CPBS 7711:
Methods and Tools in Biomedical Informatics
Tuesdays and Thursdays, 1-2:30pm
RC-1 North Tower, Room P18-6123
Anschutz Medical Campus, UC Denver
Office: RC-1 S. Room L18-6101
Phone: 303-724-3574
E-mail: Larry.Hunter@ucdenver.edu
http://compbio.ucdenver.edu/hunter/
Office hours by appointment
Chris Funk, TA
Office: RC-1S, Room L18, 6400A
Phone:
E-mail: Chris Funk
Office hours by appointment
Purpose This course is central to the educational mission of our Computational Bioscience PhD program. Please take the time to review the educational mission statement
An introduction to the theory and practice of bioinformatics and computational biology. Topics include: the analysis of macromolecular sequences, structures, gene expression arrays, proteomics, and management of the biological literature. Requirements and prerequisites
Goals for the course: The course will familiarize students with the tools and principles of contemporary bioinformatics. By the end of the course, students will have a working knowledge of a variety of publicly available data and computational tools important in bioinformatics, and a grasp of the underlying principles that is adequate for them to evaluate and use novel techniques as they arise in the future.
This course is also the beginning of the transition from well-educated students to independent researchers. The work in the course involves a series of supervised activities that introduce the activities of research. These will include:- Formulating an effective research plan
- Critiquing the research plans of others
- Revising research plans in light of critique
- Reporting on research results, orally and in writing
- Reviewing manuscripts that report on research results
This is a team-taught course. You will get a chance to meet and interact with many of the instructors in the computational bioscience program. The faculty include:
- Kevin Bretonnel Cohen
- Robin Dowell
- Debra Goldberg
- Carsten Görg
- Larry Hunter
- Michael Kahn
- Katerina Kechris
- Sonia Leach
- David Pollock
- Michael Strong
- Karin Verspoor
Much of the material presented in this course will be in the form of lectures. Generally, we dislike lecture courses, but there is so much material that you have to know in order to be a well educated researcher in bioinformatics (and to pass the preliminary exam!) that we feel we have no choice. Do know that we want you to ask questions, raise topics you'd like to know more about, and otherwise make this course more your own.
- Course Project proposals, in the form of an NIH R03 application (without a budget), are due in class on 9/29. Please bring 2 printed copies to class, and email an electronic copy to Chris Funk. We will distribute copies of each proposal to the other students, and you will write an NIH style review of your peer's proposals for presentation in class on 10/6.
Each of the following topics will be covered in one or more class lectures. This list is tentative until the lecture is posted. Lecture notes, readings and external links will be posted here before each class. The professor for each topic is indicated by last name. The dates that students present will be video broadcast to National Jewish and CU Boulder, so please note the room change on those days, all other classes will be held in RC1N - P18 6123.
- 8/30/11 Welcome/What is Bioinformatics Research Hunter
- Educational Mission
- 9/6/11 Research plans & how to claim significance Hunter
9/1/11 Course Project Overview Hunter
- 10/25/11
- 10/27/11 Expression array analysis Phang
- Slides
- 11/1/11 Manuscript review Kechris (Class will meet from 11:00-12:30pm in RC1N, 6107)
Grading
The goal of this course is to get you familiar with the use of bioinformatics techniques in addressing real scientific problems. Grading will be largely on the basis of a course project. The project will involve several stages: producing a project plan, revising your plan in light of critique, presenting a status report on your progress, a final oral presentation, and a final written presentation. In addition to this work, you will be required to produce written critiques of others' research plans, and of others' written presentations of research results. The dedication and intensity you bring to these tasks is a good predictor of your likely success as an independent researchers, so we will add a subjective component to your grade that reflects what the faculty believe is the level of effort and committment you show toward the work; this includes showing up for class prepared, participating actively in discussions and activities, and in your ability to get high quality work done in the face of the many other requirements on your time (yes, including core).
While it may be hard for you to wrap your head around, no one will ever care about the grades you get in graduate school (assuming you pass, of course). Now the important thing is to make the transition to producing significant, original research that will make an impact on a broad community. Your ability to master existing material (both in textbooks and in original research publications) is assumed, and will be tested during your preliminary exam. What we hope to teach in this course (and will be evaluating you on) is the development of a creative and scholarly approach to doing new science.
Honor Code
The Graduate School requires that this honor code be included in all course syllabi.
Education at the University of Colorado, Denver is conducted under the honor system. All students who have entered health professional programs should have developed the qualities of honesty and integrity, and each student should apply these principles to his or her academic and subsequent professional career. All students are also expected to have achieved a level of maturity, which is reflected by appropriate conduct at all times.
Note that our educational mission statement includes even stronger goals for your professional behavior. Please feel free to raise issues related to those goals in class.
