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This interactive tool allows finding genes affected by deleterious variants that segregate along family pedigrees , case-controls or sporadic samples

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babelomics/bierapp

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Overview

BierApp is the gene/variant prioritization tool of the BiER (the Team of BioInformatic for Rare Diseases). This interactive tool allows finding genes affected by deleterious variants that segregate along family pedigrees, case-controls or sporadic samples. The tool provides an easy-to-use environment in which heuristic filters can be applied to narrow down a large liste of variants found in whole exome (or genome) experiments.

Documentation

You can find BierApp documentation and tutorials at: https://github.com/babelomics/bierapp/wiki.

How to cite BiERapp

Alemán A, Garcia-Garcia F, Salavert F, Medina I, Dopazo J. A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W88-93. doi: 10.1093/nar/gku407. PubMed NAR PMC

Issue Tracking

You can report bugs or request new features at GitHub issue tracking.

Release Notes and Roadmap

Releases notes are available at GitHub releases.

Roadmap is available at GitHub milestones. You can report bugs or request new features at GitHub issue tracking.

Versioning

BierApp is versioned following the rules from Semantic versioning.

Maintainers

We recommend to contact BierApp developers by writing to OpenCB mailing list babelomics@cipf.es. The main developers and maintainers are:

Former contributors

  • Roberto Alonso
  • Mercedes Medina
  • Alejandro Aleman
Contributing

BierApp is an open-source and collaborative project. We appreciate any help and feeback from users, you can contribute in many different ways such as simple bug reporting and feature request. Dependending on your skills you are more than welcome to develop client tools, new features or even fixing bugs.

How to build

BierApp is developed in HTML5, therefore it is mainly developed in JavaScript and makes a heavy usage of HTML and CSS. It uses Bower and Grunt as building tools. BierApp also requires of OpenCB JSorolla to be built, this is a JavaScript library developed for several OpenCB web-based projects, this can be found as Git submodule in BierApp.

Stable releases are merged and tagged at master branch, you are encourage to use latest stable release for production. Current active development is carried out at develop branch, only building is guaranteed and bugs are expected, use this branch for development or for testing new functionalities. The only source code dependency of BierApp from OpenCB is JSorolla. BierApp master branch depends on stable branches in JSorolla, while develop branch of BierApp depends on JSorolla develop.

Prerequisites

The following technologies are needed to build BierApp: Node.js, npm, Bower and Grunt.

Installing Node.js and npm

To install Node.js you can visit this link.

npm stands for node packaged modules and it is the dependency manager of Node.js.

Install Bower and Grunt

After installing Node.js and npm, we can install Bower and Grunt by executing the following commands with root permission:

sudo npm install -g bower
sudo npm install -g grunt-cli

Cloning

BierApp is an open-source and free project, you can download master branch by executing:

imedina@ivory:~$ git clone https://github.com/babelomics/bierapp.git
Cloning into 'bierapp'...
remote: Counting objects: 847, done.
remote: Compressing objects: 100% (4/4), done.
remote: Total 847 (delta 0), reused 0 (delta 0), pack-reused 842
Receiving objects: 100% (847/847), 4.40 MiB | 1.10 MiB/s, done.
Resolving deltas: 100% (375/375), done.

To fetch the latest stable release at develop branch can be downloaded executing:

imedina@ivory:~$ git clone -b develop https://github.com/babelomics/bierapp.git
Cloning into 'bierapp'...
remote: Counting objects: 847, done.
remote: Compressing objects: 100% (4/4), done.
remote: Total 847 (delta 0), reused 0 (delta 0), pack-reused 842
Receiving objects: 100% (847/847), 4.40 MiB | 1.02 MiB/s, done.
Resolving deltas: 100% (375/375), don

After this, in both cases, you must execute the following command to fetch the JSorolla submodule:

git submodule update --init

Build

After install Node.js and npm we have to install npm packages for BierApp, from the the root folder execute:

npm install

This will make npm to look at file package.json and install locally all the dependencies listed there.

To install all Bower dependencies for BierApp execute from the root folder:

bower install

This will make Bower to look at file bower.json and install locally all the dependencies.

First, you must update JSorolla dependencies:

cd lib/jsorolla
npm install
bower install

Finally, to build BierApp execute:

grunt

When completed, all compiled files will be located under the build folder.

Backend

BIERapp uses Opencga 0.7 to process VCF Files.

Supporters

JetBrains is supporting this open source project with:

[Intellij IDEA] (http://www.jetbrains.com/idea/)

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This interactive tool allows finding genes affected by deleterious variants that segregate along family pedigrees , case-controls or sporadic samples

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