UC San Diego bioengineers bring functional genomics data into personal websites
San Diego, Calif., July 23, 2018 -- Bioengineers at the University of California San Diego have developed a programming library that can enable researchers to effortlessly visualize and share genomic data on their personal websites. The new open source programming library, named “GIVE” (genomic interaction visualization engine), can be used by non-experts and in many cases even eliminates the need to write any computer codes.
The work was led by bioengineering professor Sheng Zhong at the UC San Diego Jacobs School of Engineering. His team published their work recently in Genome Biology.
“The GIVE software transforms how genomics data are transferred on the internet and visualized in web browsers. It facilitates the creation of personalized genome browsers that can be customized and inserted into a user’s own website, similar to a Google map,” said Zhong.
With this vision, Zhong and his colleagues developed GIVE to automate this work and offer a portable and lightweight genome browser with complementary advantages of genome browser websites, desktop executables, and personal homepages and blogs.
“We created the open source GIVE programming library to meet the diverse needs of users with various levels of sophistication," said first author Xiaoyi Cao, a project scientist in Zhong’s research group.
|Screenshot of a custom genome browser hosting epigenome and genome interaction datasets.|
GIVE has an embedded feature called “HUG” (HTML Universal Generator), which provides a graphical interface to interactively generate HTML codes for displaying user chosen datasets. Users can save and share the HTML file with collaborators or copy and paste the HTML codes into their websites, which would lead to embedded interactive data display.
With GIVE, users can create custom genome browsers without hosting a data server, where all the data are retrieved on-demand from public data servers. Users who choose to host data on their own server can do so with commands provided in the GIVE Toolbox. With a few lines of HTML code, GIVE enables a website to retrieve, integrate, and display diverse data types hosted by multiple servers, including large public depositories and custom-built servers. Such simplicity of use comes from encapsulation of new data management, communication, and visualization technologies made available by the GIVE development team. The cores of these technologies are new data structures and a memory management algorithm.
Additional descriptions of these and other features of the GIVE programming library are in a Research Highlight from the journal: “Making genome browsers portable and personal.”
Paper title: “GIVE: portable genome browsers for personal websites.” Co-authors include Zhangming Yan, Qiuyang Wu and Alvin Zheng.
This work is funded the National Institutes of Health (U01CA200147 and DP1HD087990).
Jacobs School of Engineering