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Collection: BioQUEST Library OnLine
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- Abstract: This interactive L-system simulation produces visualizations of tree forms based on data from specimens in the field or laboratory.
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- Abstract: 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.
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- Abstract: A text chapter that introduces and explores some of the key issues in the 3Ps (Problem-posing, Problem-solving, and Persuading Peers) philosophy behind the activities of the BioQUEST Curriculum Consortium and the materials included in The BioQUEST Library.
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- Abstract: 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
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- Abstract: This tool aids in investigating relationships between interacting data elements or data clusters analysis in genetic mapping and in competition between different groups of organisms and their resource requirements.
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- Abstract: 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 important
in systems and computational biology, molecular biology, biochemistry, and genetics.
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- Abstract: 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.
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- Abstract: BIRDD is a rich collection of primary scientific data and supporting materials about the Gal·pagos Islands and Darwin's finches.
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- Abstract: The Cardiovascular Construction Kit (CVCK) allows students to design and construct a wide range of cardiovascular systems, testing each one to see how it behaves and whether it could actually exist and survive in a real organism. CVCK provides a set of basic components, e.g., pumps, vessels, capillaries and so on, which may be pieced together to construct a cardiovascular system. Gauges and measurement techniques are provided so you can draw conclusions from your experiments. Note: CVCK is a MAC Archive Module and requires System 6.05 to System 6.07.
To construct cardiovascular systems with CVCK, select components from the menu bars, drag them onto the main screen, and connect them together by making them touch.
CVCK makes it possible to construct experiments as well as systems. Such experiments allow comparisons of the performance of systems with different configurations or characteristics.
One constructs experiments by deciding what aspects of performance need to be measured and by hooking up gauges at appropriate places.
Gauges that can measure variables like pressure and blood flow can be connected to the components, and the values that are read from these gauges can be displayed in the form of a graph.
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- Abstract: The CFL simulation includes two models: the original Isolated Heart Lab, which models an isolated left ventricle, and a new Closed Circulation Lab
The Closed Circulation Lab models the entire circulatory loop: left ventricle, peripheral circulation, right ventricle, and pulmonary circulation.
Both models include numerous input parameters that can be controlled by the user. Some of these parameters are shown in Figures 1 and 2. By manipulating these physiological variables, students can design experiments to investigate a variety of questions concerning how changes affect the performance of the heart.
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- Abstract: This software can be used to investigate common molecular biology laboratory procedures using DNA or protein sequence data. These simulations and cases are based primarily on genetic and infectious disease with techniques such as: DNA electrophoresis, Southern blot, PCR, Multiplex PCR, Dot blot, ELISA, Western blot, 96-well PCR, protein electrophoresis.
Case It! is collaborative BioQUEST project between the University of Wisconsin-River Falls and Michigan State University.
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- Abstract: Cell Differentials offers a visual dataset of white blood cells that gives students practice in developing strategies and techniques for the recognition of these blood cell types.
Over 100 different cell images are randomly presented with feedback on successful identification.
In traditional labs, the recognition of white blood cell types can be compromised by several factors. Developmental changes can make recognition difficult and some cell types exhibit similar features. Microscopy can be a very individualistic kind of experience in which opportunities for instructor comments are often limited to spot checks of student comprehension. Cell Differentials was developed as a wet lab preface to provide students with abundant real-time feedback and tools to evaluate their own learning progress.
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- Abstract: CuraÁao is a computer program that simulates the sterile insect release method (SIRM) of pest population suppression, first conceived by E. F. Knipling (1955).
The user can investigate the effects of several variables on the effectiveness of the method and discover what happens when some of the basic assumptions of the model are relaxed or violated in some way. The user should gain some understanding of the sorts of things that complicate the application of the technique in situations that are more realistic than those assumed by Knipling in his simple analyses.
The simulation takes place on the Caribbean island of CuraÁao where Knipling first demonstrated the feasibility of sterile insect release. The island is divided into 2 or 3 zones, with differing numbers of cells (or levels of spatial resolution) in each zone.
The simulation can be either deterministic or stochastic. There are four factors which can be made density dependent: the probability that a female will mate, fecundity, survival, and the probability of emigration from a cell.
The Native Insect Population dialog box allows you to set the initial populations of native insects in each of 3 zones and to set the native population parameters, including the aggregation index, the probability of emigration, the proportion of females, the eggs per female and the survival to adult rate.
