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

Christopher Sullivan at CQLS

Dear CQLS Community,

Chris Sullivan, the CQLS Assistant Director of Biocomputing, has accepted a new position within OSU’s College of Earth Ocean and Atmospheric Sciences.  While we are sad to see him leave, his new position provides exciting new opportunities for him, and continues a long relationship he has had with the computing activities of CEOAS.  Please join us in congratulating Chris in his new position within OSU. 

Chris has been an integral part of CQLS (originally CGRB) since 1999.  Under his guidance the high-performance computing resources in the CQLS have grown from a few computing servers to greater than 7000 processors with more than 7 petabytes of storage and serving more than 20 departments across the University.  Chris has had great success developing bleeding edge computing research for the CQLS and the University.  He has also been phenomenal in his success at obtaining equipment grants from the likes of IBM and OpenPOWER.

Chris will remain with the CQLS at half time for the next three months to enable a smooth transition. He remains committed to the ongoing success of CQLS and to OSU. To ensure there are no interruptions in service the CQLS will fill an interim position to manage this transition before launching a full Assistant Director search in the New Year.

Again, please join us in congratulating Chris.  We will miss him, but we know that he’s just across campus.

Sincerely, 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

Oregon State University (OSU), in Corvallis and founded in 1868, is Oregon’s largest university. As a public land-grant university, conducting scientific research is part of OSU’s mission. However, the school’s new information and technology officer found it unacceptable that the university could not engage in health care research requiring HIPAA-level security standards because its previous cloud service didn’t meet security requirements. To address this challenge, the school chose to migrate its data to Microsoft Azure. As a result, the university now has reliable, compliant, and more secure data management that has positioned the school for additional research opportunities.

Read the full article on Microsoft’s website.

Hello,

We are pleased to announce the 2021 Center for Quantitative Life Sciences (CQLS) Fall Conference.  This will be a full day online event on Friday, September 17, 2021 (apologies for those who did not receive a notice about this previously. There was an issue with the list serve).  In celebration of our recent name change, the theme for this year is “Frontiers at the Intersection of the Life & Quantitative Sciences.” Because this is our first conference since our name change (and because the event is fully online this year) the conference this year is completely free for all attendees. We hope you will join us.

We strongly encourage all participants to submit a poster for the online poster session. Registered posters will be judged for cash prizes in three categories; Undergraduate Student, Graduate Student, and Post-Doctoral Fellow/Trainee. Since the event is online, a physical poster does not need to be printed. Rather, you will need to submit in advance a high-quality pdf and a stable internet connection. Lightning Talks will be limited to 5 minutes and no more than 5 slides.  Registered lighting talks will also be eligible for a cash prize.

Register in Advance

Or copy and paste the URL below into your internet browser:
https://oregonstate.qualtrics.com/jfe/form/SV_2tcSPOyfnG3beJw


On behalf of the organizing committee:

  • Kevin Brown, Pharmaceutical Sciences, OSU/OHSU
  • Molly Burke, Integrative Biology, OSU
  • Maude David, Microbiology & Pharmaceutical Sciences, OSU
  • Patrick De Leenheer, Mathematics, OSU
  • Perry Hystad, Public Health and Human Science, OSU
  • Natalia Shulzhenko, Immunology, OSU
Fall Term 2021
September 29, 2021Chris Plaisier
Arizona State University
Finding new therapies for mesothelioma
October 13, 2021TRACE
Oregon State University
TRACE COVID Community Surveillance Project
October 27, 2021David Garcia
University of Oregon
Prion-based forms of RNA-modifying enzymes
November 10, 2021Ya-chieh Hsu
Harvard University
Deep: Stem Cells at the Nexus of the Niche, Physiology, and the External Environment
Winter Term 2022
January 5, 2022TBD
January 19, 2022Carrie Hanna
Oregon Health and Science University
Using genome editing technology to create biomedical models in the nonhuman primate
February 2, 2022Jennifer Nemhauser
University of Washington
Babbage’s Cabbage: The Logic of Information Processing In Plants
February 16, 2022Yanming Di
Oregon State University
What is a replicate?
March 2, 2022Dr. Shobhan Gaddameedhi
North Carolina State University
Environmental Regulation of Genomic Stability and Human Health through the Circadian Clock
Spring Term 2022
March 30, 2022Mike Harms
University of Oregon
Ensembles, epistasis, and evolution: how biophysics shapes evolutionary outcomes
April 13, 2022Andrew Gentles
Stanford University
Atlas of Clinically Distinct Cell States and Cellular Ecosystems Across Human Solid Tumors
April 27, 2022CANCELLED – Yehenew Agazie
West Virginia University
TBD
May 18, 2022 (rescheduled for Fall2022)Elias Fernandez
University of Tennessee
TBD
June 1, 2022 (rescheduled for Fall2022)Sourav Ghosh
Yale School of Medicine
TBD

