https://github.com/lolab-msm/pydream_it
Read PySB models and generate a script for PyDREAM calibration
https://github.com/lolab-msm/pydream_it
Last synced: 12 months ago
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Read PySB models and generate a script for PyDREAM calibration
- Host: GitHub
- URL: https://github.com/lolab-msm/pydream_it
- Owner: LoLab-MSM
- License: mit
- Created: 2018-05-23T20:24:27.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2024-03-25T06:59:24.000Z (almost 2 years ago)
- Last Synced: 2025-01-04T10:16:12.102Z (about 1 year ago)
- Language: Python
- Size: 104 KB
- Stars: 0
- Watchers: 2
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# pydream_it
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[](LICENSE)
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#### pydream_it is script to that reads/imports [PySB](http://pysb.org/) models and generates a template script that is used for [PyDREAM](https://github.com/LoLab-VU/PyDREAM) calibration of the model. pydream_it inspects the model and identifies the kinetic parameters and generates the SampledParam code lines. pydream_it currently has limited functionality for #PYDREAM_IT directives that can be added to the model code alter pydream_it behavior.
## Install and basic usage
**Warning:** pydream_it is still under heavy development and may rapidly change.
#### pydream_it run dependencies
pydream_it does not have any special dependencies itself, but [PySB](http://pysb.org/) is of course needed to run the PySB models:
pydream_it does not require any special installation to use, just clone or download the GitHub repo
```
git clone https://github.com/blakeaw/pydream_it.git
```
Then to use pydream_it, simply call the script with python and passing as input the model file
```
python pydream_it.py model.py
```
The file model.py should be a PySB model file.
*NOTE:* pydream_it currently doesn't inspect for the location of model.py, so you need to be in the same directory as the model.py file when you call pydream_it.
In this case pydream_it will generate a file `run_pydream_model.py` which will contain some basic code to calibrate the model using PyDREAM.
#### pydream_it directives
The #PYDREAM_IT directives will appear as comments in the model code and are parsed by pydream_it at runtime.
pydream_it currently has the following directives that can be added to the model code file:
* **#PYDREAM_IT prior [param_name, param_index] [norm, uniform]** - tell pydream_it to use a specific prior (other than the default) for the specified parameter. The parameter can be specified by either it name (param_name) or its index (param_index). pydream_it currently supports using normal distribution (norm) of uniform priors.
* **#PYDREAM_IT no-sample [param_name, param_index]** - define a fixed parameter, i.e., pydream_it will not add it to the sample parameters list for the PyDREAM run.
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## Contact
To report problems or bugs please open a
[GitHub Issue](https://github.com/blakeaw/pydream_it/issues). Additionally, any
comments, suggestions, or feature requests for pydream_it can also be submitted as
a
[GitHub Issue](https://github.com/blakeaw/pydream_it/issues).
For any other inquiries, including questions about pydream_it use or
implementation, you can contact Blake directly via e-mail at either
blake.a.wilson@vanderbilt.edu or blakeaw1102@gmail.com; please include "pydream_it
inquiry" in the e-mail subject line.
------
## Contributing
If you would like to contribute directly to pydream_it's development please
1. Fork the repo (https://github.com/blakeaw/pydream_it/fork)
2. Create a new branch for your feature (git checkout -b feature/foo_bar)
3. Create test code for your feature
4. Once your feature passes its own test, run all the tests using [pytest](https://docs.pytest.org/en/latest/) (python -m pytest)
5. Once your feature passes all the tests, commit your changes (git commit -am 'Add the foo_bar feature.')
6. Push to the branch (git push origin feature/foo_bar)
7. Create a new Pull Request
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## License
This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details
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## Acknowledgments
* This code and the template run scripts it generates are based on the [examples](https://github.com/LoLab-VU/PyDREAM/tree/master/pydream/examples) given in the [PyDREAM](https://github.com/LoLab-VU/PyDREAM) repo.
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