Bioinformatics Brainstorm Seminar

Chemistry 202

Fall 2000

Christopher Lee

Summary

Students in Bioinformatics need to learn how to work together across disciplinary boundaries, to formulate problems succinctly and to propose solutions.  The goal of the Bioinformatics Brainstorm Seminar is to provide a structured forum where faculty and students will routinely brainstorm concrete examples of how biological problems map to (and are solved by) methodologies from other disciplines.

Course Objectives

The purpose of the seminar is to teach students collaborative problem-solving on real bioinformatics research ideas.  The seminar also serves as a forum for faculty to explore interdisciplinary project ideas and possible collaborations.  Finally, it provides the larger bioinformatics community at UCLA an open seminar for discussing research ideas and learning about the field.

Educational goals for students:

·        Learn essential concepts, problems, and vocabulary from interdisciplinary fields relevant to bioinformatics (e.g. computer science, mathematics, statistics, biology).  Students in this area must learn enough to work comfortably with collaborators from these fields.

·        Learn to explain / communicate their own individual area of expertise to collaborators from other fields.  Students must become accomplished at "translating" their own knowledge into terms others can understand.

·        Learn to identify key issues through data modeling (translating biological data and problems into information problems and theory), brainstorming (idea generation), structured critique to identify assumptions, and constructing action plans of key tests.

·        Learn to collaborate on an interdisciplinary approach to a bioinformatics problem.  Students must learn how to divide work and share results / knowledge.

Course Organization

The general model for the brainstorm seminar is a unit of two sessions: first, to introduce the problem and the theoretical framework proposed for solving it; second, to explore with specific examples the fit between the problem and proposed solution.  The two sessions are two hours each, and occur on successive Wednesdays.  The first session is intended primarily for students enrolled in the course and focuses on the separate biology and theory background, without yet moving to synthesis.  As such it is background, rather than research.  The second session is synthesis, combining the two sides to propose a new solution to a research problem.  We hope also to attract faculty and researchers to participate in these sessions.

Session I: Introducing the Problem, Proposed Solution

The student team presents essential background on the biological problem and the theory for solving it, guided by the materials and instructions of the two faculty session leaders.  These presentations do not have to synthesize the two fields or go deeply into the proposed solution.  It is sufficient to cover the two separately: to explain the biology (to theorists), and to explain the basic theory (to biologists).  In the second session we will explore the fit between the two in detail.

Each side must prepare background material for the website, including a glossary of terms, and basic introduction to the material, ideally with extensive links to more detailed expositions.  The goal is to give people information that is totally approachable (assuming no previous background) but which provides full links for drilling down to as much detailed information as the reader wants.  This material must be available on the class website at least a week before the talk.

Schedule

·        Student presentations (1 hour): Proposal overview, background presentations.

·        Discussion (1 hour): This is a chance for students to ask all questions about material that is unfamiliar or not clear to them.  Student team members answer these questions; their goal is to make sure everyone fully understands the problem and theory.  Faculty may guide the discussion or provide clarifications and elaborations.  If time permits, the proposed solution may also be discussed, with the goal of drawing out basic questions or issues which need to be thought about further.

Session II: Exploring the Fit between Problem and Solution, through Examples

A team of students led by two faculty illustrate the problem and proposed theoretical approach with clear examples on each side.  The talks should focus on examples that are comprehensible without extensive background.  It is often possible to make sophisticated concepts and issues clear by using well-illustrated examples.  The biologist's talk should state a very specific question for the theorist to answer.  The faculty and team then present their proposed solution, and lead a discussion to generate critical questions about whether it will work, whether there is a good fit between data and theory, etc.

One way to make this very concrete, is to sketch implementations of very simple example problems.

·        Start with an implementation of the "standard solution" so people can see how it translates / compares with the new approach.  This is a good starting point.

·        Choose an example problem that represents one of the simplest possible uses of the new theory.

·        Sketch how this problem would be "solved" by the new theory.  Ideally, draw an actual implementation.  The more concrete this is, the more people will be able to get a feel for whether this will work or not.

·        Choose a somewhat more sophisticated problem, and repeat the exercise.  This gives people a chance to see where this theoretical approach can go, and how hard it is to get there.

Schedule

Presentations (30 minutes)

1.   The first presenter(s) (coming from a biology viewpoint) will describe the biological problem "as simply as possible, but no more"--its essence, but without oversimplification, and illustrated with real data.

2.   The second presenter(s) (coming from a theory viewpoint) will propose a theoretical formulation of the problem: "I think this is a such-and-such kind of problem; here's what I mean by that; here's why I think it is; and here's what that means for solving the problem."  This should propose what method(s) could solve it.

Each side should take 10-15 minutes.

Open discussion (30 minutes).  Everyone can ask questions or raise points in an open forum.  All background questions should be asked during this period.  Brainstorming ideas are welcome.

Structured discussion (1 hour): The remainder of the session will be devoted to active discussion of the hypothesis, driven by an agenda to reach definite conclusions at the end of the session:

·        What are the critical issues for the problem?  Agree on a formal statement of the problem. (10 minutes)

·        What is the proposal?  Agree on a formal statement of the proposed solution. (10 minutes)

·        What are the assumptions of the proposed method? (10 minutes)

·        What tests would check these assumptions? (10 minutes)

·        What alternative methods are possible, and how do they change the assumptions? (10 minutes)

Course Requirements

Enrolled students must

·        Attend the two hour seminar each week.

·        Participate in one presentation team (two weeks).

·        Attend five meetings for their team, for collaborative preparation of their presentations, on Mondays and Fridays in the two weeks before their team presentations.

·        Prepare background material for posting to the course website, including definitions of essential vocabulary, links to basic background introductions, and further links.

·        Prepare and present material in the seminar as part of their team.

·        Write 500-750 word summaries of each brainstorm seminar including:

·        A brief description of the problem and the methodology of the solution

·        Innovative suggestions for testing assumptions inherent in the proposed solution

·        Deep, inherent problems in the proposed solution

·        Alternative approaches for solving the problem

·        Grade the summaries submitted by their peers of their presentations.

·        Write a final research paper.

·        Prepare a formal poster describing the problem and proposed solution.  The posters will be presented at the end of the course for the UCLA public to view.

Participating faculty must

·        Choose a problem and propose a solution as a subject for a seminar.

·        Provide background materials / instructions to the student team, and divide it among them according to people's strengths. (Friday meeting).

·        Advise the student team on the brainstorm presentation.  The faculty should decide the overall division of the presentation between the faculty and team members (Friday meeting).

·        Participate in the Introductory and Brainstorm seminars for their team.