Open Virtual Research Environment (openVRE)

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

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:

Requirements

• Web Server (e.g. Apache2)
• Mongo Client: mongodb-org-shell, mongodb-org-tools, php-mongo
• Oracle Grid Engine cluster queue client (formerly Sun Grin Engine): gridengine-client gridengine-common
• OpenID Connect/OAuth 2.0 client of an Identity Provider

openVRE installation

This repository contains all the code to build a functional openVRE-based analysis platform, prior installation and configuration. The final product is an online application with the virtual research environment integrating for demonstration purposes:

• one analysis tool: tool-skeleton
• one visualizer: NGL viewer)

See the installation guide for more detailed instructions.

Dependencies

• PHP (>=7.3)
• Composer : https://getcomposer.org/doc/00-intro.md

openVRE core

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