Biol 568 Syllabus

Bioinformatics: BIOL 568/ BIOMI 568
Fall 2015
COURSE INFORMATION
Lecture
Class Days:
M/W and Online

1300-1350 LSS 365
(or through BlackBoard)
Instructor: Dennis Didulo

Email: [email protected]
Office Hours by Appointment
Lab Section 1
Class Days:
Torres
Class Times:
Class Location:
2:00pm-4:40pm
LSN-126
Lab Section 2
Class Days:
Class Times:
Class Location:
Wednesday
2:00pm-4:40pm
LSN-126
Monday
Teaching Assistant: Pedro

Email: [email protected]
Description from Official Course Catalog:

Bioinformatics analysis methods and programming skills. Practical bioinformatics software for
sequence analysis, bioinformatics algorithms and programming fundamentals.
Course Content:
The content includes fundamental concepts in Bioinformatics (computational algorithms),
working knowledge of Bioinformatics software and resources and practical programming skills.
Student Learning Outcomes:
At the end of the class, the students will be able to do the following:
Understand the purpose and algorithms underlying computational biology approaches to basic
and still very widely used methods for discovery including sequence alignment, RNA structure
prediction, phylogenetics and many pattern matching approaches.
Master and apply computational algorithms for biological research.
Utilize modern biological software applications for analyzing molecular sequence data and be
able to apply it to real existing data sets.
Learn fundamental programming concepts and how they are used by Bioinformaticians. The
students will learn the widely used Python programming language.
Graduate students will learn object-oriented programming concepts and how to use the
Biopython package and gain familiarity with Unix and the R statistical package.
Real Life Relevance:
This class has extensive real-world applicability, especially for molecular biology students and
for bioinformatics students. First, students will master programs such as BLAST (and many
others) that are used in every biology lab and in most Biotechnology companies. This will be a
major advantage when applying for such positions. Second, students will learn a powerful
programming language used by Bioinfomaticians around the world as well as in companies

such as Google. Third, understanding what sequence data can do for medicine and research
will be generally useful in daily life as our society becomes every more infused with big data.
Relation to Other Courses:
Bio 568 builds upon concepts learned in introductory biology (Biol 203, 204), Chemisty (Chem
232) and molecular biology (Biol 366) This course helps prepare the students for many other
courses including upper level molecular biology courses and advanced bioinformatics
programming.
Prerequisites: Biol 366.
Adding/Dropping Procedures:
Per University policy, the last day to add this course is the 10th day of the semester. Please
note that if you have not been attending lectures through this period of time you risk falling
behind in the material and your final grade may be negatively impacted.
If you have registered for the course but do not attend class within the first two lectures, you will
be dropped from the course by the instructor. If you fail to have the required pre-requisite
courses you may also be dropped from the course by the instructor. Please note that the
instructor may not automatically drop you if you lack the pre-requisite courses - this could
negatively impact your final grade for the course.
Crashers:
Priority for crashing will be based on the number of units in the major. Open University students
will be provided add codes once all SDSU students have added the course as per University
policy.
Required Text: Think Python by Allen B. Downey
Additional online resources will be provided in lecture when applicable.
The format of the course will be online weekly lectures and a lab course. The lectures will
present material that is important for understanding Bioinformatics algorithms and fundamentals
behind the Biology. This course includes hands-on learning in lab. The first part of each lab will
include a short problem, to introduce the students to Bioinformatics concepts or programming
language basics. The rest of the lab will then be spent practicing on the computer. The graduate
TA will be available during the lab time to provide additional instruction and help students debug
their code during the completion of in-class exercises or class projects. Students will also be
encouraged to help one another with concepts and exercises.
All information for the course will be posted on Blackboard. Please be sure to consult
Blackboard for scores, PDF files, notes, etc. A separate document lists specific lecture topics
and dates, including due dates for assignments and exams.
Special Content Note: The contents of this syllabus and the schedule are subject to change at
any time. While we endeavor to make as few changes as possible, contingencies occur and the
instructors reserve the right to make changes to both content and structure of the course as
needed.
Class Etiquette:
Please be considerate of your neighbors and the lecturer. Abstain from distractions such as
carrying on conversations or entering and exiting during lectures. Cell phones must be turned
off during the lecture and lab. If you must be available for a potential emergency, set your phone
to vibrate.
Special accommodations: To request disability accommodations please make an appointment to
speak with the instructor at the beginning of the semester.
Exams and Assignments
NOTE 1: ALL ASSIGNMENTS (except Midterm) WILL BE EMAILED TO THE INSTUCTOR
USING THE FOLLOWING EMAIL ADDRESSES.
Monday Section 1 Email: [email protected]
Wednesday Section 2 Email: [email protected]
NOTE 2: YOU HAVE UP TO ONE WEEK AFTER A GRADE IS ASSIGNED TO ASK
QUESTIONS ABOUT THE GRADING OF YOUR ASSIGNMENT.
Unless the instructor says otherwise, all labs are due before the start of the next lab. If they are
not received by the start of the next lab session, you will not receive points for the lab.
How to complete non-programming lab assignments:
Download the assignment. Immediately save as under a new name: YourLastNameLab1.doc
For instance, I would name my first lab DiduloLab1.doc
Answers should be in boldface and text only (unless an image is requested) just after the
question.
You can often use screen capture and paste images into the document if necessary. Please
resize them.
Email it to yourself as a means of backing up your work. YOU ARE RESPONSIBLE FOR
MAKING SURE YOUR WORK IS SAVED, INCLUDING THE LAB PRACTICAL.
Do your own work but feel free to ask your classmates for help. Do this before asking the
instructor.
NOTE 3: These assignments and percentages are approximate and subject to change at the
instructors discretion.
The following table details the combined total assignments for lecture and lab. The labs are all
started in class and are due by the beginning of lab the next week. These labs include both the
web-based bioinformatics labs and the programming labs. The Lab Practical will cover the lab
material for the first part of the course and assignments will be completed in lab at the computer.
It will be open book and open note. The Midterm will cover the algorithms learned in lecture.
This will be a closed note exam.
The Python exams will be taken in lab. It will be open book and open note, though no internet
access will be allowed.
The Biology and Bioinformatics Masters students in the BIOMI program will be expected to
perform a sophisticated programming project by the end of the course and the BIOMI students
must also learn and apply Object-Oriented Programming for the final project.
Grading Range:
A: 93-100%
A-: 90-92%
B+: 88-89%
B: 83-87%
B-: 80-82%
C+: 78-79%
C: 73-77%
C-: 70-72%
D+: 68-69%
D: 60-67%
F: <=59%
Grades are rounded to the nearest percent.
There will be no make-up exams unless the student provides a valid written excuse, such as
from a doctor, etc. Excuses for work-related activities are not valid.
Course Etiquette:
Use of cell phones or earphones during exams will not be permitted. Use of any electronic
devices during tests is forbidden unless explicitly permitted by instructor. Also, using these
devices when the instructor is teaching is rude.
Academic Dishonesty:
Plagiarism in any form will not be tolerated. No credit will be given for plagiarized work and
students who plagiarize will be reported to the Judicial Procedures Office. Use of electronic
devices such as cell phones and earphones will not be permitted. Students who plagiarize will
be reported to the Judicial Procedures Office and receive 0 points for any assignments upon
which the student plagiarized with no opportunities to make up the lost points.
Cheating on exams or any assignments will not be tolerated. Students who cheat will be
reported to the Judicial Procedures Office and receive 0 points for any assignments upon which
the student cheated with no opportunities to make up the lost points.
Students with Disabilities:
If you are a student with a disability and believe you will need accommodations for this class, it
is your responsibility to contact Student Disability Services at (619) 594-6473. To avoid any
delay in the receipt of your accommodations, you should contact Student Disability Services as
soon as possible. Please note that accommodations are not retroactive, and that
accommodations based upon disability cannot be provided until you have presented your
instructor with an accommodation letter from Student Disability Services. Your cooperation is
appreciated.
LECTURE Schedule Fall 2015

Note: tentative schedule; subject to significant change

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Bioinformatics: BIOL 568/ BIOMI 568

M/W and Online

Instructor: Dennis Didulo

Teaching Assistant: Pedro

Description from Official Course Catalog:

programming language used by Bioinfomaticians around the world as well as in companies

LECTURE Schedule Fall 2015

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