Commits · 394d3b94098de81a32cd24987bbf909c0dcdde7b · LCSB-BioCore / COBREXA.jl

This project is mirrored from https://github.com/LCSB-BioCore/COBREXA.jl.git. Pull mirroring updated Jan 29, 2023.

25 Apr, 2021 1 commit
- move key-guessing to utils · 394d3b94
  Miroslav Kratochvil authored Apr 25, 2021
  
  394d3b94
19 Apr, 2021 39 commits
- `id` can not be represented with single models · 358547b5
  Miroslav Kratochvil authored Apr 19, 2021
  
  358547b5
- temporarily remove the functions with no tests&docs · f7ce05ce
  Miroslav Kratochvil authored Apr 19, 2021
```
(I've got backups)
```
  f7ce05ce
- change ordering so that the models are created preferably with semantic names · 7e884203
  Miroslav Kratochvil authored Apr 19, 2021
  
  7e884203
- fix the rest of the stuff · d9ff5ea0
  Miroslav Kratochvil authored Apr 19, 2021
  
  d9ff5ea0
- minor fixes · 7fc9583a
  Miroslav Kratochvil authored Apr 19, 2021
  
  7fc9583a
- balance is defaulted correctly now · 0a2d075b
  Miroslav Kratochvil authored Apr 18, 2021
  
  0a2d075b
- accomodate the JSONModel to what we have now (not much) · 5d37b353
  Miroslav Kratochvil authored Apr 19, 2021
  
  5d37b353
- added metabolic model -> JSONModel converter + small bug fixes · 34dffd23
  St. Elmo authored Apr 19, 2021
  
  34dffd23
- clean & implement some more JSON accessors · 6ecde251
  Miroslav Kratochvil authored Apr 19, 2021
  
  6ecde251
- draft · 184568fd
  Miroslav Kratochvil authored Apr 19, 2021
  
  184568fd
- test the jsonmodel conversion and interface · e2458763
  Miroslav Kratochvil authored Apr 19, 2021
  
  e2458763
- Add the constants necessary for model loading · 671f785a
  St. Elmo authored Apr 19, 2021
```
Signed-off-by: Mirek Kratochvil <exa.exa@gmail.com>
```
  671f785a
- working generic interface for JSONModel · 05f43037
  St. Elmo authored Apr 19, 2021
```
+ cylon automatic formatting changes
```
  05f43037
- implemented generic interface for JSONModel · 423d9135
  St. Elmo authored Apr 19, 2021
  
  423d9135
- started to JSONModel conversion · 217ec22a
  St. Elmo authored Apr 19, 2021
```
+ automatic formatting changes
```
  217ec22a
- working JSONModel to StandardModel convert function · 5178aa1e
  St. Elmo authored Apr 18, 2021
```
+ cylon automatic formatting changes
```
  5178aa1e
- Merge pull request #99 from LCSB-BioCore/mk-sbml-interface · c98e62ba
  Miroslav Kratochvil authored Apr 19, 2021
```
Conversion + genetics and chemical interface for SBML
```
  c98e62ba
- support n_genes · 25d7bab9
  Miroslav Kratochvil authored Apr 19, 2021
  
  25d7bab9
- Merge pull request #102 from LCSB-BioCore/mk-annotation-accessor · bd5d0a7c
  Laurent Heirendt authored Apr 19, 2021
```
add annotations
```
  bd5d0a7c
- in the end, met_id wasn't really needed · cb80b5d0
  Miroslav Kratochvil authored Apr 19, 2021
  
  cb80b5d0
- We actually need newer SBML · 6cacf30f
  Miroslav Kratochvil authored Apr 19, 2021
```
although nreleased ATM. :]
```
  6cacf30f
- add a note for the future · 5d2cd348
  Miroslav Kratochvil authored Apr 19, 2021
  
  5d2cd348
- test conversion from/to SBML · 193aee1d
  Miroslav Kratochvil authored Apr 19, 2021
  
  193aee1d
- support converting to SBMLModel · 8f8dae10
  Miroslav Kratochvil authored Apr 19, 2021
```
It would be nice if we knew how to actually _write_ the SBML model back to
disk. But that's a completely different story (and package).
```
  8f8dae10
- loosen up the dependencies · c353976a
  Miroslav Kratochvil authored Apr 19, 2021
  
  c353976a
- incomplete · 29765252
  Miroslav Kratochvil authored Apr 19, 2021
  
  29765252
- simplify chem formula parsing and unify with get_atoms · 650734e8
  Miroslav Kratochvil authored Apr 18, 2021
  
  650734e8
- balance is defaulted now · 75b51dd1
  Miroslav Kratochvil authored Apr 18, 2021
  
  75b51dd1
- skeleton of Metabolic->SBML model conversion · b8e44f72
  Miroslav Kratochvil authored Apr 18, 2021
  
  b8e44f72
- improvements · 0c31a5a8
  Miroslav Kratochvil authored Apr 18, 2021
  
  0c31a5a8
- implement the SBML accessors · d0754c8d
  Miroslav Kratochvil authored Apr 18, 2021
  
  d0754c8d
- parse gene associations correctly from SBML · 074d71b5
  Miroslav Kratochvil authored Apr 18, 2021
  
  074d71b5
- clean the types a bit · d0a208db
  Miroslav Kratochvil authored Apr 18, 2021
  
  d0a208db
- add skeleton for SBML representation of genes and chemistry · 2d29baa1
  Miroslav Kratochvil authored Apr 18, 2021
  
  2d29baa1
- add annotations · 44c13df2
  Miroslav Kratochvil authored Apr 19, 2021
  
  44c13df2
- Merge pull request #101 from LCSB-BioCore/mk-n-genes · 9e2b6ab8
  Miroslav Kratochvil authored Apr 19, 2021
```
support n_genes accessor
```
  9e2b6ab8
- support n_genes accessor · 1057a301
  Miroslav Kratochvil authored Apr 19, 2021
  
  1057a301
- Merge pull request #97 from LCSB-BioCore/mk-prepare-model-conversions · 6d782d36
  Laurent Heirendt authored Apr 19, 2021
```
Prepare accessors for genetic and chemical information
```
  6d782d36
- Merge pull request #91 from LCSB-BioCore/mk-rename-models · 85c21970
  Laurent Heirendt authored Apr 19, 2021
```
The Big Rename of LinearModel to CoreModel
```
  85c21970