I entered the workforce in 2002, just as the human genome was reaching its first completed draft. The technologies involved were amazing and required thousands of people and millions of dollars. At the same time, the new colorful consumer iMacs and Windows XP had just been released, cell phones dominated as a primary communication tool, and computers became a requirement for medical, particularly genetic research. Fascinated by both of these areas, I sought a career path that would focus on science but also allow me to continue to play with the gadgets that I love. Enter Bioinformatics, the love child of computer science and biology that connects me to both my passion for science, and my obsession with technology and gadgets. So it was a dream come true when I was recently able to work on a project that merged the human genome with a tablet computer.
Apple introduced the iPad as next generation sequencing (NGS) technologies were emerging as the gold standard for genetic sequencing. Major research institutions acquired multi-million dollar sequencers to take advantage of these improved capabilities. While NGS systems produced vast amounts of information, that information still had to be manipulated and reformatted for interpretation by scientists.
Tools began to emerge that would enable one to visualize the human genome in various ways, allowing one to put the genetic sequence data at hand, into a useful and aesthetically appealing format. Most tools, however, had limitations and navigating around the human genome, which is composed of 3 Billion bases, had its own challenges. Software tools like the UCSC Genome browser–IGB (integrated genome browser), and others were useful, but often cumbersome to navigate with a mouse and keyboard. They get the job done, but with new tools now at hand, more hands-on approaches to exploring data seemed like an obvious improvement to build upon existing technologies like these PC based browsers.
The human genome on the iPad
At CBMi we immediately realized the potential behind implementing a visualization tool that uses and benefits from a touch screen device, with “multi-touch” abilities. The programming team began developing an iPad app that would enable the UCSC browser to function in sync with touch gestures on the tablet device. The benefit seemed obvious; one could easily load up the same familiar genome browser interface, but could navigate with their hands, zooming in and out to dive into the information, and being able to simply touch items to learn more about them.
The app we developed is called Genome Wowser and it’s available for download on iTunes. It provides a functional presentation of the popular University of California, Santa Cruz (UCSC) Genome Browser that is intuitive, highly portable, and allows a “Google Maps”-like navigation experience. Users can view genomic annotation tracks, zoom in, out, and across a chromosome, search for genomic elements, and download displayed data of interest
- Standard whole genome assembly as provided by the Genome Reference Consortium.
- Comprehensive standard annotations as compiled by the UCSC Genome Bioinformatics Group via their numerous collaborations with annotators worldwide.
- Multiple annotation tracks: select the tracks you want to see and view them concurrently in an intuitive stacked configuration for any chromosome section.
- Pinch-and-spread zoom capability.
- Drag-and-swipe navigation.
There have been more than 5200 Genome Wowser downloads to date.
To download the Genome Wowser free of charge, visit the app’s iTunes page at http://itunes.apple.com/us/app/genome-wowser/id437044318?mt=8 or search for “Genome Wowser” in the iTunes store.