Introduction to ScrumPy
This is a very brief introduction to ScrumPy, with emphasis on structural analysis. A more complete documentation can be found here.
Loading and defining models
A pre-existing model is loaded by creating an instance of ScrumPy.Model(model) with model being the name of the model file (string-type ending with the ScrumPy file extension, .spy), provided that the model file is stored in the directory from where the ScrumPy shell was launched. If no name is provided, a GUI for selecting a model to open, is launched.
1 >>> m = ScrumPy.Model('toy_model.spy')
This will open a new empty editor window, copy and paste the model description below. Having done that, select "compile" from the "ScrumPy" menu, and the model is loaded.
Where toy_model.spy is a small structural model:
Structural()
A_tx:
x_A -> A
~
R_1:
A -> B
~
R_2:
B -> C
~
R_3:
C -> E
~
R_4:
B -> D
~
R_5:
D -> E
~
R_6:
D -> F
~
E_tx:
E -> x_E
~The reactions with the suffix "_tx" are transporters, i.e. they convert external metabolites (with prefix "x_") to internal metabolites.
Properties of structural models
The class Model has a range of methods, of which some are only useful for kinetic models (which are also structural models, but the oposite is not true). Among the structurally relevant methods we find ConsMoieties() - which prints a list of conserved moieties; DeadReactions() - which returns a list of reactions that cannot carry steady state flux; FindIsoforms() - which identifies reactions from the model that are redundant, i.e. a set of reactions have identical stoichiometry; ElModes() - which returns an elementary modes object; Externals() - which returns a list of external metabolites.
The stoichiometry matrix
The fields Model.sm and Model.smexterns are the two stoichiometry matrices assocciated with a model - the former is the internal matrix, the latter the external. The external matrix contains infomation about external metabolites, whereas the internal does not. All instances of ScrumPy matrices (subclasses of DynMatrix) have the fields cnames - column names and rnames - row names.
Useful methods of sm (and smexterns) include ReacToStr(reac),
and InvolvedWith(name),
Reaction reversibility
ScrumPy accepts three reversibility symbols: "->" - left to right irreversible, "<-" - right to left irreversible, and <> - reversible. Reaction reversibility is handled by the stoichiometry matrix.
Nullspace analysis
The kernel of the stoichiometry matrix can be calculated using the sm.NullSpace() method (smexterns also has the method, but the kernel of the external matrix is only related to the futile cycles of the model, not possible steady-state solutions).
Even if the signs of some of the coeffients indicate thermodynamically infeasible solutions (e.g. all active reactions in the first column have negative coefficients, even though they are irreversible) a lot of useful information can be obtained form k. For instance, we see that the row associated with R_6 is a null-vector, indicating that there is no steady-state solution involving R_6. In fact this is how ScrumPy detects dead reactions with the method DeadReactions().
Also, note that some of the row-vectors are proportional to each other - R_2, R_3; R_4, R_5; and E_tx, A_tx, R_1. This implies that these sets must carry flux in a coordinated fashion, e.g. any flux solution involving R_4 must also involve R_5. These sets of coordinated reactions are referred to as enzyme subsets and can be determined using the Model method EnzSubsets(). This method returns a dictionary object where keys are subset names (or reaction name if a reaction is in a singleton set) and values are nested dictionaries where keys are reaction names and values are the flux ratios of the reactions. The key DeadReacs maps to a list of dead reactions.
The elementary modes of a model can be analysed using the method Model.ElModes(). The field mo is a matrix similar to k.
The relationship between modes and metabolites is stored in the sto matrix.
The methods Modes() and Stos() returns a string with with same information as the matrices above.