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Peter Schubert
XBanalysis
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73bac7dbf2d0e7ffd15c12b4099d177dad0f1500
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Created with Raphaël 2.2.0
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gba_stoic_problem solved via ipopt using jax autograd and jit
main
main
gba_stoic_problem solved via ipopt using jax autograd and jit
gba_sflux_problem solved via ipopt using jax autograd and jit
gba_sflux_problem variable names aligned with gba_problem
start with scaled Flux GBA, step 1: model normalization
in GBA_problem - density constraint with scaled density
support unit definitions
support empty sboterm in reactions
reaction local parameters collect also units
support empty sboterm field
cycle free FBA implemented
version 0.3.4 - FBA and RBA refactored to sparse matrices
FBA aligned to ModelPruner (using sparce matrices)
Added fbc_gene_product and collect gene-product-association
Add package build support for sbo.owl data file
SboTerm class implemented together with branch support
implementation of RBA (resource balance analysis)
fba problem with split or reversible reactions optimized
implemented pFBA and FVA
Added Flux Balance Analysis (v 0.3.3)
Report Density Constraint, Calculate degrees of freedom
Cache last values of reaction rate related functions (v 0.3.2)
implement n_constraints
Improved calculation for growth rate wrt enzyme degradations.
GbaIpoptProblem added (version 0.3.0)
OptResults added and small adjustments
protein syntheses reaction allow sboterm 589 and 205 for now.
Initial Commit
base files
Initial commit
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