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

• Sunday’s original goal was to catch up on my reading re: methylation papers, but based on my upcoming week, I will shift to working on the biomarker manuscript and methylation analysis today instead.

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

• Saturday offers a few bonus hours of working time as I was able to wrap–up some of my other obligations earlier than expected.
  • Goal 1- get a weekly wrap-up post knocked out.
    • Summarize the week’s activities, put the priority dates on my physical wall calendar, and start to layer-in the weekly plan for the methylation manuscript.
  • Goal 2- review my writing updates on the biomarker manuscript and either update the manuscript or make notes on what can be improved.

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

• Pull the individual manuscripts from the WDFW reports to identify the original work, not the synthesis.
• Start working through the ‘Clarify’ list of edits on the biomarker draft

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

• Get my crap together! I have a multi-car pileup of tasks across so many different science projects and personal projects that today is the day to knock out what I can, schedule or delegate what I can’t, and to make a few prioritization decisions to align with some of my larger goals and deliverables.

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

• Continue to move forward with the methylation analysis.
• Lab and 1v1 Meetings

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

• Continue to move forward with the methylation analysis.
• Finish filling in the Agenda for my 1v1 with Steven tomorrow.
• Shift over to UW-RUA work for the remainder of the day. I have 8 travelers in progress and a ton of programming information to lock in.

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

• Continue to move forward with the methylation analysis.
• Knockout UW-RUA tasks, including traveler management

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

• Keep the methylation analysis moving forward
• Biomarker visualizations

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

• Keep the methylation analysis moving forward
• Review biomarker visualizations

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

• Keep the methylation analysis moving forward
• Present at the NWS Symposium

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

• The plan today is to try and focus for short working blocks in between my obligations.

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

• There are no goals nor plan for today. Nothing like being derailed because your brain cannot get out of the death- cycle of replaying everything.
• Goals for the month will be posted before the end of the week and today’s working sessions will be dedicated to knocking out the mile- long list of UW-RUA tasks I have right now.

March Goals

Reworking February’s In-Progress Goals

1. Get the biomarker manuscript over to WDFW for review and out to ICB before the March 31st submission deadline.

2. Complete DNA methylation data processing and begin exploratory analysis.

3. Finish PhD proposal and submit to committee for review.

4. Aspirational - Begin mussel experiment for Chapter 3 & 4.

Strategies for Success

Goal 1: Biomarker Manuscript

1. Re-write results section
2. Write abstract
3. Finish polished visualizations, tables, and captions for the biomarker manuscript.
4. Prepare a folder of polished supplementary materials, i.e., index maps, transformed data tables, and cleaned up R scripts.
5. Send manuscript to complete committee for feedback.

Goal 2: DNA Methylation Analysis

1. Re-familiarize myself with where I left off in late 2025 and backup the large files.
2. Move through the initial Bismark pipeline (which I believe I finished) into optimizing alignment parameters and using that outcome for subsequent steps.
3. Quantify methylation levels and visualize using IGV or JBrowse.
4. Get feedback on initial results from Steven and/or other lab members before moving into downstream analyses.

Goal 3: PhD Proposal

1. Review MS proposal and points of expansion.
2. Clarify purpose of chapters 3 & 4 and significance of the work.
3. Rework the introduction to shift the framing from identifying the problem to creating a solution to maximize the current monitoring program OR reduce the monitoring burden.
4. List and clarify the specific methods for each chapter and how they were built based on the results of chapter 2.

Goal 4: Chapter 3 & 4 Mussel Experiment

1. Put together a detailed experimental plan including timeline, materials needed, and data collection methods with 1-3 options for setup.
2. Complete the Lab Risk Assessment form from EH&S to discuss with Steven to get approval for the experiment.
3. Connect with Jon W and Sam W to work through physical space, setups, and ordering materials.

Plan of the Day

• Catch up with weekly planning and task management since I’ve been sick for the last two weeks.
• Create March Goals and plan for attainment

Projects Touched Today

• Mussel Biomarkers
• PhD Proposal
• Lab Notebook

Progress Notes

• It feels like everything is a bit messy currently, so a dedicated session to untangle the projects and required outcomes was truly necessary.
• I first worked on extending the timelines and required deliverables for my non-dissertation projects before pivoting to planning my dissertation work. I chose to do it this way so I could identify what kind of timeline my non-dissertation projects would require so I could either delegate or manage the tasks for myself.
• I reviewed the current state of the biomarker manuscript and the PhD proposal and identified some steps to complete both projects.

Products & Word Count

Tomorrow’s Plan

• Tuesday’s are UW-RUA days, so the plan is to focus on my RUA deliverables only, returning my science on Wednesday.

Plan of the Day

• Focus on UW-RUA deliverables.

Projects Touched Today

• None

Progress Notes

• Nothing relevant to my work.

Products & Word Count

Tomorrow’s Plan

• Wednesday’s plan is to map out specific tasks in completing the biomarker manuscript to get it out to my committee for review before submission to ICB at the end of the month.
• After task mapping, I will knock out 1-2 identified tasks on the manuscript.

Plan of the Week: March 2 - 8, 2026

Daily Focus

• Thursday: No science work
• Friday: Biomarker Manuscript
• Saturday: No science work
• Sunday: Biomarker Manuscript

Plan of the Day

• It feels like I just keep repeating the same tasks over and over again. Each return is an improvement, but there has to be a better way to limit the rework and encourage expeditious support from my committee.
• Based on the list of biomarker manuscript deliverables, my first task is to update my Results section to include the corrected spatial analyses. Second task is to update Figures 1 and 2.
• Finally, my current task management communication set-up is not effective. Moving forward, general weekly plans will be added to Monday notebook posts with specific daily tasks and outcome determined in the daily notebook posts. This will allow for more flexibility in task management and better communication of progress and plans.

Projects Touched Today

• Mussel biomarkers
• Lab notebook

Progress Notes

• I met my first goal of working on the results written portion of the manuscript. It is a laundry list that needs to be more succinct and focused on the key findings. To support writing that, the notes below were helpful.
• I did not meet my second goal of updating Figures 1 & 2, reworking the results took significantly longer than planned.
• I have determined that an evening versus morning check-in that has both the plan of the day, the completed tasks, and the plan for the following day is a more effective tool and cuts down on rework.

Biomarker Analysis Tests Performed

• Shapiro- Wilkes
  • Purpose: Determines if your data is normally distributed across the entirety of the dataset. The result determines parametric or non-parametric route for exploratory and subsequent analysis testing. Used at individual sample level.
  • Test H0 and assumption: Is the data normally distributed?
  • H0= Yes, p< 0.05 rejects H0
• Levene’s Test
  • Purpose: Determines if the variability of your data is consistent across different groups. This is the non-parametric test that is more robust than the Bartlett Test when facing skewed data or outliers. Used at analysis group level to verify groups are different.
  • Test H0 and assumption: Are all group variances the same?
  • H0= Yes, p< 0.05 rejects H0
• KW/ Dunn’s or ANOVA/ Tukey’s
  • Purpose: Pairwise or one-way comparison of three or more independent measurements. Test choice determined by Shapiro- Wilkes and Levene’s Test outcomes.
    • KW/ Dunn’s is the non-parametric test and post-hoc
    • ANOVA/ Tukey’s is the parametric test and pos-hoc
  • Used at the group- level (site, reporting area) to compare the measured metrics, IBRs and chemical analyte concentrations.
  • Test H0 and assumption: Are the means (ANOVA) or medians (KW) of the groups the same?
  • H0= Yes, p< 0.05 rejects H0
  • F-statistic indicates within- group and between- group variance as a ration. The higher the statistic, the more likely there is a difference to be confirmed. Should be used in interpretations verified by post-hoc testing.
  • Post-hoc testing and assumption: Any rejected null is verified with a post-hoc test to control for Type I errors (false positives) and identify which means or medians are different.
• Spearman’s Rank Correlation
  • Purpose: Non-parametric test to measure the difference in ranks of continuous variables in large datasets. Test choice determined by Shapiro- Wilkes and Levene’s Test outcomes. Used to determine any relationships between measured metrics and chemical analyte concentrations at the analysis group level.
  • Test H0 and assumption: Is there an identifiable association between variables?
  • H0= No, p< 0.05 rejects H0
  • Test interpretation: Correlation coefficient (rho) ranges from -1 to +1, and should be used in conjunction with the p-value for correct interpretation.
    • -1: Perfect negative association, as one variable increases the other variable decreases
    • 0: No association between variables
    • +1: Perfect positive association, as one variable increases, so does the other
• Kendall’s Tau
  • Purpose: Conservative, non-parametric test to assess the concordance or discordance of pairs of variables in datasets with outliers or heavy skew. Used to identify data trends or clarify Spearman’s Rho ties in measured metrics and contaminant class concentrations at the analysis group level.
  • Test H0 and assumption: Is there an identifiable association between variables?
  • H0= No, p< 0.05 rejects H0
  • Test interpretation: Kendall’s coefficient (tau) ranges from -1 to +1, and should be used in conjunction with the p-value for correct interpretation.
    • -1: Perfect discordance (disagreement), as one variable increases the other variable decreases
    • 0: No relationship between variables
    • +1: Perfect concordance (agreement), as one variable increases, so does the other
• Global Moran’s I
  • Purpose: Spatial analysis test that indicates if data is clustered, dispersed, or randomly distributed across a defined geographic area. Used to identify if there is a geographical component that affects the measured metrics, IBRs, and contaminant concentrations across all sites in the entire sampling region.
  • Test H0 and assumption: Is there a significant spatial pattern in the data?
  • H0= No, p< 0.05 rejects H0
  • Expected I= Assigned theoretical value assuming H0 is true.
  • Test interpretation: Moran’s I Index ranges from -1 to +1, and should be used in conjunction with the Expected Index (above), Z-score (determined during test if not already available) and p-value for correct interpretation.
    • -1: Negative Autocorrelation (dispersed), dissimilar data values are adjacent to each other
    • 0: No spatial relationship amongst variables (random)
    • +1: Positive Autocorrelation (clustered), similar data values are adjacent to each other
• Local Indicators of Spatial Autocorrelation (LISA) a.k.a. Local Moran’s I
  • Purpose: Spatial analysis test that indicates patterns of autocorrelation when the general Global Moran’s I identified clustered or dispersed data within the study’s geographic region. Used to identify the local spatial patterns in the measured metrics, IBRs, and contaminant concentrations across all sites within the entire sampling region.
  • Test H0 and assumption: Where are the clusters or data outliers that drove the Global Moran’s I result and are they significant?
  • H0= No, p< 0.05 rejects H0
  • LISA interpretation: There are five possible outcomes that grouped and plotted by color:
    • High-High / Hot Spot - red
    • Low-Low / Cold Spot - blue
    • High-Low / Outlier - pink
    • Low-High / Outlier - light blue
    • Not Significant - Gray

Results Overview

• KW/ ANOVA

  • 182 significant comparisons across reporting area and site that include the following metrics and indices:

    • P450, Shell Thickness, Condition Index, Raw mussel measurements

    • IBR Morph

    • Chlordanes, DDT, PAH- HMW, PBDE, Total Contaminants, Total PAH index

• Spearman’s Correlation

  • 94 total significant results

    • 78 significant correlations between individual analytes and both the measured metrics and the IBRs

    • 15 significant correlations between contaminant indices and the following:

      • SOD, IBR Bio, IBR Combined, and raw mussel measurements

• Kendall’s Tau

  • 89 total significant results

    • 79 significant correlations between individual analytes and both the measured metrics and the IBRs

      • Single P450 and single IBR Morph correlations exist in the group whereas multiples for each of the other metrics and IBRs are significant

    • 10 significant correlations between contaminant indices and the following:

      • SOD, IBR Bio, IBR Combined, and raw mussel measurements

• Global Moran’s I

  • The following chemical indices and measured metrics were significant for regional spatial autocorrelation:

    • Chlordane, DDT, HCH, PBDE, PAH- HMW, PCB, Pesticide, Total Contaminant, Total Metal and Total PAH

    • P450, Shell Thickness, Initial and Final Weights

• LISA

  • This result table is significant following the same pattern as the Global above with cluster groupings to confirm the Global pattern found significant.

Products & Word Count

Tomorrow’s Plan

• No science focus on Thursday.

Plan of the Week: March 2 - 8, 2026

Daily Focus

• Friday: No science work
• Saturday: No science work
• Sunday: No science work

Plan of the Day

• My weekly plan has shifted. I will return to science on Monday 3/9/26.

Projects Touched Today

• None

Progress Notes

• None

Products & Word Count

• None

Tomorrow’s Plan

• No science focus on Friday.

Plan of the Week: March 2 - 8, 2026

Daily Focus

• Saturday: No science work
• Sunday: No science work

Plan of the Day

• My weekly plan has shifted. I will return to science on Monday 3/9/26.

Projects Touched Today

• None

Progress Notes

• None

Products & Word Count

• None

Tomorrow’s Plan

• No science focus on Saturday.

Plan of the Week: March 2 - 8, 2026

Daily Focus

• Sunday: No science work

Plan of the Day

• My weekly plan has shifted. I will return to science on Monday 3/9/26.

Projects Touched Today

• None

Progress Notes

• None

Products & Word Count

• None

Tomorrow’s Plan

• No science on Sunday.

Plan of the Week: March 2 - 8, 2026

Daily Focus

• Last day of the week

Plan of the Day

• My weekly plan has shifted. I will return to science on Monday 3/9/26.

