v2.0.2

Main improvements in this release:

• fix:
  • getKEGGModelFromOrganism checks that fastaFile and outDir are provided as string (#146)
  • order of MIRIAM annotations in ravenCobraWrapper, and removed duplicate metSBOterms field (PR #148)
• feat:
  • alternative input for addRxns and changeRxns, using arrays of metabolites and stoichiometric coefficients (PR #147)
• doc:
  • getModelFromKEGG include note on use of generic KEGG model for use in gap-filling (PR #149)

v2.0.1

Main improvements in this release:

Solves #108 #110 #119 #120 #121 #125 #127 #128 #132

• various bugfixes
• ravenCobraWrapper supports more annotations
• libSBML 5.17 is preferred, due to significant speed improvement
• improved documentation of various functions
• deepLoc output supported in localization prediction
• new reconstruction tutorial
• include changelog of pre-GitHub development

v2.0.0

As detailed in "Wang H et al. (2018) bioRxiv doi:10.1101/321067"

Main improvements in this release:

• fix generation of folders by exportForGit
• fix dealing with grRules in model I/O
• rename addGenes to addGenesRaven for full cobra-compatibility
• remove version.txt from devel branch, only master branch has numbered releases

v2.0.0-rc.2

Release candidate 2

Various changes, including:

• updated YAML export functionality compatible with cobrapy
• new standardizeGrRules function
• Java library addition is dynamic instead of static
• rxnConfidenceScores are now of type double, consistent with cobra
• support for multiple subSystems
• progress indicator for randomSampling
• numerous bug fixes

v2.0.0-rc.1.1

Release candidate 1.1

v2.0.0-rc.1

Release candidate 1.

v2.0.0-alpha

First alpha release of RAVEN2, with many improvements, including but not limited to solvers, SBML and Excel IO, KEGG reconstruction etc.

v1.9.1

This release of RAVEN includes major changes in import/export handling, SBML L3V1 FBCv2, KEGG model reconstruction, among others. This is a pre-release, to be used at the MESB advanced course. Installation instructions can be found in the install.txt file or on the official Github page.

v1.9.0

This release of RAVEN includes support for the Gurobi optimizer. Later minor releases will include support for the glpk optimizer and an update of the sbml file formats. Installation instructions can be found in the install.txt file or on the official Github page.

v1.8.0

This is the first release of RAVEN on Github with a change to the versioning system and corresponds to the earlier RAVEN v1.08. Installation instructions can be found in the install.txt file.