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

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 Lab

The <i>Closed Circulation Lab</i> 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.

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.

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

This model of the lateblight life cycle in potatoes allows students to simulate the effects of environmental variables on the <i>Phytopthora infestans</i> 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.

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.

With the Genetics Tool, you can:
* Cross two organisms
* Self-cross one organism
* Create mutant versions of one organism

With 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 proteins

With 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

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.

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.

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.

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)