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PICS Colloquium: “How reproducible is your research?”

September 24, 2021 at 2:00 PM - 3:00 PM

Abstract: Each year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering practices, despite the increases in high-dimensional data, complexities of workflows, and computational environments. Here we show how scientific software applications can be created in a reproducible manner when simple design goals for reproducibility are met. We describe the implementation of a test server framework and 40 scientific benchmarks, covering numerous applications in Rosetta bio-macromolecular modeling. High performance computing cluster integration allows these benchmarks to run continuously and automatically. Detailed protocol captures are useful for developers and users of Rosetta and other macromolecular modeling tools. The framework and design concepts presented here are valuable for developers and users of any type of scientific software and for the scientific community to create reproducible methods. Specific examples highlight the utility of this framework, and the comprehensive documentation illustrates the ease of adding new tests in a matter of hours.

Julia Koehler Leman

Research Scientist, Systems Biology, CCB, Flatiron Institute.

Julia Koehler Leman joined the Simons Foundation in 2016 as a member of Richard Bonneau’s lab. She was previously a postdoctoral fellow in the chemical and biomolecular engineering department at Johns Hopkins University. There, she developed applications in the Rosetta software suite for biomolecular modeling, docking and design. Leman has an M.S. in physics from Leipzig University in Germany and a Ph.D. in chemical and physical biology from Vanderbilt University.


September 24, 2021
2:00 PM - 3:00 PM
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Zoom – email kathom@seas.upenn.edu


Penn Institute for Computational Science (PICS)
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