training 3/2

Was shown around the lab today. Went over safety procedures. Saw some cool fish posters. Realized I could use another fish poster at home.


Happy New Year! Today, I used ImageJ on the images. I initially had to review the process by using one of Dr. Trigg’s images but then I got into the swing of things as I used one of the clam images. I am hoping to do this on about 2 or more images tomorrow as well.

January Summary

Thursday, January 5 Happy New Year! Alright, last post I was ironing out some issues related to temperature vs. bitterness. Goals for this month (I’ll keep this short, as I’m writing this during lab meeting!) Modeling Visual Positives: For each final weighted model, create graph of each variable’s relationship to bitterness Continue writing up results and discussion Outline introduction Examining Short-Term Temperature Response: Get in touch with the journal – I’ve fixed all issues, but they haven’t gotten back to me, so need to communicate with them! Set up structure where I methodically lay out reviewer comments and my existing paper in the Google doc, start fixing up. Note: I’ve heard back from Reviewer 1 but not Reviewer 2. Start fixing up graphs to be paper-quality Overall Choose a day for thesis defense That finishes it up, let’s see how it goes!

from Aidan F. Coyle

December Summary

Monday, Dec. 5th Happy holidays – first post of December! Took the first few days of the month off to head back to Cleveland (congrats on the wedding, David!). To recap, I’ve got two papers that I’m working on at the moment. First, a paper examining the relationship of various environmental and physical variables to visual BCS positive C. bairdi by using GLMMs on a huge ADFG dataset. This is the focus of most of my work at this point – I’m in the writing up stages! The second is a paper that uses RNAseq to examine the response of infected C. bairdi to short-term temperature changes. I’ve submitted this one to Frontiers in Marine Science, but still have edits to make. My to-do lists for each task is below: Modeling Visual Positives: For each final weighted model, create graph of each variable’s relationship to bitterness Upload existing graphs to…

from Aidan F. Coyle

November Summary

Thanksgiving Update: 2022-11-23 Alright, it’s been quite a while since I’ve posted, so it’s definitely time for an update (apologies for the delay)! Big news: Got my paper submitted (the one examining gene expression in C. bairdi and Hematodinium)! Hopefully will hear back soon, but glad the bulk of it is over! Other updates: Have begun working on a paper on the modeling work I’ve been doing! Finished up the Methods section (well almost, just need to confirm my methods are sound), and have been moving on to the Results. Next goal is to produce some pretty figures for that! One big obstacle to getting there is saving the model results – I ran all four models once and the results sure look saved just fine, but to confirm I’m using the correct read-in function, I need to run the model again so I can have a before/after of reading…

from Aidan F. Coyle


This past week, I watched the video on how to splice up a video and read a bit of Grace Candall’s paper: Characterization of Reproductive Maturation in Geoduck Clams (Panopea generosa). I also begun to sort out the images that are of the males and those of the females.

10/17 Transfer of Test Tubes

Today, I worked on transferring boxes of test tubes from the smaller fridge into the larger, longer fridge. I moved half of them into a bin I labeled #11 and placed about half of them into another bin labeled #8. I documented this into a list that I have attached below.

10/05 Bottles of waste

Today, I came in to get started helping out in the lab. I spent time counting the number of waste bottles in the lab and put tape on most of the bins to label the approximate number.

September Summary

Alright, monthly goals are to do the following! Get feedback on models, use proper diagnostics Interpret modeling results Finish methods of modeling paper, start on results/intro We also have some secondary goals – these are more dependent on when I get the edits back, but Another round of edits on temperature analysis paper Thursday, September 1st Modeling: Crafted some nice loops to do some diagnostics. Found a persistent issue – when I use simulate() to check model accuracy and then compare the number of simulated BCS+ crab vs. the true number, it’s persistently underestimating (by a little for the All Crabs model, by a lot for the Females model), or overestimating (for the Males model) the number of BCS+ crab. I’m not sure exactly what is going on here. Could be a minor issue with how random effects are specified in simulate(), could be a more major issue with the…

from Aidan F. Coyle

August 10th

Today, I have been spending time working on the poster and editing my abstract.