This application displays proteomics data (Peptide/Spectrum matches and PTM quantification information) and ties them to 3D structures read from PDB files. It is aimed at being a demonstration of the capabilities of the pViz JavaScript library to display customizable protein features on the sequence.
The demo protein is ERBB2_HUMAN, where both the PSM and PTM have be randomly assigned. PDB and sequence is parsed from the Uniprot text file via the Uniprot.js JavaScript library.
Check the help menu to have more details on usage.
The application can be used live at http://research-pub.gene.com/pviz/app/proteomics-3d
Warning: you must have a WebGL enabled browser to benefit fully from the application (beware of older Internet Explorer and Mac OS X versions).
Uniprot text file is downloaded dynamically from Uniprot web site. Once a 3D structure is selected, the PDB file is downloaded from the Protein Data Bank web site. Both theses files are parsed in JavaScript to extract the meaningful information.
For the example, PSM and PTM information reside in 2 TSV files stored in the data directory (information was populated randomly).
An effort was made to decorrelate data from the application. It is straightforwards to replace the protein id and the proteomics information sources by other ones.
Clone the project, then
npm install
bower install
#if grunt was not installed with -g
alias grunt=./node_modules/grunt-cli/bin/grunt
grunt serverEt Voilà
grunt build
rsync --recursive --delete dist/* your.host:/your/path/Although GLmol.js was a key component of this application, we had to fork it and make it compatible with more recent versions of Three.js (thanks to the authors for their help on that path).
This application is based on the versatile pViz.js: a dynamic JavaScript & SVG library for visualization of protein sequence features JavaScript library, written by Alexandre Masselot and Kiran Mukhyala, from the Bioinfromatics & Computational Biology Department, at Genentech Inc. Research.
Please provide a reference to this application by citing: '''xxx.xx 2014'''
This app is aimed at demonstrating pViz library. But it would never have existed without a myriad of other useful an inspiring projects: d3.js, color brewer, GLmol.js (and more precisely the forked version to work with recent Three.js), grunt, bower, bootstrap, jQuery, backbone.js, require.js, underscore.js.
Minification, distribution etc. can be launched in a CI environment via ant tasks (./build.xml)
This library was initiated by Alexandre Masselot (masselot.alexandre@gene.com) & Kiran Mukhyala (mukhyala.kiran@gene.com) within Genentech Bioinformatics & Computational Biology Department.
The library is distributed under a BSD license. Full description can be found in LICENSE.txt