Phinch: An interactive, exploratory data visualization framework for environmental sequence data

2014-05-21T22:32:59Z (GMT) by Holly Bik

Slides from the eDNA session at #JASM2014 


Using environmental sequencing approaches, we now have the ability to deeply characterize biodiversity and biogeographic patterns in understudied, uncultured microbial taxa (investigations of bacteria, archaea, and microscopic eukaryotes using 454/Illumina sequencing platforms). However, the sheer volume of data produced from these new technologies requires fundamentally different approaches and new paradigms for effective data analysis. Scientific visualization represents an innovative method towards tackling the current bioinformatics bottleneck; in addition to giving researchers a unique approach for exploring large datasets, it stands to empower biologists with the ability to conduct powerful analyses without requiring a deep level of computational knowledge. Here we present Phinch, an interactive, browser-based visualization framework that can be used to explore and analyze biological patterns in high-throughput environmental datasets. Leveraging a close collaboration between UC Davis and Pitch Interactive (a data visualization studio in Berkeley, CA), this project takes advantage of standard file formats from computational pipelines in order to bridge the gap between biological software (e.g. QIIME) and existing data visualization capabilities (harnessing the flexibility and scalability of WebGL and HTML5).