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biomedical-jupyter-examples

This repository encodes a biomedical research analysis as reproducible and executable Jupyter Notebooks in various programming languages.

ca-imaging-ro-crate

RO-Crate bundles from Calcium Imaging experiments including research data and their retrospective provenance

cartilage_electromechanics

Python script for the manuscript_____Farooqi, A.R.; Bader, R.; van Rienen, U. Numerical Study on Electromechanics in Cartilage Tissue with Respect to Its Electrical Properties. Tissue Eng. Part B Rev. 2019, 25, 152–166. doi:10.1089/ten.teb.2018.0214.

case-study-endocytosis

Models, generated experiments, and data for the endocytosis case study of the paper "Making Simulation Experiments Explicit and Accessible using Experiment Schemas""

case-study-neurostimulator

Models, generated experiments, and data for the neurostimulator case study of the paper "Making Simulation Experiments Explicit and Accessible using Experiment Schemas"

cellpixels

R package for statistics of fluorescence microscopy images

ckan

CKAN is an open-source DMS (data management system) for powering data hubs and data portals. CKAN makes it easy to publish, share and use data. It powers datahub.io, catalog.data.gov and europeandataportal.eu/data/en/dataset among many other sites.

ckanext-disablepwreset

A CKAN extension disbaling the passwort reset functionality

ckanext-dwgviewer

A drawing (AutoCAD) file viewer for ckan

ckanext-elaine_theme

A theme for the SFB ELAINE instance of a CKAN data repository

ckanext-ldap

CKAN plugin to provide LDAP authentication

ckanext-papaya

CKAN extension using Papaya viewer to provide views for DICOM and NIFTI files.

ckanext-paraview

CKAN extension using ParaViewWeb Visualizer to add resource views for STL and VTK files.

ckanext-pdfview

PDF viewer for CKAN >= 2.3

ckanext-privatedatasets

CKAN extension that allows a user to create private datasets only visible to certain users. The extension provides also an API to specify which users can access private datasets

ckanext-videoviewer

A video Viewer extension for ckan

ckanext-vtkjs

A CKAN extension to provide views for STL and VTK files.

datapusher

A standalone service that automatically migrates data to the CKAN DataStore

detectcilia

R package to detect cilia and other colored structures in confocal fluorescence microscopy images

docker-semanticmediawiki

Repository for playing with Docker and Semantic MediaWiki

elabapy

Python package to interact with eLabFTW's API

elabdoc

Source files for generating documentation for elabftw

elabftw

:notebook: Lab manager, experiment notebook, database for research labs

elabimg

elabftw in a docker container

electro-active-hydrogels

Python script for the manuscript_____Farooqi, A.R.; Zimmermann, J.; Bader, R.; van Rienen, U. Numerical simulation of electro-active hydrogels for cartilage tissue engineering. Materials 2019, 12(18), 2913; https://doi.org/10.3390/ma12182913.

emstimtools

icinga2

imageinformation

imagejplugin_count_and_measure

Plugin for ImageJ to count and measure cells

imagesummary

R package to summarize (pixel) information of a tiff-image