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NSF grant writing advice

Some solid advice on how to write a successful NSF grant.

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Chapter on fitting various linear and nonlinear regression models using R

Assumes basic familiarity with regression modeling and quickly goes through a bunch of different types of models with sample R code to fit them on some sample datasets.

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Colin Reimer Dawson onto Computing Tools (R)

Class Notes

I use this template often for class notes.  It prioritizes margin space with margin notes and I think it promotes using the notes in a more "engaging" way.

https://www.ctan.org/pkg/tufte-latex?lang=en

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Benjamin R Morin onto Writing & Presentation Tips

Do Your Students Take Good Notes?

A blog post from Chronicles of Higher Ed with links to three other note-taking guides. The third link includes the following tips:

  • Identify key concepts in the day’s lesson: “Now here’s something you need to have in your notes. Listen carefully.”
  • Challenge students to retrieve things from their notes: “Look at your notes from November 5. What have you got about X? Nothing? That’s not good.”
  • Provide a definition, pause, and give students one minute to rewrite it in their own words. Ask students why it might be important to do so.
  • At the beginning of the period, give students three minutes to review their notes and summarize them in a sentence. Have several students share their summary, which the class then compares, revises, etc.
  • At the end of class have students trade notes with somebody sitting near them and use their partner’s notes to review the class session. Ask them to identify what was the same and different about their notes and those of their partner?
  • For frequently missed exam questions, have everyone find the date when that content was covered and see what they have in their notes that relates to the question. Ask someone who got the question correct to read what they have in their notes.
  • Tell students that any notes they take in class today can be used when they take the quiz tomorrow. Follow-up at the end of class by asking how that changed listening and note-taking.

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May Mei onto Writing & Presentation Tips

The Pen Is Mightier Than the Keyboard: Advantages of Longhand Over Laptop Note Taking

Article on difference between taking notes by hand vs on a computer.

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May Mei onto Writing & Presentation Tips

NSF DMS Math Bio Grants

Main information page for applying for math bio grants from NSF DMS. Be aware that you can apply to this program on a special RUI (Research at Undergraduate Institutions) track.

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NSF DMS Applied Mathematics Grants

Main information page for applying for applied math grants from NSF DMS. Be aware that you can apply to this program on a special RUI (Research at Undergraduate Institutions) track.

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Diversity and Inclusion in STEM

This is from Sarah Blunt, Katie Hsia, Alicia Rocha, and Doug Shea, from work they did in Bjorn Sandstede's class at Brown University, shared by Chad Topaz.

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Carrie Diaz Eaton onto Diversity and Inclusion

Adventures in Academic Year Research

An article in the Notices by Kathryn Leonard (then at Cal State Channel Islands) where she reflects on her undergraduate research experience.  Includes good tips and links to other resources.

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Tips for being a good mathematical audience member

This is a handout I use for my classes for how to listen to a mathematical presentation. It has how to dialogue with yourself and what questions that could lead you to ask a speaker.

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May Mei onto Writing & Presentation Tips

What Makes An Expert?

What the Best College Students Do
(http://www.hup.harvard.edu/catalog.php?isbn=9780674066649)

This is the second chapter from this book - this talks about deep learning vs shallow learning and the way in which motivation affects the way information is encoded. Disclaimer: This reading made my students mad.

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May Mei onto Pedagogical Readings

How Learning Works

How Learning Works: Seven Research-Based Principles for Smart Teaching
(http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470484101.html)

Great book - highly recommended! But I give the following summary of the principles from the book to my students to read.

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May Mei onto Pedagogical Readings

Pre- and Post-calculus modeling: workshop

Notes for teaching a lower-level modeling course

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GAIMME report

Great K-16 resource for mathematical modeling

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Solving DEs in R (ODE, PDE, DAE, BVP)

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Erica Graham onto Computing Tools (R)

Is this the end for Facebook...

This is a cool paper for modeling that I think students could recreate and have a great discussion about.  You don't really need a lot of background per se to understand the application area because students can use a lot of their own knowledge about social media.  There are also a lot of options to make extensions.

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Guidelines for projects

These were guidelines for a major project done as a team in an upper division modeling course

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Ami Radunskaya onto Mathematical modeling course

Module for Solve ODEs in R

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Erica Graham onto Computing Tools (R)

Article Reading Assignments

Reading questions for students to consider/answer as they read through math modeling papers. This document is constructed with the idea that a student will read the paper (or portions of the paper) in several passes. The grouping of the questions in Step 1, Step 2, etc., break the questions down into what students might consider in a first pass, a second pass, etc. with an eye towards the student developing a rubric for what makes a well written math modeling paper.

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Harvard Implicit Bias Test

The most well-known test for detecting implicit bias (which we all have!). Taking this test can be an eye-opening experience for faculty and students.

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Chad Topaz onto Diversity and Inclusion

Research Log Template

Template for research log that I use with my research students. Template contains definition of new commands in TeX for goals, log entries, meeting notes, and reflections. I have students maintain this file in a shared folder while they are doing research. My research students are expected to make goals for each week, a log entry for each day they work on their research project, and a reflection entry at the end of each week.

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Requests for New Modules

Place a comment in order to request new modules.

