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

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

STUDENTS wishing to take the workshops for credit need to register via the UI course schedule for any combination of BCB 503 01 and/or BCB 503 02. U of I registration deadlines apply.

ALL PARTICIPANTS, regardless of academic credit, must register with IMCI to attend. Space is limited. A limited number of in person seats will be offered. An online option may also be available. IMCI registration will close one week prior to the workshop.

Data Wrangling and Processing for Genomics (1 cr)

BCB 503-01 (CRN 75677) or AVS 503 (CRN 77059)

Instructors: James Van Leuven (I), Lukas Grossfurthner (I), Chava Castaneda (H)

February 15-24, T/Th, 2-5 pm

Course Title: WS: Genomics

Course 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).

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on.

Feb 14 – Introductions, Review file manipulations in shell, Setting up AWS, Installing command-line programs
Feb 16 – Overview of sequencing, data formats, input/output/synopsis of each command-line program
Feb 21 – De novo assembly, Mapping to reference sequences
Feb 23 – Graphing output in R, Understanding data quality, Putting it all together with shell scripts

Introduction to Scientific Programming in R (1 cr)

BCB 503-02 (CRN 75678)

Instructors: Julia Piaskowski

Course Title: WS: Intro/Sci Programming in R

Jan 17 – Feb 9, T/Th, 2-4 pm, Zoom

Course Description: In this workshop, participants will learn practical R programming skills for scientific data processing and analysis over the course of 16 hours of instruction and practice. The workshop will introduce the R programming language, the graphical user interface RStudio and how R can be used to manage and analyze your data. At the end of this workshop, you will be able to:

  • import & export data
  • understand data types and object types
  • filter, reshape, merge and manipulate your data
  • mathematically transform data
  • do repeat actions in R
  • plot data
  • navigate R help files

Requirements: Computer, functional speakers, and a stable internet connection. Optional but likely needed: a camera and microphone for communicating through Zoom

For more information: