KAC² Genomics Workshop

K-State Libraries

Aug 5-9, 2024

08:00 am - 5:00 pm CDT

Instructors: David Molik, Siddhartha Kanrar, Tom Misilo

Helpers: Carolyn Jackson, Carol Sevin, Gwen Sibley, Kendra Spahr, Dave Turner

General Information

The Carpentries project comprises the Software Carpentry, Data Carpentry, and Library Carpentry communities of Instructors, Trainers, Maintainers, helpers, and supporters who share a mission to teach foundational computational and data science skills to researchers.

Want to learn more and stay engaged with The Carpentries? Carpentries Clippings is The Carpentries' biweekly newsletter, where we share community news, community job postings, and more. Sign up to receive future editions and read our full archive: https://carpentries.org/newsletter/

Where: Room 359, 1117 Mid-Campus Drive North, Manhattan, KS 66506. Get directions with OpenStreetMap or Google Maps.

When: Aug 5-9, 2024; 08:00 am - 5:00 pm CDT Add to your Google Calendar.

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. They should have a few specific software packages installed (listed below).

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

We are dedicated to providing a positive and accessible learning environment for all. We do not require participants to provide documentation of disabilities or disclose any unnecessary personal information. However, we do want to help create an inclusive, accessible experience for all participants. We encourage you to share any information that would be helpful to make your Carpentries experience accessible. To request an accommodation for this workshop, please fill out the accommodation request form. If you have questions or need assistance with the accommodation form please email us.

Glosario is a multilingual glossary for computing and data science terms. The glossary helps learners attend workshops and use our lessons to make sense of computational and programming jargon written in English by offering it in their native language. Translating data science terms also provides a teaching tool for Carpentries Instructors to reduce barriers for their learners.

Contact: Please email kspahr@ksu.edu for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

Who can attend?: This workshop is open to researchers, staff, and graduate students affiliated with K-State or ARS.


Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.


Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.



Schedule

Day 1 - Genomics Carpentries 1

Before starting Pre-workshop survey
08:00 Office Hours / Prep Time
09:00 Introduction to Genomics Workshop Week
10:00 Introduction to HPC, Beocat and Scinet (Including Globus File Transfer)
11:00 Life Sciences Workshop
12:00 Lunch Hour - Partipants on Their Own
13:00 Life Sciences Workshop
14:00 Life Sciences Workshop
15:00 Life Sciences Workshop
16:00 Life Sciences Workshop

Day 2 - Genomics Carpentries 2

08:00 Office Hours / Prep Time
09:00 Library Resources and Research Support Tools
10:00 Project organization and management
11:00 Introduction to the Command Line
12:00 Lunch Hour - Lunch and Learn with Brad Olson, Evolutionary Biologist, K-State Division of Biology, bring your own lunch
13:00 Introduction to the Command Line
14:00 Introduction to the Command Line
15:00 Introduction to the Command Line
16:00 Introduction to the Command Line

Day 3 - Genomics Carpentries 2

08:00 Office Hours / Prep Time
09:00 Data Wrangling and Processing
10:00 Data Wrangling and Processing
11:00 Data Wrangling and Processing
12:00 Lunch Hour - Partipants on Their Own
13:00 Data Wrangling and Processing
14:00 Data Wrangling and Processing
15:00 Data Wrangling and Processing
16:00 Data Wrangling and Processing

Day 4 - Genomics Carpentries 3

08:00 Office Hours / Prep Time
09:00 Intro to R and RStudio for Genomics
10:00 Intro to R and RStudio for Genomics
11:00 Intro to R and RStudio for Genomics
12:00 Lunch Hour - Lunch and Learn with Phillip Shults, Entomologist, USDA REE-ARS, bring your own lunch
13:00 Intro to R and RStudio for Genomics
14:00 Intro to R and RStudio for Genomics
15:00 Intro to R and RStudio for Genomics
16:00 Intro to R and RStudio for Genomics

Day 5 - RegEx and Git

08:00 Office Hours / Prep Time
09:00 Regular Expressions
10:00 Regular Expressions
11:00 Regular Expressions
12:00 Lunch Hour - Participants on Their Own
13:00 Version Control with Git
14:00 Version Control with Git
15:00 Version Control with Git
16:00 Version Control with Git
End Post-workshop survey

Setup

To participate in a workshop, K-State affiliates will need access to a BeoCat account. If you do not already have a BeoCat account, request one by July 30. You will need access to software as described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

Install required software for the workshop or update any installations you already have. Directions and links to downloads: