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LCSB-BioCore
COBREXA.jl
Commits
181b201d
Unverified
Commit
181b201d
authored
Oct 13, 2021
by
Miroslav Kratochvil
Committed by
GitHub
Oct 13, 2021
Browse files
Merge pull request #464 from LCSB-BioCore/mo-docstring-fixes
Fix some small docstring issues + small readme changes
parents
0be294c2
30ad20fb
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#48295
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README.md
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181b201d
...
...
@@ -118,22 +118,21 @@ Dict{String,Float64} with 95 entries:
#### Model variant processing
The main feature of COBREXA.jl is the ability to easily specify and process
many analyses
at once,
in parallel.
L
et's see how the organism would perform if
some reactions were disabled:
many analyses in parallel.
To demonstrate, l
et's see how the organism would perform if
some reactions were disabled
independently
:
```
julia
# convert to a model type that is e
asy
to modify
# convert to a model type that is e
fficient
to modify
m
=
convert
(
StandardModel
,
m
)
# find the model objective value if oxygen and carbon dioxide transports are disabled
screen
(
m
,
# this specifies how to generate the desired model variants
variants
=
[
[],
# one with no modifications
# find the model objective value if oxygen or carbon dioxide transports are disabled
screen
(
m
,
# the base model
variants
=
[
# this specifies how to generate the desired model variants
[],
# one with no modifications, i.e. the base case
[
with_changed_bound
(
"O2t"
,
lower
=
0.0
,
upper
=
0.0
)],
# disable oxygen
[
with_changed_bound
(
"CO2t"
,
lower
=
0.0
,
upper
=
0.0
)],
# disable CO2
[
with_changed_bound
(
"O2t"
,
lower
=
0.0
,
upper
=
0.0
),
with_changed_bound
(
"CO2t"
,
lower
=
0.0
,
upper
=
0.0
)],
# disable both
with_changed_bound
(
"CO2t"
,
lower
=
0.0
,
upper
=
0.0
)],
# disable both
],
# this specifies what to do with the model variants (received as the argument `x`)
analysis
=
x
->
...
...
@@ -151,8 +150,10 @@ biomass production much harder:
```
Most importantly, such analyses can be easily specified by automatically
generating long lists of the modifications to apply to the model, and
parallelized:
generating long lists of modifications to be applied to the model, and
parallelized.
Knocking out each reaction in the model is efficiently accomplished:
```
julia
# load the task distribution package, add several worker nodes, and load
...
...
src/analysis/parsimonious_flux_balance_analysis.jl
View file @
181b201d
...
...
@@ -36,7 +36,7 @@ finds a minimal total flux through the model that still satisfies the (slightly
relaxed) optimum. This is done using a quadratic problem optimizer. If the
original optimizer does not support quadratic optimization, it can be changed
using the callback in `qp_modifications`, which are applied after the FBA. See
the documentation of flux_balance_analysis for usage examples of modifications.
the documentation of
[`
flux_balance_analysis
`](@ref)
for usage examples of modifications.
Thhe optimum relaxation sequence can be specified in `relax` parameter, it
defaults to multiplicative range of `[1.0, 0.999999, ..., 0.99]` of the
...
...
src/base/types/abstract/MetabolicModel.jl
View file @
181b201d
...
...
@@ -217,7 +217,7 @@ function metabolite_formula(
end
"""
metabolite_charge(model::MetabolicModel, metabolite_id::String)::Maybe{Int}
metabolite_charge(model::MetabolicModel, metabolite_id::String)::Maybe{Int}
Return the charge associated with metabolite `metabolite_id` in `model`.
Returns `nothing` if charge not present.
...
...
cylon-x
🤖
@cylon-x
mentioned in commit
95cd3a8d
·
Oct 13, 2021
mentioned in commit
95cd3a8d
mentioned in commit 95cd3a8dd6848190ad57d75954c3b7bde6d42a98
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