Bioinformatics: Sequence and Structure Analysis (323-0-1)
Instructors
Ishwar Radhakrishnan
847/467-1173
Cook Hall, Room 4135
Meeting Info
Technological Institute MG51: Mon, Wed, Fri 11:00AM - 11:50AM
Overview of class
Scientific research and knowledge-based economies rely on critical thinking and coding skills for success. The course will explore through case studies, classroom discussions, and homework assignments, the principles and practical applications of computational tools in contemporary molecular and structural biology research. Students will learn to conduct ‘experiments' in silico and critically analyze different types of sequence and structural data to establish relationships between sequence, structure, and function with an emphasis on constructing testable hypotheses. Students will also gain an appreciation for the algorithmic aspects of the computational tools along with the limitations of the tools imposed by the heuristic nature of the underlying algorithms; they will also learn to code in Python to accelerate the process of discovery. Much of the learning will occur in class; however, deep thinking and learning will occur through written homework assignments where they will learn to provide evidence-based arguments in support of their hypotheses/models. As such, the course objectives align with the empirical and deductive reasoning objectives mandated by WCAS.
Registration Requirements
Prerequisites: BIOL SCI 241, BIOL SCI 301, OR equivalent; BIOL SCI 361 OR equivalent strongly recommended. Coding experience would be advantageous but not required.
Teaching Method
Lecture and practicum (hands-on classwork assignments).
Evaluation Method
Grades will be assigned based on class participation (attendance - 10 %, asking questions in class, participating in discussions, and participating in class-work assignments and presentations - 10%), mid-term exam (40%), and final exam (40%). Homework assignments are for reinforcing concepts and will not be graded. However, students are strongly advised to attempt all the assignments including the coding exercises as these will be modeled after the mid-term and final exams. The mid-term and final exams will be comprehensive, so expect to be challenged in all areas that were covered in the course; the exams will be take-home exams.
Class Materials (Required)
Understanding Bioinformatics, 1st Ed., by Marketa Zvelebil & Jeremy Baum. Publisher: Garland Science ISBN: 0-8153-4024-9;
Python for Biologists: A Complete Programming Course for Beginners, 1st Ed., by Martin Jones. Publisher: CreateSpace Independent Publishing Platform. ISBN: 1-4923-4613-6.
Class Materials (Suggested)
Biological Sequence Analysis: Probabilistic models of proteins and nucleic acids by R. Durbin, S. Eddy, A. Krogh, and G. Mitchison. Publisher: Cambridge University Press. ISBN 0-521-62971-3;
Structural Bioinformatics, 2nd Ed., edited by Jenny Gu and Philip E. Bourne. Publisher: Wiley-Liss. ISBN 0-4701-8105-2;
Bioinformatics Programming using Python by Mitchell Model. Publisher: O'Reilly. ISBN 978-0-596-15450-9
Class Notes
Students must complete take-home exams without assistance from others. Academic integrity is taken very seriously at Northwestern. Students are responsible for reading and understanding Northwestern's Academic Integrity policies. All suspected violations of academic integrity will be reported to the Weinberg College Dean's Office. These include: cheating, plagiarism, fabrication, unfair advantage, unauthorized collaboration, and aiding and abetting of academic dishonesty. Students found in violation of academic integrity may receive a zero on the assignment or a failing grade for the course and may be suspended or permanently expelled from the University. See the WCAS website on academic integrity and Academic Integrity: A Basic Guide for more information.
Enrollment Requirements
Enrollment Requirements: Pre-Requisite: Students must have taken BIOL_SCI 241, BIOL_SCI 301, or BIOL_SCI 308 in order to register for this class.