TGQR 2010Q2 Report.pdf - Teragridforum.org

SDSC
Dash Early Users
Project Title
Principle
Investigat
or
Institution
(s)
Project Overview
Status/Outcomes
Protein
Databank
Phil
Bourne
University
of
California,
San Diego
Protein Data Bank (PDB) is a
worldwide repository of
information about the 3D
structures of large biological
molecules including proteins
and nucleic acids. Alignment-
DB, from the PDB group,
performs predictive science
with queries on pair-wise
correlations and alignments
of protein structures that
predict protein fold space and
other properties.
Initial tests show
speedup of up to
69x on a limited
set of queries
when using flash
drives. Tests are
ongoing to
evaluate the
possibility of
running test for
the full PDB. This
represents an
important use case
for Gordon, i.e., a
semi-persistent
database installed
on SSD’s. This
project is
providing a
mechanism to
assess this
architecture.
Biological
Networks
Mihail
Baitaliuc
University
of
California,
San Diego
Biological Networks
integrates over 100 public
databases for thousands of
eukaryotic, prokaryotic and
viral genomes and provides
software tools needed to
decipher gene regulatory
networks, sequence and
experimental data, functional
annotation, transcriptional
regulatory region analysis.
The software platform
supports biological pathways
analysis, querying and
visualization of gene
regulation and protein
interaction networks,
metabolic and signaling
pathways.
Generated a
synthetic
workload to
observe query
plans using
indexes and
sequential scans.
Initial tests show
speedup of up to
186x for typical
queries when the
database is
installed on
SSD’s.
Palomar
Transient
Peter
Nugent
Caltech,
UC
This project’s goal is to
support the PTF Image
PTF transient
search tested on
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