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

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.

Aaron Trippe discusses the changes and challenges of working with the PacBio Sequel since 2016. He discusses improvements in the technology since 2016 and has advice for user who would like to utilize this service.

Aaron Trippe, our long-time PacBio technician, stands next to the CGRB’s Pacific Biosciences Sequel.

Q1: How long have you been running the PacBio sequencing service at the CGRB?

The CGRB was one of the early adopters of the Sequel, the second phase of long read genomic sequencing technology from Pacific Biosciences.  It arrived here on campus in August of 2016.  Since then the technology has made significant improvements to the user-interface, and has tremendously increased read lengths and output. 

Q2: You started up the PacBio sequencing service at the CGRB. What has been the most challenging aspect about developing this service?

Aside from the continually changing and evolving technology, one of the most challenging aspects of the service is getting everything you feed the machine to produce optimal results.  One of the advantages of the technology is that you are sequencing native DNA, but that also makes it challenging when working with an organism that traditionally is difficult to work with and considered problematic.  Finding ways to produce super clean and high molecular weight DNA from just about everything is probably the largest hurdle to working with the technology as a service provider.  The keys to success are definitely within the sample quality.  Having pure, high molecular weight DNA is essential to take advantage of the long read aspect of the technology, and is directly correlated to the quality of the sequencing output.

Q3: What type(s) of project(s) would you recommend to use PacBio’s long read technology?

The technology is great for just about any sequencing application.  With the long reads, you have access to regions of DNA that were not previously accessible due to repetitive regions in genomic DNA.  There is enough output to multiplex several microbial genomes on a single SMRT Cell.  Complete sequences of multiplexed amplicons using Circular Consensus Sequencing for high fidelity reads of shorter inserts. With the read lengths exceeding that of RNA transcripts, Isoform sequencing using the Iso-seq application is also available for obtaining complete transcripts.

Q4: Favorite or most interesting project you’ve worked on?

Since managing the PacBio Sequel, I’ve gotten to work with plants, animals (vertebrates/invertebrates), fungi, bacteria, and insects for the local scientific community, and beyond.  I can’t say that I have had a favorite organism, and they have all been interesting projects, but overcoming challenges with successful results always feels rewarding.

For more information please visit the CGRB website: https://cgrb.oregonstate.edu/core/pacbio

Note: We wish Aaron the best as he purses a new opportunity and are grateful he was able to develop a successful PacBio Service at the CGRB! For future sequencing inquires please contact Katie Carter.

Close up of a PacBio SMRT cell.

The CGRB will be offering three different workshops this fall. For more information and to register, see the CGRB website.

All workshops are available for credit for students or available to non-students as non-credit workshop(s).

To give perspective students a better insight on each course, we’ve conducted short interviews with the instructors about their course.

See course descriptions and the interviews with the instructors below!


Courses Offered:

Introduction to Unix/Linux and Command-Line Data Analysis (2 modules x 5 weeks @ 2 hrs per week)

Instructor: Matthew Peterson

Course Description:

Introduction to Unix/Linux (5 weeks @ 2 hrs per week)

Logistics:
Date & Time:
Sep 25 – Oct 23, Mon/Wed 2:00pm – 2:50pm
For credit: BDS599 CRN 20579
Workshop Cost: $250


This module introduces the natural environment of bioinformatics: the Linux command line. Material will cover logging into remote machines, filesystem organization and file manipulation, and installing and using software (including examples such as HMMER, BLAST, and MUSCLE). Finally, we introduce the CGRB research infrastructure (including submitting batch jobs) and concepts for data analysis on the command line with tools such as grep and wc.

Command-Line Data Analysis (5 weeks @ 2 hrs per week)

Logistics:
Date & Time: Nov 4  – Dec 4, Mon/Wed, 2:00pm – 2:50pm
For credit: BDS599 CRN 20580
Workshop Cost: $250


The Linux command-line environment has long been used for analyzing text-based and scientific data, and there are a large number of tools pre-installed for data analysis. These can be chained together to form powerful pipelines. Material will cover these and related tools (including grep, sort, awk, sed, etc.) driven by examples of biological data in a problem-solving context that introduces programmatic thinking. This module also covers regular expressions, a useful syntax for matching and substituting string and sequence data.

Matthew Peterson in the CGRB server room

Q1: What do you hope students gain from this workshop?

My hope is that students come to appreciate the power and flexibility of using the text-based command-line interface to interact with (Linux) computational infrastructures. With practice students will become self-sufficient in utilizing the infrastructure to conduct their own research.

Q2: Favorite topic in your course?

Pipelines! The ability to chain the inputs and outputs of multiple commands to filter data is immensely powerful.

Q3: Who should register for this course?

From the first page of the course syllabus: “Linux/Unix Commands, Bioinformatics Utilities, Computational Infrastructure: If you know nothing about the above, then you are exactly in the right course! WELCOME!”

