When we announced the BaseSpace Developer’s Meeting, we encouraged attendees to enter original ideas for the “killer” next-generation sequencing app- a utility or analysis tool to significantly advance genomic understanding. And we were not disappointed; the forward-thinking innovation in the BaseSpace development community was apparent in the 100+ ideas submitted.
Now we’re excited to reveal the two winners of the BaseSpace app contest. The first winner is a visualization tool suggested by a Jack Lovell, a student at the Rhode Island School of Design. In his words, “This app would be a network visualization app with a set of tools for viewing new dimensional data with the nodes. For example, one experiment might use a network where each node contains a sequence of gene expression measurements through time. The researcher needs to compare the sequence across multiple nodes simultaneously. The idea is to develop visually intuitive links between the networks and proven graphical methods such as a standard line graph.”
The second winner is Terry Gaasterland from the Lab of Computational Genomics at the University of California San Diego. The app is a simple, elegant search tool that accepts a regular expression profile and searches one or several fastq files for reads that contain the expression of interest, such as a microRNA, to build an expression reference library directly from read data. In her words: “The reason for doing this is twofold: (a) we sequenced mRNA and microRNA from 8 tissues in eye to build an expression reference library. We need ways to peer into it for newly discovered sequence searches. Sometimes a microRNA is present but below a normal threshold cutoff, (b) many sequences of interest, e.g., a motif, a miRNA, or a short repeat, are too short to find with Blat or an alignment tool, and there are way too many such sequences to search for all of them up front.”
Congratulations to Jack and Terry! And remember, you heard about these new genomic analysis tools here first. Want to design your own killer app? More BaseSpace Developer workshops are being planned! In the meanwhile, you can find more information about the new Native App Engine in BaseSpace here, or get started as a BaseSpace Developer here.