In November, PSC received top national honors in four categories of the 2013 HPCwire Readers’ and Editors’ Choice Awards. HPCwire, the premier trade publication for the high-performance computing (HPC) community, announced the winners at the 2013 International Conference for High Performance Computing, Networking, Storage and Analysis (SC13), in Denver, Colorado.
PSC received:
• Reader’s Choice, Best use of HPC in Life Sciences, for work on PSC’s Blacklight supercomputer in overcoming limitations in complex DNA and RNA sequencing tasks, identifying expressed genes in nonhuman primates, petroleum- digesting soil microorganisms and bacterial enzymes that may help convert non-food crops into usable biofuels.
• Reader’s Choice, Best use of HPC in “Edge” HPC Application, for the VecNet Cyberinfrastructure (CI). A collaboration between PSC’s Public Health Group and Notre Dame’s Center for Research Computing is building a computational system that will enable VecNet—a partnership of academic and industrial researchers, local public health officers and foundation and national decision makers—to test ideas for eradicating malaria before applying them in the real world.
• Editors’ Choice, Best Application of “Big Data” in HPC, for PSC’s newest supercomputing resource, Sherlock. Specially designed to solve what are known as graph problems, Sherlock is optimized for questions involving complex networks that can’t be understood in isolated pieces. Topics range from cancer protein and gene interactions to performing smarter information retrieval in complex documents such as Wikipedia.
• Editors’ Choice, Best use of HPC in Financial Services, for research that led to a change in trader reporting requirements to the New York Stock Exchange and NASDAQ. Work on Blacklight enabled investigators to prove that high-volume automated traders were exploiting reporting rules to make “invisible” trades that manipulated the markets.
Two public health projects at PSC have also made HPCwire’s list of “The Top Supercomputing-Led Discoveries of 2013.” The HERMES project is analyzing public-health supply chains in lower-income countries to identify and repair under-appreciated choke points in vaccine supply efforts, for example. The VecNet Cyberinfrastructure project has created a prototype computational system to support a global malaria eradication effort (see below for more).
HPCwire named the two PSC projects among 30 supercomputing projects chosen from their new archives and which the publication believes are “set to change the world in 2014 and beyond.”
In addition to winning an HPCwire award and being cited as one of the most significant supercomputing discoveries of the year (see above), VecNet CI has also completed its prototype of a computational system for university, industry, government and funding entities to test ideas for eradicating malaria.
“After our first year of development, we have a successful prototype framework of all user tools,” says Nathan Stone, principal investigator of the infrastructure project at PSC. “Now, direct engagement with stakeholders via workshops, tutorials and online demonstrations will be important to refine these tools and get them into the hands of those who can best use them.”
The final quarter of calendar 2013 saw the completion of the prototype CI framework, which consists of four major tools. These allow users to test existing and new malaria eradication methods, investigate malaria risk factors, plan detailed intervention campaigns and assess economic impact.
To unite these user tools, the group developed a common web interface with supporting access to a digital library (for archiving data sources and provenance), compute clusters (for running the disease forecasting models) and a data warehouse (for interactive access and analysis of calculated results). The web site and tools are now in use by almost 150 users worldwide from a variety of disciplines.
“Vecnet’s work in 2014 will emphasize improvements to the malaria transmission models, and the expansion of calibrated input data to cover new geographic regions of interest to stakeholders,” Stone says.