Computational Biology Tools

Course Information

Quarter: Fall 2011

Lecture Location: Baskin, Rm 152

Lecture Times: Monday and Wednesday 5-6:45p.m.

Discussion Section: Monday 7:00-8:00p.m. in Baskin, Rm 152 & Tuesday 8:30-9:40a.m. in Engineering 2, Rm 194

Final Exam: Tuesday, December 6 4:00-7:00p.m., Baskin, Rm 152

Instructor: Brian Kidd

  • Email:
  • Office: Physical Sciences Building, Rm 405A
  • Office Phone: (831) 459-1623
  • Office Hours: Mon/Wed 4:00-5:00p.m. (before lectures) or by email appointment

Teaching Assistant: Paola Castro

Additional Assistance

If you qualify for classroom accomodations because of a disability, please submit your Accommodation Authorization from the Disability Reource Center (DRC) to the instructor during his office hours in a timely manner, preferably within the first two weeks of the quarter. Contact DRC at 459-2089 (voice), 459-4806 (TTY).


Catalog Description

Hands-on laboratory geared to teach basic tools used in computational biology (motif searching, primer selection, sequence comparison, multiple sequence alignment, genefinders, phylogenetics analysis, X-ray crystallography software). Web-based tools and databases are used. Open to all science students with basic biochemistry or permission of the instructor.

Course Objectives

This course teaches students how to access and analyze the wealth of biological data that is publicly available. The course is lab oriented to provide hands-on experience using common software tools and online databases that have been developed by the bioinformatics community. In addition, students will learn problem solving skills that apply to computational and experimental disciplines. Some examples of the topics we will cover include:

  • Accessing and searching online genomic and proteomic databases.
  • Manipulating and extracting information from a wide range of data formats.
  • Analyzing and comparing DNA, RNA, and protein sequences.
  • Analyzing and comparing protein structures.


Since this is a hands-on class, you are expected to bring your own laptop to class every day (if you do have your own laptop, you can request a loaner).
You will need a wireless network card to get on the network in class.
You will need to install the J2SE Java Runtime Environment (JRE) if you haven't already (OS X users have Java built-in already).

Textbook Information

The required textbook for the class is:
Bioinformatics for Dummies, 2nd Ed. (2006) by Claverie & Notredame

Other resources include an optional textbook:
Bioinformatics: Sequence and Genome Analysis 2nd Ed. (2004) by David W. Mount



We strongly encourage students to come to office hours or contact either the instructor or TA via e-mail. We check our e-mail regularly and you will receive a timely response.

Please do not e-mail the instructor with grading questions. If you want us to explain why we took points off, you can talk to us after class or during office hours. If you want a re-grade, please write an explanation and hand the homework and the explanation to the instructor or the TA during office hours or after class.

Occasionally we may need to broadcast a message to entire class. To make sure we can reach you, we will be using a class mailing list. The class e-mail list is: Please email the TA to join class mailing list!!!


Grades will be based on problem sets (~35%), midterm (~25%), final exam (~30%), and the combination of in-class exercises, participation* and attendance at lab sections** (~10%).

*Participation is strongly encouraged and will count for part of your grade. In addition, questions and discussion will make the class more enjoyable and allow us to better gage which of the key concepts we should be spending more or less time on.

**One discussion section absence may be allowed if cleared with the instructor ahead of time. Attendance in lab sections is mandatory. For each unexcused lab absence, you will lose 1% of your participation grade.

Homework Turn-In & Late Policy

There will be 4 problem sets given out as homework. Homeworks turned in after the deadline will have 5% deducted if turned in within 24 hours, and an additional 10% for every additional day late until homeworks are returned or answers are given in class or on-line (usually one week after homeworks are turned in).

All homework assignments will be turned in via eCommons. Acceptable formats include: simple text, PDF or Word format files.

You are encouraged to use a number of resources in solving the problems. You must give credit to these sources*** and document the tool, web site address, database, or other resource used to solve the problem (if no documentation is given, you will receive partial credit for the assignment).

***Working together -- You are encouraged to work together on in-class assignments as the process of sharing ideas and collaborating often leads to deeper understanding of a topic. However, you must acknowledge who you worked with and what each person's contribution was in the process. That said, each student must turn in their own work and write up answers to homework assignments in their own words. You may not share/trade/lend/borrow written or electronic solutions to problems, or in any way share in the act of writing or electronically sharing your answers with others (see below).

Academic Honesty and Academic Integrity

In recent years, there has been an increased number of cheating incidents in many UC campuses, and unfortunately, UCSC is no exception. The School of Engineering has a zero tolerance policy for any incident of academic dishonesty. If cheating occurs, there may be consequences within the context of the course, and in addition, every case of academic dishonesty is referred to the students' college Provost, who then sets the disciplinary process in motion. Cheating in any part of the course may lead to failing the course and suspension or dismissal from the university.

What is cheating? In short, it is presenting someone else's work as your own. Examples would include copying another student's written or electronic homework assignment, or allowing your own work to be copied. Although you may discuss problems with fellow students, your collaboration must be at the level of ideas only. Legitimate collaboration ends when you "lend", "borrow", or "trade" written or electronic solutions to problems, or in any way share in the act of writing or electronically sharing your answers. If you do collaborate (legitimately) or receive help from anyone, you must credit them by placing their name(s) at the top of your paper. 

What is Academic Integrity? This question is better answered with how we violate academic integrity. One prime example is fabrication. Fabrication:

  • In any academic exercise, submitting falsified data including bibliographic resources and experimental data, or altering graded coursework/exams and resubmitting to the instructor for a higher score.

Another example of violating academic integrity is Facilitating Academic Dishonesty:

  • One form of this is answering questions on someone else's exam or doing someone else's homework for them.
  • Another form is helping another student take a test (allowing them to cheat from you).

Official University Policy on Academic Integrity for Undergraduate Students

Instructors and Assistants