open data repository

open science framework for data sharing and collaboration. Has GitHub and AWS integrations. Free, open source from the Center for Open Science.

ropen science hackathon.

R ipython notebook bindings project

Data management tools

2015-02-25 17:01:22

Permanent repositories

Both of these are supported exports from rOpenScience

DataONE. Collab between NSF, UC Santa Barbra, Univ New Mexico, Oak Ridge, etc. Like fig share but bigger more flexible?


DMPTool from UC Digital Library for creating data management plans for funding agencies-- for collection and storage during and after projects.

UC3 from University of California Digital Library

Open models database


output to different languages, incl C, fortran, matlab, python

model of spontaneous activity in developing networks

Curated from:

Joel Tabak, Michael Mascagni, Richard Bertram, 2010, Journal of Neurophysiology, volume 103, 2208-2221. PubMed ID: 20164396

Hierarchical information visualization

MySQL Workbench is highly recommended

People have even used Omnigraffle, a classic graphviz based drawling/outlining/layout program for Mac OSX. Lots of nice graphics stencils (including programming, hardware, software, site design) at graffletopia

Stencil for drawing IDEF1X compliant data models using IEEE notation (crows feet):

Some people have used it for MySQL visualization and to export an omnigraffle hierarchy.

Gist for a Python script to convert MySQL table to omnigraffle. Uses appscript for the omnigraffle Applescript bindings in the Pro version.

Here is a gist for a ruby script that uses OSX scripting bridge to pull hierarchical omnigraffle document data to JSON


Talk (2013) by Stephen Friend at 10th annual Allen Brain Institute symposium (at youtube) on need for github for science. Introduces Synapse which is a platform which is supposed to be just that.

Core code is on Github Wiki entry

for biomedical data scientists we have created an environment that aids these users in sharing all of their digital research assets including data, code, and analysis results. These assets can be broadly shared and accessed through a unified set of RESTful APIs – through which Synapse provides integration points in R, Python, and the Linux shell in order to enable dissemination of findings across common analytical environments.

Furthermore, Synapse provides advanced capabilities for formally tracking the relationship between these digital assets through the Synapse provenance system, and for documenting and disseminating their work in ways that others can reproduce and reuse. These capabilities are key in supporting larger research teams, such as the 200+ scientists that collaborated through Synapse as part of the TCGA Pan Cancer Analysis Working Group.

Second, for clinical and biological scientists we have focused on developing Synapse as a community hub that creates a partnership between computational / analytical users and the more biologically / clinically minded scientists. In particular, the Synapse web portal is designed to enhance this communication and grow communities of scientists with diverse skill sets that can work together to interpret complex and diverse biomedical data sets.

Sage Bionetworks also makes 'Bridge Server'. Pages on Confluence and Github:

Sage Bionetworks’ Bridge Server is designed to securely manage data captured from IRB-approved human health research studies conducted through mobile technology platforms.

NeuroDebian linux distro with python psychophysics, electrophysiology, mri, and dataset access software installed.

scalable mouse brain atlas

map of developing human brain, atlas Same vtk visualization of connectivity as in mouse brain atlas.

Jupyter, Docker Sage notebook like interface for teaching. More info and python hacking tips for cognitive neuroscience and teaching at a octopress blog at berkeley

the new ipython, jupyter