NOTE Due to the GitHub enforcement of 2fa, which requires me to share my phone number with Microsoft or install an untrusted Microsoft application on my phone, any updates to this repository will be pushed to its clone at GitLab or to my personal git repository. Please see all updates here. Sorry, there should be something private in this life where Microsoft, Google or others don't put their noses.
Auditory Brainstem Project is a software framework for NEURON+Python with MPI or threading parallelization. Ultimate goal of this project is provide a simple, flexible environment to create large-scale model, run simulations and analysis results of simulations for neural networks naturally split on distinctive nuclei. For more scientific details please visit main project's webpage
This code is designed to run through NSG Portal. It allows separate single-tread code, like setting network connectivity up, generating stimuli, collecting and indexing data, statistic analysis and graphics plotting from parallel code, i.e. actual simulation. As a result one should launch the application at least twice, but in wast majority cases three times with different command line keys. First to build model, this stage is called 'preset'. Then second time to run a simulation, this may be done on different computer and/or NSG portal. And finally the third time to index recordings, make statistic analysis and figures plotting. Please find more details in User guide page
Currently this project has unstable/experimental status and totally in the developing stage. We plan to create a stable branch and make first stable commit in a few months.
The code is distributed under GNU GPL v3 License.
Although it may be downloaded as zip archive, it is better to clone latest version from repository. For MacOS or Linux operating system, you need to open the terminal and run git program:
https://github.com/rat-h/auditory-brainstem-model.git
The project requites NEURON+Python software to run a simulation and standard scientific package for Python which is
The project was tested mostly under Ubuntu or openSUSE Linux and NSG portal. The project was successfully run on MacOS computer, but terminal skills are required.
The main advantage of open source project it is fast track of bug and bug fixing system. Please use project bug report system to post any issue.
Anyone can browse the code, commits and branches using project web interface. Please feel free to make you comments on files and wiki pages.
The simplest way to do this is became a Git Hub user and add yourself to project developers. An other way is use git as main platform. So make you changes in local repository and send me your patch on ruben.tikidji.hamburyan AT gmail.com Please read Git everyday to get familiar with git terminology.
Please note that this project contains external code:
- Original C-code of Zilany, M. S. A. and Carney, L.H. auditory nerve model which is published on authors website. Please refer to original paper for proper citation:Zilany, M. S. A. and Carney, L.H. (2010), Power-Law Dynamics in an Auditory-Nerve Model Can Account for Neural Adaptation to Sound-Level Statistics. (Journal of Neuroscience 30(31):10380-10390).
- GNU libresample version 1.7 which is distributed under LGPL licence.