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Benjamin R Morin onto Computing Tools (R)

Guidelines for publishing papers containing theory and modeling

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Blerta Shtylla onto Writing & Presentation Tips

Requests for New Modules

Comment on this in order to request new modules.

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Benjamin R Morin onto Computing tools (MATLAB)

Association for Women in Mathematics

AWM has the opportunity for chapters.  It was also recently awarded a grant to renovate their site, so look for a new link soon!

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Carrie Diaz Eaton onto Diversity and Inclusion

Module on Solving ODEs in MATLAB

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Nessy Tania onto Computing tools (MATLAB)

Open community group for biocalculus

Open community group for calculus designed for biology, life science, and/or environmental science majors.

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Council for Undergraduate Research

A society committed to supporting undergraduate research

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Ten Simple Rules to Make the Most Out of Your Undergraduate Research Career

A good article to have research students read when they start doing research with you.

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Running undergraduate research groups

Presentation by Chad Topaz

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A guide to the R package manager

How to extend the functionality of R by installing and loading "packages"

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Colin Reimer Dawson onto Computing Tools (R)

Funding for applied math undergraduate student research

Presentation by Chad Topaz

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Tutorial on the curve fitting tool (CFTool)

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Julie Blackwood onto Computing tools (MATLAB)

Some plotting information

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Julie Blackwood onto Computing tools (MATLAB)

Overview of some ode solvers in MATLAB, including stiff solver

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Julie Blackwood onto Computing tools (MATLAB)

SACNAS

Society for the Advancement of Chicanos and Native Americans in Science

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Carrie Diaz Eaton onto Diversity and Inclusion

Common R Commands ("Cheat Sheet") --- based on `mosaic` package

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Colin Reimer Dawson onto Computing Tools (R)

Modeling team group contract

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Tutorial for numerical solutions of ODEs + supporting code

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Julie Blackwood onto Computing tools (MATLAB)

MATLAB intro with more ODEs, some optimization

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Julie Blackwood onto Computing tools (MATLAB)

The R Graphics Cookbook

"Recipes" for data visualization in R using the ggplot2 package

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Colin Reimer Dawson onto Computing Tools (R)

Erin Bodine's webpage: MATLAB & LaTeX tutorials

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Julie Blackwood onto Computing tools (MATLAB)

A Student's Guide to R (Simplified R for Data Analysis via Project MOSAIC)

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Colin Reimer Dawson onto Computing Tools (R)

A more detailed MATLAB intro (definitions, matrices, linear algebra, etc)

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Julie Blackwood onto Computing tools (MATLAB)

Crash Course in Basic Stats via R (DataCamp)

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Colin Reimer Dawson onto Computing Tools (R)

Machine Learning Basics in R

Introduction to basic machine learning ideas through a guided R-based tutorial (via DataCamp).

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Colin Reimer Dawson onto Computing Tools (R)

Swirl interactive tutorial to learn R programming

Instructions to download and install R and RStudio, and run an interactive tutorial within the R console.

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Colin Reimer Dawson onto Computing Tools (R)

A short intro to MATLAB (vectors, loops, an ODE script)

Written for a mathematical ecology course at Williams. Some of it is Williams-specific, but can be modified accordingly.

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Julie Blackwood onto Computing tools (MATLAB)

Chad Topaz's modeling-without-a-textbook course

Talk given at the SIAM Annual Meeting, 2016

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Chad Topaz onto Mathematical modeling course

Team Member Evaluation Rubric

We developed these team member evaluations for a summer research program where we had teams of mathematicians and biologists.  I'm not sure they were that useful after the research was done, but it might be more useful as a way to discuss what we expect from our team members.

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Research team organization

This was written for project teams in a modeling class, but it can be modified for a longer research project.

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Mathematical Writing

So this is the chapter on contrapositive proof from Book of Proof by Richard Hammack. But I'm linking this because section 5.3 is about guidelines for mathematical writing - it's more proof-y but still many applicable things.

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May Mei onto Writing & Presentation Tips

Latex and Matlab tutorials by Erin Bodine

On Erin Bodine's site

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Writing in mathematical modeling course

PRIMUS article - PRIMUS had a special issue on writing in mathematics and this is one on mathematical modeling in particular.

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Carrie Diaz Eaton onto Mathematical modeling course

Modeling contests for undergraduates

Some people structure their modeling course so that students can participate in a modeling competition. COMAP has many textbooks to support mathematical modeling as well.

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Carrie Diaz Eaton onto Mathematical modeling course

Peer-review in applied mathematics writing

This is a collaboration in calculus II with the writing director on best practices in peer-review.   This link is to the version on arxiv, but the full is published in PRIMUS.

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Carrie Diaz Eaton onto Mathematical modeling course

Bodine's Math Modeling & Scientific Writing Course

Syllabus and course assignments for a course in math modeling & scientific writing

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Erin N. Bodine onto Mathematical modeling course

Research Log Template

Template for research log that I use with my research students. Template contains definition of new commands in TeX for goals, log entries, meeting notes, and reflections. I have students maintain this file in a shared folder while they are doing research. My research students are expected to make goals for each week, a log entry for each day they work on their research project, and a reflection entry at the end of each week.