Projects Touched Today

• None

Progress Notes

• None

Products & Word Count

• None

Tomorrow’s Plan

• Monday 3/9 will be used to map out my plan for the week.

Plan of the Week: March 9 - 15, 2026

• Working week listed from Mon - Sun

Daily Focus

• Monday: Mapping out the plan of attack for the week
• Tuesday: UW-RUA & Dean’s Office Work
• Wednesday: Lab Meeting & Prep for Thursday’s eDNA ‘think tank’ session and UW-AAF events
• Thursday: eDNA process & literature ‘think tank’ session with Kassi P and Connor, Nanopore and UW-AAF events
• Friday: Writing Accountability with KPJ, focus on Biomarkers
• Saturday: NW Straits Meeting - Ecology/ Conservation/ Public Sessions
• Sunday: Biomarker Manuscript

Plan of the Day

• My goal for today is to plan out the deliverables I have for the week - including the steps for making progress on upcoming deliverables to mitigate the 11th hour push that is getting really old.
• The remainder of the day will be spent prepping UW-RUA materials.

Projects Touched Today

• Mussel Biomarkers
• Proposal Chapters 3 & 4
• Yellow Island
• Lab Notebook

Progress Notes

Planning/ Lab Notebook

• Before setting up my plan for the week, I updated my lab notebook by adding daily log posts for the weekend, archiving February and putting all of those posts into a single file, reviewing my monthly goals, and brain dumping for all projects and tasks.
• Dean Search- ConEv
  • I caught up with the Dean candidate search by watching Candidate A’s presentation and providing feedback in the survey.
  • I virtually attended Candidate B’s presentaiton and submitted my feedback in the survey provided by the search committee.

Yellow Island

• I sent my requested dates for Yellow Island surveys this spring/ summer. Since my schedule and priorities have shifted, I am able to batch surveys within the longer/ lower low tide series in late May and early June.

Chapter 3 & 4

• I worked through a scaled- down version of the lab experiment for Chapters 3 & 4
  • Using the 2021-22 WDFW data, I identified the region’s highest and lowest concentrations of the potential tx chemicals:
    • Cadmium (mg/kg) - 0.226 (Arroyo Beach) - 0.416 (Penn Cove), mean= 0.310
    • Copper (mg/kg) - 0.774 (Broad Spit) - 5.18 (Chimacum Creek Delta), mean= 1.17
    • Sum of 16 PAHs (ng/g) - 3.6 (Hood Canal Holly) - 1600 (Des Moines Marina), mean= 80.74
  • Only the 74 sites included in the biomarker work are included.
  • Values listed above are the wet tissue values (blank corrected for PAH) with the Detected qualifier only.
  • I used the Sum of 16 PAHs because they are the longest defined PAHs by the EPA for their toxicity to humans. The lowest PAH concentration was at a site not included in the earlier work (Drayton Harbor).

The individual PAHs are listed in the image below - if a mixture is not feasible for experimentation, the high molecular weight PAHs are the most persistent while the low molecular weight PAHs can have higher acute toxicity; considering long- term exposure as the baseline for molecular response, we should prioritize the high weight PAHs.

• Looking at the experimental design, there are two paths that can be taken regarding elevated water temperatures.

  • Chronic elevated water temperature at 20° C

  • Acute elevated temperature exposure through the use of resazurin assays to mimic tidal fluctuations in warmer months.

The general design without resazurin looks like the design below.

Products & Word Count

• Yellow Plan: 50 words + 2 tables/ time schedules with personnel allocation for TNC support
• Chapter 3 & 4 plan: 100 words + diagram/ sketch of tx options

Tomorrow’s Plan

• Tuesday is a UW-RUA day, and likely will include no personal science work.

Plan of the Week: March 9 - 15, 2026

Daily Focus

• Getting through the day.

Plan of the Day

• Completing my UW-RUA tasks and going back to sleep.

Projects Touched Today

• None

Progress Notes

• None

Products & Word Count

• None

Tomorrow’s Plan

• Will be made tomorrow based on how I feel.

Plan of the Week: March 9 - 15, 2026

Daily Focus

• My weekly plan will shift significantly as I try to keep myself healthy.

Plan of the Day

• My plan for today is to rest and recover.

Projects Touched Today

• None

Progress Notes

• None

Products & Word Count

• None

Tomorrow’s Plan

• Will be made tomorrow based on how I feel.

Plan of the Week: March 9 - 15, 2026

Daily Focus

• My weekly plan will shift significantly as I try to keep myself healthy.

Plan of the Day

• My plan for today is to rest and recover. Again, I have either rescheduled or canceled meetings to provide myself the time to rest. I already sent my eDNA protocols and information over to Kassi and Connor, so hopefully we just continue asynchronously until I feel better.

Projects Touched Today

• None

Progress Notes

• None

Products & Word Count

• None

Tomorrow’s Plan

• Will be made tomorrow based on how I feel.

Plan of the Week: March 9 - 15, 2026

Daily Focus

• My goal this week has been to rest and figure out some low- effort ways to get back into the work groove without overextending; overdoing it has been prolonging my actual getting down to business.

Plan of the Day

• Rather than focus on products, I focused on reading and note taking to get back into low- effort work flow that allows for breaks as needed.

Projects Touched Today

• PhD Proposal
• Literature Review

Progress Notes

• My goal today was to work through the literature to support a pivot in chapters 3 and 4 rather than do the deep work on my biomarker manuscript. I was able to clean up some sources, reinforce my historical epigenetics knowledge, and think through some ideas about shifting the lab- based experiment to support (possibly) my earlier biomarker and methylation work.

• Between medication- induced naps, I was able to go back in time to read about how epigenetics became ‘a thing’ in 1942, came to the marine invertebrate arena re: developmental bio in urchins in 1973, and then be pleasantly reminded that amongst the first marine organism non-embryonic epigenetics work was done by Steven and published in 2010 with Mac. Pretty cool. Even AI can’t make this up! Pretty dope.

Trying to find some base connections between the current work and where I can go within a dissertation and in the mytilus genome - I built out a mindmap that can definitely be expanded, but is a decent start.

Products & Word Count

• Personal literature notes + mind map above

Tomorrow’s Plan

• Will be made tomorrow based on how I feel. I expect to continue connecting the history of work with the Mytilus genome and epigenetic mechanisms sans non-coding RNAs.

Plan of the Week: March 9 - 15, 2026

• My goal this week has been to rest and figure out some low- effort ways to get back into the work groove without overextending; overdoing it has been prolonging my actual getting down to business.

Plan of the Day

• Today’s plan is to clean up my notes from yesterday and identify where I have gaps in my understanding to direct my readings.

Projects Touched Today

• PhD Proposal
• Literature Review

Progress Notes

• I took my notes, organized them into files separated by topic and keyword to help me understand what I was missing and what didn’t understand at the most fundamental level before pivoting to their application to my broader work.

• I created 3 specific documents in my Epigenetic Mechanisms in Marine Invertebrates Knowledge Library. This links to my Notion project notes and my Foundational Knowledge Library.

  • My knowledge library is a space where I keep my notes on whatever topics from the ground up. For example, if I want to understand DNA methylation in Mytilus spp., I need a fundamental understanding of Mytilus biology, physiology, their ecosystem role, population in Puget Sound, general cellular biology, the current state of genomic work with marine bivalves, and finally the other epigenetic mechanisms that influence methylation. I don’t need to be an expert at the moment, but if I cannot articulate how these pieces interact, I cannot build hypotheses worth investigating.

  • I conducted a quick literature search in both Google Scholar and Web of Science. Lots of room (see image below) and lots of reading to be done.

  • From my preliminary notes, I was able to create three areas of notes applicable to understanding the role of histone modification and chromatin remodeling in a larger context as well as add several papers to Zotero for reading beyond abstracts, methods and figures.

Products & Word Count

• Notes on epigenetic mechanisms
  • Doc 1- male bivalve research bias (it’s a bit easier): 2187 words
  • Doc 2- general history of the research: 548 words
  • Doc 3- role of epigenetic regulation in Mytilus spp.: 396 words

Tomorrow’s Plan

• Will be made tomorrow based on how I feel. I expect to build out my weekly plan and figure out what is on fire and what is just smoldering since I am super behind in just about everything.

Plan of the Week: March 9 - 15, 2026

• My goal this week has been to rest and figure out some low- effort ways to get back into the work groove without overextending; overdoing it has been prolonging my actual getting down to business.

Plan of the Day

• Today’s plan is to clean up my notes from Friday and Saturday and identify where I have gaps in my understanding to direct my readings.

Projects Touched Today

• Foundational knowledge- epigenetic mechanisms
• Literature Review

Progress Notes

• I continued the work outlined yesterday and created one additional document while diving a bit deeper into the literature from the search results on Friday and Saturday.

Products & Word Count

• Notes on epigenetic mechanisms
  • Doc 4- concept mapping the mechanisms to my research: 385 words

Tomorrow’s Plan

• Will be to plan out the week, keep it low key and start prioritizing my in- progress work.

Plan of the Week: March 16 - 22, 2026

• I am feeling marginally better, and since I didn’t map the week on Sunday, the plan today is to keep it low key so I don’t put myself back at square one.
• Monday: Map the week, catch up on UW-RUA work, confirm my spring/ summer tide schedule, build base histone and chromatin knowledge notes.
• Tuesday: UW-RUA work, no science.
• Wednesday: Return to epigenetic mechanisms to outline new Chapter 3 for my proposal.
• Thursday: Biomarker manuscript
• Friday: Biomarker manuscript
• Saturday: Return to Chapter 3 outline and start drafting options for the introduction and methods.
• Sunday: Continue Chapter 3 work.

Missing from the plan is the DNA Methylation work - it will be worked into the other priorities as time permits, or be a focus for spring break week next week.

Plan of the Day

• Today’s plan is to set up my science deliverables, catch up on my own learning, pivot from that learning into actionable application.
  • First, review the basic biology of histones and create my notes on this aspect.
  • Second, pull out the questions in my handwritten notes to compile and address later this week.
• Next, create my JKP 1v1 agenda and pivot to UW-RUA work.

Projects Touched Today

• PhD Proposal
• Literature Review

Progress Notes

• I pulled out my questions/ thoughts about linking the histone, chromatin, and methylation information to an actionable plan using current open source resources. Am I asking relevant and testable questions… we shall see!
• I spent my morning work block with Kristin building my notes about histones and their general biology. Between quick reading of lit and my good old Campbell biology textbook, I have a solid explainer of histones, their composition/ role, and a few notes about the differences in invertebrates. It took a bit longer than expected, but slow progress is better than no progress.

• I virtually attended Celeste’s defense where I learned more about tunicates than I ever thought! She did excellently. I know she worked hard, and seeing it all come together was awesome.
• I virtually attended the third Dean candidate’s presentation and submitted my feedback via the provided survey.

Products & Word Count

• Notes on epigenetic mechanisms
  • Doc 5- histone explainer: 839 words

Tomorrow’s Plan

• UW-RUA Tuesday work blocks, no science.

Plan of the Week: March 16 - 22, 2026

• I am feeling marginally better, and since I didn’t map the week on Sunday, the plan today is to keep it low key so I don’t put myself back at square one.
• Monday: Map the week, catch up on UW-RUA work, confirm my spring/ summer tide schedule, build base histone and chromatin knowledge notes.
• Tuesday: UW-RUA work, no science.
• Wednesday: Return to epigenetic mechanisms to outline new Chapter 3 for my proposal.
• Thursday: Biomarker manuscript
• Friday: Biomarker manuscript
• Saturday: Return to Chapter 3 outline and start drafting options for the introduction and methods.
• Sunday: Continue Chapter 3 work.

Missing from the plan is the DNA Methylation work - it will be worked into the other priorities as time permits, or be a focus for spring break week next week.

Plan of the Day

• Tuesday’s are UW-RUA days, no deep work done today.
• Update weekend lab notebook posts.

Projects Touched Today

• Lab Notebook
• Yellow Island

Progress Notes

• Today I pulled my notes and updated my daily lab notebook posts from the weekend and Monday.
• I was able to confirm my spring/ summer tide schedule on Yellow and working with local sites. I submitted my schedule and needs on Monday and received very quick feedback from TNC today!

Products & Word Count

• No products today

Tomorrow’s Plan

• I was unable to get to my chromatin explainer on Monday, so that will be on the agenda along with developing an outline for Chapter 3 that incorporates some of the questions I’ve been kicking around.

Plan of the Week: March 16 - 22, 2026

• I am feeling marginally better, and since I didn’t map the week on Sunday, the plan today is to keep it low key so I don’t put myself back at square one.
• Monday: Map the week, catch up on UW-RUA work, confirm my spring/ summer tide schedule, build base histone and chromatin knowledge notes.
• Tuesday: UW-RUA work, no science.
• Wednesday: Return to epigenetic mechanisms to outline new Chapter 3 for my proposal.
• Thursday: Biomarker manuscript
• Friday: Biomarker manuscript
• Saturday: Return to Chapter 3 outline and start drafting options for the introduction and methods.
• Sunday: Continue Chapter 3 work.

Missing from the plan is the DNA Methylation work - it will be worked into the other priorities as time permits, or be a focus for spring break week next week.

