Aipotu Formerly the Molecular Genetics Explorer
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Explorer molecular biology molecular genetics molecular genetics genetics explorer

Aipotu Description

Formerly the Molecular Genetics Explorer Aipotu is a software that creates a utopia that simulates the genetics, biochemistry, molecular biology, and evolution of organisms in a biologically reasonable and pedagogically relevant way.This software was formerly called the Molecular Genetics Explorer; it has been improved with the addition of an Evolution Workspace.Aipotu is a BioQUEST software simulation that integrates genetics, biochemistry, molecular biology, and evolution to study a biological phenomenon. It is designed to show students the connections between these three key disciplines of modern molecular genetics. It is based on "Botstein's Triangle".With the Genetics Tool, you can: * Cross two organisms by selecting two organisms from the Greenhouse and/or from either Work Panel and clicking Cross Two Organisms. The resulting organisms will then appear in in a Work Panel and an entry will be added to the History List. * Self-cross one organism by selecting one organism from the Greenhouse or from either Work Panel and clicking Self-Cross One organism. The resulting organisms will then appear in in a Work Panel and an entry will be added to the History List. * Create mutant versions of one organism by selecting one organism from the Greenhouse or from either Work Panel and clicking Mutate One organism. The resulting organisms will then appear in in a Work Panel and an entry will be added to the History List. * Save an organism to the Greenhouse by selecting one organism from the Greenhouse or from either Work Panel and clicking Add.... * Bring the results of a cross, etc. from the History List to a Work Panel by double-clicking the appropriate item in the History List and selecting the appropriate item from the menu that appears.With the Biochemistry Tool, you can: * Look at the structures and colors of the pigment proteins found in one organism by double-clicking the appropriate organism in the Greenhouse. * Design proteins and observe their shapes and colors by typing the single-letter code for the desired amino acids into the Amino Acid Sequence box and clicking the Fold button. The resulting folded protein will appear in the Folding Window and an entry will be added to the History List. * Compare the amino acid sequences of different pigment proteins by selecting the appropriate item from the Compare menu. * Bring a folded protein from the History List to a Work Panel by double-clicking the appropriate item in the History List and selecting the appropriate item from the menu that appears.With the Molecular Biology Tool, you can: * Look at the DNA, mRNA and protein sequences of pigment protein genes found in one organism by double-clicking the appropriate organism in the Greenhouse. * Design genes and observe the colors of the resulting proteins by editing the top DNA strand in either of the Gene Windows box and clicking the Fold Protein button. The color of the resulting folded protein will be displayed and an entry will be added to the History List. * Compare the DNA sequences of different pigment protein genes by selecting the appropriate item from the Compare menu. * Create new organisms by specifying their DNA sequences by editing the DNA sequences as above and clicking Add.... * Bring a gene from the History List to a Work Panel by double-clicking the appropriate item in the History List and selecting the appropriate item from the menu that appears.With the Evolution Tool, you can: * Load Selected organisms into the World by selecting them in the Greenhouse and clicking the Load button. * Set the relative fitness of each color by choosing values in the Relative Fitness items. * Set the rate of mutations in the Preferences panel, you can choose the per-base rates of point, insertion, and deletion mutations. * Start an evolution run by clicking Start. The organisms in the World will then be subjected to mutation and selection. * See counts of each color in each generation. * Pause the simulation by clicking the Pause button. You can re-start the simulation if you want. * Save selected organisms to the Greenhouse for study in the other sections of the program. * Save all the organisms in the World to a file. In the File menu choose Save World to file.... This file can be analyzed by other programs or loaded into Aipotu for another evolution run. Requirements: · Java 2 Standard Edition Runtime Environment What's New in This Release: · Save Greenhouse As... now works properly · Backbone trace in Biochemistry now is more visible · Return key now folds protein in Biochemistry and Molecular Biology

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