“Using Data in Undergraduate Science Classrooms” by the Science Education Resource Center (SERC) at Carleton College provides information and discussion for educators and resource developers interested in effective teaching methods and pedagogical approaches for using data in the classroom.

The National Academy of Sciences call in BIO2010 has led to the creative energy behind many new innovations in curriculum in mathematics courses, life sciences courses and interdisciplinary courses. The University of Arizona hosted a conference in June, 2012 “Making Biomath Happen” which includes online resources.

We will be looking at the use of problem spaces as a pedagogical strategy for introducing data, tools, and inquiry in the classroom. You may want to explore the Plasmodium Problem Space.

MathBench Biology Modules developed at the University of Maryland introduce students to the mathematical underpinnings of what they learn in introductory biology courses. Their goal is to integrate quantitative approaches and mathematics more deeply into the undergraduate curriculum in a way that (1) reinforces biological concepts, (2) increases math literacy, and (3) prepares students for more complicated mathematical approaches in upper-level courses.

The Numbers Count Project from the University of Minnesota – Rochester was initially funded by HHMI and focuses on biological problem solving.  Faculty workshop and classroom resources include biological data (Excel files, images, and FASTA format text files), introductory mathematical modules for biology and chemistry, concepts in statistics mapped to individual modules, our workshop resources (materials, tools, data, powerpoints, and participant products), course materials for Calculus and Freshman Statistics, and links to sites focusing on datamodeling tools, and visualization.

 

Links from the QB and BQ participants:

John R Jungck:

Mapping with Excel Data:  http://m.wikihow.com/Create-a-Google-Map-With-Excel-Data-and-Fusion-Tables

 

Pat Marsteller:

An International Look at Women’s Cancers via GapMinder | SeventyK
www.seventyk.org › Blog
Aug 24, 2011 – GapMinder is a nonprofit based out of Sweden and was acquired by … death rate in developing countries (here an HPV vaccine would be most …

HPV – Get Satisfaction
getsatisfaction.com/gapminder/topics/hpv
A description for this result is not available because of this site’s robots.txt –learn more.

Gapminder: Hans Rosling illustrates the relationship between wealth…
saveone.net/Gapminder-Hans-Rosling-illustrates-the-relationship-betwee…
Factsheet: Human Papillomavirus (HPV) ….. Gapminder: Hans Rosling illustrates the relationship between wealth and life expectancy Take Action.

Review: Gapminder Makes Statistics Fun | BlogHer
www.blogher.com › Home › Web site
Oct 21, 2010 – HPV & Our Sons: Why I’m Vaccinating My Boys ….Gapminder describes itself as “unveiling the beauty of statistics for a fact based world view.

WinCollGeog: Ageing populations – features Gapminderfounder …
wincollgeog.blogspot.com/…/ageing-populations-features-gapminder.ht…
Mar 2, 2013 – Ageing populations – features Gapminder founder Hans Rosling! Forum: The Challenge of … HPV vaccine for schoolboys? Powered by Blogger.
Breast Cancer Statistics
Breast Cancer increases with income, but so does the chances of saving women with cancer.

Herd Immunity

Evidence of Herd Immunity After Introduction of HPVVaccine …

lowrysurgery.com › Health Information

Lowry Surgery Center · Lowry Surgery Center … Significant drop in vaccine-type HPV in vaccinated, unvaccinated women. MONDAY, July 9 (HealthDay News) …How Herd Immunity Works (and Why Anti-Vaccination Is Dangerous …

www.youtube.com/watch?v=f-cKzzPkz2o

Sep 5, 2010 – Uploaded by Shane Killian

How Herd Immunity Works (and Why Anti-Vaccination Is Dangerous) … ofherd immunity. The simulation …

More videos for herd immunity simulator »

Herd Immunity Simulator – Software3D

www.software3d.com/Home/Vax/Immunity.php

Herd Immunity Simulator. written by Shane Killian modified by Robert Webb. * – Vaccinated cell * – Unvaccinated cell * – Infected cell. Click on a cell below to …

Herd Immunity Demo | MetaFilter

www.metafilter.com/124790/HerdImmunity-Demo

Feb 8, 2013 – Reminds me of the classic Zombie Simulator, which is like this but with … If they can grasp the concept of herd immunity (theoretically) they can …

How Herd Immunity Works (includes a great simulation) – Skeptics …

sguforums.com › General Discussions › Skepticism / Science Talk

Jan 19, 2011 – 14 posts – 8 authors

How Herd Immunity Works (includes a great simulation)

