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pydream_it\n------\n![Python version badge](https://img.shields.io/badge/python-2.7-blue.svg)\n[![license](https://img.shields.io/github/license/mashape/apistatus.svg)](LICENSE)\n------\n####  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.\n\n## Install and basic usage\n\n**Warning:** pydream_it is still under heavy development and may rapidly change.\n\n#### pydream_it run dependencies\npydream_it does not have any special dependencies itself, but [PySB](http://pysb.org/) is of course needed to run the PySB models:\n\npydream_it does not require any special installation to use, just clone or download the GitHub repo\n```\ngit clone https://github.com/blakeaw/pydream_it.git\n```\nThen to use pydream_it, simply call the script with python and passing as input the model file\n```\npython pydream_it.py model.py\n```\nThe file model.py should be a PySB model file.\n*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.\nIn this case pydream_it will generate a file `run_pydream_model.py` which will contain some basic code to calibrate the model using PyDREAM.\n\n#### pydream_it directives\nThe #PYDREAM_IT directives will appear as comments in the model code and are parsed by pydream_it at runtime.\npydream_it currently has the following directives that can be added to the model code file:\n* **#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.\n* **#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.\n\n------\n\n## Contact\n\nTo report problems or bugs please open a\n[GitHub Issue](https://github.com/blakeaw/pydream_it/issues). Additionally, any\ncomments, suggestions, or feature requests for pydream_it can also be submitted as\na\n[GitHub Issue](https://github.com/blakeaw/pydream_it/issues).\n\nFor any other inquiries, including questions about pydream_it use or\nimplementation, you can contact Blake directly via e-mail at either\nblake.a.wilson@vanderbilt.edu or blakeaw1102@gmail.com; please include \"pydream_it\ninquiry\" in the e-mail subject line.\n\n------\n\n## Contributing\n\nIf you would like to contribute directly to pydream_it's development please\n 1. Fork the repo (https://github.com/blakeaw/pydream_it/fork)\n 2. Create a new branch for your feature (git checkout -b feature/foo_bar)\n 3. Create test code for your feature\n 4. Once your feature passes its own test, run all the tests using [pytest](https://docs.pytest.org/en/latest/) (python -m pytest)\n 5. Once your feature passes all the tests, commit your changes (git commit -am 'Add the foo_bar feature.')\n 6. Push to the branch (git push origin feature/foo_bar)\n 7. Create a new Pull Request\n\n------\n\n## License\n\nThis project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details\n\n------\n\n## Acknowledgments\n\n* 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.\n\n------\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flolab-msm%2Fpydream_it","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flolab-msm%2Fpydream_it","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flolab-msm%2Fpydream_it/lists"}