Virtual Research Environment

VRE is a web-based collaborative working environment providing its users with a set of ready-to-use services (datasets, analysis tools and visualizaters) for supporting a research lifecycle. It is written in PHP, HTML and Javascript.

Flavors

Several research projects has adopted the VRE framework for its project-specific purposes. For example:

• MuG : https://vre.multiscalegenomics.eu
• OpenEBench : https://openebench.bsc.es/vre

Code structure

• composer.json: 3rd party software requirements
• config : configuration files
  • settings global application file
  • conf files for credentials : mail, db, oauth2, etc
  • bootstrap VRE application
• install : installation instructions and data
  • install instructions
  • database skeleton with structural collections
  • data datasets and sample schemas
• logs : paths for VRE logging files
• public : web application elements
  • 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