Front Door

Introduction

Welcome to one of the Web sites for the Fall 2011 session of Grinnell College's BIO/CSC 295, Bioinformatics, which is described relatively briefly in the official blurb. In this course, Professors Praitis and Rebelsky are hoping to have students with differing backgrounds collaborate to explore ideas that students with a single background might not be able to understand as well. Along the way, you should be learning at least a bit of Biology and at least a bit of Computer Science.

We will be using both PioneerWeb and this Web site for the course. This Web site will primarily contain Sam's notes on the course and the programming resources. The P'Web site will contain other materials.

This is an experimental course. Among other things, this means that we expect to be updating the syllabus as the semester goes on.

In an attempt to provide up-to-date information, and to spare a few trees, I am making this as much of a paperless course as I can. Hence, materials will be in a course web. If you are puzzled by the organization of the Course Web, you may want to read the basic instructions for using this course web. If you find that you want paper copies of pages, please read the notes on printing copies. If you find that you are regularly printing pages, let me know and I can provide them for you.

Important Warnings

Warning! Experience shows that biology and computer science exercise different parts of your brain, even different parts than other sciences. In general, such exercise is a good thing - one of the key points of a liberal arts education is that it exercises different parts of your brain. However, it may take a bit of time to get these new parts of your brain into shape. Expect a few difficult times, but have confidence that you can get through them and that you'll come out of the course with much more knowledge.

Warning! Bioinformatics combines biological and computational ideas in a variety of ways. Even if you have good knowledge of both biology and computer science, you will find some aspects of this course difficult and puzzling.

Warning! Computers are sentient, stupid, and malicious. When things go wrong, don't blame yourself. Ask one of the faculty, a tutor, or the class mentor for help.

Basics

Meets: TuTh 1:15-3:05 p.m., Science 3819

Instructor (CS): Samuel A. Rebelsky, Science 3824. 269-4410 (office). 236-7445 (home). Office hours: TuTh 10:00-11:00, MWF 2:15-3:05. I also tend to follow an open door policy: Feel free to stop by when my door is open or to make an appointment for another time. I have children, so please do not call my house before 7 a.m. or after 10 p.m.

Instructor (Biology) Vida Praitis. Science 1204. 269-4390. Office hours: Monday 2:15-3:15, Wednesday 10:00-11:00. I tend to have my door closed because noise distracts me. Feel free to knock whenever you see me in my office. We can talk then or make an appointment for another time.

Class Mentor: Chase Felker. Mentor session: Sunday 8-9 p.m. Office hours: Sunday 9-11 p.m., Wednesday, 8-9 p.m.

Grading (subject to change):

• Class participation: 5%;
• Response Papers: 15%;
• Programming Projects: 10%;
• Other assignments (Web explorations, peer review, etc.): 10%;
• Final Project: 15%;
• Portfolio: 10%;
• Mid-semester examination: 10%;
• Final: 20%
• Best of (responses, programming, project, final): 5%

More information on grading can be found in the grading policies page and the types of work page.

Labs: Computer science 295 includes a collaborative workshop component. On many days, you will work on laboratory problems with other students in the class. Your partners on labs (and on group programming exercises) will be assigned.

Extra Credit: We will often offer 1/2 point of extra credit for attending a particular talk (e.g., a computer science talk or College convocation) or for supporting your classmates in their public endeavors (e.g., attending a concert or a dance recital). Each category is capped at 1.5 points. You will report on this extra credit at the end of the semester, using a prepared checklist.

Good-Faith Grade Guarantee: Because we realize that bioinformatics may be particularly difficult as students attempt to synthesize two different disciplines, we will reward effort as well as outcome. Hence, students who make a good faith effort in this class will pass the class, with at least a C+. A good-faith effort includes missing no more than two classes, turning in every homework assignment, and spending the requisite time on each examination.

Printing Pages: Most of these pages are designed for viewing onscreen. If you'd like to print them, you may want to use PDF versions, which are designed for paper. Many pages have links directly to the PDF version. If there isn't such a link, simply replace the html at the end of the URL with pdf.

If you do decide to print, you should also consider printing the document double-sided and two-up (that is, two pages side-by-side on one physical page) so as to conserve paper. When I distribute documents, I will do my best to distribute them in this form.

Textbook

St. Clair, Caroline & Visick, Jonathan (2010). Exploring Bioinformatics: A Project-Based Approach. Sudbury, MA: Jones and Bartlett.

Programming Language

Exploring Bioinformatics uses Perl as its primary programming language. We, however, will be using Python. Why the switch? Most importantly, Python supports an interactive environment. That is, you can enter code and immediately see a response, rather than building a program that you need to run separately. In addition, evidence suggests that Python is a bit easier for novice programmers to learn. Finally, Python is also a language of growing importance in bioinformatics.

The Python supplement for our text can be found at the ExBioPy link on each page and at http://www.cs.grinnell.edu/~rebelsky/ExBioPy/. Note that this supplement is being developed as the semester progresses.

Optional Books and Other Readings

Forthcoming.