Aipotu

(Formerly the Molecular Genetics Explorer)

• Information about the authors
• Using this tool for Genetics
• Using this tool for Biochemistry
• Using this tool for Molecular Biology
• Using this tool for Evolution
• Download Aipotu
• Lab Manuals
• Acknowledgments
• More Software by the Authors

• Life can be explained in terms of The Individual Functions of Living Things.
• Genetics explains The Individual Functions of Living Things in terms of Genes.
• Biochemistry explains The Individual Functions of Living Things in terms of Proteins.
• Molecular Biology connects Genetics and Biochemistry by explaining how Genes encode Proteins.
• Evolution provides a context that explains how these features changed over time to become what they are.

You are provided with a starting set of flowers in the Greenhouse; these organisms are saved as organism files, each of which contains two DNA sequences. These organisms are loaded into the Greenhouse when the program starts.

BW gave a PowerPoint Presentation about Aipotu at the Evolution 2008 conference.

• Power-point format
• .pdf format

• Brian White (UMB Biology): web page, e-mail.
• Ethan Bolker (UMB Computer Science): web page, e-mail.

Genetics

Use the Genetics Tool by clicking the Genetics tab.

• 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.

Biochemistry

Use the Biochemistry Tool by clicking the Biochemistry tab.

• 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.

Molecular Biology

Use the Molecular Biology Tool by clicking the Molecular Biology tab.

• 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.

Evolution

Use the Evolution Tool by clicking the Evolution tab.

• 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.

• Aipotu for Windows
• Aipotu For Mac OS X
• Aipotu For UNIX/Linux

• Part I:Genetics:
• MS Word format.
• Adobe Acrobat (.pdf) format.
• Part II: Biochemistry:
• MS Word format.
• Adobe Acrobat (.pdf) format.
• Part III: Molecular Biology:
• MS Word format.
• Adobe Acrobat (.pdf) format.
• Part IV: Evolution:
• MS Word format.
• Adobe Acrobat (.pdf) format.

• Version 1.2.3 as of October 29, 2009.
• Save Greenhouse As... now works properly
• Backbone trace in Biochemistry now is more visible
• Return key now folds protein in Biochemistry and Molecular Biology
• Version 1.2.2:
• Allows running one generation at a time in Evolution
• Greenhouse automatically saves at every change
• Misc bug fixes
• Version 1.2.1:
• Can disable mutations with one button click
• Deals with extinction properly
• Version 1.2:
• Now takes better screen snapshots and can save these to file
• Now has pop-up windows that give the names of the colors for colorblind students. This can be turned off in the Preferences.

• Sumana Adma
• Vinod Aggawal
• Bogdan Calota
• Ruchi Dubey
• Tao-Hung Jung
• Pradeep Kadiyala
• Chitra Karki
• Prasoon Kejriwal
• Nikunj Koolar
• Wei Ma
• Naing Naing Maw
• David A. Portman
• Namita Singla
• Chung Ying Yu
• Ziping Zhu