BIO/CSC 243
Bioinformatics

Syllabus

Prof Hours Office Phone Email
Steve
Horton
Mon, Thurs, Fri 4-5
and by appt.
Office: 222 Wold
Lab: 206 Wold
388-6328
hortons@union.edu
Chris
Fernandes
Mon 12-2, Tues 3-5, Fri 1-3
and by appt.
Steinmetz Hall
Room 220
388-6401
fernandc@union.edu

Course Web page: http://nexus.union.edu

Course Summary

Bioinformatics is the study of how information technology, computer science principles, and algorithmic techniques have affected and informed the study of biology in the 21st century (and vice versa). Specifically, the field of genomics (the study of the function of genes) has generated a tremendous amount of data to be analyzed. Bioinformatics brings to bear data management and analysis techniques found in the information processing field to discover pertinent knowledge in this sea of data that has applications in research and medicine.

In this course, you will learn about both biological and computer science concepts, how they interact with each other, and how they are used together to further research in genomics. Specifically, you will learn:

in Biology:

in Computer Science:

in Bioinformatics:

Texts (2-3 required)

Prerequisites and Course Format

The prerequisite for this course is BIO 225 (Molecular Biology) OR any introductory programming course CSC 10x. Because of this, it is expected that the student population of this course will consist of a mix of Biology and Computer Science students, each student bringing their own knowledge base, skill set, and perspective to the course. Given this diverse population, the first half of the course will concentrate on exposing students from one discipline to the fundamental concepts of the other (and vice versa) in order to gain a working knowledge of the field. Computer Science students will be taught the principles of Molecular Biology, and Biology students will be exposed to the essentials of Computer Science. In the second half of the course, we will assemble teams consisting of both types of students to work on a series of directed projects, the goal of which is to get students to creatively work in the inter-disciplinary fashion that is central to the emerging field of Bioinformatics.

Evaluation and Grading

Evaluation will be done via exams and both individual and group assignments. Groups will be assigned later in the term. Here is the breakdown:

First half of course

Biologists
Program 1 7%
Program 2 8%
Program 3 10%
Midterm
Thurs, April 28, 2016
15%
Computer Scientists
Assignment 10%
Term-Test
Thurs, April 14, 2016
15%
Term-Test
Thurs, April 28, 2016
15%

Second half of course

Biologists and Computer Scientists together
Group Project #1 20%
Group Project #2 20%
Final Exam 15%

The remaining 5% is based on participation. The final exam is not cumulative.

Programming projects must be turned in both on paper and electronically via Nexus. Your instructor will show you how to turn in your e-copies. All programs will be done in the Python programming language. CS students will be expected to learn this language on their own during the first five weeks.

No lates will be accepted for any of the projects. All exams are closed-book, closed-notes.

Academic Dishonesty

Your enrollment here at Union is taken to signify implicit agreement with the Academic Honor Code, available at honorcode.union.edu. It is each student's responsibility to ensure that submitted work is his or her own and does not involve any form of academic misconduct. Students are expected to ask their course instructors for clarification regarding, but not limited to, collaboration, citations, and plagiarism. Ignorance is not an excuse for breaching academic integrity.

Students are also required to affix the full Honor Code Affirmation, or the following shortened version, on each item of coursework submitted for grading: "I affirm that I have carried out my academic endeavors with full academic honesty." [Signed, Jane Doe]. For programming projects, this can be included as a comment in your code.

So what is plagiarism for this course? Here's some concrete examples to help. This is not an exhaustive list, but helps to set some ground rules.

What you need to do

To prepare for class, you are required to do the following:

The Bottom Line

Ask questions and seek help. This is the most important point of all. We live to answer questions. It's better for everybody (you AND us) if you understand things sooner rather than later. And you'll get the help you need faster by starting on projects sooner rather than waiting until the last minute.

Any student with a documented learning disorder is welcome to come talk to us privately about options for completion of course assignments and exams.