isee Exchange™

Number of items: 29

Date joined: Apr 05 2016

Jon Darkow's Work

Lactase simulation with variable sample sizes

sim ⋮ 98 runs

Photosynthesis Model with Sample Size

sim ⋮ 13 runs

HPV and Adaptive Immune Response

sim ⋮ 930 runs

HPV Antibodies feedback loops vaccine

Photosynthesis Model

sim ⋮ 29097 runs

Cardiovascular Model

sim

Ground Finch (Geospiza fortis) on Daphne Major

Adaptation of ground finch

sim ⋮ 51 runs

evolution biology

Lactase Enzyme Simulation with Data Analysis

sim ⋮ 77574 runs

Extinction Vortex

sim ⋮ 918 runs

Recombination and Gene Linkage

sim ⋮ 1882 runs

#10

Apterous Genetics

Apterous is an allele that results in a fly without wings. Wild-type variants have normally function ... Read more

Apterous is an allele that results in a fly without wings. Wild-type variants have normally functioning wings. The goal of this simulation is to determine the pattern of inheritance for the apterous phenotype. Is apterous dominant or recessive? Sex-linked or autosomal? Complete, incomplete, or codominant?

sim ⋮ 6011 runs

Genetics

#11

Thyroid Hormone - Negative Feedback

sim ⋮ 136 runs

negative feedback thyroid hormone metabolism biology

#12

Water Potential and Osmosis

Factors that affect the flow across a semi-permeable membrane.

sim ⋮ 3021 runs

#13

Chaos Theory: Strange Attractor

Manipulate the main variables of the Lorenz equation.

sim ⋮ 2 runs

chaos theory Lorenz attractor manifold

#14

Logistic Growth Model and the Butterfly Effect

Model allows users to test the starting population size (N), the carrying capacity of the populatio ... Read more

Model allows users to test the starting population size (N), the carrying capacity of the population (K), and the intrinsic rate of growth (r max). Iterations are discrete, not continuous.

sim ⋮ 104 runs

logistic growth carrying capacity

#15

Transformation Simulation

Simulation allows students to test the transformation principle. Two major goals of the experiment a ... Read more

Simulation allows students to test the transformation principle. Two major goals of the experiment are: 1. Allow users to see that supernatant from heat-killed bacteria can transform the genes of another bacterium. 2. What transforms the inheritance of the bacteria is DNA, not RNA or proteins.

sim ⋮ 660 runs

transformation DNA biology

#16

Evolution and Natural Selection

sim ⋮ 7046 runs

#17

Neurophysiology and Neurotoxicity

The main dependent variable measured in the model is the membrane potential (millivolts) of a motor ... Read more

The main dependent variable measured in the model is the membrane potential (millivolts) of a motor neuron and the muscle fiber it innervates. You will be able to add excitatory and inhibitory neurotransmitters, and compare how neurotransmitters modulate the electrical impulses of the motor neuron and the muscle fiber. Additionally, you will be able to compare the effects of four neurotoxins: Tetrodotoxin, botulinum toxin, sarin nerve gas, and VX. While extremely lethal, these toxins are very instructive in understanding neurons because of the specific way the toxins act. Each toxin modifies or inhibits a specific molecule in neurons that help process and transmit information.

sim ⋮ 1 run

Neurophysiology toxins sarin VX TTX

#18

Evolution of LAP Allele in Mussels

sim ⋮ 2799 runs

Evolution Natural Selection Cline

#19

Evolution

Evolution of Populations: Genetic Drift, Natural Selection, and Mutations

sim ⋮ 1105 runs

evolution natural selection genetic drift

#20

Trp Operon

Tryptophan is an amino acid that is synthesized by plants and bacteria from other molecules in a bio ... Read more

Tryptophan is an amino acid that is synthesized by plants and bacteria from other molecules in a biochemical pathway (see diagram below). The trypophan operon is a series of sequential genes found on a bacterial genome. The genes of the operon produce the enzymes that direct the synthesis of tryptophan. In this model you will experiment with the negative feedback loop of the repressible system.

sim ⋮ 671 runs

Feedback loop operon biology tryptophan repressible

#21

Steady State in Freshwater Ecosystems

sim ⋮ 2249 runs

#22

Cellular Respiration Accounting Model

The purpose of the model is to understand how glucose is metabolized, and how the energy stored in i ... Read more

The purpose of the model is to understand how glucose is metabolized, and how the energy stored in its chemical bonds is transfered.

sim ⋮ 5903 runs

cellular respiration aerobic respiration ATP biology

#23

Lactose Operon: An Inducible System

In this simulation users explore the negative feedback system of the Lactose Operon found in bacteri ... Read more

