Topics in Bioinformatics

BIOI 7713; (4 credits)	Prof. Larry Hunter
Topics in Bioinformatics	RC-1 L18-6101
RC-1 North 6th Floor Lecture Hall (Room P18-6107)	(303)724-3574
Tuesdays and Thursdays, 11:00am-12:15pm	Larry.Hunter@uchsc.edu
Office hours by appointment	http://compbio.uchsc.edu/hunter

Course Description

Grading

Course Materials

Important Notices

I will be out of town March 11, 24, 29, 31 and April 7. I will try to arrange for alternative discussions on those days, but given the nature of the class, I may just have to cancel.

Course description

This course looks at current research topics and recent results in bioinformatics and computational biology. Students will become familiar with the requirements for productive research in bioinformatics. They will be able to define, execute and report on a significant and achievable bioinformatics research project, as well as present and evaluate bioinformatics research projects of others..

Goal for the course: To help advanced students make the transition to beginning researchers. Also, to gain experience with key forms of academic writing, such as grant proposals, conference posters and journal articles.

Course Requirements:

Prerequisite: Bioinformatics 7712 with a grade of B or higher, or permission of the instructor.
Readings: Recent research publications, primarily drawn from conferences such as the Pacific Symposium on Biocomputing (PSB) and the conference on Intelligent Systems for Molecular Biology (ISMB) and journals such as Bioinformatics. Course readings will be available on-line.
Computational: Access to a computer with an internet connection. In general, you will need access to the computational resources necessary to accomplish your course project. If additional university supplied tools are necessary, please contact the instructor as soon as possible.

Grading

Grades will be a combination of class participation, presentations and a project.

Participation: Each student is expect to attend all classes, and to participate regularly and meaningfully. At a minimum, I insist that each student say at least one thing in each class
Presentations: Each student will make several classroom presentations, including:
1. A bioinformatics paper from the primary literature.
2. Background material necessary to place a paper from the primarily literature (which will be presented by another student) in appropriate context. The backgrounder should describe significant biological and/or computational aspects of the problem being addressed, alternative methods that have been used by other researchers, and other useful contextual material. Backgrounders will follow the presentation of the primary paper.
3. A report on the student's course project. Depending on the number of students in the course, an additional, earlier presentation of the project plans may also be required.
Project: Each student will define and execute a bioinformatics project. Although it is not expected that student projects result in publishable contributions, student projects should be of roughly the same scope as a PSB or ISMB paper. Project efforts will be due on the following schedule:
- March 22 Draft project proposal due (in R-03 format)
- April 5 Project proposal due (in R-03 format)
- April 12-19 Proposal study section
- April 21 Manuscript reviews due.
- April 26 Paper presentations begin
- May 10 Project presentations begin
- May 23 Final reports due.

Course materials

NIH Materials

PHS 398 grant forms and instructions
The Program Announcement for the National Library of Medicine's Individual Biomedical Informatics Fellowships (including predoctoral fellowships!)
One of the NIH R-03 Program announcements
NIH's instructions to reviewers of R-03s
NIH's general grant review proceedures
Revised review criteria for all NIH grants.
Policy documents about peer review, including (scroll down) a comparison of the old and new review criteria.
Recent changes to federal regulations about NIH grants

Advice

Here are some pointers that will be useful to you during the class:

How to write a project proposal
How to present a paper
How to provide context for a paper
How to present your work as a lecture
How to present your work in written form

Readings

Here is the current edition of the Bioinformatics journal, and the conference proceedings for the last few years. The journal and the ISMB proceedings will only be available from within the UCHSC address range (or with access to the Bioinformatics journal site some other way).

Journals and Conferences in Bioinformatics

Articles relevant to bioinformatics can be found throughout the biomedical literature. Many publications in particular application areas contain important methods developments. However, there are a core set of conferences and journals where many bioinformatics methods are published.

You can generally get access to these resources (often online) through the Dennison Library Bibliographics search tools such as PubMed (note that the previous link has the UCHSC library holdings qualifier), CiteSeer, MedMiner, PubGene and Chilibot are also your friends... Consider signing up for some of the table of contents alert services, too.

Conferences

You can find a useful calendar of bioinformatics events at the ISCB website. [By the way, I encourage you to join the ISCB -- it's quite cheap for grad students and worth it if you go to one conference or subscribe to one journal.]

Intelligent Systems for Molecular Biology (ISMB)
Pacific Symposium on Biocomputing (PSB, "The Hawaii Meeting")
Research in Computational Biology (RECOMB)
The Genome Informatics Workshop (GIW, "The Japan Meeting")
European Conference on Computational Biology (ECCB, "The European Meeting")
The American Medical Informatics Association meeting (AMIA)
Rocky Mountain Regional Meeting on Bioinformatics (Last year's site; next year's coming soon). (Rocky)

Journals (specifically bioinformatics)

Other journals that often contain bioinformatics papers (incomplete!)

Project Reports:

Your presentation your project should be in the form of a conference talk. You should prepare a 20 minute presentation, and leave 5 minutes for questions.