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SDSC Creates PDB Focus Group as First Step Toward Cell-Phone Enabled Bioinformatics

A research team at the San Diego Supercomputing Center is building a focus group of Protein Data Bank users in an effort to create a suite of bioinformatics tools that will run on so-called “smart phones” — cell phones with the capabilities of personal digital assistants.
Eventually, the technology aims to enable researchers to have immediate access to a variety of biological information outside the lab or in remote locations.
Greg Quinn, principal investigator in the mobile data visualization lab at SDSC, told BioInform that Microsoft Research provided funding for the effort, called the Mobile Life Sciences Platform, a few months ago, and that work is just beginning to get underway.
The goal of MLSP is to create a development framework for bioinformatics applications that will run on smart phones. The first application under the effort will be a version of the Protein Data Bank called PDB Mobile.
Quinn and his colleagues are seeking PDB users with access to a smart phone running Windows Mobile 5.0 who can provide feedback during the development process. While Windows will serve as the “reference version” of MLSP, Quinn said that the system will ultimately be “platform agnostic.”
The long-term goal, Quinn said, is “being able to access life science information any time and anywhere,” although he acknowledged that there is a fair degree of skepticism regarding the demand for that kind of capability — particularly among government funding agencies.
“The question that’s sometimes thrown at me is, ‘What the hell’s the use of seeing protein molecules on a PDA or on a smart phone?’” he said, noting that there are a number of scenarios in which mobile bioinformatics might make sense.
“One might imagine that a field researcher — like a researcher working in hot springs, for example, trying to collect thermophilic bacteria — might want to pull up phylogenetic data rather quickly and be able to access that kind of information. Or someone who’s chained to the lab doing PCR or cloning might want to pull up a molecule quickly with one hand using their smart phone. Or someone listening to a lecturer talking about a particular protein sequence who wants to look at another sequence that he thinks is similar. Or a postdoc traveling between levels in a building who needs to look at Blast results quickly.”
Quinn said that the MLSP isn’t intended to be a replacement for current bioinformatics computing platforms, but an alternative that will enable new scenarios for accessing data.
There are a number of formidable challenges, however, in modifying current bioinformatics resources for smart phones. Even though many cell phones are currently web-enabled — meaning that a researcher could technically access unmodified PDB files from the current PDB site — the PDB and other websites are not optimized for the tiny displays used in most hand-held electronics.
It’s not just a question of using smaller pictures and type sizes, Quinn said. “There are real issues about how you present data on a small form-factor device — it’s not simply that you present data in a smaller format. … What we’re talking about is really visualization, being able to quickly glean data without looking at huge amounts of text. That’s a very interesting challenge.”
In addition, he noted, “there are issues with network latency” for wireless connections, particularly in the case of cell phones, where mobile users are likely to wander in and out of range, which would disrupt data downloads.  
The end result, Quinn said, is that smart phones currently provide “a poor end-user experience that really pushes life science researchers not to use this medium at the moment, and we see that as being a shame.”
One key aspect of the MLSP, therefore, will be the development of new user interface capabilities to overcome some of those obstacles. Quinn said that his team will explore easier ways to interact with handheld devices “through one hand, through quick button presses, and maybe even through voice activation.”
In the case of the PDB, there are also data format issues. “You can’t simply create an application that accesses these huge PDB files. These things have a huge amount of information in them that often isn’t used by a program that simply renders structure,” he said. “There needs to be a sort of rationalization of the data that’s actually sent through the handset. Part of that will be developing the software interface that will sit between a regular life science database and the actual handset.”

“There are real issues about how you present data on a small form-factor device — it’s not simply that you present data in a smaller format. … What we’re talking about is really visualization, being able to quickly glean data without looking at huge amounts of text. That’s a very interesting challenge.”

Quinn said that an initial version of PDB Mobile should be available publicly by the second quarter of 2007, although PDB focus group participants will have earlier access.
The SDSC team will also publish the API for writing applications — called microapps —for the framework so that researchers can create their own mobile visualization toolkits, Quinn said.
Quinn said that PDB was chosen as the first MLSP application for several reasons. One is his physical proximity to the PDB group at the SDSC. PDB co-director “Phil [Bourne] is just around the corner and it’s easy to get interaction with them. And I knew that they had a very well-defined setup internally for developing applications, for getting feedback from users, and basically I wanted to tap into that,” he said.
In addition, he confessed, “in terms of eye candy and catching people’s attention, I think it’s a very good area to be working in because it’s very visual. With protein structures, in terms of manipulation, you get immediate feedback.”
Eventually, Quinn said he hopes to extend the MLSP effort into phylogenetic analysis as well as to Blast and other alignment tools, but he acknowledged that those applications are more challenging from a visualization perspective. “One of the things that was thrown back at me for my last NIH proposal was, ‘How does someone look at Blast data?’ and that’s a very good question,” Quinn said. “One needs to look at ways of graphically doing that, and then being able to quickly drill down to data and have that data presented to you in a way that you can quickly and easily assimilate.”
Ultimately, he said, “the task is not only the technical aspects of engineering an application that works efficiently on a smart phone device — which in itself is really quite a challenge — but it’s also how you present complex scientific data on small form-factor device that end users will want to actually use.”
Further information about the MLSP is available here.

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