RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

Abstract

Here a new release of the RAVEN toolbox (for Reconstruction, Analysis and Visualization of mEtabolic Networks) is presented. Its main new features are its redefined pipeline, now constructed around the KEGG and MetaCyc databases, and improved performance/compatibility with the COBRA toolbox. I was mainly involved in the latter feature, working in achieving proper conversion between RAVEN & COBRA model structures. The ease of use of RAVEN is exemplified with the de novo reconstruction of Sco4, a GEM of the antibiotic-producing bacterium Streptomyces coelicolor.

Benjamín J. Sánchez

Senior Scientist

Biology, math, programming, running, and many other fun things