Unverified Commit 3c78af74 authored by Miroslav Kratochvil's avatar Miroslav Kratochvil Committed by GitHub
Browse files

Merge pull request #332 from LCSB-BioCore/mk-fix-screening

fix screening doc build

and HOPE for the best
parents 029adb51 0ac06267
Pipeline #43064 failed with stages
in 18 minutes and 15 seconds
......@@ -3,6 +3,7 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
JuMP = "4076af6c-e467-56ae-b986-b466b2749572"
OSQP = "ab2f91bb-94b4-55e3-9ba0-7f65df51de79"
Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
Tulip = "6dd1b50a-3aae-11e9-10b5-ef983d2400fa"
[compat]
......
......@@ -57,12 +57,9 @@ bar(reactions(model), productions, orientation = :hor, dpi = 600)
# ## Knocking out reaction combinations
#
# With a bit of help from `IterTools` package, it is very easy to prepare
# matrices of biomass productions from all possible two-reaction knockouts. To
# make it more interesting, we will restrict one of the reactions of the pair a
# bit less, to see more possible outcomes.
#
using IterTools
# It is very easy to prepare matrices of biomass productions from all possible
# two-reaction knockouts. To make it more interesting, we will restrict one of
# the reactions of the pair a bit less, to see more possible outcomes.
# We do not process all reactions here to make the notebook rendering
# efficient, but you can easily remove the restriction, and speed the process
......@@ -74,8 +71,8 @@ rxns = reactions(model)
productions = screen_variants(
model,
[
[with_limited_rate(rxn1, 3), with_limited_rate(rxn2, 0.1)] for
(rxn1, rxn2) in product(rxns, rxns)
[with_limited_rate(rxn1, 3), with_limited_rate(rxn2, 0.1)] for rxn1 in rxns,
rxn2 in rxns
],
model -> get_biomass(flux_balance_analysis_dict(model, Tulip.Optimizer)),
)
......
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