Algorithmic and Complexity Results for Decompositions
of Biological Networks into Monotone Subsystems
Supplementary Material: Matlab Implementation Files
This link provides a zip file which unpacks to directory (folder) containing all programs. The subdirectory is named dasgupta_enciso_sontag_zhang_programs_directory.
The files in this directory are Matlab functions and scripts in .m format.
They can be opened using any text editor, and each contains descriptions regarding its purpose and use.
Two useful packages to be used when running these functions are:
The Systems Biology Toolbox for Matlab, which allows for networks in SBML format to be imported into the Matlab environment. This toolbox also allows for processing of the Matlab structures as well as the creation of SBML format files from Matlab structures. It can be downloaded at http://sbml.org/.
The SeDuMi Optimization Toolbox, one of the most popular implementations of the SDP algorithm for Matlab. It is freely available for downloaded from http://sedumi.mcmaster.ca/.
The most important functions in this directory are listed below.
ReactionDigraph.m: this function receives a model in SBML format and produces the associated reaction digraph associated to the reaction.
RepeatPartition.m: this function produces a partition p which optimizes the number of consistent edges of a given signed digraph G. It implements the SDP-based ULP algorithm.
DLPtrim.m: this function implements the hybrid ULP-DLP algorithm mentioned in the end of the discussion of the SGFR network.
PlunderNTriangle.m: this function uses a greedy algorithm to eliminate odd parity, pairwise disjoint triangles from a given subgraph of a signed digraph G (to be used in connection to the discussion regarding changes of variables to eliminate inputs in the decomposition).
For questions or comments regarding this code please contact:
german.enciso@gmail.com