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Diversifying the faculty: A guidebook for search committees

by Turner, Caroline Sotello Viernes

"This monograph suggests ways in which an institution can diversify its faculty and facilitate the work of the search committee before a candidate ever reaches the interview stage. It outlines a step-by-step process to improve the likelihood of a successful search, and it recommends items to consider after a hire is confirmed to ensure that the new faculty member will be more likely to stay. The sections are: (1) Before the Search Begins; (2) The Search Process; and (3) After the Search. Appendixes contain a checklist of best practices, a list of leading institutions for minority Ph.D.s, a list of baccalaureate institutions identified as producers of numbers of female doctorates; and a list of Web resources of programs for building diverse faculties. An annotated bibliography lists 59 sources for additional information. (Contains 36 references.) (SLD)"

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Carrie Diaz Eaton onto Diversity and Inclusion

Mentoring undergraduate applied math research

Chad Topaz discusses personal values, college mission, undergraduate research management tips, being a productive scholar, and more

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Carrie Diaz Eaton onto AALAC presentations

Using Kurator Tools for Data Quality and Cleaning Biodiversity Data - Tracy Barbaro

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Molly Phillips onto Workshop Presentations

Getting to Know the Data - Libby Ellwood

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Molly Phillips onto Workshop Presentations

Where to Find Collections Data - Molly Phillips

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Molly Phillips onto Workshop Presentations

Backward Design - Deb Linton

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Molly Phillips onto Workshop Presentations

Resources For Collections-Based Undergraduate Education - Anna Monfils

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Molly Phillips onto Workshop Presentations

Module 4: An Investigation of the Island Rule

Module 4: Mammal Size on Islands [Island Biogeography]

Course:

  • Upper Level Ecology (Juniors or Seniors)

Length:

  • This exercise is designed as a 2-3-hour experience, but could be spread over several days or include a take-home component.
  • The assessment is completed as a take-home assignment.

Objectives:

  • Interpret patterns of species morphology on islands using natural history collections data.
  • Apply the process of science by the development and testing of hypotheses.
  • Collect, clean, and analyze data from a digitized natural history collection.

Activities:

  1. Students make a prediction about the relationship between mammal body size and island vs mainland habitat.
  2. Students use the Arctos online database to download species collection records from islands in the Alexander Archipelago and from the nearby Alaska mainland.
  3. Students determine the average mass of different mammal species collected on the islands and mainland. This activity requires significant time for data “cleaning”.
  4. Students do statistical analyses of the data (t-test) to test their hypotheses.

Assessment:

  • Students complete a standard laboratory report detailing their methods and findings.

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Molly Phillips onto Workshop Modules

Module 3: The Effect of Climate Change on Phenology and Interspecific Interactions

Module 3: The Effect of Climate Change on Phenology and Interspecific Interactions

Course:

  • Introductory Ecology (Sophomores or Juniors)

Length:

  • This exercise is designed as a 3-hour laboratory experience.
  • The assessment is completed as a take-home assignment.

Objectives:

  • Measure shifts in the timing of life history events due to climate change.
  • Predict the effects of phenology shifts on interspecific interactions.
  • Collect, clean, and analyze data from a digitized natural history collection.

Activities:

  • Students collect temperature data from weather/climate database.
  • Students collect data on butterfly plants phenology from digitized natural history collections.
  • Students collect data on butterfly phenology from digitized natural history collections.
  • Students analyze the three data sets to identify correlations between temperature change and shifts in the phenology of butterfly food plants and butterflies.
  • Students make predictions about the effects of phenology shifts on the population sizes of the plants and butterflies.
  • Students read parts of a primary literature article about the phenology of the pied flycatcher and its prey, butterfly larvae, and draw conclusions about the interactions between all three groups (butterfly food plants, butterflies, and flycatchers).

Assessment:

  • Students complete a case study assessment investigating phenology shifts in the early spider orchid (Ophyrs sphegodes) and its pollinator, the solitary bee (Andrena nigroaenea).
  • Students graph provided temperature, flowering time, and date of first bee flight data to visualize the changes in phenology.
  • Students make predictions about the effects of the phenology shifts on the orchid population.

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Molly Phillips onto Workshop Modules

Module 2: Angiosperm Reproduction and Coevolution

Module 2: The Evolution (and Coevolution) of Flowering Plants

Course:

  • Introductory Biology, Ecology, or Evolution (Freshmen or Sophomores)

Length:

  • This exercise is designed as a 3-hour laboratory experience, but activities could be used individually.
  • The assessment is completed as a take-home assignment.

Objectives:

  • Describe the role of flowers in angiosperm reproduction.
  • Identify the parts of a flower.
  • Describe the role of fruits in angiosperm reproduction.
  • Identify the parts of a fruit.
  • Identify different types of fruits.
  • Explain the role of pollinators in the life history of angiosperms.
  • Define coevolution and identify selection pressures that exist between pollinators and the plants they pollinate.
  • Predict pollinator/plant pairs based on morphological traits.
  • Collect data from digitized natural history collections.
  • Analyze spatial co-occurrence data for pollinators and the plants they pollinate.

