Blätke Mary-Ann
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, Corrensstrasse 3, 06466 Seeland OT Gatersleben, Germany.
J Integr Bioinform. 2018 Sep 6;15(3):20180021. doi: 10.1515/jib-2018-0021.
While high-throughput technology, advanced techniques in biochemistry and molecular biology have become increasingly powerful, the coherent interpretation of experimental results in an integrative context is still a challenge. BioModelKit (BMK) approaches this challenge by offering an integrative and versatile framework for biomodel-engineering based on a modular modelling concept with the purpose: (i) to represent knowledge about molecular mechanisms by consistent executable sub-models (modules) given as Petri nets equipped with defined interfaces facilitating their reuse and recombination; (ii) to compose complex and integrative models from an ad hoc chosen set of modules including different omic and abstraction levels with the option to integrate spatial aspects; (iii) to promote the construction of alternative models by either the exchange of competing module versions or the algorithmic mutation of the composed model; and (iv) to offer concepts for (omic) data integration and integration of existing resources, and thus facilitate their reuse. BMK is accessible through a public web interface (www.biomodelkit.org), where users can interact with the modules stored in a database, and make use of the model composition features. BMK facilitates and encourages multi-scale model-driven predictions and hypotheses supporting experimental research in a multilateral exchange.
尽管高通量技术、先进的生物化学和分子生物学技术变得越来越强大，但在综合背景下对实验结果进行连贯解释仍然是一项挑战。生物模型工具包（BMK）通过提供一个基于模块化建模概念的生物模型工程综合通用框架来应对这一挑战，其目的是：（i）通过以配备定义接口的Petri网形式给出的一致可执行子模型（模块）来表示有关分子机制的知识，这些接口便于它们的重用和重组；（ii）从一组临时选择的模块（包括不同的组学和抽象层次）构建复杂的综合模型，并可选择整合空间方面的内容；（iii）通过交换竞争模块版本或对组合模型进行算法突变来促进替代模型的构建；以及（iv）提供（组学）数据集成和现有资源集成的概念，从而促进它们的重用。可通过公共网络界面（www.biomodelkit.org）访问BMK，用户可以在该界面与存储在数据库中的模块进行交互，并利用模型组合功能。BMK促进并鼓励多尺度模型驱动的预测和假设，在多边交流中支持实验研究。
