2025 November Daily Posts

This page compiles all daily posts made in November 2025.

2025-11-01 — Monthly Planning & Goal Setting

• The focus of today is to set my goals for the month of November, but I am still stuck in trying to get the rest of my life online for the month… gotta love this time of year. Everything is urgent until something truly urgent comes along.
• November goals
  • Finish biomarker manuscript draft
  • Finish MS thesis proposal
  • Finish mussel methylation analysis

2025-11-02 — From Kenya to Tacoma and Back

• Today’s work was
  • Finalizing my presentation on the biomarker work for Alison’s class tomorrow.
  • Creating the sediment sampling protocol, metadata collection steps, building the data tables and providing open- source resources to gather the data for the NMK team. They go out to our Lake Victoria field sites next week.
  • Reading papers to help me clarify the experimental design for my chapter 3.

2025-11-03 — Biomarkers

• I ran through my ecotox presentation and headed down to Tacoma to give it!
• I met with Alison to discuss transitioning from chapter 2 outcomes to chapter 3 validation and that was super helpful. Our current lab- based plan doesn’t achieve what we are looking for, so I’ll do some more reading and work through some alternatives before meeting with Steven.
• I lectured on biomarkers, conservation, Puget Sound organizations and what it means to be a non-traditional student. It was awesome and I enjoyed getting to practice talking about the biomarker and preliminary DNA methylation work.

2025-11-04 — No Science Today

• No science work done today.

2025-11-05 — ENVIR Lecture

• I knocked out my Research as Resistance lecture for Friday’s ENV 100 class. I’m definitely nervous about speaking in front of more than 300 students, but if I don’t practice now, I’ll never get used to it.

2025-11-06 — Writing

• I spent the majority of today making an annotated bibliography for the biomarker paper while struggling through writing the introduction. It is still crap, but at least something is on the page.

2025-11-07 — King Tides

• I presented to the ENV 100 class and it was very cool! It is very fun to chat through what I am doing and where I want to go with my work.
• After class I got home, packed my gear in the car and headed out to the coast for the weekend so I could take pictures of the tides, read without interruption, and write.

2025-11-08 — Tides in Tokeland

• I spent the majority of the day photographing the coast, the tides, intertidal critters at night, and the towns of Westport and Tokeland.

2025-11-09 — Tides, Again

• I caught the last of the king tides at the Ocean Shores N jetty before heading home and setting up for the week.

2025-11-10 — No Science Today

• No science today, tons of personal errands and tasks to knock out.

2025-11-11 — Methylation Analysis

• Today’s mission was to get the ‘simple’ version of the methylation work up and running on Raven. Last week, I built my bioinformatics environment on my local computer so that I could run the initial QC, trimming and alignment on 1-2 sequences so I could understand what I was doing.
  • I was able to take the code from Steven’s Mytilus Project repo, strip it down to the barest of essentials (so I could understand it) and run through the Bismark alignment. I was able to do this with one sample (read 1 and 2), but my computer didn’t have enough storage/ memory to do the second. Looking at the QC reports, I understand what I see, but I do not understand the Bismark output. This will be a topic in our 1v1 this week.
• I finally got my repo up on Raven, cleared the cache on my GH Desktop app so that I could actually work with the remote repo, and made script adjustments so that I could call the programs like FastQC, MultiQC, Bismark and Bowtie outside of my locally- created container.
  • First - and possibly most important, if you update your gitignore file after the first commit without clearing the cache of your GH Desktop app, you will commit/ push files that are listed in the gitignore resulting in a never ending compressing/ writing/ failing loop that will prevent you from doing anything. Thank you StackOverflow for the fix.
  • Second - I will 100% have to move up from Raven to Klone for this work and beyond. Just running the QC work on Raven has taken hours - will most likely take overnight for the process to finish. Not feeling great about it, but it is a tool that must be used.

2025-11-12 — More Methylation

• Started today’s work by checking on the status of my QC work I left running last night. It is still running and I anticipate the trimming and QC will take equally as long, so I will use the Bismark output from my local single sample run to touch base with Steven in our 1v1 tomorrow.
• While I keep checking in on these things, I am wrapping the introduction for my MS thesis proposal.
• Returning to the methylation analysis, it has taken far longer to get through the QC steps before trimming and repeating the QC and I am going to have to just keep at it to get through it. I am a bit disappointed, but it is how it goes. I will get through the trimming and start the QC again tonight to hopefully have some results in the morning.
  • One thing I noticed is that there are a ton of sequences that look like maybe they are from the sequencer, possibly the absolutely raw data instead of the ‘processed raw’ data that is named in alignment with what I named the samples. I will ask about it when I talk to Steven tomorrow.
  • I opened a second terminal window to get the trim and QC rolling while the multiQC runs on the fastqc reports.
  • I moved the additional sequences from the raw directory to the raw_other directory to hopefully speed up this part of the process.

2025-11-13 — Advisor Check-Ins and Writing

• I met with Steven today to go over my current steps in the methylation analysis, clarify the lab based experiment for my dissertation chapters and review the past two weeks of work.
• I worked on changing the second chapter of my MS proposal from eDNA to DNA methylation.