Activities:

  1. Flower dissection and drawing [30 min] – each pair of students is assigned a flower to dissect and draw.
  2. Plant/Pollinator match game [30 min] – each student receives either a pollinator or plant “card” and must locate their match using information provided on the card.
  3. Bat/Agave case study using digitized Natural History Collection data [60 min] – students use the iDigBio Portal to investigate the distribution of several bat and plant species to analyze spatial co-occurrence data to make inferences about interspecific interactions.
  4. Fruit dissection, drawing, stations [45 min] – each pair of students is assigned a fruit to identify, dissect, and draw. The team then produces a “station” displaying their fruit for other class members to view.

Assessment:

  • Students complete a case study assessment investigating the relationship between the early spider orchid (Ophyrs sphegodes) and its pollinator, the solitary bee (Andrena nigroaenea).
  • Students use images to identify characteristics of the orchid flower and fruit, use the iDigBio Portal to investigate the co-occurrence of the two species, and write about the selection pressures involved in the co-evolutionary relationship.

 

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Molly Phillips onto Workshop Modules

Module 1: An Investigation of the Relationship between Island Size and Species Richness using Data from Online Natural History Collections

Module 1: The Relationship between Island Size and Species Richness [Island Biogeography]

Suited for Upper-Level Undergraduates

Course:

  • Introductory Biology or Ecology (Freshmen or Sophomores)

Length:

  • This exercise is designed as a 2-3-hour experience, but could be spread over several days or include a take-home component.
  • The assessment is completed as a take-home assignment.

Objectives:

  • Interpret patterns of species distribution on islands using natural history collections data.
  • Apply the process of science by the development and testing of hypotheses.
  • Collect, clean, and analyze data from a digitized natural history collection.

Activities:

  1. Students make a prediction about the relationship between island size and species richness.
  2. Students use an aggregated online database to download species collection records from islands of different size classes in the Alexander Archipelago.
  3. Students determine the number of mammal species collected on each of the selected islands. This activity requires significant time for data “cleaning”.
  4. Students do statistical analyses of the data (t-test, ANOVA, or regression) to test their hypotheses.

Assessment:

  • Students complete a standard laboratory report detailing their methods and findings.

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Molly Phillips onto Workshop Modules

Basta Lab Exercise: Metabolism

This lab activity merges the HHMI Biointeractive lactase resources with additional data analysis opportunities for a 300-level Anatomy and Physiology lab (2 hours).

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Holly Basta onto Lactase & Amylase

pixabay

All images and videos on Pixabay are released free of copyrights under Creative Commons CC0. You may download, modify, distribute, and use them royalty free for anything you like, even in commercial applications. Attribution is not required.

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Drew LaMar onto Web Images

Awards Banquet May 10, 2017 Mebane Arts Center

May 10, 2017.  Mebane Arts Center.  170 students received invitations for the recognition ceremony. Each honoree were allowed to bring family. Approximately 80 students RSVP'ed. 53 eighth graders and 10 ninth graders were in attendance. Total attendance was approximately 225 inclusive of honorees, guest, and speakers.

Middle schools Represented Broadview Graham Hawfields Southern Turrentine Western Woodlawn

High schools Respresented Cummings Eastern Graham Southern Williams Western

DISCUSSION funded the Dinners and Gave the Charge to Students and Parents

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Greg Goins onto Closing the Achievement Gap Inc. ABSS

Calculus II Unity College

Calculus II 3-credit course at Unity College for life and environmental science. Matlab, Integration, ODEs and intro to systems.

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Carrie Diaz Eaton onto Syllabi

Calculus I Unity College

3 credit calculus for life and environmental science majors. Covers beginning of sequences, difference equations, limits, and derivatives with applications.

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Carrie Diaz Eaton onto Syllabi

People profiles to be used to discuss global lactase persistence. 

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Melissa Csikari onto Lactase & Amylase

Photos from DISCUSSION II

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Greg Goins onto Photos of People Events and Materials

Smashing Magazine

Online website for web designers and web developers.

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Jenny Kwan onto Web Design

Hong Kiat

Design weblog for designers, bloggers and tech users. Covering useful tools, tutorials, tips and inspirational artworks.

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Jenny Kwan onto Web Design

NATURE | NEWS Darwin’s iconic finches join genome club

Scientists pinpoint genes behind famous beak variations.
by Geoff Marsh published 11 February 2015

This is a nice update on recent research into the finch phylogeny. It includes video and an interview with Leif Andersson about his research on the evolutionary relationships between species based on genomic sequences. 

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Data Wrangling Cheat Sheet

from RStudio

Covers dplyr and tidyr

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Drew LaMar onto Resources for R

Base R Cheat Sheet

from RStudio

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Drew LaMar onto Resources for R

Two locus selection and gametic disequilibrium

These are the teacher notes associated with the student activity. This activity uses Populus software to have students run simulations with gametic frequency data.

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Gabriela Hamerlinck onto Example problem sets

Two locus gametic disequilibrium

These are the teacher notes associated with the student activity. Students will work with phenotypic data from Drosophila populations to understand allele frequencies and Hardy-Weinberg equilibrium. Students are asked to calculate and interpret a variety of population genetic statistics, including X2 and D (gametic disequilibrium).

