The CQLS has experienced significant change in the last few years.  Throughout this we have increased CQLS staffing, developed new research collaborations, and continued CQLS services without interruption.  As we move forward the CQLS will be increasing community outreach and events including restarting the Fall Conference (November 22^nd) and working with faculty committees and our users and community to direct the future of the CQLS.

The CQLS is composed of four interconnected functional groups:

CQLS Core Laboratory – Four laboratory staff run the services provided in Genomics Core, Shared Instrumentation Core, and Microscopy Core.  Recently the laboratory has been working with the Division of Research and Innovation to move CQLS into the new RELMS instrument billing system.

CQLS Research Computing HPC – Two CQLS staff run and maintain the CQLS HPC, the largest and most widely used computing cluster at OSU.  Recent upgrades outlined in this newsletter combine the CQLS HPC with other OSU HPC to create a consolidated OSU research computing cluster.

CQLS Bioinformatics and Data Science – Six CQLS staff consult on computational research and teach our computing and bioinformatics courses.  CQLS scientists consult on experimental design, grant proposals, research, and programming projects and are highly utilized in many labs across OSU.

CQLS Health Data Informatics – Led by Denise Hynes, the CQLS provides support and tools for analyzing health data including protected and secure data.

In this newsletter you will find information on CQLS changes and new services, research projects in the CQLS, spotlight on CQLS service, and information on upcoming CQLS events.

Brent Kronmiller

CQLS Interim Director

The Division of Research and Innovation is combining Center and Institute facility ordering systems into RELMS (https://research.oregonstate.edu/relms) to streamline user management, ordering and billing, instrument usage, and equipment calendar reservations. The CQLS is beginning to transfer our weborder system into RELMS.

The CQLS will create 3 separate RELMS sites, each containing multiple CQLS services:

1. CQLS Shared Instrumentation and Microscopy
2. CQLS Genomics Core
3. CQLS HPC, Research Consulting, and Training

We will move services individually as we transition to RELMS. A service that has transitioned to RELMS will not be available in CQLS weborder. When a service moves we will notify users via the CQLS-Community email list and with a notification on the weborder site. Once a service has moved you will need to create a RELMS account to order this service.

Effective September the following services will be moved to RELMS:

• Extractions (DNA and RNA)
• Genotyping by Sequencing (GBS)

Effective October the following additional CQLS services will move to RELMS:

• Illumina Sequencing (MiSeq and NextSeq)
• Sample preparations
• Bioanalyzer
• DNA size selection
• PacBio Sequencing
• TapeStation
• Bioinformatics Consulting

Effective November the following services will be moved to RELMS:

• Biocomputing (HPC)

Please request a RELMS account using one of the following links:
OSU Faculty/Staff Students: https://oregonstate.qualtrics.com/jfe/form/SV_782PHrAZwIFVilM
External Users: https://oregonstate.qualtrics.com/jfe/form/SV_7OKXvp5M5Q5VpI2
and visit https://relms.oregonstate.edu/facilities to find the CQLS service that you want to order.

Thank you again for your patience and support as we transition to RELMS. If you need assistance please contact the CQLS, visit the RELMS website (https://research.oregonstate.edu/relms), or email RELMS staff directly (relms@oregonstate.edu).

Thank you,

The CQLS and RELMS support teams

Colleagues,

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

Dr. Kronmiller has been at OSU and affiliated with CQLS for 11 years. Most recently, he has served as the CQLS Assistant Director of the Bioinformatics and Data Science Group that helps consult and collaborate on bioinformatics and data science research across the university. He is also an Assistant Professor (Senior Research) in the Department of Botany and Plant Pathology in the College of Agricultural Sciences.

In the CQLS, he has provided technical and scientific advising to staff and the OSU community and provided guidance and direction to both the CQLS Biocomputing group and the CQLS Core Laboratory group. He also manages the CQLS teaching effort, courses and workshops for students and employees to learn high-performance computing (HPC), bioinformatics and data science skills. Dr. Kronmiller also provides scientific leadership for designing experiments, providing laboratory quotes and troubleshooting errors and issues.

Dr. Kronmiller succeeds Dr. Kathy Higley, who has served as CQLS interim director since December 2021. My special thanks to Kathy for leading the CQLS during this transition period for the center. While Kathy will remain as OSU faculty, she will also be assuming the duties as the President of the National Council on Radiation Protection and Measurements.

Please welcome Dr. Brent Kronmiller to this new role as we take the CQLS to the next stage in support of Prosperity Widely Shared.

Best,

Irem

Irem Y. Tumer, Ph.D., ASME Fellow
Vice President for Research and Innovation
Professor, School of Mechanical, Industrial, and Manufacturing Engineering 

Division of Research and Innovation
Oregon State University | 541-737-0664

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