The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox is a software suite for MATLAB that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or the KEGG database, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology.
The latest stable release is RAVEN 2.11.4, maintained in SysBioChalmers/RAVEN.
This repository is where RAVEN 3 is under active development, with the upcoming 3.0.0b1 beta as its first release, targeting a final 3.0.0. RAVEN 3 is a deliberate breaking release: the codebase has been reorganized into functional folders, optional function arguments can now be passed positionally, by name, or both, external binaries and KEGG reference data are fetched on demand instead of bundled in the repository, several MATLAB toolbox dependencies were dropped, and a number of low-value or duplicate functions were removed alongside new capabilities. Until 3.0.0 is tagged, the code can still change. See the migration guide for the full list of changes for users upgrading from RAVEN 2.
For context-specific model extraction, use ftINIT; getINITModel and runINIT are the original tINIT implementation, kept for reproducing models built with it.
Installation instructions, a user guide and the API reference are published at raven-docs.
Full user documentation, including a migration guide for users upgrading from RAVEN 2 to RAVEN 3, is published at raven-docs.
If you use RAVEN in your scientific work, please cite:
Wang H, Marcišauskas S, Sánchez BJ, Domenzain I, Hermansson D, Agren R, Nielsen J, Kerkhoven EJ. (2018) RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor. PLoS Comput Biol 14(10): e1006541. doi:10.1371/journal.pcbi.1006541.
All releases are also archived in Zenodo, so you can cite the specific version of RAVEN used in your study
If you use ftINIT in your scientific work, please cite:
Gustafsson J, Anton M, Roshanzamir F, Jörnsten R, Kerkhoven EJ, Robinson JL, Nielsen J. (2023) Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data. Proc Natl Acad Sci 120(6): e2217868120. doi:10.1073/pnas.2217868120
For crediting supporting work, please cite doi:10.1002/msb.145122 (tInit); doi:10.1371/journal.pcbi.1000859 (randomsampling). For crediting RAVEN 1, cite doi:10.1371/journal.pcbi.1002980. For more details, see wiki#cite-us.
Use GitHub Discussions for support, to ask questions or leave comments.
Contributions are always welcome! Please read the Contributor guidelines to get started. RAVEN 3 development happens on the develop branch of this repository; RAVEN 2.x is maintained in SysBioChalmers/RAVEN.