This blog post is by UT Austin graduate students Rayna Harris and April Wright.
It is our pleasure to report back on the 2nd Annual Big Data in Biology Symposium that was held at UT Austin on May 16, 2014. Hosted by UT’s Center for Computational Biology and Bioinformatics (CCBB), this event showcased the cutting-edge research done at The University of Texas at Austin and neighboring institutions that takes advantage of high throughput approaches, complex data, and/or high performance computing. Twenty three of the more than 120 attendees were BEACONites! We hope the BEACON presence at the Symposium will grow even more in the coming years.
After everyone had coffee and breakfast bagels, CCBB Director and BEACONite Dr. Hans Hofmann and Dr. Dan Stanzione (Acting Director, Texas Advanced Computing Center) welcomed everyone to the event and shared their vision for Big Data research here at UT and beyond. Dr. Rosalind “Roz” Eggo, a postdoc in Lauren Meyer’s lab (BEACON Lab), presented her compelling research linking asthma to cold transmission and the academic calendar in school age children. Dr. Claudio Casola from Texas A&M discussed permutation methods for detecting interlocus gene conversion. BEACON member Dr. Clause Wilke discussed his research into the biophysical properties of molecular that hinder or accelerate rates of molecular evolution.
The keynote address was supposed to be given by Dr. Pamela Silver from Harvard Medical School; she is a world leader in synthetic and systems biology, but her flight was cancelled due to inclement weather. Fortunately, Dr. Edward Marcotte stepped in at the last minute and delivered an excellent talk on how his lab using large datasets to study the evolution of gene and protein networks and the biomedical implications of his research. Dr. Vishy Iyer presented ENCODE research that used ChIP-seq to detect functionally important SNPs that are linked to disease. Elizabeth Milano, a graduate student in Tom Juenger’s lab, presented her work using ddRAD to identity genes underlying phenotypics traits in different ecotypes of switch grass. Dr. Matt Cowperthwaite, who oversees medical informatics programs at the Texas Advanced Computing Center (TACC), discussed informatic approaches to estimating the mutation rate in untreated Glioblastoma multiforme. Dr. Scott Hunicke-Smith, who directs UT’s Genome Sequencing and Analysis Facility (GSAF, which has supported many a BEACON project!) concluded the symposium with a thanks to all our sponsors, volunteers, and participants for helping making the event a huge success.
The Lunch Breakout Sessions
This year, the symposium offered researchers an opportunity to have small-group discussions with various big data professionals over lunch. These sessions were aimed at helping attendees network with other like-minded researchers and discover resources for different aspects of and opportunities in data science.
The Big Data in Teaching Panel provided an opportunity, for grads, postdocs, and faculty to discuss the challenges and opportunities for designing undergraduate curricula that gives students hands on training in data analysis, interpretations, and statistics. Andy Ellington (BEACONite), Claus Wilke (BEACONite), and Erin Dolan (the newly appointed Director of the Texas Center for Science Discovery and coordinator of the popular Freshman Research Initiative program) sat on the lunch panel. The lunch discussion centered around how to integrate your science research with teaching, learning, and mentoring; what topics modernized syllabi should include; online resources for teaching programming in the classroom (such as Appsoma and Code Academy); and research projects for undergrads.
The Big Data in Medicine Panel provide the opportunities for trainees and faculty to discuss challenges and opportunities for high-performance computing for the medical community. This panel consisted of Dr. Robert Messing (Vice Provost for Biomedical Sciences), Dr. Matt Cowperthwaite (Texas Advanced Computing Center), Dr. Peter Mueller (Department of Statistics and Data Sciences), and Dr. Bill Rice (St. David’s Heath Care). Discussion between medical panel members and the audience covered topics such as the evolution of medical research, which emphasized the need to integrate larger data sets into this area of study; common obstacles medical researchers face when attempting to work with these data sets; and modern tools available that may help with big biomedical research.
The Big Data in Industry Careers Panel provided an excellent opportunity for undergrads and grads to gain exposure to the wide world of STEM careers for Big Data scientists. Scott Hunicke-Smith (Director, Genome Sequencing and Analysis Facility), William Honea (T-Systems North America), Dr. Krista Ternus (Signature Science), and Dr. Dennis Wylie (Asuragen) lead the discussion. After the Panelists introduced themselves, each described the types of career options and associated salaries for PhD-level “big data scientists” within their respective companies. The industry panel had strong representation in the life sciences, but also provided insight into data science jobs that do not involve biology. Topics of discussion included desirable software skills for students seeking industry positions, adapting curriculum vitae for industry, corporate culture and compensation, and types of roles a PhD might have within industry, individual control of science, and science support of business objectives. The session concluded with a discussion about how to identify job opportunities and network in the realm of “Big Data in biology.”
The Poster Session
Twenty one trainees presented posters on a wide range of topics in diverse disciplines such as ecology, neuroscience, biochemistry, computer science, and molecular biology. Most posters were presented by UT Austin graduate students and postdocs, but two students from UT San Antonio made the drive north to participate. Six attendees participated as poster judges (including two BEACONites: Dr. Jeffrey Barrick and Dr. Rebecca Young of Hans Hofmann’s Lab). Nathan Abell and Amelia Hall from Vishy Iyer’s lab, Alberto Ghezzi for Nigel Atkinson’s lab, and Carly Kenkel from Misha Matz’s lab all received prizes for best poster presentation. Rayna Harris (BEACONite) organized the poster session, selected the judges, and presented the poster awards. All who stayed to hear the poster announcement were entered into a raffle, and two students each won prizes for a free CCBB short course offered in the fall.
The week after the event, over 50% of participants responded to our online survey, and the responses were overwhelmingly positive. Specifically, 80% of survey respondents agreed that the breadth of talks was Excellent/Very Good, 94% said the same about the poster session, and a staggering 97% considered the lunch breakout sessions to be of Excellent/Very Good value! Regarding demographics, 48% of attendees were female, with 54% self-identified as trainees and 38% as PIs or research staff. Finally, 12% of attendees came from industry or from institutions other than UT Austin. Again, we hope to increase the number of outside participants next year, particularly from BEACON institutions.
For more information about the Big Data in Biology Symposium, visit the website at http://www.ccbb.utexas.edu/dataconference.html, follow April on twitter at WritingApril #bdib, or contact Rayna Harris rayna.harris at utexas.edu or Hans Hofmann at hans at utexas.edu.