This interactive L-system simulation produces visualizations of tree forms based on data from specimens in the field or laboratory.
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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.
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.
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.
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 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.
The CFL simulation includes two models: the original Isolated Heart Lab, which models an isolated left ventricle, and a new Closed Circulation LabThe 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.
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.
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.
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.
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.
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.
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.
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 policiesThe direct-manipulation, graphical interface encourages exploration, and makes the program accessible to introductory students.
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 modelsA Windows version in currently in beta-testing.
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.
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.
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.
This text module focuses on the use of narrative cases as a way to initiate student-centered investigation. Cases are descriptions of richly complex, realistic situations and the people, organisms, and systems involved in those situations. In the first version of this module, three cases in multiple parts are presented in Kingdoms Entangled: Molecules, Maize, and Malaria. The cases all share a central event that organizes the action, namely a blight of corn caused by a fungus. Its main characters are two graduate biology students studying corn genetics and ecology. The current version expands on implementation and assessment issues as well as the role of resources in case development. Over 60 faculty developed investigative cases can be found at: http://bioquest.org/icbl
Java Demography, an application that simulates exponential growth in age-structured populations, enables users to manipulate values for age-specific mortality rates, fertility rates, and initial population characteristics.Through observation of how population characteristics change through time, users of Java Demography can investigate important questions in population biology, develop a deeper understanding of fundamental population concepts, and explore issues related to population policy.
This model of the lateblight life cycle in potatoes allows students to simulate the effects of environmental variables on the Phytopthora infestans life cycle.Crop scientists frequently use simulations to try to convince themselves and others of the reasonableness of a new control method. They can use simulation results to support their claims.
Lateblight allows students * to manipulate the variables that affect the development of late blight * to adjust the economic parameters that determine the cost-effectiveness of the disease management proceduresStudents can also simulate the use of potato cultivars by altering: * the level of resistance to the fungus * the time of initiation of tuber production * the yield potential of the crop in the absence of disease
MacRetina simulates data from retinal ganglion cells in the eye to the brain.By sampling neural activity while stimulating the retina with small spots of light, students can see the dynamic excitatory and inhibitory responses of these neurons in the simulation, and map the organization of the retinal region that drives the cell's receptive field.MacRetina is modeled accurately on published data and is a realistic simulation of a lab experiment that would otherwise be beyond the reach of the typical undergraduate laboratory. The program models 10 retinal ganglion cells with overlapping receptive fields. A cell may be an on-center type cell or an off-center type cell and may have either sustained or transient response dynamics.
A µGCK problem starts with a field collection of bacteria, either in a test tube or plated onto a petri plate. Each of the gray circles on the plate represents one colony. These colonies result from bacteria collected from the field. The colonies are of unknown genotype and phenotype, although all bacteria within a colony share a genotype and phenotype.µGCK includes several tools to help organize and analyze the data that are collected during an experiment. The Media Matrix window displays the media used by all current plates and tubes; phenotype worksheets record the phenotypes of colonies; complementation worksheets record the complementation behavior of a plate's colonies.µGCK comes with several predefined problems designed to present a different aspect of microbial genetics or to illustrate a particular problem. In addition, using the problem editing utility, it is possible to customize a problem to meet your specific needs.
Modeling: A Primer - The crafty art of making, exploring, extending, transforming, tweaking, bending, disassembling, questioning, and breaking models. Explore how to use, analyze, and criticize some important and historically influential models in biology in this text only module. See Modeling Tools to simulate modeling.
The simulation program Logistic Growth provides the user with a number of ways to graphically analyze, interpret, and understand the behavior of the logistic growth equation and minimum density limited logistic growth equation.The second simulation program allows users to generate a binomial distribution model of blending inheritance.
With the Genetics Tool, you can: * Cross two organisms * Self-cross one organism * Create mutant versions of one organismWith the Biochemistry Tool, you can: * Look at the structures and colors of the pigment proteins found in one organism * Design proteins and observe their shapes and colors * Compare the amino acid sequences of different pigment proteinsWith the Molecular Biology Tool, you can: * Look at the DNA, mRNA and protein sequences of pigment protein genes * Design genes and observe the colors of the resulting proteins by editing the top DNA strand * Compare the DNA sequences of different pigment protein genes * Create new organisms by specifying their DNA sequences
PEACH simulates the annual carbon supply and demand in peach trees. Calculations represent the amount of carbon produced in photosynthesis and the amount of carbon used for growth and respiration. The program simulates tree growth on a daily basis for one growing season. Students may use PEACH to test their understanding of integrated plant growth. It models typical horticultural operations such as thinning and pruning.Fruit, leaf, current-year stem, branch, trunk, and root weight are the state variables in PEACH. The minimum and maximum air and soil temperatures, degree-days, solar radiation, and canopy light interception are the driving variables. The rate variables that characterize photosynthesis, maintenance respiration, and growth are derived from experimental studies on PEACH.
This simulation allows students to manipulate environmental variables in a life cycle model of a normally benign dinoflagellate to produce an outbreak of its toxic form.The dinoflagellate Pfiesteria piscicidais an intriguing microbe with complex interactions that has been linked to large fish kills in the waters of North Carolina and the Chesapeake Bay.Examine the effect of environmental variables associated with outbreaks such as flooding and fish density with a model of the Pfiesteria life cycle.
Phylogenetic Investigator (PI) is a software package designed to facilitate creative problem-solving in phylogenetic analysis for the purpose of teaching and learning phylogenetic inference. Users can identify characters and states, polarize characters, and engage in directed-search phylogenetic tree construction.PI also allows the user to * make inferences and represent them one step at a time * vary representational features of their trees (such as angle of divergence and time between speciation events) * create reticulate tree patterns * view all of the character transformations at one time. In addition, PI can generate plausible data stochastically for modeling and practicing tree construction.
