GIVE is an open source programming library that allows anyone without much programming experience to build custom genome browser websites or apps. With a few lines of codes, one can set up GIVE service on a local machine, manage custom data and build an interactive genome browser. Besides, we established GIVE Data Hub, a data center providing GIVE service and hosting public/customer data sets, such as ENCODE data. It takes only a few minutes to build a genome browser website using GIVE-Hub.

This portable library encapsulates novel data communication and data visualization technologies, including new data structures and new memory management methods that enable efficient data transfer between the data-hosting website and internet browsers. GIVE is the acronym of Genomic Interaction Visualization Engine, although GIVE’s utilities have outgrown its original name.

A 2-minute tutorial

Just copy paste the following HTML codes to jsfiddle, an online HTML testing website for testing of your own HTML codes. 1) Go to jsfiddle, 2) copy paste the following lines to the HTML panel (top left), 3) hit “run” button. Congratulations! You have built your first genome browser webpage using GIVE Data Hub data source in less than 1 minute.

<!-- header source -->
<script src="https://www.givengine.org/bower_components/webcomponentsjs/webcomponents-lite.min.js"></script> 
<link rel="import" href="https://www.givengine.org/components/chart-controller/chart-controller.html">

<!-- embed the browser in the web page -->
<chart-controller 
  title-text="A 2-minute starter of building a genome browser with GIVE" 
  ref="hg19" 
  num-of-subs="2" 
  coordinates='["chr18:19140000-19450000", "chr18:19140000-19450000"]'
  group-id-list='["genes", "CHi-C_promoter"]'
></chart-controller>

So you have enough time to learn some essential tips for customizing your genome browser. Please read the GIVE Tutorial 0: Start from a 2 minutes example. The following GIF animation shows the whole process of the 2 minute tutorial. It’s so easy.

2 minute show

How to use your own data instead of GIVE Data Hub data source? It’s easy! Just learn more from GIVE tutorials! You can set up your own GIVE service and build a powerful genome browser with you own data in less than 2 hours!


Examples of custom genome browsers built with GIVE using GIVE-Hub data source

   
Single-cell transcriptome website
A web browser for human ENCODE datasets      
A website for genome-wide RNA-DNA interactions
A website for displaying genome interaction (Capture Hi-C) data
A website for displaying genome interaction (ChIA-PET) data

Citation: Xiaoyi Cao, Zhangming Yan, Qiuyang Wu, Alvin Zheng, Sheng Zhong, Building a genome browser with GIVE, bioRxiv, 2017, https://doi.org/10.1101/177832.


© COPYRIGHT 2017 GIVE Authors. Code Licensed under the Apache License 2.0. Documentation licensed under CC BY 3.0.