General Neuroscience resources
A list of freely available resources for Neuroscience community. This list is regularly updated, any suggestions or changes are very welcome at deepti.mittal12@gmail.com or https://deeptimittal12.github.io/neuroscience/ This list includes:
Research Data Management
- RDA - Research Data Sharing without barriers
- LabFolder - Electronic lab notebook, All your data in one place
- DMPonline - Electronic lab notebook, All your data in one placeOnline tool created by the Digital Curation Centre (DCC) to help researchers create and share data management plans.
- Data Management Costing Tool - UK Data Service
- Nextjournal - The notebook for reproducible research
- Code Ocean - a research collaboration platform.
- Jupyter Notebook -services for interactive computing across dozens of programming languages.
Current resources provided by Heidelberg University’s Kompetenzzentrum Forschungsdaten:
- Research data management
- bwFDM - German-language information portal on research data management (FDM)
- heiDATA - Heidelberg University’s repository for research data
- heiBOX - data sharing for smaller data sets
- heiCLOUD - The Heidelberg cloud infrastructure, configurable virtual analysis machines
- heiArchive - the central data archiving service at Heidelberg University, 10 year storage for data sets with metadata
SFB1158 Data management Support and Services
The above list contains some resources that might be more useful for the projects under SFB1158 Pain Project. It is a collaborative effort to gather the information about all the tools, resources, services and trainings related to neurophsyiology.
International and National Organisations, Training space, Communities
- INCF - International Neuroinformatics Coordinating Facility - A standards organization for open and FAIR neuroscience,
- INCF Training Space
- G-NODE - German Neuroinformatics Node
- Neurostars - A question and answer forum for neuroscience researchers, infrastructure providers and software developers.
- Human Brain Project - Neuroscience, computing, and brain-related medicine
- CodeNeuro - Bringing neuroscience and data science together
- OCNS - Organization for Computational Neuroscience
- NeuralEnsemble - a community-based initiative to promote and co-ordinate open-source software development in neuroscience. NeuralEnsemble hosts a number of software projects for computational and systems neuroscience, including PyNN, NeuroTools, Brian, Neo, OpenElectrophy, libNeuroML and Sumatra.
- Organization for Human Brain Mapping
- SFN - Society for Neuroscience
- FENS - Federation of European Neuroscience Societies
- IBI - International Brain Initiative
- INM - Institute of Neuroscience and Medicine - Forschungszentrum Jülich
Data Formats, Softwares and Computational tools
This is a list of standard tools, software packages, data types and formats that are popular in the neuroscience community.
Electrophsyiology Data Analysis
- Syntalos(formerly known as MazeAmaze) - a software for in-vivo behavior tracking, electrophysiology and control of automated mazes
- Open Ephys - Open source, Well-documented tools for electrophysiology research
- SpikeInterface - simplifies the process of running multiple spike sorters on the same dataset
- Spike Sorting Software Comparison: links and descriptions of publicly available code for spike sorting
- SpykeViewer - a multi-platform GUI application for navigating, analyzing and visualizing data from electrophysiological experiments or neural simulations. It is based on Neo format
- Neo - a hierarchical data model well adapted to intracellular and extracellular electrophysiology and EEG data with support for multi-electrodes
- Elephant - Software for common electrophysiological data analysis operations, built on the Neo data format
- Wave_Clus - a fast and unsupervised algorithm for spike detection and sorting
- Kilosort2: automated spike sorting with drift tracking and template matching on GPUs
Data Formats
- NIX - Neuroscience information exchange format data model for storing fully annotated datasets
- HDF5 - Hierarchical Data Format Version 5
- Neurodata Without Borders: Neurophysiology (NWB:N)
- Open Ephys - Open source, Well-documented tools for electrophysiology research
- Neuroshare - Open data specifications and software for neurophysiology
- NSDF - Neuroscience Simulation Data Format
- DICOM - Digital Imaging and Communications in Medicine) - An international standard to transmit, store, retrieve, print, process, and display medical imaging information.
- NIfTI - Neuroimaging Informatics Technology Initiative
- OpenNEURO - A free and open platform for sharing MRI, MEG, EEG, iEEG, and ECoG data
- BIDS - Brain Imaging Data Structure - A simple and intuitive way to organize and describe your neuroimaging and behavioral data)
Events, workshops and Conferences (and Virtual events)
- NWB User Days Workshop - Remote May 12-15, 2020
- Allen Insitute for Brain Science Events
- FENS Calender for upcoming events
- Neuroscience conference and events calendar 2020/21
Other relevant resource pages
- FENS resource list
- Open Computational Neuroscience Resources list
- Computational neuroscience resources by Dan Goodman
Online courses
- Coursera
Basic Neurobiology:
- Understanding the Brain: The Neurobiology of Everyday Life
- Advanced Neurobiology I
- Advanced Neurobiology II
- Synapses, Neurons and Brains
Medical Neuroscience:
NeuroImaging:
- MRI Fundamentals
- Principles of fMRI 1
- Principles of fMRI 2
- Fundamental Neuroscience for Neuroimaging
GitLab/Github basics guides
- GitLab basics guides
- Git Tutorials
- A bunch of good git tutorials
- Pro Git book, written by Scott Chacon and Ben Straub
- GitLab University
- All GitLab Courses by Udemy
Additional Resources
Plugins
| Plugin | README |
|---|---|
| Website | plugins/website/ |