Commits · 996c02182090fb70c0c4a9c8b478d3c85862ef3f · Peter Schubert / XBanalysis · GitLab

Snippets Groups Projects

Sep 19, 2022
- gba_sflux_problem solved via ipopt using jax autograd and jit · 996c0218
  Peter Schubert authored 2 years ago
  
  996c0218
Sep 14, 2022
- gba_sflux_problem variable names aligned with gba_problem · abd06b7d
  Peter Schubert authored 2 years ago
  
  abd06b7d
- start with scaled Flux GBA, step 1: model normalization · 798da8ba
  Peter Schubert authored 2 years ago
  
  798da8ba
- in GBA_problem - density constraint with scaled density · bd0ccaeb
  Peter Schubert authored 2 years ago
  
  bd0ccaeb
Sep 09, 2022
- support unit definitions · 29170105
  Peter Schubert authored 2 years ago
  
  29170105
- support empty sboterm in reactions · 961ba3d4
  Peter Schubert authored 2 years ago
  
  961ba3d4
- reaction local parameters collect also units · 64c34134
  Peter Schubert authored 2 years ago
  
  64c34134
- support empty sboterm field · 25504b56
  Peter Schubert authored 2 years ago
  
  25504b56
- cycle free FBA implemented · 5b066c06
  Peter Schubert authored 2 years ago
  
  5b066c06
Jul 27, 2022
- version 0.3.4 - FBA and RBA refactored to sparse matrices · b573771b
  Peter Schubert authored 2 years ago
  
  b573771b
Jul 26, 2022
- FBA aligned to ModelPruner (using sparce matrices) · a250486e
  Peter Schubert authored 2 years ago
  
  a250486e
Jul 12, 2022
- Added fbc_gene_product and collect gene-product-association · 0710e3bb
  Peter Schubert authored 2 years ago
  
  0710e3bb
Jul 08, 2022
- Add package build support for sbo.owl data file · 010bef12
  Peter Schubert authored 2 years ago
  
  010bef12
- SboTerm class implemented together with branch support · 948c03e8
  Peter Schubert authored 2 years ago
  
  948c03e8
Jul 07, 2022
- implementation of RBA (resource balance analysis) · 73bac7db
  Peter Schubert authored 2 years ago
  
  73bac7db
Jul 02, 2022
- fba problem with split or reversible reactions optimized · 45ab9851
  Peter Schubert authored 2 years ago
  
  45ab9851
Jul 01, 2022
- implemented pFBA and FVA · 1dc4ede4
  Peter Schubert authored 2 years ago
  
  1dc4ede4
- Added Flux Balance Analysis (v 0.3.3) · a1b14bc7
  Peter Schubert authored 2 years ago
  
  a1b14bc7
Jun 13, 2022
- Report Density Constraint, Calculate degrees of freedom · d2d0de9d
  Peter Schubert authored 2 years ago
  
  d2d0de9d
Jun 12, 2022
- Cache last values of reaction rate related functions (v 0.3.2) · 5ee09d74
  Peter Schubert authored 2 years ago
  
  5ee09d74
Jun 11, 2022
- implement n_constraints · c8bf47ae
  Peter Schubert authored 2 years ago
  
  c8bf47ae
- Improved calculation for growth rate wrt enzyme degradations. · 90fc6f25
  Peter Schubert authored 2 years ago
  
  90fc6f25
Jun 07, 2022
- GbaIpoptProblem added (version 0.3.0) · 4908ba43
  Peter Schubert authored 2 years ago
  
  4908ba43
- OptResults added and small adjustments · 7c80ca04
  Peter Schubert authored 2 years ago
  
  7c80ca04
May 16, 2022
- protein syntheses reaction allow sboterm 589 and 205 for now. · 19dd0cff
  Peter Schubert authored 3 years ago
  
  19dd0cff
May 13, 2022
- Initial Commit · 341b1550
  Peter Schubert authored 3 years ago
  
  341b1550
- base files · 49e369f0
  Peter Schubert authored 3 years ago
  
  49e369f0
- Initial commit · 4e718317
  Peter Schubert authored 3 years ago
  
  4e718317