Simulation analysis of the effect of herd immunity and age structure …

www.ncbi.nlm.nih.gov/pubmed/9234438

by MP Ward – 1997 – Cited by 7 – Related articles

Prev Vet Med. 1997 Feb;29(4):299-309. Simulation analysis of the effect of herd immunity and age structure on infection of a cattle herd with bluetongue viruses …

Calculating Risks

Tutorial for R | Memorial Sloan-Kettering Cancer Center

www.mskcc.org/research/epidemiology-biostatistics/health…/tutorial-r

tutorial for running decision curve analysis using R (download PDF) takes the … of published models; application to censored data, including competing risk.

Decision Curve Analysis – Memorial Sloan-Kettering CancerCenter

www.mskcc.org/research/epidemiology…/decision-curve-analysis-0

Decision curve analysis is a simple method for evaluating prediction models, diagnostic tests, … Using relative utility curves to evaluate risk prediction. …Tutorials are available for both Stata and R. The tutorials include data sets, code and an …

NHANES Analysis Web Tutorials – Risk Factor Monitoring & Methods …

riskfactor.cancer.gov/tools/nhanes_tutorial.html

May 17, 2012 – NHANES Analysis Web Tutorials. Data from the National Health and Nutrition Examination Surveys (NHANES) have provided unique …

A note on competing risks in survival data analysis

www.ncbi.nlm.nih.gov › Journal List › Br J Cancer › v.91(7); Oct 4, 2004

by JM Satagopan – 2004 – Cited by 234 – Related articles

Oct 4, 2004 – A note on competing risks in survival data analysis … A patient who dies of breast cancer during the study period would be considered to have….. 2003b) provide a detailed tutorial review of various survival analysisconcepts, …

GenePattern: Tutorial – Broad Institute

www.broadinstitute.org/cancer/software/genepattern/tutorial/gp_tutorial

Cancer Program ©2006-2013 … The GenePattern Tutorial introduces you to GenePattern by providing step-by-step instructions for analyzing gene expression. It takes … The server must have the following GenePattern analysismodules installed: …. If the security message appears, accept the risk and click Run to continue.

RAIS Main Tutorial – The Risk Assessment Information System

rais.ornl.gov/tutorials/tutorial.html

This tutorial is designed to assist the user in understanding and applying available RAIS tools to the risk assessment process. Using the tutorial, the user is …

White Papers: Risk & Decision Analysis, Monte Carlo Simulation …

www.palisade.com/articles/whitepapers.asp

For over twenty years, the use of Monte Carlo simulation to analyze risk in project cost …. Monte Carlo simulation is used to evaluate the risk of cancerafter radiation exposure …. The Use of Video Tutorials in a Mathematical Modeling Course

the tutorial on prostate pathology.

library.med.utah.edu/WebPath/TUTORIAL/…/PROSTATE.html

Return to the tutorial menu. …. Men at higher risk for prostate cancer at earlier ages, including men of African American ancestry or a family history of prostate …

[PDF]

Survival Analysis Part I: Basic concepts and first analyses – slaop

www.slaopweb.org/pdf/MBOncology/Journ7.pdf

by TG Clark – 2003 – Cited by 156 – Related articles

Tutorial Paper. Survival … In many cancer studies, the main outcome under assessment is the  (instantaneous) risk of death appears to be high in the…

Amylase Problem Space

http://en.wikipedia.org/wiki/Sequence_alignment

Lab 10: Constructing an Amylase Evolutionary Tree

biologywithsaxe.blogspot.com/…/constructing-amylaseevolutionarytree

Feb 11, 2009 – In this lab you will be constructing an evolutionary tree by comparing amino acid sequences in amylase. The biggest thing to remember in this ..

Close evolutionary relatedness of alpha-amylases from Archaea …

www.ncbi.nlm.nih.gov/pubmed/10079280

by S Janecek – 1999 – Cited by 44 – Related articles

Since the results for alpha-amylases belonging to all three domains (Eucarya, Eubacteria, Archaea) offered by both evolutionary trees are very similar, it is …

Phylogeny and the evolution of the Amylase multigenes in the …

www.ncbi.nlm.nih.gov/pubmed/12574858

by Z Zhang – 2003 – Cited by 15 – Related articles

Phylogeny and the evolution of the Amylase multigenes in the Drosophila montium species … On our tree the sequences of the auraria, kikkawai, and jambulina …

Diversity and evolution of the α-amylase genes in animals – Biologia …

biologia.savba.sk/Suppl_11/Dalage.pdf

by JL Da Lage – Cited by 15 – Related articles

amylase tree and a reliable phylogenetic tree are good indications of peculiar evolutionary histories in the relevant lineages, or divergence between par-.