Resistan is a mechanistic simulation model of the process of selection of fungicide-resistant biotypes of a hypothetical fungal pathogen of a hypothetical crop.The fungus is a polycyclic organism with many generations per season. There is no genetic component in this simulator. Reproduction is assumed to be asexual. A small proportion of the initial inoculum is designated as the fungicide-resistant biotype at the start of the season, and the response of that population to various fungicide spray programs is observed as the season progresses.Resistan can be made to simulate different fungi and different fungicides by changing the parameters that control the model.One interesting feature of this simulation is the ability to include economic factors in the simulation. Total costs, total revenue, and profit are calculated at the end of each season based on the following parameters: * Fungicide Cost is used in the benefit-cost analysis at the end of the simulation. * Application Cost is the cost of a single spray application in dollars per acre. This does not include the cost of the fungicide. * Fixed Costs are the total crop production costs, excluding the fungicide spray application cost and the cost of the fungicides. * Maximum Revenue is the expected revenue from the crop without any losses resulting from the disease.
Sampling is a computer tool designed to help biology students obtain a qualitative understanding of basic concepts related to estimation and statistics.Sampling presents the user with a group of hypothetical populations distributed throughout an area, and with tools for sampling these populations to estimate characteristics such as population size and density, the nature of each population's spatial patterning, and spatial correlations in abundance between populations. By manipulating the number of samples, the size of each sample, and the spatial location and patterning of samples, users of Sampling can investigate important questions in population estimation and, especially in conjunction with field studies, develop a much deeper understanding of fundamental concepts than would likely be obtained solely from limited field studies that can be conducted in introductory courses.
Using this simulation, you can manipulate virtual tubes of bacteria in a virtual lab to discover the transforming principle and recreate classic experiments in the discovery of DNA. How was the hereditary molecule isolated and identified? What decisions do we need to make as we recreate the lab work of researchers like Oswald Avery and his colleagues?
SequenceIt! is a simulation program that allows you to experience the art and logic of protein sequencing through experimentation.Your objective is to deduce the sequence of this polypeptide using many of the tools available to a practicing protein chemist.You specify the operations and the order of their application. Success in determining the protein sequence depends on your understanding of the experimental procedures and on the logic you use in executing those procedures. Operations available range from simple cleavage reactions (enzymatic and chemical) which break a polypeptide into smaller fragments to complex sequential analyses (e.g., Edman degradation) that provide sequence information.
From 1991 until 1993 the Biosphere system supported people, plants, and animals. Experiments offered the opportunity for tracking in great detail the interactions among land and water ecosystems and the atmosphere.SimBio2 offers several scenarios in which students can generate simulation graphs using actual data from the Biosphere 2 experiment. Studentscan explore some of the problems that affected Biosphere 2 such as higher levels of carbon dioxide than expected and the resulting decrease oxygen. Students can also create their own models and experiment with alternative strategies.
TB Lab is a simulated microbiology laboratory that allows users to explore how the bacteria responsible for the disease tuberculosis develop resistance to antibiotics. Students perform simulated experiments on strains of Mycobacterium tuberculosis to investigate how antibiotics affect bacteria and how bacteria can become resistant to antibiotics. The simulation is designed to help students understand the direct connection between genetic and structural differences, particularly as they potentially lead to a survival advantage in the face of a selective pressure.Facilities allow growth and antibiotic sensitivity experiments, biochemical assays to examine how antibiotics affect the bacteria's metabolism, and DNA sequencing experiments that allow students to look for genetic differences between strains of bacteria, and mutation experiments to observe the development and effects of spontaneous mutations.Students can produce three different kinds of data to support their investigations. They can grow bacteria with antibiotics, run chemical tests to discover how antibiotics affect cellular processes of bacteria, and compare certain DNA sequences of bacteria.
The simulation program is based on the Nobel Prize winning Hodgkin-Huxley model for excitation of the squid axon. The program simulates an excised squid axon by applying stimuli or clamps after setting the environment of the axon, changing its properties, and/or adding drugs or toxins.By using the program tools, experiments can be developed that explore a variety of nerve properties, ranging from classical phenomena such as threshold, summation, refractory period, and impulse propagation to more modern concepts of channels, gates, and eventually even molecular events.The simulation provides insight into the hypothesized mechanisms of excitation in a way that is not practical with animal preparations. These ideas can be explored at both beginning and advanced levels. You can dive into a full blown propagating action potential with 15 recording electrodes or you can begin with an unexcitable axon and gradually patch in the component parts. In every case there are animations linked to the computations which will help interpret any experiment.
The Visual Datasets text module discusses the concept of visual learning and presents some suggestions for ways to design learning environments that support students in developing visual literacy skills. Three visual datasets that can be used for problem solving activities in evolution, classification, development, and botany are included:Caminacules: A dataset of imaginary animals that can be used as the basis for a variety of problem-posing and problem-solving activities in evolution, classification, development, and others. Originally generated by J. H. Camin and described by Robert Sokal in an article in the 1983 Journal of Systematic Zoology, 32 (2) 161-163. Dendrogrammaceae: A dataset of imaginary plants that can also be used for problem-posing and problem solving activities in evolution and classification. Warren H. Wagner (The University of Michigan)Oh Phlox!: Close-up images of late season garden phlox plants and selected leaves with leaf miner damage provide opportunities for visual learning practice for the field and for exploration with the use of NIH Image or other graphics packages in biological investigations. Ethel Stanley (Beloit College and Illinois State University)