Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories
Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories
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DOI：
10.1021/acssynbio.7b00423
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发表时间：
2018-04-01
影响因子：
4.7
通讯作者：
Sonnenschein, Nikolaus
中科院分区：
文献类型：
--
作者：
Cardoso, Joao G. R.;Jensen, Kristian;Sonnenschein, Nikolaus
计算系统生物学方法使得能够在基因组规模上合理设计细胞工厂，从而加速细胞工程以生产有价值的化学品和蛋白质。不幸的是，大多数这些方法的实现要么没有发布，要么依赖于专有软件，要么不提供文档化的接口，这阻碍了它们在该领域的主流采用。在这项工作中，我们提出了cameo，一个独立于平台的软件，使在硅片设计的细胞工厂和目标都有经验的建模人员以及新的用户到该领域。它是用Python编写的，并实现了最先进的方法，用于枚举和优先考虑敲除，敲入，过表达和下调策略及其组合。Cameo是一个开源软件项目，在Apache许可证2.0下免费提供。可以在http://cameo.bio上找到一个专门的网站，其中包括文档、示例和安装说明。用户也可以在http://try.cameo.bio上尝试cameo。
Computational systems biology methods enable rational design of cell factories on a genome-scale and thus accelerate the engineering of cells for the production of valuable chemicals and proteins. Unfortunately, the majority of these methods' implementations are either not published, rely on proprietary software, or do not provide documented interfaces, which has precluded their mainstream adoption in the field. In this work we present cameo, a platform-independent software that enables in silico design of cell factories and targets both experienced modelers as well as users new to the field. It is written in Python and implements state-of-the-art methods for enumerating and prioritizing knockout, knock-in, overexpression, and down-regulation strategies and combinations thereof. Cameo is an open source software project and is freely available under the Apache License 2.0. A dedicated Web site including documentation, examples, and installation instructions can be found at http://cameo.bio. Users can also give cameo a try at http://try.cameo.bio.