January 2012   Modeling SNPs to Understand Bacterial Evolution

Introduction:  Turning a scientific paper into an open‐ended classroom experience.

Bacterial Evolution  Presentation
EMBL EBI   Link to bioinformatics tools and databases

Paper:   Lieberman, T.D. et al. Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes. Nature Genetics 43:1174‐1176 doi:10.1038/ng.1011

Project I Worksheet
modified ng.977-S2.xlsx
isolates file

Project II Worksheet

Modified burkisolates

ClustalW2 Link to tool

Project III Worksheet

June 11, 2011   Exploratory Data Analysis and Visualization

Introduction:   We will explore the data and discover patterns, reanalyze the data based on results from the accompanying paper to deepen our grasp of statistical analysis, “unpack” the paper to consider how a scientific paper in this discipline is written and how results can be succinctly communicated, and focus on a specific aspect of the paper and develop a poster where the results are visually displayed.

Gapminder www.gapminder.org

Exploratory Data Analysis.pdf


Paper:  Garfinkel, Alan, et. al. “Prognostic Value of Dobutamine Stress Echocardiography in Predicting Cardiac Events in Patients With Known or Suspected Coronary Artery Disease.” Journal of the American College of Cardiology 33(3) (1999) 708‐16.

Introduction to Concepts in Statistics.pdf

Introduction to Concepts in Statistics.docx

March 19, 2011   Cancer: A Global View

Introduction:  Use the topics of cancer and global health and the resource Gapminder to focus on reading graphs and emphasize the differences between linear, semi-log, and log-log views of the data. Use Excel to model tumor growth in order to make predictions based on re-sampling data.

CancerGlobalView pdf

CancerGlobalView doc

Gapminder  http://www.gapminder.org/

Interactive visual statistics with access to global data

Excel Modeling



Links of Interest:

June 12, 2010   Numbers Count:  Using Excel with Gapminder

Introduction:  HHMI Numbers Count Project features data, tools, and curricular materials for use in the classroom to support student observation, experimentation and modeling quantitative exploration.

Interactive visual statistics with global examples

Gap Minder Tables (pdf)

Phenomenological Models and Sustainability using Gapminder (pdf)

Oil Consumption Gapminder Spreadsheet (xls)

Oil Consumption Person Gapminder Spreadsheet (xls)

Population Growth Gapminder Spreadsheet (xls)

Sustainability BioQUEST Spreadsheet (xls)

Total CO2 Emissions Gapminder Spreadsheet (xls)

Total Income Gapminder Spreadsheet (xls)


AAMC-HHMI Report (pdf)

March 5, 2010    Measurement and Error

Introduction:  Discuss measurement and data gathering in the workplace. Could physicians rely on medical data without calibration? Follow-up Excel activity that clearly demonstrates why error control is essential in insuring that data is reliable.


Calibration ppt


Measuring America: How the United States Was Shaped


June 12, 2010  Image J Analysis:  Counting Sheep

Introduction:  Using image data through measurements of distance and area as well as counts.

ImageJ   Image processing and analysis
A Brief Introduction to Using ImageJ.pdf