Cellgoal project

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

Requirements for ADMM solver

1. Fortran compiler.
   • tested on PGI 18.4 and 18.10: required for OpenACC-based parallelization
   • tested on gfortran 8.2.0
2. cmake
3. make
4. Linear solver:
   1. umfpack: provided by suitesparse package in Linux
   2. MA57: please obtain from www.hsl.rl.ac.uk/catalogue/ma57.html

Requirements to run test suite

1. Python >= 2.7
2. cobrapy
   • to load metabolic models
   • to generate synthetic fluxes
   • to validate the estimated goal reaction

Installation

1. Install MA57 linear solver
   1. it needs metis-4, not metis-5 that is commonly in package managers. Get metis-4.0.3 from Karypis lab.

ADMM solver

1. cd admm
2. mkdir build
3. cd build
4. cmake ..
5. make

Test suite

1. python setup.py develop