A Metabolic Reaction Balancing Web Service for Computational Systems Biology
A Metabolic Reaction Balancing Web Service for Computational Systems Biology
复制标题
计算系统生物学的代谢反应平衡 Web 服务
DOI：
10.1101/187328
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发表时间：
2017
期刊：
影响因子：
--
通讯作者：
Dobson P
中科院分区：
文献类型：
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作者：
Dobson P
背景在代谢网络重建中，反应的化学计量平衡对于创建现实的基于约束的模型至关重要。在基因组规模上，平衡是一项重复性任务，会消耗可以部署在其他地方的宝贵资源。自动反应平衡是可能的，并且可能在计算系统生物学中有用，但适当代码的广泛使用受到该领域使用的不可互操作编程语言的多样性的限制。 RESTful Web 服务提供了一种与语言无关的将服务绑定在一起的方法。结果反应平衡可以作为混合整数线性规划问题来识别化学计量系数并推断通常缺失的组件。此功能已公开为 Web 服务，该服务使用 JSON 或 SBML 形式的反应列表。反应平衡 Web 服务已部署在 http://www.nactem.ac.uk/balancer。代码可通过 Github 获取。通过演示，该服务已应用于中国仓鼠卵巢细胞代谢重建，使另外 219 个反应达到平衡。 结论 由于缺乏特定于语言的绑定，大多数系统生物学软件无法访问现有的自动反应平衡工具。 Web 服务通过使用广泛使用的 Web 通信协议来桥接不同的语言，这意味着一种绑定适用于几乎所有语言。现在，任何系统生物学软件都可以通过 RESTful Web 服务使用自动反应平衡。
BackgroundIn metabolic network reconstruction the stoichiometric balancing of reactions is essential to create realistic constraint-based models. At the genome scale, balancing is a repetitive task that consumes valuable curator resource that could be deployed elsewhere. Automatic reaction balancing is possible and could be useful across computational systems biology, but widespread use of the appropriate code has been limited by the diversity of non-interoperable programming languages used in the field. RESTful web services offer a language-agnostic way of binding services together.ResultsReaction balancing can be posed as a mixed integer linear programming problem to identify stoichiometric coefficients and infer commonly missing components. This functionality has been exposed as a web service that consumes a list of reactions as JSON or SBML. The reaction balancing web service has been deployed at http://www.nactem.ac.uk/balancer. Code is available via Github. By way of demonstration the service has been applied to a Chinese hamster ovary cell metabolic reconstruction to bring a further 219 reactions into balance.ConclusionsThe majority of systems biology software cannot access existing automatic reaction balancing tools due to a lack of language-specific bindings. Web services bridge different languages by using widely-spoken web communication protocols, meaning that one binding works for almost all languages. Automatic reaction balancing can now be consumed by any systems biology software via a RESTful web service.
构建系统生物学中交互式数据探索的应用程序
DOI：
--
发表时间：
2017
期刊：
bioRxiv
影响因子：
--
作者：
Bjørn Fjukstad;V. Dumeaux;K. Olsen;Michael Hallet;E. Lund;L. A. Bongo
通讯作者：
L. A. Bongo
影响因子：
9.3
作者：
Hefzi H;Ang KS;Hanscho M;Bordbar A;Ruckerbauer D;Lakshmanan M;Orellana CA;Baycin-Hizal D;Huang Y;Ley D;Martinez VS;Kyriakopoulos S;Jiménez NE;Zielinski DC;Quek LE;Wulff T;Arnsdorf J;Li S;Lee JS;Paglia G;Loira N;Spahn PN;Pedersen LE;Gutierrez JM;King ZA;Lund AM;Nagarajan H;Thomas A;Abdel-Haleem AM;Zanghellini J;Kildegaard HF;Voldborg BG;Gerdtzen ZP;Betenbaugh MJ;Palsson BO;Andersen MR;Nielsen LK;Borth N;Lee DY;Lewis NE
通讯作者：
Lewis NE