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Gabriela Hamerlinck onto Example problem sets

Fixation index with one locus and three alleles

These are the teacher notes for the student activity. Working with allozyme genotype data, students are asked to compute and interpret genotype frequencies and fixation indices.

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Gabriela Hamerlinck onto Example problem sets

"Beyond Darwin"

This lesson plan, created by Discovery Channel, is for grades 6-8 and its goal is to study native vs introduced species and their effects. It's been hard to find resources for older kids.

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Sarah Scott onto Galapagos Islands Teaching Resources

Galapagos Education Site

Very rudimentary. The "Classroom Investigations" are for grades 5-8. However it is not uninteresting and includes links to simulations and worksheets. It was created by the National Science Teachers Association. Could be a fun resource to included if for no other reason than because it's cute. The "Galapagos Guide" is within the site, explaining different areas of the islands. The "Resources for Teaching Evolution" tab does not have designated grades and appear to be a little more intensive. It contains things like discovery channel videos and a virtual tour of a volcano. 

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Sarah Scott onto Galapagos Islands Teaching Resources

Code My UI

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Drew LaMar onto Web Design

The project homepage contains the Activity Feed. Collected here are updates about activity within the project. Some updates are posted automatically, for example, when a file is uploaded or a...

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Anne Kruchten onto QUBES Help

Projects are workspaces for collaboration. Often team members will need to share and store files in an area accessible by other team members. The Files area of a project can be found on the...

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Anne Kruchten onto QUBES Help

To add or delete members, you must be a manager of the project.

To add or delete members, from the project's home screen, click on the "Team"...

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Anne Kruchten onto QUBES Help

Bowman: THE EVOLUTION OF VOCAL COMMUNICATION IN DARWIN'S FINCHES

John recommended looking into the work of Robert Bowman and this is his section from the larger work about galapagos finches Notícias de Galápagos 1 (which would probably be helpful but most of the rest of the work is in Spanish) much of it is comparing the giospiza to other species of song birds, and goes into why the galapagos finch is the perfect subject for studying bird song in an evolutionary focus. 

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Sarah Scott onto Song Scientific Literature

Connection Article

This article is really nice because it connects song and beak morphology all in the realm of evolution. It's a quick read and good for beginners but also pretty interesting for anyone

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Sarah Scott onto Song Scientific Literature

Sorting


  •  

Will have to look into more, but from what I've seem it's an evolution focused lab based in separating finch species. Seems to be a premade lab 

Ok so it's actually really cool! The premise is you're trying to sort finches into two groups based on song sound, spectrograms, beak shape and appearance, at the end you can check how close you were. Theres another activities for differentiating finches that's not quite as related and tabs to learn about spectrograms and  Daphne Major. Both are pretty basic crash courses but would be very helpful for a beginner or an introductory activity. I'll definitely provide a walk through because it's super fun!!

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Sarah Scott onto Bird song teaching resources

All about Birds

Very cool multimedia

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Hayley Orndorf onto Bird song teaching resources

Resources for Teaching with Bird Data

A bit outdated, but links out to other interesting bird data sources, which include a lot of citizen science. 

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Hayley Orndorf onto Bird song teaching resources

Cornell Lab of Ornithology Teaching Resources

The modules, "Species Concepts in Birds" and "Sound Trees" use song data. Lessons are well developed with learning objectives, instructor guides, student handouts, how-to's on the Macaulay library and RavenViewer, and some assessment ideas.

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Hayley Orndorf onto Bird song teaching resources

House of Representatives Committee on Science, Space, and Technology Twitter account

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Drew LaMar onto In the News

What Does It Mean When Cancer Findings Can't Be Reproduced?

The first results from a major project to measure the reliability of cancer research have highlighted a big problem: Labs trying to repeat published experiments often can't.

That's not to say that the original studies are wrong. But the results of a review published Thursday, in the open-access journal eLife, are a sobering reminder that science often fails at one of its most basic requirements — an experiment in one lab ought to be reproducible in another one.

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Drew LaMar onto In the News

How statistics lost their power – and why we should fear what comes next

The ability of statistics to accurately represent the world is declining. In its wake, a new age of big data controlled by private companies is taking over – and putting democracy in peril

by William Davies

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Drew LaMar onto In the News

How statistics lost their power – and why we should fear what comes next

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Cell Cycle and Cancer

The goal of these multi-week activities is to use Cancer Biology as a theme to introduce concepts in the cell cycle, cell biology, genetics and signal transduction.

These activities are appropriate for high school and Introductory Biology classes.

Learning Objectives:

  1. Identify the different stages of the cell cycle.
  2. Estimate the duration of the different stages of the cell cycle from microscopic examination of onion root tips slides.
  3. Relate deficiencies in cell cycle regulation to development of cancer
  4. List the names, chromosomal location and functions of genes identified in various types of cancer
  5. Describe how mutations in cancer driver genes can result to abnormal cell biology and development of cancer cells

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Alice Tarun onto Cancer Genomics

Using HHMI BioInteractive modules to link global warming, ocean acidification and coral reef health

Through the use of HHMI modules on Earth Systems, Ocean Acidification and Coral Bleaching  and lab activities, students will be able to discern the complex inter-relationship of carbon cycling, global warming, ocean acidification and coral reef health.

