学家构建模型和与模型交互的方式。最近，全细胞和器官的多尺度模型的兴起，以及单细胞测量和实时成像等新数据源，促成了将数据与模型集成的新方法。我们就这些发展所带来的挑战以及SBML Level 3如何提供支持这一发展所需的基础提供了我们的观点。在过去的二十年里，来自不同领域的科学家一直在开发SBML，这是一种用于编码生物学和医学计算模型的标准格式。本文总结了最近的进展，并对新出现的挑战提出了看法。
Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction‐based models and packages that extend the core with features suited to other model types including constraint‐based models, reaction‐diffusion models, logical network models, and rule‐based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single‐cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution. Over the past two decades, scientists from different fields have been developing SBML, a standard format for encoding computational models in biology and medicine. This article summarizes recent progress and gives perspectives on emerging challenges.
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影响因子：
14.9
作者：
Caspi R;Billington R;Ferrer L;Foerster H;Fulcher CA;Keseler IM;Kothari A;Krummenacker M;Latendresse M;Mueller LA;Ong Q;Paley S;Subhraveti P;Weaver DS;Karp PD
通讯作者：
Karp PD
影响因子：
--
作者：
Büchel F;Rodriguez N;Swainston N;Wrzodek C;Czauderna T;Keller R;Mittag F;Schubert M;Glont M;Golebiewski M;van Iersel M;Keating S;Rall M;Wybrow M;Hermjakob H;Hucka M;Kell DB;Müller W;Mendes P;Zell A;Chaouiya C;Saez-Rodriguez J;Schreiber F;Laibe C;Dräger A;Le Novère N
通讯作者：
Le Novère N
影响因子：
3
作者：
Bergmann FT;Adams R;Moodie S;Cooper J;Glont M;Golebiewski M;Hucka M;Laibe C;Miller AK;Nickerson DP;Olivier BG;Rodriguez N;Sauro HM;Scharm M;Soiland-Reyes S;Waltemath D;Yvon F;Le Novère N
通讯作者：
Le Novère N
影响因子：
5.8
作者：
Bornstein, Benjamin J.;Keating, Sarah M.;Hucka, Michael
通讯作者：
Hucka, Michael
DOI：
10.1007/978-1-4419-5797-9_7
发表时间：
2010-01-01
期刊：
SYSTEMS BIOLOGY FOR SIGNALING NETWORKS
影响因子：
--
作者：
Draeger, Andreas;Schroeder, Adrian;Zell, Andreas
通讯作者：
Zell, Andreas