The document summarizes a genome sequencing project aimed at mapping the genome of California's sugar pine tree. A key partner in the project is Jill Wegrzyn, a CSRC alumna recently appointed as an assistant professor at the University of Connecticut. The project led by UC Davis scientists and Steven Salzberg from Johns Hopkins University seeks to provide information to help preserve the iconic but imperiled sugar pine tree. Funding from the USDA will allow the partnership to apply new diagnostic tools from sequencing to accelerate finding disease-resistant parent trees, whose seeds can then help protect future generations of sugar pines.

1. CSRC Alumna Jill Wegrzyn, a bioinformatician, was
recently appointed to assistant professor at the University
of Connecticut. She is a key partner in a sequencing project
aimed to map the genome of California’s legendary sugar
pine, which naturalist John Muir declared to be “king of the
conifers.” The project led by UC Davis scientists and Steven
Salzberg, a computational biologist professor at John Hopkins
University, is expected to provide useful information that
may help preserve the iconic but imperiled tree.
Being one of the tallest tree species in the world, the
sugar pine has an important environmental worth as
a key element of California’s forests. It has ecological
and recreational value as well as a source of timber.
With funding provided from the U.S. Department of
Agriculture’s National Institute of Food and Agriculture,
the partnership of UC Davis and Dr. Salzberg, Dr.Wegrzyn
and scientists are able to apply the new diagnostic tools
taken from sequencing which will accelerate the finding of
disease-resistant parent trees directly. The seeds planted
from parent trees will help protect new generations of
sugar pines from diseases such as the blister rust pathogen.
On November 30, 2015, San Diego State
University became the first California
State University (CSU) system member to
obtain 100Gbps connectivity to the Internet.
Working with network engineers from the
Corporation for Education Network Initiatives
in California (CENIC) and faculty from Calit2
at the University of California, San Diego,
Christopher Paolini, from the Computational
Science Research Center (CSRC) and College
of Engineering, implemented a dedicated
100Gbps connection to the SDSU campus.
SDSU has joined a handful of other prominent
research universities such as Stanford, Caltech,
UCSD, UC Berkeley, UC Davis, UC Riverside,
UC Santa Cruz, and UC Irvine on a 100Gbps
backbone that connects to Internet2 and the
Pacific Wave wide-area advanced research
network that interconnects Los Angeles,
Sunnyvale, Seattle, Denver, Albuquerque, El
Paso, and Chicago. This major project began
Wednesday, June 17, 2015 and was completed
November 30, 2015. In order to accommodate
100Gbps connectivity, an existing Cisco
CWDM-MUX8Aeight-channel passive coarse
wavelength-division multiplexer (CWDM)
and a Cisco Catalyst 4900M Ethernet switch,
which had been providing SDSU with 10 Gigabit Ethernet connectivity (funded in 2009
through NSF Office of CyberInfrastructure MRI Grant 0922702 awarded to CSRC), was
replaced by a new Cisco ONS 15454 M6 Multiservice Transport Platform (MSTP) and
a new Cisco ONS 15216 Exposed Faceplate Mux/Demux 40-Channel Patch Panel, as
shown in the figure above. The new patch panel provides SDSU with 40 odd-numbered
frequencies, as defined by ITU G.694.2, for dense
wavelength-division multiplexing (DWDM) point-
to-point data center interconnections. The Cisco
ONS M6 shelf includes a 100GE line card to provide
100Gbps California Research and Education
Network (CalREN) High Performance Research
(HPR) connectivity to the SDSU Science DMZ.
The 100Gbps circuit from the M6 MSTP terminates
at a new Brocade MLXe-4 router recently purchased
using NSF CC-NIE award funds.The MLXe includes
one eight-port 10-GbE module to support Science
SDSU
Computational Science
Graduate Programs:
PhD. in Computational Science
Master Degree in Computational Science
Contact the CSRC or Be Placed on
the Mailing List:
Computational Science
Research Center
GMCS Building, Room 206
San Diego State University
5500 Campanile Drive
San Diego, CA 92182-1245
Telephone: (619) 594-3430
csrc@mail.sdsu.edu
Give to the Computational Science
Research Center for the Graduate
Student Research Projects Fund:
Donations to the CSRC can be made in the
following ways:
By check made out to:
The SDSU Campanile Foundation
or through credit card by contacting the
Computational Science Research Center
GMCS Building, Room 206
College of Sciences
San Diego State University
5500 Campanile Drive
San Diego, CA 92182-1245
Telephone: (619) 594-3430
csrc@mail.sdsu.edu
Executive Board
Director
Jose E. Castillo, PhD
Associate Directors
Andrew Cooksy, PhD
Satchi Venkataraman, PhD
Paul Paolini, PhD
Computer Support Coordinator
James Otto, PhD
Industry Projects Coordinator
Ezra Bejar, PhD
COMPUTATIONAL SCIENCE
ODYSSEY is published bi-annually by the
Computational Science Research Center
for the faculty, friends and supporters of San
Diego State University.
