STATEMENT OF INTEREST
I have chosen to focus on bioinformatics because it is clear that analysis of large datasets is increasingly important to the biological sciences. I find this quickly evolving field rich with opportunities to learn new skills and to further develop those skills by training and collaborating with other scientists.
Working with data from existing and emerging technologies in an open and collaborative environment is preferred. I am interested in both optimizing heuristics for informative but speedy initial data analysis and more open ended exploration of new kinds of data to identify unanticipated sources of information.
I have worked primarily on de novo assembly and draft assembly improvement projects for NGS and genome map data. However I am also very interested to work on projects involving cancer genomics.
PERSONAL SCHOLARLY DEVELOPMENT
As a graduate student I studied genomics applications, chromosome and genome analysis, and bioinformatics. This prepared me for assembling my own transcriptomes for two wild grasses in my master research project.
As the Bioinformatics Core Outreach Coordinator I learned to code in Perl and BASH as well as work on an SGE Cluster by collaborating with bioinformatics specialists and cluster administrators. As I accrued these skills I made completed scripts available for use through Github as “kstatebioinfo". As these scripts developed into workflows I created tutorials that I used to train students in the lab portion of an introductory Bioinformatics course. Students in this course became interested in learning how to code, prompting the creation of a month long coding workshop. The workshop, NGS Analysis on Beocat, turned into a collaboration between the Division of Biology and KSU Center for Scientific Supercomputing. I developed most of the exercises and taught the first two weeks of the workshop. Greg Wilson from Software Carpentry (SWC) met with us at an early stage of workshop development and I adjusted the NGS Analysis on Beocat material to fit the SWC training model.
In addition to coding, codesharing and training I ,created the Applied Bioinformatics Journal Club (ABJC) as a forum to discuss workflows and projects within and between Bioinformatics Cores. At the ABJC, methods articles are discussed weekly by an interdepartmental group of biologists and computer scientists from KSU, KUMC, and KU-L’s Bioinformatics Cores via video conference. Usage of the ABJC’s archived topics has already exceeded 90,000 views.
I am also collaborating with scientists at BioNano Genomics to develop workflows for BioNano molecule maps. These can be used to assemble physical maps or order/orient sequence assemblies. Working in a beta test site for this new technology and working with my Bioinformatics Core to start our certified BioNano Pro service center brought together the dynamic and collaborative aspects that draw me to bioinformatic analysis. This was perhaps the most engaging collaborative experience I have had so far.