KappaNEURON 0.2.0rc3

KappaNEURON integrates the SpatialKappa simulator with NEURON to allow rule-based simulations of molecular systems embedded in neurons.

KappaNEURON

KappaNEURON integrates the SpatialKappa simulator with NEURON to allow rule-based simulations of molecular systems embedded in neurons.

For example, the package facilitates simulation of dynamic models of the postsynaptic proteome in the context of the spine head.

Further details

• Sterratt, D. C., Sorokina, O. and Armstrong, J. D. (2015). ‘Integration of rule-based models and compartmental models of neurons’. Lecture Notes in Bioinformatics 7699: 143-158. Presented to the Third International Workshop on Hybrid Systems Biology Vienna, Austria, July 23-24, 2014 at the International Conference on Computer-Aided Verification 2014. doi:10.1007/978-3-319-27656-4_9. Preprint at arXiv:1411.4980
• Presentation given to Hybrid Systems Biology 2014

Installation & testing

1. Install NEURON v. 7.4 with python enabled, follow the instructions in step 1 of KappaNEURON installation from source

2. Run pip install KappaNEURON

KappaNEURON has been tested on the following combinations of software:

KappaNEURON	OS	gcc	Python	Java	py4j	NEURON
0.1.0	Ubuntu 14.04	4.8.4	2.7	openjdk 7	0.10.4	trunk of NEURON mercurial repository on 2014-09-23
0.2.0	Ubuntu 14.04	4.8.4	2.7	openjdk 7	0.10.4	7.4 as of 2017-01-13
0.2.0	Ubuntu 16.04	5.4.0	2.7	openjdk 7	0.10.4	7.4 as of 2017-01-13

Authorship & License

KappaNEURON is Copyright © 2013-2014, 2017 David C. Sterratt <[e-mail]> and is released under the GPL Version 3.

We thank Anatoly Sorokin for his help with SpatialKappa and Vincent Danos for helpful discussions.

Acknowledgements

The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement nos. 241498 (EUROSPIN project), 242167 (SynSys-project) and 604102 (Human Brain Project).