---
title: "December 2023, Daily Log"
author: "Kathleen Durkin"
date: "2023-12-29"
categories: ["daily log"]
format:
  html:
    toc: true
---

# Daily Log

## 29 December 2023

#### Friday

-   Looked into more TTS tools, this time testing out some paid ones. Will be making a dedicated post about this once I've gotten through all the ones on my list.

## 28 December 2023

#### Thursday

-   Lab meeting -- Grace, Ariana, and Chris gave practice talks/outlines for SICB next week

-   Meeting w/ Laura and Ingrid to go over Laura's RNAseq data analysis workflow and scripts.

## 27 December 2023

#### Wednesday

-   Prepped for meeting w/ Laura & Ingrid tomorrow by reviewing RNAseq data analysis [notes](https://docs.google.com/document/d/1HzMTreqnY2BD-oyjEJRA-JECpFE4CXlEoWKkmiaTYis/edit) Laura sent.

-   Started modifying sRNAseq trimming/QC script from E5 work for use with the cod RNAseq data (once it's back). May test with snow crab data used in Laura's shared workflow

## 26 December 2023

#### Tuesday

-   Out

## 25 December 2023

#### Monday

-   Out -- university holiday

## 22 December 2023

#### Friday

-   Out

## 21 December 2023

#### Thursday

-   Lab Meeting

-   Joined Paperpile with lab license

## 20 December 2023

#### Wednesday

-   Read Chpt.3 of "Race After Technology" for lab meeting tomorrow

-   Read some papers reviewing sRNA analysis techniques using RNAseq data

## 19 December 2023

#### Tuesday

-   Lit review

-   Looking for good text-to-speech platform/app/etc. and tried some out. The free one I tried doesn't work well with academic papers, so want to get an academia-focused service through the lab.

## 18 December 2023

#### Monday

-   Finished Zotero paper-entry

-   Read some of those papers

## 15 December 2023

#### Friday

-   E5 molecular group meeting

-   Started reading about the nitty gritty of some ncRNA stuff (evolution, function, etc.) and then my brain started melting, so I'm gonna postpone that for a day when I've had more sleep 🙃

-   more Zotero paper-entry!

## 14 December 2023

#### Thursday

Hackathon 2023, Day Three!

-   Finished pulling and subsampling cod samples, and consolidated to send for RNAseq on Monday -- details [here](../../projects/pacific_cod/2023_12_14_pacific_cod.qmd)
-   Common recommendation for citation managers during lab meeting was [Paperpile](https://paperpile.com/) (for collaboration and easy integration with the Google environment) *with* a supplementary manager like [Zotero](https://www.zotero.org/) (for easier indexing, more detailed metadata, working offline). This sounds like a good plan to me! Messaged Steven about getting access to the lab paid Paperpile, and downloaded Zotero to start adding all my current lab-relevant literature.
-   Started the tedious process of adding all of the papers I have downloaded to my laptop and iPad to Zotero, and transferring my highlighting/notes for each

## 13 December 2023

#### Wednesday

Hackathon 2023, Day Two!

-   Finished overhauling my lab notebook site (for now). I reformatted the home page and added a site section for each of the projects I'm working on. For each project, have "about" page and posts for all the work I'm doing in that project (instead of having everything in just my daily logs). Still want to do something about all of the lit review notes/questions I currently have cluttering up my daily logs, but haven't 100% decided how I want to do that yet...

-   [Compiled spreadsheets](../../projects/pacific_cod/2023_12_13_pacific_cod.qmd) detailing the samples we plan on sending out for RNAseq and methylation

## 12 December 2023

#### Tuesday

Hackathon 2023, Day One!

-   Backed up all E5 deep-dive work to-date on Gannet

-   Added sRNA investigation results for *P.meandrina* to the "E5 - Descriptive ncRNAs in corals" doc, including links to associated data/outputs

-   Met with Steven to go over some long-term project plans and outlined a (very preliminary) timeline of degree progess

-   Started overhauling my lab notebook site, will finish tomorrow

## 11 December 2023

#### Monday

With the end of the quarter and no more classwork, today's the day for lots of little things!

-   Updated calendars (mine and lab) for the next few weeks and next quarter

-   Moved all code/data from Autumn 2023 classes to github repo for future reference, and saved local copies of relevant class materials before end of quarter.

-   Still no access to TREQ system, so emailed around again about that

-   Registered for UW eScience Institute Software Carpentry Workshop in January -- Python focused!

-   Brainstormed some stuff to talk about w/ Steven related to long-term plans for my degree work

## 08 December 2023

#### Friday

Took QSCI482 midterm (last assignment of the quarter!) and read some papers.

## 07 December 2023

#### Thursday

Lab meeting! Started [sampling cod liver tissue samples]() for RNAseq.

## 06 December 2023

#### Wednesday

-   Studied and took practice midterm for QSCI 482 (test on Friday) -- got a 95!

-   Read Chpt.2 for DEI -focused lab meeting tomorrow

## 05 December 2023

#### Tuesday

Office setup supplies arrived and I unpackaged and setup my new monitor, laptop stand, keyboard, and mouse! Still need to find some batteries for the wireless keyboard though.

Finished *P.meandrina* sRNA work, and compiled comparison of approaches across the three species ([here](../../projects/E5_coral/2023_12_05_E5_coral.qmd)).

## 04 December 2023

#### Monday

Classes. Learned about Celeste's work with tunicates!

## 01 December 2023

#### Friday

-   E5 Molecular working group meeting -- reviewed sRNA progress

-   Science Hour -- talked with Sam about some of my recent questions/confusion spots for miRNA stuff
