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https://github.com/inab/openvre

Open Virtual Research Environment
https://github.com/inab/openvre

html javascript mongodb php vre

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Open Virtual Research Environment

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README

        

Open Virtual Research Environment (openVRE)
=========

### :information_source: Please, visit the [Wiki Pages](https://github.com/inab/openVRE/wiki) to learn more on 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](https://github.com/Multiscale-Genomics/VRE) |
| OpenEBench | ELIXIR Benchmarking Platform | https://openebench.bsc.es/vre | [Code](https://github.com/inab/openEBench_vre) |
| euCanSHare | Computational environment for cardiovascular research | https://vre.eucanshare.bsc.es/ | [Code](https://github.com/euCanSHare/vre/) |
| IPC | Individualized Paediatric Cancer Analysis Platform | https://vre.ipc-project.bsc.es/ | [Code](https://gitlab.bsc.es/inb/ipc/openvre) |
| euCanImage | Cancer imaging analysis platform enhanced by Artificial Intelligence| https://vre.eucanimage.eu/ |[Code](https://gitlab.bsc.es/inb/eucanimage/vre) |
| Disc4All | Computational simulations in translational medicine, applied to intervertebral disc degeneration.|https://vre.disc4all.eu/ |[Code](https://gitlab.bsc.es/inb/eucanimage/vre) |

### 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:

![arch](https://github.com/inab/openVRE/raw/master/public/assets/layouts/layout/img/wiki/architecture_overview.png)

### 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](./config) : configuration files
- [settings](./config/globals.inc.php.sample) sample for the global application settings
- [bootstrap](./config/bootstrap.php) bootstrap VRE application
- [install](./install) : installation instructions and data
- [install](./install/README.md) instructions
- [database](./install/database) skeleton with structural collections
- [data](./install/data) datasets and sample schemas
- [public](./public) : web application elements under the web server root directory
- **web pages**
- [home](./public/home) pages for 'Homepage' section
- [workspace](./public/workspace) pages for 'User Workspace' section
- [getdata](./public/getdata) pages for 'Get Data' section
- [launch](./public/launch) pages for 'Run Tool / Visualizers' section
- [help](./public/help) pages for 'Help' section
- [helpdesk](./public/helpdesk) pages for 'Helpdesk' section
- [admin](./public/admin) pages for 'Admin' section
- [user](./public/user) pages for 'User Profile' section
- [cookies](./public/cookies) notification
- **libraries**
- [applib](./public/applib) : pages' backend
- [assets](./public/assets) : pages' client scripts
- [phplib](./public/phplib) : VRE libraries and classes
- [htmlib](./public/htmlib) : html templates
- **content**
- [tools](./public/tools) : web form, assets and summart page for integrated tools
- [visualizers](./public/visualizers) : visualizers code
- [scripts](./scripts) : maintainance scripts