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.

Publications

Please cite Sterratt & al. (2015) when using KappaNEURON:

• 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 using these instructions for Ubuntu 18.04

2. Create a virtual environment:

   sudo apt install virtualenv
   virtualenv --python=python2.7 /tmp/KappaNEURON
   source /tmp/KappaNEURON/bin/activate
   

3. Run pip install KappaNEURON

4. Run an inital test:

   python2.7 -i -m unittest KappaNEURON.tests.TestCaAccumulation.test_injectCalcium
   

   The test should return OK and the following figure window should appear The figure will be saved in PNG format to the directory test_figs.

5. At present is not possible to run the entire test suite in one go, because completely clean tear down of the test environoment is not possible with the current version of KappaNEURON. Therefore individual tests can be run as follows:

    python2.7 -m unittest KappaNEURON.tests.TestCaAccumulation.test_injectCalciumGHK
    python2.7 -m unittest KappaNEURON.tests.TestCaAccumulation.test_injectCalciumPump
    python2.7 -m unittest KappaNEURON.tests.TestCaAccumulation.test_injectCalciumPumpGHK
    python2.7 -m unittest KappaNEURON.tests.TestCaAccumulation.test_injectCalciumPump2
    python2.7 -m unittest KappaNEURON.tests.TestCaAccumulation.test_injectCalciumPump2k2
    python2.7 -m unittest KappaNEURON.tests.TestCaAccumulation.test_twoMembraneSpecies
    python2.7 -m unittest KappaNEURON.tests.TestCaAccumulation.test_twoMembraneSpeciesOneUncharged
   

   Most of these tests save figures to test_figs. The red ("mod") and blue ("kappa") curves in these figures should more-or-less overlap. The kappa curves will be more irregular, because of the stochstic simulation.

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
0.3.x	Ubuntu 18.04	5.4.0	2.7	openjdk 7	0.10.4	7.4 as of 2017-01-13

Getting started

Code for the two demo simulations in Sterratt & al. (2015) paper are the demos subdirectory:

1. Calcium pump in response to calcium pulse
2. Ca-CaM-CaMKII pathway in the postsynaptic density

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.

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

Acknowledgements

This open source software code was developed with 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), and in the Human Brain Project, funded from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreements No. 720270 and No. 785907 (Human Brain Project SGA1 and SGA2).