Meeting 3.29

Set Events seems to fix our issue.

Setting 4/7 tasks to zero in order to achieve more fitness disparity between tasks.

We'll see how this works out when our runs are done tomorrow.

Meeting March 21

Looking at the outcomes of early runs we discovered that EQU was evolving despite lack of incentive!

Troubleshooting: Discovered that events file was not reading in Environment.cfg files, we did not realize that actual environment information needs to be in Events.cfg

Fix: Combining Emily Jane and Erkin's python scripts to generate events files with randomized environment files within them.

Problem: When avida reads a change environment line, that doesn't work, it doesn't throw any errors, so we thought it was running fine, when avida was actually using the default environment file.
We need errors to let us know when some thing has gone wrong!!
Also, it would be much better if we could change Environment files on the fly!

Meeting 3.10.11

Tasks!

TASKS!

Did we do them?

Erkin has his files, so hurrah.

April has her script and will be generating 4 sets of 50 avida.cfg, each using a separate events file. Naming convention: avidaTA.cfg for avida "treatment" "a". Put each of these groupings of 50 in their own folder. Emily will share the events files that she generates with me once this is done.

Erkin will parallelize the runavida script.

We will reconvene Monday to do things. Same time, same place.

writing a python script to alter a text file

Actually kind of stupidly complicated.

But whatever, done, except for specifying directory paths (since I don't know how we're setting things up).

Meeting 3.1.2011

Meeting:

This is mostly stuff we're making calls on since our last post (which was like ten seconds ago).

So, we're going 250,000 updates for each treatment (equals will not be rewarded). And then, we'll switch to equals being rewarded (and nothing else being rewarded) for 50,000 updates.

When we do our bottlenecks, we'll do random kill-offs since there is no spatial structure to our experiment.

Decrease mutation rate - Art says default is high.

We don't need to do competition trials since we're doing the 50k updates with equals being rewarded.

Erkin: Generating randomized environment files. Art suggested making a pool of environment files (maybe 500 of them). Naming scheme: environmentxxx.cfg in which "xxx" is a number.

Emily: Generate a script to choose an environment file to use for the events file. eventx.cfg

April: Set up avida.cfg (100x100 grid, mut. rate=.003) and make iterate for 50 consecutive runs. Needs to open a avida.cfg file and choose a new eventsx.cfg file.

Concluding remarks: None.

To do list.

Things we need to do:

1) Make our set of randomized environment files:
These files will consist of a set of values
where sum(abcdefg)=7, 0=h=i
REACTION NOT not process:value=a:type=add requisite:max_count=1
REACTION NAND nand process:value=b:type=add requisite:max_count=1
REACTION AND and process:value=c:type=add requisite:max_count=1
REACTION ORN orn process:value=d:type=add requisite:max_count=1
REACTION OR or process:value=e:type=add requisite:max_count=1
REACTION ANDN andn process:value=f:type=add requisite:max_count=1
REACTION NOR nor process:value=g:type=add requisite:max_count=1
REACTION XOR xor process:value=h:type=add requisite:max_count=1
REACTION EQU equ process:value=i:type=add requisite:max_count=1


2) Set up 4 events files (python script to generate events files)

1-(Control A) Constant environment where 1=a=b=c=d=e=f, 0=h=i, every 500 updates kill off 95% of population
2-(Control B) Constant environment where 1=a=b=c=d=e=f, 0=h=i, every 5,000 updates kill off 95% of population
(these second two need to be x50, with different random environments)
3-(Treatment A) Changing environment, every 500 updates, change to random environment.cfg, kill off 95% of population
4-(Treatment B) Changing environment, every 5000 updates, change to random environment.cfg, kill off 95% of population

IN ALL EVENTS FILES at 250,000 updates switch to environment file: where 0=a=b=c=d=e=f=g=h, 10=i .
allow to run for 50,000 more updates, log time EQU evolves


3) Set up avida.cfg
100 x 100 grid
Decrease mutation rate to 0.02
run for 300,000 updates


4) Run all 4 treatments x50.


5) Analysis!!