2023 January Daily Bits

First day of environmental data science course (FISH 549), went over course expectations, overview, and data science principles
Worked on first committee meeting slides – used GSS lightning talk slides as a jumping off point. Mussel work is pretty easy and almost set for final analysis. Long non-coding RNA work is a little harder to nail down.
Troubleshooting lab notebook (unsuccessful)

Lab meeting and pub-a-thon
Met with Steven to discuss first committee meeting
- Need to focus on the story and add some additional context, each chapter adds a layer of complexity, should add additional info on bypass and additional chapter
Finishing up first draft of committee meeting slides, send to Steven when complete
Steven helped me fix lab notebook

Incorporated Steven’s edits for committee meeting slides
1st committee meeting (need to do a quick write up from my written notes in notebook)
SAFS Cafe
Had chat with Sarah Tanja about lab notebooks and elicit.org for lit reviews
CoEnv strategic planning meeting

Catch up on Environmental Data Science class I missed yesterday for committee meeting, covered “research compendia” which is already very similar to how we organize repos in the Roberts lab, also started this week’s homework

Compendium general structure:

FISH 549 class, intro to git
- Really feels like an extended software carpentry workshop, homework for this week is essentially working with git in command line and then setting up a project repo
Worked on my methods section for pub-a-thon tomorrow

Pub-a-thon
Worked on the methods section of mussel heat stress paper, at the vomitting on the page stage, need to get in an edit
Finished lab notebook post with committee meeting updates
- TLDR: Basically re-working second chapter to work with coral data Hollie mentioned in meeting. She brought up the great point of making sure my chosen data set actually works for seeing environmental responsiveness in lncRNAs.New tentative timeline reflects focusing on wrapping up mussel work and continuing to re-work second chapter, with the overall intent of applying for by-pass by the end of this summer (by the end of spring ideally).
Bevan Seminar with William Cheung from UBC Ocean and Fisheries

Environmental Data Science class, working with git in command line
Realized in class that I need to do an Xcode update, but I don’t have the space on my computer. Using this as an opportunity to clean up my computer, do some organization, and delete old files. Need to make sure I won’t have any issues working in command line.

Worked with Zoe over the weekend and set up my to-do for this week (17th-20th). List is in this post.

Lab meeting, Rosalind had us think about possible lessons we would be comfortable teaching
- Seems like this could turn into some cool field invasives stuff, and I could always develop a lesson plan for coastal remote sensing
Hit a wall in using command line git, need to update Xcode
- My computer storage is out of hand, can’t update until I get this under control
Spent a lot of today organizing and moving files around (a clean up that was longer overdue)

Environmental data science class, we’re working in R using Git version control
- Confirmed with Mark that Xcode was holding me up, he recommended trying to just update command line tools
Spent a little too much time trying to figure out how to parse out certain parts of the Xcode update to no avail
Deleted a ton of system files and documents I don’t need, still needed more space so I got an SD card and moved a ton of files over
Successfully updated Xcode which fixed my Git command line and R Studio issues
- Also decluttered my computer a lot
- Definitely was a case for using Raven, but nice to have everything all set up on my personal computer

PSD lunch
Chat with prospective grad students about the Roberts Lab
Bevan Seminar and TGIT
- Presenter - Marco Hatch
- Nice conceptual framework for working with indigenous communities, really focused on boundary spanners (those who have a relationship with a community and work with western scientists)

I was super sick this week, so didn’t get too much done…
Need to reschedule qPCR with Grace, we were both out sick wednesday
Attended a SAC meeting where we discussed tuition increases and more about the budget, probably worth bringing up to FINS
E5 Molecular Mechanism meeting, we discussed how we get from epigenetic state to environment and what metrics we could be assessing from a molecular perspective to get at this aim.
- Set up a meeting with Jill Ashey (Putnam lab grad student) to discuss our projects on non-coding RNA.
- Bow-tie model of what we’re trying to get at has epigentics/molecular mechanisms on one side, environmental factors on the other side, and physiology in the middle.
Complete assignment 2 for class, pull request

Went to lab meeting, we discussed larval rearing methods
- Matt is looking for help in April to create HUDL system
Went to class, guest lecture by Jenn Scheurell about relational databases
- Played a lot of catch up for class after missing last week

Created my February goals
Currently working on an idea related to Danielle and Ariana’s E5 nutrient gradient project. They have sequencing data from colonies at high, mid, and low nutrient levels along a gradient in the Moorea Coral Reef. I wonder if I could use this data to compare expression to other metrics, the work has already been done for nutrients, but could this data be compared to remotely sensed chlorophyll data? Is there only a nutrient gradient? What other environmental factors might be at play across this area?
Chatting with Yaamini about what remotely sensed data is available to replace some environmental data lost by a storm for one of her projects.
- Need to dig around and see if I can find any modeled datasets that provide daily data at relatively high spatial resolution. I know of a couple land-based datasets like this, but I don’t know if one exists for water quality.
Finished catching up in class from absence last week and installed PostgreSQL for the relational database exercises we’ll be doing. Interesting to see how other labs are managing their data.