Introduction to Bioinformatics (CMPSC 300 and BIO 300)

Spring 2016

Lecture, Discussion and Group Work Session: Alden 101, Tuesdays and Thursdays 9:30am to 10:45am

Laboratory Session: Alden 101, Fridays 2:30pm to 4:20pm

Dr. Jumadinova's Office Hours:

Monday and Wednesday: 10am-12pm (15 minute slots)

Thursday: 1pm-2pm (10 minute slots)

Friday: 11am-12pm (10 minute slots)

Schedule an appointment with Janyl Jumadinova using the Google calendar or by email: jjumadinova@allegheny.edu

Dr. Webb's Office Hours:

Monday: 11am-12pm (15 minute slots)

Tuesday: 1:30pm-3:30pm (15 minute slots)

Thursday: 11:30pm-12:30pm (15 minute slots)

Friday: 10am-12pm (15 minute slots)

Schedule an appointment with Kristen Webb during the office hours, please click on the schedule an appointment link, and select the desired date and time. You can schedule an appointment outside of the office hours by email.

Course Resources:

  • Course Syllabus

  • Course Schedule

  • Course Material: Resources

  • Crash Course in Biology

  • Crash Course in Computer Science

  • Course Slack channel for questions, discussions and other communication

  • Bitbucket repository, a cloud-based course repository for obtaining the latest course materials from the instructor and for submitting assignments

  • Sakai page for viewing course grades and accessing online quizzes and exams

    • Required Textbook: "Exploring Bioinformatics: A Project-based Approach", second edition, by Caroline St. Clair and Jonathan E. Visick Loftus.

      Along with the required books and handouts, you will be assigned to read additional articles from a wide variety of conference proceedings, journals, and the popular press.

      The description of the course:

      An introduction to the development and application of computational approaches to answer biological questions. Students use state-of-the-art bioinformatics software to gain insights into the functionality of the information contained within genomes as well as learn the algorithms behind such applications. Topics include data management, analysis of large-scale biological datasets, genome annotation, and genetics of disease. Unique challenges in the field and the wide range of existing solutions are examined. Prerequisites: BIO 221 and FSBIO 201, or CMPSC 111.

      The course follows two parallel tracks. In the lectures we will learn basic bioinformatics fundamentals and applications, while in the laboratory sessions you will have a larger hands on experience with problem solving and writing programs. The laboratory sessions will be usually tied to the lectures.