03511 - Policies

Computational Molecular Biology and Genomics - Course Policies

[Lectures] [Electronic Devices] [Attendance and Participation] [Course Work] [Grading] [Due Dates] [Collaboration] [Academic Integrity] [Exams] [Accommodations and Resources]

If you have any questions about the policies explained here, or any other aspect of the course, please do not hesitate to ask. I am here to help you learn this material and succeed. My course policies are designed to explain my expectations of students and foster an open learning environment, while ensuring a fair and honest system.


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.


Electronic Devices

Unexpected noises and movement automatically can divert and capture your classmates' attention, which means you are affecting everyone's learning experience if your device makes noise or is visually distracting during class. Personally, I find laptops and other electronic devices in class distracting. When I am distracted, I am a poor lecturer.

Further, evidence from learning research suggests that laptops in the classroom do not enhance the academic performance of the student using the laptop - taking notes by hand helps you retain information better!

For this reason, I ask you to turn off your mobile devices and close your laptops during class.

Classroom Recording Allowed for Personal Educational Use

Classroom activities may be recorded by a student for the personal, educational use of that student or for all students presently enrolled in the class only, and may not be further copied, distributed, published or otherwise used for any other purpose without the express written consent of Dr. Stolzer. All students are advised that classroom activities may be taped by students for this purpose.


Attendance and Participation

Attending class is one of the best ways to gain a better understanding of the material. Being attentive for lectures, taking notes, and engaging in examples are important to your success in this course. In order to learn, you must be present both physically and mentally!

Because your presence and engagement in learning is so vital to your success, I want to reward you for this work. A small portion of your grade will be based on class attendance and participation. You will be rewarded with a perfect score if you frequently come to class and actively contribute to the class either during lectures or office hours.


Take the time to look over the schedule for this course (the syllabus). Please let me know as soon as possible, preferably through email, if you will miss class for any excusable reason (religious observance, illness or injury, personal or family emergency, conference or job interview, university-sanctioned event, etc.). Sometimes, life happens, and you won't be able to make class for some other reason. Everyone is permitted one unexcused absence without the deduction of points. Further absences will be docked 10% of the attendance and participation grade. If extenuating circumstances will cause you to miss more classes, and they are not for excusable reasons, please come and discuss this issue with me in advance of your absence(s).


Tardiness (being late to class) disrupts the lecturer and the learning environment of your fellow classmates. Please respect your peers and show up to class on time. If you are tardy more than three times, I will start docking points from your attendance and participation grade - 5% for every tardy. Being more than 5 minutes late to class will be considered a tardy. If there are extenuating circumstances, please contact me.


Participation makes class more valuable for everyone. During class, I expect students to be attentive and actively engaged in the learning process (i.e., taking notes and following along with the lecture). Asking questions during class will help you, me, and the rest of the class. Chances are, if something is confusing to you, it's confusing to at least one other person in class. I will ask questions of the class and ask for participation in walk-through examples. This helps me assess whether a concept has been effectively conveyed or areas that need more discussion. I understand that public speaking can be more difficult for some than others. Therefore, I will also consider your attendance at office hours and questions submitted electronically as part of your participation.


Course Work

Course work for both sections includes 10 homework assignments, two in-class exams, and a final exam. Homework assignments focus on problem solving and most do not require programming. The emphasis is on applied algorithms, not implementation. 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 03-711 (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 for 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

In calculating your final score, I will drop your lowest grade of the homework assignments, but only if you have submitted all assignments 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.


Due dates and late assignments

Due dates for every assignment are provided on the course syllabus. Due dates are also included on the assignments. Unless otherwise stated, course work is due by the day and time listed. 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

Problem Set 0 (PS0) 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 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, websites, and campus learning resources while preparing your assignments. Again, students must write a summary of the sources and information consulted on the front of their homework assignments. This information is to help me understand each individual student's comprehension of the material. Students are not penalized for collaborating. I stongly encourage discussion of class and homework topics with your fellow, current classmates, especially when it enhances your understanding and learning.

You should not follow a procedure described by classmates or in sources, unless you understand it well enough to explain it. In general, if you cannot solve a similar problem on a test, you shouldn't submit the work as your own.

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.
  3.   getting help from a classmate or source without acknowledgement.
  4.   receiving answers from students who have taken the course in previous years.
You may not consult solution sets from previous years. Nor may you quote from any source without attribution.


Academic Integrity

Integrity and honesty are integral aspects of good science.

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. Any act of cheating or plagiarism will be treated in accordance with Carnegie Mellon's Policy on Academic Integrity. Depending upon the individual violation, students could face penalties ranging from failing the assignment to a penalty as severe as failure in the course for a single violation.



Exams are closed book. You may bring two 8.5"x11" pages (or one page, front and back) of your own notes. 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, family emergency, religious observation, or disability. This policy applies to both in-class exams and the final exam. The dates of the two in-class exams are provided on the course syllabus. If you are unable to take an exam in class on the posted date, for any of the listed exception, please let me know as soon as possible.


Accommodations and Resources

Please see the course resources page for more information on resources available to help you succeed at CMU.

Accommodations for Students with Disabilities

If you have a disability and have an accommodations letter from the Disability Resources office, I encourage you to discuss your accommodations and needs with me as early in the semester as possible. I will work with you to ensure that accommodations are provided as appropriate. If you suspect that you may have a disability and would benefit from accommodations but are not yet registered with the Office of Disability Resources, I encourage you to contact them at access@andrew.cmu.edu .

Student Health & Well-being

Take care of yourself. Do your best to maintain a healthy lifestyle this semester by eating well, exercising, avoiding drugs and alcohol, getting enough sleep and taking some time to relax. This will help you achieve your goals and cope with stress.

All of us benefit from support during times of struggle. You are not alone. There are many helpful resources available on campus and an important part of the college experience is learning how to ask for help. Take the time to learn about all that's available and take advantage of it. Ask for support sooner rather than later – this always helps.

If you or anyone you know experiences any academic stress, difficult life events, or feelings like anxiety or depression, we strongly encourage you to seek support. Consider reaching out to a friend, faculty or family member you trust for assistance connecting to the support that can help. Counseling and Psychological Services (CaPS) is here for you: call 412-268-2922 and visit their website. Over 25% of students reach out to CaPS some time during their time at CMU.

If you or someone you know is feeling suicidal or in danger of self-harm, call someone immediately, day or night:

CaPS: 412-268-2922

Re:solve Crisis Network: 888-796-8226

If the situation is life threatening, call the police
On campus: CMU Police: 412-268-2323
Off campus: 911


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Last modified: August 26, 2019.
Maintained by Maureen Stolzer.