Jan 02 - Jan 06

Jan 08

  • Quarterly planning doc
  • Reviewing RA responsibilities, setting up reporting reminders, set up daily log for Jan 24
  • Week 01 Goals
  • SICB work lab notebook post

Jan 09

  • NMFS-Sea Grant population dynamics budget documents
  • CEABiGR oyster lncRNA size and location figures
  • NMFS-Sea Grant population dynamics model covariate emails to Stephanie Moore and Simone Aln

Jan 10

  • Undergrad chat with two SAFS students
  • [CEABiGR] Re-run kallisto count matrix generation
  • [CEABiGR] Re-run DESeq2 for males
  • [CEABiGR] Re-run DESeq2 for females
  • [CEABiGR] Re-run combined DESeq2
  • [CEABiGR] Final pipeline for count matrix and DESeq2 Runs

Jan 11

  • Lab meeting
  • Check-in with Grace to fix my heatmap figures
  • [CEABiGR] fix DESeq2 heatmap figures
  • [CEABiGR] Size & Final pipeline for count matrix and DESeq2 Runs lab notebook posts
  • Bevan Seminar: Why is fisheries management so hard? An industry perspective on the challenges before us!

Jan 12

  • e5 molecular mechanism meeting
    • Work with Sam and Kathleen on ncRNA ID sections
  • [CEABiGR] differential expression lab notebook post
  • Sea Grant funding opportunities meeting
  • Meeting with Steven
  • [CEABiGR] RNAcentral blast recap

Jan 16

  • [CEABiGR] Run kallisto count matrix generation for coding sequences
  • [CEABiGR] DESeq2 for coding sequences in males
  • [CEABiGR] Run DESeq2 for coding sequences in males
  • [CEABiGR] Run combined DESeq2 for coding sequences
  • [CEABiGR] Final coding sequence pipeline for count matrix and DESeq2 runs
  • Modeling chat with Emily Jameson for Pop Dy fellowship

Jan 17

  • [CEABiGR] Finish final coding sequence pipeline for count matrix and DESeq2 runs
  • [CEABiGR] Get image assets for mRNA DE lab notebook post
  • [CEABiGR] Dug up prior work on methods
  • [e5 Deep Dive] Chat with Kathleen about our portion of the e5 deep dive descriptive manuscript
  • [e5 Deep Dive] Edits for lncRNA discovery section of e5 deep dive descriptive manuscript

Jan 18

  • Lab meeting
  • [CEABiGR] mRNA DE lab notebook post
  • [CEABiGR] Edit doc for methods as they stand so far through DESeq2
  • Prospective students lunch
  • Weekly meeting with Steven
  • [CEABiGR] WGCNA so far female lncRNAs lab notebook post, add to methods with this info

Jan 19

  • [CEABiGR] Cont. WGCNA so far female lncRNAs lab notebook post, add to methods with this info
  • Pop Dy Fellowship App
  • Week 3 planning

Jan 22

  • Working on Pop Dy Fellowship Materials
  • Week 3 goals lab notebook post

Jan 23

  • Faculty meeting note taking
  • Work on Pop Dy Fellowship App

Jan 24

  • Work on Pop Dy Fellowship App

Jan 25

  • Final work on Pop Dy Fellowship
  • Submit Biology TA and Friday Harbor TA applications

Jan 26

  • [CEABiGR] Finished re-run and summary notebook post of WGCNA for females
  • [CEABiGR] Started male lncRNA WGCNA
  • [CEABiGR] WGCNA methods so far
  • Meeting with Steven:
    • Discussed CEABiGR paper, it needs to include comparison on lncRNAs with other Crassostrea (BLAST), size and expression distribution, location in the genome, and a full background of experimental design since this will be the first paper with CEABiGR data.

Jan 29

  • [CEABiGR] Finished male WGCNA
  • [CEABiGR] Male lncRNA WGCNA notebook post
  • Week 4 goal adjustment and notebook post
  • [CEABiGR] CDS FASTA confirmation issue

Jan 30

  • [CEABiGR] CDS FASTA confirmation issue closed, CDS fasta already used is appropriate
  • [CEABiGR] mRNA WGCNA
  • [CEABiGR] Add to results and methods sections

Jan 31

  • [CEABiGR] Add to results and methods sections
  • [CEABiGR] mRNA WGCNA
  • Peer mentoring meeting
  • [CEABiGR] mRNA WGCNA issue post to settle on pOverA settings

Feb 1

  • Lab meeting, project planning with Ariana
  • RA monthly reporting Google submission form
  • Weekly meeting with Steven
  • [CEABiGR] Weekly oyster meeting (spurious transcription paper)
  • [CEABiGR] WGCNA meeting with Ariana, established settings and what figures to generate
  • [CEABiGR] mRNA WGCNA

