Sasha Ames


Email: sasha@llnl.gov
Phone: 925-424-4644


Sasha Ames is a postdoctoral researcher in the Center for Applied Scientific Computing at the Lawrence Livermore National Laboratory.  Sasha primarily works for the AIMS group led by Dean Williams, for which he is heavily involved in the development and operation of the Earth System Grid Federation ESGF.  For that effort, he leads working teams that handle data publication and autonomous node management.  He is also involved in distributed computation for ESGF, PCMDI site and archive administration, and ACME Data Management task leadership.  In addition to his work with AIMS, Sasha works with Jonathan Allen on an LDRD effort to develop a genomic sequence DeBruijn graph for antibiotic microbial resistance detection.

Sasha received his PhD from UC Santa Cruz in 2011 while working at LLNL as part of the Lawrence Scholar Program (since 2008) with Prof. Carlos Maltzahn.   This work was part of the SISC and PerMA LDRD efforts, in which he developed the QUASAR query language and QMDS file system software prototype.  Previously, he earned a B.A. in computer science from Columbia University, spent several years in industry, working on a financial web application and intrusion detection software, and received a M.S. from UCSC, prior to working at LLNL.   At LLNL as a postdoc he worked on the "Metagenomics Search" LDRD (also with JE Allen) where he was primarily he was primarily responsible for the framework to create searchable genome reference databases and has co-managed the software development and release efforts for the Livermore Metagenomics Analysis Toolkit (LMAT).  He also worked for the DCA LDRD with Maya Gokhale and Brian Van Essen on evaluating the DI-MMAP runtime module.

Awards:
 

2015 ESGF community award

2014 Global Security Gold Award

 

Publications:

 

Sasha K Ames, Shea N Gardner, Jose Manuel Marti, Tom R Slezak, Maya B Gokhale, Jonathan E Allen. "Using populations of human and microbial genomes for organism detection in metagenomes" Genome Research 25 (7) July 2015, 1056-1067 

Sasha Ames, Jonathan E. Allen, David A. Hysom, G. Scott Lloyd and Maya B. Gokhale. "Design and Optimization of a Metagenomics Analysis Workflow for NVRAM." 13th IEEE International Workshop on High Performance Computational Biology. May 2014

Brian Van Essen, Henry Hsieh, Sasha Ames, Roger Pearce, Maya Gokhale. “DI-MMAP—a scalable memory-map runtime for out-of-core data-intensive applications.” Cluster Computing (online), October 2013

Sasha K. Ames, David A. Hysom, Shea N. Gardner, G. Scott Lloyd, Maya B. Gokhale, Jonathan E. Allen. "Scalable metagenomic taxonomy classification using a reference genome database.” Bioinformatics,  29 (18) July 2013, 2253-2260.
 
Brian Van Essen, Henry Hsieh, Sasha Ames, Maya Gokhale, “DI-MMAP: A High Performance Memory Map Runtime for Data-Intensive Applications,” Data intensive scalable computing systems workshop at SC12, November 2012.
 
Brian Van Essen, Roger Pearce, Sasha Ames, Maya Gokhale:  “On the role of NVRAM in data intensive HPC architectures: an Evaluation” in Proceedings of the 26th IEEE International Parallel & Distributed Processing Symposium.  May 2012
 
Sasha Ames
, Maya B. Gokhale, Carlos Maltzahn.  "QMDS: a file system metadata management service supporting a graph data model-based query language." International Journal of Parallel, Emergent, and Distributed Systems,  28 (9), 2013 159-183.

Sasha Ames, Maya B. Gokhale, Carlos Maltzahn.QMDS: A File System Metadata Management Service Supporting a Graph Data Model-based Query Language.  in Procedenings of the 2011 IEEE Conference on Networking, Architecture, and Storage (NAS 2011). Dalian, China, July 2011. LLNL-CONF-45494

Jonathan Koren, Yi Zhang, Sasha Ames, Andrew Leung, Carlos Maltzahn, Ethan L. Miller. Searching and Navigating Petabyte Scale File Systems Based on Facets. Proceedings of the 2007 ACM Petascale Data Storage Workshop (PDSW 07), November 2007.

Sasha Ames, Nikhil Bobb, Kevin Greenan, Owen Hofmann, Mark W. Storer, Carlos Maltzahn, Ethan L. Miller, Scott A. Brandt. LiFS: An attribute-rich file system for storage class memories. Proceedings of the 23rd IEEE / 14th NASA Goddard~ Conference on Mass Storage Systems and Technologies, May 2006.

Ames, A., Bobb , N., Brandt, S.A., Hiatt, A., Maltzahn, C., Miller, E. L., Neeman, A., Tuteja, D.: "Richer File System Metadata Using Links and Attributes", in Proceedings of the 13th NASA Goddard Conference on Mass Storage Systems and Technologies (MSST '05)