The students will be able to apply concepts in carbon cycling, pH, and ecosystem health  in modeling the effect of increased carbon dioxide to climate, acidification and coral reef ecosystems. An extension of these activities is to connect these activities to the application of the scientific method to make predictions on which areas of the world are at risk to coral bleaching.

 

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Found the book!!

Ecology and Evolution of Darwin's Finches by Peter R. Grant

Published by Princeton University Press 1999 

Overview of useful sections:

Chapter 9

Song and Bill Morphology as Species Cues 

Song is the way of expressing ones species from over a large distance, which beak shape is how it would be expressed in the short distance 

Beyond Species-Recognition: Mate Choice 

In this section, Grant reports on 14 females he watched, after observing the songs of their fathers. Though statistically speaking 2-3 of the females should have mated with males that shared their fathers song if it were random, not a single female did. This implies that song could act as a prevention method against inbreeding to keep the gene pool healthy.

 

Chapter 14

Other Features

"The distribution of sound energy in songs varies in such a way that it might be transmitted best in the particular configuration of vegetation in which the song is sung." In other words, the plants in an area have a large effect on the songs of the finches that live there. 

 

 

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Sarah Scott onto Song Scientific Literature

The Syntax of Bird Songs

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Sam S Donovan onto Bird song teaching resources

Finch Song Articles

The first article is a transition into Grants work concerning differentiation in bird songs. The article briefly discusses the allopatric divergence, and the interesting concept of song being a culturally inherited trait. Paragraph 22-4 delves into the song in relation to the hybridization of finch species due to song and how this revolves around the males. The end of paragraph 24 states "The barrier to gene exchange erected by song differences has been breached, and environmental change appears to have been the most important factor" It ends by explaining that the variety of finch songs likely has to do with both sexual selection along with a random shift in learned behavior. 

This article cited the works of Grant which are extremely relevant to the study of song and evolution however the publication is a full book and I could not track it down anywhere free so I will delve into the library when I get the chance. 

 

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Sarah Scott onto Song Scientific Literature

Bird Song Hero

This is a fun little game created by The Cornell Lab of Ornithology that can help you familiarize yourself not only with the songs of various birds, but also with the general idea of a spectrogram. With enough practice, just looking at a spectrogram with allow you to imagine a pretty accurate song before even listening to it.

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Dylan Chase McHugh onto Bird song teaching resources

Melissa Haswell - Cancer Genomics Implementation

Uses:

  • Cell cycle introduction/review 
    • High school
    • Undergraduate introductory biology course
    • Upper level biology course for review/introduction to an advanced topic such as cancer pathophysiology
  • Benefits:  Helps students identify the importance of the cell cycle and its relationship to cancer cell development
  • How I use this activity:
    • Student population: BSN nursing students enrolled in a pathophysiology course
    • Review the cell cycle & introduce relationship of cell cycle to cancer in the genetic disease unit (genetic disease unit covers epigenetics, inherited diseases, diseases of nondisjunction, and cancer)

       

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Melissa Haswell onto Cancer Genomics

Moore-Lactase Persistence

Overview of implementation of bio interactive modules

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John Morton Moore onto Lactase & Amylase

Kill Math

This one is really a combination of blog and demos of digital tools that highlight the bloggers math philosophy.

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Kristin Jenkins onto Math Education Blogs I Like

Soulver

A calculator that allows words and numbers in equations.  Possibly a way to help students through initial problem set ups?

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Discrete Maps: The Logistic Model

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Drew LaMar onto Timeline

Possible clicker questions for HIV and phylogenetic trees

These are just Powerpoint slides at the moment, not 'live' clicker questions.  Two are for HIV, two are for phylogenetic trees.

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Elizabeth F Ryder onto Teaching HIV Evolution

From Agent-Based to Population Models: Logistic Growth (Part 3)

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From Agent-Based to Population Models: Logistic Growth (Part 2)

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From Agent-Based to Population Models: Logistic Growth (Part 1)

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ESA announces new journal

Letter from ESA:

Dear Colleagues,
I'm pleased to announce a new resource for students, faculty, educators, professionals, and policymakers: Case Studies in the Environment (cse.ucpress.edu). This journal will consist of peer-reviewed case study articles with slides and teaching notes, articles on case study pedagogy, and a preprint server for editor-reviewed case study slides. Case Studies in the Environment is organized around a broad collection of cases within six domains, with the first three domains—Climate Change Mitigation and Adaptation, Ecology and Biodiversity Conservation, and Environmental Law, Policy and Management—coming in mid-2017.

The journal website is now live, and you can find information on the criteria for cases and how to submit cases here: http://cse.ucpress.edu/author-information/. If you have a relevant case study, I encourage you to submit it. You can also sign up for periodic email alerts about Case Studies in the Environment at http://cse.ucpress.edu/contact/.
 
Best wishes,
Cynthia A. Wei, PhD
Section Co-Editor for Ecology and Biodiversity Conservation
and
Associate Director of Education
National Socio-environmental Synthesis Center (SESYNC)
1 Park Place Suite 300/ Annapolis, MD 21401
(410)919-4991
www.sesync.org

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John Roach onto Potential Publication Venues

Instructions for phylogeny.fr and reading distance trees

Content pulled from a larger resource intended for AP students. These sections contain exercises and material surrounding phylogenetic trees, using Phylogeny.fr, and phylogenetic analysis. 

