solveME: fast and reliable solution of nonlinear ME models

solveME toolbox for solving nonlinear ME models. Includes interfaces (as external modules) to the quad MINOS-based Fortran 90 code by Ding Ma and Michael A. Saunders at Stanford University

If you use solveME in a scientific publication, please cite:

Yang, L., Ma, D., Ebrahim, A., Lloyd, C. J., Saunders, M. A., & Palsson, B. O. (2016). solveME: fast and reliable solution of nonlinear ME models. BMC Bioinformatics, 17(1), 391. doi:10.1186/s12859-016-1240-1

and the following for the Quad MINOS solver:

Ma, D., Yang, L., Fleming, R.M.T., Thiele, I., Palsson, B.O., Saunders, M.A. (2017). Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression. Scientific Reports, 7, 40863. doi:10.1038/srep40863

Author: Laurence Yang

Systems Biology Research Group, UCSD

Requirements

1. Python
   • tested on Python 2.7 and 3.6
2. cobrapy
   • tested on 0.5.11
   • not yet fully compatible with cobrapy 0.6 release
3. cobrame (0.0.7): follow Installation instructions here: https://github.com/SBRG/cobrame
   • git clone --branch v0.0.7 https://github.com/SBRG/cobrame.git
4. gfortran (>=4.6)
   • (Ubuntu) sudo apt-get install gfortran
   • (Arch) sudo pacman -S gcc-fortran
5. quadMINOS (available for academic use from Prof. Michael A. Saunders at Stanford University)

Installation

1. Compile quadMINOS

   • copy Makefile.defs into quadLP_root/minos56/ and quadLP_root/qminos56/
     • this step ensures the compiler flags needed to interface with Python are set
   • cd qminos_root
   • cd minos56; make clean; make
   • cd ..
   • cd qminos56; make clean; make

2. Copy shared libraries to solveme root directory

   • cd [solveme_root]
   • cp [qminos_root]/qminos56/lib/libquadminos.a ./
   • cp [qminos_root]/minos56/lib/libminos.a ./

3. Run: python setup.py develop

   • or python setup.py develop --user
   • or sudo python setup.py develop to install for all users
     • (if getting an error, [undefined reference to main], try sudo python setup.py develop)

4. Special NERSC installation steps

   • (shell) module swap PrgEnv-intel PrgEnv-gnu
   • python setup.py config_fc --f90exec=ftn develop --user
     • (need to use the ftn gfortran Cray wrapper, or else get symbol not found error during import)

5. Troubleshooting common errors

   1. ImportError: .../solveME/solvemepy/qminospy/qwarmLP.so: symbol _gfortran_transfer_real128_write, version GFORTRAN_1.4 not defined in file libgfortran.so.3 with link time reference
      • Problem: setup.py picked up the wrong libgfortran during installation. Typically, if anaconda is installed, an older version is installed, which seems to be used by default.
      • Solution (workaround): pre-load the desired libgfortran version, bypassing the anaconda one:
        • export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libgfortran.so.3
        • (then, proceed with setup) python setup.py develop --user
      • Link to original solution

Use qminos to solve ME models in python

For (reduced) ME models prior prototype 44

1. Import qminospy to access the solver methods:

from qminospy.me2 import ME_NLP
me_nlp = ME_NLP(me)
# Solve directly using LCL (linearly constrained Lagrangian) NLP method
x,stat,hs = me_nlp.solvenlp()
# Access the solution that is saved in the original minime object
sol = me.solution
sol.f
sol.x_dict

24 Feb 2016: for ME models after prototype 44

1. Import

py to access the solver methods:

from qminospy.me1 import ME_NLP1
# The object containing solveME methods--composite that uses a ME model object 
# Provide growth_key = 'mu' for minime models,
me_nlp = ME_NLP1(me, growth_key='mu')
# Use bisection for now (until the NLP formulation is worked out for the new prototype 44
muopt, hs, xopt, cache = me_nlp.bisectmu(precision=1e-6)    
# Access the solution that is saved in the original minime object
sol = me.solution
sol.f
sol.x_dict

If your ME model is based on ME 1.0 code (iOL1650, iJL1678):

1. Same as above but use growth_key='growth_rate_in_per_hour'

from qminospy.me1 import ME_NLP1
# The object containing solveME methods--composite that uses a ME model object 
me_nlp = ME_NLP1(me, growth_key='growth_rate_in_per_hour')
# Bisection
muopt, hs, xopt, cache = me_nlp.bisectmu(precision=1e-3)    
# Access the solution that is saved in the original minime object
sol = me.solution
sol.f
sol.x_dict

Use qminos to solve LP problems in quad-precision:

See the notebook: examples/test_quadLP.ipynb