Your comments, suggestions and bulletin
submissions are welcome. Please call Parisa
Plant at (619) 594-2260 or e-mail: parisa.
plant@sdsu.edu
Ezra Bejar Editor-in-Chief
Parisa Plant Editor/Publication
Diana Prout Graphic Designer
CSRC Alumni Spotlight
O D Y S S E YO D Y S S E Y
C O M P U TAT I O N A L S C I E N C E
Director
Jose E. Castillo, PhD
Industry Advisory Board
John Newsam, Chair
Tioga Research, Inc.
Gary Fogel
Natural Selection, Inc.
Mark E. Pflieger
Cortech Solutions, Inc.
Anton Zajac
Eset Foundation
Bill Bartling
California Dept. of Conservation
Bob Parker
SPAWAR
Scott Kahn
Illumina, Inc.
Victor Pereyra
Stanford University
Antonio Redondo
Los Alamos National Laboratory
SPRING
2016
C C - N I E c o n t i n u e d o n P a g e 3
After James Mullinix completed his service in the
U.S. Marines, he began his studies at SDSU majoring
in Applied Mathematics. He also found employment with
a local research company, NanoComposix, Inc., where
James worked as a research associate for seven years. Upon
receiving his B.S. in Math, he made the decision to apply for
an M.S. at SDSU in Applied Mathematics with an emphasis
in Dynamical Systems, which he completed in the Summer
of 2015. James learned from being a mathematician and a researcher that there is a
great need for those who work well in an interdisciplinary environment along with
a strong need for managing big data. The CSRC is the perfect environment to learn
both skills-- this was the compelling reason to further his education. Additionally,
James has found a place in Professor Antoni Luque’s lab where he is studying
current problems facing the global coral reef population. Doing research in Dr.
Luque’s lab provides great meaning and depth to James’ studies as he knows he is
working towards solving an important issue of today.
CSRC New Students Spotlight
NSF Campus Cyberinfrastructure - Network
Infrastructure and Engineering Program (CC-NIE)
THE
In This Issue
CC-NIE Article ..............Page 1
Director’s Corner ............Page 2
CC-NIE & Newsworthy ..Page 3
Alumni & New Students ..Page 4
Stephanie Lauber started attending SDSU as a Master's student in Astronomy of
2013 after completing her B.S. in Physics with a concentration in Astrophysics
at SFSU. During her time in the Astronomy Department, she was able to take two
elective courses, Computational Physics and Quantum Mechanics with Dr. Calvin
Johnson. It was through Computational Physics and several courses that Stephanie
became interested in the computational aspects of physics and astronomy.
When deciding on a PhD program, Stephanie applied to Computational Science
due to the encouragement from Dr. Johnson and fellow CSRC students. During
the fall semester, she spent time transitioning to focus on computational nuclear
physics. As an undergraduate, Stephanie knew she wanted to work in astrophysics
when constantly asking herself "why?" when confronted with the astronomical
processes. After completing her degree, Stephanie hopes to find a post-doc position
at a national laboratory.

2. Dear Friends,
As we move into 2016, the CSRC is excited to have 50 Doctoral and 11 Master’s students in the
Computational Science Program. We had three Master’s students graduate in the fall of 2015, and
offer our congratulations to the following students: Gregori Clarke, Eric Su, and Raul Vargas Navarro.
Also, we are proud to congratulate Lingjun He, Martin Kandes and Mariangel Garcia for completing
their Doctoral Programs! These graduates represent research groups that span Mathematics, Computer
Science, Condensed Matter Physics, and Biology-- there’s no better demonstration of the importance
and success of the interdisciplinary nature of CSRC at San Diego State University. Rounding out the
research focus of each student was a broad exposure in our colloquia from state-of-the-art computational
applications to internationally recognized research projects and courses designed to strengthen their
foundations in applied mathematics. The CSRC is proud to prepare the next generation of scientists to meet the need for an
increasingly flexible and well-balanced workforce.
