Online databases

== (mostly) Data ==
* Collaborative Research in Computational Neuroscience (CRCNS)
** "Neurodata Without Borders" data format
* 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 ==
=== Data analysis ===
* STRFPak "The spatio- and spectro- temporal receptive field estimation package"
* nSTAT neural Spike Train Analysis Toolbox
* Stan
* Brain Connectivity Toolbox
=== E-phys ===
* 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 ===
* 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) ===
* 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 ===
* 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 ===
* Jakob Macke
** pop_spike_dyn
** more lds estimation
* Chris Burgess
* Byron Yu
* Srini Turaga
* Mauro Maggioni Duke applied mathematics professor working on manifold learning.
* Sayan Mukherjee Duke applied math professor 
* John Cunningham
** preconditioned_GPs
* Mark Churchland
== Resources ==
* 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
** Neuroscience subgroup
* Synapse (from Sage bionetworks) 
** "github for research"?
* "Statistics for biologists" web collection from Nature webpage
== Forward-thinking publication systems ==
* F1000Research
* elife
* biorXiv
* arXiv, Neurons and Cognition