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Spring 2021 Carpentries Workshops Announced

Spring 2021 Carpentries Workshops Announced

The Carpentries training program aims to improve data literacy and reproducible science. IMCI sponsors the University of Idaho as a member in the organization.

Postdocs and graduate students will run 3 workshops this spring for upper-level undergraduate students, new graduate students and anyone else interested in good-practices in data management and analysis.

STUDENTS can register for academic credit

Students wishing to take the workshops for credit need to register via the UI course schedule for any combination of BCB 503 01, BCB 503 02, and/or BCB 503 03. Each workshop is 1 credit each.

NON-STUDENTS must also register to attend

If you do not want academic credit, you may attend any workshop for free but must still register. Space is limited.

Unix, Git, and Programming (R/Python) for Novices

Workshop dates: January 19 – February 4; T/Th, 2-5 p.m.

Instructors: Breanna Sipley, Travis Seaborn, Chava Castaneda, Li Huang, Erich Seamon, Angela Crabtree, Akorede Seriki

Description: Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation in Unix, GitHub, R, and Python. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. The course is aimed at graduate students and other researchers but is open to all. You don’t need to have any previous knowledge of the tools that will be presented at the workshop. Participants must have a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. All participants should attend the Unix/Git sections (first week). The R (second week) and Python (third week) sections will each be taught as independent sections.

View Code of Conduct, Detailed Schedule & Set Up Requirements

Data Wrangling and Processing for Genomics

Workshop dates: March 2-11; T/Th, 2-5 p.m.

Instructors: JT Van Leuven, Angela Crabtree, Lukas Grossfurthner, Amanda Stahlke, Travis Seaborn, Breanna Sipley

Description: Data Carpentries aims to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain. This hands-on workshop will cover basic concepts and tools, including best practices for organization of bioinformatics projects and data, use of command-line utilities, use of command-line tools (shell and R) to analyze sequence quality and perform variant calling, connecting to and using cloud (AWS) computing, and visualizing genomic data. The course is aimed at graduate students and other researchers but is open to all. While the course is designed for learners that have no prior experience with the tools covered in the workshop, some familiarity with biological concepts (DNA, mutation, population variation) will be useful. Participants must have a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on.

View Code of Conduct, Detailed Schedule & Set Up Requirements

Advanced Geospatial Analysis

Workshop dates: April 20-29; T/Th, 2-5 p.m.

Instructors: Erich Seamon, Li Huang, Travis Seaborn, Lukas Grossfurthner

Description: This hands-on workshop will focus on managing and understanding spatial data formats, understanding coordinate reference systems, and working with raster and vector data in R for analysis and visualization. The course is aimed at graduate students and other researchers but is open to all. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. Introductory knowledge of R is suggested.

View Code of Conduct, Detailed Schedule & Set Up Requirements

Get Involved, Seminars & Workshops

Register to Attend a Carpentries Course

The topics of upcoming workshops are always up for discussion and depend on your input. If you have workshops suggestions or requests, please email JT Van Leuven.

If you are a student wishing to take any of these courses for academic credit, please register via the U of I Course Schedule.

SPRING 2021 WORKSHOPS

Unix, Git, and Programming (R/Python) for Novices

Workshop dates: January 19 – February 4; T/Th, 2-5 p.m.

Instructors: Breanna Sipley, Travis Seaborn, Chava Castaneda, Li Huang, Erich Seamon, Angela Crabtree, Akorede Seriki

Description: Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation in Unix, GitHub, R, and Python. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. The course is aimed at graduate students and other researchers but is open to all. You don’t need to have any previous knowledge of the tools that will be presented at the workshop. Participants must have a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. All participants should attend the Unix/Git sections (first week). The R (second week) and Python (third week) sections will each be taught as independent sections.

NON-STUDENT REGISTRATION: Unix, Git, and Programming (R/Python) for Novices

(If you are a student, please register via the Course Catalog.)

Data Wrangling and Processing for Genomics

Workshop dates: March 2-11; T/Th, 2-5 p.m.

Instructors: JT Van Leuven, Angela Crabtree, Lukas Grossfurthner, Amanda Stahlke, Travis Seaborn, Breanna Sipley

Description: Data Carpentries aims to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain. This hands-on workshop will cover basic concepts and tools, including best practices for organization of bioinformatics projects and data, use of command-line utilities, use of command-line tools (shell and R) to analyze sequence quality and perform variant calling, connecting to and using cloud (AWS) computing, and visualizing genomic data. The course is aimed at graduate students and other researchers but is open to all. While the course is designed for learners that have no prior experience with the tools covered in the workshop, some familiarity with biological concepts (DNA, mutation, population variation) will be useful. Participants must have a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on.

NON-STUDENT REGISTRATION: Data Wrangling and Processing for Genomics

(If you are a student, please register via the Course Catalog.)

Advanced Geospatial Analysis

Workshop dates: April 20-29; T/Th, 2-5 p.m.