2025-11-14 — Writing

• Today was a writing day. I have toggled between personal writing and proposal writing throughout the day; this helps me refocus when I feel like I am dragging.
• One major thing I will need to adjust moving forward is my literature review setup. I built a database in Notion that hold all of my papers, annotations, and purpose for the papers, but most of the papers I read and worked on before doing that in September don’t align with the new system and I cannot afford to go back and redo things at this moment… but I will need to make an adjustment so that when my MS proposal is finished, I don’t run into this again.
  • I also need to ensure the current setup is effective for me since I feel like I spend more time aligning my notes with the system rather than using the system to help me manage my notes.
  • One thing that helps that doesn’t exist yet is a place to keep an annotated bibliography by project - this will help me move quicker though the literature.
  • Another thing is to use a category versus tagging system as the tags are out of hand. My Notion + Zotero integration already imports the keywords from the papers as tags, having my own ‘tags’ group is just making a confusing mess,
  • Finally, I need a better way to see my notes in my properties - more aligned with how I take the notes, that make it easier to read without having to click through a million things.

2025-11-15 — No Science Today

• No science today

2025-11-16 — No Science Today

• No science today

2025-11-17 — No Science Today

• No science today

2025-11-18 — FISH 510 & Methylation Analysis

• Today is a slow working day after some other responsibilities took me away from my work the last few days.
• I started with adjusting my code like Steven and I discussed so I could reduce the time to run Bismark on the sequences to understand the output and optimize the parameters so that I’m balancing mapping efficiency while monitoring some of the cytosine parameters to ensure no artificial inflation of methylation ID.
• I also started to catch up on my FISH 510 discussion posts by working backwards from the most recent one due to the posts that are overdue.
• Finally, I attended class and participated in the polar bear epigenetic clock conversation.

2025-11-19 — Wednesdays are for Writing

• I realized today that my MS proposal format is wrong. I am actually doing more than needed. During a writing block with KPJ, we realized I was framing the chapters individually rather than weaving together the common goal of both. This means I have been writing too much detail for each chapter rather than focusing on the overall narrative. I need to reframe my proposal to highlight the connections between chapters and how they contribute to my research question. This is relieving.

2025-11-20 — FISH 510 Coursework

• Today’s work was dominantly task- centered as I am a bit behind.
  • I first knocked out the discussion post for next week’s class. That led me to do a bit of a deeper dive to understand how Botryllus is able to invade, survive and possibly thrive under challenging climate conditions; dominantly the asexually reproducing ones since the paper called out using both asexual and sexually reproductive colonies to interrogate genomic and epigenomic contributions to survival.
  • I outlined my final deliverables and chose to go with the blog post. This was fun because translating complex scientific topics to a general audience made me map out what folks need to know to understand the topic, what I knew, and creating a fun roadmap to discuss epigenetics.
• I am continuing the methylation analysis, but there have been many stalls and lags with Raven today. Slow and steady…

2025-11-21 — Writing

• I started the day by trying to streamline the lab- based experiment that should be conducted in the winter. It is a bit larger and more involved right now than I think it needs to be.
• I moved next to updating my daily lab notebook entries for the week, I didn’t realize I was this far behind.
• Finally, I finished the introduction to my MS proposal. I have got to get it to Steven for editing before passing off to my committee. I need to have it uploaded and confirmed by my committee by 12/12/25 and this is far tighter a window than I anticipated providing for edits and feedback.

2025-11-22 — Mussels & Epigenetics

• I jumped back into Raven to get my alignments going again- my connection timed out two days ago and I have finally finished cleaning out the pieces of files, fixing my script to find the executable version of Bowtie and set it off and running.
• I outlined my blog post for FISH 510, drafted my reflection statement and set up the plan for the presentation for class on 12/2.

2025-11-23 — Sundays are for Reading

• I spent today reading about the history of Puget Sound waterway accesses and industrialization. Mostly historical non-fiction, not scientific articles.

2025-11-24 — MS Writing

• I finally finished the draft of my MS proposal and got it over to Steven. I have lost the doc I started with my annotated bibliography - before I switched over to Notion, so I will have to go back and tighten up my sources before submitting the draft to my committee.

2025-11-25 — FISH 510

• Tuesdays are for RUA, so the only ‘science’ I did today was prepare for and participate in class.

2025-11-26 — FISH Blog

• I completed the draft of my blog for class and my reflection statement… Now on to prep for Thanksgiving tomorrow.

2025-11-27 — Thanksgiving

• The only science being done today was of the culinary fashion…

2025-11-28 — No Science

• No science today

2025-11-29 — Mentoring & Recommendations

• I completed three recommendation letters for three former mentees, and one reference for a job for a fourth. These young adults are keeping me busy!

2025-11-30 — Citing for MS Proposal

• I cannot find my annotated bibliography, so I had to comb back through all of my sources to match with what I wrote based on the first- pass notes in Zotero… 0/10 do not recommend.
• I built in the annotated bib section into my Notion literature review database so that as I’m redoing the work, I won’t lose it again.