Metadata-Version: 1.2
Name: KappaNEURON
Version: 0.3.0rc1
Summary: KappaNEURON integrates the SpatialKappa simulator with NEURON to allow rule-based simulations of molecular systems embedded in neurons.
Home-page: https://github.com/davidcsterratt/KappaNEURON
Author: David C Sterratt
Author-email: david.c.sterratt@ed.ac.uk
License: UNKNOWN
Description: 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)
        
        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](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
        ------------------------
        
        1. Install NEURON v. 7.4 with python enabled using [these instructions
           for Ubuntu 18.04][INSTALL-neuron]
        
        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
           ![KappNEURON result of test_injectCalcium](doc/figs/test_injectCalcium_2018-09-05.png)
           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                                | 
        
        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](demo/ca_pulse)
        2. [Ca-CaM-CaMKII pathway in the postsynaptic density](demo/psd)
        
        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.md "NEURON installation instructions"
        
        <!--  LocalWords:  KappaNEURON SpatialKappa KappNEURON Sterratt Danos
         -->
        <!--  LocalWords:  Anatoly Sorokin FP EUROSPIN SynSys
         -->
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 2
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Requires-Python: <3
