Daily Notes

Stuff that did not make the bar to postworthy

Note (2025-03-04 06:59:36)

62-7174 | CLIMATE RESILIENCE | CC100950 CoEnv | Aquatic and Fishery Sciences (SAFS) - R&E | PG107267 | GR014587 | FD200 | RS100077 | FN111 |

Note (2025-03-01 11:45:01)

Get the Peve time series methylation array, stuff in a notebook

Note (2025-03-01 08:14:36)

Run deep expression on symbiont

Note (2025-02-28 12:40:04)

https://gannet.fish.washington.edu/spartina/project-oyster-oa/Haws/

Note (2025-02-28 07:40:26)

One thing that I really want to get done, let’s put it on a to do item and maybe if we search for to do it’ll come up, but I’d like to develop some research retrospective to come up on my website to look at kind of past effort and and summarize in particularly if we’re not there, they’re not active areas you know I’m thinking Olympia oyster I just changed that I’m also thinking active efforts to might be might be valued #todo

<!— block assistant —> Develop a research retrospective section on my website:

  1. Plan where to incorporate the section on the website, consider where it can be easily accessed and seen.
  2. Begin to gather and compile the information for past projects, focusing on non-active ones like the Olympia oyster.
  3. Write thorough summaries of each project, detailing the process, findings, and why the project ended or is currently inactive.
  4. Design the website section to be engaging and easy to understand.
  5. Build out ‘active efforts’ section as well, keeping it updated with current projects and research.
  6. Once the section is ready, test for usability and functionality.
  7. Upload and monitor the performance of the new section.
  8. Consider promoting the new section through various channels to ensure it catches the attention of site visitors.

This could be a great way to showcase past achievements and pursuits. It could also aid in sparking interest in currently active projects. #todo <!— endblock —>

Note (2025-02-28 06:36:47)

Goal today is getting e5 lncrna discovery pipeline up.

Note (2025-02-25 16:45:09)

My Afternoon

•   I met with the research administration team to discuss my grants
•   I need to carefully manage my budgets for grants ending this summer
•   I’m still waiting to hear back from NSF about a no-cost extension
•   I’m having some challenges finding postdocs to hire
•   Around 3:15 PM, I had a discussion about my course and research
•   We talked about the effectiveness of online vs. in-person recitations

Note (2025-02-25 16:25:35)

Today I did not do much coding- class stuff and admin meetings

Note (2025-02-24 20:05:58)

I am done for now

Note (2025-02-24 19:51:44)

docs/notes.txt

Note (2025-02-24 19:50:12)

OK, can I get a QMD file to a text file?

Note (2025-02-24 19:25:04)

From phone to render

Note (2025-02-24 18:41:04)

Install R

sudo apt update sudo apt install -y r-base

Install Quarto

wget https://github.com/quarto-dev/quarto-cli/releases/download/v1.3.450/quarto-1.3.450-linux-amd64.deb sudo dpkg -i quarto-1.3.450-linux-amd64.deb rm quarto-1.3.450-linux-amd64.deb quarto –version # Verify installation

Install R Packages in a User-Writable Directory

mkdir -p ~/R/library echo ‘R_LIBS_USER=~/R/library’ >> ~/.Renviron Rscript -e ‘install.packages(c(rmarkdown, knitr), repos=http://cran.rstudio.com/, lib=~/R/library)’

Render Quarto document to docs/

export R_LIBS_USER=~/R/library # Ensure R finds the installed packages mkdir -p docs # Ensure docs/ exists before rendering quarto render notes.qmd –to html –output-dir docs

Note (2025-02-24 17:20:26)

Note (2025-02-24 16:28:07)

Tasks

  1. Email Matt about triploid oysters.
  2. Review Arianna’s proposal.
  3. Review Eva’s proposal.
  4. Send an email to EarthLab.

Note (2025-02-24 16:12:50)

Started my morning with a burst of productivity! 🚀 Spent several hours creating something I’m really excited about - an automated system for my notebook posts. Finally figured out how to use iOS shortcuts with GitHub to make posting updates a breeze. It’s amazing how a morning of coding can make life so much easier. Already used it to post about Sam’s DNA extraction and Ariana’s work.

By midday, found myself troubleshooting with some colleagues. Someone was having issues with file management in Raven - you know how these technical hiccups can be. Helped sort that out while discussing plans for time series methods and methylation analysis. It’s satisfying when you can help others get unstuck.

The afternoon brought a fascinating research meeting about our three-species analysis project. We dove deep into differential expression analysis and gene ontology work. The team’s making good progress, though we need to secure some additional funding for sequencing. The Wildlife Diseases Conference abstract deadline is coming up on March 1st - always keeping us on our toes!

Later in the day, had a lengthy session reviewing a scientific paper. Spent quite a bit of time fine-tuning the visualizations for symbiont-host interactions. Also tackled some grant management tasks - budgets, personnel, supplies, you name it. Earthlab and BIMS funding discussions always keep things interesting.

