Computational Neuroscience

BigPint Bioconductor package that makes BIG (RNA seq) data pint sized

The BigPint package can help examine any large multivariate dataset. However, we note that the example datasets and example code in this package consider RNA-sequencing datasets. If you are using this software for RNA-sequencing data, then it can help you confirm that the variability between your treatment groups is larger than that between your replicates and determine how various normalization techniques in popular RNA-sequencing analysis packages (such as edgeR, DESeq2, and limma) affect your dataset.

neurolib

Easy whole-brain modeling for computational neuroscientists 👩🏿‍🔬💻🧠 In its essence, neurolib is a computational framework for simulating coupled neural mass models written in Python. It helps you to easily load structural brain scan data to construct brain networks where each node is a neural mass representing a single brain area.

YAPiC

With YAPiC you can make your own customized filter (also called model or classifier) to enhance a certain structure of your choice with a simple Python based command line interface, installable with pip.

Computational Cognitive Neuroscience 4th Ed

This is the 4th edition of the online, freely available textbook, providing a complete, self-contained introduction to the field of Computational Cognitive Neuroscience, where computer models of the brain are used to understand a wide range of cognitive functions, including perception, attention, motor control, learning, memory, language, and executive function.

Emergent Neural Network Simulation Software

Neural network simulation software written in Go and Python, for developing biologically-based but also computationally functional neural models. Features an interactive 3D interface for visualizing networks and data, and has many implemented models of a wide range of cognitive phenomena.

Uncertainpy A python toolbox for uncertainty quantification and sensitivity analysis tailored towards computational neuroscience

Uncertainpy is a python toolbox for uncertainty quantification and sensitivity analysis tailored towards computational neuroscience. Uncertainpy is model independent and treats the model as a black box where the model can be left unchanged.

PsychRNN: An Accessible and Flexible Python Package for Training Recurrent Neural Network Models on Cognitive Tasks

PsychRNN is designed for neuroscientists and psychologists who are interested in RNNs as models of cognitive function in the brain. Despite growing interest in RNNs as models of brain function, this approach poses relatively high barriers to entry to researchers, due to the technical know-how required for specialized deep learning software (e.

INCF NeuroStars

Neurostars is an open source question and answer site that serves the INCF network and the global neuroscience community as a forum for knowledge exchange between neuroscience researchers at all levels of expertise, software developers, and infrastructure providers.

INCF TrainingSpace

TrainingSpace is an online hub that aims to make neuroscience educational materials more accessible to the global neuroscience community developed by the Training and Education Committee composed of members from the INCF network, HBP, SfN, FENS, IBRO, IEEE, BD2K, and iNeuro Initiative.

Open Source Brain

Open Source Brain, a platform for sharing, viewing, analyzing, and simulating standardized models from different brain regions and species. Model structure and parameters can be automatically visualized and their dynamical properties explored through browser-based simulations.