Sequence similarities and evolutionary relationships of microbial …

imb.savba.sk/~janecek/Papers/PDF/EJB_94.pdf

by S JANECEK – 1994 – Cited by 78 – Related articles

conserved regions. These sequence regions were examined from structure/function and evolutionary perspectives. An unrooted evolutionary treeof a-amylases …

Thermostable α-amylase from moderately halophilic Halomonas sp …

journals.tubitak.gov.tr/biology/issues/biy-12…/biy-36-3-11-1106-7.pdf

by KS UZYOL – 2012 – Cited by 1 – Related articles

The phylogenetic tree constructed using the maximum-parsimony method showed essentially the same relations (Figure 2). α-Amylase production. Time profiles ..Close evolutionary relatedness of α-amylases from archaea and …

www.academia.edu/…/Close_evolutionary_relatedness_of_-amylases_fro…

Jan 1, 1999 – Since the results for –amylases belonging to all three domains (Eucarya, Eubacteria, Archaea) offered by both evolutionary trees are very …

Evolution of α-Amylases: Architectural Features and Key Residues …

mbe.oxfordjournals.org/content/18/1/38.full

by G Pujadas – 2001 – Cited by 38 – Related articles

α-Amylase (AAMY) (EC 3.2.1.1; 1,4-α-d-glucan glucanohydrolase) is an enzyme ….. There is some scattered clustering in the unrooted evolutionary tree

PDF(491K) – Wiley Online Library

 onlinelibrary.wiley.com/doi/10.1046/j.1432-1033.2003.03404.x/pdf

by Š Janeček – 2003 – Cited by 71 – Related articles

starch-binding domain; evolutionary tree; domain evolution. The a-amylasefamily (glycoside hydrolase family 13, with close relatives in families 70 and 77) …

Sequence Similarities and Evolutionary Relationships of Microbial …

onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.1994.00519.x/pdf

by Š Janeček – 1994 – Cited by 78 – Related articles

conserved regions. These sequence regions were examined from structure/function and evolutionary perspectives. An unrooted evolutionary tree of a-amylases …

Relation between domain evolution, specificity, and taxonomy of the …

onlinelibrary.wiley.com › … › Vol 270 Issue 4

by Š Janeček – 2003 – Cited by 71 – Related articles

Jan 24, 2003 – α-amylase family;; glycoside hydrolase family 13;; starch-binding domain;; evolutionary tree;; domain evolution. The α-amylase family …

Close evolutionary relatedness of alpha-amylases from Archaea …

www.researchgate.net/…/13212241_Close_evolutionary_relatedness_of_al…

Since the results for alpha-amylases belonging to all three domains (Eucarya, Eubacteria, Archaea) offered by both evolutionary trees are very similar

molecular biology webpage – Biology @ Davidson – Davidson College

www.bio.davidson.edu/Courses/Molbio/MolStudents/…/orthologs.html

With this knowledge of the sequence similarities in α-amylases, Janecek (1994) was able to create an evolutionary tree for all the different α-amylases.

Parallel β/α-barrels of α-amylase, cyclodextrin glycosyltransferase …

www.sciencedirect.com/science/article/pii/0014579394010196

by Š Janeček – 1994 – Cited by 47 – Related articles

The structures of functionally related β/α-barrel starch hydrolases, α-amylase, …They enable one to construct a phylogenetic tree common for the whole AMY …

Amylase Gene Structures in Primates – Molecular Biology and …

mbe.library.arizona.edu/data/1996/1306/5samu.pdf

by LC Samuelson – Cited by 35 – Related articles

Department of Physiology, University of Michigan. Amylase transcription in the human salivary gland results from the evolutionary juxtaposition of two inserted.

Classification and evolution of a-amylase genes in plants

www.pnas.org/content/89/16/7526.full.pdf

by N Huang – 1992 – Cited by 71 – Related articles

Because KS values for monocot/dicot a-amylase genes were not available (Table 1), KA values were used to con- struct the phylogenetic tree shown in Fig. 1.