CatReNet：（自动）催化反应网络的交互式分析。

CatReNet: interactive analysis of (auto-) catalytic reaction networks.

机构信息

Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076 Tübingen, Germany.

Department of Chemistry, Imperial College, London SW7 2BX, United Kingdom.

出版信息

Bioinformatics. 2024 Aug 2;40(8). doi: 10.1093/bioinformatics/btae515.

DOI:10.1093/bioinformatics/btae515

PMID:39163485

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11361791/

Abstract

SUMMARY

Catalytic reaction networks serve as fundamental models for understanding biochemical systems. CatReNet is a novel software designed to facilitate interactive analysis of such networks. It offers fast and exact algorithms for computing various types of self-sustaining autocatalytic subnetworks, including so-called CAFs (constructively autocatalytic food-generated networks), RAFs (reflexively autocatalytic food-generated networks), and pseudo-RAFs. It provides dynamic visualizations to aid exploration and understanding.

AVAILABILITY AND IMPLEMENTATION

This open-source Java application runs on Linux, MacOS, and Windows. It is available at https://github.com/husonlab/catrenet under a GPL3 license.

摘要

催化反应网络是理解生化系统的基本模型。CatReNet 是一款新软件，旨在方便对这类网络进行交互式分析。它提供了用于计算各种自维持自催化子网的快速精确算法，包括所谓的 CAFs（建设性自催化食物生成网络）、RAFs（反射性自催化食物生成网络）和伪 RAFs。它还提供动态可视化功能，以帮助探索和理解。