[WIP] DistributedData FVA

Project.toml

@@ -7,6 +7,7 @@ version = "0.1.0"
 Clp = "e2554f3b-3117-50c0-817c-e040a3ddf72d"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
+DistributedData = "f6a0035f-c5ac-4ad0-b410-ad102ced35df"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 GLPK = "60bf3e95-4087-53dc-ae20-288a0d20c6a6"
 HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"

src/COBREXA.jl

@@ -8,6 +8,7 @@ using JuMP
 using MAT
 using Distributed
 using SBML
+using DistributedData
 import Pkg
 
 # import src files
@@ -45,8 +46,8 @@ export speye, LinearModel, nReactions, nMetabolites, nCouplingConstraints,
        removeCouplingConstraints!, removeCouplingConstraints,
        changeCouplingBounds!, changeCouplingBounds,
        verifyConsistency, findExchangeReactions, findExchangeMetabolites,
-       solveLP, loadModel, loadSBMLModel, writeModel,
-       fluxBalanceAnalysis, fluxVariabilityAnalysis, parFVA,
+       solveLP, loadModel, loadSBMLmodel, writeModel,
+       fluxBalanceAnalysis, fluxVariabilityAnalysis, parFVA, parFVA2,
        convertToExportable, createParPool
 
 end

src/analysis/fva.jl

@@ -87,3 +87,34 @@ function allocateReacs(reactions::Array{Int64, 1}, nWorkers::Int)
 
    return allocatedReacs
 end
+
+function parFVA2(model::LinearModel, reactions::Vector{Int}, optimizer, workers)
+    if any(reactions .> length(model.rxns))
+        throw(ArgumentError("reactions contain an out-of-bounds index"))
+    end
+
+    γ = 1.
+    fluxes = zeros(length(reactions), 2)
+
+    (optimization_model, x₀) = fluxBalanceAnalysis(model::LinearModel, optimizer)
+    Z₀ = JuMP.objective_value(optimization_model)
+    x = JuMP.all_variables(optimization_model)
+    @constraint(optimization_model, model.c' * x ≥ γ * Z₀)
+
+    fetch.([save_at(w, :cobrexa_parfva_model, optimization_model) for w in workers])
+
+    fluxes = vcat(dpmap(reactions, rid -> :(begin
+        var = JuMP.all_variables(cobrexa_parfva_model)[$rid]
+        @objective(cobrexa_parfva_model, MOI.MIN_SENSE, var)
+        JuMP.optimize!(cobrexa_parfva_model)
+        min_flux = JuMP.objective_value(cobrexa_parfva_model)
+
+        @objective(cobrexa_parfva_model, MOI.MIN_SENSE, var)
+        JuMP.optimize!(cobrexa_parfva_model)
+        max_flux = JuMP.objective_value(cobrexa_parfva_model)
+        [min_flux max_flux]
+    end), workers)...)
+
+    fetch.([remove_from(w, :cobrexa_parfva_model) for w in workers])
+    return fluxes
+end