Plan of the Day

• Today is chromatin’s day to shine!
  • Compile current notes, identify basic biology, any applicable marine invert knowledge, and develop some questions around the mechanism in the context of my work.
• Format and render my lab notebook posts so they look less like an unhinged diary…

Projects Touched Today

• Lab Notebook
• PhD Proposal
• Foundational Knowledge

Progress Notes

• I caught up the notebook posts, archived February’s posts to a single doc, and added a few images to make things more fun!
• I started by prepping for my afternoon meetings
  • UW-RUA applicants X 2 re: research statement feedback
  • NW Straits April 3rd Caroline Gibson ‘Conference’ prep re: posters and abstract submission guidelines
  • Henry Art Gallery re: my written accompaniment piece for a summer showcase
  • Alternate paths to marine science for a high school group related to the IG cohort
• I completed a one- pager for a STEM/social science collaboration in late 2026/ early 2027 if accepted
• I completed the initial pass on the chromatin explainer, but found that it is mostly questions and connections to histones (obviously), so this may be the shorted explainer yet!
  • Once I clean this up, I will add it to the digital notes but right now my handwritten notes are all over the place.
  • Next steps are to put all three mechanisms together and make a plan for how to use current open source data to develop an analysis plan.

Products & Word Count

• Building Bridges in Conservation: 765 words
• Chromatin raw notes (handwritten): 230 words

Tomorrow’s Plan

• Clean up chromatin notes and add to epigenetics explainers in my foundational knowledge db.

• Pivot to using the notes to create a plan for Chapter 3.

• Review biomarker manuscript and make a plan for completion.

Plan of the Week: March 16 - 22, 2026

• I am feeling marginally better, and since I didn’t map the week on Sunday, the plan today is to keep it low key so I don’t put myself back at square one.
• Monday: Map the week, catch up on UW-RUA work, confirm my spring/ summer tide schedule, build base histone and chromatin knowledge notes.
• Tuesday: UW-RUA work, no science.
• Wednesday: Return to epigenetic mechanisms to outline new Chapter 3 for my proposal.
• Thursday: Biomarker manuscript
• Friday: Biomarker manuscript
• Saturday: Return to Chapter 3 outline and start drafting options for the introduction and methods.
• Sunday: Continue Chapter 3 work.

Missing from the plan is the DNA Methylation work - it will be worked into the other priorities as time permits, or be a focus for spring break week next week.

Plan of the Day

• I originally slated time today to work on biomarkers, but I want to finish the chromatin work so I can mull over the mechanisms while working on the biomarker manuscript.
• Today is chromatin’s day to shine… again!
  • Compile current notes, identify basic biology, any applicable marine invert knowledge, and develop some questions around the mechanism in the context of my work.
• I did not get through finalizing my chromatin notes and outlining Chapter 3, so I’m going to focus on that before moving into Biomarker work.
  • First, review existing notes. Second, pull the questions out and put them with the rest and format notes like the others. Third, use the questions and notes to identify alternate ways to work with open source data for Chapter 3.
• After note taking, I will begin outlining a plan for Chapter 3.
  • Pivoting to a bioinformatics chapter rather than a lab based one will allow me to make better decisions for the experiments, more strongly tie the mechanisms to the outcomes, and pull together the complete work cleanly.

Projects Touched Today

• PhD Proposal
• Foundational Knowledge
• DNA Methylation

Progress Notes

• I started by wondering how I ever made it out of Catholic school with this handwriting!
  • My Chromatin notes are a bit all over the place, so after a quick review I identified some gaps I have in understanding. I’m filling those in as best as I can to knock out the cleaner notes.
  • I moved my questions over to the running doc and realized that chromatin remodeling is possibly the most straightforward of all of the mechanisms.
• When I shifted over to DNA methylation, I found myself with more analysis/ workflow questions than mechanistic questions.
  • I pivoted to creating a more comprehensive checklist and process to follow for myself since it is easy for me to rattle a few high-level steps, but unpacking them has been a process.
  • I then created a decision outline with some guiding questions for the analysis.
  • For both I chose to start at the point of sequences in hand - I will need to go back and make a section for sampling/ experimental design. Probably when I work on the methods for the manuscript.
  • This exercise took an embarassingly long time, but really helped me get down to the ‘bones’ of the process and set myself up to comprehensively answer any questions with something more robust than “that’s how my lab does it”.
• For all of my explainers/ note docs I am certain there is plenty of room to make them better, and when the time is appropriate, I will, but for now I need to get back to basics and reinforce information or decisions I have been treating as ‘set-in-stone’ facts.
• I was feeling pretty ‘ready to apply’ this reinforced knowledge and quickly learned that sorting through old code and outputs after dinner is a recipe for instant despair.
  • I went back to the DNA methylation analysis work to see where I left off and possibly move forward… I did this because evening writing is often akin to trying to sharpen a pencil with a blade of grass - not smart. So, I thought, maybe tangible do X get Y work would do it. Instead, I am now questioning every decision and trying to figure out how my maping efficiency has not gotten above 27%, and if that is even a problem… Key sign to pack it up for the day.

Products & Word Count

• Doc 6- Chromatin Explainer: 498 words
• Doc 7- DNA Methylation Analysis Checklist: 573 words
• Doc 8- DNA Methylation Analysis Decisions: 875 words

Tomorrow’s Plan

• Friday starts with creating a specific task list for the biomarker manuscript, executing a reasonable amount of it, and then turning my attention to methylation.

Plan of the Week: March 16 - 22, 2026

• I am feeling marginally better, and since I didn’t map the week on Sunday, the plan today is to keep it low key so I don’t put myself back at square one.
• Monday: Map the week, catch up on UW-RUA work, confirm my spring/ summer tide schedule, build base histone and chromatin knowledge notes.
• Tuesday: UW-RUA work, no science.
• Wednesday: Return to epigenetic mechanisms to outline new Chapter 3 for my proposal.
• Thursday: Biomarker manuscript
• Friday: Biomarker manuscript
• Saturday: Return to Chapter 3 outline and start drafting options for the introduction and methods.
• Sunday: Continue Chapter 3 work.

Missing from the plan is the DNA Methylation work - it will be worked into the other priorities as time permits, or be a focus for spring break week next week.

Plan of the Day

• Today’s goal was to work on biomarkers, but I am shifting to mussel methylation.
  • Because I am behind basically everywhere in every aspect of my life, I have a heavy task day. That equates to a lack of time to focus on deep work, the kind of work that I need to do with the biomarker manuscript.
  • I don’t want to not touch something science today, so I’m going to get something else cooking that is more formulaic going.

Projects Touched Today

• Mussel Methylation

Progress Notes

• My first step was to re-acclimate myself with where the project was in the pipeline, where it needed to go, and what the next tangible steps are.
  • First, I have not yet gotten myself sorted on Klone, so I am still working on Raven.
  • Reviewing the sequences and alignments, I realized three major things.
    • No documentation of matching checksums for my sequences or for the reference genome.
    • No notes on potential parameter testing/ mapping efficiency percentages and what was adjusted to get there, or what needed to be done.
    • I didn’t remove the sequencer artifacts from the work, so my QC reports are 99% unnecessary and not useful.
  • Since I just made a list of steps and decisions, I went back and used them!
    • First, I removed all of the old, second, I reviewed and updated the code files that I created from Steven’s originals and modified for running on my machine, not Raven. Most important, I added some echoes so I wasn’t flying blind in the process.
  • Next up, I cleaned up the repo folders, added code to concatenate the individual checksums into a single text file so I didn’t have to open 48 files…
    • Once my sequences were uploaded/ downloaded/ pulled into Raven, I pulled out one sample (reads 1 & 2) from the high PAH (69M) and low PAH (272M) to run through the complete process before analyzing the complete dataset.
    • I moved all other sequences out of the raw data folder and committed.

Products & Word Count

• Updated code docs for QC, trimming, reference pull and alignment: ~100 words

Tomorrow’s Plan

• Moving forward with the preliminary sequence run through QC, trimming, and alignment.
• Continuing to knock out the other non-lab tasks and work I was not able to complete today.

Plan of the Week: March 16 - 22, 2026

• I am feeling marginally better, and since I didn’t map the week on Sunday, the plan today is to keep it low key so I don’t put myself back at square one.
• Monday: Map the week, catch up on UW-RUA work, confirm my spring/ summer tide schedule, build base histone and chromatin knowledge notes.
• Tuesday: UW-RUA work, no science.
• Wednesday: Return to epigenetic mechanisms to outline new Chapter 3 for my proposal.
• Thursday: Biomarker manuscript
• Friday: Biomarker manuscript
• Saturday: Return to Chapter 3 outline and start drafting options for the introduction and methods.
• Sunday: Continue Chapter 3 work.

Missing from the plan is the DNA Methylation work - it will be worked into the other priorities as time permits, or be a focus for spring break week next week.

Plan of the Day

• Today’s goal is to work on my new Chapter 3 outline and keep pushing the methylation work forward

Projects Touched Today

• Mussel Methylation

Progress Notes

• The day started with running FastQC and MultiQC on the representative samples.
  • I did not properly move the sequencer artifacts, so my QC rerun failed repeatedly until I realized it was because I needed to properly move those files and not adjust the code… that took a little too long.
  • FastQC went well and reminded me that I need to ask again what some of the quality parameters mean in the broader analysis-impact pov.
  • I spent the better part of the day checking why I was stuck in MultiQC purgatory… I am doing something wring because it should not take half a day to run MultiQC on 4 samples, but after some troubleshooting, I can’t figure out what it is. I will ask for help on this one before I screw up something in the shared drives on Raven.
• I moved over to trimming, bypassing MultiQC while keeping FastQC.
  • Based on on the FastQC returns, the standard 20by at the beginning and end of the raw sequences makes sense. I see we use fastp, but TrimGalore is everywhere - I will try to sort out the differences or create a comparison at another less time-restricted moment.
  • I completed trimming, reviewed those FastQC files (bypassing MultiQC until I can figure out where it is getting stuck), and moved on to grabbing the reference genome from NCBI and starting the alignment.
• Once I started the alignment script, I let that run while I worked on some of my UW-RUA deliverables for the week.

Products & Word Count

• No tangible products today.

Tomorrow’s Plan

• No science on Sunday. I am exhausted, still taking my cold meds and hoping to shake this off for good.

Plan of the Week: March 16 - 22, 2026

• I am feeling marginally better, and since I didn’t map the week on Sunday, the plan today is to keep it low key so I don’t put myself back at square one.
• Monday: Map the week, catch up on UW-RUA work, confirm my spring/ summer tide schedule, build base histone and chromatin knowledge notes.
• Tuesday: UW-RUA work, no science.
• Wednesday: Return to epigenetic mechanisms to outline new Chapter 3 for my proposal.
• Thursday: Biomarker manuscript
• Friday: Biomarker manuscript
• Saturday: Return to Chapter 3 outline and start drafting options for the introduction and methods.
• Sunday: Continue Chapter 3 work.

Missing from the plan is the DNA Methylation work - it will be worked into the other priorities as time permits, or be a focus for spring break week next week.

Plan of the Day

• Today’s goal is to monitor my alignments running in Raven and knockout household tasks.

Projects Touched Today

• Mussel Methylation

Progress Notes

• I checked in on the alignments that I started running last night.
  • The reference was downloaded and checksums confirmed.
  • The first sample alignment was completed around midday.
  • The second sample was completed in the evening.
• I began looking at the next steps by reviewing the lab handbook, Steven’s Mytilus methylation repo, and Sam’s workflow for methylation analysis in oysters.
  • I know that deduplication, methylation extraction and parameter testing are the next general steps, but my BASH code is pretty rudimentary and I spent an awfully long time just sorting what some of the commands do before building a base version.
  • I built the ‘simple’ version by first writing out, in full words, what steps needed to be taken before turning to write out the script.
  • In the process, I also noticed that I have some data files that saved to the code directory, so I need to remember to move them and ensure I am setting up my data and output paths properly in the scripts.
• I have not started the deduplication; that will be a task for next week while I am working on getting some of my other projects moving forward as well.

Products & Word Count

• Simple deduplication script: 1
• Written process for deduplication, methylation extraction, and parameter testing: ~200 words

Tomorrow’s Plan

• Working on UW-RUA programming and traveler management.

Plan of the Week: March 23 - 29, 2026

• I am still not at full capacity and my plan for the week is to map out the rest of March and Spring Quarter since I have some very real, very important deadlines I’d like to hit.
  • A full plan will be added to my daily post for Tuesday 3/24/26.

Plan of the Day

• Today’s goal is to make progress with some of my UW-RUA deliverables and to map out the week before pivoting to mapping out the upcoming quarter.

Projects Touched Today

• None

Progress Notes

• I managed to make decent headway on the data analysis of the UW-RUA program outcomes.
  • I pulled in the program stats, cleaned them and made some base plots to illustrate traveler demographics, colleges/ departments within UW, and the host institutions visited.
  • I worked on writing up some more testimonials (that will accompany the data) based on the interviews I’ve completed since the end of Fall Quarter.
• I put together the flyer text for the Scholarly Skill Building professional development programming series for review and edit.

Products & Word Count

• No science products today.

Tomorrow’s Plan

• More UW-RUA work and planning of science deliverables, not just the UW-RUA ones.

Plan of the Week: March 23 - 29, 2026

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

• I am still not at full capacity and my plan for the week is to map out the rest of March and Spring Quarter since I have some very real, very important deadlines I’d like to hit.

Plan of the Day

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

• Today’s goal is to map out the week before pivoting to mapping out the upcoming quarter and tackling the highest priority identified from the planning.
  • Since I was unable to do more than the UW-RUA work yesterday, planning shifted to today.
  • Based on the planning session (in progress notes below), my first priority is the biomarker manuscript and that will be the primary project I work on today.

