ScrumPy

The ScrumPy modelling software is developed at Oxford Brookes univeristy by the cell systems modelling group:

http://mudshark.brookes.ac.uk/ScrumPy

http://mudshark.brookes.ac.uk/

This documentation is for the scrumpy_to_cobra utility and associated functions. Gsmodutils is capable of converting ScrumPy structural models to cobrapy objects. However, it should be noted that additional constraints on reactions are not specified within the ScrumPy modelling format. As a consequence, these will have to be specified manually (or through supported json formats).

Example usage

$ scrumpy_to_cobra --model SCRUMPY_FILE.spy --output OUTPUT_FILE.json

As scrumpy spy files do not include constraints for models, the following options are probably required to get a working model

--media a json file for growth media

--atpase_reaction

--atpase_flux

--objective_reaction Objective to maximise (multiple objectives currently not set)

--objective_direction

Alternatively, use the python interface to load a model and set the constraints with the cobrapy interface

from gsmodutils.utils.scrumpy import load_scrumpy_model
cobra_mdl = load_scrumpy_model('model.spy')
cobra_mdl.objective = cobra_mdl.reactions.Biomass
cobra.mdl.reactions.ATPase.lower_bound = -8.0
cobra.mdl.reactions.ATPase.upper_bound = -8.0

Scrumpy formatted strings can also be loaded in to gsmodutils models on the fly. For example, after a gsmodutils project model is loaded:

from gsmodutils import GSMProject
project = GSMProject()
model = project.model

spy_reactions = """
External(PROTON_i, "WATER")

NADH_DH_ubi:
    "NADH" + "UBIQUINONE-8" + 4 PROTON_i -> "UBIQUINOL-8" + 3 PROTON_p + "NAD"
    ~

NADH_DH_meno:
    "NADH" + "Menaquinones" + 4 PROTON_i -> "Menaquinols" + 3 PROTON_p + "NAD"
    ~
"""
model.add_scrumpy_reactions(spy_reactions)

A further usage is to load cobra models directly from scrumpy strings:

from gsmodutils.utils.scrumpy import load_scrumpy_model
spy_reactions = """
Structural()
External(PROTON_i, "WATER")

NADH_DH_ubi:
    "NADH" + "UBIQUINONE-8" + 4 PROTON_i -> "UBIQUINOL-8" + 3 PROTON_p + "NAD"
    ~

NADH_DH_meno:
    "NADH" + "Menaquinones" + 4 PROTON_i -> "Menaquinols" + 3 PROTON_p + "NAD"
    ~
"""
model = load_scrumpy_model(spy_reactions)

Naturally, any constraints additional to reaction directionality (such as uptake) will have to be specified manually.

Code docs

exception gsmodutils.utils.scrumpy.ParseError

Bases: Exception

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

gsmodutils.utils.scrumpy.get_tokens(line)

Goes through each charachter in scrumpy file attempting to find tokens

FIXME: if there is a numeric after a direction token this fails e.g. ‘->2 “PROTON”’ fails but ‘-> 2 “PROTON”’ works :param line_dt: :return:

gsmodutils.utils.scrumpy.load_scrumpy_model(filepath_or_string, name=None, model_id=None, media=None, objective_reactions=None, obj_dir='min', fixed_fluxes=None)

Specify a base scrumpy structural model file and returns a cobra model. This hasn’t be thoroughly tested so expect there to be bugs

To get a solution from the returned object you need to specify nice stuff like the atpase reaction and media

Parameters:

• filepath_or_string – filepath or scrumpy string
• name –
• model_id –
• media –
• objective_reactions –
• obj_dir –
• fixed_fluxes –

Returns:

gsmodutils.utils.scrumpy.parse_file(filepath, fp_stack=None, rel_path='')

Recursive function - takes in a scrumpy spy file and parses it, returning a set of reactions

Note this code is not fully tested. Expect some bugs. :param filepath: :param fp_stack: :param rel_path: :return:

gsmodutils.utils.scrumpy.parse_fobj(infile, fp_stack, rel_path, source_name)

gsmodutils.utils.scrumpy.parse_string(spy_string, rel_path='.')