Data Carpentry lesson to learn how to use command-line tools to perform quality control, align reads to a reference genome, and identify and visualize between-sample variation. A lot of genomics analysis is done using command-line tools for three reasons: 1) you will often be working with a large number of files, and working through the command-line rather than through a graphical user interface (GUI) allows you to automate repetitive tasks, 2) you will often need more compute power than is available on your personal computer, and connecting to and interacting with remote computers requires a command-line interface, and 3) you will often need to customize your analyses, and command-line tools often enable more customization than the corresponding GUI tools (if in fact a GUI tool even exists). In a previous lesson, you learned how to use the bash shell to interact with your computer through a command line interface. In this lesson, you will be applying this new knowledge to carry out a common genomics workflow - identifying variants among sequencing samples taken from multiple individuals within a population. We will be starting with a set of sequenced reads (.fastq files), performing some quality control steps, aligning those reads to a reference genome, and ending by identifying and visualizing variations among these samples. As you progress through this lesson, keep in mind that, even if you aren’t going to be doing this same workflow in your research, you will be learning some very important lessons about using command-line bioinformatic tools. What you learn here will enable you to use a variety of bioinformatic tools with confidence and greatly enhance your research efficiency and productivity.

Software Carpentry lesson that teaches how to use databases and SQL In the late 1920s and early 1930s, William Dyer, Frank Pabodie, and Valentina Roerich led expeditions to the Pole of Inaccessibility in the South Pacific, and then onward to Antarctica. Two years ago, their expeditions were found in a storage locker at Miskatonic University. We have scanned and OCR the data they contain, and we now want to store that information in a way that will make search and analysis easy. Three common options for storage are text files, spreadsheets, and databases. Text files are easiest to create, and work well with version control, but then we would have to build search and analysis tools ourselves. Spreadsheets are good for doing simple analyses, but they don’t handle large or complex data sets well. Databases, however, include powerful tools for search and analysis, and can handle large, complex data sets. These lessons will show how to use a database to explore the expeditions’ data.

This open educational resource (OER) was compiled for use in ENGL 1010 – Expository Writing, the first of Middle Tennessee State University’s two first-year writing courses. This OER is divided into five main sections, all of which are designed with ENGL 1010’s course objectives in mind. Each of those sections contains a number of readings related to the section’s topic, with many of those readings curated from other open-access texts.

The first-year writing sequence at Middle Tennessee State University takes a rhetorical approach to writing. This means that students are asked to consider how “good” writing is situational. There are no hard and fast “rules” for writing. Instead, there are conventions or norms and expectations specific to particular contexts. In ENGL 1010: Expository Writing, students practice identifying writing conventions across modes and contexts.

This lesson in part of Software Carpentry workshop and teach novice programmers to write modular code and best practices for using R for data analysis. an introduction to R for non-programmers using gapminder data The goal of this lesson is to teach novice programmers to write modular code and best practices for using R for data analysis. R is commonly used in many scientific disciplines for statistical analysis and its array of third-party packages. We find that many scientists who come to Software Carpentry workshops use R and want to learn more. The emphasis of these materials is to give attendees a strong foundation in the fundamentals of R, and to teach best practices for scientific computing: breaking down analyses into modular units, task automation, and encapsulation. Note that this workshop will focus on teaching the fundamentals of the programming language R, and will not teach statistical analysis. The lesson contains more material than can be taught in a day. The instructor notes page has some suggested lesson plans suitable for a one or half day workshop. A variety of third party packages are used throughout this workshop. These are not necessarily the best, nor are they comprehensive, but they are packages we find useful, and have been chosen primarily for their usability.

By the mid 1960s, Americans’ interpretation of the Civil Rights Movement was split. While many white Americans perceived laws like the Civil Rights Act and Voting Rights Act as solving the problem of segregation and civil rights, the experiences of many black Americans proved that there was still a great discrepancy in their treatment, opportunities, and economic status. The philosophy of black nationalism, which argued for …, grew in influence during this time. This lesson examines how black nationalism impacted not only the larger aims of the civil rights movement, but institutions like schools, universities, local economies, and the arts.

This lesson is organized as a warm up quote and mini-lecture to affirm student understanding of black nationalism and the ongoing struggle faced by black Americans even after many civil rights “milestones.” Students will then explore in a gallery walk/station format the different ways that black nationalism impacted society in the late 1960s and 1970s. Depending on time, teachers may want to have students visit multiple stations or focus on one and then share findings with the class. A final class discussion will ask students to compare their findings and to find connections with our society today.

Many of the sources in this lesson were found in the August Wilson archives at the University of Pittsburgh. August Wilson was a Pittsburgh playwright whose work chronicled the experience of black America, and the sources found there speak to both the desire within the arts for more artwork about the experience of people of color in the United States and more arts organizations to support it; as well as sources that reflect on the growth within the University of Pittsburgh of a Black Studies program and the Black Action Society, a student group. While local in focus, these changes reflect national movements in the 1960s and 1970s.