Projects Touched Today

• Yellow Island
• Kenya eDNA
• Biomarker Manuscript
• DNA Methylation

Progress Notes

• I started with a massive brain dump of all of the projects, tasks, ideas, thoughts, etc that I want to prioritize, delegate, or put in order for next- up.
  • I didn’t do a monthly retro moving into March, so some of that was done after the brain dump and revealed a few things that I will try to keep in mind moving into April and spring quarter.
    • First, no matter how I time block, my brain does not appreciate pivoting projects in the same day. One or the other project gets the attention, and no matter how I try to force myself, I cannot give full attention (for deep work) to more than one. This is a problem.
    • Second, my highest focus times of day are shifting to a bit later than what I’m used to; typically my most productive times are between 6:00 am - 12:00 pm, and are now shifting back to more like 9/ 10:00 am - 3:00 pm. This is a conflict with how my current meetings are scheduled and anything I can shift moving forward, I will.
    • Third, while I am continually saying no to things, I am still underwater. I cannot currently identify what needs to be cut out, but my ‘no thank you’ game has got to get stronger.
  • My priorities for March/ April are as follows:
    • Biomarker manuscript out to ICB
    • PhD proposal for bypass to my committee NLT April 1st
      • Getting back into weekly meetings with Steven to go over the updates
      • A committee meeting scheduled for sometime between 4/13 - 4/24
    • Finishing initial DNA methylation analysis
      • Getting through the 2 sequence test run (deduplication, methylation extraction and then moving into bio/ phys impact via gene ID/ annotation)
      • Adjusting the parameters to ensure we’re getting the most out of the data without inflating error or over-representation of results.
      • Visualizing the results of the test run
      • Completing the workflow with the rest of the sequences
    • Pulling together my complete bypass package for May 15th submission deadline
      • Biomarker manuscript
      • Truncated MS proposal & cover letter explaining expansion from MS to PhD
      • Polished PhD proposal based on committee feedback
  • Auxiliary work that must move forward, but can do so slowly
    • Yellow Island surveys
    • Kenya eDNA + mormyrid gut content data
    • Refining PromethION protocols for the Kenya data
    • Preparing for the Climate Wayfinders training over the summer
• Shifting gears from project & task identification, and into delegation:
  • I confirmed my spring/ summer travel date adjustments with TNC to push my survey window back.
  • I met with Connor and Kassi P. to help them build out the eDNA pipeline and gave them next steps they can accomplish without me.
  • I met with a former GEODUC student who was interested in post-bac opportunities in the lab; not sure our goals are aligned at this time.
• Before hopping into my next round of tasks, I wanted to check off an easy transition task - updating my GitHub landing page to more accurately represent what I am working on. Mainly because it will be linked to my work showcased on April 3rd at the NW Straits Foundation Caroline Gibson ‘conference’.
  • I updated my work description, order of the sections, and removed some of the one-off work that was done a long time ago.
• Next, I went back to the biomarker manuscript and folder of figures/ tables/ results and made a list of next steps:
  • Fully updating results (not just comments)
  • Putting the figures into the manuscript where they belong, regardless of how polished or not they look
  • Identifying where better citations or more detail should be added
    • I really phoned it in in the discussion/ conclusion and tying our results back to the problem identified in the introduction
    • The introduction can be more straight forward
    • I need to decide what I am calling the geographic groupings and stick to it
  • Write the abstract! (totally forgot about that…)
• After reviewing it, I read it for coherence, gaps and line edits. I worked on reworking the results section; it is not great, but I think I have a good idea of how I want the most important spatial results to read while the rest are just added to the supplement.
• I wrapped up by reviewing my deduplicating and parameter checks code for the methylation data.
  • Again, I took examples from the lab and built a version that I understand from those examples.
  • I got it up on Raven and if the spinning sparkle of death ever stops, I will find out shortly if it was successful from a coding point of view…

Outcomes: Products & Word Count

• Biomarker results edits: 237 words

Next Up: Tomorrow’s Plan

• Will be determined by the end of the day!

Plan of the Week: March 23 - 29, 2026

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

• I am still not at full capacity and my plan for the week is to map out the rest of March and Spring Quarter since I have some very real, very important deadlines I’d like to hit.

Plan of the Day

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

• Today’s goal is to return to the plan mapping I finished yesterday and complete the task breakdown, refine the project priorities, and start plugging the tasks into my planner dashboard in Notion.

Projects Touched Today

• DNA Methylation

Progress Notes

• I kicked off the day with a new paper from my Google alerts, One Health perspectives on veterinary residues and bioaccumulation in marine mussels. DOI link to the paper.
  • This is a review paper focused on contaminant mixtures and their potential impacts to mussels, and how those outcomes link to human health outcomes using the One Health framework.
  • The authors focus on heavy metals and pharmaceuticals as the perturbation/ mixture.
  • Call to Action: Integrate monitoring programs, molecular ecotox, and new tech to mitigate contaminant’s entry into waterways.
• I moved into task planning. I identified the main projects that must be pushed forward, the secondary projects that are moving forward under delegated efforts, and potential upcoming project work.
  • This took a significantly longer time to get through, so I focused on the priority project tasks in the allotted time block.
  • Thursday will see a revisit of the task defining and scheduling since I need to pivot to meeting prep.
• First ‘meeting’ was my working block with KPJ.
  • I walked myself through the Bismark results so I could understand what I was seeing and what questions I actually needed to ask.
  • I returned to my problem trying to access the qc programs. I haven’t been able to run a successful MultiQC yet. So, I created an environment in Raven where I can run FastQC and MultiQC without searching for the tools to only find the directories - this means I either don’t get a result, or the result returns an error after running for days.
  • I updated my QC, trim, alignment and deduplication scripts to reflect this new environment.
  • I ran the QC and trim files for all remaining sequences; I hadn’t done that yet, only for the two I am working with.
• I left that work block and joined lab meeting. We shared progress and upcoming plans.
  • I need to update the lab calendar with my availability next quarter.
• I moved over to my weekly eDNA meeting with Connor and Kassi P
  • We went over the introductory literature I shared, field protocols (for Connor’s upcoming work), and next steps for our meeting in two weeks.
• I completed my second of three total high school marine bio sessions after that.
• Once meetings were out of the way, the remainder of the day was spent monitoring the QC and trimming scripts on Raven and knocking out some UW-RUA tasks for travelers.

Outcomes: Products & Word Count

• No direct products

Next Up: Tomorrow’s Plan

• To complete the task ‘scheduling’ and prepare for the smaller project deliverables upcoming between March 31st - April 6th.

Plan of the Week: March 23 - 27, 2026

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

• I am still not at full capacity and my plan for the week is to map out the rest of March and Spring Quarter since I have some very real, very important deadlines I’d like to hit.

Plan of the Day

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

• Today’s goal is to complete the followings:
  • NWStraits abstract and poster mock-up
  • Locate open source sequences for Chapter 3
  • Update or refine and add my figures to the biomarker manuscript
  • Prep for my meeting with PSP and Tiara for the social science project
  • Complete the task mapping for the lower-priority projects

Projects Touched Today

• DNA Methylation
• NWStraits Caroline Gibson Conservation Symposium
• Conservation Ecology

Progress Notes

• I knocked out my abstract and followed up with my current and former mentees to remind them to get the requested information to me by the end of their day on Friday.
  • My poster is about increasing access to increase larger opportunities in conservation ecology
  • The plan is to link programs like Yellow, REU, and DDCSP to their larger impacts in conservation
• Somehow, I managed to lock up Raven on my end. I thought the additional script I started yesterday was MultiQC only, not the alignment script, and that caused everything to just hang in the air.
  • I force- quit all terminals running
  • I attempted to commit the files that I changed and managed to stare at a ‘commit’ screen that would not respond to any staging. I realized far too late that I checked one of the huge packages with about a gazillion parts while I was clicking around to see if I had just lost my mouse or if the interface was lagging…
  • Now, I can’t get Raven to load without crazy lagging - I haven’t waited this long to accomplish anything since dial-up days- so I know I screwed something up on my side.
  • I have shut it all down, killed all processes, and am going to restart it after my afternoon meeting.
• I added a timeline, products, notes, and a revised research question section to my proposal idea with PSP.
  • Tiara and BIMS will be the non-profit partner with me as the lead researcher - if our proposal is accepted.
  • Next steps are to polish the plan slightly for the next meeting with PSP, BIMS and WA SeaGrant to ensure we are aligned in the mission.
• Next up, finding RNA-seq in NCBI for some gene expression and mussel methylation comparisons for Chapter 3.
  • I created a Bookmarked folder of all 47 of the SRAs and GEO datasets for Mytilus spp., focusing on RNA-seq data in mantle tissue, including both non-stressed and treatment stressed samples. I then added a few that were other tissue types just in case. As a reminder, I chose mantle tissue because that is the tissue type I am exploring in the methylation analysis.
  • I read the abstracts to confirm data type, treatment, and preparation process. Anything without an abstract was flagged for removal.
  • I started working my way through a quick skim of the methods section of papers related to the sequences so I can confirm fully the availability, sequencing platform, and sample preparation process. This helped me flag those prepared for immuno-assays and immune function chromosome tags that weren’t clear in the abstract nor the sequence name in the NCBI databases.
  • I set a 90 minute time block on this, so I marked where I left off, and will return during another ‘transition task’ work block.
• Returning to Raven. I had to reach out to Sam to kill anything I had going on because I very effectively put a pause on the work…
  • I dug a bit more and realized it was a GitHub issue - one cannot simply commit using terminal and then attempt to push or pull with the interface without creating an issue..
  • Once I solved my issue, I cleaned out the old mussel methylation repo taking up huge space, cleaned up my commit, and restarted Raven.
  • Success was getting my MultiQC reports for the raw and trimmed files after looping through the output folders to ensure the downloads, checksums, and trimmed files existed with their respective FastQC files.
  • I moved over to running the full alignments with Bismark after verifying that the reference was downloaded, checksum match confirmed, and Bismark bisulfite genome created. Now we wait…
• I brainstormed some ideas for the Black Opportunity Fund call, something art and environment related.
  • Put out a few feelers for artists, branding/ marketing, and venues.
• I started pulling together all of my project notes for the 3 projects I have listed on my lab notebook site
  • Biomarkers- Google docs analysis notes doc
  • Methylation - will need to pull from daily notebook posts
  • Yellow - my UW Google drive, my personal Google drive, and daily posts.
  • I’m certain the handwritten notes on all projects won’t make it in for now, but will be in future projects because I just don’t want to waste time pulling them for projects reaching their end.
• I wrapped up the day by updating my CV using Vitae and finally getting to my About Me GitHub page since I will be presenting myself and my work in 2 weeks and I’d like folks to have something more substantial than my GH landing page only.

Outcomes: Products & Word Count

• NWStraits Abstract: 107 words
• PSP Social Science Proposal Update: 412 words
• BOP Art x Environmentalism Ideas: 277 words
• Creating my About Me .qmd page: 528 words
• NWStraits poster mock-up based on mentee responses so far

Next Up: Tomorrow’s Plan

• Will be determined by the end of the day!

Plan of the Week: March 23 - 29, 2026

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

• I am still not at full capacity and my plan for the week is to map out the rest of March and Spring Quarter since I have some very real, very important deadlines I’d like to hit.

Plan of the Day

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

• Today’s goal is to complete the followings:
  • Backup my methylation data from Raven on Gannet
  • Get my full sequence alignments running
  • Outline Chapter 3 with research questions
    • Finish review of bookmarked sequences
    • Identify usable NCBI data sources and plan for them
    • Identify other ways to integrate epigenetic mechanisms to make the chapter more robust

Projects Touched Today

• DNA Methylation
• Chapter 3

Progress Notes

• I have two meetings and a doctor’s appointment today, spread out at the most inconvenient intervals, so my plan today is to knock out tasks and work that is easy to put down and pick back up.
• First, I dropped into science hour to get Sam’s help in completing the rsync from Raven to Gannet for my methylation repo.
  • I cleaned up old files, removed old repos, and made sure to commit anything necessary to github via terminal instead of the interface before completing the sync.
  • We also chatted about the difference in parameters used to align the methylation sequences. I’m going with the standard choice in the lab re: stringency since the outputs don’t seem to show any significant differences.
• Next I worked on creating the deduplication script for the full sequences (not just the two I was working on, and not just the first 10k pairs) with a MultiQC output.
• I reviewed the methylation extraction code from both Sam and Steven and started to put that together.

Outcomes: Products & Word Count

• SACNAS Abstract: 213 words
• Something else: 0 words
• Created scripts for the methylation analysis: 2 scripts

Next Up: Tomorrow’s Plan

• Will be determined by the end of the day!

Plan of the Week: March 23 - 29, 2026

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

• I am still not at full capacity and my plan for the week is to map out the rest of March and Spring Quarter since I have some very real, very important deadlines I’d like to hit.

