Bioinformatics for environmental metagenomics:
We are increasingly aware of the invisible & ubiquitous microbial component of our lives - in & on our bodies, in our environment. But, how do you actually measure that? What if you wanted to find out what bacteria are living around you? In this workshop we will learn the methods for identifying microbial species with DNA sequencing data, & understand what their functions are & how that can inform decisions or urban design.
We will use the Pathomap dataset & each participant will obtain the metagenomic sequences of their favorite subway station. We will explain the file formats used for sequencing data & how to manipulate them, & gain hands-on experience on using the computational tools to identify bacterial species & their genes with that data, & visualize the results.
About the instructor:
Dr. Elizabeth Hnaff is a computational biologist & designer. Her academictrajectory started with a Bachelors in Computer Science, followed by a Master's inPlant Biology (both from UT Austin) & a PhD in Bioinformatics from theUniversity of Barcelona.At the center of her research is a fascination with the way living beingsinteract with their environment. This inquiry has produced a body of work thatranges from scientific articles in peer-reviewed journals, to projects with landscapearchitects, to working as an artist in environments from SVA to the MIT Media Lab.She has made contributions to understanding how plants respond to the force ofgravity, how genome structure changes in response to stress, & most recently hasturned her attention to the ubiquitous & invisible microbial component of ourenvironment.
Some recent highlights include the design for the bioremediation of alocal toxic Superfund site which won a design competition, had a gallery exhibit, anda scientific publication. Her work with the MIT Media Lab led to the development ofa novel approach to urban microbiome sampling using honeybees, an exhibit at the2016 Venice Architecture Biennale, & a curriculum for international workshops.She has consistently makes the tools - software, wetware, hardware - neededto answer her research questions.She currently holds an Assistant Professor position in the Integrated DigitalMedia department at the NYU Tandon School of Engineering in New York City,where she teaches courses in biodesign.