General Information

WHAT IS ABOUT?

This workshop will cover data management and analysis for genomics research including: best practices for organization of bioinformatics projects and data, use of command-line utilities, use of command-line tools to analyze sequence quality and perform variant calling, and connecting to and using cloud computing.

AUDIENCE

This lesson assumes that learners have no prior experience with the tools covered in the workshop. However, learners are expected to have some familiarity with biological concepts, including the concept of genomic variation within a population. An equipped informatics classroom is available for the participants.

When: Mar 07-14-21, 2023. Add to your Google Calendar.

Requirements: Participants should have computer with a Mac, Linux, or Windows operating system. They should have a few specific software packages installed (listed below).

Accessibility: We are committed to making this workshop accessible to everybody.

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance.

Contact: Please email mcmelek@msn.com 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?: Anyone interested in genomics, bioinformatics, molecular biology and related fields.

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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.

Report a Code of Conduct Incident

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Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

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Schedule

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Setup

To participate in a Data Carpentry workshop, 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 the videoconferencing client

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

• Two monitors: If you have two monitors, plan to have the tool you are learning up on one monitor and the video conferencing software on the other.
• Two devices: If you don't have two monitors, do you have another device (tablet, smartphone) with a medium to large sized screen? If so, try using the smaller device as your video conference connection and your larger device (laptop or desktop) to follow along with the tool you will be learning about.
• Divide your screen: If you only have one device and one screen, practice having two windows (the video conference program and one of the tools you will be using at the workshop) open together. How can you best fit both on your screen? Will it work better for you to toggle between them using a keyboard shortcut? Try it out in advance to decide what will work best for you.

This blog post includes detailed information on how to set up your screen to follow along during the workshop.

The setup instructions for the Data Carpentry Genomics workshops can be found at the workshop overview site

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