Genomics Lab Technician opening in the Center for Genome Research and Biocomputing

The Center for Genome Research and Biocomputing at Oregon State University is searching for a lab technician for its genomics core facility. The appointee will be conduct services for Center collaborators spanning DNA and RNA extraction, DNA sequencing, genotyping, high throughput sequencing, and PCR assays as needed. A significant portion of the work will involve viral detection and sequencing. The position is a full-time 1 year appointment. Minimum qualifications include a relevant undergraduate degree and at least 12 months’ experience working in a molecular biology research or service laboratory. For more information, and to apply for the position go to jobs.oregonstate.edu and search for posting P04217UF.

The Center for Genome Research and Biocomputing at Oregon State University collaborates with and assists life scientists of all levels in their research using cutting-edge genomics, informatics and computational techniques. An important component of the CGRB’s activities is the molecular biology and genomics laboratory.

To ensure full consideration, applications must be received by March 18, 2021. Applications will continue to be accepted until March 25, 2021. The closing date is subject to change without notice to applicants. For questions, contact Brett Tyler brett.tyler@oregonstate.edu

OSU commits to inclusive excellence by advancing equity and diversity in all that we do. We are an Affirmative Action/Equal Opportunity employer, and particularly encourage applications from members of historically underrepresented racial/ethnic groups, women, individuals with disabilities, veterans, LGBTQ community members, and others who demonstrate the ability to help us achieve our vision of a diverse and inclusive community.

Matthew Peterson

Congratulations to our very own Matthew Peterson, who has been appointed a 2021 Trusted CI Fellow. Trusted CI is a National Science Foundation (NSF) Cybersecurity Center of Excellence. The Trusted CI Fellows program empowers members of the scientific community with knowledge of cybersecurity and trains fellows to serve as cybersecurity liaisons to their respective communities. Six fellows are selected across the nation each year. To read more about Trusted CI and the other five fellows for 2021, check out the Trusted CI blog post about the 2021 fellows.

INTRODUCTION TO PYTHON

Introduction to Python I:
This module introduces programming concepts, driven by examples of biological data analysis, in the Python programming language. Topics covered will include variables and data types (including strings, integers and floats, dictionaries and lists), control flow (loops, conditionals, and
some boolean logic), variable scope and its proper use, basic usage of regular expressions, functions, file input and output, and interacting
with the larger Unix/Linux environment.

Introduction to Python II:
Part II expands on basic programming and explores using ‘objects’ (and their blueprints: classes) in encapsulating functionality into easily used blocks of code that more closely match the biological concepts at hand. Other topics include APIs, syntactic sugar, and creating and using packages such as BioPython.

January 4 – March 12

Monday/Wednesday 2:00-2:50 PM, BDS 599 (CRN:38557 and 38558) or as a workshop
Instructor: Matthew Peterson, matthew@cgrb.oregonstate.edu
for more information, email the instructor or visit: https://cgrb.oregonstate.edu/training/workshops

ENVIRONMENTAL SEQUENCE ANALYSIS

Gain practical experience with, 16s rRNA amplicon sequencing and shotgun metagenomics. No command line / R-studio experience required! Starting with raw FASTQ files, learn how to 1) profile rRNA sequences and 2) determine the taxonomy and functional composition of metagenomics samples!

January 4 – March 12

Tuesday/Thursday 10:00-10:50 AM, BDS 599 (CRN 38546) or as a workshop
Instructor: Andrew Black, andrew@cgrb.oregonstate.edu
For more information, email the instructor or visit: https://cgrb.oregonstate.edu/training/workshops