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Hayley Orndorf onto Resources for Phylogenetic Trees

Modelling coral calcification accounting for the impacts of coral bleaching and ocean acidification

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Carrie Diaz Eaton onto Marine Bio/Coral links

Coral Reef learning modules

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Carrie Diaz Eaton onto Marine Bio/Coral links

Factors affecting the evolution of bleaching resistance in corals.

This is not a link to the article for rather the summary.

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Carrie Diaz Eaton onto Marine Bio/Coral links

QUEST Virtual Institute

Quantitative Ecology and Socioeconomics Training (QUEST) Virtual Institute

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Full Issue on Fisheries Education

AFS Special Issue on Education

The article on p. 436, "Are we preparing the next generation of fisheries professionals to succeed in their careers" comes highly recommended.

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Is There a Shortage of Fisheries Stock Assessment Scientists?

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Full report on shortage of stock assessment scientists

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COPUS observation protocol for teaching practice

Link to information on observing teaching practice.

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Engage to Excel PCAST report

Presidential Council of Advisors Report on Science and Technology

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Carrie Diaz Eaton onto Bio Ed reports

Vision and Change report

Guiding document for life science curricula

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Carrie Diaz Eaton onto Bio Ed reports

Quantatitive literacy to modeling for biology

Contact Joe Dauer (UNL) and Robert (Bob) Mayes (Georgia Southern) for information on their Quant Skills pilot project.

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quantitative skills inventory for biologists

Contact Pam Bishop/Lou Gross at University of Tennessee - designed for stats/calc/discrete foundational courses.

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biology attitudes about math

Contact Melissa Aikens at UNH (biology dept)

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Increase the impact project

How to increase the impact of your curriculum development project in terms of sdoptibility by other institutions

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NIBLSE Core Competencies

The competencies are skills that NIBLSE recommends all life science students be able to do by the time they graduate.

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Hayley Orndorf onto Teaching HIV Evolution

Journal Club assignment

This is the link to the journal club assignment that accompanies the Markham et al. 1998 PowerPoint slides.  The home page of the course is here: http://www.openwetware.org/wiki/BIOL368/F16

from which you can get to the other assignments in the series and student work.

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Kam Dahlquist onto Teaching HIV Evolution

Markham et al. (1998) Journal Club slides

These are the slides I use for the group journal club in my upper division bioinformatics lab class.  I usually keep them behind a firewall to avoid having to deal with copyright issues, so we will need to address that if they will be publicly available.  Some of this presentation is left vague so that the students will provide the information and I don't give out the "answers" ahead of time.

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Kam Dahlquist onto Teaching HIV Evolution

Molecular Forensics

This is an exercise that is designed to help get students oriented to the logic of sequence comparison and interpreting evolutionary relationships to answer biological questions. Maybe we can use this instructional flow with some of the HIV Evolution unit data as a low tech way to get at competency 1. 

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Sam S Donovan onto Resources for Phylogenetic Trees

Slide set for Exploring HIV Evolution

Slides from the Bedrock site and Liz for teaching this material. 

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Hayley Orndorf onto Teaching HIV Evolution

Testing your program

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Dryad Digital Repository

The Dryad Digital Repository is a curated resource that makes the data underlying scientific publications discoverable, freely reusable, and citable. Dryad provides a general-purpose home for a wide diversity of datatypes.

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Quandl

Contains large datasets on many topics including demography, environment, and health.

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Drew LaMar onto Data Repositories

Long Term Ecological Research (LTER) Network

The LTER Network Information System Data Portal contains ecological data packages contributed by past and present LTER sites. Please review the LTER Data Policy before downloading any data product. We request that you cite data sources in your published and unpublished works whenever possible. Digital object identifiers (DOI) are provided for each dataset to facilitate citation.

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Montgomery, S. (2004). Of towers, walls, and fields: perspectives on language in science. Science, 303(5662), 1333-1335.

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Kam Dahlquist onto Resources for the Language paper

PULSE: Partnership for Undergraduate Life Science Education

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Anne Kruchten onto Vision and Change

Vision and Change website

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Anne Kruchten onto Vision and Change

Study finds straightforward way to model growth of vein networks

October 3, 2016 by Patrick Ammerman

A new study by Eleni Katifori, an assistant professor in the Department of Physics & Astronomy of the University of Pennsylvania School of Arts & Sciences, and Henrik Ronellenfitsch, a postdoc in her lab, described how a simple rule guides the development of the vasculature in both animals and plants.
They used mathematical modeling to show that this rule, known as adaptive feedback, can produce the most efficient possible network of veins for any organism.