Director’s Corner - Andy Cooksy
DMZ data transfer notes (DTNs) with 10Gbps network
interfaces, one four-port 40-GbE module, and one two-port
100GbE module with two 100 GbE CFP2 LR4 optics for
distances up to 10km over single mode fiber (SMF). The
40-GbE module provides inter-router connectivity between
CSRC’s older Alcatel-Lucent OS10K router and the new
MLXe-4. CSRCisnowabletoprovideSDSUresearchfaculty
with 100 and 40Gbps connectivity to support demanding
scientific data transfer requirements. The Science DMZ
has been enabling “BigData” intensive science at SDSU in
such areas as Earthquake Rupture and Wave Propagation
Simulation (Kim Olsen and Steven Day), Parallel 3-D
Unified Curvilinear Coastal Ocean Modeling (Jose Castillo),
and High-Order PSIC Methods for Simulation of Pulse
Detonation Engines (Gustaaf Jacobs). Access to the Science
DMZ network is currently available in the CSL, EBA, GMCS,
Physics, Physical Science, and Engineering buildings. We
are in the process of installing a new network switch in the
Physics Astronomy building to support the research of the
Dengue Prevention Consortium at SDSU.
In addition to the implementation of 100Gbps connectivity to
our Science DMZ, SDSU was invited by UCSD to become an
CC-NIE continued from Page 1
N E W S W O R T H Y. . .
Intellisis Corporation Fellowship Awards Lunch
The Parallel Computing Summer Research Internship review committee at Los Alamos National Laboratory has recently
announced internships awarded to three CSRC students. They are Priscilla Kelly, Neelam Patel, and Stephanie Lauber.
The review committee was extremely impressed with the quality of students from CSRC/SDSU, which is evident in the high
acceptance rate into LANL’s program. Los Alamos had over 50 applicants for nine spots and three of those spots went to our
students. We hope the students’ time at the Laboratory over the summer can strengthen the relationship between LANL and
SDSU.
Congratulations to Genivaldo Silva, Computational Science PhD student and Alexandru Popescu, Master’s student in
Aerospace Engineering (CSRC-STEM scholarship recipient) in receiving the Provost’s Award at the 2016 SDSU Student
Research Symposium.
Behrouz Babakhani, PhD student, has been awarded Honorable Mention for his submitted paper to the 2016 IEEE AP-S
Student Paper Competition. Behrouz will receive a $1000 stipend to offset his travel expenses to the AP-S/URSI 2016
Symposium. This year, the IEEE AP-S Society Advisory Committee received 158 paper submissions for the contest.
PhD student, Luis Escalona recently received the Graduate Student Travel Fund - Student Success Fee for $1000. The
funding will be used for the 2016 SPIE Smart Structured/NDE Conference, March 20th - 24th, held in Las Vegas, NV.
Computational Science Doctoral Program Reaches New Milestone... The Computational Science Ph.D. Program reached
a new milestone when doctoral student James Turtle defended his PhD dissertation on March 24, 2016. He becomes
the 50th doctoral student to successfully finish the Computational Science Doctoral Program in Computational Science. The
program, that was started in 2002, has produced outstanding graduates that have entered and flourished in academia, national
research labs, and industry. To learn more about our alumni visit http://www.csrc.sdsu.edu/alumni.html.
active participant in the recent NSF funded Pacific Research
Platform: A Science-Driven Big-Data Freeway System. NSF
has provided UC San Diego and UC Berkeley with a $5 million,
five-year award to establish a Pacific Research Platform (PRP),
a science-driven high-capacity data-centric “freeway system”
on a large regional scale. The goal of this project is to give
participating universities and other research institutions the
ability to move data 1,000 times faster compared to speeds on
today’s inter-campus shared Internet. The PRP links most of
the research universities on the West Coast (the 10 University
of California campuses, San Diego State University, Caltech,
USC, Stanford, and University of Washington) via the CENIC/
Pacific Wave 100G infrastructure. Christopher Paolini
and Jose Castillo are participating in the PRP as one of the
science driver teams to pursue research in CO2
sequestration
simulation. On October 14, 2015, Paolini presented a talk
entitled Pacific Research Platform Enabled Geologic CO2
Sequestration Simulation at Calit2’s Qualcomm Institute,
University of California, San Diego. The research goals of
this effort will be to study the effect of aqueous electrolytic
reactions on reservoir temperature during supercritical CO2
injection, and the effect of induced fracturing on carbonate
mineral saturation.
The CSRC is proud to announce three of our graduate students: Anna Ma, Uyen Hoang and Jonathan Matthews
have received a fellowship award from Intellisis Corporation. This award provides a $5,000 fellowship for
graduate students in the Computational Science Program.
The awardees’ areas of interests are as follows: Anna Ma - Machine Learning and Big Data; Uyen Hoang - Image
Informatics; and Jonathan Matthews - Numerical Partial Differential Equations.
Here are some snapshots from the Intellisis Corporation Fellowship Awards Lunch held at the Faculty-Staff Club on
campus.