compneuro

DLCISNN

Cerebellum-inspired spiking neural network(DLCISNN), a hybrid of Spiking Neural Network and Deep learning networks with the architecture and firing behaviour inspired from cerebellar microcircuitry.

BST_PD_ComplexNetworks2019

A computational model of mapping TNFa signalling in Parkinson's disease(PD) has been developed to understand how it mediates glutamate excitotoxicity and neuroinflammation leading to disease pathogenesis and progression. Pathways were modeled and simulated using the biochemical pathway visualization program CellDesigner, a modeling tool for gene-regulatory and biochemical networks that support graphical notation and listing of symbols. The model allows a qualitative analysis of PD and a key signalling pathways for evaluating PD treatment conditions relating pathophysiology to molecular concentration changes recordable from biological experiments.

ReConv-LFP-modeling-algorithm-for-Neuron-Python

Repetitive convolution (ReConv) algorithm for LFP reconstruction coded for Neuron+Python (ModelDB: 139883)

LFPsim

Simulation scripts to compute Local Field Potentials (LFP) of cable compartmental models implemented with NEURON

ABioNLP

ABioNLP tool - A Biological Natural Language Processing Tool for Systems Biology, Translational science and Medicine. This tool is part of the paper "Mining Scientific Articles for Inter-Relationships and Visualisation: Natural Language Processing for Systems Biology Modeling" by Nidheesh Melethadathil, Priya Chellaiah, Jaap Heringa, Bipin Nair and Shyam Diwakar.

compneuro.github.io

TCOB_Neuron

TCOB is a constrained-object programming language, a temporal extension of the constrained-object language COB. This document contains instructions to create and run TCOB programs in Swi-prolog environment. In this implementation, we show how modeling neural and microcircuit network dynamics can be achieved using TCOB. Developed by Manjusha Nair, Jinesh Manchan Kannimoola, Shyam Diwakar Amrita Vishwa Vidyapeetham (University), Kollam, Kerala, India. and by Bharat Jayaraman State University at Buffalo, NY, USA. Last updated 26-February-2018 More details will be made available. This is a preliminary version of the code for results in the paper titled "A Temporal Constrained Object based Declarative Programming Paradigm for Modelling Neuronal Dynamics" (manuscript submitted).

compneuro

GitHub pages for Amrita Computational Neuroscience Laboratory, Amrita University, India

PD_BiochemicalSystemsTheory

Major pathways involving in Parkinson's disease (PD) such as alphasynuclein aggregation, dopamine synthesis, lewy body formation, tau phosphorylation, parkin, and apoptosis were modeled using stochastic differential equations. Pathways were modeled and simulated using the biochemical pathway visualization program CellDesigner, a modeling tool for gene-regulatory and biochemical networks that support graphical notation and listing of symbols. The model allows a qualitative analysis of PD and a key signalling pathways for evaluating PD treatment conditions relating pathophysiology to molecular concentration changes recorded in experiments.

Amrita-Neuron-Simulator

A graphical web-based Neuron simulator (implemented on JS) and models neuronal spiking dynamics replicated in the soma or in a section of excitable neuronal membrane using the Hodgkin-Huxley equations. Developed as a virtual lab, several experiments on vlab.amrita.edu will be based on this educational tool. This JS based implementation allows simulating HH-style dynamics, AdEx integrate and fire neuron models.

GrC

Cerebellum Granule Neuron Model (working copy as on Modeldb)

reconv

working version of Repetitive Convolution Code (works on NEURON simulator and Matlab)

Repetitive-Convolution-LFP-reconstruction

Reconstructing evoked LFP in cerebellar granular layer using jittered repetitive convolution (ReConv)