CabFriendly is a cloud-based mobile web application to match users who request similar trips and would like to share a cab. The application is hosted on Amazon's EC2 service and combines several open-source frameworks (Django, PostgresQL, Redis, Node.js, JQuery Mobile) with social networking (Facebook), mapping, and location-awareness (Google) APIs. The modularity of our design allows the service to easily scale in the cloud as the user base grows. It was initially developed as a project for Eric Brewer's CS 262 course at UC Berkeley, but we will soon release it into the wild and extend its functionality by adding an interface for taxi drivers to "claim" rides.
eXpress: Streaming RNA-Seq analysis [link]
eXpress is a general quantification tool for target DNA/RNA sequences. While its primary use currently is RNA-Seq it has the potential for applications in many other areas including as allele-specific expression and metgenomics. What makes eXpress different is that it is an online (or streaming) algorithm, meaning it only makes one pass through the data. This allows it to be very light-weight and efficient using a constant amount of memory and time linear in the number of sequenced fragments being processed. Furthermore, it accepts piped SAM/BAM input, allowing users to avoid storing extremely large alignment files. eXpress models fragment biases (sequence-specific and positional), fragment lengths, and errors, allowing it to also be one of the most accurate quantification methods available.
Cufflinks: Transcript assembly, differential expression, and differential regulation for RNA-Seq [link]
Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, with the option of controlling for sequence-specific biases.