Data Science for Biologists

Preparing Biologists for the Data Era

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Syllabus

Data Science for Biologists

BIOL 691, 3 Credits, Fall 2020

Professor

Dr. Catherine Hulshof

Email: cmhulshof@vcu.edu

Class Location

Online

Times

Asynchronous (reserve 1:00 pm - 3:50 pm W for occasional online meetups)

Office Hours

Times: Online

Location: Online

Or by appointment.

Note: my schedule gets busy during the semester so please try to schedule appointments in advance. In general it will be difficult to set up appointments less than 24 hours in advance.

Website

The syllabus and other relevant class information and resources will be posted at https://catherinehulshof.github.io/Fall2020-biology/. Changes to the schedule will be posted to this site so please try to check it periodically for updates.

Course Communications

Email: cmhulshof@vcu.edu

We will also use Canvas to submit assignments and for other course announcements and communications.

Required Texts

There is no required text book for this class.

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 to provide context for exercises.

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:

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

Attendance will not be taken or factor into the grades for this class. However, experience suggests that students who regularly miss class struggle to learn the material.

Quiz/Exam Policy

All quizzes are online, open-book, honor system.

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 Canvas. This timing 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.

VCU Policies

Students should visit http://go.vcu.edu/syllabus and review all syllabus statement information. The full university syllabus statement includes information on safety, registration, the VCU Honor Code, student conduct, withdrawal and more.

Most importantly, if you are struggling for any reason please come talk to me and I will do my best to help.

Grading Policies

Grading for this course is based on 14 equally weighted assignments (75%), and 14 equally weighted quizzes (25%).

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:

Grading scale

Course Schedule

The detailed course schedule is available on our course website at: https://catherinehulshof.github.io/Fall2020-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.