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…
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.
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.
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.
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…
Today, I have been spending time working on the poster and editing my abstract.
Today, I came into lab to work on R studio with Professor Roberts and Sam. They walked me through using R studio to form a box plot, teaching me the ways in which I can play around to make other graphs from the data. I also worked on finishing the draft of my abstract and putting my poster together. Professor Roberts and I talked about how the poster will be structured, and on Thursday, we will meet to continue working on this.
This morning begun with a lab meeting where we dived into the last chapter of Fresh Banana Leaves. The chapter focused on colonialism, eco-tourism and invasive species, among other topics. I will continue to work on the abstract today and tomorrow, I will come into lab to learn about using R studio with Professor Roberts.
Today, I came into lab to weigh the dried somatic and gonad tissues of the mussels 31-40. I placed a clean empty weigh boat and then tared it to zero before I weighed each dried tissue. Afterwards, I placed the tissues back into the oven and recorded the weights into the spreadsheet. Sam worked with me to get familiarized with using R by creating an account for me and walking me through parts of R studio. We played around with downloading the data into R, creating a graph and working with the labels.
Today, I begun this morning by working on the spreadsheet, and then I met with Professor Roberts to talk about the spreadsheet and to plan what will happen in the coming days. I asked questions about the RNA extraction process that I was unsure about, and what it could have meant to have no Cq values expressed. Professor Roberts showed me ways I need to consolidate information into one sheet – measurements of mussels (length, width and height), dry weight of the somatic and gonad tissues – along with the Cq mean values. This would allow us to find any relationship between any of the conditions. I was also introduced to the formula used to convert the Cq mean values into larger quantities that I can understand more easily, since the smaller the Cq, the more expression of the gene within the mussel. I will come in to weigh the dried out tissues tomorrow. We will also work on R next week Tuesday.