Two-Species Model

19 Aug 2024 | Contributor(s): Anton E Weisstein, Rene Salinas, John Jungck | doi:10.25334/VGXD-SE94

These two Excel worksheets simulate the population growth of two interacting species. In isolation, each species grows logistically, but interaction effects between species may limit or enhance that growth.

Split Decomp

19 Aug 2024 | Contributor(s): Anton E Weisstein, John Jungck | doi:10.25334/1SCD-8P78

This Excel worksheet performs split decomposition on a set of four DNA sequences and their associated amino acid sequences. The user can type in the sequences or paste them in from a text file.

Phylogeography Simulator

19 Aug 2024 | Contributor(s): Anton E Weisstein | doi:10.25334/NS40-AB64

This Excel workbook simulates the phylogeography of an asexually reproducing species.

Operon

19 Aug 2024 | Contributor(s): Anton E Weisstein | doi:10.25334/0HM4-A428

This Excel workbook models lac operon function in a partial diploid E. coli. The user chooses the bacterial genotype and the sugars present in the surrounding medium: the workbook then determines which structural genes will be expressed.

Linkage Analysis

18 Aug 2024 | Contributor(s): Anton E Weisstein | doi:10.25334/H2Y4-SB61

This Excel workbook simulates a linkage analysis problem with up to four alleles. Based on the offspring produced by a multihybrid testcross, the user builds a model of the gene order, recombination frequencies, and linkage phase in the hybrid parent.

Hidden Markov Model

17 Aug 2024 | Contributor(s): Anton E Weisstein | doi:10.25334/C0HE-TY17

Hidden Markov models are a set of mathematical tools that can be used to draw inferences about genomic and evolutionary processes.

GeoPhyl

17 Aug 2024 | Contributor(s): Anton E Weisstein | doi:10.25334/SWB4-1N16

This Excel workbook allows students to explore evolution over space and time using published data on the invasive plant Tamarix (salt cedar).

Genetic Code

17 Aug 2024 | Contributor(s): Anton E Weisstein | doi:10.25334/FB7F-XQ32

This Excel workbook allows the user to recreate the steps in breaking the genetic code. The user enters the sequence of repetitive synthetic mRNA strands, which are translated in vitro to produce repetitive polypeptides.

Dynamic Programming

17 Aug 2024 | Contributor(s): Anton E Weisstein | doi:10.25334/M8TG-1K91

In bioinformatics, dynamic programming is mainly used to align nucleotide and amino acid sequences, and to predict RNA and protein folding from primary sequence data.

Deme 2.0

16 Aug 2024 | Contributor(s): Anton E Weisstein | doi:10.25334/QRCF-8649

This workbook simulates the population genetics of a single gene with two alleles. It can simultaneously model up to three local populations, which may differ in their selection coefficients.

DeFinetti 1.0

16 Aug 2024 | Contributor(s): Anton E Weisstein, John Jungck, Tia Johnson, Ed Louis | doi:10.25334/M1QT-VB37

This Excel workbook simulates evolution of a single gene with three alleles. The user assigns fitness values to each of the six possible genotypes, then enters starting allele frequencies for each of up to 22 individual populations.

Continuous Growth Models

16 Aug 2024 | Contributor(s): Anton E Weisstein | doi:10.25334/PE67-JN93

This Excel worksheet compares user-input growth data with predictions under linear, exponential, and logistic models of growth. Introduces concepts of statistical analysis that can be additionally explored with statistics software (e.g. JMP, SAS).

Biostatistical Tools

15 Aug 2024 | Contributor(s): Anton E Weisstein, Rama Viswanathan, Sheldon Gordon, Jennifer Spangenberg | doi:10.25334/JFKP-HK74

This Excel collection of workbooks has tools for: 1. Linear regression through the origin 2. Linear regression not through the origin 3. Polynomial fit 4. A simple chi-square analysis to test whether a data set is in Hardy-Weinberg Equilibrium.

Teaching biostatistics using the Rule of Four

19 Mar 2023 | Contributor(s): Rachel Hartnett, Qingxia Li, Stacey Kiser, Anton E Weisstein | doi:10.25334/FHZB-ZG48

A guide to helping intro bio students develop a deeper understanding of key statistical concepts by translating among numeric, graphical, verbal, and symbolic representations.

SIR BuildIt

03 Apr 2020 | Contributor(s): Anton E Weisstein | doi:10.25334/MF1T-WV05

An introduction to epidemiological models using interactive Excel worksheets

A Hands-on Introduction to Hidden Markov Models

04 Jan 2019 | Contributor(s): Tony Weisstein, Elena Gracheva, Zane Goodwin, Zongtai Qi, Wilson Leung, Christopher D. Shaffer, Sarah C.R. Elgin | doi:10.25334/Q4ZM88

A lesson in which students will understand the basic structure of an HMM, the types of data used in ab initio gene prediction, and its consequent limitations.

Michaelis-Menten Enzyme Kinetics

11 Sep 2018 | Contributor(s): Tony Weisstein | doi:10.25334/Q4VT6N

In this simulation, equations used in enzyme kinetics (Michaelis-Menten, Eadie-Hofstee, Dixon, and Lineweaver-Burk) are modeled under various conditions.

Luria-Delbruck

11 Sep 2018 | Contributor(s): Tony Weisstein, John R Jungck, Doug Green | doi:10.25334/Q40H75

These two workbooks model the evolution of phage resistance in a bacterial population under two alternative hypotheses.

EvolSeq

11 Sep 2018 | Contributor(s): Tony Weisstein, John R Jungck | doi:10.25334/Q44B01

An Excel worksheet that simulates the molecular evolution of DNA sequences.

The effects of Avian Malaria On Pigeon Fledging Growth

19 Jun 2018 | Contributor(s): Qingxia Li, Lauren Gollahon, Tony Weisstein, Xinyao Yang | doi:10.25334/Q4BH8N

Poster on a case that combined Biology and Statistics in a student research project presented at the 2018 QUBES/BioQUEST Summer Workshop

The effects of Avian Malaria On Pigeon Fledging Growth

30 May 2018 | Contributor(s): Qingxia Li, Lauren Gollahon, Tony Weisstein, Xinyao Yang | doi:10.25334/Q46H58

Poster on a case that combined Biology and Statistics in a student research project presented at the 2018 QUBES/BioQUEST Summer Workshop

Effects of Laptop Use on Student Learning

17 Jan 2018 | Contributor(s): Tony Weisstein | doi:10.25334/Q4QM36

Resource from the 2015 BioQUEST Summer Workshop

Exploring HIV Evolution

05 Jun 2017 | Contributor(s): Sam S Donovan, Tony Weisstein

In this activity you will study aspects of sequence evolution by working with a set of HIV sequence data from 15 different subjects (Markham, et al., 1998). You will first learn about the dataset, then study the possible sources of HIV for these...

Exploring HIV Evolution

05 Aug 2016 | Contributor(s): Sam S Donovan, Tony Weisstein

In this activity you will study aspects of sequence evolution by working with a set of HIV sequence data from 15 different subjects (Markham, et al., 1998). You will first learn about the dataset, then study the possible sources of HIV for these...