Plan of the Day

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

• Today’s goal is to knock out the first version of the NWS poster to ask for feedback early next week

Projects Touched Today

• DNA Methylation

• NWS Symposium

Progress Notes

• After going over the parameters that Sam and I talked about yesterday, I annotated the scripts so I wouldn’t forget.
  • I am still running the methylation analysis with the standard alignment parameters (L,0, -0.6) because this aligment stringency is the best balance between mapping efficiency and not inflating the CHH or CHG percentages; methylation percentage changes marginally (11.5% to 11.7%)
  • Clarifying what I mean re: parameters below. When running Bismark and Bowtie2, the list of parameters below tell the programs what to do.
    • First, The goal is to convert the reference genome to a bisulfite- ready version for alignment, and then Bowtie2 aligns my sample sequences with the bisulfite- converted reference genome.
    • Alignment ‘matching’ stringency. This parameter check was done on the first 10k sequences of the aligned test sequences (69M- high PAH and 272M- low PAH) scores ranging from L,0,-4 to L,-1,-0.6). This is basically a ‘how many mismatches are too many’ check - the smaller the number (more negative), the more relaxed the matching and potentially the driver behind mapping efficiency differences. L- linear function, first number is the intercept, second number is the slope. These are impacted by read length… will add read length thresholds as a later- knowledge project.
    • Output order. The Reorder call just puts the outputs in the same order as the inputs and supports future troubleshooting. This is for organization/ file management.
    • Quality score. The call to ignore-quals is just a way to bypass any PHRED/ quality scores and treat all of the sequences the same. This is a data management command.
    • R1 and R2 are a team. The —no-mixed command tells Bowtie2 to keep sequence pairs together, when one aligns but the other does not, the whole thing has to go. This makes the mapping more conservative and supports downstream analysis/ interpretation.
    • Direction. Non-directional versus directional calls either release or restrict the directional library assumptions. Library prep should have preserved strand directionality and this is the default call for the program, so no need for changing up now!
    • Discordancey. A no-discordant call forces the alignments to follow paired-end logic (supporting the —no-mixed command).
    • Dovetail and maxins: next up to double check they are actually commands to ensure fragments and overlapping reads aren’t discarded, but I have to double check that because all of the online resources use descriptions that are as clear as mud.
• I shifted over to sketching out a few poster ideas, settling on one that is too conceptual, and returning to square one.

Outcomes: Products & Word Count

• Bismark & Bowtie2 Command Breakdown: 578 words

Next Up: Tomorrow’s Plan

• Taking the day off to hang out with the kid

Plan of the Week: March 23 - 29, 2026

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

• I am still not at full capacity and my plan for the week is to map out the rest of March and Spring Quarter since I have some very real, very important deadlines I’d like to hit.

Plan of the Day

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

• Today’s goal is to brain dump the tasks and priorities for the week, check the status of the methylation data on Raven, and hang out with the kid.

Projects Touched Today

• DNA Methylation

Progress Notes

• The only science I did today was to check the alignment script I am running on Raven.
  • I had to restart the Bismark code, I made tool path adjustments in the script and made a coding mistake, so the reference portion ran again because I forgot to un-comment the skip loop when I was making other changes. It is the same reference, so that’s fine- just a time waster.

Outcomes: Products & Word Count

• No tangible products

Next Up: Tomorrow’s Plan

• Use my brain dump list to set up the week, knock out the NWS poster, and prep for the TNC meeting next week.

Grab progress notes from Notion - note on 3.31.26

Plan of the Week: March 30 - April 5, 2026

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

• I am finally as close to healthy as I have been in awhile, so as long as the anxiety of being so behind doesn’t take me out, I will be solid!

Plan of the Day

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

• Today’s goal is to
  • Complete NWS poster
  • Check on methylation alignment progress

Projects Touched Today

• DNA Methylation
• NWS Symposium

Progress Notes

• The notes are in Notion

Outcomes: Products & Word Count

• Some product…

Next Up: Tomorrow’s Plan

• Tuesdays are UW-RUA days.

Plan of the Week: March 30 - April 5, 2026

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

• I am finally as close to healthy as I have been in awhile, so as long as the anxiety of being so behind doesn’t take me out, I will be solid!

Plan of the Day

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

• There is no science goal today.

Projects Touched Today

• None

Progress Notes

• None

Outcomes: Products & Word Count

• No science products

Next Up: Tomorrow’s Plan

• Working block with KPJ. A full plan will be made based on UW-RUA outcomes today as we prep for the programming series that starts at the end of the month.

February Goals

1. Get the biomarker manuscript over to WDFW for review and sign-off for 31 March 2026 ICB submission deadline.

2. Begin mussel experiment for Chapter 3 & 4.

3. Complete DNA methylation data processing and begin exploratory analysis.

Strategies for Success

Projects Touched Today

• lab notebook
• mentoring
• mussel pilot experiment

New Knowledge

• I first knocked out Darian’s recommendation letter for a summer internship; had to get back into the writing groove.
• Next, I put together a weekly wrap-up post on my 1/25/26 resazurin trial with my pilot experiment mussels.
• I built the table with the observations of the pilot experiment to add to the pilot repo, and I made a few notes about what should go in the README for a small task later this week.
• I finished by moving my Notion daily notes to my daily notebook post template and updating the entire month of January. The ease of just adding a few lines in Notion (via my button) doesn’t really translate into an easy post setup, so I need to think about how to streamline that process. I like that I can capture what I’m doing or questions I have in the moment, but those are a bit too loosey- goosey.

Old Tricks

• It was a RUA day, so getting some of my admin tasks out of the way was a bigger win than I expected.

Word Count (Productivity)

A note on word count/ productivity: I do not include task- based writing, for example the recommendation letter and cleaning up my January notebooks posts, because those don’t directly move my work forward. I do count the resazurin post, because it was a synthesis of the work, a reflection on the results, and a plan for next steps.

• Resazurin post: 713 words
• Today’s total: 713 words
• Monthly total to date: 713 words
• Annual total to date: 10,969 words

Questions or Concerns?

• None.

Tomorrow’s Plan

• Will be made tomorrow to include resazurin analysis, editing and refining biomarker viz, and updating February noteboook posts.

Projects Touched Today

• lab notebook
• mussel experiment planning and design
• mussel pilot experiment

New Knowledge

• I created my February Goals Post with specific steps and strategies to complete them.
• I worked with KPJ for a 3-hour writing block where I collated and cleaned up about half of my lit notes to support the mussel experiment design choices.

Old Tricks

• Continued refining my literature support for the mussel experiment (second bullet point)
• Returned to mapping for the biomarker visualizations (from yesterday). I cleaned up the sampling site map, and went to work on the individual biomarker activity maps for p450 and sod but didn’t finish those today.

Word Count (Productivity)

A note on word count/ productivity: I do not include task- based writing, for example the recommendation letter and cleaning up my January notebooks posts, because those don’t directly move my work forward. I do count the resazurin post, because it was a synthesis of the work, a reflection on the results, and a plan for next steps.

• February Goals + Strategy Post: 191 words
• Viz made: 1 map

Questions or Concerns?

• None.

Tomorrow’s Plan

• Will be made tomorrow to include resazurin analysis, editing and refining biomarker viz, and continuing experimental planning for my 2/11 meeting with Steven.

Projects Touched Today

• mussel biomarkers

New Knowledge

• So, in my quest to wrap up mapping, I found a mistake in my spatial analysis of the biomarker metrics and indices. When I mapped my spatial results, I started with the geographic clusters designated using K-Means clustering that I verified with variance and significance testing ensure the groups were statisically different enough to be meaningful. When I threw the groups in the map, it looked like I just threw out a handful of fruit loops and said ‘ok’…
  • First, I went back and double checked the sites and assigned color palette were correct. Next I went to the data table to verify the values were in the correct format and not mistakenly overwritten. Finally, I moved over to check the code I used to analyze the clusters.
  • One seven letter word got me- degrees. I completed the SPATIAL analysis in degrees, not distance. I made a note in the R code, and moved back over to GIS to redo the analysis.
• To redo the analysis, I did the following:
  • Imported a clean table of the metrics and identifiers, and formatted the columns from characters to actual numbers for next steps
  • Next we need to link the table to the map, so I created a point layer to link the Puget Sound map. This takes the lat/ long data and converts it from coordinates (degrees) to actual distances. I confirmed the projection and moved to confirm the results.
  • To verify that worked, beyond the points showing up on the map, I ran a distance matrix summary (by site_id, k=5) to verify the point layer and to guide the parameters I select in the Moran’s I analysis. The summary gives you a quick table of minimum and mean distances and the standard deviation; these guide the distance bands (scale) for Moran’s.
  • I confirmed the distance matrix by running a linear matrix that shows if the distances are actually varying, there aren’t any self-comparisons, and verify both tests returned consistent results.
  • Happy with the confirmation, I ran the Moran’s I (spatial autocorrelation- regional or global) for p450, mapped the result, and then moved to sod.
    • P450 showed a few significant clusters, SOD did not. This aligns with the KW comparisons and the Spearman’s correlations results. Thank goodness.
• Tomorrow, I will return to the Moran’s I analysis of the remaining metrics (18 of 20 total), the LISA analysis (all 20), and begin mapping the results one metric at a time.

Old Tricks

The log of mapping decisions I may need to return to:

• Returned to the sampling site map, added insets for Seattle and Tacoma, and threw it in canva to clean up the format.

• I chose to add the following city labels:

  • Olympia, Tacoma, Seattle, Everett, Penn Cove, and San Juan Islands

• The insets have the city label only for Tacoma and both the city label and Bainbridge Island for the Seattle one because of the geography captured in the inset

• Next maps will most likely not need the Canva step since I figured out how to do adjust borders independently in QGIS, but we’ll see.

  • I created a specific color palette for reporting areas in QGIS to be used in all plotting/ mapping for consistency. Hex codes follow a pound sign with no spaces, and are as follows:

    • 6 - 0f6f6c (dark teal)

    • 7 - 6a4c93 (plum)

    • 8.1 - c7352d (brick red)

    • 8.2 - d4a437 (gold)

    • 9 - e07a5f (coral/ salmon)

    • 10 - 4fb3a2 (light teal)

    • 11 - ff7f00 (orange)

    • 12 - 33a02c (yellow)

    • 13 - 1f3c5b (navy blue)

  • My sampling site basemap is in purple with black borders

    • Seattle inset is framed in black

    • Tacoma inset is framed in white - may need to change to yellow or something brighter

  • My sites by reporting area map is just like the sites map, except color coded as outlined above.

    • The legend is framed in the same weight as the other frames, and has no background so that it doesn’t stand out so starkly.

    • This map feels VERY busy, feedback will help for refining

Questions or Concerns?

• I made a quick protocol for converting non-geometric data into geometric data in QGIS. Mainly to help myself not miss a step, but secondarily to make sure I am creating mapping layers in the right projections with the right formats before I start mapping, rather than get stuck in the middle because nothing is working correctly.

• This and the maps will be in my weekly wrap-up.

Tomorrow’s Plan

• Tomorrow (2/6), I will return to the Moran’s I analysis of the remaining metrics (18 of 20 total), the LISA analysis (all 20), and begin mapping the results one metric at a time.
• The documentation and analysis of the mussel pilot experiment and resazurin trials will get put back in the queue behind finishing the biomarker work.

Projects Touched Today

• Mussel biomarkers

Plan of the Day

• Complete spatial analyses in QGIS and R, complete mapping for the biomarker manuscript and supplement, and possibly get back to working on the resazurin analyses.

Progress Notes

• Today’s work started with drafting presentation text for our Student Technology Proposal: PromethION 2 Solo: Advancing UW Genomics Research Through Enhanced Access to High-Quality Long-Read DNA Sequencing. The proposal is being led by Mike Sadler in Oceanography. We have 3 minutes to pitch our submission followed by 10 minutes of Q&A from the panel, so it has to be clear and quick.

• After that, I spent my work block with KPJ reworking the spatial analyses for all metrics in QGIS and confirming in R so I can build the tables to be plotted on the maps succinctly.

  • Picking up from the p450 and sod analysis from the day before, I plotted the results on a scatter plot to confirm no self- autocorrelation across the sites and was pleased to see it worked!
  • I continued with the Global Moran’s I analysis for the remaining 17 metrics, there are 19 metrics not 20- I misspoke in yesterday’s post. Global Moran’s was run first because the results answer the question of whether or not there is a statistically significant spatial structure to the measured metrics (p450, sod, shell thickness, condition index), the integrated response indices (IBR biomarker, morphometric, combined), and the contaminant indices (chlordanes, ddt, hch, metals, 4 pah groups, pbde, pcb, pesticides, and total contaminants).

• 

  • Next up was the ‘local moran’s’ also known as LISA (local indicators of spatial autocorrelation). Since there were 9 metrics indicating a ‘global’ significance, the LISA test tells us what kind of spatial structure exists and if the pattern is consistent across the metrics.
  • While I don’t expand this into a connection to the physical geography of each of the sampling sites, that can be easily done as a point in the Discussion/ Conclusion of the manuscript or left to assess at a later time.

• Once I had the QGIS results, I then went back to see if I could fix the errors I made in R to replicate the results. The main reason is to confirm the outcome, and the secondary reason is to create data tables of the results that aren’t GeoPackages so they can be used to plot, build a supplementary spatial results table, and export as a csv in the correct format.

  • Rather than try to adjust the existing markdown script, I built the script from the beginning, paying special attention to the conversion from coordinate (degrees) to a distance matrix that matched the QGIS matrix.
  • I ran an analysis of variance between the ‘clusters’ and used the K Nearest Neighbors statistical grouping of geographic groups to continue the analysis. My last attempt used K-Means Clustering, which is not effective in non-normal data since it is built on response variables, not geographic location first- something that was very unclear in my earlier understanding of the test. The K-NN test resulting in an n=6 that was statistically significant and balanced the number of sites per group.
  • Once that was established, I spent a ridiculous amount of time building a loop to assess all of the metrics for each test. With the help of ChatGPT, I found that I was building the function sandwich in the wrong order… should have just checked that earlier.
  • The outputs of each of the tests were saved as csv’s, then only the statistically significant results were saved in another csv. Those outputs were then joined to the full csv of identifiers (site number, site name, lat/ long) and metric values, converted to GeoPackages for mapping, and added to QGIS for visualization.

