piandpower / arachne

Software for the synthesis of realistic neural networks and their numerical processing on remote clusters using parallel computing

ARACHNE

version 2.0

Update is expected to be released at 01.04.2017

ARACHNE is a newly designed simulation environment in which neural and neuroglial network organisation, optimisation and execution take advantage of the pre-set, optimised parallel algorithms for remote computations, and of a friendly user interface located on a local computer. In these settings, a neuroscientist without IT background should be able to incorporate the representative variety of biophysical mechanisms pertinent to nerve (or astroglial) cells, within a single network model in which the network complexity is limited only by the availability of remote computing resources, and not by the modelling kernel or its interface.

Installation.

There are 4 versions of ARACHNE. Each version has its own parameters of installation.

1. "Demo-version" - contains executables and the directory "Core", to create and to compute networks on a cluster with preinstalled kernel. These executables were compiled in MATLAB version 8.1.0.604 (R2013a). To run the demo on a local computer where this version of MATLAB is not installed (or the computer does not have any version of Matlab), a user has to install corresponding version of MATLAB Runtime (R2013a). It is a free package that can be downloaded from the webpage: https://www.mathworks.com/products/compiler/mcr/. The entire contents of Demo-version must be copied and installed anywhere on the local computer. To run GUI of ARACHNE the executable file START_Arachne.exe must be launched. (See Manual.docx for details)

2. "Full-version" contains two directories "host" and "worker" for installation ARACHNE in any cluster operating under Linux/Windows and any host computer operating under Windows with preinstalled Matlab.

3. "Matlab-version" contains only "host" files with MatLab codes and the bat-files that control the communication between host computers and the preinstalled cluster. This catalogue can be downloaded at any place of "host" computer operating under Windows. The file Readme.md has a detail instruction about a set of steps of working with the soft.

4. "Mobile-version" contains files for the mobile device operating under Mobile OS.

Examples

There are five files with a set of parameters for different configurations of ARACHNE https://github.com/LeonidSavtchenko/Arachne/tree/master/ExamplePLOS A set of basic input parameters necessary for reproduction plots in the manuscript published in PLOS Comp Biology

Documentation

Manual and API documentation can be found at https://github.com/LeonidSavtchenko/Arachne

Written by Leonid Savtchenko.
Visit us at:
http://www.ucl.ac.uk/ion/departments/epilepsy/themes/synaptic-imaging
Department of Clinical and Experimental Epilepsy
Institute of Neurology
University College London
UK