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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 2.7 and 3.3+.

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

  • Python (2.7 or 3.3+)
  • numpy
  • scipy
  • matplotlib
  • pip

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

Installation

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

$ pip install stimator

or, in a Anaconda/Miniconda installation, install from the aeferreira channel:

$ conda install -c aeferreira stimator
Release History

Release History

This version
History Node

0.9.110

History Node

0.9.102

History Node

0.9.101

History Node

0.9.99

History Node

0.9.98

History Node

0.9.97

History Node

0.9.96

History Node

0.9.95

History Node

0.9.90

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File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
stimator-0.9.110.zip (84.0 kB) Copy SHA256 Checksum SHA256 Source Mar 20, 2017

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