Online Resource for:
L Yang, MA Saunders, JC Lachance, BO Palsson, J Bento (2019). Estimating Cellular Goals from High-Dimensional Biological Data. In The 25th ACM SIGKDD Conference on Knowledge Discovery and Data Mining pp. 2202-2211 | arXiv :1807.04245
- Fortran compiler.
- tested on PGI 18.4 and 18.10: required for OpenACC-based parallelization
- tested on gfortran 8.2.0
- cmake
- make
- Linear solver:
- umfpack: provided by suitesparse package in Linux
- MA57: please obtain from www.hsl.rl.ac.uk/catalogue/ma57.html
- Python >= 2.7
- cobrapy
- to load metabolic models
- to generate synthetic fluxes
- to validate the estimated goal reaction
- Install MA57 linear solver
- it needs metis-4, not metis-5 that is commonly in package managers. Get metis-4.0.3 from Karypis lab.
- cd admm
- mkdir build
- cd build
- cmake ..
- make
- python setup.py develop