BIO/CSc 283
Bioinformatics: Information Technology in the Life Sciences
Syllabus
| Prof |
Hours |
Office |
Phone |
Email |
Steve
Horton |
By appt. |
Science & Engg.
Room S304
(Lab: S206) |
388-6328 |
hortons@union.edu |
Chris
Fernandes |
M 11-12,
W 10-11:30,
W 3:30-4:30,
F 9:30-10:30
and by appt. |
Steinmetz Hall
Room 229 |
388-6401 |
cfernand@union.edu |
Course Web page: http://cs.union.edu/bio283
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:
- basic Mendelian genetics
- the flow of genetic information from DNA to proteins
- molecular biological approaches and their applications
- genomic projects and comparative genomics
in Computer Science:
- algorithm design as a means of problem solving
- basic programming using the Python programming language
- data organization schemes, analysis techniques, and how they apply to biological applications
- further understanding of what computers can and cannot solve easily
in Bioinformatics:
- pairwise and multiple alignment matching of gene sequences
- polymerase chain reaction (PCR) techniques
- automated primer detection
- phylogenetic trees
Texts (2-3 required)
- Jean-Michel Claverie, Cedric Notredame,
Bioinformatics for Dummies, For Dummies, 2006.
- Allen B. Downey, Jeffrey Elkner, and Chris Meyers,
How to Think Like a Computer Scientist: Learning with Python,
Green Tea Press. This book is free! Read it online
at
http://www.greenteapress.com/thinkpython/thinkCSpy/html/
- Aydin Tozeren, Stephen W. Byers,
New Biology for Engineers and Computer Scientists,
Pearson Education, Inc., 2004. Only CS students need buy this
book.
Prerequisites and Course Format
The prerequisite for this course is Bio 225 (Molecular Biology)
OR CSc 140 (Data Structures). 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% |
Term-Test
Thurs, Feb 5, 2009 |
15% |
|
| Computer Scientists |
| Assignment |
10% |
Term-Test
Tues, Jan 20, 2009 |
15% |
Term-Test
Thurs, Feb 5, 2009 |
15% |
|
Second half of course
| Biologists and Computer Scientists together |
| Group Project #1 |
20% |
| Group Project #2 |
20% |
| Final Exam (Thurs, March 19, 1-3pm, BUTR 106) |
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
BlackBoard.
Your instructor will show you how to use BlackBoard 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. Web-based exercises will be assigned
to ensure that CS students are learning at an appropriate pace.
No lates will be accepted for any of the projects. All
exams are closed-book, closed-notes.
For the Graduate Students
Grad students taking this course will be required to do
an extra independent project in addition to the requirements
listed above. This project should incorporate both the
biological and CS aspects of the course. You should set up
a meeting with your instructors by the 4th week
of classes (week of Jan 26) to propose and get approval for
your idea. Once approved, the project will be due on
Thursday, March 12. The project will be worth 10% of
your overall grade, and the remaining items above will be
prorated to be worth 90% of your grade.
Academic Dishonesty
Students often have some confusion about what might or might not be
considered "cheating" in a class where computer programs are written.
In general, you should take advantage of your instructors
and fellow students in working out
solutions to assignments. However, we also need to make sure that you are
actually learning, and not simply using all of
these resources as a crutch. As with writing a paper for an English
class, there is a point at which working together
becomes plagiarism. As a rule of thumb, feel free to discuss
general solutions to problems, but the writing down of an
actual solution must be done solo by you. (Exception: for group
projects, the actual code must be written by you and your teammates,
but no one else.) Here are some concrete examples of what's
plagiarism and what's not:
It is plagiarism...
- to look at someone else's code and copy what's written there
- for two people to write code together on a computer or on paper
- to look at someone's code for "inspiration"
and then change all of the variable names and comments
- to take code from the Internet or from other textbooks besides our own
but it's perfectly fine to use code...
- that we hand out in class
- that is part of a demo that we leave on BlackBoard
- that is in the textbook that we use for this course
Here's the bottom line: if you find yourself turning in work
that looks substantially like the work of
someone else, you should seriously examine whether you have crossed
the line. If you have any doubts, talk to us
before turning in the assignment.
In all cases, you must give credit to any source
(like a written work or help from some individual) that you use to help
complete an assignment. Again, this is similar to writing an English
paper;
if you use a quote or material from someone else,
you have to give credit where credit is due. Otherwise you are
inappropriately plagiarizing or borrowing ideas.
What you need to do
To prepare for class, you are required to do the
following:
Show up
You are expected to be present for every class. However, we
realize that sometimes other things come up (interview, illness, etc.) so just
please let us know in advance or by phone/email if you're going to be absent.
If you miss class, get notes from someone and do the readings before coming to
see us. We're happy to explain things, but we won't repeat lectures for you.
Read the texts
You should do the reading for that week before
coming to class so that questions you have about the material can be answered
during class time. There will always be a time for questions about the
readings or previous class sessions at the beginning of each class. Take
advantage of it.
Check the web page
The reading assignments (and other announcements)
will be posted regularly on the course web page. You are required to check it
at least once a week. The address is at the top of this document.
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.
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