Exhaustive_double_deletion: Exhaustive_double_deletion, a function for computing...

In abcdeFBA: ABCDE_FBA: A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package.

Description

Exhaustive_double_deletion enables parallel computing of double knockouts by splitting and running the simulation as different instances on the same multi-core machine. The results of the simulation are stored into files named result1, result2 etc.which may be reassembled using the BFDProcessor function

Usage

Exhaustive_double_deletion(fba_object,thread_no,core_number)

Arguments

fba_object	Is a list containing the data required to perform flux balance analysis. The elements of the list are mat which is the stoichiometric matrix, dir which gives the direction of the equality constraints, obj specifies the objective function for the simulation, bounds specifies the lower and upper inequality constraints, rhs is the right hand side of the steady state expression, types refers to the numeric nature of the variables which in case of FBA happens to be "Continuous", max is a Boolean specifying the type of optimization, "Maximization" by default, all_genes is all the genes present in the model, gpr contains boolean expressions of gene essentiality for the corresponding reactions in the model, metabolite_name contains list of all the metabolites, reaction_list contains all the reactions present in the model, compartment is a numeric identifier for each reaction the key for which is in comp_name.
thread_no	This specifies the thread number, it is useful to think of the thread number as a chunk of the complete combination of all pairs of reactions that can be formed. This depends on the number of the cores you are employing which must obviously be a fixed number. For instance if you have a 40 core computer you can divide the double-knockout simulation into 40 chunks. In that case the thread number would refer to the chunks of simulation as 0-39, with thread 0 performing the first 1/40th part of the simulation
core_number	core_number specifies the number of cores that are available to you for performing double knockout simulations. It should be a fixed number for a particular instance of simulations on one model

Examples

#Performing double knockouts in a 2 core computer 
data(Ecoli_core)	
#Exhaustive_double_deletion(Ecoli_core,0,2)
#New instance of R
data(Ecoli_core)
#Exhaustive_double_deletion(Ecoli_core,1,2)

abcdeFBA documentation built on May 2, 2019, 9:19 a.m.