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Drew LaMar onto Primary and news articles

Introduction to Agent-Based Modeling (ABM)

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Information Theory: Practice

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Self-paced, rolling dates online ODE w/linear systems course from UIUC NetMath

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Carrie Diaz Eaton onto Online ODE courses

Self-paced, rolling admission ODE course at NetMath (UIUC)

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Carrie Diaz Eaton onto Online ODE courses

Online ODE course at University of Illinois

Online ODE course at University of Illinois

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Carrie Diaz Eaton onto Online ODE courses

Review Session for Exam #1

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Information Theory

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The ASM-NSF Biology Scholars Program: An Evidence-Based Model for Faculty Development

Biology Scholars Program

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Carola Haas onto Faculty Development

Parsimony and Collinearity

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Data and Models

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Phenology module online at Cleveland State University

Resource Type: lab description, prelab quiz, grading rubric

Classroom Type: Introductory lab for biology majors

Modifications: Because our campus was closed for one week, we implemented the phenology module online through Blackboard. Each section was a separate submodule that could be turned in separately. I included a prelab quiz from how we are implementing this lab in the classroom this fall; prelab quizzes are meant to test whether students prepared for the lab by reading the introduction and part I procedures.  An optional excel graphing assignment was for students with little to no graphing skills (the practice_data.xls file is for the optional excel exercise).

 

 

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A Faculty-Development Model for Transforming Introductory Biology and Ecology Courses

D'Avanzo et al. 2012

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Gabriela Hamerlinck onto Assessment papers

The ASM-NSF Biology Scholars Program: An Evidence-Based Model for Faculty Development

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Gabriela Hamerlinck onto Assessment papers

Post Vision and Change: Do we know how to change?

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Gabriela Hamerlinck onto Assessment papers

Errors in Hypothesis Testing; Linear Regression

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How I used A / B testing to hack my kids

A/B testing is used to test one or more “treatments” or experiments over a “control” or the existing experience. A metric is measured, usually based on a user action such as a click through or “conversion” with a baseline against the control.

Sounds like science to me!

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Drew LaMar onto Primary and news articles

Intro to Statistical Inference (cont'd)

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Modified Student Report Rubric

Looking through the two different types of student reports, I found that neither one was useful, the short version didn't include near enough information, and the long form was way too detailed. I modified the rubric to be a nice intermediate for me. I hope it is useful for others too.

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Introduction Powerpoint

This is the a bare bones powerpoint introduction that I used to introduce some of the topics related to bald eagle biology. I taught this activity in an upper-level Ecology class. 

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Lecture: Intro to Models and Modeling

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Lecture: Understanding Science

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Lab: Introduction to R, RStudio, and RMarkdown

  1. Download and install R on your laptop (http://cran.at.r-project.org/)
  2. Download and install RStudio on your laptop (https://www.rstudio.com/home/)
  3. Complete the following two OpenIntro Statistics labs:
  4. Read the following sections of the OpenIntro Statistics book:  1.1-1.3, 1.6-1.7 (this will help with the Introduction to Data lab)

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Lecture: Introduction and Overview of Course

Download  Syllabus

Download  Essay to students about the fallacy of fixed math ability

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Toward 'hybridised' faculty development for the twenty-first centry: blending online communities of practice and face-to-face meetings in instructional and professional support programmes

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Researching the community of inquiry framework: Review, issues, and future directions

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How blended learning can support a faculty development community of inquiry

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Epidemics: Modelling with mathematics

The following are resources for disease modeling dynamics that are age appropriate for upper middle school, high school, and undergraduate. There are hands-on activities such as disease on networks.

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Carrie Diaz Eaton onto SMB/ECMTB presentations

Mathematical Modeling in Systems Biology: An Introduction

by Brian P. Ingalls

Chapters Used:

  • Chapter 1: Introduction
  • Chapter 2: Modeling of Chemical Reaction Networks
  • Chapter 3: Biochemical Kinetics
  • Chapter 4: Analysis of Dynamic Mathematical Models
  • Chapter 5: Metabolic Networks
  • Chapter 6: Signal Transduction Pathways
  • Chapter 7: Gene Regulatory Networks

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Drew LaMar onto Books

Fundamentals of Molecular Evolution

by Dan Graur and Wen-Hsiung Li

Chapters Used:

  • Chapter 2: Dynamics of Genes in Populations

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Drew LaMar onto Books

Agent-Based and Individual-Based Modeling: A Practical Introduction

by Steven F. Railsback and Volker Grimm

Chapters Used:

  • Chapter 1: Models, Agent-Based Models, and the Modeling Cycle
  • Chapter 2: Getting Started with NetLogo
  • Chapter 3: Describing and Formulating ABMs:  The ODD Protocol
  • Chapter 4: Implementing a First Agent-Based Model
  • Chapter 5: From Animations to Science
  • Chapter 6: Testing Your Program
  • Chapter 7: Introduction to Part II
  • Chapter 8: Emergence

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OpenIntro Statistics

by David M Diez, Christopher D Barr, and Mine Çetinkaya-Rundel

Chapters Used:

  • Chapter 1: Introduction to Data
  • Chapter 4: Foundations of Inference
  • Chapter 7: Introduction to Linear Regression
  • Chapter 8: Multiple and Logistic Regression

 

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Model Based Inference in the Life Sciences

by David R. Anderson

Chapters Used:

  • Chapter 1:  Introduction: Science Hypotheses and Science Philosophy
  • Chapter 2:  Data and Models
  • Chapter 3:  Information Theory and Entropy
  • Chapter 4:  Quantifying the Evidence About Science Hypotheses

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