28 June 2024
Friday
- Point Whitney field day, hardening oysters (see post for details)
27 June 2024
Thursday
admin for Point Whitney field work
Submit receipts from 6/25 trip
Figure out timing/ferry schedules for trip out tomorrow
Note: Mileage reimbursement for personal vehicle usage is $0.67/mile
Reserve UCars for Monday, Wednesday, and Friday of next week. Pickup @ 8:00am, drop off at 7:00pm each day. Car from UW Tower on Monday, from Central Parking Garage on Wednesday and Friday. Confirmation numbers 101491, 101492, 101493.
emailing Andy & Zach to schedule meeting for Ray’s Winter biodiversity seminar
Met with Colby and Steven about Resazurin oyster assays
Reading through E5 deep dive manuscript
26 June 2024
Wednesday
data entry for oyster lengths
Point Whitney notebook post
troubleshooting problems pushing github changes
reading some papers for experimental design
25 June 2024
Tuesday
- Field day at Point Whitney (details in notebook post)
24 June 2024
Monday
Reading Ariana’s Sea Grant biomarker proposal
submit treq for additional disk space on laptop
meeting w steven
some review of C.gigas thermal tolerances
21 June 2024
Friday
Checked on Madeline’s stress test oysters @ 42C in FTR 228 (at Steven’s request). Visually inspected larger oysters, removed smaller oyster plate for ~1min and manually checked each. No gaping in any, suggesting no mortality?
Lit review (see ongoing notebook post)
Meeting w Ariana about oyster planning
20 June 2024
Thursday
Lit review (see ongoing notebook post)
19 June 2024
Wednesday
Lit review (see ongoing notebook post)
18 June 2024
Tuesday
admin stuff – TA offer for Autumn 2024, updating class schedule, scheduling weekly summer appointments with Steven
Started compiling a list of conferences to keep track of dates/locations of ones I might want to present at or attend. And they’re all during the summer, which means I have to wait a whole year to present at my first real conference…?😭
meeting with Ariana to talk about oyster stuff
completed driver safety training and UCAR registration
Looking into NSF GRFP rules, esp on aquaculture
17 June 2024
Monday
Completed GSAR form for end of year (EOY) meeting with Steven
Reading through a bunch of Ariana’s lab notebook posts to try to finalize what I can contribute to with the oysters
EOY meeting with Steven
generate basic outline of oyster project
14 June 2024
Friday
E5 meeting
reading some more papers on ShortStack, miRNA biogenisis/structure and siRNAs following E5 meeting discussion
Some more looking through ShortStack outputs and added a bit to the manuscript
Reading some papers on the mechanisms of triploid mortality and associated physiological indicators to think about which biomarkers might be the best place to start. Learned that triploid mortality has been associated with triploid fecundity/gametogenisis, which is whack since I thought they were largely sterile
13 June 2024
Thursday
12 June 2024
Wednesday
Continue rerunning Pacific cod analyses
writing in the E5 manuscript, discussion section
did some prep for Chris’s Yellow Island Graduate Student Panel
11 June 2024
Tuesday
still rerunning Pacific cod analyses
Running into some issues while converting SAM files to sorted BAM. Occasionally quits and I have to restart it, and I’ve also started running out of disk space on Raven. Clearing some old files.
Added plots of top DEGs and their abundance across all treatments
noticed that in a lot of these plots, there’s sort of a bimodal distribution in the 16C treatment, with ~5 samples clustering away from the median…
10 June 2024
Monday
07 June 2024
Friday
continue with Pacific cod analysis rerun
some reading on mature v star miRNA for E5 issue (updated notebook post)
06 June 2024
Thursday
started rerunning full Pacific cod analysis with sample 92 included
- troubleshooting trimming code that suddenly wont run – realized the code on Raven somehow reverted to an older version, so just needed to copy over the correct code from github
reading on miRNA biogenisis/transport/function
05 June 2024
Wednesday
talked with Ariana about oyster stuff
helped Divya with github/raven problems to finish out FISH541 work
04 June 2024
Tuesday
more looking into that shortstack issue, also found that Pmea shortstack needs to be rerun because it’s using the wrong database file (see github issue)
Did some reading on miRNA biogenisis and updated Shortstack notebook post from yesterday
Set up daily posts and goals for this month
Trying to figure out how to incorporate the star miRNA sequences in comparison analysis (if we decide that would be useful because of possible incorrect mature/star ID). It wouldn’t work perfectly just subbing in a different list of sequences to current workflow. Star sequences are getting blast hits to the sets of stars associated with already known conserved mature miRNAs, and I’m not exactly sure how I might want to change the filtering to get what I want. After manually investigating it in Google sheets though, it looks like including star sequences wouldn’t have a huge impact. Instead of 4 miRNAs conserved in all three species and 1/1/1 for each pair of species, including stars as possible mature miRNA sequences would shift the conserved counts to 5 miRNAs in all three species and 0/1/1 for the Apul-Peve, Apul-Pmea, and Peve-Pmea pairs.
03 June 2024
Monday
Some writing in E5 manuscript
doing some manual investigation of the ShortStack outputs and db matches
noticed potential problem with ShortStack ids, full post here