Current To-do List

  • Make posts about DEA pipeline and non-coding RNA function prediction tools
  • Confirm normalizing primer for mussel work

Feb 1-2

  • Environmental data science class, working with PostgreSQL for database management
    • Have to load the Lake Washington data file before class Friday
  • Rescheduled qPCR with Grace for Friday
  • Did an inventory and prep for qPCR run of HSC70 for my mussel chapter
    • Need to order more plates and caps
  • Learning how to complete a differential expression analysis
    • chatGPT was actually really helpful for this
    • Will be doing a DEA on CEABiGR oyster data specifically for lncRNA, should allow me to setup my own pipeline to use for coral work later on

Feb 3

  • Had a chat with Jill Ashey from the Putnam Lab about non-coding RNAs
    • Sounds like we have similar interests in moving away from DNA methylation to look at other mechanisms of gene regulation
    • Should probably set up a monthly (if not more frequent) meeting
  • Joined science hour briefly
  • Environmental data science class, PostgresSQL database building
    • I’m intrigued by PostgresSQL data management, but it doesn’t really seem appropriate for my work (or really any work happening at the individual grad student level), but it makes sense for larger scale environmental monitoring work or for an organization
  • Ran mussel HSC70 qPCR with Grace

Feb 6

  • Lab meeting: chapter 13 of The Disordered Cosmos
  • Environmental data science class, discussion about metadata and the best ways to store data about your data, couple of cool R packages…
  • Had coffee with Olivia, Celeste, and Gabi
  • Went to SAFS Cafe
    • Need to follow up with some of the other grad students about which stats classes they found most useful
  • Chatted with an undergrad from the class I TA-ed last quarter, I think he might be a good undergrad to have help out in the lab
  • Did some coastal erosion lesson planning with Ariana and Rosalind, we’re going to meet with an MHS math teacher next Monday
  • SAC meeting
    • We discussed the new CoEnv-wide mentoring program
    • Seems like a great opportunity for undergrads but not sure we have enough grad students interested
    • It will be largely informal with the intention of not being too time intensive

Feb 7

  • Wrote a letter of rec for one of my students last quarter for NSF ETEP
    • Have a nice letter of rec template now
  • Had a chat with Anna
  • Had an issue with Github Desktop not opening, but was able to fix it with this solution

Feb 8

  • Environmental Data Science class, visualization and graphics
    • Showed us some cool sources for R figure generation
    • Particularly liked the R Graphics Gallery
  • Retrieved HSC70 qPCR data, updated the plate info, and put it in the appropriate place in my notebook
    • Looks like amplification was low for a few of the samples, but the NTCs looked good
  • Going to register for FISH 546 (Bioinformatics) and QERM 514 (Analysis of Ecological and Environmental Data I) on Friday
    • Probably going to drop QERM 514, but a lot of people have been recommending it for more quantitative training (not sure I need it though)
  • Worked on putting together a differential expression analysis pipeline, making a separate posting about this

Feb 9-10

  • Subbed in for one of the sustainable agriculture faculty interviews, was really interesting to see how this works, the position also appears to be calling for something I wasn’t expecting
  • E5 Molecular Mechanism Meeting
    • Currently wondering how Danielle’s nutrient experiment data could be useful to me, centers around nutrient exposure, so does get me on a more narrowed down route for what I want to do
    • It seems like an lncRNA analysis on her data would be a natural extension of her already completed work, so maybe this is something she would want to pursue
    • Emma’s data seems much more difficult to use since her analysis was confounded by ploidy, but it might be cool to do a diploid-triploid comparison of non-coding RNAs
  • Environmental data science class, R markdown
    • Mark did a great job of showcasing R markdown functionality
    • This is something I feel like I should already know, but does beauftiful-jekyll allow me to use Rmd instead of md? Because Rmd looks so much more functional and easier. I think the answer to this is no but I’ll figure it out.
  • DESeq2 protocols I’m filtering through:

Feb 13-15

  • Lab meeting, tidy tuesday
    • Forgot to prep for this, but I think I’m going to still work through it on my own
    • This was a very telling way to see which lab members prioritize what when it comes to displaying data
  • Environmental data science class x 2
    • R markdown knitting, creating docs and pdfs, formatting - This was a great perspective on publishing R markdown files, but I can’t help thinking that some of this is unnecessary. The most utility I saw was in creating webpages and having an easy to update CV. Using this for regular doc creation honestly feels like pushing it to me.
    • Designing presentations - A bit of the same as last class, and to reiterate, I feel like this might be overcomplicating powerpoint or google slides, but I do see the utility.
  • MHS/UW Collaboration Meeting: Coastal Erosion Lesson Plan
    • Rosalind, Ariana, and I are working with a math teacher from the Maritime High School to create a coastal erosion lesson plan
    • Ariana will focus on the hands-on simulation activity
    • I’m working on the real-world context slides and showing a computer model that display coastal inundation
    • Some great Washington specific options can be found here
  • E5 Monthly Team Meeting
    • Review of basically all the material we covered in our last molecular mechanisms meeting, plus a look at Ferdi’s most recent publication
    • I need to be more aware of what is going on in the modeling team, especially taking a peek at the E5 papers already published

Feb 16

  • Long non-coding RNA data analysis options are really well documented in this paper
  • Paperpile updated with E5 modeling papers, went a little off the rails but got a bit of a sample of each of the modeling members work and 2 in progress papers
  • Wanted to add a table of contents to my lab notebook posts, but was having trouble with it, will come back to later
  • Basic DESeq2 pipeline post is live here
  • LncRNA tool post is up next…

Feb 17

  • Science hour
    • Confirmed ordering of beta-actin, 18S rRNA could also work, but might have issues with the magnitude of its expression, budget is in purchasing slack
    • Purchasing
      • I feel like I’m missing something with this
    • First step with P. verrucosa needs to be filtering GFF to see if lncRNAs are identified, which it seems like they aren’t
    • Reference deepdive repo and Danielle’s repo
    • Start from the beginning, I want to try lncPipe, I think it’s the guidance I need it’s under development, but it just brings together pieces I think we already have
  • Env data sci, creating your own website

Feb 21

  • Lab meeting, last chapter of disordered cosmos
  • Set-up oyster lncRNA repo
  • Ran kallisto on Raven to get lncRNA count matrices

Feb 22

  • Caught up with SAC mentor program planning
    • SAC will be hosting a more informal program for undergrads to be mentored by grad students
    • Need to start doc with organization and planning info
  • Also discussed other SAC activities, most notably ADDEI SAC meetings happening next week
    • Need to send out emails to remind member to attend
    • Must update questions doc with Julia’s edits
  • Environmental data science class, creating a function