January 2024 Goals

January 2024 goals and daily notebook entries.

Goals

Writing and manuscripts

  1. SICB conference presentation
  2. Write full methods, physiological results, introduction, and abstract for A. pulchra gametogenesis paper (Ch.2)
  3. Send Knauss Fellowship for reviews
  4. ICRS apps? Ruth Gates?
  5. Map sequences for heatwave manuscript to de novo transcriptome
  6. Use methylseq kits for heatwave samples
  7. Histological image analyses
  8. JEB paper review

Sample processing

  1. Methylseq library preparation for heatwave samples, n = 12

Data analysis

  1. Finish stats for A. pul gametogenesis paper
  2. Work on DEG analysis after mapping sequences to de novo transcriptome
    • See about duplication errors through trinity pipeline approach
  3. Histological image/gonad analyses

Daily log

January 1

  • Edits to SICB presentation
  • Set up OSF for Acropora images
  • Began organizing images and analyzing a few for practice

January 2

  • SICB conference, arrived in SEA
  • Student training meeting
  • Final edits to presentation

January 3

  • SICB presentation
  • SICB conference
  • Looked at more histology images, edited staging guide

January 4

  • SICB conference
  • Updated prompts for section 1 and section 2 for Knauss Fellowship application

January 5

  • SICB conference
  • Updated prompts for section 1 and section 2 for Knauss Fellowship application
  • Completed edits for CV for Knauss app
  • Wrote three paragraphs for introduction of A. pul gametogenesis and edited methods section

January 8

  • Completed relevant coursework and future plans document for Knauss
  • Completed sections 1 and 2 for personal education and career development statements for Knauss
  • Delivered samples to PacBio for A. pul genome re-processing

January 9

  • Continued revising Knauss app, asked reviewer (Deme) to look full draft over on Friday
  • Ran

January 10

  • Checked LN2 and dry ice in lab
  • Worked in aquarium room, cleaned BT 1/2 and part of BT 3/4, all daily tasks
  • Calculated alignment statistics for samples against de novo transcriptome >95 percent for all :)

January 11

  • Aquarium work, cleaned rest of BT 3/4, daily tasks
  • Met w/ Jill and Hollie for transcriptome, discussed multiQC, look into duplication errors
  • Worked on IDP and smart goals
  • Ran bowtiebuild for de novo transcriptome

January 12

  • IDP + SMART goals
  • E5 ncRNA meeting
  • Lab meeting
  • Sent full draft of Knauss Fellowship to Deme for reviews/edits

January 13

  • Worked on Knauss edits

January 14

  • Worked on Knauss edits

January 15

  • Worked on review for JEB paper
  • Completed edits for Knauss to share to SeaGrant office for review and three other reviewers
  • Sent LOR request to Hollie and Nyssa
  • Created GitHub issues for private GitHub with Hollie and submitted IDP, SMART goals sheets, and Fall 2023 assessment

January 16

  • Sent out Knauss to three reviewers and SeaGrant office for review
  • Edited trinity mapping script, testing on two samples to check for issues for duplication from Hollie and Jill meeting
  • Reviewed TA google drive for BIO 101 to prep for meeting tomorrow
  • A.pul gametogenesis manuscript methods, introduction, and abstract section writing

January 17

  • Trinity script finished running, got RSEM output files for transcript count matrix
  • Aquarium things, all daily responsibilities, cleaned BT 3/4, fed all corals
  • BIO 101 general meeting
  • Austin +5 meeting
  • Knauss working hour questions meeting
  • Read papers on RSEM to understand calculation of counts
  • Got QuPath to work for histological images, meeting with Abby tomorrow to confirm gonad observations
  • Created A. pul functional annotation workflow, working on Diamond BLAST scripts on Andromeda are not working
  • Created histology image analyses notebook post

January 18

  • Fixed Diamond BLAST scripts and write git issues and closed on PutnamLab GitHub
  • Wrote functional annotation workflow, waiting to run Diamond till new scripts done running
  • BIO 101 TA meeting Unit 1 10-12pm
  • Financial meeting 12:30-1:30
  • Histology image review with NSU Prof
  • Apul gametogenesis phys analysis, methods, results section work

January 19

  • Running blastp on transcriptome predicted protein file for functional annotation
  • Mapping all sequences using Trinity align and estimate abundance script for downstream Deseq2
  • Hollie meeting
  • Lab meeting
  • Histology image review with Chloe
  • Apul wrote more of abstract from story perspective
  • Apul write staging method section
  • Received Knauss feedback from SeaGrant

