Comments (3)
stelmo
commented on May 30, 2024
1
I like the modeling/linearmodel.jl approach (but will the file names being similar confuse anyone? not sure)
More functions that need new homes:
- everything in src/analysis/fluxes.jl (maybe modeling? but these are more analysis type functions...)
- the
check_duplicate_annotationsfunctions (types/agene.jl, /areaction.jl and /ametabolite.jl) check_same_formulain types/ametabolite.jlget_atomsin types/ametabolite.jlcheck_duplicate_reactionandis_mass_balancedin types/areaction.jl
I can do all of this schnell in a PR when we decide on the folder structure.
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exaexa
commented on May 30, 2024
Possibly related to #38 (reorganizing the contents of types/ could just fix it)
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stelmo
commented on May 30, 2024
#53 addressed point (1) above
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Related Issues (20)
- Gapfilling not giving any solutions HOT 6
- Add stoichiometry to gene reaction rules HOT 3
- Sampling size parameters are not very intuitive
- Organize everything into submodules HOT 2
- Add support for ME models HOT 4
- Drop OSQP and use Clarabel instead for QPs HOT 4
- tINIT algorithm HOT 7
- Parse common attributes from notes HOT 3
- Collect package download information HOT 5
- .mat model not loading HOT 6
- Conversion from MATModel produces opaque errors if fields are missing HOT 3
- Incorrect gene reaction rule parsing HOT 7
- JSON model format incompatible with escher HOT 8
- Mapping through delimited IDs into inner models HOT 2
- `removeReaction!` etc. doesn't update all fields in a `CoreModel` HOT 1
- Pretty print model semantics HOT 2
- Check that function return types inferred in documentation make sense HOT 2
- `check_duplicate_reaction` does not consider reaction directionality HOT 2
- Implement Tables.jl interface for `ModelWithResult` HOT 1
- Document forwarding the `--project` exeflag with ClusterManagers HOT 1
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