Frank Austin Nothaft

I am currently focused on distributed and parallel computing and bioinformatics applications, and computer-aided design for RF/mixed-signal systems. Previously, I have worked on energy efficient computer architecture.

Publications

Refereed Journal Articles

1. John Vivian, Arjun Arkal, Frank Austin Nothaft, et al. Toil enables reproducible, open source, big biomedical data analyses. In Nature Biotechnology, April 2017.
2. Zhao Zhang, Kyle Barbary, Frank Austin Nothaft, Evan Sparks, Oliver Zahn, Michael J. Franklin, David A. Patterson, and Saul Perlmutter. "Kira: Processing Astronomy Imagery Using Big Data Technology." In TBD – IEEE Transactions on Big Data, August 2016. Extended version of Zhang BigData '15.
3. Benedict Paten, et al. "The NIH BD2K center for big data in translational genomics." JAMIA – Journal of the American Medical Informatics Association, July 2015.

Refereed Conference Publications

1. Zhao Zhang, Kyle Barbary, Frank Austin Nothaft, Evan Sparks, Oliver Zahn, Michael J. Franklin, David A. Patterson, and Saul Perlmutter. "Scientific computing meets big data technology: An astronomy use case.". BigData '15 – Proceedings of the IEEE International Conference on Big Data, 2015. Originally posted as ArXiv:1507.03325, July 2015.
2. Frank Austin Nothaft, et al. "Rethinking Data-Intensive Science Using Scalable Analytics Systems". SIGMOD '15 – Proceedings of the SIGMOD International Conference on Management of Data, 2015.
3. Frank Austin Nothaft, Luis Fernandez, Stephen Cefali, Nishant Shah, Luke Darnell, and Jacob Rael. "Pragma-based floating-to-fixed point conversion for the emulation of analog behavioral models". ICCAD '14 – Proceedings of the International Conference on Computer-Aided Design, 2014.
4. Krishna T. Malladi, Frank Austin Nothaft, Karthika Periyathambi, Benjamin C. Lee, Christos Kozyrakis, and Mark Horowitz. "Towards energy-proportional datacenter memory with mobile DRAM". ISCA '12 – Proceedings of the International Symposium on Computer Architecture, 2012.

Technical Reports

1. Matt Massie, Frank Austin Nothaft, Christopher Hartl, Christos Kozanitis, André Schumacher, Anthony D. Joseph, and David Patterson. "ADAM: Genomics Formats and Processing Patterns for Cloud Scale Computing". University of California, Berkeley Technical Report UCB/EECS-2013-207.

Preprints

1. John Vivian, Arjun Rao, Frank Austin Nothaft, et al. "Rapid and efficient analysis of 20,000 RNA-seq samples with Toil". BioRxiv:062497. July 2016.

Theses

1. Frank Austin Nothaft, "Scalable genome resequencing with ADAM and avocado." Masters Thesis, May 2015. University of California, Berkeley Technical Report UCB/EECS-2015-65.
2. Frank Austin Nothaft, "Design Strategies for Compiler Managed Instruction Stores", Honors Thesis, Stanford University, June 2011.

Selected Presentations

Conference Talks

"Rethinking data-intensive science using scalable analytics systems"

• International Conference on Management of Data, June 2015 (SIGMOD '15). (Slides)

"Reproducible Emulation of Analog Behavioral Models"

• International Conference on Computer Aided Design, November 2014 (ICCAD '14). (Slides)

"ADAM: Fast, Scalable Genome Analysis"

• Bioinformatics Open Source Conf., July 2014 (BOSC '14). (Slides, Video)
• Spark Summit, June 2014. (Slides, Video)

Invited Talks

"Fast Variant Calling with ADAM and avocado"

• KTH Kista/SICS, February 2015. (Slides, Video)

"ADAM: Fast, Scalable Genome Analysis"

• Human Longevity, June 2015.
• DNANexus, December 2014. (Slides)
• Novartis Institutes, October 2014. (Slides)
• Wellcome Trust Genome Center, July 2014. (Slides)

"Automation For Validating Behavioral Models Against Schematics"

• Cadence Mixed Signal Design Summit, September 2012. With Nishant Shah.