Eduard Kerkhoven
Eduard Kerkhoven
### Description of the issue: In the style of [human-GEM](https://sysbiochalmers.github.io/Human-GEM-guide/), a brief tutorial showing some yeast-GEM functionality would be useful. **I hereby confirm that I have:** - [ ] Tested...
### Description of the issue: Various reactions are chemically unbalanced. Many are caused by H+, but this is not the only culprit (see list below). In some cases, the `metFormula`...
### Main improvements in this PR: Duplicate of #356, reverting the revert by #359 :) (see explanation there). The changes made in PR are based on the discussion and consensus...
### Description of the issue: Adapt https://github.com/SysBioChalmers/Human-GEM/pull/392 for native support in RAVEN. #### System information * Please report: 1. RAVEN version (stabile [release](https://github.com/SysBioChalmers/RAVEN/releases), `devel` branch?) 2. Operating system (Windows/Mac/Linux; include...
The `testing/unit_tests` folder now already includes tests for many functions (as of 5a65fe0455ac41e6cab4826981cf268a4127f057). Ideally this should cover all functions (`*.m` files, except from those in the `legacy` and `software` folders)....
RAVEN should support writing a [cobrapy](http://cobrapy.readthedocs.io/en/latest/_autogen/cobra.io.yaml.html)-compatible yaml format, as this format is very concise. - [x] make `writeYaml` function that writes a text file, and parses through the model structure....
### Description of the issue: Leveraging on the work done for [`yeast-GEM`](https://github.com/SysBioChalmers/yeast-GEM/pull/175), the contribution guidelines should be updated, to clarify the following: - [ ] when major, minor and patch...
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...
### 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...
### Main improvements in this PR: As suggested in #171 - feat: - `findMetSmiles` function for querying PubChem for SMILES using metabolite names. - DLKcat in- and output files have...