The course has no class final exam - the grade is based on the following
components:
1. Scribe
Each 2-3 students (the number depends on
final course enrollment) will scribe (i.e., to prepare lecture notes for) one
lecture. The notes should be prepared in LaTeX, and
corrected according to guidelines and marks given by the TA and/or the
instructor. Precise instructions and schedule are given here
. Notes should contain all the material presented in class, written in clear
and accurate fashion, as well as the relevant references. Using figures
and diagrams when necessary in order to clarify things is recommended. In most
lectures, the scribes of lectures given in
a previous year in the course can be used as a basis.
2. Literature Review Project
Students who will not be assigned a scribe task
should do a literature review project instead.
The project can be done in pairs.
The subject of the project
can be chosen from the list of topics covered in
the course, or a related topic. Each pair is required to schedule a meeting with the
instructor/TA to obtain consent to the topic, discuss relevant papers and
the direction for your project.
The project should include (i) a summary of the literature on this subject, (ii) a
short summary of tools available, (iii) a clear description of the biological
goal of the framework, (iv) a clear description of the computer
science/mathematics tools used to solve the problem, (v) clear examples, (vi) a
short summary of open computational problems in the area, (vii) either a small
implementation of one of the algorithms/concepts in the paper with some
experimentation or a theoretical investigation of a computational problem from
one of the papers, and (viii) bibliography.
Upon completion of the project, it will be presented in writing and also orally in a 15 minute meeting with the TA/instructor.
3. Theoretical Exercises
3-4 theoretical exercise sets will be given during the course. Solutions should
be done independently by each student and without help from others.
Use of books and articles for the solutions is allowed and will not affect the
grading, but the sources should be noted in the solutions. Most
assignments contain built-in bonus, so by completing some 90% worth of all
exercises you will be given full score.
4. Programming Project
Students will be assigned a project which will require writing code
(implementing algorithms from the literature), applying it to public gene expression
datasets and reporting the results. The project can be done in pairs.
Breakdown of final grade (tentative) :
1. Scribe / Literature Review: 25%
3. Theoretical Exercises: 50%
4. Programming Project: 25%
Tardiness:
Scribe preparation is done in two steps, each of which has its own
deadline. Scribe grade will lose one point for each late day past each of
the two deadlines. This is done in order to ensure that scribes are
completed and made available to the whole group promptly.
Deadlines for theoretical exercises are strict - no late submission is allowed
without prior authorization from the instructor /TA.
Projects should be handed in not later than June 10th. Late projects will
lose one point for each late day.