Schäuble Sascha, Stavrum Anne-Kristin, Bockwoldt Mathias, Puntervoll Pål, Heiland Ines
Jena University Language & Information Engineering (JULIE) Lab, Friedrich-Schiller-University Jena, Jena, Germany.
Department of Informatics, University of Bergen, Bergen, Norway.
BMC Bioinformatics. 2017 Jun 24;18(1):314. doi: 10.1186/s12859-017-1722-9.
Systems Biology Markup Language (SBML) is the standard model representation and description language in systems biology. Enriching and analysing systems biology models by integrating the multitude of available data, increases the predictive power of these models. This may be a daunting task, which commonly requires bioinformatic competence and scripting.
We present SBMLmod, a Python-based web application and service, that automates integration of high throughput data into SBML models. Subsequent steady state analysis is readily accessible via the web service COPASIWS. We illustrate the utility of SBMLmod by integrating gene expression data from different healthy tissues as well as from a cancer dataset into a previously published model of mammalian tryptophan metabolism.
SBMLmod is a user-friendly platform for model modification and simulation. The web application is available at http://sbmlmod.uit.no , whereas the WSDL definition file for the web service is accessible via http://sbmlmod.uit.no/SBMLmod.wsdl . Furthermore, the entire package can be downloaded from https://github.com/MolecularBioinformatics/sbml-mod-ws . We envision that SBMLmod will make automated model modification and simulation available to a broader research community.
系统生物学标记语言（SBML）是系统生物学中的标准模型表示和描述语言。通过整合大量可用数据来丰富和分析系统生物学模型，可以提高这些模型的预测能力。这可能是一项艰巨的任务，通常需要生物信息学能力和脚本编写。
我们展示了SBMLmod，一个基于Python的Web应用程序和服务，它可以自动将高通量数据集成到SBML模型中。随后的稳态分析可以通过Web服务COPASIWS轻松访问。我们通过将来自不同健康组织以及癌症数据集的基因表达数据集成到先前发表的哺乳动物色氨酸代谢模型中，来说明SBMLmod的实用性。
SBMLmod是一个用于模型修改和模拟的用户友好平台。该Web应用程序可在http://sbmlmod.uit.no上获得，而Web服务的WSDL定义文件可通过http://sbmlmod.uit.no/SBMLmod.wsdl访问。此外，整个包可以从https://github.com/MolecularBioinformatics/sbml-mod-ws下载。我们设想SBMLmod将使更广泛的研究社区能够进行自动模型修改和模拟。
