Update 3/25

Good job this week with presentation stuff (Great slides, Sara!). Alex is chugging along with the code (thanks!), and I hope that we're all starting to outline (mentally? on paper?) how we're going to support him. Nick, as things calm down in lab, please meet with Ian about the stats; he seemed to indicate our stats are going to be complex.

Update 3/19: A few additional notes

In the meeting with Phil, it was suggested that we email Chris Chandler to see if some of the issues he's solved will be useful to us. I just emailed Chris, so we're waiting on a response now.

Also, Phil suggested sending him notes and code the night before meetings on issues we're having so he can think about it overnight. Let's try to do that in the future. He also suggested that we should use something similar to his send/retrieve code for broadcasting and look at the devo lab wiki and the Avida documentation (online and within copy) more as we run into problems.

Update 3/19

Alex and I had a productive meeting with Phil, we've relaxed some assumptions, and hopefully we will have some running code soon. Additionally, Sara has made some wonderful slides, so everyone please look at them in prep for Tuesday.

TerraGrid

Hey everyone,
I just got an email that our TerraGrid account has been added! I will email you all with login info once it is made available.

3/16 Update -- Presentation Slides

I've sent around a draft of our update presentation for next Tuesday. If there's anything that isn't clear about our experimental design and plans, please let me know so that I can make changes.

Update 3/14

Today was productive! Alex and Nick discussed the code and runs, and Emily and Sara discussed the experimental design with Ian.

Updates to the experimental design:
1. Threshold loss: "Loss" is now defined as the point when 95% of the population no longer has the signaling genes. This is to combat a small number of signalers hanging out but the population as a whole losing the signal much earlier.

2. Runs will be at least 2500 and intended to measure the effect of linkage and population size on signal loss. Check my math.
genotype (2; linked or unlinked) X percentage of guaranteed success of signal (5; 100%, 75, 50, 25, 0%) X population size (5; 200%, 100, 50, 25, 10%) X runs (50) =2500

Update 3/3

Alex has gotten Avida to compile and will be working on getting things going. Unfortunately, Phil had to cancel this week, but we're still shooting for after the break to begin runs. Also, Sara is working with the updated proposal to begin writing the introduction.

Chugging along... but everyone still enjoy your breaks!

Update: 3/1

Alex and I have now scheduled things with Phil, and Alex is working to get Avida going to better understand how to modify the existing code. We'll discuss this Friday with Phil, but I just wanted to keep you guys posted. Also, I've been updating the proposal as we go, so hopefully we'll be able to used this as a skeleton for out paper.

Sara, can you find the PLOS guidelines? If we've got to write to those, it would be good if we know what they are.