Downloading, Installing, and
Running Aipotu

System Requirements:

• Hardware: The software will run on computers with 500mHz processors and 512mB RAM but protein folding will be slow; at least 1GHz processor and 1Gb RAM is best.
• Operating System:
  • Windows XP or higher. You may also need to install Java; it is available for free.
  • Mac OS X version 10.5 or higher. Java comes installed with OS X.
  • Linux it is compatable with many versions of linux. You may also need to install Java; it is available for free.

Download Aipotu from the link below for your particular operating system and follow the instructions below the link:

• Aipotu for Mac OS
1. This will put a .zip file in the folder where your downloaded files go (usually Downloads).
2. Double-click that .zip file and it will expand to the Aipotu app.
3. The Greenhouse is built in to the .app so you won't see a Greenhouse folder but Aipotu will run normally.
4. If you save any organisms to the Greenhouse, a Greenhouse folder will be created in your /Users/{your username}/Library/Application Support/Aipotu/ folder.
• Aipotu for Windows XP and above
1. This will put a .zip file in the folder where your downloaded files go (usually Downloads).
2. Go to your Downloads folder and find the Aipotu.zip file; it will look like a folder with a zipper on it.
3. Double-click that folder to open it.
4. Drag the Aipotu folder you find in that folder to your Desktop. This will un-zip the Aipotu folder. You must do this step or the program will not run!
5. In the Aipotu folder on your Desktop, you will find Aipotu.exe; double-click it to run it.
• Aipotu for Unix/Linux
  1. This will put an Aipotu.tar.gz file where your downloaded files go.
  2. What you do next is very dependent on your linux distribution. You must un-zip and un-tar the file.
  3. In the resulting directory, double-click the Aipotu.sh file to run Aipotu.

Version History

• Version 1.3.3 as of May 24, 2017.
  • Created single-app Aipotu for Mac OS to work with new security.
• Version 1.3.2 as of June 17, 2011.
  • Fixed bug where typed-in protein sequences were folded but not displayed.
  • Fixed some layout issues.
  • Fixed text selection in MoBo.
• Version 1.3.1 as of March 17, 2011.
  • "Non-foldable" or "toxic" proteins are no longer replaced, but are treated as lethal. Organisms with these proteins are dead (fitness = 0) and shown in gray
  • Added Average Fitness display to Evolution
  • Added Relative Fitness calculation and display to Evolution
  • Made both orange and purple colors easier to see
  • Refactored folding code to be cleaner
• 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.
  • OS X version signed to be compatible with Mountain Lion

Thanks to:

Aipotu and its components are the result of a multiyear collaboration among the two authors and the second author's computer science students. We thank (in alphabetical order) the following for their contributions to the code.

• 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