https://github.com/matthiaskoenig/sedml-script
https://github.com/matthiaskoenig/sedml-script
Last synced: 3 months ago
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- Host: GitHub
- URL: https://github.com/matthiaskoenig/sedml-script
- Owner: matthiaskoenig
- Created: 2019-07-23T07:14:09.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2019-07-26T17:08:16.000Z (almost 6 years ago)
- Last Synced: 2025-01-04T20:24:46.440Z (5 months ago)
- Language: Jupyter Notebook
- Size: 1020 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# SED-ML script
Python based implementation of the SED-ML script examples.
For the reference SED-ML script and antimony code see:
https://docs.google.com/document/d/1HzX0GcwoG_dcA_Zwuud0r7ICyH9WfSuJX_4lXxdJImc/edit?ts=5d37846b#
## Installation
All examples can be run with a minimal virtual environment.
Requirements are listed in
```
# create virtualenv
mkvirtualenv sedml-script --python=python3.6
(sedml-script) pip install -r requirements.txt
(sedml-script) pip install jupyterlab
# run jupyter lab with kernel
(sedml-script) ipython kernel install --user --name=sedml-script
(sedml-script) jupyter lab
```
## Notebook examples
The notebook with outputs is [here](sedml-script.ipynb).
## TODO
- read data and plot
- read data and parameterize
- parameter scan and plot areas
- initial condition scan