Dear CQLS Community,

As the fall term is underway, I recognize that it is long-past time to provide an update on CQLS activities.  Just a reminder, the Center has four distinct competencies, including: laboratory services; bioinformatics and data science; high performance computing (HPC); and health data and informatics.  Each of our four functional groups has had substantial undertakings over the last year. A very brief overview of key activities is offered below

o   Laboratory services:

  • We’ve expanded and reorganized our core lab footprint; this now includes ALS 3012 (A-B), 3020, 3131, 3137 (A-F), 3139 and 2070.  Multi-user and drop-off are now through ALS 3139.
  • Our Core lab is working on proposals to bring updated microscopy instrumentation to OSU.
  • We have a new QuantStudio Absolute Q digital PCR for multi-users.
  • We’ve updated our Genotyping Software.
  • Amplicon sequencing and longer 300 base-pair runs are now available on the NextSeq2000.
  • We have access to Pacific Biosystem’s Revio long read sequencing.
  • Our workflows have improved with the purchases of hoods and minor equipment.
  • Most significantly, the core lab has developed and posted a new position: Assistant Director for the Core Laboratory.  This role will take the lead on maintaining and expanding our core laboratory services, including working with our oversight boards, coordinating support among our constituencies, large scale project management, and coauthoring grants for new equipment which aligns with the evolving science. This open position closes at the end of the month.

o   High Performance Computing (HPC):

  • The CQLS HPC represents nearly 50% of the research computing capabilities at OSU (both for processing and storage).  Over the years CQLS (largely through the efforts of our past Assistant Director Chris Sullivan and current HPC manager Ken Lett) has developed an HPC model that provides a robust, resilient, cost-effective, cutting edge, and accessible computing resource for our users.  
  • The CQLS is highly engaged with campus-wide discussions on the future of OSU’s HPC needs for research computing.  Through this re-imagining the University intends to develop the next generation of HPC users and create a widely available HPC resource while still maintaining expert computing support for individual research domains.
  • We continue to upgrade the CQLS HPC.  Earlier this year our zfs storage server nfs0 was retired as users moved to newer servers.  We continue to upgrade servers and transition users to new hardware.

o   Bioinformatics and Data Science

  • CQLS instructors continue to train OSU researchers on HPC and research computing. Six CQLS workshops were taught last year including “Introduction to Linux”, “Introduction to Python Programming”, “RNAseq Analysis”, “Environmental Sequence Analysis”, and “Genotyping by Sequencing”.  Several courses were also taught in conjunction with the Oregon Data Science Collaborative. 
  • The CQLS maintains an isolated HPC for instruction, the ACTF.  This HPC provides a sandbox learning experience for HPC instruction.
  • Six CQLS Bioinformatics and Data Science consultants are available for collaboration on grant proposals, project discussion, experimental design, pipeline development, and data analysis on projects in bioinformatics and data science.

o   Health Data and Informatics

  • Working with Protected Health Data (PHI) and Personally Identifiable Information (PII), requires incredible attention to the safety and security of the information. Denise Hynes and Matthew Peterson, along with UIT and the Office of Information Security (OIS), coordinate the development of secure cloud resources within Microsoft Azure to facilitate the collection and processing of sensitive data for OSU researchers.
  • In particular, Denise and Matthew have worked to secure Oregon Health Authority (OHA claims data) and deployed Vanderbilt’s Research Electronic Data Capture (REDCap) software in production for multiple NIH grant-funded projects. 
  • The Health and Data Informatics group also maintains a ‘Community of Learning and Practice’ that serves an educational mission for the University, empowered by the CQLS’ newest part-time hire, Joe Spring, who has a wealth of REDCap training and administrative experience.
  • At the Center Level and Beyond:
    • Konnie Handschuch has joined us to provide administrative support to the Center.  Konnie had provided interim support and has now joined CQLS as a permanent member. She divides her time between CQLS and the Research Office.
    • As part of an overall effort to streamline our activities and achieve efficiency, we have handed off much of our budget and expense as well as HR activities to the Research Office.
    • Liz Zepeda has taken on the job of Building manager, stepping into the role after long-time manager, Chris Sullivan moved to CEOAS.
    • While Chris Sullivan moved to CEOAS he left his heart in CQLS.  He remains an incredible advocate for our Center and has worked with Ken Lett (appointed as Infrastructure Manager) to provide seamless support for researchers in CEOAS that are prime users of the CQLS infrastructure.
    • Chris Sullivan, Ken Lett, Chris Thompson (of the College of Engineering) and DRI (Mark Keever) have made tremendous strides in creating single logins, shared storage, and unified job scheduling for consistent access across OSU’s HPC infrastructure, while staying aligned with the security policy of the university.  This is incredibly important for ease of access of users from across and outside of OSU.
    • The next item on our to-do list is the zero-based budget effort, which will kick off soon. Don’t be surprised if some of you are asked to participate in that effort.

