Path2Models: large-scale generation of computational models from biochemical pathway maps.
Path2Models: large-scale generation of computational models from biochemical pathway maps.
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DOI：
10.1186/1752-0509-7-116
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发表时间：
2013-11-01
影响因子：
--
通讯作者：
Le Novère N
中科院分区：
文献类型：
--
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
系统生物学项目和组学技术导致了越来越多的生化途径模型和重建。然而，这些模型中的大多数仍然是基于文献挖掘和路径数据的手动处理重新创建的。为了提高模型创建的效率，Path 2 Models项目使用一套免费软件从路径表示自动生成数学模型。数据来源包括KEGG、BioCarta、MetaCyc和SABIO-RK。根据源数据，提供了三种类型的模型：动力学，逻辑和基于约束的。来自2600多种生物的模型在SBML中一致编码，并通过BioModels Database（http://www.ebi.ac.uk/biomodels-main/path2models）免费提供。每个模型都包含参与者列表、它们的交互、相关的数学构造和初始参数值。大多数模型也可作为易于理解的图形SBGN地图。到目前为止，该项目已经产生了14万多个免费提供的模型。这种资源可以通过提供用于模拟和分析的初始启动模型来极大地加速数学模型的开发，这些模型可以随后进行管理和进一步参数化。
Systems biology projects and omics technologies have led to a growing number of biochemical pathway models and reconstructions. However, the majority of these models are still created de novo, based on literature mining and the manual processing of pathway data. To increase the efficiency of model creation, the Path2Models project has automatically generated mathematical models from pathway representations using a suite of freely available software. Data sources include KEGG, BioCarta, MetaCyc and SABIO-RK. Depending on the source data, three types of models are provided: kinetic, logical and constraint-based. Models from over 2 600 organisms are encoded consistently in SBML, and are made freely available through BioModels Database at http://www.ebi.ac.uk/biomodels-main/path2models. Each model contains the list of participants, their interactions, the relevant mathematical constructs, and initial parameter values. Most models are also available as easy-to-understand graphical SBGN maps. To date, the project has resulted in more than 140 000 freely available models. Such a resource can tremendously accelerate the development of mathematical models by providing initial starting models for simulation and analysis, which can be subsequently curated and further parameterized.
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影响因子：
5.8
作者：
Bornstein, Benjamin J.;Keating, Sarah M.;Hucka, Michael
通讯作者：
Hucka, Michael
影响因子：
5.8
作者：
Hucka, M;Finney, A;Wang, J
通讯作者：
Wang, J
影响因子：
2
作者：
GLASS, L;KAUFFMAN, SA
通讯作者：
KAUFFMAN, SA
影响因子：
9.5
作者：
Bernard, Thomas;Bridge, Alan;Pagni, Marco
通讯作者：
Pagni, Marco
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