BIO/CSC 243
Bioinformatics
Syllabus
| Prof |
Office Hours |
Office |
Phone |
Email |
Steve
Horton |
Tue, Thurs 4-5:30
and by appt. |
Office: 222 Wold
Lab: 206 Wold |
388-6328 |
hortons@union.edu |
Chris
Fernandes |
Tue, Thurs 2-4
Wed 12-2
and by appt. |
Steinmetz Hall
Room 219 |
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:
- 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
- gene prediction
Texts (2-3 required)
- Jean-Michel Claverie, Cedric Notredame,
Bioinformatics for Dummies, 2nd ed, Wiley Publishing, 2007.
- 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
https://greenteapress.com/thinkpython2/html/index.html
- Kratz, R.F., Molecular & Cell Biology for Dummies,
Wiley Publishing, 2020. Only students who have not taken BIO 205 should buy this
book.
Prerequisites and Course Format
The prerequisite for this course is BIO 205 (Current Topics in 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 each discipline to the fundamental
concepts of the other 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.
Attendance at Lecture
COVID-19 AWARENESS: As we are all aware, we are still in the midst
of the Covid-19 pandemic, and therefore we will be taking these safety precautions
in and out of class:
- In class, wearing masks is optional.
- When visiting our offices, wearing masks is mandatory. I'll provide
one for you if you forget yours.
For more information, regularly check the appropriate Union website listed below
for community updates:
https://www.union.edu/where-you-are/community-updates
If you are quarantined or isolated for COVID-19-related reasons, we will be notified
by the Dean of Students Office that you will not be able to attend classes during
the specified time frame and that you may require additional flexibility with regard
to your participation in this course. Your responsibility will be to contact us as
soon as you are able so that we can discuss your needs. We will make arrangements to
provide you with material missed from classes.
If you are feeling ill, however, DO NOT come to lecture. We expect you to be
responsible and consider others who may be vulnerable in the classroom.
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, 2022 |
15% |
|
| Computer Scientists |
| Assignment |
10% |
Term-Test
Thurs, April 14, 2022 |
15% |
Term-Test
Thurs, April 28, 2022 |
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
electronically via
Nexus.
You should also turn in a copy on paper.
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.
-
Working together on an individual homework is ok, but you should only discuss problems in
general terms like, "I think this problem looks like the ice cream demo from class."
Never write the actual answer together -- always write it by yourself and don't compare them afterwards.
If you're really questioning your own answer, talk to your instructor about it. For group projects,
you can discuss in as much detail as you like within your group. However, the same rules above apply
for those not in your group.
-
If someone asks you for help on a part of some problem, help them by doing a different example on
a separate sheet of paper. Or by going over a class demo together that is similar. If the person
is really stuck or doesn't even know when to start, that person should be talking to the instructor.
-
NEVER look at someone else's code when you're stuck. This is plagiarism. Ask someone else to
look at your code to see if they can help you debug it. You should only look at another's
code when you are giving help, not getting help. This applies to individual
as well as group projects. Of course, seeking out Chris for
help is always an option too.
-
DO compare answers after you get your graded homework back. There are many ways of writing a correct
answer and looking at others' ways of thinking can help you.
-
You must cite everything and everyone you worked with, including people you worked with, CS helpdesk,
Bio Backup, and URLs of web sites. You don't need to cite our own textbooks or your own teammates
for group projects.
-
Here's a quick list of what's
plagiarism and what's not with respect to code:
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 Nexus
- 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.
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 Nexus. You are required to check it
at least once a week.
Check your email twice a day
We know: it's old tech, but this school runs on email. We send out
tips, hints, announcements, error corrections, and
lecture addendums over email. Check it at least twice daily.
Accommodations
Union College facilitates the implementation of reasonable accommodations,
including resources and services, for students with disabilities, chronic
medical conditions and temporary disabilities resulting in difficulties
accessing learning opportunities. All students needing services must first
register with Accommodative Services located in Reamer 303. It is strongly
recommended that accommodations be requested within the first two weeks
of the term (by April 8th). Last minute requests can be denied.
Any student with a documented learning disorder is welcome to come talk to
us privately about options for completion of exams and homework assignments.
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.