| BNFO 301 |
Topic: Research Project |
Spring 2013
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Rationale
OK, this is the main event.
Why 'What is a Gene'? Why codons? Why BioBIKE? ...all of that so that you could be prepared
for the analysis of phage genomes, a project that will consume most of the remainder
of the semester.
There's too much to learn about genome analysis. There's WAY too much to learn. Never mind you,
there's too much for ME to learn, or any other human for that matter. Fortunately, humans have made
significant progress despite the fact that no single human is an expert in all areas. The strategy
for your research project is similar to the strategy for all large research projects: each person
becomes expert in a small slice of the pie and conversent about other people's slices. Each person
contributes to the whole, even though the whole is too big for any single person to comprehend.
To facilitate this, you'll be part of a small group with a common interest in a large topic.
You'll each have a smaller topic within that focus. Each group will meet with me once a week, but
I anticipate you will want to communicate in some way amongst yourselves more frequently than that.
Along the way, you'll develop an exhaustive bibliography on your topic (to gain the sense of expertise),
and you'll write a summary of one (possibly computational) experiment taken from one of those articles.
A summary of an experiment is like a miniature research proposal and will give you practice in writing one.
At the end of the semester, you'll present your work first to your colleagues and then to the world
and also write a report detailing your progress.
General Advice and Examples
Overview: What and Why Research Proposal?
Advice:
How to find a research topic
Advice:
How to address a protein-centered problem
Advice:
How to address a DNA-centered problem
Advice: How to build an exhaustive bibliography
Advice and examples:
How to write a summary of a research article
Advice:
How to annotate genes
Advice:
How to prepare a presentation on your work
Groups
Each group is defined by a core focus, which comes with at least one
suggested article. Group members may use this article as inspiration, a
starting point to find other pertinent articles, and an aid
in defining and subdividing the project. A group is under no obligation
to stick to any predetermined
agenda, so long as it goes in a direction that is even more interesting
than the original. Here's a brief overview
of the nature of each group, but it is no substitute for reading the articles suggested at
each group's web page.
Each person will have an individual project. Since our sister class,
BNFO252 (Phage Discovery Lab), is analyzing newly sequenced mycobacteriophages,
it would be interesting if your project considered their phage genomes, but
in some cases this may not be possible. Your project will probably something
greater than a single phage or small group of phages -- perhaps mycobacterial phages
or some other group.
Starting the week of April 2, I will be meeting with each group at
the specified time (time and place yet to be determined). Groups are
encouraged to meet before this time to figure out who will be covering
what subtopic and to exchange insights useful to all. Click Phage
Analysis Groups for alternate times.
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