3D FractaL-Tree allows scientists to collect data from actual specimens in the field or laboratory, insert these measurements into a spatially explicit L-system package, and then visually compare to the computer generated 3D image with such specimens. The measurements are recorded and analyzed in a series of worksheets in Microsoft ExcelíŹ and the results are entered into the graphics engine in a Java applet. 3D FractaL-Tree produces a rotatable three-dimensional image of the tree which is helpful for examining such characters as self-avoidance (entanglement and breakage), penetration of sunlight, distances that small herbivores (such as caterpillars) would have to traverse to go from one tip to another, and Voronoi polyhedra of volume distribution of biomass on different subsections of a tree. These and other factors have been discussed in the Adaptive Geometry of Trees (Horn, 1971). Three different representations are available in 3D FractaL-Tree images: wire frame, solid, and transparent. Easy options for saving and exporting images are included.
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BioGrapher is an Excel front-end for the AT&T GraphViz graphical visualization and layout package (http://www.graphviz.org/). BioGrapher is unique in that it (1) allows users to enter data into an Excel spreadsheet in one of three ways: adjacency matrices, nodal lists, and Newick format for phylogenetic trees; (2) displays graphs in four different layouts: radial, circular, hierarchical, and tree; (3) properties of graphs, e.g., diameter, connectedness, and average clustering can be computed and displayed; (4) data can be read from standard comma separated value (CSV) text files. A VBA custom menu interface for the Windows and Mac OS X versions of GraphViz has been programmed and added to the standard Excel menu bar so that the user can easily invoke the graphical layout and computation routines.
This module includes both linear cellular automata and 2D cellular automata. For linear CA, users can choose from a set of popular rules or define their own. For 2D CA, examples of a toroidal, cylindrical, and walled spatial configurations are presented, with a library of preset patterns and the ability to customize patterns. The original 3 rules for survival, death, and birth are implemented in this module, but users with some ExcelíŹ knowledge can implement variations on these rules. Cellular automata have been extensively used in biology to model the development of pigmentation in textile cone shells, the spread of forest fires, and epidemics, for example.
This worksheet compares user-input growth data with predictions under linear, exponential, and logistic models of growth. Students can input parameters for each model; the program graphs the results and computes a crude goodness-of-fit measure. Introduces concepts of modeling and statistical analysis that can be more thoroughly explored using standard statistics software (JMP, SAS, etc.)
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. The program tracks each population through 100 generations and plots the results in a ternary graph. Additional output includes a 3D adaptive landscape and a time plot of local populations' mean fitness, genetic variance in fitness, and expected heterozygosity.
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.
This worksheet simulates the molecular evolution of DNA sequences. The program begins with a single (random) sequence, then follows that sequence through time as it reproduces and mutates. Eventually, up to 20 evolutionary related sequences are generated. EvolSeq then calculates the genetic distances between each pair of DNA sequences, and also between the associated amino acid sequences.
This workbook simulates the population genetics of a single gene with two alleles, allowing the user to set the initial allele frequencies and enter parameters for a variety of different selection models; the program then tracks the population through up to 10,000 generations.
This excel workbook demonstrates the principles of the MacArthur-Wilson theory of Island Biogeography. It allows the user to define the mainland species pool, area of the island, and distance of the island from the mainland. Graphical output included species richness equilibrium at varying island size and distance. The workbook also allows the user to calculate a species-area function for data entered into the data input page. Several datasets on island area and species richness are included for various types of islands and species. Variables and formulas are defined in the accompanying tutorial.
This excel workbook uses the Leslie matrix model for population projection of age-class structured populations, and also allows Lefkovitch matrix models for stage-class structured populations. The user enters age or stage specific fecundity and survival rates as well as the populationí˘óťs initial proportions. The workbook calculates the matrix with corresponding eigenvalues for finite growth rate and eigenvectors for stable age/stage distribution and reproductive value. The graphical output included illustrates the stabilization of population structure, reproductive values and the finite rate of increase. It also includes exponential growth curves and semi-log plots of the population growth. The user can view population projections for four actual datasets.
This workbook allows the analysis of sample or imported protein sequences. The model can analyze protein sequences up to 500 amino acids long. The program analyzes five aspects of the protein sequence: the highest potential charge along the protein sequence, the amino acid composition of the protein sequence, the isoelectric point of the protein sequence at varying pHs, the hydrophobicity to predict surface and membrane spanning regions of the protein sequence and the protein structure using the Chau and Fassman algorithm.
This worksheet implements an SIR (Susceptible/ Infected/ Resistant) model of epidemiology for vector-borne diseases. Up to three microbial strains with different virulence and transmission parameters can be modeled and the results graphed. Originally designed to explore coevolution of myxoma and rabbits, the model is easily generalized to other systems.
This 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. The program then translates the DNA sequences into amino acid sequences and calculates split indices and four-point conditions for each of the three possible unrooted phylogenies. The user can use these values to assess the data support for each of these topologies.
These two 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. Graphical output includes phase diagrams and return graphs as well as conventional plots of population size vs. time.