Centre of Biological Engineering, University of Minho, Braga, Portugal.
Bioinformatics. 2019 Dec 15;35(24):5361-5362. doi: 10.1093/bioinformatics/btz598.
CoBAMP is a modular framework for the enumeration of pathway analysis concepts, such as elementary flux modes (EFM) and minimal cut sets in genome-scale constraint-based models (CBMs) of metabolism. It currently includes the K-shortest EFM algorithm and facilitates integration with other frameworks involving reading, manipulation and analysis of CBMs.
The software is implemented in Python 3, supported on most operating systems and requires a mixed-integer linear programming optimizer supported by the optlang framework. Source-code is available at https://github.com/BioSystemsUM/cobamp.
CoBAMP 是一个用于枚举通路分析概念的模块化框架，例如基因组规模约束基模型（CBM）中的基本通量模式（EFM）和最小割集。它目前包括 K-最短 EFM 算法，并便于与其他涉及读取、操作和分析 CBM 的框架集成。
该软件是用 Python 3 实现的，支持大多数操作系统，并需要由 optlang 框架支持的混合整数线性规划优化器。源代码可在 https://github.com/BioSystemsUM/cobamp 上获得。
