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Title: Funding Opportunities
at the National Science Foundation and Tips for Writing
Successful Proposals
Presenter: V.
Celeste Carter, Ph.D., Biotechnology and Bioinformatics
Program Director Division of Biological and Health Sciences,
Foothill College, CA
Description:
Dr. Carter will talk about her experience as a program officer
at the National Science Foundation and describe the NSF's
programs for funding educational activities and curriculum
development. The workshop will include information about
applying for funding and the important points to consider.
Presentation:
Funding
Opportunities at the National Science Foundation and Tips
for Writing Successful Proposals (.ppt, 1.7 Mb)
Title: OnLine Bio-Databases & Bioinformatics
Tools for the Educator
Presenter: Christopher Smith, Ph.D., Program
Manager, Integrative BioSciences / Integrative Computational
Sciences, San Diego Supercomputer Center, University of
California San Diego, CA
Description:
An overview of the plethora of biology-related databases
and bioinformatics tools will be presented, as well as web
portals and guides that provide educator-friendly interfaces
to the plethora of resources. The focus of this workshop
will be a presentation on and hands-on activity detailing
how these tools have been integrated into laboratory/classroom
activities.
CMSMolecular Biology Resource: http://restools.sdsc.edu
CMSMBR Discovery Tools: http://restools.sdsc.edu/discovery_tools/discovery_tools.html
Using Internet Resources in Molecular Biology:
http://www.sdsc.edu/pb/edu/pharm207/7/7.html
Presentation:
Online
Databases and Bioinformatics Tools for the Educator (.ppt,
2.1 Mb)
Title:
Analysis of Microarray Data in the Classroom
Presenter: Laurie Heyer, Ph.D., Department
of Mathematics Davidson College, Davidson, NC
Description:
Dr. Heyer will lead participants through the process of
analyzing microarray data using MAGIC Tool, a program developed
in her laboratory. MAGIC Tool is described in more detail
at http://www.bio.davidson.edu/magic
Title: Bioinformatics
resources at Geospiza and the Dolan DNA Learning Center
at Cold Spring
Harbor Laboratory
Presenters: Linnea
Fletcher, Ph.D., Bio-Link
Regional Director, and Biotechnology Program Director,
Austin Community College, Austin, TX
Description:
Computers have become a standard piece of equipment in modern
biology labs. We use them to control laboratory equipment;
to gather, store and analyze data; and to share our results
with others over the Internet. Now, with a wealth of data
from genome and proteome projects, students can do hypothesis-driven
and discovery-based research, as well. Some of the most
widely used bioinformatics tools have been those that allow
biologists to search literature, compare biological sequences,
and visualize the organization of genes and introns and
models of three-dimensional structures.
Dr. Linnea Fletcher has investigated and used a wide variety
of materials that are available for instructors who wish
to use bioinformatics in their classes. These include the
Green Arrow® Tutorials
(Geospiza, Inc.), DNA
interactive (Cold Spring Harbor Laboratories), the Biology
Student Workbench, and others. In this workshop, Linnea
Fletcher will provide an overview of existing materials
and illustrate how she uses bioinformatics in several courses
in her biotechnology program.
Presentation:
Green Arrow Tutorials http://www.geospiza.com/outreach
DNA interactive http://www.dnai.org
Biology Student Workbench http://peptide.ncsa.uiuc.edu
Title:
NCBI WWW Genome Resources in the Biology Curriculum
Presenter: Peter Cooper, Ph.D., National
Center for Biotechnology Information
Description:
Molecular databases and analysis tools available on the
World Wide Web are now invaluable resources for biological
research. Familiarity with these resources is expected
for all working in the biological sciences. Undergraduate
students in biology therefore should receive as much experience
as possible in the use of these online resources. Moreover,
the availability of, well-annotated, complete mammalian
genomes provides a rich area for exploration and valuable
learning experiences that can be used to enhance and reinforce
the key concepts in a wide variety of undergraduate life
science settings.
This tutorial will provide participants with instructor-led
hands-on practice using the molecular biology databases
and tools available at the National Center for Biotechnology
Information. Participants will gain experience using
worked examples designed to be easily incorporated
into undergraduate
courses. The focus will be on complete genomes and emphasize
the integration of various types of data, including literature,
sequence and structure, and analysis tools, including
the NCBI BLAST services.
Presentation:
NCBI
Resources in Bioinformatics Education (.ppt, 8.9 Mb)
NCBI
Resources in Bioinformatics Education (.pdf, 2 Mb)
NCBI
Handout and Problem Set (.pdf, 3 Mb)
Title:
BEDROCK
Presenter: Sam
Donovan, Ph.D., BEDROCK, BioQUEST Curriculum
Consortium, University of Pittsburgh, Department of Instruction
and Learning, Pittsburgh, PA
Description:
The National Science Foundation funded BEDROCK initiative
(Bioinformatics
Education Dissemination: Reaching Out,
Connecting and Knitting-together) is a new BioQUEST project
with the goal of enhancing, expanding, and empowering a
national community of bioinformatics educators.
Presentation:
http://bioquest.org/bedrock
Title:
Exploring DNA Land with Regular Expressions
Presenter: Mark
LeBlanc, Ph.D., Computer
Science, and Betsey
Dyer, Ph.D., Department
of Biology; Wheaton College, Norton, MA
Description:
We have developed a set of lab exercises to teach students
to write
regular expressions (RegEx) useful in searching files of
DNA
sequences. Our central theme is "word play".
Students visualize
the results of their searches by applying regular expressions
to
both English word lists and DNA motif lists.
We have found that the enjoyment of
seeing patterns in words (and in motifs) is an excellent
motivator
for learning RegEx syntax and using it for creative exploration.
Participants in this workshop will quickly learn some basic
RegEx
rules and will use them to seek interesting words and motifs.
Presentation:
Regular
Expression Lab (.pdf, 412 kb)
Title: Phylogenetics
in the Classroom
Presenter: Stuart Brown, Ph.D., Research
Computing Resource, NYU School of Medicine, NY, NY
Description:
This workshop will contain both a lecture and practical
exercises
so that attendees will become familiar with both
the theory and practical aspects of building phylogenetic
trees from molecular sequence data. First we will look at the history of taxonomic
classification and the theoretical basis of grouping organisms by the number
of shared characters (cladistics). Then we will examine the relationship between
sequence alignment, clustering, and the various phylogentic algorithms (simple
similarity, neighbor joining, parsimony, and maximum likelihood). Finally, we
will look at a range of phylogenetics computer software that is available
for free download and on the Web.
Presentation:
Phylogeny
workshop powerpoint slides (.ppt, 564 kb)
Phylogeny
workshop web page
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