Unverified Commit 181b201d authored by Miroslav Kratochvil's avatar Miroslav Kratochvil Committed by GitHub
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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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...@@ -118,22 +118,21 @@ Dict{String,Float64} with 95 entries: ...@@ -118,22 +118,21 @@ Dict{String,Float64} with 95 entries:
#### Model variant processing #### Model variant processing
The main feature of COBREXA.jl is the ability to easily specify and process The main feature of COBREXA.jl is the ability to easily specify and process
many analyses at once, in parallel. Let's see how the organism would perform if many analyses in parallel. To demonstrate, let's see how the organism would perform if
some reactions were disabled: some reactions were disabled independently:
```julia ```julia
# convert to a model type that is easy to modify # convert to a model type that is efficient to modify
m = convert(StandardModel, m) m = convert(StandardModel, m)
# find the model objective value if oxygen and carbon dioxide transports are disabled # find the model objective value if oxygen or carbon dioxide transports are disabled
screen(m, screen(m, # the base model
# this specifies how to generate the desired model variants variants=[ # this specifies how to generate the desired model variants
variants=[ [], # one with no modifications, i.e. the base case
[], # one with no modifications
[with_changed_bound("O2t", lower=0.0, upper=0.0)], # disable oxygen [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("CO2t", lower=0.0, upper=0.0)], # disable CO2
[with_changed_bound("O2t", lower=0.0, upper=0.0), [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`) # this specifies what to do with the model variants (received as the argument `x`)
analysis = x -> analysis = x ->
...@@ -151,8 +150,10 @@ biomass production much harder: ...@@ -151,8 +150,10 @@ biomass production much harder:
``` ```
Most importantly, such analyses can be easily specified by automatically Most importantly, such analyses can be easily specified by automatically
generating long lists of the modifications to apply to the model, and generating long lists of modifications to be applied to the model, and
parallelized: parallelized.
Knocking out each reaction in the model is efficiently accomplished:
```julia ```julia
# load the task distribution package, add several worker nodes, and load # load the task distribution package, add several worker nodes, and load
......
...@@ -36,7 +36,7 @@ finds a minimal total flux through the model that still satisfies the (slightly ...@@ -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 relaxed) optimum. This is done using a quadratic problem optimizer. If the
original optimizer does not support quadratic optimization, it can be changed original optimizer does not support quadratic optimization, it can be changed
using the callback in `qp_modifications`, which are applied after the FBA. See 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 Thhe optimum relaxation sequence can be specified in `relax` parameter, it
defaults to multiplicative range of `[1.0, 0.999999, ..., 0.99]` of the defaults to multiplicative range of `[1.0, 0.999999, ..., 0.99]` of the
......
...@@ -217,7 +217,7 @@ function metabolite_formula( ...@@ -217,7 +217,7 @@ function metabolite_formula(
end 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`. Return the charge associated with metabolite `metabolite_id` in `model`.
Returns `nothing` if charge not present. Returns `nothing` if charge not present.
......
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