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- Abstract: The Data Collection and Organization (DC&O) text module provides background on useful, general-purpose software tools. The aim is to discuss types of generic software that virtually every well-equipped scientist uses. This includes: spreadsheets, database programs, statistics packages, graphics programs, and word processors.
DC&O includes several examples of the use of these tools in biology. These include 'An Embryological Example with Tips and Tricks' and the complete text and dataset of a classic evolutionary study published in 1899 by Hermon Bumpus ('The Elimination of the Unfit as Illustrated by the Introduced Sparrow, Passer domesticus'). The Bumpus data can be used to investigate problems in natural selection.
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- Abstract: The Developmental Selection module is a research simulation that allows students to investigate the possible causes of incomplete embryo development in perennial legume fruits.
Two competing hypotheses are proposed to explain patterns of seed abortion - the pollen tube competition hypothesis and the maternal resource limitation hypotheses. Students can explore these competing hypotheses by setting up experimental problems and then collecting and analyzing their data.
The Developmental Selection interface includes three sliders that the student can control to influence seed abortion rates (Seed/Ovule Ratio) and the relative influence of pollen tube competition (PTC) and maternal resource limitation (MRL).
Other interfaces emphasize data collection, data analysis and a summary of observations.
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- Abstract: Using the Extend 'connect-the-components' visual programming, students can model and simulate ecosystems including social and economic forces as well as study parameter variations to develop an understanding of ecosystem function and productivity.
By making 'what if...' changes in the model, the effects of various proposed decisions about the environment can then be shown.
EDM includes three ecological systems: Ponds, Grasslands, and Logging. Students can predict results of changes in the models and explore relationships.
First, you diagram a model of the system showing parts and connections among them. For example, components of the model, such as the sun, are placed on the computer screen. Each component is linked to the others with a mathematical relationship, such as the transfer of the sun's energy to plants.
Values are entered into block dialog boxes to characterize the interactions of the components, such as the amount of sunlight at a particular location or the initial number of bluegill in a pond. When the simulation is run, you can see the growth curves of the various components of the system.
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- Abstract: This program allows users to graphically enter population and disease characteristics (e.g., the virulence of the pathogen, the likelihood of transmission), to set up an initial population, and then observe the changes in population characteristics and the prevalence of the disease through time.
Using modified SIR-type models (Susceptible-Infected-Recovered), Epidemiology allows students
* to ask a variety of "what if" questions
* to design and perform their own investigations
* to explore the implications of various public health policies
The direct-manipulation, graphical interface encourages exploration, and makes the program accessible to introductory students.
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- Abstract: Evolve allows students to model evolution and get quick results from population genetics experiments.
With Evolve, you can control:
* the starting population size
* overall population size
* intensity of natural selection
* pattern of inheritance
* proportion of migration in a hypothetical population
Learners could develop:
* a better understanding of evolutionary processes and their interactions
* the ability to differentiate between the effects of fecundity and survival in natural selection
* a firmer grasp of some important concepts of Mendelian genetics
* a greater understanding of experimental design and the use of models
A Windows version in currently in beta-testing.
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- Abstract: Genetics Construction Kit is a simulation of a classic Mendelian genetics laboratory. It provides students with a set of organisms with unknown patterns of inheritance, and gives them the tools to design and perform a series of experiments to discover these inheritance patterns.
Students will be able to cross the unknown organisms and analyze their crosses in ways much like those used by practicing scientists.
GCK provides several tools for analyzing and organizing data:
* Vial Summary Chart summarizes the contents of a vial or set of vials
* Cross Matrix records the crosses made so far and indexes the vials generated by these crosses
* Chi Squared Worksheet allows students to test whether observed numbers differ significantly from the ratio expected under a given hypothesis.
GCK comes with several predefined problems designed to present a different aspect of genetics or to illustrate a particular problem. In addition, by using the problem editing utility, it is possible to customize a problem to meet your specific needs.
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- Abstract: Sampling of aquatic microorganisms reveals a surprising feature of many open water systems - stratification.
Students can model the effects of reducing nutrient loads to surface waters on microbial populations and oxygen levels within the Mississippi River basin and Gulf of Mexico Hypoxia Zone.
Planktonic and benthic microbes occupy distinct zones in stratified water columns. Explore how the benthic consumer populations respond to environmental cues such as changes in sunlight, wind effects, or increases in organics due to pollution with the model HypoxiaZone.
Although hypoxia zones are natural phenomena, increasing pollution from human activities and natural events is affecting the size and persistence of these zones in ways that threaten to disrupt the natural ecology of the systems.
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