Course

Data Carpentry for Biologists

WIS 6934, 3 Credits, Fall 2019

Instructor

Dr. Ethan White (he/him)

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, 3-3:50

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

An introduction to data management, manipulation, and analysis, with an emphasis on biological problems. Class consists of short introductions to new concepts followed by hands on computing exercises using R and SQLite, but the concepts apply to programming languages and databases more generally. No background in computing 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 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.

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 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.

Materials and Supplies Fees

There are no materials and supplies fees for this course.

UF Policies

University Policy on Accommodating Students with Disabilities

The Disability Resource Center coordinates the needed accommodations of students with disabilities. This includes registering disabilities, recommending academic accommodations within the classroom, accessing special adaptive computer equipment, providing interpretation services and mediating faculty-student disability related issues.Students requesting classroom accommodation must first register with the Dean of Students Office. The Dean of Students Office will provide documentation to the student who must then provide this documentation to the Instructor when requesting accommodation0001 Reid Hall, 352-392-8565, www.dso.ufl.edu/drc/

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

Online Course Evaluation Process

Student assessment of instruction is an important part of efforts to improve teaching and learning. At the end of the semester, students are expectedto provide feedback on the quality of instruction in this course using a standard set of university and college criteria. These evaluations are conducted online at https://evaluations.ufl.edu. Evaluations are typically open for students to complete during the last two or three weeks of the semester; students will be notified of the 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.

Academic Honesty

As a student at the University of Florida, you have committed yourself to uphold the Honor Code, which includes the following pledge:“We, the members of the University of Florida community, pledge to hold ourselves and our peers to the highest standards of honesty and integrity.”You are expected to exhibit behavior consistent with this commitment to the UF academic community, and on all work submitted for credit 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.”

It is assumed that you will complete all work independently in each course unless the instructor provides explicit permission for you to collaborate on course tasks (e.g. assignments, papers, quizzes, exams). Furthermore, as part of your obligation to uphold the Honor Code, you should report any condition that facilitates academic misconduct to appropriate personnel. It is your individual responsibility to know and comply with all university policies and procedures regarding academic integrity and the Student Honor Code.Violations of the Honor Code at the University of Florida will not be tolerated. Violations will be reported to the Dean of Students Office for consideration of disciplinary action. For more information regarding the Student Honor Code, please see: http://www.dso.ufl.edu/sccr/process/student-conduct-honor-code

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.

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 Helping Resources

Students experiencing crises or personal problems that interfere with their general well-being are encouraged to utilize the university’s counseling resources. The Counseling& Wellness Center provides confidential counseling services at no cost for currently enrolled students. Resources are available on campus for students having personal problems or lacking clear career or academic goals, which interfere with their academic performance.

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, 392-1575.

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 Connections Center: Reitz Union, 392-1601. Career assistance and counseling. https://career.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

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.