Working Session & Re-Focusing

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Mussel Methylation
Mussel Biomarkers
Yellow Island
Published

April 15, 2026

Plan of the Week: April 13 - April 19, 2026

High- level outline for the week. Adjusted daily to reflect progress of the day before

  • This week is all about biomarkers and methylation.

Monday - Methylation, methylKit run

Tuesday - UW-RUA, biomarkers

Wednesday - Biomarkers

Thursday - Biomarkers

Friday - Task management & ferry to FH/ Yellow

Saturday - Yellow Island Surveys

Sunday - Yellow Island Surveys

Plan of the Day

Granular level task list to accomplish the high- level goal outlined above

  • My primary goals for today are as follows:
    • Continue working through the biomarker draft updates
    • 1v1 with Steven
    • Verify my supplies, working gear, and transportation are set for Yellow.

Projects Touched Today

  • Mussel Biomarkers
  • Mussel Methylation
  • Yellow Island

Progress Notes

  • I started the day by making ferry reservations up through my 4th tide series. Holding off on the 5th series until I know if I need it.
  • I wrapped up UW-RUA tasks I couldn’t get to yesterday.
  • Returned to Yellow work by verifying my survey sheets, guides, gear, and Rite in the Rain paper are all good to go for the last preparation steps on Thursday.
    • Have to check the boxes in the office to see if I am out after this series.
  • Met with Steven for our first of this new style of working session. The key takeaways are:
    • Biomarker draft to committee on 4/17 with a feedback deadline of 5/8.
    • Shifting the methylation manuscript timeline to to use this DML table, determine the number of DMLs (17), the number of DMLs that are annotated, and have a drafted methods and results prepared for out 4/20 meeting.
    • An agenda with the deliverables will be prepared and sent to Steven no later than Sunday morning, 4/19.
    • Next week during our working session we will review the drafted methods and results, choose the key result, and start framing the discussion.
  • Next up, I did a quick review of the DML table and associated outputs to ensure I have what I need to move forward with our plan.
    • There are 17 DMLs using 55% difference and a q-value = 0.01.
      • Difference= mean methylation of tx 0 - mean methylation of tx 1
      • Q-value = false discovery rate
    • When you put these parameters together, at these levels, we get biologically meaningful (%) and statistically sound (q) results.
    • A later task is to play around with both to see what is the same, different, defensible.
    • The annotated gene list is in Steven’s notebook post. A quick review shows the following:
      • 12 of 17 DMLs mapped to genes that are hypo-, hyper- methylated, or both.
      • 4 are hyper-methylated, 6 are hypo-methylated, and 2 have both instances.
      • The magnitudes of methylation in either direction are the same.
      • 10/12 have a characterized gene function, and 2/10 are uncharacterized.
    • A task for Friday will be to dig into the result a little deeper to understand what I am seeing.
  • I shifted to editing and reworking some of the results of the biomarker paper with a focus on:
    • Shifting the results section from a laundry list to a key result, supporting results, and a brief section of non-results that were anticipated.
    • Next, aligning the discussion with both the key results and the introduction.
      • This was a bit surface as I already worked on aligning it with the introduction; fresh eyes and a critical editing pass will fix this tomorrow morning.
    • I flagged a few pieces of information that will support a coherent read of the paper and deeper look should the committee decide. Since that was not the focus, or a strict necessity for the draft, only a list of notes was created before moving back to reinforcing the citations with the annotated pieces I took from the WDFW reports last week.
  • Finally, I wrapped up the day by making a priority list of ‘first to tackle’ edits for tomorrow morning, updated this post, and shifted to making sure my deliverables for tomorrow’s meetings were ready so I didn’t derail the morning by already running behind.

Outcomes: Products & Word Count

  • Biomarker edits to results: 274 words

Today’s total: 274 words

Monthly total to date: 4694 words

Annual total to date: 37,367 words

Annual target total to date: 51,000 words

Next Up: Tomorrow’s Plan

  • Biomarkers, biomarkers, biomarkers!