Online databases
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Jump to navigationJump to search(mostly) Data[edit | edit source]
- Collaborative Research in Computational Neuroscience (CRCNS)
- Allen Institute data
- Allen Institute data wiki-guide
- German Neuroinformatics Node (G-Node)
- Mosers' online datasets
- Human Connectome Project
- Gene Expression Omnibus
- Janelia Research Campus (HHMI) Several labs at Janelia have data available, however (unlike for their tool-sharing endeavors) there does not seem to be a central web-hub for data sharing. Here is what we have found:
- Hippocampus RNA-seq atlas
- FlyEM Drosophila connectome project. Data is available upon request (see page for relevant details). Possibly this is due to the size of the data?
- MouseLight claims that data will be available starting summer of 2016
- Spruston lab Some interesting looking materials, including cell morphologies and some other info about single cells in hippocampus
- Scalable Brain Atlas
- Anne Churchland data a dataset and code from Anne Churchland. The CSH Information Repository doesn't have much data now, but maybe in the future it will have more.
- open connectome
- NeuroElectro "organizing information on cellular neurophysiology"
- Hippocampome "The Hippocampome is a curated knowledge base of the circuitry of the hippocampus of normal adult, or adolescent, rodents at the mesoscopic level of neuronal types"
- Digital Reconstruction of Neocortical Microcircuitry from the Blue Brain Project
- SenseLab
- The Neural Prediction Challenge
- Data Dryad
- The R-fMRI Network A network for supporting resting-state fMRI related studies
- BrainMaps.org "BrainMaps.org, launched in May 2005, is an interactive, multiresolution next-generation brain atlas that is based on over 140 million megapixels of sub-micron resolution, annotated, scanned images of serial sections of both primate and non-primate brains and that is integrated with a high-speed database for querying and retrieving data about brain structure and function over the internet."
- Temporal-lobe.com "Temporal-lobe.com offers 1) Descriptions of all known anatomical connections of the rat hippocampal formation. 2) A graphical interface to search and display these connections. 3) A way to quickly find the original articles describing these connections."
- mouseconnectome.org
- Fruit Fly Brain Observatory
Code and Software Packages[edit | edit source]
Data analysis[edit | edit source]
- STRFPak "The spatio- and spectro- temporal receptive field estimation package"
- nSTAT neural Spike Train Analysis Toolbox
- Stan
- Brain Connectivity Toolbox
E-phys[edit | edit source]
- Klusta framework (associated with the Cortical Processing Laboratory at UCL, as well as György Buzsáki at NYU).
- associated paper: Spike sorting for large, dense electrode arrays (Nature Neuroscience 19, 634–641 (2016))
- KiloSort also associated with the Cortical Processing Laboratory at UCL. This package uses GPU computing and therefore is faster than Klusta. Unclear what the relationship between the two is.
Calcium imaging[edit | edit source]
- Suite2P image processing and ROI detection software from the Cortical Processing Laboratory at UCL. Can take advantage of (but does not require) GPU's.
Simulations (neurons and networks)[edit | edit source]
- NEURON "for empirically-based simulations of neurons and networks of neurons"
- Brian The Brian spiking neural network simulator
- NEST The Neural Simulation Tool
- PyNN "A Python package for simulator-independent specification of neuronal network models"
- NeuroML "A Model Description Language for Computational Neuroscience"
- XPPAUT from Bard Ermentrout. A flexible software tool for solving a variety of differential equations, for example in the context of neuron membranes. Incorporates AUTO and PHASEPLANE.
Group repositories[edit | edit source]
- Code neuro
- The Cortical Processing Laboratory at UCL
- main website: Cortical Processing Laboratory
- Janelia
- The Blue Brain Project
- International Neuroinformatics Coordinating Facility (INCF)
Personal and lab repositories[edit | edit source]
- Jakob Macke
- Chris Burgess
- Byron Yu
- Srini Turaga
- Mauro Maggioni Duke applied mathematics professor working on manifold learning.
- Sayan Mukherjee Duke applied math professor
- John Cunningham
- Mark Churchland
Resources[edit | edit source]
- NeuralEnsemble NeuralEnsemble is a community-based initiative to promote and co-ordinate open-source software development in neuroscience.
- Open Source Brain
- ModelDB
- Brain Architecture Project
- SciCrunch
- Neuroscience Information Framework
- International Neuroinformatics Coordinating Facility
- wikipedia list of neuro databases
- What is this list?
- Simons Center for Data Analysis
- Synapse (from Sage bionetworks)
- "github for research"?
- "Statistics for biologists" web collection from Nature webpage