gillespy2 1.0.3

Python interface for Gillespie style biochemical simulations

Gillespy2

      Every living thing is composed of complex interlocking systems. These systems determine how tall a tree grows, how bright a firefly is, and how an immune system fights diseases. Systems are composed of a variety of biochemical compounds that interacting in complex ways, creating or breaking into new compounds in response to the environment around them. Quantifying and observing the behavior of these systems requires us to abstract the behavior of these interactions, but even this simplification can be difficult to understand and quantify mathematically.Software libraries exist to assist researchers in this field, but many are so complex in operation that require an in-depth understanding of computer science to utilize or they do not offer specific capabilities that the system of inquiry requires.
      We present GillesPy2, a software library intended to solve the needs of many scientists; from the result seeking wet-lab biologist to the performance seeking bioinformatician. GillesPy2 is a next-generation of the original GillesPy library, an open source cross-platform Python library used for creating statistically correct trajectories for biochemical ordinary differential equations. GillesPy2 has been designed with a focus on providing both ease of use and clarity to the end user, using a unique modular solver system that allows the end user to specify the algorithm to solve their system of inquiry. This granularity is coupled with high-level functionality allowing the researcher to communicate and export their findings seamlessly.

Build Status

Master Branch	Develop Branch

Installation

Please install gillespy2 through the following methods.

Linux

python3 -m pip install --upgrade pip
python3 -m pip install gillespy2

Mac

(Pip should work, same as Linux)

Windows

(Pip should work, same as Linux)

Deployment

Built With

• Numpy
• Scipy
• MatplotLib

Contributing

If you have any problems, or want to request a feature, please submit an issue to this repository. If you want to contributed to GillesPy2, please send a pull request. If you have any questions, contact Brian Drawert.

Authors

• Dr. Brian Drawert
• Dr. Kevin Sanft
• Ghilman Brock
• Eliot Dixon
• Dalton Nickerson
• Sean Matthew
• George Hall
• W.R. Jackson

License

GillesPy2 is licenced under GPLv3, see [LICENCE] for details.

Acknowledgments

This work has been funded by National Institutes of Health (NIH) NIBIB Award No. 2R01EB014877-04A1