Metadata-Version: 2.1
Name: KappaNEURON
Version: 0.2.0rc3
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)
        
        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
        ------------------------
        
        1. Install NEURON v. 7.4 with python enabled, follow the instructions
           in step 1 of [KappaNEURON installation from source][INSTALL]
        
        2. Run `pip install KappaNEURON`
        
        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                                | 
        
        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"
        
        <!--  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
Description-Content-Type: text/markdown
