October 2024 Goals

October 2024 goals and daily notebook entries.

Goals

Writing and manuscripts

  1. Dissertation proposal submission to grad school
  2. e5 ncRNA complete methods + results + outline of discussion
  3. Pacuta manuscript submission
  4. AST results for manuscript
  5. JEB app
  6. EGRA
  7. Methods for Apul genome paper
  8. Resubmit Astrangia review to Biology Letters

Sample processing

  1. Re-amp 6 WGBS e5 deep dive samples
  2. Phys stuff for AST and Mcap DT
  3. Find and send DNA for e5 samples

Data analysis

  1. 3’UTR for AST 2021 (GENE EXT) and rerun miRanda with that info
  2. Run mirtarrnaseq for AST
  3. Run mirtarrnaseq for deep dive (Apul)
  4. Mcap DT 2023 mRNA + miRNA counts matrix
  5. Compiling all phys stuff for AST 2021

Field work / travel

  1. Figure out travel for cbass workshop - chat w/ Sofia
  2. Apply for travel $$$ for cbass workshop
  3. Apply for travel $$$ for sicb

Daily log

20241001

  • e5 writing meeting

20241002

  • e5 writing meeting

20241003

  • e5 writing meeting

20241004

  • Writing accountability
  • e5 meeting

20241007

  • Prepping for various meetings
  • Hollie meeting
  • Lab meeting
  • Aquarium room stuff
  • Finding DNA for e5
  • JEB app stuff

20241008

  • Found e5 DNA + sent to Azenta
  • Random lab stuff
  • Reformat manuscript for Astrangia review

20241009

  • Writing accountability
  • SICB travel w/ Zoe
  • Astrangia review talks
  • Met w/ prospective grad student
  • Met w/ Amy re topgo
  • Created fisher return order
  • Astrangia review edits + responses
  • Skype a scientist

20241010

  • Writing meeting
  • Astrangia review
  • Bank for wire transfer and various other errands

20241011

  • Writing accountability
  • Astrangia review
  • Aquarium room stuff

20241013

  • Astrangia review

20241014

  • Dissertation proposal
  • PCR adapter cleanup w/ POR samples
  • First part of pico prep
  • Catching up on notebook posts
  • Started applying to HI job
  • Updated e5 DNA master list

20241015

  • Looked at Chloe & Yasmin GRFP materials
  • Completed pico prep + QC
  • Therapy
  • github learnin

20241016

  • Writing accountability
  • Pico write-up + checks
  • Ariana meeting
  • Astrangia review
  • Lirman lab app

20241017

  • Writing meeting
  • Astrangia review
  • Aquarium room larval setup

20241018

  • submitted EGRA
  • Writing accountability
  • Remaking e5 ncRNA figs
  • e5 meeting
  • Clam sam visit!

20241020

  • Astrangia review

20241021

  • Lab meeting
  • Aquarium room stuff
  • Died from vaccines

20241022

  • Astrangia review
  • Therapy

20241023

  • Astrangia review
  • Submitted dissertation proposal lol
  • Random code things
  • Trimming RNAseq reads for Mcap 2023 DT
  • Aquarium stuff
  • Aligning RNA reads for Mcap 2023 DT

20241024

  • Mcap rnaseq alignment and assembly
  • JEB app
  • DESeq2 mcap mRNA data
  • Trimming mcap smRNA data

20241025

  • Submitted JEB app
  • URI policy comments
  • Writing accountability
  • Trimming mcap smRNA data
  • Pacuta discussion section
  • Colloquium

20241027

  • Got on unity!
  • Ran merge bam for e5 apul
  • Ran gene ext for e5 apul
  • Running shortstack for mcap data (raw)

20241028

  • Looking at shortstack output - fail
  • Looking at gene ext output
  • Manually extending Apul genes that didnt get gene extended
  • Started running miranda on new Apul 3’UTRs
  • Lab meeting
  • Lab things
  • Attempted to ship, fail
  • Running miranda with -scale 8

20241029

  • Freezer chaos
  • TAR + putnam lab travel form
  • Lots of miranda code with Apul e5
  • Changed water for larvs
  • Attempted to submit Astrangia review

20241030

  • Miranda with e5 apul
  • Writing accountability
  • Pacuta paper
  • Miranda for e5 deep dive
  • GO enrichment on mirna targets for e5
  • Species comparisons for mirna targets e5

20241031

  • Halloween!
  • Writing meeting
  • e5 ncRNA paper writing
  • Species comparisons for shared mirnas
  • Resubmitted Astrangia review

October reflection

How did I do with my goals for this month?

Writing and manuscripts

  1. Dissertation proposal submission to grad school - done
  2. e5 ncRNA complete methods + results + outline of discussion - done for the most part. finishing up miRNA target results
  3. Pacuta manuscript submission - nope but close to sending to coauthors for more edits
  4. AST results for manuscript - nope
  5. JEB app - yes submitted
  6. EGRA - yes submitted
  7. Methods for Apul genome paper - done
  8. Resubmit Astrangia review to Biology Letters - done

Sample processing

  1. Re-amp 6 WGBS e5 deep dive samples - yes, still need to send
  2. Phys stuff for AST and Mcap DT - nope
  3. Find and send DNA for e5 samples - done

Data analysis

  1. 3’UTR for AST 2021 (GENE EXT) and rerun miRanda with that info - can move forward
  2. Run mirtarrnaseq for AST - no but can move forward
  3. Run mirtarrnaseq for deep dive (Apul) - no but have all miranda data for this project
  4. Mcap DT 2023 mRNA + miRNA counts matrix - yes for mRNA
  5. Compiling all phys stuff for AST 2021 - nope

Field work / travel

  1. Figure out travel for cbass workshop - chat w/ Sofia - kinda? flights booked
  2. Apply for travel $$$ for cbass workshop - yes
  3. Apply for travel $$$ for sicb - yes

This was a very busy month and a lot of my data analysis goals got thrown off by revisions to the Astrangia review. I did get a lot of writing done! And several apps are submitted for travel support.

to do

  • HI job app
  • Lirman lab job app
  • pacuta discussion
Written on October 1, 2024