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.
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 |
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:
- 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
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.
- PHP (>=7.3)
- Composer : https://getcomposer.org/doc/00-intro.md
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
- install : installation instructions and data
- 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