January 20

  • Blastp finished, issue with .xml -f option, need 5 but only 0 working
  • Edited Knauss application with feedback from SeaGrant

January 21

  • Finished editing Knauss application with feedback from SeaGrant, sent to Basia and Deme for review
  • Solved diamond blast .xml issue by using older version of diamond blast

January 22

  • Created workflow for deep dive samples and ran trinity align_and_estimate_abundance script for mapping
  • TA 11-11:50 am in Chafee 271
  • TA meeting 12- 1 pm
  • Ran diamond blastx for .cds file
  • Apul staging guide 3 sample example of 3 pictures of each of the stages

January 23

  • Knauss edits for Brady added
  • Meeting with Ariana
  • Meeting with writing center
  • Made PolyA and rRNA depletion compare document, sent to Hollie and Jill
  • Continued looking at photos for histology and making 3 pictures at each stage
  • Finished new approach for Apul gametogenesis manuscript

January 24

  • TA 11-11:50
  • Writing and journal club meeting
  • Molecular underpinnings edits
  • Sent Apul gametogenesis abstract and staging methods section to Hollie
  • Looked into RiboFree and PolyA for express compare data, way forward, Hollie sent comparisons
  • Knauss writing group
  • Knauss edits from Deme and Basia
  • Continued looking at photos for histology and making 3 pictures at each stage

January 25

  • TA meeting 11:30-12:30
  • TA grading
  • Writing and journal club meeting
  • Knauss edits from Deme and Basia
  • Working on trinity output files to matrices, realized I need to do them separately

January 26

  • TA 11-11:50
  • E5 meeting 12-1pm
  • Worked on trinity mapping script on Andromeda that streamlines files so no individual scripts needed
  • Wrote deep dive notebook post for mapping for comparison
  • Edited some molecular underpinnings comments
  • Histology images meeting with NOVA tech 5-6:30pm

January 27

  • Worked on trinity mapping script that streamlines files so no individual scripts needed

January 28

  • Ran updated script on Andromeda for trinity mapping streamlined, ran in four hours
  • Running gene count matrix script on Andromeda for heatwave samples
  • Edited Knauss for Deme and Basia final comments
  • Edited molecular underpinnings general comments

January 29

  • Working through matrix output error
  • TA 11-11:50
  • TA meeting 12-1
  • Editing and completing lab presentation
  • Moorea meeting with Terava and Ariana, methods section for marine heatwave manuscript
  • Deep dive trinity script ran on Andromeda
  • Ariana Knuass edits meeting
  • Knauss edits

January 30

  • Finished lab meeting presentation
  • Lab meeting 11-12:30
  • Hollie meeting 1-2:15
  • TA grading
  • Histological sizing testing
  • One intro paragraph for molec underpinnings

January 31

  • Molecular underpinnings addressing comments
  • TA 11-11:50
  • Lab writing and readings meeting 12-1:30p,
  • TA grading
  • Knauss writing 3-5pm

Reflection on monthly goals:

  1. SICB conference presentation
    • Well done on restructuring and presentation, good feedback overall. Can improve on being more concise throughout, give the audience the information they want and need to hear the story and get excited about the research!
  2. Write full methods, physiological results, introduction, and abstract for A. pulchra gametogenesis paper (Ch.2)
    • Completed all methods for A.pul manuscript, completed general introduction and abstract outline. Continue working on flushing out the story completely.
  3. Send Knauss Fellowship for reviews
    • Came leaps and bounds on this application with ~5 reviewers feedback and finally feeling like it is at the final stages :)
  4. ICRS apps? Ruth Gates?
    • Not necessary for more funding at the moment, have a draft from previous years I can work on if needed
  5. Map sequences for heatwave manuscript to de novo transcriptome
    • Got through mapping phase for both approaches, ran into error at creating matrices, probably linked to the duplication we are seeing, revisit after we hear back from Azenta
  6. Use methylseq kits for heatwave samples
    • On hold, not immediately necessary without genome construction, can revisit down the line for my chapter specific objectives
  7. Histological image analyses
    • Created general diagrams for each stage, flushed out characteristics for each step for oogenesis and spermatogenesis, working through troubleshooting for size measurements.
  8. JEB paper review
    • Pushed back till this month and was approved by JEB since applying for USAjobs and Knauss this month.

Ways forward:

JUST KEEP SWIMMING, keep up on your organizing of hours, daily, weekly goals and stick to them! End of the month got a bit busy with new TA responsibilities and office hours taking a big chunk of time. Make sure to include this in plans whenever I set my intentions for the week.

Written on January 2, 2024