Feb 2

  • e5 coral meeting
  • Required UW Trainings
  • CoEnv SAC agenda
  • [CEABiGR] mRNA & settings for WGCNA

Feb 5

  • Buying a new computer (which I desperately need)
  • [CEABiGR] mRNA WGCNA documentation

Feb 6

  • [CEABiGR] create list of differentially expressed mRNAs for each DESeq2 run
  • [CEABiGR] mRNA WGCNA

Feb 7

  • [CEABiGR] mRNA WGCNA
  • [CEABiGR] methods and results
  • CoEnv SAC meeting

Feb 8

  • Lab meeting
  • [CEABiGR] Oyster meeting and methylation manuscript
  • NW CASC Fellowship opportunity webinar
  • UW Violence Prevention training
  • [CEABiGR] Comparison between hisat/stringtie and kallisto mRNA counts
  • [CEABiGR] WGCNA lab notebook post
  • Final Sea Grant Crab Team hiring tasks

Feb 9

  • [e5] molecular meeting
  • [e5] work on ncRNA descriptive manuscript
  • [e5] planning meeting for all hands Feb 23
  • Re-orienting goals

Feb 12

  • [e5] confirm/add lncRNA fastas and beds in deep-dive repo wiki, closed issue
  • [CEABiGR] wrap up male lncRNA WGCNA
  • [e5] status of transcriptomes, count matrices, etc.

Feb 13

  • figure out how to get my dying computer to survive until my new one arrives
  • birthday amnesty

Feb 14

  • Weekly goal planning
  • Reboot winter daily log
  • [CEABiGR] Updated WGCNA settings post
  • [Olympia Oysters] Got in touch with Mark about NW CASC Fellowship

Feb 15

  • Lab meeting
  • CEABiGR meeting
  • Meeting with Steven
  • [CEABiGR] lncRNA location and expression distribution

Feb 20

  • Meeting with Kathleen to discuss co-expression for e5
  • Meeting with Jose to discuss course
  • Faculty meeting note taking
  • New computer set-up

Feb 21

  • Finished setting up computer for work (RStudio, Git, VPN, notebook repo clone, etc.)
  • [CEABiGR] lncRNA location and expression distribution
  • Meeting with Andy about crab lab

March 1

  • Started WSG crab team job
    • Orientation
    • Tour of resources and facilities
    • Meetings with other team members
  • Meeting with Jose and Andy to plan FISH 497 lab

March 4

  • [Crab Team] HOBO logger configuration
  • [Crab Team] Molt training kits
  • [Crab Team] Check in with Emily

March 5

  • Work on NW Fellowship App
  • [CEABiGR] Methods and intro blurbs

March 6

  • [Crab team] Monitor training (online)
  • [Crab team] Strategery Meeting
    • Upcoming in-person trainings
    • HOBO logger retrievals and planting
  • NW CASC Fellowship app budget
    • Send to Lisa ASAP

March 7

  • Lab meeting
  • Meeting with Steven
  • [Crab team] species ID webinar
  • [CEABiGR] manuscript intro chunks and methods
  • Pub-a-thon
  • NW CASC Fellowship budget and app components

March 8

  • [e5] molecular mechanism meeting
  • Serena Hackerott defense
  • NW CASC Fellowship proposal

March 11

  • Crab team monitor training and temp logger placement preparations
  • Finished and submitted NW CASC Fellowship

March 12

  • [Crab Team] In the field placing temp loggers and doing site checks throughout the Puget Sound

March 13

  • [Crab Team] Port Townsend New Monitor and Refresher Trainings (All day)

March 14

  • Lab meeting
  • Weekly Check-in
  • Pub-a-thon
  • CEABiGR lncRNA paper (methods)

March 15

  • Udpate CEABiGR lncRNA results
  • Descriptive e5 manuscript
  • Crab team scheduling
  • Meeting with Jose about class

March 18

  • Crab team
    • Check in and season launch tasks
    • Website migration
  • WSG staff meeting intro

March 19

  • Off

March 20

  • Crab team strategery meeting
  • Look over Yaamini’s CEABiGR manuscript (didn’t have anything to add)
  • ORCID registration
  • CEABiGR descriptive code

March 21

  • Lab meeting
  • Pub-a-thon
  • Weekly update
  • CEABiGR descriptive manuscript

March 22

  • e5 molecular mechanism meeting
  • meeting with Jose about FISH 497
  • FISH 497 content prep
  • CEABiGR descriptive methods