Data Carpentry for Biologists

WIS 6934, 3 Credits, Fall 2018

Professor

Dr. Ethan White

Office: Room 1 in Building 150 (just north of Newins-Zeigler)

Email (best way to contact us): ethanwhite@ufl.edu

Phone: 352-294-2081

Location

Times

Tuesdays, 12:50-1:40

Fridays, 11:45-1:40

Office Hours

Times: Monday 2-3:15

Location: Newins-Zeigler 203

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

Course TA

Andrew Marx

Email: andrewjmarx@ufl.edu

Website

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

Course Communications

Email: ethanwhite@ufl.edu

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.

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 to the ‘Quantitative Skills’ and ‘Conducting and Analyzing Independent/Original Research’ Student Learning Outcomes specified in the Ph.D. and MS in Wildlife Ecology and Conservation Academic Assessment Plans, by providing students the skills and knowledge they need to manage and analyze the data used in research.

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

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 Canvas. 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.

UF Policies

University Policy on Accommodating Students with Disabilities

Students requesting accommodation for disabilities must first register with the Dean of Students Office (http://www.dso.ufl.edu/drc/). The Dean of Students Office will provide documentation to the student who must then provide this documentation to the instructor when requesting accommodation. You must submit this documentation prior to submitting assignments or taking the quizzes or exams. Accommodations are not retroactive, therefore, students should contact the office as soon as possible in the term for which they are seeking accommodations.

University Policy on Academic Misconduct

Academic honesty and integrity are fundamental values of the University community. Students should be sure that they understand the UF Student Honor Code at http://www.dso.ufl.edu/students.php.

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.

Getting Help

For issues with technical difficulties for E-learning in Canvas, please contact the UF Help Desk at:

Any requests for make-ups due to technical issues MUST be accompanied by the ticket number received from LSS when the problem was reported to them. The ticket number will document the time and date of the problem. You MUST e-mail your instructor within 24 hours of the technical difficulty if you wish to request a make-up.

Other resources are available at http://www.distance.ufl.edu/getting-help for:

Should you have any complaints with your experience in this course please visit http://www.distance.ufl.edu/student-complaints to submit a complaint.

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 13 equally weighted assignments. 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.

Grading scale

Course Schedule

The details course schedule is available on the course website at: http://www.datacarpentry.org/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.