Because of the nature of bioinformatics, there will necessary be a variety
of kinds of work for this course. For example, you will be expected to read
and respond to material from the primary literature and you will be expected
to collaboratively develop some programs that solve interesting problems
in bioinformatics. (As Sam's statement on teaching
and learning suggests, such a variety is good for all courses. It is
particularly important for bioinformatics.) Because some forms of work are
likely to be new to students, this document provides some detail about the
different kinds of work.
In addition to having you read our textbook, we will also ask you to read
some pieces from the primary literature. For some of these readings, we will
ask you to prepare a one-page response in advance of the class discussion of
the reading.
Because of the nature of response papers, we will not accept late responses.
Reading papers are generally individual work. However, you should feel
free to discuss readings with your colleagues, provided you then cite them
in the work you turn in.
More details can be found in Writing Response Papers.
In studying how students use and benefit from their class work, reseachers
have found that students too rarely reflect retrospectively on their work
in a course, or consider how their work and thought processes change
throughout a course (or an academic career). Portfolios have proven to be
a successful mechanism for helping students to reflect on past work and to
consider growth.
A typical portfolio consists of a few pieces of student work, selected by
the student. The student writes a short narrative for each piece, explaining
what the piece demonstrates (or fails to demonstrate). The student also writes
an introductory essay that summarizes the content and ideas of the portfolio.
Toward the end of the semester, we will ask you to prepare a portfolio of
work from this course. At that point, we will provide further details about
how much work to include and how much and what kind of narrative writing is
required.
To prepare yourself for creating your Bioinformatics portfolio, you
should make sure to keep a copy of all of your work for the course.
You may also find it beneficial to keep both ungraded and graded copies
of each assignment.
While portfolios are primarily individual work, students should feel free
to consult with their colleagues as they prepare the portfolio.
See the guidelines for portfolios
for more information.
In each chapter, our textbook includes a series of Web Exploration
Questions
that ask you to use standard bioinformatics resources to
find out more about an issue or problem. At times, we will devote class
time to these Web explorations. At others, we will ask you to do them on
your own time. In a few cases (including both in-class and out-of-class
explorations), we will ask you to turn in a write-up of the Web explorations.
Web explorations are group work. When you explore the Web, you should do
it with your (assigned) peers and discuss each question. When you turn in
answers to Web exploration questions, you need turn in only one assignment
for the whole group.
In addition to discussing the Web explorations with your colleagues in the
group, you may also discuss them with members of other groups. In such cases,
you should make sure to include a citation when you turn in your assignment.
There are basically two kinds of programming projects that you will do in
this class: guided projects and open-ended projects. There will also be
a significant programming component to the final
project.
Guided projects, usually taken through the book, guide you
through a series of exercises to help you develop a working solution
to a standard program in bioinformatics, such as protein matching or
gene sequencing. We will typically allocate a full class period for a
guided project, but you may also need time beyond the class period to
complete the guided project. We will rarely ask you to turn in your work
on a guided project.
On-Your-Own projects provide followup work to the guided
projects. TYpically, the ask you to extend your programs from the guided
projects in novel and interesting ways. At times, we will also ask you to
use these programs to explore new domains and to explain the results of
our explorations.
Toward the end of the semester, we will ask each group to pick an interesting
problem in bioinformatics, to write a program that helps gather information
that can be useful in exploring that problem, and to analyze the results that
the program produces. Ideally, the project will require significant
contributions from both biology experts
and computer science
experts
.
A sample project is that of finding olfactory receptor genes. In order to write
a program to find such receptors, one would first determine typical patterns
of DNA that make it likely that the code for a receptor is nearby (biologic
expertise). One would then write a program that detects such patterns,
handling possible variations and approximation (computer science expertise).
Next, one would run the program to ensure that it identifies known olfactory
receptor genes and to see if it also identifies new areas of the geneome that
may code for olfactory receptors (mixed expertise).
Throughout the semester, we will try to suggest possible projects based on
the current topic.
The final project is, necessarily, group work. Students should certainly
work closely with other members of their group. They may also discuss
their project with colleagues outside the group.
Further details about the project will follow after fall break.
We will regularly ask you to review the work of your colleagues. Details
on what we expect for each peer review will be distributed with that
peer review assignment.
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