August 2017

For those who are interested. Here are the slides from the Beanbag Biology workshop from Monday. Please contact Holly Gaff for any questions: hgaff@odu.edu or holly.gaff@gmail.com.

Mentioned in the models and modeling workshop

Visit our website to download the BIOMAAP materials presented at our workshop.  You can also sign up for our monthly email newsletter to find out about upcoming workshops, faculty mentoring networks, and new BIOMAAP materials.

These slides have an overview of what was discussed in the Invitation to Modeling Workshop, with links to resources embedded in presentation and listed below.

• Aikens, M., Dahlquist, K.D., Dauer, J.T., Donovan, S., Eaton, C.D., Highlander, H.C., Jenkins, K.P., Jungck, J.R., LaMar, M.D., Ledder, G., Mayes, R.L., Schugart, R.C. (2017) An Invitation to Modeling:  Building a Community with Shared Explicit Practices, to be submitted to CBE: Life Sciences Education in mid-August, draft available: https://docs.google.com/document/d/168826jQsv5zoNVXKJLaQeWC-VvXyKSB2cF28R1opZmY/edit?usp=sharing
  • Please give us feedback by commenting on this draft!

• Eaton, C.D., Callendar, H.L., Dahlquist, K.D., LaMar, M.D., Ledder, G., Schugart, R.C.  (2016)  A “Rule of Five” Framework for Models and Modeling to Unify Mathematicians and Biologists and Improve Student Learning, submitted on 20 June 2016 to the journal PRIMUS:  Problems, Resources, and Issues in Mathematics Undergraduate Studies https://arxiv.org/abs/1607.02165v2

• Kam and Drew’s Lactase Persistence Activity is based on this article:

  • Morales, E., Azocar, L., Maul, X., Perez, C., Chianale, J., & Miquel, J. F. (2011). The European lactase persistence genotype determines the lactase persistence state and correlates with gastrointestinal symptoms in the Hispanic and Amerindian Chilean population: a case–control and population-based study. BMJ open, 1(1), e000125. http://dx.doi.org/10.1136/bmjopen-2011-000125

• Carrie’s HWE model lesson plan: https://docs.google.com/documen/d/1Re58_Gs1SMEEPhXUwcvgblpHG2mC6LT0vzhigjtPBoA/edit

  • PopGen: http://www.radford.edu/~rsheehy/Gen_flash/popgen/

• Glenn’s Resource-limited Population Growth materials: https://qubeshub.org/collections/post/3101

• HHMI Biointeractive modules on Lactase and Amylase

Invitation to Modeling draft paper

Rule of Five paper

Lactase persistence paper

Evolutionary forces with HWE

Evolutionary forces with HWE

PopGen software

Resource-limited growth

Slides takes you to the HTML presentation.  Many, if not all, images are clickable.

Slides

Slides on GitHub

DataCamp Group (FREE)

QUBES Software

Jupyter Notebooks

R/RStudio

Serenity

Most students have seen an exponential model for population growth and know that it predicts unlimited growth. Better models, such as the logistic growth model, should incorporate assumptions to account for limitation of resources. In this activity, participants collect data from a physical simulation of resource-limited growth, prepare a variety of graphs to visualize the data, construct a verbal model based on their observations and the graphs, and (for those who want to go this far) construct a symbolic model from the verbal model.

Presentation describing how the Double Helical model of DNA was determined and how it has helped us understand various biological processes and also design new molecules.

A collections of Video tutorials for using UCSF Chimera for:

1: Loading PDB coordinates into the software, manipulating the structure in 3D, and saving session.

2: Menus

3: Selecting parts of a protein structure

4: Analyzing and exploring a protein structure

5: Comparing the structures of two related proteins/domains and visualizing the superposed structures of these proteins/domains.

This file guides you to use UCSF Chimera to explore the structures of substrate-DNA and product-DNA bound complexes with a restriction enzyme.

Instructions for preparing your computer for visualizing and exploring structures from the Protein Data Bank

The central theme of this workshop is exploring the molecular basis of insecticide resistance in a case study approach that enforces a conceptual understanding of a variety of topics in the context of preventing the spread of Zika virus. The interactive models used in this workshop can be borrowed from the MSOE Model Lending Library or purchased from 3D Molecular Designs. I've included "briefs" that describe activities associated with a wide range of models that lay the conceptual foundation for the case study, as well as case study files (which are numbered). More information about using various models can be found at the 3D Molecular Designs website under Teaching Resources.

Materials include:
Avida-ED Lab Book; Homepage; Direct program link; YouTube intro video; Evolution Education and Outreach journal article on this curriculum; and a shortened link to a Google Drive repository containing Google Docs versions of the Introduction, Exercises 1-4, the Independent Research assignment and other activities/resources.

Markdown workflow in R (PDF)

A quick reference guide to markdown. 

swirl teaches you R programming and data science interactively, at your own pace, and right in the R console!

For teachers:

swirl is a platform for teaching R programming and data science. However, an educational platform is only as good as the content it delivers to students. Although we have contributed some content ourselves, swirl is designed in such a way that you can create your own interactive content and share it freely with students in your classroom or around the world.

"This is a great source for basic R functionality like importing and manipulating data.  It also has very helpful information on making graphs (see this page). "

Excel workbooks, PowerPoint presentation, and (partial) list of resources on stochastic modeling.

Most students have seen an exponential model for population growth and know that it predicts unlimited growth. Better models, such as the logistic growth model, should incorporate assumptions to account for limitation of resources. In this activity, participants collect data from a physical simulation of resource-limited growth, prepare a variety of graphs to visualize the data, construct a verbal model based on their observations and the graphs, and (for those who want to go this far) construct a symbolic model from the verbal model.