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

NOVEMBER 12, 2020

Photo courtesy of The Corvallis Advocate

From The Corvallis Advocate: “Oregon State University brought its TRACE Community COVID-19 testing program to Eugene, sending three-member teams – one OSU student, one UO student and one professional –to city neighborhoods to collect nasal-swab samples from hundreds of residents and sewage samples from around Eugene and Springfield. This will further expand TRACE’s coverage, which includes five similar sweeps in Corvallis, as well as some study in Bend, Hermiston and Newport. TRACE will be working in tandem with UO’s Monitoring and Assessment Program (MAP).” See the full article for more information.

Another great term of the CGRB’s Bioinformatics User Group (BUG) is in the books!

This term we had a wide range of presenters—graduate students to Principle Investigators. It was nice to get the perspective of folks who are in different parts of their careers.

A special thanks to all of our presenters:

Sept 25: Christopher Sullivan and Ken Lett (Center for Genome Research & Biocomputing)

  • Title: CGRB’s new DFS for one and all!, i.e., Don’t know what a Distributed File System is? Come find out!
  • Abstract: The CGRB works with researchers to provide the most robust computational infrastructure available today. Many group rely on file services at the heart of their research computing needs and the CGRB has worked for over 2 decades to provide redundant high speed file services.  Over the years users have grown to expect the best solution at a very cheap price. Because of this model the CGRB spends a great deal of time evaluating the available systems to ensure we always have the best at the lowest price. In the past year the CGRB has worked to evaluate and purchase new file service hardware that will replace our existing setups. We will be explaining the pathway taken to bring the new service online and some of the new exciting features.

Oct 9: Lillian Padgitt-Cobb (David Hendrix Lab, Biochemistry & Biophysics)

  • Title: A phased, diploid assembly of the hop (Humulus lupulus) genome reveals patterns of selection and haplotype variation, i.e., Resolving functional and evolutionary mysteries of a large, complex plant genome with genomic data science
  • Abstract: Hop (Humulus lupulus) is a plant valued for its use in brewing and traditional medicine. Efforts to determine how biosynthetic pathways in hop are regulated have been challenged by its complex genomic landscape. The diploid hop genome is large, repetitive, and heterozygous, which challenged early attempts at sequencing with short-reads. Advances in long-read sequencing have improved detection of repeats and heterozygous regions, revealing that the genome is nearly 78% repetitive. For our assembly, PacBio long-read sequences were assembled with FALCON and phased into haplotype assemblies with FALCON-Unzip. Using the phased, diploid assembly to assess haplotype variation, we discovered genes under positive selection enriched for stress-response, growth, and flowering functions. Comparative analysis of haplotypes provides insight into large-scale structural variation and the selective pressures that have driven hop evolution. The approaches we developed to analyze the phased, diploid assembly of hop have broader applicability to the study of other large, complex genomes.
  • Lillian’s GitHubhttps://github.com/padgittl/CascadeHopAssembly
  • Hop Genome Browserhttp://hopbase.org/

Oct 23: Kelly Vining (Kelly Vining Lab, Horticulture)

  • Title: R/qtl, i.e., Applications and methods for analysis of quantitative traits
  • Abstract: R/qtl is an R package that is used for genetic mapping and marker-trait association. This presentation will explore specific features of R/qtl applied to plant breeding populations. Data types, functions, and interpretation of results will be explored.

Nov 6: Ed Davis (Center for Genome Research & Biocomputing)

  • Title: Introductory microbiome analysis using phyloseq, i.e., How to generate exploratory diversity plots and what they mean
  • Abstract: Generating high quality, publication ready figures for a microbiome study can be somewhat difficult. An understanding of both the statistical tests and how to effectively use R to produce figures is required, so the learning curve can be somewhat steep. Fortunately, there are several easy-to-use packages in R that facilitate the analysis of microbiome studies using 16S amplicon data, including the phyloseq package that will be the focus of my talk. I will cover the basics of analyzing alpha and beta diversity and provide some code and example images to show how to generate publication ready figures starting from the base phyloseq output. I will also generate some exploratory charts and graphs such that one would be able to form and later test hypotheses using microbiome data. I will be happy to share the examples and code as well, so that I might catalyze the analysis of your own microbiome studies.
  • Follow up blog post: https://tips.cgrb.oregonstate.edu/posts/phyloseq-bug-meeting-presentation-fall-2019/

Nov 20:  Cedar Warman (John Fowler Lab, Botany & Plant Pathology)

  • Title: High-throughput maize ear phenotyping with a custom-built scanner and machine learning seed detection, i.e., Computer counts corn, correctly.
  • Abstract: Near-incomprehensible amounts of maize are produced each year, but our understanding of the dominant North American crop is fundamentally incomplete. Of particular interest is the seed-producing structure of maize, the ear. Here, we present a novel maize ear phenotyping system. Our system captures a video of a rotating ear, which is subsequently flattened into a projection of the ear’s surface. Seed positions and genetic markers can be quantified manually from this projection. To increase throughput, we applied deep learning-based computer vision approaches to seed and marker quantification. Our progress towards a completely automated phenotyping system will be described, in addition to challenges we continue to face adapting computer vision technology to maize ears.
  • Links from Cedar’s presentation:
  • Movie flattening: github.com/fowler-lab-osu/flatten_all_videos_in_pwd
  • Seed distribution analysis: github.com/vischulisem/Maize_Scanner
  • Also here’s a preprint describing the scanner: https://www.biorxiv.org/content/10.1101/780650v2

Dec 4: Christina Mulch (Kelly Vining Lab, Horticulture)

