Computational Molecular Biology and Genomics Policies

[Lectures] [Course Work] [Grading] [Due Dates] [Collaboration] [Academic Integrity] [Exams]

Lectures and course work

Most lectures will be presented at the chalk board. Lecture summaries will be posted on the syllabus page. These are not comprehensive notes and are not guaranteed to cover all the material discussed in class. You are responsible for taking notes in class and learning the material from your notes and reading assignments. Occasionally, lectures will include powerpoint presentations, software demonstrations, and guest lectures.

I find laptops and other electronic devices in class distracting. When I am distracted, I am a poor lecturer. For this reason, I ask you to turn off your mobile devices and close your laptops during class. In addition, evidence from learning research suggests that laptops in the classroom do not enhance the academic performance of the student using the laptop and distract students sitting around them.

Course work for all sections includes 6 to 8 problem sets, two in-class exams, and a final exam. The final exam is cummulative, although there will be greater emphasis will be on material covered in the last third of the course.

Students taking the 12 unit version of the course will be assigned additional homework problems. These assignments will focus on extensions of the course material to topics in genomics and will involve designing or applying algorithms or discrete mathematics approaches in more complex or open-ended scenarios. Typically a reading assignment, focussed on a specific problem in genomics, will be included that will prepare you to solve the problem solving section of the assignment. This material will not be covered extensively in class. Most assignments will involve problem-solving, rather than coding, and none will involve extensive programming tasks.

You will be graded on the scientific content of your work, not your English language skills.

Grading policy

Due dates and late assignments

Assignments are due by 4pm on the due date. Homework may be submitted in class, in MI-646, or by email to

In calculating your final score, I will drop your the lowest grade of the homework assignments, but only if all assignments have been submitted by the last day of classes. Your mid-term grade will be based on in-class examinations and all homework assignments administered before mid-semester. No homework scores will be dropped at midterms.

The penalty for late homework is 10% per day. No late homework will be accepted once graded homework has been returned to the class and the solution set has been posted. Extensions will be granted only in extraordinary circumstances (e.g., an extended illness). There will be no "makeup" homework assignments.

Collaboration on homework

Problem Set 0 is a self-administered placement quiz, to help you (and me) determine if you have the background for the course or need to read additional material.

Your score on Problem Set 0 counts towards your final grade.

All other problem sets: Discussion and collaboration on homework problems between students is allowed, but each student must prepare his or her own assignment. Students may not copy any portion of a homework assignment from another student, nor may they jointly prepare all or part of an assignment. An example of acceptable collaboration would be the discussion of strategies for a particular task, followed by each student implementing the strategy independently. Examples of unacceptable collaboration are:

  1. jointly doing an analysis and then handing in multiple copies of the results.
  2. following a method suggested by someone else without being able to explain the method.
Students who collaborate on homework assignments must write the names of their collaborators on the front of their homework assignments, with a short explanation of what was discussed.

You may consult textbooks, articles and websites while preparing your assignments. You should not follow a procedure described in such sources, unless you understand it well enough to explain it. You may not consult solution sets from previous years. Nor may you quote from any source without attribution.

Academic Integrity

All students are responsible for familiarizing themselves with the Carnegie Mellon policies on Academic Integrity, Cheating, and Plagiarism, and adhering to those policies.    In order to deter and detect plagiarism, online tools and other resources may be used in this class.

You should be aware that plagiarism, cheating and other violations of the academic integrity policy are considered to be serious infractions at Carnegie Mellon. CMU policy allows me to exact a penalty as severe as failure in the course for a single violation.

Exam policy

Exams are closed book. You may bring two 8.5"x11" pages (or one page, front and back) of your own notes. Bring a calculator. The final exam will be cumulative. You are responsible for all material covered during the semester.

The time and date of the final exam are determined by the registrar's office and are beyond my control.     Until the date of the final is determined, you should not make plans to leave for winter vacation before the end of the exam period. No student will be permitted to take the final exam early.

No student is required to take more than two scheduled examinations that start within a 25-hour period. If you have more than two final examinations scheduled within a 25-hour period or another examination scheduled at the same time as the exam for this course, please see me immediately to discuss how to resolve this conflict.

With the exception of the above, make-up exams will not be offered, except in the case of documented illness or family emergency. This policy applies to both in-class exams and the final exam.

Last modified: August 28th, 2017.
Maintained by Dannie Durand (