https://github.com/davidcsterratt/KappaNEURON
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README.md
KappaNEURON
===========
KappaNEURON integrates the [SpatialKappa][SpatialKappa] simulator with
[NEURON][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.
![KappNEURON demonstration simulation of postsynaptic proteome in context of spine head - first 6 seconds](doc/figs/neuron_kappa_Very_short_6000.png)
![KappNEURON demonstration simulation of postsynaptic proteome in context of spine head - first 65 seconds](doc/figs/neuron_kappa_Very_short_65000.png)
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](http://dx.doi.org/10.1007/978-3-319-27656-4_9). Preprint at <a title="Abstract"
href="http://arxiv.org/abs/1411.4980">arXiv:1411.4980</a>
* [Presentation given to Hybrid Systems Biology 2014](doc/2014-07-24-rb-compartmental-method.pdf)
Installation & testing
------------------------
* To install, follow the instructions in [doc/INSTALL.md][INSTALL]
* KappaNEURON has been tested on Ubuntu 14.04 (gcc version 4.8.4,
python 2.7, openjdk 7) with py4j 0.10.4 and NEURON from the trunk of
its mercurial repository on 2014-09-23.
Authorship & License
--------------------
KappaNEURON is Copyright © 2013-2014, 2017 David C. Sterratt
<<david.c.sterratt@ed.ac.uk>> and is released under the
[GPL Version 3](http://www.gnu.org/copyleft/gpl.html).
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).
[SpatialKappa]: https://github.com/davidcsterratt/SpatialKappa "SpatialKappa"
[NEURON]: http://neuron.yale.edu/neuron/ "NEURON"
[INSTALL-neuron]: doc/INSTALL-neuron "NEURON installation instructions"
[INSTALL]: doc/INSTALL.md "KappaNEURON installation instructions"
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