Ever wonder what happens when you put the most brilliant minds in bioinformatics together in one room?
You may not have needed shades indoors on April 9, but some truly stellar research was presented by the institute’s faculty, as well as a patent reminder of the groundbreaking history of the field by bioinformatics founder and keynote, Dr. Michael Waterman of the University of Southern California.
The symposium, which highlighted the institute’s latest and greatest research, was kicked off by Executive Director Dr. Chris Barrett. He set the tone by noting that “Bioinformatics has changed and changed everything in the last fifteen years…Genes and genomes occur in context. In order to understand what they do, you need to understand what they do in context.”
The rest of the day was spent delivering that context in a dazzling array of research and technology, with Dr. Shiv Kale acting as moderator and emcee throughout the day.
Energy was high as members of each laboratory or research team presented both individually and on panels, sharing information, questioning one another, and unveiling new nodes of connection and collaboration. Dr. Silke Hauf asked particularly penetrating questions about how research is done, wondering about how useful data might be made more accessible. Truly, as she noted in her own presentation, “Complexity is the enemy of reliability.”
From Dr. Allan Dickerman’s exceptionally apt metaphor of finding ways to “kayak the firehose of information” to a discussion of how projects like the PAThosystems Resource Integration Center (PATRIC) have grown from a sample size of 8 to 40,000 genomes, the symposium emphasized the spirit of team science that has truly become the hallmark of the institute’s research portfolio.
Similarly, the Network Dynamics and Simulation Science Laboratory has also grown its program and ability to synthesize increasingly complex and large sets of data, from city-based projects like the TranSims project in Portland in 2000 up to the global simulation project that is currently underway. Today, with the use of the Shadowfax computing environment, runtime on projects is seconds (as opposed to weeks), and the response time for emergent projects, as with Ebola last summer, has been shaved down to a matter of hours. In the future, NDSSL expects even greater compute power to continue to whittle away runtimes, with the addition of 300+ cores imminent.
The Nutritional Immunology and Molecular Medicine Laboratory, led by Drs. Bassaganya-Riera and Hontecillas, discussed new discoveries in computational immunology and immunoinformatics that advance our understanding of the immune responses and accelerate the path to cures. “The fully integrated computational modeling and experimental validation capabilities of NIMML are unique and help revolutionize how we understand immune responses in the gut from cells to systems,” said Dr. Bassganya-Riera. Under the Center for Modeling Immunity to Enteric Pathogens, NIMML in collaboration with NDSSL developed Enteric Immunity Simulator (ENISI), an HPC-driven modeling tool that simulates 108 cells in the gut and it is being used to guide the design of immunology studies.
The Medical Informatics and Systems team, which has been focusing on microsatellite repeats, has leveraged the Genomics Research Laboratoryr’s one-stop shop approach to genomic analysis to discover new and better tests for cancer. Likewise, the Kale Laboratory has found through precise experimentation and genomic analysis that anti-fungal medications of the future will likely require very individually tailored medicines to combat fungal infection.
Led by Dr. Sallie Keller, the Social Decision and Analytics Laboratory, traveled to Blacksburg from its home base in Arlington at the Virginia Tech Research Center. They gave a rousing presentation, complete with banjo stylings from Dr. Mark Orr. The team demonstrated how the variety of disciplines from economics to psychology housed under their roof adds value to understanding Big Data or the All-Data Revolution. As Dr. Orr quoted, "Theory without data is myth, and data without theory is madness."
Both the Genomics Research Laboratory and the Computational Core discussed moving forward with advanced technology to match the institute’s cutting-edge research portfolio. The GRL now serves 105 laboratories in over 21 departments on campus. The Computational Core will be adding an iRODs (integrated Rule-Oriented Data Systems) management system in a new data center with over 800 new cores soon to come online. All of these technologies enhance and enable further collaboration between researchers both within VBI and the Virginia Tech campus and beyond.
The institute also celebrated the addition of its newest laboratory, the Mathematical Biocomplexity Laboratory, led by Dr. Christian Reidys. Reidys discussed his team’s focus on RNA pseudoknots, and how their group is re-envisioning cross-serial RNA interactions via mathematical algorithms. Eventually, this may allow them to predict structure and further deduce the role of RNA in a variety of situations. For instance, Reidys posited the union yet again of microbiology and network dynamics when he said, "If we want to understand viral infection, we must understand its evolution via network interactions."
The Mathematical Biocomplexity presentation served as the perfect prelude to Dr. Waterman’s presentation, wherein he recapped the history of bioinformatics and the discovery of the famous Smith-Waterman algorithm, which is the basis for sequence comparisons. Dr. Waterman emphasized that our concept of genomes and how to understand them is consistently changing. We have come a long way in understanding the genome, but we still have a long way to go. As he so slyly noted at the end of his keynote, "My only prediction is that in the next 85 years, there is still yet more to learn about sequencing."
All in all, it was a wonderful recap of where the institute has been and a tantalizing glimpse of where it’s headed. The future’s so bright, we truly might all need shades.
April 16, 2015