Molb 4485/5485 – Computers in Biology – Syllabus Fall Semester

Vikram E. Chhatre, PhD & Instructor 2

Wyoming INBRE Bioinformatics Core
Dept. of Molecular Biology
University of Wyoming


1. Course Description

Technological advances have led to exponential increase in the size of biological data sets. Handling of these large datasets has become intractable without some level of bioinformatic literacy. Many biologists find that there is a steep learning curve to develop the skills required to explore their datasets effectively because of their size or complexity. This bioinformatics short course includes a rich collection of hands-on instruction and lectures specifically intended to help novice users become comfortable with a range of tools currently used to analyze such data. All coursework will be implemented in linux on local workstations or a remote server.

1.1 Prerequisites

There is no prerequisite for this course other than a willingness to learn and to work hard throughout the 5 weeks.

2. Student Learning Outcomes

(also represents expectations for student performance)

3. Course Structure:

The course is organized into 5 modules

4. Text(s), Readings, and Access to Materials:

All course materials will be disseminated during (or before) class meetings. These materials will also be available after each class meeting through WyoCourses. Additional reference or working materials will be suggested throughout the course for those interested in exploring topics in a deeper manner.

5. Assignments and Grading Standards:

All grading will be done on an individual basis, even for activities that involve some group work and applies to both undergraduate as well as graduate students. For additional requirements for graduate students, see below. All of the assessments for this course are made during class meetings. Please note: every class meeting is worth 20% of your grade. Thus, you can not pass this class without attending class meetings. Grades will be calculated using the following scale, after conversion of the total number of points acquired to percentages:

A: ≥ 90%    B: 80-89%    C: 70-79%    D: 60-69%    F: < 60%

5.1 Grading summary:

Grading Component Undergraduate Graduate
Assignments (weekly tutorials) 70 45
Participation (ind & group) 30 30
Research Project N/A 25
Total 100 100

Graduate Students will choose a research data analysis project with instructors to be completed before November 30, 2018.

5.2 Grading details:

Assignments: Working with computers in biology often requires collaboration and input from others. Almost all assignments for this course will be completed during class meetings. At the end of each class meeting you will save the entire commandline session with history command.

Participation: Students are expected to work together to foster an atmosphere of inquiry and respect. While you will be working with computers, creative-problem solving skills will be required to enter into dialogue during class meetings and to complete tasks throughout the 5 weeks.

6. University Policies and Information

Attendance Policy, and Policy for Late and Make-up work/examinations: To succeed in this course, it is essential to show up. Twenty points will be subtracted from your grade for every absence that is not University-sponsored or deemed acceptable by the instructor. University-sponsored absences are cleared through the Office of Student Life. Please discuss anticipated absences with the instructor in advance. Make-up work will only be offered for students with acceptable absences.

Academic Honesty: The University of Wyoming is built upon a strong foundation of integrity, respect and trust. All members of the university community have a responsibility to be honest and the right to expect honesty from others. Any form of academic dishonesty is unacceptable to our community and will not be tolerated [from the University Catalog]. Teachers and students should report suspected violations of standards of academic honesty to the instructor, department head, or dean. Other University regulations can be found here.

Disability Statement: If you have a physical, learning, sensory or psychological disability and require accommodations, please let the instructor know as soon as possible. You will need to register with, and provide documentation of your disability to University Disability Support Services (UDSS) in SEO, room 330 Knight Hall.

UW Writing Center: The Writing Center in Coe 302 is able to help writers at any stage of the writing process. With a focus on teaching and learning, the Writing Center is not a “fix-it shop”, but they help writers identify, articulate, and implement improvements and corrections to their writing. Drop in to see if a consultant is available, or schedule an appointment online

7. Semester Schedule:

Please note that with the exception of our first meeting, other events are TENTATIVELY scheduled, because we will work at a pace that is appropriate for the cohort.

Module 1: Course introduction, command line interface

Week 1

Module 2: Computer cluster, sequence similarity searches

Week 2

Module 3: Sequence alignments and phylogenetics

Week 3

Module 4: Next-generation sequencing and quality assessment of human genomic data

Week 4

Module 5: Analysis of Human Genomic Variation Across Global Populations

Week 5