Bioinformatics has been defined as the science of
examining the structure and function of genes and proteins
through the use of computational analysis, statistics, and
pattern recognition. A number of recent workforce studies
have shown that there is a high current and unmet demand for
people trained to various levels of expertise in
bioinformatics, from technicians and technical librarians to
developers of new and improved methodologies and
applications. National estimates of needed positions in the
field in the next four to five years is about 20,000.
Bioinformatics is a rapidly evolving and developing field
both in terms of breadth of scope of useful applications and
in terms of depth of what can be accomplished. This course is designed to introduce bioinformatics at a
level appropriate for biology majors having completed the
lower-division core, and for chemistry, computer science,
and math majors with an interest in biology. This course is
designed so that the content and curricula can rapidly
adjust as required to meet changing circumstances during the
course of the semester and to evolve with the topics of
interest in bioinformatics over time. Students will learn to
use conventional software, web-based applications, and
software which they download to their machine. By using the
well-tested and successful approach of problem-based
learning, students will learn through applying the
strategies and tools used in bioinformatics to topical
problems drawn from ongoing research and applications in a
variety of fields. There is to be an integration of the
basics of computation and analysis along with chemistry and
biology throughout the course. A well designed course should prepare students to meet
the expected outcomes of having taken that course. As a
minimum at the end of this course, there should be a solid
understanding of the scope of bioinformatics. It is expected
that the basic knowledge can be applied in many different
fields of interest. Students should gain substantial
competency in content, skills, and awareness within the
field of bioinformatics. Many of the problems presented in
the course will serve as launch points for further inquiry
and exploration as students move on into other courses. The fields of study in molecular and cell biology
continue to grow rapidly. The field of bioinformatics
changes so rapidly that it is nearly impossible to keep up
with all the different areas of progress. It is therefore
necessary to learn how to access new information and how to
assimilate it into the whole, in order to continue to learn
beyond the limits of this course. It is also necessary to
become aware of the tools and techniques used in research
and in applications. Therefore, while learning the
essentials of bioinformatics, you will also begin to learn
to use some of these tools. In doing so, you should find
that they help you in learning beyond this course and to see
the connections in other courses. This course is expected to attract students from a
variety of backgrounds, with different levels of experience
and preparation. As a way of accommodating the broadest
possible range of students, a pre-module has been
designed with two purposes in mind. One is to assess initial
preparation and readiness for the course. The other is to
provide access to quality web-based tutorials in several
support subjects to assist students in reviewing or learning
the necessary basics needed to be successful in this course.
The pre-module exercise will given during the first week of
the semester. Although ungraded, successful completion is
expected before proceeding in the course. Grading in the course will be based on the
following activities. See below for an explanation of each.
Note: This breakdown may be
modified slightly following the unit revisions. There will
be an announcement and discussion in class on
this. Assignments must be turned in on time. Exercises
will be due either 1) by midnight on the day of the lab, or
2) if you stay for the full lab period, you may turn them in
at the beginning of the following class meeting. Discussion participation 20 Unit exercise summaries [6 sets] 60 Unit projects [6 problems] 120 Mid-semester summary problems 50 End-semester problem proposal 50 Unit assessments/critiques [6] 60 Total 360 Cheating and plagiarism: This will result in
dismissal from class and a failing grade. The lecture/discussions are designed to be highly
participatory. Therefore, it is fair and just that points
are awarded for effort and participation in these
discussions. Participation will include such activities as
group discussions of topics; discussions with faculty and
guest presenters on topics, research, and/or application
problems; short presentations on relevant papers and project
results; and critiques of resource material, software, and
other things related to bioinformatics. The course is divided into six units: The unit exercises are one of the key means of learning
how to find and search databases, use a variety of
application software, and analyze results. For each set of
exercises, there will be a series of summary questions.
These exercises are posted on this web site under "Computing
Materials Home". Points will be earned for completing the
exercises. Grading on these will be lenient; the key point
is to learn something in the process of doing them. You will
be able to explore while you gain some familiarity of how to
find sequences, to make comparisons of sequences, and to
locate original literature related to the sequences. You
will be shown where and how to continue learning more about
bioinformatics beyond the basic introduction given during
this course. You will also gain experience which should help
you in completing the projects. Two short projects in the first unit, and one project per
unit thereafter, will be introduced in the context of
real-world applications and research in a variety of fields.
One purpose of these projects is to demonstrate the diverse
utility of bioinformatics, while appealing to the diverse
interests of the students. Another purpose is to gain
expertise in analyzing problems, finding approaches to
obtain solutions, analyzing results, and presenting
summaries of project outcomes and conclusions. These
projects will be done in small groups. Group effort will
facilitate brainstorming and breaking the problem up into
smaller chunks manageable by individual students. Grading
will be based on individual effort and overall group
outcomes. Mid-semester problem set:
["Not-the-midterm"] The problem set will consist of two key types of
questions. One type will be practical, requiring use of some
of the databases and applications used so far. The other
type will focus on approaches to finding solutions and
evaluating results. Thought and analysis will be
stressed. After a semester of exploring bioinformatics through
problem-based learning, it is time to move beyond and think
ahead. Here is the opportunity to get serious about asking
some relevant questions and generate a problem or
independent project relating bioinformatics to a topic of
your interest. The problem or project will be independently
designed by you or by a small group of your choice. Here you
can enjoy a little freedom and creativity. You can
capitalize on the experiences gained during the semester.
Grading will be based on project design, including the
quality of development and description of the approach to be
taken. For those interested, the proposal can serve as the basis
for a senior research project or special study project in a
later semester. Unit assessments and
critiques: In addition to assessing individual student performance
and progress, it is important to critique the function and
quality of the unit materials and activities. This will
allow for further development and improvement of the course.
For each unit, there will be unit surveys to identify
difficulties and to solicit suggestions for improvement.
Your input will be a valuable resource to future offerings
of this and related courses. Points will be awarded for
completing the surveys. .
Assessment & Grading
.
Course Objectives
Assessment & Grading
Note on final grade calculation: The top score of the
class earned by an undergraduate will be essentially valued
as a perfect 100%. This creates a "fudge factor". All other
scores will be computed on that basis. This will compensate
for possible assignments or problems which may be too
difficult or unclear. Letter grades will be assigned as
follows:
Course Requirements
Discussion participation:
End-semester problem/project proposal:
["Not-the-final"]
Updated 8/28/03 by thatcher@sonoma.edu