RAVEN

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feat: align RAVEN and COBRA model fields

18

There are many benefits in having RAVEN functioning as submodule of the [COBRA toolbox](https://github.com/opencobra/cobratoolbox). While RAVEN 2.0 is largely compatible with COBRA through use of the `ravenCobraWrapper` function and using...

edkerk

feat: support for metSmiles field

1

### Main improvements in this PR: - feat: - support in various functions for a `model.metSmiles`, which contains SMILES for each metabolite. Note: SBML currently does not have a dedicated...

edkerk

fix: various minor fixes

1

### Main improvements in this PR: - fix: - `simplifyModel` with irreversible backwards-only reactions (solves #529) - `writeYAMLmodel` do not write lines with empty entries (e.g. reactions without subsystems) -...

edkerk

fix: add "G_" prefix when exporting model to SBML

1

### Main improvements in this PR: - Fix: - `exportModel` now adds the "G_" prefix to gene IDs. It is needed for the genes which begin with numeral chars **I...

simas232

Error in getModelFromHomology function

3

### Description of the issue: An existing function, "getModelFromHomology," is not working. I am attempting to create a draft metabolic model of Plasmodium vivax. I have conducted BLAST searches on...

SANDRA-ui-rgp

### Description of the issue: Reactions that are defined backwards-only (so lb - [x] Checked that a similar issue does not [already exist](https://github.com/SysBioChalmers/RAVEN/issues?q=is%3Aissue) or is already [discussed](https://github.com/SysBioChalmers/RAVEN/discussions).

edkerk

### Description of the issue: Hi everyone, I have this issue on exporting models to Excel format. Systems Biology Ontology (SBO) terms are not properly handled in the `exportToExcelFormat()` function,...

pranasag