BIOL 419

BIOL 419
Introduction to Bioinformatics

Catalog Entry

Biology 419. Introduction to Bioinformatics
Three hours lecture. (3).

Prerequisites: A grade of "C" or better in BIOL 131, 132, 231, and 232; or a grade of "C" or better in BIOL 111, BIOL 112, and BIOL 222; or permission of the instructor.

This course will provide a broad introduction to bioinformatics. Bioinformatics is a field that lies at the interface of biology, statistics, and computer science. The purpose of Bioinformatics is to analyze very large datasets and interpret the results in a biological framework. It often relies on scripting (writing computer code), which is the implementation of algorithms in a chosen programming language. Topics will include: basic genetics, open-source biosequence databases and search tools, sequence alignment algorithms, introductory genomic and transcriptomic analysis, gene annotation, and basic coding skills.

Detailed Description of Content of the Course

This is a general introduction to bioinformatics with an emphasis on the use of available open-source databases and computer software to address biological questions using biosequence data. Emphasis of the class will follow existing trends and tools available and may cover the following concepts and applications, via problem solving.

Data and databases:

Biosequence file formats
Biosequence databases
Gene expression databases
Data retrieval, storage, and organization
Shared version control
Metadata
Reproducibility

Basic coding skills:

File paths
R statistical computing language
UNIX / MS-DOS
Python
Automating data pipelines / writing loops
Remote servers

Data analysis topics:

Cancer genomics
Conservation genetics
Biodiversity informatics
Metabarcoding
Molecular ecology
Phylogenetics
Genome annotation
Gene annotation
RNA-seq / transcriptomics
Comparative genomics

Detailed Description of Conduct of Course

This will be a hands-on problem-solving based course supplemented with lecture and discussion. Individual assignments may be given to familiarize students with the databases and methods being covered. Reading the scientific literature to explore how the tools used in the course can be applied to a wide-range of topics in genomics will be a foundation of the course.

Goals and Objectives of the Course

The ability to access and search bioinformatics databases is now a key component of most biological research. This course will provide an overview of the nature and breadth of these databases and general search strategies will be practiced. Student will test hypotheses and determine the most appropriate bioinformatic approach to answer those questions given a suite of available tools and data. In this course, students will learn: self-reliance, logic, patience, attention to detail, abstract thinking, problem solving, and how to ask good questions.

Upon completion of this course students will:

Define bioinformatics in broad terms.
Describe basic computer concepts and their use in a biological laboratory setting.
Provide example questions that can be answered using bioinformatic tools.
Navigate several open-source biosequence databases.
Analyze biosequence data using R or Python.
Manipulate biosequence data using the command-line.
Annotate a section of a genome.
Conduct steps for troubleshooting.
Create reproducible work.
Communicate results from data analysis in written, visual, and oral formats.

Assessment Measures

Students may be assessed using quizzes, exams, data analysis assignments, participation on group projects, in-class presentations, and written summaries of their own and others work.

Other Course Information

Review and Approval

DATE ACTION REVIEWED BY
October, 2007

Revised 4/13/09 Gary Coté

February 27, 2024