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.
You can find BierApp documentation and tutorials at: https://github.com/babelomics/bierapp/wiki.
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
You can report bugs or request new features at GitHub issue tracking.
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.
BierApp is versioned following the rules from Semantic versioning.
We recommend to contact BierApp developers by writing to OpenCB mailing list babelomics@cipf.es. The main developers and maintainers are:
- Joaquin Dopazo (jdopazo@cipf.es) (Founder and Project Leader)
- Ignacio Medina (im411@cam.ac.uk)
- Susi Gallego (agallego@cipf.es)
- Francisco Salavert (fsalavert@cipf.es)
Former contributors
- Roberto Alonso
- Mercedes Medina
- Alejandro Aleman
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.
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.
The following technologies are needed to build BierApp: Node.js, npm, Bower and Grunt.
To install Node.js you can visit this link.
npm stands for node packaged modules and it is the dependency manager of Node.js.
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-cliBierApp 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
After install Node.js and npm we have to install npm packages for BierApp, from the the root folder execute:
npm installThis 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 installThis 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 installFinally, to build BierApp execute:
gruntWhen completed, all compiled files will be located under the build folder.
BIERapp uses Opencga 0.7 to process VCF Files.
JetBrains is supporting this open source project with:
