Biological Sciences 1540
Computational Biology
Fall Term 2016-2017

General Info

Meeting Times:
2:00-2:50pm MWF (Lectures in 241 Crawford Hall, Labs in 266 Chevron Hall)

Office Hours:

12-1pm Tuesdays in 165 Crawford Hall

Prerequisites:

BioSc 0150 and 0160 or permission from Instructor.

Class Web Page:

http://www.pitt.edu/~epolinko

Instructor Info

Coordinator (& Lecturer):

Dr. Eric Polinko
103F Clapp Hall
(412) 624-0419
epolinko@pitt.edu

Lecturers:

Course Materials
Required: Optional:

Really Optional:


All books above are available through the Pitt library system.



Course Info
Description:

Due to the incredible wealth of biological sequence information generated since the turn of the century, the use of computational methods has become an invaluable tool for the molecular, genetic, and biomedical scientist. A wide variety of computational techniques have been created to organize, analyze, and manipulate this data - and this course seeks to give students a broad view of these from a biological and computational point of view. Several techniques will be covered in depth - including sequence analysis, comparative genomics, structural analysis, and molecular dynamics. A hands-on approach to learning these programs will be coupled with discussions of the models and assumptions used to generate them. In addition, students will be exposed to a variety of bioinformatic experts and career paths - including the Biological Sciences department & Health Sciences Library here at Pitt, the National Center for Multiscale Modeling of Biological Systems at the Pittsburgh Supercomputing Center, the Department of Biomedical Informatics at UPMC, and the private company BioTeam .
Objectives:

To provide students with a broad understanding of current computational techniques available to biological and biomedical scientists. This will be accomplished through lectures from experts in the field, coupled with lab sessions where students will interact with the resources discussed in class. Student comprehension of concepts will be assessed through two exams during the course of the semester. Student comprehension of techniques will be assessed through individual projects whicthath will evolve through the course of the semester. In addition, students will be exposed to a variety of research avenues available to the computational scientist.
Policies
Exams, Homework, & Projects:

The schedule for all meetings of this course is attached. Please note the dates of the two exams and project due dates to avoid any future scheduling conflicts. Both examinations will be given during regular class times. The final will consist of individual project presentations during finals week (three alternative day/time windows will be scheduled for this). There will be no make-up examinations. If you miss one of the exams due to an excused emergency absence, your final grade will be based on the total points from the one exam you did take, attendance, and projects. If you miss an examination due to an emergency (illness, serious injury or a death in your immediate family), you must submit, in writing, your request for an excused absence. Failure to comply with these guidelines could result in a zero recorded for the missed exam. No one will be excused from more than one examination. If you miss more than one examination you should discuss possible options available to you with your advisor or the CAS Dean's Office.

Projects 1-4 must be submitted by 9am on their scheduled due date. Ten points will be deducted for each day a project version is late, and five points for each day a homework assignment is late.
Exam Regrades

A student may request that the instructor regrade any portion of their graded mid-term examinations. The student must write out an explanation detailing the reasons for requesting a regrade. This request must be submitted to Dr. Polinko within one week after the date that the graded examinations were returned to the class. You are advised to consult the answer key and your textbook prior to submitting your request. Please be aware that your entire exam may be evaluated and any question that was graded incorrectly (in your favor) may also be regraded and could result in points deducted from your total.
G Grades:

Students who wish to petition for a G grade must submit to Dr. Polinko, in writing, a specific request documenting your reason(s) for this grade change. You will be required to make arrangements with Dr. Polinko for the specific tasks you must complete to remove the G grade. Remember that G grades, according to CAS guidelines, are to be given only when students who have been attending a course and have been making regular progress are prevented by circumstances beyond their control from completing the course after it is too late to withdraw (University of Pittsburgh Undergraduate Bulletin, 1999-2002, p.29). If you miss the final and have a valid excuse, you may receive a G grade, but only after the excuse is documented and arrangements to finish the course work are finalized with Dr. Polinko.
Disability:

If you have a disability for which you are or may be requesting an accommodation, you are encouraged to contact both your instructor and the Office of Disability Resources and Services, 140 William Pitt Union, 412-648-7890/412-624-3346 (Fax), as early as possible in the term. Disability Resources and Services will verify your disability and determine reasonable accommodations for this course.  For more information, visit www.studentaffairs.pitt.edu/drsabout.

Academic Integrity:

Cheating/plagiarism will not be tolerated. Students suspected of violating the University of Pittsburgh Policy on Academic Integrity, from the February 1974 Senate Committee on Tenure and Academic Freedom reported to the Senate Council, will be required to participate in the outlined procedural process as initiated by the instructor. A minimum sanction of a zero score for the quiz or exam will be imposed. View the complete policy at www.cfo.pitt.edu/policies/policy/02/02-03-02.html.

Students agree that by taking this course all required papers may be subject to submission for textual similarity review to Turnitin.com for the detection of plagiarism. All submitted papers will be included as source documents in the Turnitin.com reference database solely for the purpose of detecting plagiarism of such papers. Use of Turnitin.com page service is subject to the Usage Policy and Privacy Pledge posted on the Turnitin.com site.

E-mail Communication:

Each student is issued a University e-mail address (username@pitt.edu) upon admittance. This e-mail address may be used by the University for official communication with students. Students are expected to read e-mail sent to this account on a regular basis. Failure to read and react to University communications in a timely manner does not absolve the student from knowing and complying with the content of the communications. The University provides an e-mail forwarding service that allows students to read their e-mail via other service providers (e.g., Hotmail, AOL, Yahoo). Students that choose to forward their e-mail from their pitt.edu address to another address do so at their own risk. If e-mail is lost as a result of forwarding, it does not absolve the student from responding to official communications sent to their University e-mail address. To forward e-mail sent to your University account, go to http://accounts.pitt.edu, log into your account, click on Edit Forwarding Addresses, and follow the instructions on the page. Be sure to log out of your account when you have finished. (For the full E-mail Communication Policy, go to www.bc.pitt.edu/policies/policy/09/09-10-01.html.)

Grading
Final grades will consist of attendance, homework, two standard exams, and an individual project based on a student-selected family of sequences. This project grade will consist of four progressive versions due during the course of the semester, culminating with a final written project and a brief (10 min) PowerPoint presentation of your findings during the final exam period. A breakdown of the grading is provided below.

Attendance 10% 100
Homework 10% 100
Midterm Exam 1 20% 200
Midterm Exam 2 15% 150
Project part 1 1.5% 15
Project part II 6% 60
Project part III 10% 100
Project part IV 12.5% 125
Final Project 15% 150
TOTAL 100% 1000 pts



Class Schedule

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Last Updated: 25 August 2016
Question or Comments: epolinko@pitt.edu
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