Q4: Advice for users new to bioinformatics and/or programming?

Practice, practice, practice! Learning how to use the command-line effectively is like making a clay pot, you need to get your hands dirty!


RNA-Sequencing (10 weeks @ 2 hrs per week)

Instructor: Dr. Andrew Black

Course Description:

Logistics:
Date & Time: Sept 25 – Dec 5, Tue/Thur 11:00am – 11:50am
For credit: BDS 599, CRN 20581
Workshop Cost: $500

This course provides an introduction to, and practical experience with, the computational component of bulk-RNA-sequencing. After a general overview, participants will obtain a working introduction to command line, R-studio, and accessing and utilizing a computing infrastructure. Students with then work through a series of exercises cleaning raw FASTQ files, aligning reads to a reference genome, quasi-mapping reads to a transcriptome / de novo assembly, followed by data visualization and Differential Gene Expression analysis.

Dr. Andrew Black will teach the RNA-seq workshop this term.

Q1: What do you hope students gain from this workshop?

I hope that students gain an understanding of the computational workflow involved with RNA-seq and an appreciation of the methodology! My overarching goal with this course is that people can use material from this course as scaffolding for analyzing their own data on the CGRB infrastructure.

Q2: Favorite topic in your course?

I added a lord of the rings theme to my course; students are looking for differentially expressed genes between hobbits and golems. I’m a dork, I know, but I had fun spiking different genes into the data and enjoy having students visualize this.

Q3: Who should register for this course?

Graduate students, postdocs, faculty, or anyone outside of OSU that are interested in receiving an introduction to RNA-seq or for those that are needing to learn the workflow for their own project(s).

Q4: Advice for users new to bioinformatics and/or programming?

Take it one step at a time and get comfortable with several commands before expanding your scope. Also, record your commands / code in a text document, because if you aren’t using it on a daily basis, you’ll forget it!


Data Programming in R (6 weeks @ 3 hrs per week)

Instructor: Dr. Shawn O’Neil

Logistics:
Date & Time: Sept. 25 – Nov. 6, Mon/Weds/Fri 9:00am – 9:50am
For credit: ST 599, CRN 17196
Workshop Cost: $500


The R programming language is widely used for the analysis of statistical data sets. This course introduces the language from a computer science perspective, covering topics such as basic data types (e.g. integers, numerics, characters, vectors, lists, matrices, and data frames), importing and manipulating data (in particular, vector and data-frame indexing), control flow (loops, conditionals, and functions), and good practices for producing readable, reusable, and efficient R code. We’ll also explore functional programming concepts and the powerful data manipulation and visualization packages dplyr and tidyr, and ggplot2.

Q1: What do you hope students gain from this workshop?

I really hope that students gain an appreciation for programming as a creative activity. It’s not just a means to an end, even with a statistical language like R; there’s a lot of room for play and exploration. Simulation, for example, is a great way to explore complex systems and ask ‘what if’ questions. Many languages (including R) support programmatic drawing and data visualization which can be quite fun.

Q2: Favorite topic in your course?

I always enjoy the point when we first start scaling analyses to thousands of statistical tests. It’s an eye-opening moment, and doing so in R introduces ‘functional programming,’ a powerful and increasingly important paradigm for software design. 

Q3: Who should register for this course?

Anyone who is interested in doing data analysis, especially of a statistical sort. For those interested in learning programming in a broader sense, our winter Intro to Python series is an excellent overview of fundamental concepts. Although we cover the same topics in the R course, R organizes its features differently than most mainstream programming languages like Python, Java, and C++. Learning both Python and R provides a solid foundation for data science!

Q4: Advice for users new to bioinformatics and/or programming?

I do recommend learning more than one programming language, eventually, as this helps separate deeper concepts from syntax. Find what motivates you and explore it via programming — this could be your primary research project, some field you’ve been wanting to learn more about, or even a hobby. 


This blog post was originally published on September 10, 2018 and written by Christopher M. Sullivan, Assistant Director for Biocomputing. Read the whole article here.

The Oregon State University’s Center for Genome Research and Biocomputing (CGRB) and the Plankton Ecology Lab at OSU Hatfield have been collaborating in implementing an image processing pipeline to automate the classification of in situ images of plankton: microscopic organisms at the base of the food web in the world’s oceans and freshwater ecosystems. The imagery collection from a 10-day cruise typically contains approximately 80 TB worth of video, which, in some cases, may convert into image data yielding several billions of segments representing individual plankton and particles that need to be identified; a near impossible task to carry out manually by human experts. While we have a fully functional Convolutional Neural Net (CNN) algorithm that does an excellent job at predicting the identity of the plankton organisms or particles, we have been limited by GPU computational capabilities. We started working with PCI bus based Tesla K40 and K80 GPUs, which were good enough to manage millions of segments. However, when it came to billions of segments, it became a near insurmountable challenge.

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