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

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.

KappNEURON demonstration simulation of postsynaptic proteome in context of spine head - first 6 seconds KappNEURON demonstration simulation of postsynaptic proteome in context of spine head - first 65 seconds

Publications

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

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_injectCalciumgit commit -m "EU acknowledgement
    

    The test should return OK and the following figure window should appear KappNEURON result of test_injectCalcium 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
    ```git commit -m "EU acknowledgement
    
    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

EU flag

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).
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