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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This interactive L-system simulation produces visualizations of tree forms based on data from specimens in the field or laboratory.
Action Potential Experiments is a demonstration/simulation laboratory for neurophysiology based on the 'sodium theory' as originally formulated and tested by A. L. Hodgkin and his colleagues. The application includes simulations of the original experiments of Hodgkins and his colleagues, and of the classic voltage clamp and patch clamp experiments and an animated illustration of the 'sodium theory' explanation of Nernst potentials for potassium and sodium ions. The student can perform simple ion concentration experiments to test the predictions of the theory.
The osmotic controlled passage of polar water through fundamentally nonpolar biologic lipid bilayers (membranes) wasn't understood until the work of Peter Agre and Roderick MacKinnon on aquaporins resulting in the Nobel prize in Chemistry in 2003. We decided to examine conservation in aquaporins. A Google search provided us with both the PDB id (1h6i) of the human aquaporin A chain from RBCs, and a clearer understanding that the aquaprorins represent a related group of proteins present in multiple species. At http://www.rcsb.org/pdb/ we conducted an initial investigation of the structure of 1h6i. At consurf (http://consurf.tau.ac.il/) we were able to obtain the protein sequences for the best 20 matches in nearly FASTA form. After text editing we ran Clustalw and retrieved both rooted and unrooted trees. In the trees, it is easy to see the families of aquaporins (type 1, 2 etc; see tree.doc below).
Avida-ED allows users to design and perform experiments to test hypotheses about evolutionary mechanisms using evolving digital organisms. Avida-ED is an NSF-funded project to develop a digital evolution educational software platform for use in biology courses. The co-PIs on the project are Charles Ofria, Richard Lenski, and Diane Ebert-May. There are several on-line tools to help with problems with the Avida-ED program
BIRDD is a rich collection of primary scientific data and supporting materials about the Gal·pagos Islands and Darwin's finches.
Medical personnel investigate differences in response in individuals exposed to staph.
BeeVisit enables students to evaluate the relative contributions of different pollinator species to a plant's reproductive success through an interactive model of pollen transfer.The model tracks a plant's presentation of pollen through time; pollen may be presented gradually or all at once, and the program lets you choose from a family of power curves to model the shape of the cumulative pollen presentation curve over a set number of time intervals (usually 100). Then, 'bees' of 1, 2, or 3 types are allowed to visit the plant.You specify the expected number and type of visits; this sets the probability of a visit occurring during each interval, and visits occur stochastically according to these probabilities.
PURPOSE: A simple Excel-based workbook with worksheets as a front end for the AT&T GraphViz Graph Layout software suite. BioGrapher enhances Excel-based tools developed in the Chemistry and Biology Departments at Beloit College to allow for convenient visualization of graphs and graphical connections that are importantin systems and computational biology, molecular biology, biochemistry, and genetics.
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 site from BioQuest briefly explains how scientific knowledge is created, modified, and used. By using problem posing, problem solving and peer persuasion, students will experience science from the point of view of a practicing biologist.
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 text manual introduces statistical analysis and its underlying philosophy, enabling students to understand how to describe the confidence they have in their analysis.Statistical analysis is one of the most widely used, and abused, techniques in the biological sciences. Statistics are ostensibly used to allow an investigator to be objective. That is, the researcher uses statistical tests to determine whether or not his/her hypothesis is supported by the data collected.Unfortunately, the choice of the particular statistical test is often not objective and the underlying limitations of individual tests are often ignored or unknown by the researcher. Yet statistical analysis, when appropriately applied, allows scientists to examine the probability that their hypotheses are or are not supported by the data collected.
The Biosphere 2 project of the early 1990s failed dramatically because the planners overlooked the metabolic activities of naturally occurring soil microorganisms. The simulation program SimBio 2 allows us to gain insights into the complexity of this closed ecosystem. Here we can manipulate and monitor variables within a virtual Biosphere 2. We will explore oxygen availability by taking a closer look at the relationship between organic materials and living microbial populations in the soil. Alternative models can be constructed and simulated. * run simulations of a model of the Biosphere 2 to explore the unexpected impact of microbial metabolism on closed system dynamics
The discovery of anthrax spores in the Senate Office Building in Washington in October 2001 as well as in several post offices caught microbiologists unprepared for their central role in the War on Terrorism. Infection control specialists were challenged to think of new strategies to confront the anthrax problem. How would you respond to this crisis? * develop a plan to decontaminate areas in the Senate Office Building where anthrax spores have been found
Images of a flock of black-backed gulls off the coast of Dunedin, New Zealand in February 2009. The original image is divided into nine contiguous quadrats.