Proteus: a web-based, context-specific modelling tool for molecular networks.
Proteus: a web-based, context-specific modelling tool for molecular networks.
复制标题
Proteus：一种基于网络的、针对特定上下文的分子网络建模工具。
DOI：
10.1093/bioinformatics/bts126
复制
发表时间：
2012
期刊：
影响因子：
--
通讯作者：
Gunawardena,Jeremy
中科院分区：
文献类型：
--
作者：
Gnad,Florian;Estrada,Javier;Gunawardena,Jeremy
分子网络通常在不同的细胞或实验环境中进行研究，具有高度特定的细节。建模引入了关于数学描述层次的进一步选择。由此产生的可能性很难迅速探索，阻碍了建模和实验的整合。我们已经开发了Proteus，一个基于网络的，特定于上下文的工具，用于构建划分的常微分方程（ODE）模型。它的灵感来自于Ca 2+信号传导的分子“工具箱”的想法。Proteus中的工具箱是生物系统作为组件集的上下文无关的表示，这些组件可能对应于不同复杂程度的机制。用户从工具箱中挑选组件，对于每个组件，从不同的机制中挑选，每个机制描述组件机制的不同实例化。Proteus将这些选择组合成ODE系统，然后可以以SBML（系统生物学标记语言），Matlab或Fortran格式下载并独立分析。工具包，组件和机制是用户可构建的，无论是通过蚕食现有模型，包括Biomodels数据库中的所有模型。可用性和实施：Proteus，在C#中实现，以及用于模拟钙信号的原型工具包可以在www.modularmodeling.com上免费和普遍地获得联系人：gnad.florian@ gene.com;哈佛补充信息：补充数据可以在Bioinformaticsonline上获得。
Summary:Molecular networks are often studied in diverse cellular or experimental contexts, with highly context-specific details. Modelling introduces further choices as to levels of mathematical description. The resulting possibilities are difficult to explore rapidly, hampering the integration of modelling and experiment. We have developed Proteus, a web-based, context-specific tool for building compartmentalized, ordinary differential equation (ODE) models. It is inspired by the idea of a molecular ‘toolkit’ for Ca2+signalling.Toolkitsin Proteus are context-independent representations of biological systems as sets ofcomponents, which may correspond to mechanisms of differing levels of complexity. Users pick and choose components from a toolkit and, for each component, pick and choose from differentmechanisms, each of which describes a different instantiation of the component's mechanism. Proteus combines these choices into a system of ODEs, which may then be downloaded in SBML (Systems Biology Markup Language), Matlab or Fortran format and independently analyzed. Toolkits, components and mechanisms are user-constructible, eitherde novoor by cannibalizing existing models, including all those in the Biomodels database. A wide variety of context-specific models may thereby be rapidly built, modified and explored.Availability and implementation:Proteus, implemented in C#, and a prototype toolkit for modelling calcium signalling are freely and universally available at www.modularmodeling.comContact:gnad.florian@gene.com; jeremy@hms.harvard.eduSupplementary information:Supplementary data are available atBioinformaticsonline.