Open Virtual Research Environment (openVRE)

ℹ️ Please, visit the Wiki Pages to learn more on openVRE

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openVRE is a cloud-based working environment that allow to rapidly build your own computational platform. It offers:

• a user-friendly web-based interface that integrates a number of pluggable resources:
  • analysis tools or pipelines,
  • interfaces to external data repositories,
  • visualizaters
• an scalable backend for cloud computing compatible with OCCI middlewares like OpenNebula or OpenStack.

Flavors

Several research projects have adopted openVRE as the framework for rapidly prototying their computational platforms:

Project	Title	URL	Repository
MuG	Virtual Research Enviroment for Multiscale Complex Genomics	https://vre.multiscalegenomics.eu	Code
OpenEBench	ELIXIR Benchmarking Platform	https://openebench.bsc.es/vre	Code
euCanSHare	Computational environment for cardiovascular research	https://vre.eucanshare.bsc.es/	Code
IPC	Individualized Paediatric Cancer Analysis Platform	https://vre.ipc-project.bsc.es/	Code
euCanImage	Cancer imaging analysis platform enhanced by Artificial Intelligence	https://vre.eucanimage.eu/	Code
Disc4All	Computational simulations in translational medicine, applied to intervertebral disc degeneration.	https://vre.disc4all.eu/	Code

Components

This repository contains the code of the openVRE core, the central web server managing and distributing the executions to plugged-in elements. However, a fully functional infrastructure include other elements depicted here:

Code repository structure

openVRE cores is a server-side web application mainly written in PHP modules, as well as some Java Script based libraries. Following, a short description of the content of this repository.

• composer.json: 3rd party software requirements
• config : configuration files
  • settings sample for the global application settings
  • bootstrap bootstrap VRE application
• install : installation instructions and data
  • install instructions
  • database skeleton with structural collections
  • data datasets and sample schemas
• public : web application elements under the web server root directory
  • web pages
  • home pages for 'Homepage' section
  • workspace pages for 'User Workspace' section
  • getdata pages for 'Get Data' section
  • launch pages for 'Run Tool / Visualizers' section
  • help pages for 'Help' section
  • helpdesk pages for 'Helpdesk' section
  • admin pages for 'Admin' section
  • user pages for 'User Profile' section
  • cookies notification
  • libraries
  • applib : pages' backend
  • assets : pages' client scripts
  • phplib : VRE libraries and classes
  • htmlib : html templates
  • content
  • tools : web form, assets and summart page for integrated tools
  • visualizers : visualizers code
• scripts : maintainance scripts