Biological Simulation using Reaction-Like Arrows
Jupyter Notebook Python
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cellerator
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README.md

pycellerator

Pycellerator provices python libraries, a command line interface, and an ipython notebook interface for Cellerator arrow notation.


To install pycellerator:

(1) Download the latest file release.

(2) Unzip the archive and copy the folder "pycellerator" in the file release to the folder where you want to keep your pycellerator files.

(3) Inside the pycellerator folder is detailed documentation in the file pycellerator.pdf. Chapter 2 gives detailed instructions on how to install Python (if you don't already have it installed); and what additional Python libraries are needed and how to get them.

(4) Begin working either on the command line (read chapter 3) or using an ipython notebook. A demonstration notebook "demo.ipynb" is included in the archive.


quickstart (command line)

In the terminal, cd to the folder that contains pycellerator.py and enter:

  python pycellerator.py solve -in Gold1.model -plot

This will run a simulation based on the file Gold1.model, generating and saving a python code file, a csv file, and plotting results on the screen.


quickstart (ipython notebook)

In the terminal cd enter

  ipython notebook

Navigate to the notebook demo.ipynb and click to open that notebook.


To uninstall pycellerator

Drag the folder "pycellerator" to the trash.


To Cite Pycellerator

Shapiro, BE, Mjolsness E (2016) Pycellerator: an arrow-based reaction-like modelling language for biological simulations. Bioinformatics. 2016 Feb 15; 32(4):629-31. doi: 10.1093/bioinformatics/btv596. Epub 2015 Oct 26. Journal web site: http://bioinformatics.oxfordjournals.org/content/32/4/629