Releases: opencobra/MASS-Toolbox
Updated Documentation
Minor Updates
Minor codebase updates including:
- model2escher becomes model2json
- Fixes in example data pfk and pk modules
Introducing Annotations and Pathway Attributes
Two new attributes have been added, one for MIRIAM annotations, and one for pathway visualization. These can also be imported/exported to SBML.
In addition, a new Toolbox Palette has been added to easily add Toolbox specific types. Minor bugfixes are also included in this release.
Switched back to AutomaticUnits
The M10 units package results in severe issues with computation time for large models, so the MASS Toolbox has switched back to using AutomaticUnits. Other minor bugfixes and new functions are added in this update.
Removed dependency on MathSBML
Revamped the model2sbml function which originally used MathSBML. The current version uses SBML Level 3 and also supports the FBC extension. Miriam annotations can now be imported, viewed, and exported.
Other changes in this release include the addition of more modules for the SB2 example data, and minor bug fixes.
Updates for SB2 Book
- Minor updates to functions including drawNodeMaps and getElementalMatrix.
- Capitalized all species and reactions in example data
- Added a model2escher function that creates JSON files for MASS models to be imported into Escher
Updated examples for SB2 textbook
Updated various examples for the SB2 textbook, including reordering species/reactions and adding in elemental matrices.
Also added the minspan function to find the minimal spanning vectors of a null space, and the function toMASSunits, which converts all units to Liters, Hours and Millimoles.
Updated Example Data
The example data for SB2 has been updated to reflect the order of metabolites in the textbook tables. In addition, the PFK module has been added to the example data
Elemental Matrix
Use getElementalMatrix[model] to generate the elemental matrix for the model.
Minor bug fixes
- Added Minutes to Units package
- Fixed Units context shadowing bug
- Fixed elementallyBalancedQ function