• I felt very comfortable in stopping at this point since I was making silly mistakes reviewing them in QGIS - time to throw in the towel for the day.

Tomorrow’s Plan

• Continue mapping the spatial results.

Projects Touched Today

• Mussel biomarkers

Plan of the Day

• Map the analysis results.

Progress Notes

• Back at the mapping in QGIS.
  • First map to make is the Global Moran’s I outcomes. Since just plotting the Moran’s value or p-values isn’t helpful, I am exploring ways to plot the 9 significant results to tell the story with the actual stats in the caption. Using the significant results, I will go back to my complete metrics and indices table, convert the columns to the format I need, add geometry, and test plotting each of the 9 significant metrics.
  • The mapping choices are as follows:
  • A multi-panel layout will have P450, Total contaminants, PAH, PBDE and PCB in the top row in that order, and DDT, pesticides, chlordanes and HCHs in the bottom row in that order.
  • P450 will use a different single color gradient than the contaminant ones; all contaminants will use the same single color gradient for consistency. The higher the value, the darker the color.
  • For visual consistency, the category breaks for all 8 of the contaminants will be exactly the same - all of the concentrations are in ng/kg, so the comparison is super important to make clearly.
  • As a reminder, the contaminants are in ng/g, and p450 is in activity/mg protein
  • Using the histogram of values in p450, I moved the default from 30 bins to 7 to clearly visualize the values gradient between -1 to 2.7 without inflating the activity values and remembering that these are the values scaled based on the reference site. A zero means the value is the same at the reference site, and negative number means it is lower than the reference site, and any positive number is higher than the reference.
  • The basemap is at 75% opacity to allow the symbols to stand out. The p450 symbol is a 4mm purple diamond with an outline/ stroke of dark grey (#2b2b2b) and a weight of 0.4 and a round join style. This is important because each of these settings, except for the color will be used in the contaminant maps.
  • I added a duplicate symbol layer below the one described above to add a bit of depth. It is the same symbol shape, drug below the primary, set to 5.5mm, color is very pale grey (#f7f7f7), opacity at 30%, stoke/ outline off. This halo effect helps makes the higher density sites clearer without an inset.

• Shifting gears a bit, I pulled the summary stats for the contaminant indices, put them in a quick view table, and then thought through how to make consistent groupings, or how to explain the differences in scale.
  • None of the contaminant indices will follow a uniform color gradient, so I am trying to group similar scaled classes together rather than group them as I had planned earlier.
  • There are three groups that are zero- dominant and 5 groups that have a significant range in concentrations, so I am splitting them into two groups for mapping. Group 1 will go to the supplement as detected/ not detected and group 2 will be in maps alongside the p450 map; the main difference is that the contaminants in group two will be broken down into percentiles of concentrations for consistency and p450 activity will remain scaled to the reference site to prevent inflation or deflation of variability.
  • I created the templates for both groups, created the base maps for all 8 indices, and began refining them in the print layout to export. I need to create a single legend that can be displayed for them all, and tweak the details, but the base information and outcomes are complete - finally!
• Putting two maps per print layout
  • Width- 139.640
  • Height- 205.216

Products & Word Count

• STP Presentation Draft: 327 words

• Complete Spatial Analysis RMD (excluding header, doc settings & library loads): 487 words

• Viz made: 1 map

  Today’s total: 814 words

  Monthly total to date: 1718 words

  Annual total to date: 12,878 words

Tomorrow’s Plan

• Watch the Seahawks win the Super Bowl.

Plan of the Day

• While the OG plan of the day was to watch the Seahawks redeem the worst decision in football… I really wanted to complete the draft maps of the significantly spatially autocorrelated contaminant classes so I could start fresh on some of the other tasks for the week on Monday.

Projects Touched Today

• Mussel Biomarkers

Progress Notes

• Started off today reviewing what I knocked out yesterday, and picked back up on mapping the contaminant indices.

  • Splitting the significant indices into percentiles and detected/ not detected, that makes my layout simpler - I am going to put a grid together for the percentile maps; one shared legend. The top row will be (L-R) pah, pcb, pbde; the bottom row will be (L-R) ddt, total contaminants, legend.

  • Set my print layout to ANSI B - Landscape; 431.8mm x 279.4mm to make sure I can get 3 across without crowding.

  • The maps have the same exact setup, only the data varies, so this feels like it should be a clean way to compare the information.

  • Can’t forget to add the map attribution: Basemap: Esri World Ocean | © Esri, and the projection: base- EPSG: 3857, points- EPSG:4326 - WGS 84 - Geographic

• NOTE: When I return to the sampling site and P450 maps- they need to match the extent, scale, and labeling of these maps.

  • Fix the city/ location labels

  • Everett is misspelled

  • Olympia may be misplaced

  • Add Port Angeles or Port Townsend, lots of sites= label

  • Consider adding waterway labels, like Commencement Bay, Elliott Bay, greater Salish Sea and/ or Puget Sound

• Back to the contaminant maps

  • There is an asterisk indicating the reference site - orange and just slightly larger than the map points; don’t forget to add this in the caption

  • This is a bit dramatic on the page - adjust when refining the maps

• I am so excited to have finally gotten much closer to aligning the figures with the story in the manuscript draft - since the whole thing is on the shorter side, the figures really have to deliver. There is definite room for improvement; small cleanups on things like aligning frames, text styles, naming convention (I don’t think I should pluralize the contaminant abbreviations), and larger refinements for clarity and overall message delivery will be tackled after committee feedback.

Products & Word Count

• Viz made: 5 maps + captioning (357 words)

  Today’s total: 357 words

  Monthly total to date: 2,075 words

  Annual total to date: 14,953 words

Tomorrow’s Plan

• Reminder to committee to review my MS proposal so I can get it submitted

  • MS proposal must be submitted and signed off NLT 2/20/26

  • Schedule a meeting for end of February, early March to discuss PhD proposal and manuscript (full committee will receive NLT MS feedback/ submission is completed)

• Spend some time reviewing the status of my current projects

  • I have spent so much time in the QGIS rabbit hole that I need to refresh myself on where everything else stands

  • Map plan for the week based on that review (including blocks for non-dissertation projects that have also lagged)

  • Put up outline of 1v1 agenda/ statuses to be completed in advance of my meeting with Steven on 2/11

Plan of the Day

• Today’s plan is to catch up on tasks outside of my direct dissertation work; only the two below are science related.
  • Continue to prepare to deliver the presentation to STP for the P2Solo
  • Compile my notes in preparation for SAFS 10 year graduate group meeting

Projects Touched Today

• None

Progress Notes

• None that are applicable

Products & Word Count

• No dissertation/ thesis products today

  Today’s total: 0 words

  Monthly total to date: 2,075 words

  Annual total to date: 14,953 words

Tomorrow’s Plan

• Shifting Monday’s plan (below) to Tuesday 2/10/26

• Reminder to committee to review my MS proposal so I can get it submitted

  • MS proposal must be submitted and signed off NLT 2/20/26

  • Schedule a meeting for end of February, early March to discuss PhD proposal and manuscript (full committee will receive NLT MS feedback/ submission is completed)

• Spend some time reviewing the status of my current projects

  • I have spent so much time in the QGIS rabbit hole that I need to refresh myself on where everything else stands

  • Map plan for the week based on that review (including blocks for non-dissertation projects that have also lagged)

  • Put up outline of 1v1 agenda/ statuses to be completed in advance of my meeting with Steven on 2/11

Plan of the Day

• Today’s plan is to add a few science tasks into a medium- lift for UW-RUA since I don’t have any events or major travelers this week.
  • After RUA office hours, my plan is to spend 30 minutes the specific deliverables for my current science work in progress
  • Create my 1v1 agenda to send Steven before our meeting on 2/11
  • Send the reminder email to my committee for proposal feedback and scheduling of our next meeting
  • Aspirationally - complete a draft of the CIL grant application for potentially free chems

Projects Touched Today

• 1v1 prep

Progress Notes

• The only science I did today was put together my agenda for my meeting with Steven for tomorrow.

Products & Word Count

Today’s total: 0 words

Monthly total to date: 2,075 words

Annual total to date: 14,953 words

Tomorrow’s Plan

• 1v1 with Steven

• Lab Meeting

• Meet with interested undergrad for potential bench work support through the mussel experiment

Plan of the Day

• Advisor 1v1
• Lab Meeting
• Potential UG for lab

Projects Touched Today

• MS proposal

Progress Notes

• Weekly meeting with Steven. He wants me to add more more detail on the Chapter 2 approaches as well as a more expanded results expectation and research questions. Will work on that.
• The rest of the agenda was a run- through of the statuses of current and upcoming with no additional steps.
• Lab meeting did not yield any tasks or extra responsibilities
• Met with the Bio undergrad about what they are looking to gain and looking to contribute. Based on skills and interests, I think I have a 2- prong plan where we can gain some skill exposure, and get them linked to some of the summer opportunities that align with their interests.

Products & Word Count

Tomorrow’s Plan

• Tomorrow is pretty meeting heavy. I have 2 UW-RUA debrief meetings post traveler return, the NW CASC Info-session, the first of 3 ESA Future-Proofing Your Science Career sessions, and a meeting with a former mentee to work through the stats and visualizations for his capstone project featuring the data we collected on Yellow Island from 2023 - 24.

• Specific steps in my own work will be determined post today’s meetings.

Day 1 of 365: January Goals

January Goals

1. Finish these proposals and get them out to my committee by the end of the month for a chance at submitting a bypass package by the February deadline.
2. Get the biomarker manuscript polished enough to go to WDFW for review and sign-off.

Today’s Work

• Day 9. Mussel Check 1430

• Visual tank inspections looked good for airflow and water clarity; clear reduction in food since yesterday. Mussels were still aggregated in their respective bags/ coolers. The airflow in blue remains a bit lower than in red. Will continue to monitor.

• Temperature

  • Blue= 11° C

  • Red= 15° C

• Salinity

  • Blue= 26 psu

  • Red= 25 psu

• Mortality

  • Blue= 0

  • Red= 0

Mussels and King Tides

Projects Touched Today

• Mussel pilot experiment

New Knowledge

Day 10. Mussel Check at 0600

Visual tank inspections looked good for airflow and water clarity; continued reduction in food since yesterday. Mussels were still aggregated in their respective bags/ coolers. The airflow in blue remains a bit lower than in red. Will continue to monitor.

• Temperature

  • Blue= 11° C

  • Red= 15° C

• Salinity

  • Blue= 26 psu

  • Red= 25 psu

• Mortality

  • Blue= 0

  • Red= 1

Old Tricks

• I will not be checking on the mussels on 1/3 since I’m leaving for the coast after this morning’s check. I will check upon return on 1/4.

Questions or Concerns?

• None

Tomorrow’s Plan

• Photograph the tides off of La Push and tidepool!

Quiluete Land & Coastal Wanderings

Projects Touched Today

• None

New Knowledge

• The Quiluete Resort is the perfect place to unplug and is central to awesome tidepooling for the night low tides.

Old Tricks

• Hiking along the coast during low tide feels like treasure hunting!

Questions or Concerns?

• None

Tomorrow’s Plan

• Return home, check on my mussels, and prepare for the first day of the next quarter.

Mussels

Projects Touched Today

• Mussel pilot experiment

New Knowledge

Day 12. Mussel Check at 1520

Visual tank inspections looked good for airflow and water clarity. Mussels were still aggregated in their respective bags/ coolers. The airflow in blue remains a bit lower than in red. Will continue to monitor.

• Temperature

  • Blue= 11° C

  • Red= 15° C

• Salinity

  • Blue= 27 psu

  • Red= 26 psu

• Mortality

  • Blue= 3

  • Red= 0

• Of course 3 kick the bucket! I do not know if all died today or yesterday, but since they are the control temp, it feels odd but could be due to air flow. I swapped the air stones between Red and Blue after wiping both down. The stronger air stone is now in Blue, with the less strong in Red since adjusting flow didn’t seem to make enough of a change.

Old Tricks

• Time to prep for the new quarter by updating calendars, planning time off and mapping daily goals.
• One of my 2026 goals is to write at least 500 new words a day. Ultimately, those words have to be in projects that move my work and my professional presence forward. The word count doesn’t include emails or task- based writing.
• I may adjust that to include coding work, visualizations created, etc., since those all contribute to completing the deliverables in front of me.

Questions or Concerns?

• None

Tomorrow’s Plan

• Review the status of my proposals and make a daily plan for completing the drafts this month.

Welcome to Winter Quarter

Projects Touched Today

• Mussel pilot experiment

New Knowledge

Day 13. Mussel Check at 1049

Visual tank inspections looked good for airflow and water clarity. Mussels were still aggregated in their respective bags/ coolers. The air stone swap seems to be ok. Will continue to monitor.

• Temperature

  • Blue= 11° C

  • Red= 15° C

• Salinity

  • Blue= 27 psu

  • Red= 26 psu

• Mortality

  • Blue= 0

  • Red= 0

Old Tricks

• Not a lot of science beyond the mussel check. Prepping for a RUA day tomorrow.

