R Programming for Biologists

Teaching the tools to get computers to do cool science

Creative Commons License

Abridged Syllabus

*Note: See eLearn site for official syllabus.

R Programming for Biologists

BIO XVI, 3 Credits, Summer 2019

Professor

Dr. Robert Harbert

Office: Shields 204

Email (best way to contact us): rharbert@stonehill.edu

Phone: 508-565-1248

Location

Times

Office Hours

Times: Monday 2-3:15

Location: eLearn Collaborate Portal

Website

The syllabus and other relevant class information and resources will be posted at http://rsh249.github.io/semester-biology. Changes to the schedule will be posted to this site so please try to check it periodically for updates.

Course Communications

Email: rharbert@stonehill.edu

Required Texts

There is no required text book for this class. However, I recommend Hadley Wickham’s R for Data Science which is available as a free eBook here or for purchase on Amazon.

Course Description

Computers are increasingly essential to the study of all aspects of biology. Data management skills are needed for entering data without errors, storing it in a usable way, and extracting key aspects of the data for analysis. Basic programming is required for everything from accessing and managing data, to statistical analysis, to modeling. This course will provide an introduction to data management, manipulation, and analysis, with an emphasis on biological problems. Class will typically consist of short introductions or question & answer sessions, followed by hands on computing exercises. The course will be taught using R and SQLite, but the concepts learned will easily apply to all programming languages and database management systems. No background in programming or databases is required.

Prerequisite Knowledge and Skills

Knowledge of basic biology.

Purpose of Course

In this course you will learn all of the fundamental aspects of computer programming that are necessary for conducting biological research. By the end of the course you will be able to use these tools to import data into R, perform analysis on that data, and export the results to graphs, text files, and databases. By learning how to get the computer to do your work for you, you will be able to do more science faster.

Course Goals and Objectives

Students completing this course will be able to:

How this course relates to the Student Learning Outcomes in Wildlife Ecology and Conservation

This course contributes much needed content in quantitaive reasoning and data skills to the natural science curriculum. Though designed for Biology students other science majors will benefit from the material.

Teaching Philosophy

This class is taught using a flipped, learner-centered, approach, because learning to program and work with data requires actively working on computers. Flipped classes work well for all kinds of content, but I think they work particularly well for computer oriented classes. If you’re interested in knowing more take a look at this great info-graphic.

Instructional Methods

As a flipped classroom, students are provided with either reading or video material that they are expected to view/read prior to class. Classes will involve brief refreshers on new concepts followed by working on exercises in class that cover that concept. While students are working on exercises the instructor will actively engage with students to help them understand material they find confusing, explain misunderstandings and help identify mistakes that are preventing students from completing the exercises, and discuss novel applications and alternative approaches to the data analysis challenges students are attempting to solve. For more challenging topics class may start with 20-30 minute demonstrations on the concepts followed by time to work on exercises.

Course Policies

Attendance Policy

You must be present in this course through active participation in discussion forums, timely completion of assignments, and communication with the instructor.

Quiz/Exam Policy

There are no quizzes or exams in this course.

Make-up policy

Life happens and therefore there is an automatic grace period of 48 hours for the submission of late assignments with no need to request an extension. However, it is highly recommended that you submit assignments on time when possible because assignments build on one another and it can be hard to catch up if you fall behind. Reasonable requests for longer extensions will also be granted.

Assignment policy

Assignments are due Monday night by 11:59 pm Eastern Time. Assignments should be submitted via eLearn. This allows you to be finished with one week’s material before starting the next week’s material.

Course Technology

Students are required to provide their own laptops and to install free and open source software on those laptops (see Setup for installation instructions). Support will be provided by the instructor in the installation of required software. If you don’t have access to a laptop please contact the instructor and they will do their best to provide you with one.

Netiquette and Communication Courtesy

All members of the class are expected to follow rules of common courtesy in all email messages, threaded discussions and chats.

Homework Grading Policies

One problem from each assignment (selected at the instructors discretion after the assignments have been submitted) will receive a thorough code review and a detailed grade. Other problems will be graded as follows:

Independent projects may focus on databases, programming, or a combination or the two.

Course Schedule

The details course schedule is available on the course website at: http://rsh249.github.io/semester-biology/schedule.

Disclaimer: This syllabus represents my current plans and objectives. As we go through the semester, those plans may need to change to enhance the class learning opportunity. Such changes will be communicated clearly both on the website and in class.