Getting started

What this package does

The purpose of this package is to allow the end user to easily define a set of ordinary differential equations (ode) and obtain information about the ode by simply invoking the the appropriate methods. Here, we define the set of ode’s as

\[\frac{\partial \mathbf{x}}{\partial t} = f(\mathbf{x},\boldsymbol{\theta})\]

where \(\mathbf{x} = \left(x_{1},x_{2},\ldots,x_{n}\right)\) is the state vector with \(d\) state and \(\boldsymbol{\theta}\) the parameters of \(p\) dimension. Currently, this package allows the end user to find the algebraic expression of the ode, Jacobian, gradient and forward sensitivity of the ode. A numerical output is given when all the state and parameter values are provided. Note that the only important class is DeterministicOde all the functionality described previously are exposed.

The current plan is to extend the functionality to include

Solving the ode analytically when it is linear
Analysis of the system via eigenvalues during the integration
Detection of DAE

Obtaining the package

The location of the package is current on GitHub and can be pulled via https from:

https://github.com/PublicHealthEngland/pygom.git

The package is currently as follows:

pygom/
    bin/
    doc/
    pygom/
        loss/
            tests/
        model/
            tests/
        sbml_translate/
        utilR/
    LICENSE.txt
    README.rst
    requirements.txt
    setup.py

with files in each of the three main folder not shown. You can install the package via command line:

python setup.py install

or locally on a user level:

python setup.py install --user

Please note that there are current redundant file are kept for development purposes for the time being.

Testing the package

Testing can be performed prior or after the installation. Some standard test files can be found in their respective folder and they can be run in the command line:

python setup.py test

which can be performed prior to installing the package if desired.