diff --git a/docs/src/distributed/1_functions.md b/docs/src/distributed/1_functions.md index e0e94f36..1deefc18 100644 --- a/docs/src/distributed/1_functions.md +++ b/docs/src/distributed/1_functions.md @@ -29,7 +29,7 @@ locally](2_parallel.md) and [running distributed analysis in HPC clusters](3_slu As of COBREXA 1.3, the list of functions that accept the `worker` argument is as follows: -- `affine_hit_and_run`](@ref) sampling, together with [`warmup_from_variability` +- `affine_hit_and_run` sampling, together with `warmup_from_variability` - `flux_variability_analysis` - `max_min_driving_force` - `objective_envelope` @@ -40,12 +40,10 @@ Notably, the screening functions are reused to run many other kinds of analyses which, in turn, inherit the parallelizability. This includes a wide range of functionality, including analyses such as: -- [single and multiple gene deletions](../examples/07_gene_deletion.md) (and other - genetic modifications), -- [modifications of the reaction - spectrum](../examples/07_restricting_reactions.md) (e.g., disabling reactions) -- advanced envelope-scanning analyses, -- [growth media exploration](../examples/11_growth.md) (e.g., metabolite depletion) +- single and multiple gene deletions (and other genetic modifications) +- modifications of the reaction spectrum (e.g., disabling reactions) +- advanced envelope-scanning analyses +- growth media exploration (e.g., metabolite depletion) ## Mitigating parallel inefficiencies diff --git a/src/COBREXA.jl b/src/COBREXA.jl index 9719c4b5..c3b3feb2 100644 --- a/src/COBREXA.jl +++ b/src/COBREXA.jl @@ -31,7 +31,7 @@ by copy-pastable examples. To start quickly, load your favorite JuMP-compatible solver, use [`load_model`](@ref) to read a metabolic model from the disk, and solve it with -[`flux_balance`](@ref). +[`flux_balance_analysis`](@ref). """ module COBREXA @@ -65,7 +65,7 @@ include("builders/compare.jl") include("builders/enzymes.jl") include("builders/fbc.jl") include("builders/interface.jl") -include("builders/knockouts.jl") +include("builders/knockout.jl") include("builders/loopless.jl") include("builders/objectives.jl") include("builders/scale.jl") diff --git a/src/builders/knockouts.jl b/src/builders/knockout.jl similarity index 100% rename from src/builders/knockouts.jl rename to src/builders/knockout.jl