Multiscale Systems Biology Collaboration
In silico models
- 78 M models from BiGG
JSON data files for 78 Flux Balance Analysis models (LP problems)
from the BiGG database.
Python code to apply Double MINOS and Quad MINOS to these models
is here:
quadLPpy.zip.
- 83 FBA models
MPS data files for 83 Flux Balance Analysis models (LP problems)
corresponding to 83 Matlab structures in a file “all_models.mat” generated
by running the following notebook written by Ali Ebrahim, UC San Diego:
load_models.ipynb.
The MPS files were generated by these Matlab scripts:
dumpMPS2.m and dumpMPS2all.m.
- quadLP data
MPS data files for 14 multiscale LP models used in this paper:
D. Ma, L. Yang, R. M. T. Fleming, I. Thiele, B. O. Palsson and M. A. Saunders,
Reliable and efficient solution of genome-scale models of
Metabolism and macromolecular Expression,
Sci. Rep. 7, Article number: 40863 (2017); doi:10.1038/srep40863.
- openCOBRA toolbox
COnstraints Based Reconstruction and Analysis toolbox for MATLAB.
- BiGG Database, Systems Biology Research Group,
University of California, San Diego
- Molecular Systems Physiology Group,
University of Luxembourg (Dr Ines Thiele)
Algorithm NCL for nonlinearly constrained optimization
- Optimal taxation policy
AMPL scripts, documentation, and results for solving Optimal Taxation problems
with many nonlinear constraints that don't satisfy the LICQ.
Algorithm NCL generates a sequence of nonlinearly constrained
augmented Lagrangian subproblems analogous to the bound constrained subproblems
generated by LANCELOT. The taxation problem and Algorithm NCL are modeled
in AMPL and solved by the interior method IPOPT.
The files here illustrate how Algorithm NCL can be implemented in a
high-level language when first and derivatives of the problem objective
and constraints are available via that language (as in AMPL and GAMS).
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