Questions or Concerns?

• None.

Tomorrow’s Plan

• Tuesdays are RUA days again this quarter, so only mussel checks.

Mussels & RUA

Projects Touched Today

• Mussel pilot experiment

New Knowledge

Day 14. Mussel Check at 1700

Visual tank inspections looked good for airflow and water clarity. Mussels were still aggregated in their respective bags/ coolers. The air stone swap is ok. Will continue to monitor.

• Temperature

  • Blue= 11° C

  • Red= Increasing from 15° C to 18° C

• Salinity

  • Blue= 28 psu

  • Red= 26 psu

• Mortality

  • Blue= 2

  • Red= 0

• Partial water changes in both coolers. Salinity recheck

  • Blue= 25 psu

  • Red= 25 psu

Old Tricks

• Tuesday is a RUA workday.

Questions or Concerns?

• None

Tomorrow’s Plan

• Continue to knockdown the lit notes for biomarkers and my proposals.

Mussels and Biomarker Manuscript Work

Projects Touched Today

• Mussel biomarkers
• Mussel pilot experiment

New Knowledge

Day 15. Mussel Check at 1558

Visual tank inspections looked good for airflow and water clarity. Mussels were still aggregated in their respective bags/ coolers. The air stone swap seems to be ok. Will continue to monitor.

• Temperature

  • Blue= 11° C

  • Red= 18° C

• Salinity

  • Blue= 25 psu

  • Red= 25 psu

• Mortality

  • Blue= 0

  • Red= 0

• Feeding

  • Using the same calculations as on 12.31, a 400mL slurry was made and divided between Red and Blue, with slightly more going to Blue.

Old Tricks

• Returned to working on the manuscript for biomarkers. I cleaned up the methods and results sections to make them more succinct and separate from the discussion.

Questions or Concerns?

• None.

Tomorrow’s Plan

• Limited time tomorrow as the quarterly cross- institution RUA meetings are all morning with ‘working groups’ in the afternoon.

Mussels and RUA Working Groups

Projects Touched Today

• Mussel pilot experiment

New Knowledge

Day 16. Mussel Check at 0915

Visual tank inspections looked good for airflow and water clarity. Mussels were still aggregated in their respective bags/ coolers. The air stone swap seems to be ok. Will continue to monitor.

• Temperature

  • Blue= 11° C

  • Red= 18° C

• Salinity

  • Blue= 25 psu

  • Red= 25 psu

• Mortality

  • Blue= 0

  • Red= 0

Old Tricks

• Full RUA day.

Questions or Concerns?

• None.

Tomorrow’s Plan

• Breakdown my daily plan to smaller bites. Even the smallest tasks are taking a lifetime, which is an indicator that I am making them too big.

Mussels and MS Proposal Work

Projects Touched Today

• Mussel pilot experiment
• MS proposal

New Knowledge

Day 17. Mussel Check at 1628

Visual tank inspections looked good for airflow and water clarity. Mussels were still aggregated in their respective bags/ coolers.

• Temperature

  • Blue= 11° C

  • Red= 18° C

• Salinity

  • Blue= 26 psu

  • Red= 25 psu

• Mortality

  • Blue= 0

  • Red= 0

Old Tricks

• Returned to the MS proposal draft and made significant progress on the literature review to help me write the introduction section in a way that is a bit preachy, but done.

Questions or Concerns?

• None.

Tomorrow’s Plan

• Pull all of my pilot observations out of my notebook and into their own table. I will need this information to help guide the continuation of the experimental design for the larger experiment.

• Return to lit review/ note taking for biomarker manuscript. Progress I made there really helped me knock out the MS proposal intro and I will need to expand for the intro to the PhD proposal.

Mussels and Proposal Work

Projects Touched Today

• Mussel pilot experiment
• MS proposal
• PhD proposal

New Knowledge

Day 18. Mussel Check at 1624

Visual tank inspections looked good for airflow and water clarity. Mussels were still aggregated in their respective bags/ coolers. There is a smell to the tanks, but that has to be waste products since there are no mortalities.

• Temperature

  • Blue= 11° C

  • Red= 18° C

• Salinity

  • Blue= 26 psu

  • Red= 27 psu

• Mortality

  • Blue= 0

  • Red= 0

Old Tricks

• Reviewed previous day’s work in both proposals
• Total new words added across both proposals: 941

Questions or Concerns?

• None.

Tomorrow’s Plan

• Nothing concrete except for checking the mussels. 1/11 is Sunday.

• Didn’t complete today, so will move this to next week. Pull all of my pilot observations out of my notebook and into their own table. I will need this information to help guide the continuation of the experimental design for the larger experiment.

Sunday - No Science Today

Projects Touched Today

• Mussel pilot experiment

New Knowledge

Day 19. Mussel Check at 1429

Visual tank inspections looked good for airflow and water clarity. Mussels were still aggregated in their respective bags/ coolers. There remains a smell to the tanks, but that has to be waste products since there are no mortalities.

• Temperature

  • Blue= 11° C

  • Red= 18° C

• Salinity

  • Blue= 25 psu

  • Red= 27 psu

• Mortality

  • Blue= 1

  • Red= 0

Old Tricks

• None

Questions or Concerns?

• None

Tomorrow’s Plan

• Map the week ahead to include the following: continue work on the proposals and supplementary visuals for the biomarkers, finalize a draft experimental design to inform the PhD proposal.

Mussels and Proposals

Projects Touched Today

• Mussel pilot experiment
• MS proposal
• PhD proposal

New Knowledge

Day 20. Mussel Check at 1209

Visual tank inspections looked good for airflow and water clarity. Mussels were still aggregated in their respective bags/ coolers. There remains a smell to the tanks, but that has to be waste products since there are no mortalities.

• Temperature

  • Blue= 11° C

  • Red= 18° C

• Salinity

  • Blue= 26 psu

  • Red= 27 psu

• Mortality

  • Blue= 1

  • Red= 0

• Partial Water Change completed for Blue and Red by emptying half of the existing water and adding fresh seawater.

  • Salinity rechecked

    • Blue= 25

    • Red= 25

Old Tricks

• Writing, writing, writing. I continued to move forward with adding a better outline for Chapter 3 and 4 in the PhD proposal, went back and revised the introduction to the MS proposal, and reworked the biomarker manuscript discussion/ future directions to align a bit better with the intro and results.

Word Count (Productivity)

• Editing biomarker manuscript: 520 words
• MS proposal writing: 140 words
• PhD propsal writing: 131 words
• Today’s total: 791 words
• Monthly total to date: 1732 words

Questions or Concerns?

• None.

Tomorrow’s Plan

• Tomorrow is a RUA day, so no real science will be done.

Mussels and RUA

Projects Touched Today

• Mussel pilot experiment

New Knowledge

Day 21. Mussel Check at 1017

Visual tank inspections looked good for airflow and water clarity. Mussels were still aggregated in their respective bags/ coolers. There smell is almost non- existent now.

• Temperature

  • Blue= 11° C

  • Red= 18° C increasing to 20° C

• Salinity

  • Blue= 26 psu

  • Red= 26 psu

• Mortality

  • Blue= 0

  • Red= 0

Old Tricks

• None.

Word Count (Productivity)

• No science writing today
• Today’s total: 0 words
• Monthly total to date: 1732 words

Questions or Concerns?

• None.

Tomorrow’s Plan

• Continue to last of selected papers for my proposals, work on the experimental design constraints and scale.

Mussels and Proposals

Projects Touched Today

• Mussel pilot experiment
• Mussel experimental design

New Knowledge

Day 22. Mussel Check at 1752

Visual tank inspections looked good for airflow and water clarity. Mussels were still aggregated in their respective bags/ coolers. There remains a smell to the tanks, but that has to be waste products since there are no mortalities.

• Temperature

  • Blue= 11° C

  • Red= 20° C

• Salinity

  • Blue= 26 psu

  • Red= 29 psu

• Mortality

  • Blue= 0

  • Red= 0

• Partial Water Change completed for Red by emptying half of the existing water and adding fresh seawater.

  • Salinity rechecked
    • Red= 26

• Mussels were fed using the same calculations and method as outlined on 12.31.25 except tissue mass has been reduced to 170g for total tissue weight in the remaining mussels.

Old Tricks

• Today I brain dumped all of the experimental design thoughts I was having from both the planning and the reading. It is possible to maintain an experiment that has treatments that include two temps (elevated and control), two metal concentrations and two PAH or PCB concentrations with interactive treatments. There would be 15 treatments that way, including controls. A fully expanded setup would be 21+ and that is excessive for not just the information it may not yield, but for the costs associated.
• Based on the ‘streamlined’ setup, I created a folder in Zotero that has all of the associated papers to support the experimental design and endpoints. This will be useful for both the MS proposal and the PhD proposal.

Word Count (Productivity)

• 1 draft experimental design outline for MS proposal: ~400 words (handwritten across 6 pages, A4 size)
• Today’s total: 400 words
• Monthly total to date: 2132 words

Questions or Concerns?

• None.

Tomorrow’s Plan

• Continue writing proposals to get them to the committee sooner rather than later. It’s getting too close to offer a fair window of return.

Mussels and Proposals

Projects Touched Today

• Mussel pilot experiment
• PhD proposal
• Mussel experiment planning

New Knowledge

Day 23. Mussel Check at 1503

Visual tank inspections looked good for airflow and water clarity. Mussels were still aggregated in their respective bags/ coolers.

• Temperature

  • Blue= 11° C

  • Red= 20° C

• Salinity

  • Blue= 27 psu

  • Red= 26 psu

• Mortality

  • Blue= 0

  • Red= 0

• Partial Water Change completed for Blue by emptying half of the existing water and adding fresh seawater.

  • Salinity rechecked
    • Blue= 25

Old Tricks

• Returned to the PhD proposal after working on mussel experiment design. Made good progress on writing the methods sections, objectives and research questions. I feel like I matched the tone of the rest of the proposal and the MS proposal.
• I messaged with Sam and emailed with Jon Whittock re: tank help and any guidance he had on using contaminants in lab experiments. I followed that up with a phone call and subsequent email to EH&S re: anything other than physical lab requirements and waste disposal of water with metals/ contaminants in it.

Word Count (Productivity)

• PhD Proposal: 1340 words
• Today’s total: 1340 words
• Monthly total to date: 3472 words

Questions or Concerns?

• None.

Tomorrow’s Plan

• Same as yesterday. Continue writing proposals to get them to the committee sooner rather than later. It’s getting too close to offer a fair window of return.

More Mussels and Proposals

Projects Touched Today

• Mussel pilot experiment
• PhD proposal

New Knowledge

Day 24. Mussel Check at 1121

Visual tank inspections looked good for airflow and water clarity. Mussels were still aggregated in their respective bags/ coolers.

• Temperature

  • Blue= 11° C

  • Red= 20° C

• Salinity

  • Blue= 26 psu

  • Red= 26 psu

• Mortality

  • Blue= 0

  • Red= 0

Old Tricks

• Returned to the PhD proposal after working on mussel experiment design. Made good progress on writing the methods sections, objectives and research questions. I feel like I matched the tone of the rest of the proposal and the MS proposal. I continued with creating a shortened version for chapters 1 and 2, and read two papers that I previously only read the abstract for.

Word Count (Productivity)

• PhD Proposal: 1105 words
• Today’s total: 1105 words
• Monthly total to date: 4577 words

Questions or Concerns?

• None.

Tomorrow’s Plan

• Same as yesterday. Continue writing proposals to get them to the committee sooner rather than later. It’s getting too close to offer a fair window of return.

Mussel Check and Errands

Projects Touched Today

• Mussel pilot experiment

New Knowledge

Day 25. Mussel Check at 1004

Visual tank inspections looked good for airflow and water clarity. Mussels were still aggregated in their respective bags/ coolers.

• Temperature

  • Blue= 11° C

  • Red= 20° C

• Salinity

  • Blue= 26 psu

  • Red= 26 psu

• Mortality

  • Blue= 0

  • Red= 0

Old Tricks

• None. Lot of personal stuff to knockout today.

Word Count (Productivity)

• Today’s total: 0 words
• Monthly total to date: 4577 words

Questions or Concerns?

• None.

Tomorrow’s Plan

• Will be made tomorrow.

Mussel Check and… You Guessed it, Proposal Writing

Projects Touched Today

• Mussel pilot experiment
• Proposal writing

New Knowledge

Day 26. Mussel Check at 1137

Visual tank inspections looked good for airflow and water clarity. Mussels were still aggregated in their respective bags/ coolers.

• Temperature

  • Blue= 11° C

  • Red= 20° C

• Salinity

  • Blue= 27 psu

  • Red= 26 psu

• Mortality

  • Blue= 0

  • Red= 0

Old Tricks

• Right back at it refining, aligning and ensuring my proposal is clear without getting too into the weeds. I’m super close to a draft that isn’t totally embarrassing to share with the committee.

Word Count (Productivity)

• MS & PhD Proposal: 556 words
• Today’s total: 556 words
• Monthly total to date: 5133 words

Questions or Concerns?

• None.

Tomorrow’s Plan

• Will be made tomorrow.

Mussels, Mussels Everywhere

Projects Touched Today

• Mussel pilot experiment
• Mussel resazurin trial
• Mussel experimental design
• Proposal writing

New Knowledge

Day 27. Mussel Check at 1630

Visual tank inspections looked good for airflow and water clarity. Mussels were still aggregated in their respective bags/ coolers.

