Using Avida

For the moment, the best version of Avida to use is available on the CSE linux machines. If you are in the department, you can use room 3340 where we have our labs (which other labs are linux labs?). If you are connecting in remotely, you should ssh into adriatic.cse.msu.edu.

The full avida documentation can be found here.

Obtaining Avida

Once on one of the linux machines, you can find all of the files you will need in the directory:

To copy these into your own account, cd into the directory you want them in and just type:

The quotas on the CSE accounts are relatively small; if you can fit the Avida files in your account, you can create a directory under /tmp and put them there. There is a much larger quota on these directorys, but they are periodically erased, so you don't want to keep anything there that you need.

We will also be making these files available for Mac and Windows relatively soon so that you'll be able to run them on your own machines.

Once you have the Avida files, there are two executables available to you.

avida is the "primitive" version, which will generate the output files, and denote its progress to the screen, but with no interaction.

avida-viewer is a text-based interface, which you used in class.

The remainder of these directions are assuming that you are using the text-based interface.

Extracting Organisms

When you are running Avida, sometimes you may wish to extract a specific organism for further study. To do so, follow these instructions:

• Pause the run by hitting 'p'
• Press 'c' for to choose a specific organism
• Move around the map screen to find an organism you like. Press enter when you find it.
• Press 'x' to eXtract the organism. This will tell you the name of the file it is being placed in.

You will now be able to find an file by this name in the data directory.

Alternatively, you can choose a specific organism from the Zoom screen. To do so:

• Pause the run by hitting 'p'
• Press 'z' to move to the zoom screen.
• Press '>' to shift modes to the component zoom.
• Press TAB to focus on the map in the zoom.
• Use the arrow keys to choose an organism. (You can use '<' to shift back to see stats about that organism).
• Press 'x' to eXtract the organism.

Other Notes:

In order to use the ncurses interface properly the TERM environment variable must be set properly. TERM=xtermc does not work properly.

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