Working with custom models

It may happen that the intuitive representation of your data does not really match what is supported by a given COBRA package. COBREXA.jl attempts to avoid this problem by providing a flexible framework for containing any data structure that can, somehow, represent the constraint-based model.

The task of having such a polymorphic model definition can be split into 2 separate concerns:

• How to allow the analysis functions to gather the required information from any user-specified model data structure?
• How to make the reconstruction functions (i.e., reaction or gene deletions) work properly on any data structure?

To solve the first concern, COBREXA.jl specifies a set of generic accessors that work over the abstract type MetabolicModel. To use your data structure in a model, you just make it a subtype of MetabolicModel and overload the required accessors. The accessors are functions that extract some relevant information, such as stoichiometry and bounds, returning a fixed simple data type that can be further used by COBREXA. You may see a complete list of accessors here.

A good solution to the second concern is a slightly more involved, as writing generic data modifiers is notoriously hard. Still, there is support for easily making small changes to the model using the modifications system, with functions such as with_added_reactions and with_changed_bound.

Writing the generic accessors

Let's write a data structure that represents a very small model that contains N metabolites that are converted in a circle through N linear, coupled reactions. (E.g., for N=3, we would have a conversion of metabolites A, B and C ordered as A → B → C → A.) This may be useful for testing purposes; we will use it for a simple demonstration.

The whole model can thus be specified with a single integer N that represents the length of the reaction cycle:

struct CircularModel <: MetabolicModel
    size::Int
end

First, define the reactions and metabolites:

COBREXA.n_reactions(m::CircularModel) = m.size
COBREXA.n_metabolites(m::CircularModel) = m.size

COBREXA.reactions(m::CircularModel) = ["rxn$i" for i in 1:n_reactions(m)]
COBREXA.metabolites(m::CircularModel) = ["met$i" for i in 1:n_metabolites(m)]

It is useful to re-use the already defined functions, as that improves the code maintainability.

We can continue with the actual linear model properties:

function COBREXA.objective(m::CircularModel)
    c = spzeros(n_reactions(m))
    c[1] = 1 #optimize the first reaction
    return c
end

COBREXA.bounds(m::CircularModel) = (
    zeros(n_reactions(m)), # lower bounds
    ones(n_reactions(m)), # upper bounds
)

function COBREXA.stoichiometry(m::CircularModel)
    nr = n_reactions(m)
    stoi(i,j) =
        i == j ? 1.0 :
        (i % nr + 1) == j  ? -1.0 :
        0.0

    sparse([stoi(i,j) for i in 1:nr, j in 1:nr])
end

You may check that the result now works just as with CoreModel and StandardModel:

julia> m = CircularModel(5)
Metabolic model of type CircularModel

  1.0  -1.0    ⋅     ⋅     ⋅
   ⋅    1.0  -1.0    ⋅     ⋅
   ⋅     ⋅    1.0  -1.0    ⋅
   ⋅     ⋅     ⋅    1.0  -1.0
 -1.0    ⋅     ⋅     ⋅    1.0
Number of reactions: 5
Number of metabolites: 5

This interface is sufficient to run most of the basic analyses, especially the flux balance finding ones:

julia> flux_balance_analysis_dict(m, Tulip.Optimizer)
Dict{String, Float64} with 5 entries:
  "rxn5" => 1.0
  "rxn2" => 1.0
  "rxn1" => 1.0
  "rxn3" => 1.0
  "rxn4" => 1.0

Writing generic model modifications

The custom model structure can also be made compatible with many of the existing variant-generating functions and analysis modifiers.

The functions prepared for use as "variants" in screen, usually prefixed by with_, have their generic variants that only call simpler, overloadable functions for each specific model. This choice is based on the overloading dispatch system of Julia. For example,with_removed_metabolites is implemented very generically by reducing the problem to some specific remove_metabolites functions selected by the dispatch, as follows:

with_removed_metabolites(args...; kwargs...) =
    m -> remove_metabolites(m, args...; kwargs...)

To be able to use with_removed_metabolites in your model, we can just overload the actual inner function. For the simple circular model, the modification might as well look like this:

COBREXA.remove_metabolites(m::CircularModel, n::Int) =
    return CircularModel(m.size - n)