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"author": "David C Sterratt",
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"description": "KappaNEURON\n===========\n\nKappaNEURON integrates the [SpatialKappa][SpatialKappa] simulator with\n[NEURON][NEURON] to allow rule-based simulations of molecular systems\nembedded in neurons.\n\nFor example, the package facilitates simulation of dynamic models of\nthe postsynaptic proteome in the context of the spine head.\n\n\n\n\nPublications\n------------\n\nPlease cite Sterratt & al. (2015) when using KappaNEURON:\n\n* Sterratt, D. C., Sorokina, O. and Armstrong,\n J. D. (2015). \u2018Integration of rule-based models and compartmental\n models of neurons\u2019. Lecture Notes in Bioinformatics 7699: 143-158.\n Presented to the Third International Workshop on Hybrid Systems\n Biology Vienna, Austria, July 23-24, 2014 at the International\n Conference on Computer-Aided\n 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 arXiv:1411.4980\n* [Presentation given to Hybrid Systems Biology 2014](doc/2014-07-24-rb-compartmental-method.pdf)\n\nInstallation & testing\n------------------------\n\n1. Install NEURON v. 7.4 with python enabled using [these instructions\n for Ubuntu 18.04][INSTALL-neuron]\n\n2. Create a virtual environment:\n ```\n sudo apt install virtualenv\n virtualenv --python=python2.7 /tmp/KappaNEURON\n source /tmp/KappaNEURON/bin/activate\n ```\n\n3. Run `pip install KappaNEURON`\n\n4. Run an inital test:\n ```\n python2.7 -i -m unittest KappaNEURON.tests.TestCaAccumulation.test_injectCalcium\n ```\n The test should return `OK` and the following figure window should\n appear\n \n The figure will be saved in PNG format to the directory\n `test_figs`.\n\n5. At present is not possible to run the entire test suite in one go,\n because completely clean tear down of the test environoment is not\n possible with the current version of KappaNEURON. Therefore\n individual tests can be run as follows:\n ```\n\tpython2.7 -m unittest KappaNEURON.tests.TestCaAccumulation.test_injectCalciumGHK\n\tpython2.7 -m unittest KappaNEURON.tests.TestCaAccumulation.test_injectCalciumPump\n\tpython2.7 -m unittest KappaNEURON.tests.TestCaAccumulation.test_injectCalciumPumpGHK\n\tpython2.7 -m unittest KappaNEURON.tests.TestCaAccumulation.test_injectCalciumPump2\n\tpython2.7 -m unittest KappaNEURON.tests.TestCaAccumulation.test_injectCalciumPump2k2\n\tpython2.7 -m unittest KappaNEURON.tests.TestCaAccumulation.test_twoMembraneSpecies\n\tpython2.7 -m unittest KappaNEURON.tests.TestCaAccumulation.test_twoMembraneSpeciesOneUncharged\n ```\n\n Most of these tests save figures to `test_figs`. The red (\"mod\")\n and blue (\"kappa\") curves in these figures should more-or-less\n overlap. The kappa curves will be more irregular, because of the\n stochstic simulation.\n\nKappaNEURON has been tested on the following combinations of software:\n\n| KappaNEURON | OS | gcc | Python | Java | py4j | NEURON | \n|-------------|--------------|-------|--------|-----------|--------|-----------------------------------------------------| \n| 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 | \n| 0.2.0 | Ubuntu 14.04 | 4.8.4 | 2.7 | openjdk 7 | 0.10.4 | 7.4 as of 2017-01-13 | \n| 0.2.0 | Ubuntu 16.04 | 5.4.0 | 2.7 | openjdk 7 | 0.10.4 | 7.4 as of 2017-01-13 |\n| 0.3.x | Ubuntu 18.04 | 5.4.0 | 2.7 | openjdk 7 | 0.10.4 | 7.4 as of 2017-01-13 |\n\nGetting started\n---------------\n\nCode for the two demo simulations in Sterratt & al. (2015) paper are\nthe `demos` subdirectory:\n1. [Calcium pump in response to calcium pulse](demo/ca_pulse)\n2. [Ca-CaM-CaMKII pathway in the postsynaptic density](demo/psd)\n\nAuthorship & License\n--------------------\n\nKappaNEURON is Copyright \u00a9 2013-2014, 2017 David C. Sterratt\n<> and is released under the\n[GPL Version 3](http://www.gnu.org/copyleft/gpl.html).\n\nWe thank Anatoly Sorokin for his help with SpatialKappa and Vincent\nDanos for helpful discussions.\n\nAcknowledgements\n----------------\n\nThe research leading to these results has received funding from the\nEuropean Union Seventh Framework Programme (FP7/2007-2013) under grant\nagreement nos. 241498 (EUROSPIN project), 242167 (SynSys-project) and\n604102 (Human Brain Project). \n\n[SpatialKappa]: https://github.com/davidcsterratt/SpatialKappa \"SpatialKappa\"\n\n[NEURON]: http://neuron.yale.edu/neuron/ \"NEURON\"\n\n[INSTALL-neuron]: doc/INSTALL-neuron.md \"NEURON installation instructions\"\n\n\n\n\n\n",
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