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Created with Raphaël 2.2.05Oct23Sep1914927Jul2612872113Jun1211716May13gba_stoic_problem solved via ipopt using jax autograd and jitmainmaingba_stoic_problem solved via ipopt using jax autograd and jitgba_sflux_problem solved via ipopt using jax autograd and jitgba_sflux_problem variable names aligned with gba_problemstart with scaled Flux GBA, step 1: model normalizationin GBA_problem - density constraint with scaled densitysupport unit definitionssupport empty sboterm in reactionsreaction local parameters collect also unitssupport empty sboterm fieldcycle free FBA implementedversion 0.3.4 - FBA and RBA refactored to sparse matricesFBA aligned to ModelPruner (using sparce matrices)Added fbc_gene_product and collect gene-product-associationAdd package build support for sbo.owl data fileSboTerm class implemented together with branch supportimplementation of RBA (resource balance analysis)fba problem with split or reversible reactions optimizedimplemented pFBA and FVAAdded Flux Balance Analysis (v 0.3.3)Report Density Constraint, Calculate degrees of freedomCache last values of reaction rate related functions (v 0.3.2)implement n_constraintsImproved calculation for growth rate wrt enzyme degradations.GbaIpoptProblem added (version 0.3.0)OptResults added and small adjustmentsprotein syntheses reaction allow sboterm 589 and 205 for now.Initial Commitbase filesInitial commit