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Cellular goal estimation
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admm
docker
tests
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README.md
setup.py

README.md

Cellgoal project

Online Resource for Estimating Cellular Goals from High-Dimensional Biological Data

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
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