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README.md

GIVE (Genomic Interactive Visualization Engine)

DOI Contributor Covenant

GIVE (Genomic Interactive Visualization Engine) is a HTML5 library that lets you embed genomic visualization panels as you would standard HTML elements to build a customized genome browser to visualize data from public deposits (such as ENCODE) and/or in-house data.

GIVE uses Web Components, specifically Polymer Library for user interface and Scaled Vector Graphics (SVG) 1.1 for graphics. These components are supported by all major browsers.

<!-- Polyfill Web Components for browsers without native support -->
<script src="https://www.givengine.org/bower_components/webcomponentsjs/webcomponents-lite.js"></script>

<!-- Import GIVE component -->
<link rel="import" href="https://www.givengine.org/components/chart-controller/chart-controller.html">

<!-- Embed the browser in your web page -->
<chart-controller ref="mm10" title-text="My GIVE Browser"
  coordinate='["chr17:35504032-35512777"]'
  group-id-list='["genes", "singleCell", "customTracks"]'></chart-controller>

Table of Contents

Installation

Installation of GIVE is optional and not required for the use of any of the Web Components of GIVE. By installing GIVE components, you can serve codes and/or data sources directly from your own server.

GIVE consists of three major parts: GIVE Web Components, the client-side codes running in browsers, implemented by HTML5, GIVE server, including bare server codes, implemented by PHP, and GIVE Data Source.

To install any part of GIVE, a web-hosting environment is needed on your server. Please refer to GIVE Tutorial 2.2: Custom Installation of GIVE for detailed instructions. Alternatively, you can use GIVE-Docker (recommended), a Docker image delivering an already configured GIVE server and GIVE Web Components. Please refer to GIVE Tutorial 2.1: Easy local deployment of GIVE with GIVE-Docker

Usage

You may use GIVE-HUG (HTML Universal Generator) on the GIVE Data Hub page to generate the HTML code needed for embedding. The GIVE Data Hub is accessible on the public GIVE instance at https://www.givengine.org/give-data-hub.html and will be at the same relative location after you install your own GIVE instance. If you would like to code the HTML files by yourself, you can use GIVE Web Components by importing the component and using the tags directly.

Importing GIVE Web Components

To use GIVE Web Components, just use HTML import to import Web Components polyfill and the required Web Components.

All components, including Web Component polyfill, are available on our website, the public GIVE instance, for direct HTML import without any installation.

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

If you already installed GIVE Web Components on your server, please use your own path.

<script src="/bower_components/webcomponentsjs/webcomponents-lite.js"></script>
<link rel="import" href="/components/chart-controller/chart-controller.html">

Implementing A Customized Genome Browser by Embedding GIVE Components

After you have imported the components in your HTML page, you can use them in several ways. The most straightforward way is to use them as if you are using common HTML tags (like <div> or <video>):

<chart-controller ref="mm10" title-text="My First GIVE Browser"
  group-id-list='["genes", "singleCell", "customTracks"]'></chart-controller>

You can also use Document.createElement() to create the element in your JavaScript code:

var myChart = document.createElement('chart-controller')
myChart.titleText = "My First GIVE Browser"
myChart.groupIdList = ["genes", "singleCell", "customTracks"]

Or to use the built-in JavaScript constructors:

var myChart = new GIVE.ChartController({
  titleText: "My First GIVE Browser",
  groupIdList: ["genes", "singleCell", "customTracks"]
})

Supported Tracks

Currently GIVE supports three types of tracks:

Tutorial

We have compiled a series of tutorials for different GIVE functionalities and components. Please check out the Tutorial Homepage.

Manual

The GIVE Manual is available under the Manual Homepage.

How to contribute to GIVE

Any kind of contributions to GIVE development are welcome. Please read the Contribution Guides and the Covenant Code of Conduct first.

Credits

GIVE is developed by Xiaoyi Cao, Zhangming Yan, Qiuyang Wu, Alvin Zheng from Dr. Sheng Zhong's lab at University of California, San Diego.

License

Copyright 2017 GIVe Authors

This project is licensed under the Apache License, Version 2.0 (the "License"); you may not use this project except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

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