https://github.com/lolab-msm/corm
COX2 Reaction Model
https://github.com/lolab-msm/corm
Last synced: 4 months ago
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COX2 Reaction Model
- Host: GitHub
- URL: https://github.com/lolab-msm/corm
- Owner: LoLab-MSM
- Created: 2014-12-09T21:30:56.000Z (about 11 years ago)
- Default Branch: master
- Last Pushed: 2017-02-28T20:17:55.000Z (almost 9 years ago)
- Last Synced: 2025-10-13T16:14:08.945Z (4 months ago)
- Language: Jupyter Notebook
- Homepage:
- Size: 27.6 MB
- Stars: 1
- Watchers: 13
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
COX-2 Reaction Model (CORM)
=============
CORM provides a proposed model of cyclooxygenase-2 (COX-2) allosteric and catalytic interactions with arachidonic acid (AA) and 2-arachidonoylglycerol (2-AG).
COX-2 turnover of AA or 2-AG produces prostaglandins (PGs) or prostaglandin glyceryl esters (PG-Gs), respectively.
Quickstart
----------
To facilitate easy use of CORM, we provide a virtual machine with everything you need to run CORM already installed. You can download it [here](http://puma.mc.vanderbilt.edu:8000/virtual_machines/CORM_demo.ova). Warning: 1.4G file.
Installation
------------
CORM is encoded as a Python Systems Biology (PySB) model. To download and install PySB and its dependencies, [see the PySB documentation](http://docs.pysb.org/en/latest/installation.html#option-2-installing-the-dependencies-yourself).
If you would like to run Bayesian Markov Chain Monte Carlo (MCMC) fitting of the CORM parameters, you will also need the LoLab-VU fork of PyMC 3.
Clone the repository:
```
git clone https://github.com/LoLab-VU/pymc
```
Enter the cloned directory and switch to the branch that has the DREAM MCMC stepping method:
```
git checkout dream
```
Then install PyMC:
```
python setup.py install
```
Running CORM
------------
The CORM model file is defined in the file [corm.py](https://github.com/LoLab-VU/CORM/blob/master/corm.py).
You can import the model for exploration by typing:
```python
from corm import model
```
from an iPython session.
We also provide an iPython notebook that will walk you through how CORM is defined [here](http://nbviewer.ipython.org/urls/raw.githubusercontent.com/LoLab-VU/CORM/master/corm_tutorial.ipynb).
Fitting CORM Parameters
-----------------------
The file [run_pymc_sampling.py](https://github.com/LoLab-VU/CORM/blob/master/run_pymc_sampling.py) provides a Python script for fitting CORM parameters using PyMC.
To run the fitting, simply type:
```
python run_pymc_sampling.py
```
Parameter traces for all MCMC chains will be saved to a pickled Python dictionary as specified in run_pymc_sampling.py.