Skip to main content

Analysis of ODE models with focus on model selection and parameter estimation.

Project description

S-timator is a Python library to analyse ODE-based models (also known as dynamic or kinetic models). These models are often found in many scientific fields, particularly in Physics, Chemistry, Biology and Engineering.

Features include:

  • A mini language used to describe models: models can be input as plain text following a very simple and human-readable language.

  • Basic analysis: numerical solution of ODE’s, parameter scanning.

  • Parameter estimation and model selection: given experimental data in the form of time series and constrains on model operating ranges, built-in numerical optimizers can find parameter values and assist you in the experimental design for model selection.

S-timator is in an alpha stage: many new features will be available soon.

Requirements

S-timator supports Python versions 2.6 and up, but support of 3.x is coming soon.

S-timator depends on the “scientific python stack”. The mandatory requirements for S-timator are the following libraries:

  • Python (2.6 or 2.7)

  • numpy

  • scipy

  • matplotlib

  • pip

  • pandas

  • seaborn

One of the following “scientific python” distributions is recommended, as they all provide an easy installation of all requirements:

The installation of these Python libraries is optional, but strongly recommended:

  • sympy: necessary to compute dynamic sensitivities, error estimates of parameters and other symbolic computations.

  • IPython and all its dependencies: some S-timator examples are provided as IPython notebooks.

  • wxPython: although S-timator is a python library meant to be used for scripting or in IPython literate programming interface, a simple GUI is included. This interface requires wxPython.

Installation

After installing the required libraries, (Python, numpy, scipy, matplotlib, pandas and pip) the easiest way to install S-timator is with pip:

$ pip install stimator

The classical way also works, but is not recommended:

$ python setup.py install

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

stimator-0.9.98.zip (246.5 kB view hashes)

Uploaded Source

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page