Elmo-Knocks

ElMo-Knock - Enumeration of reaction knockouts for optimal metabolic network design

Description
Commands And Options
Elmo-Knock input file format
Elmo-Knock output file format
Example
See Also

DESCRIPTION

ElMo-Knock is a tool which enumerates reaction knockout subsets for optimal design of metabolic networks. 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 and yields matrix computed using Elmo-Comp

COMMANDS AND OPTIONS

elmoknock [options]
OPTIONS:

-c / --configs_file <str> name of configuration file

ELMO-KNOCK INPUT FILE FORMAT

The input to the ElMo-Knock is a configuration file generated previosly by ElMo-Comp program following the computation of elementary modes. It contains (name,value) pairs in the format field_name : value as given in the table :

name value

algorithm "direct, "indirect" or "optstar" enumeration algorithms

network capacity "low" or "high"

efm_file file name with elementary modes (use -b option in elmocomp)

efm_meta_file meta file name

use_transport_reacs "yes" or "no" to use transport reactions in knockouts

max_efm_cands (indirect algorithm ONLY) number of modes to consider in every enumeration step

max_reac_cands (used in direct, indirect and optstar algorithms) number of reactions to consider in every enumeration step

max_reaction_knockout_subset_length maximal length of reaction knockout subset

init_knock_reacs reactions knocked out from network prior to searching for knockout subsets

substrate_reacs substrate reactions

target_reacs target reactions

transport_reacs transport reactions

efficient_growth_coupled_min_yield minimal yield values required for modes which are efficient as well as coupled to growth (biomass reaction); 2 values required

efficient_growth_uncoupled_min_yield minimal yield values required for modes which are efficient but not coupled to growth (biomass reaction); 2 values required

yields_file file containing yield values for all elementary modes for the target/substrate reactions specified in the configuration file it should be computed using the elmocomp and elmocompga software using -y option. it has to be matrix (NUM_EMS x 2)

output_file name of the output file to save the enumerated reaction subsets

name	value
algorithm	"direct, "indirect" or "optstar" enumeration algorithms
network capacity	"low" or "high"
efm_file	file name with elementary modes (use -b option in elmocomp)
efm_meta_file	meta file name
use_transport_reacs	"yes" or "no" to use transport reactions in knockouts
max_efm_cands	(indirect algorithm ONLY) number of modes to consider in every enumeration step
max_reac_cands	(used in direct, indirect and optstar algorithms) number of reactions to consider in every enumeration step
max_reaction_knockout_subset_length	maximal length of reaction knockout subset
init_knock_reacs	reactions knocked out from network prior to searching for knockout subsets
substrate_reacs	substrate reactions
target_reacs	target reactions
transport_reacs	transport reactions
efficient_growth_coupled_min_yield	minimal yield values required for modes which are efficient as well as coupled to growth (biomass reaction); 2 values required
efficient_growth_uncoupled_min_yield	minimal yield values required for modes which are efficient but not coupled to growth (biomass reaction); 2 values required
yields_file	file containing yield values for all elementary modes for the target/substrate reactions specified in the configuration file it should be computed using the elmocomp and elmocompga software using -y option. it has to be matrix (NUM_EMS x 2)
output_file	name of the output file to save the enumerated reaction subsets

ELMO-KNOCK OUTPUT FILE FORMAT

EXAMPLES

After unpacking and compiling the program, run the included example of E. coli central metabolism grown on xylose substrate (folder ecoli_xyl/) :

$ ./elmocomp -f data/iCT_Ecoli_xylose.txt -b ecoli_xyl.bin -y targets_substrate.elmo

where targets_substrate.elmo has the content:

substrates: TRA8
target: BIO TRA1

This will produce ecoli_xyl.bin, ecoli_xyl.bin.meta and yields.txt files.

After unpacking and compiling the program, run the included example of E. coli central metabolism grown on xylose substrate (folder ecoli_xyl/) :

$ ./elmoknock -c ecoly_xyl/configs.knock

CONTENTS

DESCRIPTION

COMMANDS AND OPTIONS

ELMO-KNOCK INPUT FILE FORMAT

ELMO-KNOCK OUTPUT FILE FORMAT

EXAMPLES

SEE ALSO