Scalable Software Infrastructure for the Lab and a Specific Investigation of the Yeast Transcription Factor Eds1
Date of Award
Master of Science (MS)
Individual biology labs handle increasingly large data sets. Ensuring accurate data entry, consistent sample metadata, and ease of access to the data once it is stored, are critical for both the integrity of analysis as well as productivity of the lab. Chapter 1 one of this thesis describes three implementations of software meant to facilitate handling data and metadata in the lab as the size of the data and complexity of analysis scale. The first piece of software is a database and entry interface for storing a large and varied amount of data on biological samples. The second is a software package which uses established bioinformatics tools to further build upon the database API to facilitate analysis. The third is a Nextflow pipeline for the Calling Cards protocol for assaying transcription factor binding via sequencing.
Chapter two focuses on EDS1, a gene encoding a transcription factor present in Saccharomyces cerevisiae. EDS1 is a paralog of RGT1, an important regulator of sugar uptake. We show that Eds1p has both functionally redundant and divergent roles in response to external nutrients.
Jeremy Buhler, Rob Mitra