NAME
ElMo-Proc - Processing of elementary flux modes
CONTENTS
Description
Commands And Options
Examples
Notes On Elementary Flux Modes
See Also
Author
License And Citation
History
DESCRIPTION
ElMo-Proc is a tool which allows the processing of elementary flux modes and computation of various features, statistics and information from them. It is developed in C++ as a serial and parallel software based on MPI library of functions. It takes as input the bit-compressed matrix of elementary flux modes computed using Elmo-Comp
COMMANDS AND OPTIONS
elmoproc [options] OPTIONS:
-b / --bit_efm_file <str> file name for bit-compressed EFM matrix [no] -c / --cef <str> computation of control effective fluxes [no] -d / --debug_file <str> debug file name [debug.info] -e / --efm_file <str> file name for real-valued EFM matrix [no] -f / --file <str> metabolic network file name -s / --sort <str> sort modes by first given target yield in decreasing or increasing way [dec|inc] -t / --endianess <str> endianess [little] -u / --show_mem <str> show memory usage [no] -v / --verify <str> verification of elementar flux modes using rank test [no] -y / --yield <str> name of file contianing names of substrate and target reactions for yield computation [no]
ELMO-PROC INPUT FILE FORMAT
The inputs required for program ElMo-Proc can be compulsory such as: (1) bit-compressed EFM file, (2) bit-compressed EFM meta file, (3) original file with metabolic network in METATOOL format used for computing EFMs, or it can be optional: (4) yield computation input file.
ELMO-PROC OUTPUT FILE FORMAT
ElMo-Proc as output may generate (1) expanded floating-point elementary flux mode matrix, (2) yields matrix, (3) sorted bit-compressed elementary flux modes matrix in increasing/decreasing order of the first listed target reaction, (4) array of control effective fluxes.
EXAMPLES
Make sure that as input you have the bit-compressed file from previous computation using ElMo-Comp and the associated meta file. To perform the expansion of the bit-compressed elementary flux mode matrix into a full floating-point value matrix on the E. coli metabolic network with 59 reactions, call the following command:
$ ./elmoproc -f data/iCT_Ecoli_59.txt -b efm59.bin -e efm59.txt
requesting that the output is saved in expanded format in file efm59.txt.
In addition, as in ElMo-Comp yield computation may be requested as:
$ ./elmoproc -f data/iCT_Ecoli_59.txt -b efm59.bin -y comp_yield.elmo
where comp_yield.elmo contains a list of substrate and target reactions.
NOTES ON ELEMENTARY FLUX MODE PROCESSING
Computation of various statistics and quantitative features from EFM
Metabolic networks used in this software are described as a stoichiometry matrix where dimensions correspond to metabolites and reactions. Pathways are analytically represented as vectors which lie in the nullspace of the stoichiometry matrix, and the elementary flux modes are the subset of such vectors.
Enumeration of efficient reaction knockouts
One of many applications of elementary flux modes is the computation of efficient reaction knockouts which is implemented in the tool ElMo-Knock
Memory Requirements
Accuracy
SEE ALSO
ElMo-Comp
EFMTools
METATOOL v5.1
| Last change: August 2012 |