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https://github.com/inab/openvre

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

html javascript mongodb php vre

Last synced: 5 days ago
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Open Virtual Research Environment

Host: GitHub
URL: https://github.com/inab/openvre
Owner: inab
License: apache-2.0
Created: 2019-02-22T12:37:58.000Z (over 5 years ago)
Default Branch: master
Last Pushed: 2024-10-29T12:36:57.000Z (16 days ago)
Last Synced: 2024-10-29T15:04:02.627Z (16 days ago)
Topics: html, javascript, mongodb, php, vre
Language: JavaScript
Homepage:
Size: 12.6 MB
Stars: 6
Watchers: 10
Forks: 2
Open Issues: 0
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG
- License: LICENSE

Awesome Lists containing this project

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