Course Requirements
and Grading
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) 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 is 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 some lectures, the
scribes of lectures given in previous years in the course Algorithms in Molecular Biology can be used as a
basis.
2.
Literature Review Project
Each pair of students will do a literature review project. The project must be
presented orally to the instructor or the TA. Students who will not have
assigned scribes have to submit that project in writing as well. 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 15 minute 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
theoertical investigation of a computational problem from one of the papers,
and (viii) bibliography.
3. Theoretical Exercises
Several 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 exression datasets and reporting
the results. The project can be done in pairs.
Breakdown of final grade:
1. Scribe / Written Literature Review: 30%
2. Oral Literature Review: 15%
3. Theoretical Exercises: 40%
4. Programming Project: 20%
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 30th. Late project will
lose one point for each late day.