Award Abstract # 2018432
CC* Networking Infrastructure: A Science DMZ For Quantitative Biology and Precision Agriculture

NSF Org: OAC
Office of Advanced Cyberinfrastructure (OAC)
Recipient: MICHIGAN STATE UNIVERSITY
Initial Amendment Date: May 15, 2020
Latest Amendment Date: May 15, 2020
Award Number: 2018432
Award Instrument: Standard Grant
Program Manager: Kevin Thompson
kthompso@nsf.gov
 (703)292-4220
OAC
 Office of Advanced Cyberinfrastructure (OAC)
CSE
 Directorate for Computer and Information Science and Engineering
Start Date: July 1, 2020
End Date: June 30, 2022 (Estimated)
Total Intended Award Amount: $483,122.00
Total Awarded Amount to Date: $483,122.00
Funds Obligated to Date: FY 2020 = $483,122.00
History of Investigator:
  • Brian O'Shea (Principal Investigator)
    oshea@msu.edu
  • Melissa Woo (Co-Principal Investigator)
Recipient Sponsored Research Office: Michigan State University
426 AUDITORIUM RD RM 2
EAST LANSING
MI  US  48824-2600
(517)355-5040
Sponsor Congressional District: 07
Primary Place of Performance: Michigan State University
426 Auditorium Rd, Room 2
East Lansing
MI  US  48824-2600
Primary Place of Performance
Congressional District:
07
Unique Entity Identifier (UEI): R28EKN92ZTZ9
Parent UEI: VJKZC4D1JN36
NSF Program(s): Campus Cyberinfrastructure
Primary Program Source: 01002021DB NSF RESEARCH & RELATED ACTIVIT
Program Reference Code(s):
Program Element Code(s): 808000
Award Agency Code: 4900
Fund Agency Code: 4900
Assistance Listing Number(s): 47.070

ABSTRACT

Moore?s Law has ushered in a scientific data revolution. This is particularly acute in the life sciences, where the devices used to collect data and the theoretical tools used to generate models have benefited tremendously from the advent of inexpensive digital sensors and general-purpose graphics processing units, which have led to an explosive increase in the volume of high-quality data. Sharing large amounts of this data for analysis by other researchers will result in tremendous benefits to the scientific community.

This project creates a Science DMZ at Michigan State University, which will facilitate MSU researchers? ability to share huge volumes of data with the external research community at very high bandwidth. The project supports the networking hardware and software necessary to implement up to 100Gbps network connections used for sharing data already stored at MSU?s High Performance Computing System and on the NSF-funded MI-OSIRIS file system. The project uses data provided by four research groups on campus as a testbed, making cryo-electron microscopy images, hyperspectral imaging of crops using drones, three-dimensional volumetric images of plants generated via X-ray computed tomography, and a databank of biomolecular simulation data available to other researchers and the public. This project enhances the impact of MSU scientists and leverages prior NSF scientific and cyberinfrastructure investments. In addition, it involves the participation of students in the deployment and usage of the science DMZ.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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Amézquita, Erik J and Quigley, Michelle Y and Ophelders, Tim and Landis, Jacob B and Koenig, Daniel and Munch, Elizabeth and Chitwood, Daniel H "Measuring hidden phenotype: quantifying the shape of barley seeds using the Euler characteristic transform" in silico Plants , v.4 , 2022 https://doi.org/10.1093/insilicoplants/diab033 Citation Details
Soltani, Ali and Walter, Katelynn A. and Wiersma, Andrew T. and Santiago, James P. and Quiqley, Michelle and Chitwood, Daniel and Porch, Timothy G. and Miklas, Phillip and McClean, Phillip E. and Osorno, Juan M. and Lowry, David B. "The genetics and physiology of seed dormancy, a crucial trait in common bean domestication" BMC Plant Biology , v.21 , 2021 https://doi.org/10.1186/s12870-021-02837-6 Citation Details

PROJECT OUTCOMES REPORT

Disclaimer

This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.

The goal of this project was to build a high-speed research network at Michigan State University (MSU) that will facilitate MSU researchers' ability to share huge volumes of data both within MSU and with the external research community at very high bandwidth - up to 100 Gbps.  The funding from this grant was used for the networking hardware and software necessary to implement the high-speed network connections used for sharing data already stored at MSU's High Performance Computing Center (HPCC) and the NSF-funded MI-OSiRIS data storage systems, as well as to individual facilities on campus.  As a testbed, we used data provided by four research groups on campus whose work focuses on data-intensive applications in biology and agriculture.

The intellectual merit of this project is that it has immediately accelerated data transfer for MSU's data-intensive core research facilities (i.e., the MSU HPCC, MI-OSiRIS, and MSU's cryogenic electron microscopy facility), to the benefit of all research and educational efforts that use these facilities.  In addition, research groups whose work focuses on precision agriculture with hyperspectral drone imaging and LIDAR, and molecular simulations of plant interactions, have experienced speedups in data transfers to and from their labs. Serendipitously, speeds between the Atlas Great Lakes Tier 2 data center locations at MSU and the University of Michigan, as well as to CERN, were increased and their connectivity was made more robust.  Beyond these immediate and significant impacts, additional research groups with data-intensive experimental equipment will be brought onto the high speed research network in the near future.

The broader impacts of this project are as follows.  A significant number of undergraduate students, graduate students, and postdoctoral researchers  participated in either the construction and optimization of the high speed research network or used it for their own research, thus giving them experience with cutting-edge research cyberinfrastructure and (in the latter case) accelerated their own research projects.  In particular, undergraduate students participated in the network controllers used in this project, giving them real-world experience with high end networking equipment.  In addition, the new network has enhanced the ability to share large datasets in a variety of research areas (most notably, computational plant science) that will be used to train students in computational biology.

 


Last Modified: 10/09/2022
Modified by: Brian W O'shea

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