  • Title: IsoSeq pooling and HiSeq multiplexing comparison for Rubus occidentalis samples to explore Aphid resistance, i.e., Utilizing RNA to find differences between Aphid Resistant and Susceptible plants.
  • Abstract: Black raspberry (Rubus occidentalis L.) is a small specialty crop produced primarily in the Pacific Northwest of the U.S. A major challenge for its success is Black raspberry necrosis virus vectored by the Large Raspberry Aphid (Amphorophora agathonica A.). We used Pacific Biosciences IsoSeq long read sequencing technology to study the gene expression patterns in leaves following aphid inoculation. We collected samples from a segregating population for resistance to the pest. High quality RNA was extracted from 20 samples, 10 resistant (R) and 10 susceptible (S) using a modified RNA extraction protocol. Data processing was preformed using the IsoSeq3 pipeline. Alignment of each R and S pool to the latest chromosome level black raspberry reference genome used minimap2 according to recommended options for IsoSeq. Reads were filtered based on mapping quality, alignment length, and presence or absence in multiple samples. This study seeks to reveal the genetic underpinning of aphid resistance with the ultimate goal of enabling marker assisted selection.

Thank you for attending and we look forward to seeing you in 2020!

All of the slots for winter 2020 are full, but please contact us if you’re interested in presenting in the future.

The CGRB 2019 Fall conference registration is now open! Please join us for our annual event this September for informative talks, posters and a reception. This year the Fall Conference will also include lighting talks.

Important Information:

  • When: Friday, September 20, 2019
  • Where: CH2M Hill Alumni Center – Oregon State University
  • Registration: here
    • Registration fee: $25 (includes lunch and social hour)
    • NOTE: registration fee is waved for:
      • Undergrads presenting their research poster
      • Lightning talk presenters
  • Deadlines:
    • Lightning Talk Submission: August 15th
    • Poster Registration: September 7th
    • Conference Registration: September 13th (registration fee increases to $35 after Sept 13)

Featured Speakers

Ed Kelly
Associate Professor
School of Pharmacy
University of Washington

Daniel Liefwalker
Research Assistant Professor
Molecular and Medical Genetics
Oregon Health and Science University

Doris Taylor
Director
Regenerative Medicine Research
Texas Heart Institute

Conference Agenda

Time
8:00-8:50Registration & refreshments (Poster & sponsor setup)
8:50-9:15Brett Tyler,
Director, CGRB
Introduction, CGRB update
Morning
Session
Hosted By Jaga Giebultowicz
9:15 – 9:40Andrew Annalora,
Environmental and Molecular Toxicology
Exploring Splice Variant Biology in Nuclear Receptor and
Cytochrome P450 Genes
9:40 – 10:30Ed Kelly,
University of Washington
Organs on a Chip – Chips in Space
10:30 – 10:55Break (Poster and Sponsor displays)
10:55 – 11:35Morning Lightning Talks (8 talks) –
moderated by Jeff Anderson
11:35– 12:00Felipe Barreto,
Integrative Biology
Genomics in the Tidepool: Functional and Population
Genetics of Adaptation and Speciation in a
Tiny Crustacean
12:00 – 12:25Kevin Brown,
College of Pharmacy
Adventures in Complex Systems
12:25 – 1:25Lunch (Poster and Sponsor displays)
Afternoon
Session
Hosted By Craig Marcus
1:25 – 1:50Afua Nyarko,
Biochemistry and Biophysics
Selectivity and Specificity in Cancer Regulatory Proteins
1:50 – 2:40Daniel Liefwalker,
Oregon Health and Science University
Therapeutic strategies targeting c-MYC
2:40 – 3:20Afternoon Lightning Talks (8 talks) –
Moderated By Viviana Perez
3:20 – 3:45Break 25 mins (Poster and Sponsor displays)
3:45 – 4:10Morgan Giers,
Chemical, Biological, and Environmental Engineering
Regenerating the Intervertebral Disc: Developing Effective
Therapies in a Nutrient Limited Environment
4:10 – 5:00Doris Taylor,
Texas Heart Institute
Building Solutions for Heart Disease: A 2019 Update
5:00 – 7:30Poster Session / Reception, Sponsor Displays

Call for posters!

Invitation to present a Poster at the 2019 CGRB FALL CONFERENCE (Sept 20, 2019)
Students, Post Docs, Research Staff and Research Faculty are invited to present their research as a Poster. Presenters are strongly encouraged but not required to consider utilizing a revolutionary new trend in poster format: https://twitter.com/mikemorrison

https://osf.io/ef53g
(Posters in any format displayed at recent meetings are also welcome)
Prizes for Best Posters: $100 (Undergraduate, Graduate and Post Doc Categories).

All fields and research topics welcome. To submit a Poster, please navigate to https://beav.es/ZPd
DEADLINE Sept. 7, 2019.

Call for lightning talks!

Invitation to present a Lightning Talk at the 2019 CGRB FALL CONFERENCE (Sept. 20, 2019)
https://cgrb.oregonstate.edu/fall-conference
Students, Post Docs, Research Staff (FRA, Res. Associates, etc.), and Research Faculty are invited to present their research as a 5-minute Lightning Talk at the annual CGRB Fall Conference, Friday Sept. 20, 2019.
First Prize for Best Lightning Talk = $100
Conference Registration Fee is waivedfor all Lightning Talk Presenters

All fields and research topics welcome. To submit a lightning talk: Please navigate to beav.es/ZPA

Talks are limited to 5 minutes and 5 slides maximum. Please Submit no Later Than: August 15, 2019.
Talks will be selected by the Program Committee and Presenters notified by Aug. 31, 2019.

Committee Members

Thank you to our 2019 Fall Conference Committee:

Jaga Giebultowicz, Department of Integrative Biology
Craig Marcus, Environmental and Molecular Toxicology
Jeff Anderson, Department of Botany and Plant Pathology
Viviana Perez, Department of Biochemistry and Biophysics