Patrice Koehl
Department of Computer Science
Genome Center
Room 4319, Genome Center, GBSF
451 East Health Sciences Drive
University of California
Davis, CA 95616
Phone: (530) 754 5121
koehl@cs.ucdavis.edu




Computational Structural Bioinformatics: Winter 2022

General information

Lecture Time and Location:

Mon-Wed-Fri 1:10 pm- 2:00 pm; Wellman Hall 6

Discussion session:

M 2:10 am - 3:00 pm; Teaching and Learning Complex 1215

Instructor:

Prof. Patrice Koehl
koehl at cs.ucdavis.edu
This is the only email address that will be answered.
Your subject line MUST include “ECS129″.

Course homepage:

http://www.cs.ucdavis.edu/~koehl/Teaching/ECS129

Office Hours:

Wed 4:00 pm - 5:00 pm, 3059 Kemper
Fri 4:00 pm - 5:00 pm, 3059 Kemper

Midterm:

Midterm 1: Wed, Feb 2
Midterm 2: Project based, due Wed, Mar 2

Final:

Tue, March 15, 8:00 am - 10:00 am

Information sheet:

Word document or PDF file

 

Overview

Tangible success of the many genome sequencing projects currently underway (from human to dog, mouse, rat, tomatoes,...) will come from the unraveling of the information contained in the corresponding sequences, and from constructing models that relate the genotype (i.e. the information coded in the genes) to the phenotype (the physical manifestation) of an organism. Our goal in this course is to provide an overview of the challenges faced by bioinformatics, a new branch of both computer science and biology whose aims are to collect, organize and analyze the data coming from these genomics projects. We will focus in particular on the importance of structural data.

The Tree of Life

Being responsible for your grades

Regrading Policy

Regrading requests, if any, should be done within a week after the announcement/distribution of the graded papers. All requests may be submitted in writing by email, or directly in office hours. Those requests need to explain why additional credit is requested. Reevaluation may result in a decrease as well as an increase or the grade and is not limited to the specific question addressed by the student.

Late policy

If you turn in your projectlate, you will only receive partial credit. If it is less than 24 hours late, you will receive 75% credit; if it is between 24 hours to 48 hours late, you will receive 50% credit; if it is more than 48 hours late, you will receive 0 credit. The only exception is when you bring me a doctor's note.

Grade breakdown

Midterm 20%
Project 50%
Final exam 30%

Grades for the project and midterm will be posted one week after the due/exam date. Please go to https://canvas.ucdavis.edu/ to check your grades. It is very important you do check your grades.

Canvas (http://canvas.ucdavis.edu)

  • The project must be turned on Canvas by 4:00 pm on the due date.
  • Course gradebook will be maintained on Canvas, it is your responsibility to ensure that the scores recorded there match the scores on materials passed back to you.

Academic Conduct

The rules for conduct in UC Davis classes can be summarized with three principles:

  • Be polite.
  • Don’t cheat.
  • Don’t lie.

Be polite

As adults meeting in a professional context, we should all behave professionally: this means being polite and respectful to everyone we deal with.

As the instructor, it is my responsibility to teach as well as I can and to be available, polite and respectful to you.

You are responsible for treating me and your fellow students politely and with respect.

Don’t cheat

As the instructor, it is my responsiblity to make tests and assignments that are fair, to grade fairly, to look for cheating, and to refer students who cheat to Student Judicial Affairs for possible sanctions. The English department made the largest number of referrals to SJA last year, but Computer Science was in the top 10.

As students, it is your responsibility to avoid cheating and to discourage other students from cheating.

Don’t lie

Cheating is one form of lies, but there are other. Manipulating data, false claim of ownership of an assignment/idea, plagiarism are all forms of lies. Do not lie to the instructor, and even more importantly, do not lie to yourself!

Acknowledgements






  Page last modified 19 April 2022 http://www.cs.ucdavis.edu/~koehl/