In this simulation users explore the negative feedback system of the Lactose Operon found in bacteria. Lactose induces the system by inhibiting and inhibitor.

sim ⋮ 3142 runs

Inhibition negative feedback biology lactose operon

#24

Information Processing and Neurophysiology Model

The main dependent variable measured in the model is the membrane potential (millivolts) of two diff ... Read more

The main dependent variable measured in the model is the membrane potential (millivolts) of two different neurons in a series. You will be able to add excitatory and inhibitory neurotransmitters, and compare how these modulate electrical impulses of the two neurons. Additionally, you will be able to compare the effects of three neurotoxins: Tetrodotoxin, botulinum toxin, and sarin nerve gas. While extremely lethal, these toxins are very instructive in understanding neurons because of the specific way the toxins act. Each toxin modifies or inhibits a specific molecule in neurons that help process and transmit information.

sim ⋮ 15232 runs

infromation processing neurophysiology biology

#25

Tryptophan Operon: A repressible system

sim ⋮ 10 runs

#26

White-Eyed Genetics

White-eyed is an allele that results in a fly white eyes. Wild-type variants have red eyes. The ... Read more

White-eyed is an allele that results in a fly white eyes. Wild-type variants have red eyes. The goal of this simulation is to determine the pattern of inheritance for the white-eyed phenotype. Is yellow body dominant or recessive? Sex-linked or autosomal? Complete, incomplete, or codominant?

sim ⋮ 2935 runs

Genetics

#27

Growth Factors, Cyclins, and Cancer

Explores the feedback loops that regulate the cell cycle. Model focuses on manipulating stimuli (gro ... Read more

Explores the feedback loops that regulate the cell cycle. Model focuses on manipulating stimuli (growth factors), to stimulate the cell cycle feedback loops.

sim ⋮ 2857 runs

growth factors cyclins cell cycle cancer

#28

Phenology of the Karner Blue Butterfly

Karner Blue butterfly is an endangered species. Habitat loss and climate change are contributing fac ... Read more

Karner Blue butterfly is an endangered species. Habitat loss and climate change are contributing factors to the reduction in the butterflies' population sizes. Climate change can alter the timing of lifecycles. When climate change disproportionally affects the timing of life cycles of species in an ecosystem asynchrony within a food web occurs.

sim ⋮ 190 runs

asynchrony timing phenology climate change butterfly

#29

Population dynamics of white footed mouse

sim ⋮ 14165 runs

Uploading a Bundle from Zip

Instead of creating bundles, categories, and assemblies one by one, you can upload a single zip file that contains all of your bundle's content. To create your zipped bundle, make a folder with your bundle's name and add subfolders with your categories' names. The folder tree should have the same structure that you want the categories to have in your bundle. Place your assembly .stmx files in the appropriate category folders, then zip your bundle folder and upload it using the Upload Bundle from Zip link above.

Assemblies, Bundles, and Categories

Assemblies are self contained models that demonstrate common ways to connect together building blocks and that can be used as parts of other models. This is analogous to using prefabricated wall and roof pieces to construct a house.

Bundles are groups of assemblies with a common use or theme. For example, a Health Care bundle might contain a variety of assemblies that aid in creating health care models. When you download assemblies from the isee Exchange™, you download an entire bundle, rather than individual assemblies.

Categories are subgroups of assemblies within a bundle. For example, a Health Care bundle might contain a Funding category for assemblies related to the management of hospital funds. All assemblies must be assigned to a category—they cannot be assigned to the root of a bundle.

Assemblies, bundles, and categories can be created and uploaded to the isee Exchange™ via the options on the Manage My Assemblies page. To learn more, visit our help pages, or take our assemblies tutorial.

Sim App (Sim)

An interface that allows users to interact with a model.

Sim apps allow users to interact with a model using buttons, sliders, knobs, tables, graphs, and storytelling. These interactions help users understand how parts of a system interact.

Interfaces are created by model authors in the Stella desktop software and can be uploaded to the isee Exchange™.

Model

A diagram that represents how elements in a system influence one another.

Models are mathematical representations of how elements in a system are connected and interact (e.g., ecosystems, organizations, supply chains). When running models on the isee Exchange™, results can be viewed in output devices like graphs and tables.

Models appear in the isee Exchange™ directory when authors upload them from the Stella® desktop software or create them with Stella Online™.

Causal Loop Diagram (CLD)

A map that represents the feedback structure of a system.

CLDs are high-level maps that represents the feedback structure of a system and easily communicate the essence of a model. They appear in the isee Exchange™ when authors upload them from the Stella desktop software or create them with Stella Online™.

Jon Darkow's Profile