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Bioinformatics:

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Course Goals ... Lists of and links to these resources are available on the course website. ... part of a new biochemistry & biophysics Superlab course ... – PowerPoint PPT presentation

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Title: Bioinformatics:


1
Bioinformatics  A HHMI Faculty Development
Course
  • Physics
  • Suzanne Amador Kane
  • Biology
  • Phil Meneely
  • Jenni Punt
  • Rob Fairman
  • Chemistry
  • Rob Scarrow
  • Mathematics
  • Jeff Tecosky-Feldman
  • Curtis Greene
  • Computer Science
  • John Dougherty
  • Funding from HHMI
  • Many thanks to Kim Minor

Haverford College May 2002
2
Course Goals
  • Its unrealistic for us to hire a bioinformatics
    faculty member or teach entirely new courses on
    the subject, so we instead chose to
  • Educate faculty about theory behind and use of
    bioinformatics tools
  • Stimulate development of research applications
  • Stimulate use of bioinformatics in courses
  • Get faculty talking across departmental
    boundaries

Haverford College May 2002
3
Course Format
  • Eleven weekly 1 ½ lectures
  • Six 1 ½ hour hands-on computer workshops
  • Dinner with instructors in between lecture
    workshop
  • Informal homework graded by instructors
  • Assigned readings lecture notes
  • Follow-up subgroup meetings throughout the spring
    term
  • Faculty received one course stipend or release

Haverford College May 2002
4
The Instructors
  • Greg Grant
  • Elisabetta Manduchi
  • Warren Ewens
  • U. Penn. Center for Bioinformatics
  • Guest lecturers
  • Jessica Carol Kissinger
  • Jonathan Crabtree (both of U.Penn.)
  • Stephen Bryant (NIH National Center for
    Biotechnology Information)

Haverford College May 2002
5
Course Content Syllabus
  • Topics covered
  • Statistics
  • Sequence alignment
  • Gene finding
  • Gene expression/DNA microarrays
  • Phylogenetic analysis
  • Protein structural alignment
  • Kim Minor has made a very comprehensive course
    website
  • http//www.haverford.edu/biology/genomicscourse/ge
    nomics.htm

Haverford College May 2002
6
Textbooks, software, other resources
  • We have compiled a list of useful textbooks,
    Powerpoint presentations, and course materials
    from other institutions.
  • Lists of and links to these resources are
    available on the course website.

Haverford College May 2002
7
Research applications
  • Phil Meneely, Curtis Greene Rob Manning will
    perform a phylogenetic analysis of the RCC-1
    protein family this summer with rising junior
    Ethan Roland.
  • John Doughertyongoing research with David Barkan
    (HC undergrad) on A Parallel Implementation of
    the Needleman-Wunsch Algorithm for Global Gapped
    Pair-Wise Alignment. (poster presented April
    2002 at Consortium for Computing at Small
    Colleges 7th Annual NE Conference.)
  • Jenni Punt will perform a PSI-BLAST analysis of
    CDK2 in order to understand possible targets for
    its unexpected role in programmed cell death

Haverford College May 2002
8
Current curricular development
  • Bio 100 What is life? Phil Meneely BLAST and
    clustalw used to understand phylogenetic
    relationships of beta globins of humans and other
    mammals.
  • Bio 200 Cellular Molecular Biology. Jenni
    Punt DNA Microarray/Gene expression
    examplestumor classification Rob Fairman
    Sample BLAST analysis of a-amylase.
  • Physics 320 Intro Biophysics Suzanne Amador
    Kane sequence analysis, DNA chip technology for
    gene expression, protein structual prediction)
  • CS392 Parallel Computing J.D. assignment
    implementing a sequential and parallel version
    of the Needleman-Wunsch algorithm for DNA
    sequence alignment.
  • Math 218 Probability Statistics Curtis
    Greene dishonest casino example of hidden
    Markov chains probability statistics of
    sequence alignments.

Haverford College May 2002
9
Ongoing curricular development
  • Bio 303 Protein Structure/Function Rob Fairman
    New modules on PSI-BLAST sequence analysis and
    protein structural alignments (threading
    algorithms)
  • Bio 300 PSI-BLAST lab module on anthrax porins
  • CS206 Data StructuresJ.D. Assignment on
    phylogeny to provide experience with trees and
    matrices in a bioinformatics context
  • Chem 351 Bioinorganic Chemistry Rob Scarrow
    J.D. phylogenetic analysis of metalloproteins
    to understand how the binding of different metals
    has evolved.
  • Bioinformatics will be an important part of a new
    biochemistry biophysics Superlab course

Haverford College May 2002
10
Conclusions
  • The Faculty Development course structure has been
    very successfully applied in Computing across
    the Sciences (Spring 2001) and Bioinformatics
    (Fall, 2001).
  • Faculty participation has been strong and
    consistent.
  • New research and curricular applications have
    resulted as a consequence.
  • The next installment will be a course next spring
    on Science and Society which we hope will draw
    in faculty from other divisions.

Haverford College May 2002
11
  • Faculty enjoyed the chance to meet and talk
    across disciplinary divisions
  • I felt like learning about different teaching
    styles and different approaches to science was
    the most important thing to come out of this
    experience.

Haverford College May 2002
12
  • Positive outcomes include my understanding of
    bioinformatics, and my appreciation for the use
    of probability and statistics in biology.  I also
    consider the professional relationships forged in
    the lab trying to"BLAST" protein sequences or
    construct SQL queries a positive outcome.
  • I knew absolutely NOTHING about bioinformatics
    prior to the course. I've learned a lot about the
    tools and strategies, and the central problems of
    a whole area of inquiry of which I was ignorant.
    This was a terrific way to get to know colleagues
    in the Biology dept. Our collaboration has
    spawned other discussions about ways that the
    Mathematics dept can serve the Biology major.

Haverford College May 2002
13
  • Mainly, working cohesively with my colleagues
    on bringing bioinformatics into our curriculum.
    It has gotten me to appreciate how we can work
    together as a Department on such goals and to
    articulate the need for expertise in this area
    for the long-term goals of this Department.
  • I wanted to find out what all the fuss was
    about.  I had some general ideas about what
    bioinformatics could do and what tools were out
    there, but I'd only used one or two and I wasn't
    sure how they worked. I realized that the things
    that will be most useful to me are things I'd
    already heard of, but I was glad for the
    increased level of under-standing of the
    bioinoformatic tools. It was great to get
    together with other faculty in working toward a
    common intellectual project.

Haverford College May 2002
14
  • On a more cosmic level, I am now much more
    "available" to offer advice to seniors who are
    thinking about research problems in this area. I
    can imagine it leading to specific mathematical
    projects in the future (for example, studying the
    statistics in Greg and Warren's book).
  • I understand the power of PSI-BLAST a lot more
    now. I would never have thought of this research
    project without the course.

Haverford College May 2002
15
  • Drawbacks
  • Time constraints in working out the examples and
    doing background reading
  • Time constraints in implementing curricular
    development.
  • Requests for more hands-on workshops.
  • More application-driven emphasis to math stats
    (less abstraction).

Haverford College May 2002
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