live interactive learning @ your desktop nsdl/nsta web seminar: computational biology tuesday,...
TRANSCRIPT
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LIVE INTERACTIVE LEARNING @ YOUR DESKTOP
NSDL/NSTA Web Seminar:
Computational Biology
Tuesday, December 11, 2007
6:30 p.m. - 8:00 p.m. Eastern time
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1. Introductions
2. Tech-help info
3. Web Seminar tools
4. Presentation
5. Evaluation
6. Chat with the presenter
Agenda:
http://nsdl.org
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Jeff LaymanTech Support, NSTA
Supporting the NSDL Presenting Team are…
For additional Tech-help call:
Elluminate Support,
1-866-388-8674 (Option 2)
http://nsdl.org
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ScreenshotElluminate Screenshot
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We would like to know more about you…
http://nsdl.org
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How many web seminars have you attended?
A. 1-3
B. 4-5
C. More than 5
D. More than 10
E. This is my first web seminar
Use the letters A-E located at the top left of your actual screen to answer the poll
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Where are you now?
http://nsdl.org
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What grade level do you teach?
A. Elementary School, K-5.
B. Middle School, 6-8.
C. High School, 9-12.
D. I teach undergrad and/or grad students.
E. I am an Informal Educator.
http://nsdl.org
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LIVE INTERACTIVE LEARNING @ YOUR DESKTOP
Tuesday, December 11, 2007
NSDL/NSTA Web Seminar:
Computational Biology
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Dr. Jeff KrauseStaff Computational Biologist and EducatorShodor Foundation, Inc
http://nsdl.org
Today’s NSDL Expert:
http://www.shodor.org http://cserd.nsdl.org http://www.nsta.org
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Agenda
• Introduction
• Background on contemporary
(computational) biology
• Protein structure and molecular motion
• Protein networks and systems biology
• Tools for teaching system thinking
http://nsdl.org
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Stamp all the categories that apply to you. I teach….
Biology Math General Science
Computation/ Programming
None of these
http://nsdl.org
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Introduction: My Neuro-Computational Perspective
http://nsdl.org
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Introduction: My Neuro-Computational Perspective
http://nsdl.org
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Introduction: My Neuro-Computational Perspective
http://nsdl.org
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Introduction: My Neuro-Computational Perspective
http://nsdl.org
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Contemporary Biology: A short history
Biology as a “hard” science
Use reductionism to deal with biological complexity
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Contemporary Biology: A short history
High-throughput biomolecular measurement technologies and the “genomic revolution”
http://nsdl.org
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Contemporary Biology: A short history
http://nsdl.org
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The molecular world is unintuitive to most students (and teachers). How does the molecular world differ from our everyday experience?
Write your ideas on the chat
http://nsdl.org
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The Molecular Literacy Projecthttp://molit.concord.org
http://nsdl.org
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Seeing Real Protein Structure, Function and Dynamics
http://nsdl.org
Typical textbook molecular structure
Molecular dynamics simulation
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The Protein Data Bankhttp://www.rcsb.org/pdb
http://nsdl.org
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Additional Collections for Protein Structure and Dynamics….
Go to the NSDL K-12 page resource list for this seminar
http://nsdl.org
http://nsdl.org/resources_for/k12_teachers
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VMD: Visual Molecular Dynamics
http://ks.uiuc.edu/research/vmdhttp://nsdl.org
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How many of you have seen or used any of these tools before?
A. I haven’t seen or used them before
B. I knew about some of them as research resources
but not educational resources
C. I have used them in class to positive effect
D. I have used them in class but they weren’t helpful
http://nsdl.org
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An Example: Calcium-Induced Structural Change in Calmodulin
Calmodulin was PDB Molecule of the
Month for August 2003
Calmodulin is a molecular switch:
• If no calcium
– Then keep sticky spots closed
• Else, calcium binds
– Then open up the sticky spots
http://nsdl.org
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An Example: Calcium-Induced Structural Change in Calmodulin
http://nsdl.org
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One Role of CaM at the Synapse
http://nsdl.org
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How many calmodulin binding proteins can you name? Stamp your answer:
More than 20 More than 5
At least 1 zzzzzz
http://nsdl.org
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Some of the CaM Targets in the Cell
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From Parts Lists to Systems-Level Understanding
Two tasks:
1. System identification
2. Behavior analysis
http://nsdl.org
How do the parts go together to make the functional system?
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Additional Collections for Major Systems Biology Resources on the Web and Standards Movements in Systems Biology …
Go to the NSDL K-12 page resource list for this seminar
http://nsdl.org
http://nsdl.org/resources_for/k12_teachers
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Which of the following is not one of the “Big 3” cellular networks?
Cell division metabolic
signaling gene-regulatory
http://nsdl.org
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How Big is the Task of Systems Biology?
http://nsdl.org
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How should we prepare students to contribute to, or at least understand post-genomic biology?
http://nsdl.org
Write your ideas on the chat
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Have any of you mentioned systems biology in class? If so, what activities or lessons did you conduct on the topic?
Write your responses
on the chat
http://nsdl.org
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Under Development at Shodor:Dynamic Modeling Workbench
• Analyze time-course data
from a virtual experiment
• Diagram the system
using data
• Build a system diagram
(Vensim model)
• Run the simulation
• Compare results to time-
course data
http://www.shodor.org/~jeffk/dynModWB.html (temporary site)
http://nsdl.org
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Step 1: Analyze Time-Course Data
from a Virtual Experiment in Excel
http://nsdl.org
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Step 2: Diagram the System, and
Create and Run a Vensim Model
http://nsdl.org
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Step 3: Explore and modify the original Agent-Based Model that was used to produce the data
http://nsdl.org
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Agent Sheets allows model building
with a graphical interface, but…
http://nsdl.org
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THANK YOU!
Dr. Jeff [email protected] http://www.shodor.org
http://www.cserd.nsdl.org
Shodor is always looking to work with passionate educators!
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• Download our Seminar Resource List
• Utilize our blog featuring our presenters for the Fall Series sharing their insights on careers in science and science education:
http://expertvoices.nsdl.org/2007fall-nsta-sems/
http://nsdl.org
Go to http://nsdl.org and click on the K-12 audience page to:
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Elluminate logo
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http://learningcenter.nsta.org
NLC screenshot
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National Science Teachers AssociationGerry Wheeler, Executive Director
Frank Owens, Associate Executive Director Conferences and Programs
Al Byers, Assistant Executive Director e-Learning
LIVE INTERACTIVE LEARNING @ YOUR DESKTOP
NSTA Web SeminarsFlavio Mendez, Director
Danielle Troiano, Project CoordinatorJeff Layman, Technical Coordinator
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http://learningcenter.nsta.org
• NASA: Successful Strategies for Involving Parents in Education
December 12, 2007
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Changing Climate System
December 13, 2007