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Biological ESTEEM - Resources by Category

Author(s): 
John Jungck

Biochemistry

Balancing Chemical Equations Using Matrix Algebra. This Excel workbook introduces using matrix algebra to balance chemical reactions.

Buffer Preparation. This workbook calculates the necessary components to create a buffer solution.

Bioinformatics

Protein Analysis. This workbook allows the analysis of sample or imported protein sequences.

Biometrics

BioBayes. This Excel workbook and documentation lead the user through several different methodologies for applying Bayesian probabilities to real life examples and problems.

Biostatistical Tools A collection of workbooks for linear regression, polynomial fit, and chi-square analysis to test whether a data set is in Hardy-Weinberg Equilibrium.

Database Construction and Sampling. The construction of three simple databases using a spreadsheet is described here and basic summary statistics are provided for each.

Fractal Fern Generator. This Excel workbook creates graphical images of a certain type of fractals that can be constructed by linear transformations.

PopTools. This downloadable Windows program allows the construction, analysis, and simulation of complex models in a simple spreadsheet format.

Botany

Three-D FractaL-Tree. This module allows scientists to collect data from specimens, insert the measurements into a spatially explicit L-system package, and visually compare to the computer generated 3D image with such specimens. The module consists of an Excel workbook and a Java applet.

Developmental Biology

Biological Cellular Automata Laboratory (BioCA Lab). This Excel workbook includes linear cellular automata and 2D cellular automata. Users can choose from a set of popular rules or define their own.

Developmental Allometry: Scaling in Growth. This Excel workbook illustrates a number of allometric equations in animal growth.

Ecology

Biodiversity.  This Excel workbook allows the diversity of a biological population to be estimated with both the Shannon and Simpson biodiversity indices.

Continuous Growth Models. This worksheet compares user-input growth data with predictions under linear, exponential, and logistic models of growth.

Island Biogeography. This Excel workbook demonstrates the principles of the MacArthur-Wilson theory of Island Biogeography.

Java Food Web. This Java applet is accompanied by 100 Excel worsheets that provide food web matrices for analysis by the applet.

Leslie Matrix for Age-structured Populations. This Excel workbook uses the Leslie Matrix Model for population projection of age-class or stage-class structured populations.

Two-Species Model. This worksheet simulates the population growth of two interacting species.

Epidemiology

SIR Model. This worksheet implements an SIR (Susceptible/ Infected/ Resistant) model of epidemiology for vector-borne diseases.

Evolution

DeFinetti 1.0. This workbook simulates evolution of a single gene with three alleles.

ESS: Evolutionary Stable Strategies Game Theory Module. This workbook illustrates a number of ESS examples. 

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

Genetics

ABO Blood Group Frequencies. The purpose of this workbook is to compare several methods for calculating allele frequencies for ABO blood groups.

Birthday Problem & Class Phenotypic Probabilities. This Excel workbook as two related applications, the Birthday Problem and Class Phenotypic Probabilities.

Deme 2.0. This worksheet simulates the population genetics of a single gene with two alleles.

Linkage Analysis. This workbook simulates a linkage analysis problem with up to four alleles.

ORF Finder. This workbook performs six-frame translation on a short user-input nucleotide sequence and highlights the position of stop codons.

Operon. This workbook models lac operon function in a partial diploid E. coli.

Phylogenetics

EvolSeq. This worksheet simulates the molecular evolution of DNA sequences.

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

Split Decomp. This worksheet performs split decomposition on a set of four DNA sequences and their associated amino acid sequences.

Sequence Alignment

Multiple Alignment. These two worksheets implement a dynamic programming algorithm for simultaneous alignment of multiple sequences.

Pairwise Alignment. These two worksheets implement a dynamic programming algorithm for pairwise sequence alignment.


 

The Biological ESTEEM project is part of the BioQUEST Curriculum Consortium at 
http://www.bioquest.org/esteem

John Jungck, "Biological ESTEEM - Resources by Category," Loci (December 2005)

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