PEER 2011

Use these links to jump to sections of the schedule:

Go To a Day: Wednesday | Thursday | Friday | Saturday

Go To an Activity: Online Research | Excel Modeling | Image Analysis | Protein Structure | Other Tools | Final Projects

All workshop sessions will be held in Room 136 of the Haslam Business Building.

9:00-9:15 Welcome

Cynthia Peterson, PEER

9:15-9:45 Cyberlearning in Higher Education

Sam Donovan, University of Pittsburgh

• Cyberlearning Survey – this has some questions about teaching which may not fit for you. However, it would be helpful if you would complete the short survey so we can learn a bit about your background.

• Launch page – In this session we will be getting some hands-on experience with online, collaborative productivity tools that every graduate student should know about.

10:45-11:00 Break 11:00-12:30 Online Resource Management Tools (part 2)

• Launch page – We will continue the session and share our work.

Here’s what we have accomplished:

12:30-1:30 Lunch

Gretchen A. Koch, Goucher College

Resources

• Num3er5 Count
• Gapminder
• Gapminder Breast Cancer Video
• Gapminder Lung Cancer Video
• WolframAlpha
• World Health Organization (WHO): Cancer
• Centers for Disease Control and Prevention (CDC):  Cancer

Materials

• Cancer Global View Lab (PDF)
• Cancer Tumor Kinetics Lab (PDF)
• Excel Data Sheet
• Friberg 1997 Article
• Cancer: Global View PowerPoint
• Cancer Tumor Kinetics PowerPoint
• Excel Data Sheet with Graphs and Complete Calculations

3:00-3:15 Break 3:15-4:30 Modeling Cancer Growth (part 2)

Here’s what we have accomplished – Gapminder:

Here’s what we have accomplished – Cancer Modeling:

4:30-5:00 Wrap up blog posts for the day

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8:30-9:00 Breakfast 9:00-10:45 Data from Images: Image J

Ethel Stanley, BioQUEST Curriculum Consortium

Using-ImageJ-UTK2011

• Tree Rings:  
  • Sheep

• ImageJ To Analyze Graphs
• Visualization in Singapore
  • article in the economist
  • video examples

Here’s what we have accomplished:

10:45-11:00 Break 11:00-12:00 Invited Talk

Dr. Jerome Baudry. Assistant Professor Biochemistry and Cellular and Molecular Biology

 

• Title: Computational drug discovery: a cocktail of biology, physics, computer sciences and chemistry

12:30-1:30 Lunch 1:30-3:00

Stephen Everse, University of Vermont

This afternoon we will be exploring protein structures (some background on proteins, folding, and structural biology techniques can be found here)–  we’ll examine where they live, what we can learn from them, how we can view them, how to make journal quality images, and how to contribute back to the community. Here’s a list of links that we will be making use of:

• Protein Database
• PyMOL

• Proteopedia – http://www.proteopedia.org
• Conserf Server – http://consurftest.tau.ac.il/
• Molecule of the Month – http://www.pdb.org/pdb/explore/motm.do

Some PyMOL tutorials that might be handy:

• Introduction to PyMOL (PDF)
• PyMOL tutorial (MS Word)
• Using PyMOL (PDF)
• PyMOL Tutorial (PDF)
• PyMOL Laboratory #1
• PyMOL Laboratory #2

So your first assignment I’d like you to generate an image of any protein. We will be blogging about it — please make sure you describe your protein and what you did to display it. Please use some descriptive tags (3 to 5) and click on the Structural Projects #1 category so that it displays on the right page!

Here’s what we have accomplished:

3:00-3:15 Break 3:15-4:30 Molecular Visualization (part2)

Here’s what we have accomplished:

4:15-4:45 Blogging

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8:30-9:00 Breakfast 9:00-Noon  

• Thoughtful Integrating of  Videos in the Classroom
  • Inner Life of the Cell
  • Bad Project
  • Large Hadron Rap
  • A biologists St Patty’s Song
  • Powering the Cell: Mitochondria
  • BioRAD PCR Song
  

• Tree Thinking – Sam Donovan
  • Tree Thinking Paper – Baum et al
  • Tree Thinking PowerPoint

• Wordle – Ethel Stanley
• CMap Tools
  • The Theory Underlying Concept Maps
  • Pollen Concept Map

 

• Social Networking – draft

• WolframAlpha
• Khan Academy

Here’s what we have accomplished:

Introduction to projects:

The primary goal of the group project is to help you connect what we have done during the workshop with your future as a graduate student. This could include using some of the tools that have been introduced, pushing your own thinking about your interests, exploring data resources, analysis tools and literature in your research area. We would like you to work in groups of 2 or 3 for several reasons. First, it will allow you to build a stronger working relationship with a colleague. Secondly, by collaborating with someone we hope you will get a chance to gain insights and resources from other disciplines.

We have set aside 2.5 hours this afternoon for you to work. You will have a chance to share your project Saturday morning. Please post your project material and tag them as “project”.

As with most independent work identifying a suitable project and negotiating how to share it with your collaborators is probably the most difficult step. Think creatively about what will be useful for you down the line.

Noon-1:30 Lunch

1:30-2:30 Invited Talk

Dr. Lynne Parker. Professor and Associate Head, Dept. of Electrical Engineering & Computer Science

Title: Overview of Research in the UTK Center for Intelligent Systems and Machine Learning

2:45-4:30 Problem Space Collaboration Discussion and Work Session

4:30-5:00 Project Groups Checkin

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8:30-9:00 Breakfast 9:00-11:00 Group Work Presentations and Survey

• Shalanda & Raphael – Comparison between HIV & SIV
• Stefan & Mauricio – Drug Delivery
• Pawel & Tara – Phylogenetics
• Jessica, Ann & Sara – Transportation
• Joanna & Anna – Lucky: Canine Parovirus Type 2
• Thomas, Steven & Rachel – Automated Research Assistant
• Jennifer, Kate & Anastasia – What is luciferase?
• Kyle, Ben & Thomas – Walk the line: Kinesin

Final Survey – Thanks!

Here are our projects: