psamm
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zhanglab
Curation and analysis of metabolic models
- [ ] Tests. - [x] Option to select condition when there are multiple. - [ ] Documentation. - [ ] References to correct papers.
This is one attempt at finding an alternative implementation of GapFind that works correctly on larger models instead of marking almost all compounds blocked. Does not depend on v_max, instead...
Adds properties to `NativeModel` to make it look more like the model representation in psamm-import. Then, copies over code from psamm-import which can now be applied to `NativeModel`.
Add specialized `argparse` type for reaction references. This type guards against using non-existing ID since the actual ID string can only be obtained (through `resolve()`) if the reaction is defined...
Currently, the code that is responsible for writing YAML model files is embedded in psamm-import. This means that API users will have to copy this code from psamm-import or reimplement...
It was proposed that additional features should be allowed in the medium table format. Currently the medium table format consists of 4 column (2 required, 2 optional), specifying compound ID,...
Currently the gene associations are interleaved with the reaction database. This makes it hard to use shared reaction databases for different organisms. @keitht547 suggested moving the gene associations from the...
When solving the LP10 problem in Fastcore with GLPK, the objective becomes very small so that GLPK seems to consider it equal to zero. It may be possible to solve...