Instructors: Erich Seamon, Li Huang, Travis Seaborn, Lukas Grossfurthner

Description: This hands-on workshop will focus on managing and understanding spatial data formats, understanding coordinate reference systems, and working with raster and vector data in R for analysis and visualization. The course is aimed at graduate students and other researchers but is open to all. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. Introductory knowledge of R is suggested.

NON-STUDENT REGISTRATION: Advanced Geospatial Analysis

(If you are a student, please register via the Course Catalog.)

Get Involved, Seminars & Workshops

Disease Deadliness And Willingness To Vaccinate Linked, Study Shows

Congratulations to IMCI participants on their recent publication in PLOS Medicine. The following news story was produced by the Mountain West News Bureau. View the original article here.

A newly published study out of the University of Idaho suggests that the higher perceived risk of a disease, the more likely someone is to vaccinate.

The researchers surveyed about 2,400 people back in 2018, and the analysis of those answers shows that perceived deadliness played a big role in vaccination decisions.

Participants were randomly given different hypothetical disease scenarios, and, as a news release explains, “vaccination willingness was greater for participants who were given information about the potential deadliness of a disease, versus those told how severely it could impact daily life.”

It also found that certain demographics – like those with higher incomes, older people and men – were also more willing to vaccinate.

University of Idaho philosophy professor Bert Baumgaertner, who co-authored the study, said another factor was at play, too – politics.

“Especially the very liberals and the very conservatives, they actually behave quite similarly in terms of how their ideology seems to be influencing their decisions,” Baumgaertner said.

Essentially, they both stuck to their guns regardless of the risk, with conservatives less willing to vaccinate and liberals more willing.

There are caveats, though: This survey didn’t measure for changes in confidence around a vaccine’s safety. It was also done with hypothetical diseases, not the one everyone is focused on right now: COVID-19.

Still, according to the study, “This information can be helpful for campaigns that aim to reduce vaccine hesitancy and is useful for modeling feedback between human decision-making and the spread of disease.”

Congratulations, Publications

Pilot Grant Slides Available for Download

Pilot Grant Slides Available for Download

For future reference or if you weren’t able to attend the Brown Bag Lunch yesterday, here are the slides presented by IMCI Director Holly Wichman regarding our Pilot Grant program. Please remember, you are welcome to reach out to the leadership team directly and at any time if you have questions about whether your research fits within the goals and objectives of IMCI.

Download slides from the Information Session held on Oct. 22, 2020.

Brown Bag Lunch, Funding Opportunities, Pilot Programs

3-D Printer to Revolutionize Biofluids and Biomechanics Research

This news article comes from central University of Idaho Communications and Marketing. View the original here. While IMCI was not involved in the funding of this research project, we are honored to have Dr. Tao Xing as one of our IMCI participants.

October 20, 2020 – With the help of a more than $300,000 major research instrumentation grant from the U.S. National Science Foundation (NSF), the University of Idaho College of Engineering’s Department of Mechanical Engineering is installing a high-resolution, mixed-material 3-D printer. To be housed in the Integrated Research and Innovation Center (IRIC), this state-of-the-art 3-D printer can print large, geometrically detailed and flexible 3-D structures. The printer can also produce pieces in extremely high resolution, 16 microns, about one-third the average cross-section of a human hair. This complex printing is not currently possible using other 3-D printers on the Moscow campus.

Mechanical Engineering Associate Professor and project lead Tao Xing said 3-D printed materials on the U of I Moscow campus are currently printed in several components that are later connected, which can introduce additional errors in the geometry and add difficulty in conducting high-fidelity experimental measurements.

“Using this new printer, researchers can analyze the physical constructs of complex structures to improve understanding of different mechanisms in the body, from breathing to brain-drug delivery, the effect of brain cancer drugs in-vitro and therapeutic approaches to traumatic brain injury,” said Xing. “This instrument will facilitate and enhance multidisciplinary research and expand academic-industrial collaborations at U of I.”

The NSF grant was awarded to a team consisting of nine faculty from four U of I colleges, including engineering, the College of Science, College of Agricultural and Life Sciences and the College of Natural Resources.

The installation of the printer is expected in spring 2021.

The printer will be part of a new lab in the IRIC focused on 3-D printing for studying biofluids and biomechanics. Both undergraduate and graduate students will have access to the printer and future lab. A one-credit course is currently being developed to provide training to use the new printer. The printer will also be used in 3-D-printing projects and competitions, including a partnership with the U of I chapter of the Society of Women Engineers (SWE) during their Women in Engineering events, held twice annually. Equipment time and training will be provided to advisors at local K-12 schools, including the Moscow High School Science Club and Near Space Engineering Club through the mission of the U of I Library’s Making, Innovating, Learning Laboratory training programs.

“Students will be exposed to structure-function relationships in tissues, 3-D drawing, mechanical analysis and state-of-the-art multi-material 3-D printing,” Xing said. “These outreach capabilities will broaden the participation of underrepresented minorities in engineering and related fields.”

This project was funded to University of Idaho by National Science Foundation under award 2019231. The total project funding is $360,774.00 of which 70% is the federal share.

About Us, Congratulations, Equipment