This README gives a short summary of the code used in my master's thesis "Mixed-Integer Optimization for Loopless Flux Distributions in Metabolic Networks".
The code for the different methods is located in /src. The code for FBA, ll-FBA and for the decomposition with combinatorial Benders' and with no-good cuts is on the main branch.
To run ll-FBA on the model e_coli_core, type the following in the julia REPL:
include("loopless_fba.jl")
loopless_fba_data("e_colicore")To solve ll-FBA on the model e_coli_core with the combinatorial Benders' decomposition, run in the REPL:
include("cuts_decomposition.jl")
combinatorial_benders_data("e_coli_core", fast=true, indicator=true, big_m=false)If fast=true, we use combinatorial Benders' cuts, otherwise, no-good-cuts will be used. With indicator=true and big_m=false, the structure of the master problem is defined. If we want to block several cycles at once, we set multiple_mis=0.5, where we block k cycles and the number k is 0.5% of the number of reactions in the model.
We provide several tests in /test including tests for FBA, ll-FBA and for the decomposition with combinatorial Benders' and with no-good cuts. To run the tests, start a session in the folder with julia --project and run the command: include("run_tests.jl").
The files to reproduce the experiments with the methods on the branch are in /experiments. The models used for the experiments are located in /molecular_models. The files for the thesis are found in /latex. Some code we did not use in the thesis is still in /not_used, including some experiments with MOMA.
| Branch | Content |
|---|---|
| enzyme_data | includes the randomized data generation for the enzyme models |
| disjunctive_programming | contains the code for the big-M reformulation and the convex-hull formulation using DisjunctiveProgramming.jl |
| intersection_cuts | contains the preliminary code for intersection cuts and the code for plots; the test file covers several tests including the implementation of an intersection cut for a simple MIP |
| plots_and_tables | contains the code for the performance plots and the code for selecting a subset of columns for the tables |
| cycle_free_flux | contains the code for blocking cycles and the code for generating the box plot |
| constraint_handler | contains the preliminary experiments with using a constraint handler for the combinatorial Benders' approach |