• Temperature

  • Blue= 11° C

  • Red= 20° C increasing to 22° C

• Salinity

  • Blue= 28 psu

  • Red= 29 psu

• Mortality

  • Blue= 0

  • Red= 0

• Water Change

  • Partial water change for Blue and Red. Salinity recheck:

    • Blue= 26

    • Red= 26

Old Tricks

• Same as 1.18: Right back at it refining, aligning and ensuring my proposal is clear without getting too into the weeds. I’m super close to a draft that isn’t totally embarrassing to share with the committee.

• I finished up the experimental design at a balanced scale for outcomes and size. I will be checking-in with Ariana later this afternoon to chat about Resazurin as the metabolic measure rather than straight-up respiration testing if possible. The goal is to try it out on the pilot mussels and see if we can see a difference between the heat treated v ‘control’ ambient mussels.

Word Count (Productivity)

• MS & PhD Proposal: 346 words
• Experimental Design, Justification & Resazurin modified protocol/ questions: 1265
• Today’s total: 1611 words
• Monthly total to date: 6744 words

Questions or Concerns?

• None.

Tomorrow’s Plan

• Will be made tomorrow.

Mussels, Mussels Everywhere + RUA

Projects Touched Today

• Mussel pilot experiment
• Mussel resazurin trial

New Knowledge

Day 28. Mussel Check at 1354

Visual tank inspections looked good for airflow and water clarity. Mussels were still aggregated in their respective bags/ coolers. You can smell the mussels when you enter the cold room, this temperature increase may get us to 50% mortality.

• Temperature

  • Blue= 11° C

  • Red= 22° C

• Salinity

  • Blue= 27 psu

  • Red= 30 psu

• Mortality

  • Blue= 0

  • Red= 2

• Water Change

  • Partial water change for Blue and Red. Salinity recheck:

    • Blue= 25

    • Red= 25

• Feeding

  • Mussels were fed using the same calculations and method as outlined on 12.31.25 except tissue mass has been reduced to 140g for total tissue weight in the remaining mussels.

Old Tricks

• Same as 1.18: Right back at it refining, aligning and ensuring my proposal is clear without getting too into the weeds. I’m super close to a draft that isn’t totally embarrassing to share with the committee.

• I finished up the experimental design at a balanced scale for outcomes and size. I met with Ariana this morning to chat about Resazurin as the metabolic measure rather than straight-up respiration testing if possible. The goal is to try it out on the pilot mussels and see if we can see a difference between the heat treated v ‘control’ ambient mussels. She helped me identify some key safeguards and ‘insurances’ when running this for the first time with these samples.

Word Count (Productivity)

• RUA working day
• Today’s total: 0 words
• Monthly total to date: 6744 words

Questions or Concerns?

• None.

Tomorrow’s Plan

• Will be made tomorrow.

Mussels, Mussels Everywhere + eDNA

Projects Touched Today

• Mussel pilot experiment
• Kenya eDNA
• Proposal writing

New Knowledge

Day 29. Mussel Check at 1813

Visual tank inspections looked good for airflow and water clarity. Mussels were still aggregated in their respective bags/ coolers. You can smell the mussels when you enter the cold room, this temperature increase may get us to 50% mortality.

• Temperature

  • Blue= 11° C

  • Red= 22° C

• Salinity

  • Blue= 28 psu

  • Red= 29 psu

• Mortality

  • Blue= 0

  • Red= 6

• Water Change

  • Partial water change for Blue and Red. Salinity recheck:

    • Blue= 25

    • Red= 25

Old Tricks

• Same as 1.18, 1.19, and 1.20: Right back at it refining, aligning and ensuring my proposal is clear without getting too into the weeds. I’m super close to a draft that isn’t totally embarrassing to share with the committee. I have finally finished verifying my lit, polishing what I can and have setup a schedule-send email because I do not need to share what time I finished this…

• I met with Mollie Ball to go over the nuances between standard eDNA metabarcoding and using it for analyzing gut contents. This was super helpful and I now have a better idea of how to get my bench protocols cleaned up a bit.

Word Count (Productivity)

• Proposals: 938
• Today’s total: 938 words
• Monthly total to date: 7682 words

Questions or Concerns?

• None.

Tomorrow’s Plan

• Will be made tomorrow.

Mussels & Biomarkers

Projects Touched Today

• Mussel pilot experiment
• Mussel biomarkers

New Knowledge

Day 30. Mussel Check at 1944

Visual tank inspections look ok-ish for airflow and water clarity; water is very cloudy in comparison to previous checks. Mussels were still aggregated in their respective bags/ coolers. You can smell the mussels when you enter the cold room, this temperature increase may get us to 50% mortality.

• Temperature

  • Blue= 11° C

  • Red= 22° C

• Salinity

  • Blue= 26 psu

  • Red= 26 psu

• Mortality

  • Blue= 0

  • Red= 3

Old Tricks

• I had some personal obligations to knock out today, so my main productive activity was making the maps of the contaminant indices and IBRs for the supplement of the biomarker paper.

Word Count (Productivity)

• Maps Made: 16
• Today’s total: 0 words
• Monthly total to date: 7682 words

Questions or Concerns?

• None.

Tomorrow’s Plan

• Will be made tomorrow.

More Mussels and Biomarkers

Projects Touched Today

• Mussel pilot experiment
• Mussel biomarkers

New Knowledge

Day 31. Mussel Check at 1709

Visual tank inspections look fine for airflow but not for water clarity. Water is cloudier than yesterday and in comparison to previous checks. Mussels were still aggregated in their respective bags/ coolers. You can smell the mussels when you enter the cold room, this temperature increase may get us to 50% mortality.

• Temperature

  • Blue= 11° C

  • Red= 22° C

• Salinity

  • Blue= 27 psu

  • Red= 28 psu

• Mortality

  • Blue= 0

  • Red= 7

• Water Change

  • Partial water change for Blue and Red. Salinity recheck:

    • Blue= 25

    • Red= 25

• With today’s mortalities, we have reached 19 out of 30 (>50%) in the elevated temperature treatment. Since we were aiming for a full 30-days, including acclimation, this is great. 22° C, despite a ramp-up is the max over time. Potentially feeding every 5 days instead of 7, and tighter salinity management with more frequent water changes may also increase resilience to the higher temp.

Old Tricks

• The biomarker paper is my focus for editing, expanding the introduction to better scaffold the problem we are solving, and fixing the method’s subsection for analysis was my focus today. I also worked out some tentative captions for the figures, based on feedback from Alison about which viz is most effective. I am super excited about it is shaping up.

Word Count (Productivity)

• Biomarker manuscript and figure captions: 2574 words
• Today’s total: 2574 words
• Monthly total to date: 10,256 words

Questions or Concerns?

• None.

Tomorrow’s Plan

• Will be made tomorrow.

Mussels, Thy Name is Icarus

Projects Touched Today

• Mussel pilot experiment
• Mussel biomarkers

New Knowledge

Day 32. Mussel Check at 1246

Visual tank inspections look fine for airflow but not for water clarity. Water is CLOUDY. Mussels were still aggregated in their respective bags/ coolers. You can smell the mussels when you enter the cold room, this temperature increase has pushed us past 50% mortality.

• Temperature

  • Blue= 11° C

  • Red= 22° C

• Salinity

  • Blue= 27 psu

  • Red= 28 psu

• Mortality

  • Blue= 0

  • Red= 4

• Water Change

  • Partial water change for Blue and Red. Salinity recheck:

    • Blue= 26

    • Red= 26

• With today’s mortalities, we have reached 23 out of 30 (>50%) in the elevated temperature treatment. Since we’re notching daily mortalities now, I will run the Resazurin trial tomorrow, 1/25 to hopefully ensure some of the elevated temp mussels can also be tested.

Old Tricks

• The biomarker paper is my focus for editing, expanding the introduction to better scaffold the problem we are solving, and fixing the method’s subsection for analysis was my focus today. I also worked out some tentative captions for the figures, based on feedback from Alison about which viz is most effective. I am super excited about it is shaping up.

Word Count (Productivity)

• Biomarker manuscript and figure captions: 2574 words
• Today’s total: 2574 words
• Monthly total to date: 10,256 words

Questions or Concerns?

• None.

Tomorrow’s Plan

• Will be made tomorrow.

Testing Resazurin Assay Protocols for Mussels

Projects Touched Today

• Mussel pilot experiment

New Knowledge

• Resazurin trials with the mussels that have undergone the 30-day survivability testing; modified protocol, notes and experiment raw data are in the January 25th weekly post and the mytilus_pilot repo.

Day 33. Mussel Check and Experiment Take Down at 1020

Visual tank inspections look fine for airflow but not for water clarity. Water is CLOUDY. Mussels were still aggregated in their respective bags/ coolers. You can smell the mussels when you enter the cold room, this temperature increase has pushed us past 50% mortality.

• Temperature

  • Blue= 11° C

  • Red= 22° C

• Salinity

  • Blue= 26 psu

  • Red= 27 psu

• Mortality

  • Blue= 0

  • Red= 5

Old Tricks

• The 30-day survivability test for mussels is completed today, actual day 33. The mussels not used for the resazurin trials were removed from their mesh bags, visually inspected for any signs of slow response or shell damage, and then frozen in the -80 for potential baseline biomarker work to inform the full mussel experiment.
• The tanks and equipment were taken down, cleaned and kept together since it is a short period of time between takedown and setup for the full experiment.

Questions or Concerns?

• Next week Need to-do’s: Following up with EH&S for guidance around tank/ physical space requirements.
• Will chat with Sam re: the location of the Hazardous Waste labels.

Tomorrow’s Plan

• Continue working through resazurin results and protocol optimization.

Mytilus is the Main Character

Projects Touched Today

• Mussel pilot experiment
• Mussel experiment planning

New Knowledge

• I updated the metadata and ImageJ measurements in the data tables for the pilot resazurin trial ran on Sunday (1/25).
• Put together some experimental design options for the isotopes of PAHs or PCBs that we can use in the lab. Cambridge Isotope Labs has a good selection of isotopes that we can order at various price points ranging from $150 on the lower end and well over $2000 on the higher end.
• In addition, the Cambridge Isotope Labs has a grant section that is an easy lift to potentially attain the chemicals for no cost.

Old Tricks

• Continued to update my literature review notes since determining many of those notes have been incorrectly discarded.

Questions or Concerns?

None

Tomorrow’s Plan

• Prep for a full RUA day and events, not much but task management will be done tomorrow.

STEM Socializing - No Science Today

Projects Touched Today

No project work today. Tuesdays are UW-RUA days.

New Knowledge

I held an event to explain what UW-RUA can do, what the postdocs and PhD-C’s need to apply, and generally trying to facilitate conversations and getting to know each other beyond just asking about the program. I learned far more about engineering than I expected, but enjoyed the clarity into how different graduate programs work.

Old Tricks

Data cleaning and analysis for the historic UW-RUA program (all three iterations) has been a nice way to keep my exploratory visualization skills up.

Questions or Concerns?

No.

Tomorrow’s Plan

Fly home.

Document or it didn’t happen..

Projects Touched Today

• Lab Notebook

  • The goal of the work today is to get my daily and weekly lab notebook back up to date!

New Knowledge

I created a new template that makes staging my daily and weekly posts much easier to create. My current system is to drop updates into Notion using a button, and that helps me remember days whwere one or two things were going on without a lot of detail, but this format may be an easier capture of the details that are important.

Old Tricks

Thank goodness for the Notion setup or I would have forgotten all that has been done!

Questions or Concerns?

Why did I keep pushing this off?!?! Definitely going to give it a better run in February.

Tomorrow’s Plan

Reviewing and updating my written proposals and figures for the biomarker manuscript will be the plan for the remainder of the week.

No Science Today

No science today. I am home until February 2nd.

No Science Today

No science today. I am home until February 2nd.

No Science Today

No science today. I am home until February 2nd.

Notes from 10.06.2025 Lab Meeting

Progress as of 10/06/25
After dusting off the docs and taking an inventory of where each of the pieces stand, I have the 3 PhD chapters outlined and pivoted to working on my first MS chapter. I chose to shift away from the PhD proposal focus so that I could knock out the MS chapter since it is my required manuscript for the package and needs to be reviewed/ approved by both the committee and WDFW.

1st- the Graduate School Funding Guide has a huge database (GFIS) of funding opportunities that you can search, download into a csv and explore on your own time. It also has the college-wide Assistantships database you can explore. There are dedicated support resources through the library if you have questions.

2nd- If you use Zotero and want to clean up your literature review process, link it to something like Notion or any other organizational platform that supports integration and keep all of your notes and annotations in one place. This video from The Grad School Coach shows you how to integrate Notion & Zotero, and this video from Aynur Science on how to create a literature review workflow using Notion that supports information recall.

3rd- Wondering where your time is going? I did my own time trials using Toggl this summer to see how long my most frequent tasks (reading and annotating a paper, coding plots, setting up data cleaning scripts, etc.) take me to complete so that I could better schedule my day and not demoralize myself when I’m not meeting my productivity goals. I used daily to track my time, help me build my weekly time blocking schedules, and review where I’m getting lost, and as a bonus, I can see just how much work on each project I am putting in and how to adjust for the upcoming week. Toggl is platform that you can use for free, but there are paid upgrades if you want them. I’ve been using it since July and haven’t needed to upgrade at all, all of the free functions are great.