Data Carpentry for Biologists

Teaching the tools to get computers to do cool science

Creative Commons License

Syllabus

Course

Data Carpentry for Biologists

WIS 6934, 3 Credits, Fall 2018

Instructor

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.

Teaching Assistant

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.

All needed material is openly available on the course website. If you are interested in additional reading on the topics we are covering I highly recommend R for Data Science, which is freely available on the web.

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 Objectives and Goals

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.

Attendance policy

Attendance is not required but it is recommended that you attend class as often as possible to get the most out of the 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. Assignments turned in after the 48 hour grace period without an extension will be be graded with a 20% penalty.

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.

Materials and Supplies Fees

There are no materials and supplies fees for this course.

UF Policies

University Policy on Accommodating Students with Disabilities

Students with disabilities requesting accommodations should first register with the Disability Resource Center (352-392-8565; http://www.dso.ufl.edu/drc/) by providing appropriate documentation. Once registered, students will receive an accommodation letter which must be presented to the instructor when requesting accommodation. Students with disabilities should follow this procedure as early as possible in the semester.

My policy: If you are in my class I want to help learn and will happily work with you to make the learning environment equitable for you and others.

University on Course Evaluations

Students are expected to provide feedback on the quality of instruction in this course by completing online evaluations at https://evaluations.ufl.edu. Evaluations are typically open during the last two or three weeks of the semester, but students will be given specific times when they are open. Summary results of these assessments are available to students at https://evaluations.ufl.edu/results/.

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.

University Honesty Policy

UF students are bound by The Honor Pledge which states, “We, the members of the University of Florida community, pledge to hold ourselves and our peers to the highest standards of honor and integrity by abiding by the Honor Code. On all work submitted for credit by students at the University of Florida, the following pledge is either required or implied: “On my honor, I have neither given nor received unauthorized aid in doing this assignment.” The Honor Code (https://www.dso.ufl.edu/sccr/process/student-conduct-honor-code/) specifies a number of behaviors that are in violation of this code and the possible sanctions. Furthermore, you are obligated to report any condition that facilitates academic misconduct to appropriate personnel. If you have any questions or concerns, please consult with the instructor or TAs in this class.

Software Use

All faculty, staff, and students of the University are required and expected to obey the laws and legal agreements governing software use. Failure to do so can lead to monetary damages and/or criminal penalties for the individual violator. Because such violations are also against University policies and rules, disciplinary action will be taken as appropriate. We, the members of the University of Florida community, pledge to uphold ourselves and our peers to the highest standards of honesty and integrity.

Student Privacy

There are federal laws protecting your privacy with regards to grades earned in courses and on individual assignments. For more information, please see: http://registrar.ufl.edu/catalog0910/policies/regulationferpa.html

Grading Policies

Grading for this course is based on 13 equally weighted assignments.

Exercises in assignments will be graded as follows:

Grading scale

UF grading policies for assigning grade points

https://catalog.ufl.edu/UGRD/academic-regulations/grades-grading-policies/

Campus Resources

Health and Wellness

U Matter, We Care: If you or a friend is in distress, please contact umatter@ufl.edu or 352 392-1575 so that a team member can reach out to the student.

Counseling and Wellness Center: http://www.counseling.ufl.edu/cwc, and 392-1575; and the University Police Department: 392-1111 or 9-1-1 for emergencies.

Sexual Assault Recovery Services (SARS): Student Health Care Center, 392-1161.

University Police Department: 392-1111 (or 9-1-1 for emergencies), or http://www.police.ufl.edu/.

Academic Resources

E-learning technical support: 352-392-4357 (select option 2) or e-mail to Learning-support@ufl.edu. https://lss.at.ufl.edu/help.shtml.

Career Resource Center: Reitz Union, 392-1601. Career assistance and counseling. https://www.crc.ufl.edu/.

Library Support: http://cms.uflib.ufl.edu/ask. Various ways to receive assistance with respect to using the libraries or finding resources.

Teaching Center: Broward Hall, 392-2010 or 392-6420. General study skills and tutoring. https://teachingcenter.ufl.edu/.

Writing Studio: 302 Tigert Hall, 846-1138. Help brainstorming, formatting, and writing papers. https://writing.ufl.edu/writing-studio/.

Student Complaints Campus: https://www.dso.ufl.edu/documents/UF_Complaints_policy.pdf.

On-Line Students Complaints: http://www.distance.ufl.edu/student-complaint-process.

Course Schedule

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