It’s been nearly two years since I assumed the role of Interim Director, with my focus on making changes to operations that will position CQLS for long-term success, and its next Director.  We are nearly there.

Sincerely,

Kathryn A. Higley, Ph.D., CHP, HPS Fellow
Interim Director CQLS – Center for Quantitative Life Sciences,
Professor, School of Nuclear Science and Engineering

Dear members of the CQLS Community,

I wanted to reach out and give you an update on the status of the Center.  It has been, as they say, an interesting year.  We have seen an easing of COVID restrictions, and with that return of staff to the Center.  We have had several personnel changes: Bo (Finance Manager), Dana (Bioinformatics Analyst), Matt (Bioinformatics Analyst), and Lynn (Admin. Assistant) have left for new opportunities.  Max Schmidt (Computational Scientist) and Steven Carrell (Bioinformatics Scientist) have joined the Center.  Konnie Handschuch has been serving as our part time Admin Assistant.

There have been changes within our laboratory space as well.  With closing of the previous Director’s lab, we’ve began the process of expanding our core laboratory into that space. A consultant has reviewed laboratory workflows for spatial optimization, and we are excited that this effort will help streamline sample processing and provide better staff space.

As part of functional realignment efforts in the Research Office, we have transferred several administrative duties to them.  Parts of CQLS billing, ordering, and HR efforts now take place in the Research Office.  This change will provide substantial capacity and personnel overlap and minimize bottlenecks.

The biocomputing side of CQLS has continued its efforts to replace and upgrade our computational infrastructure.  That has required us to retire some systems and move researchers on to newer (and improved!) components.  We have also engaged with University Information and Technology (UIT) to aggressively maintain the security posture of our systems.

Chris Sullivan has recently accepted an exciting position within the College of Earth, Oceans and Atmospheric Sciences (CEOAS) but, for the next two months, will work half time with the CQLS to enable a smooth transition. The CQLS will hire an Acting Assistant Director for Biocomputing, and we anticipate a search for a permanent position.

CQLS Bioinformatics and Data Science group continues to teach CQLS workshops and offer research consulting services.  The CQLS trainers teach introductory level workshops for learning high performance computing and Python programming, and bioinformatics workshops to learn analysis of RNAseq, genotyping, and environmental sequencing.  Bioinformatics research consulting analyzes weekly samples for COVID wastewater testing as well as many custom bioinformatics projects across the University.  The newly formed Oregon Data Science Collaborative (ODSC), in conjunction with UO and PSU, brings data science research into the CQLS.  The ODSC teaches workshops and offers research consulting on data analytics, data integration, and machine learning.  The ODSC just hosted its first state-wide data science symposium.

The coming year we will undertake several processes that will help shape the future of the CQLS. First, we will reengage with our stakeholders and steering committees, revisiting the components of the strategic plan.  Secondly, we will undertake a budget analysis in cooperation with the OSU Research Office.  This will help ensure the continued success of the Center.  Third, our Core Laboratory will work with the RO and help them construct CQLS-centered components for the new Research Equipment Laboratory Management System (RELMS).  This will, in turn, help CQLS better serve its customers.

When I accepted the position of Interim Director, I knew that there were challenges that needed to be addressed. Some involved our emergence from the restrictions imposed by the pandemic.  Others were more structural.  One thing that was certain, however, was that the Research Office is very committed to the success of CQLS.  They have been unwavering in their support and continue to help us navigate these challenging times.  CQLS will continue to be here, to provide support, guidance, and a place to grow your research.

Looking forward to this year,

Kathy

Kathryn A. Higley, Ph.D., CHP, HPS Fellow
Interim Director CQLS – Center for Quantitative Life Sciences,
Professor, School of Nuclear Science and Engineering

December 1, 2021

Colleagues,

It is my pleasure to announce that Dr. Kathryn A. Higley has been selected to serve as the Interim Director of the Center for Quantitative Life Sciences (CQLS) effective December 1.

Dr. Higley has been at OSU for 27 years, and most recently served as the Associate Director for the TRACE-OSU effort. She has a long record of both administrative and academic experience at OSU. She is a Professor and former Head of the School of Nuclear Science and Engineering in the College of Engineering at Oregon State University. She has managed OSU’s Radiation Health Physics program, including developing its online graduate degree into the largest in the country. Dr. Higley has been at Oregon State University since 1994 teaching undergraduate and graduate classes on radioecology, radiation biology, and more. She is a Council Member of the National Council on Radiation Protection and Measurements, a board member and fellow of the Health Physics Society, and a Certified Health Physicist. Dr. Higley and her students have done research in radiologically contaminated environments around the globe.

I am excited to start working with Dr. Higley, CQLS staff and affiliated faculty to take the center to the next stage. Please join me in welcoming her to the CQLS and RO community!

Sincerely, Irem Y. Tumer, Ph.D., ASME Fellow
Vice President for Research