Note to self: Yesterday’s impromptu Seattle trip without a raincoat was not my brightest moment! 🌧️ Got soaked and learned my lesson - need to start checking the weather forecast more regularly.

Looking ahead, we’ve got some exciting projects in the pipeline - Yellow Island sampling, biomarker analysis, and that trip to plan for. Never a dull moment!

Today was one of those full but satisfying days. The new automated notebook system might be my favorite achievement - it’s the little things that make work life smoother, isn’t it?

Note (2025-02-24 13:58:36)

What is the best way to save time writing ✍️ science notebook posts?

  1. Organize Your Thoughts: Before you start writing, have a clear outline of the content you want to share. This will help you write in a streamlined manner and avoid wasting time changing things later.

  2. Use Templates: If you often write about similar topics, consider creating a template that includes all the sections you typically include. This way, you won’t need to start from scratch each time.

  3. Write Regularly: The more you do it, the quicker you’ll get. Regular practice will help you familiarize with scientific language and structure, thus speeding up your process.

  4. Use Technology: Make use of science writing software tools, plagiarism checkers and grammar correction software to assist in creating quality content quickly.

  5. Write First, Edit Later: Avoid editing as you write. Instead, focus on getting all your ideas down first. Once you’ve finished, you can review what you’ve written and make necessary changes.

  6. Use Visuals: It often takes less time to explain complex scientific concepts using images, graphs, or charts.

  7. Break Down Complex Ideas: Instead of spending time writing lengthy explanations, break complex ideas down into simpler ones. This will make your posts easier to understand and quicker to write.

  8. Reuse Content: If you’ve written about a topic in the past, it’s okay to reuse some of that content. Just make sure to update any outdated information.

  9. Set Time Limits: Determine how much time you want to spend on each post. This will help you stay focused and avoid wasting time on unnecessary details.

  10. Delegate: If there are too many tasks on your plate, consider delegating. A collaborator or an assistant can help with research, editing, or even writing portions of the post.

Note (2025-02-24 13:14:08)

Is my time zone correct?

February 21, 2025

ffs Why These Class Codes for lncRNA Discovery?****

  1. Intergenic lncRNAs (lincRNAs) → Class code “u”****

• They exist outside known protein-coding genes.

• Tend to be truly novel transcripts.

  1. Intronic lncRNAs → Class code “i”****

• These are found inside introns of known genes.

• Some intronic lncRNAs are functional and could be regulatory.

  1. Antisense lncRNAs → Class code “x”****

• Found on the opposite strand of known genes.

• Might regulate sense-strand transcription.

  1. Potential lncRNAs Overlapping Known Genes → Class code “o”****

• Need further filtering to ensure they are not protein-coding isoforms.

Research Notes: February 20, 2025

Today provided several valuable insights across multiple marine science domains:

From seminar, learned about novel approaches to enhancing resilience in commercially important species. Key points:

•   Integration of multiple OMICS technologies (metabolomics, proteomics, transcriptomics) for comprehensive analysis
•   Successful application in various species:
•   Green-lipped mussels (summer mortality resistance)
•   Pacific oysters (viral infection response)
•   Chinook salmon (feed efficiency optimization)
•   Geoduck cultivation
•   Abalone heat wave resilience

Particularly interesting: The development of encapsulated feed technology for abalone, showing promising results in both land-based and open-water aquaculture systems.

Oyster Genetics Analysis

Data analysis session with Benjamin revealed interesting patterns:

•   Observed distinct differences in copy number variance between diploid and triploid oysters
•   Potential implications for stress response mechanisms
•   New insights into gene loss patterns

Phage Therapy Applications

Emerging therapeutic approach for aquaculture diseases:

•   Discussion with Scripps collaborators highlighted potential applications for oyster pathogens
•   Integration with existing disease management strategies
•   Possibility for targeted bacterial control in aquaculture settings

Future Directions

•   Further investigation needed on specific genes involved in stress response
•   Potential for combining phage therapy with resilience enhancement strategies
•   Cross-disciplinary applications of OMICS technologies in aquaculture

Note: Planning follow-up collaborative work with Scripps Institution of Oceanography to expand phage therapy research.

This synthesis of today’s learnings highlights the increasing convergence of molecular techniques, traditional aquaculture, and innovative therapeutic approaches in marine science. The integration of these methods could provide new solutions for industry challenges.

February 15, 2025

Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools found here: '/usr/bin/samtools'
Reference genome folder provided is ../data/    (absolute path is '/home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/data/)'
FastQ format assumed (by default)
Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4
Each Bowtie 2 instance is going to be run with 10 threads. Please monitor performance closely and tune down if necessary!

Input files to be analysed (in current folder '/home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/code'):
../data/22-Apul-meth/ACR-140-TP2_R1.fastp-trim.fq.gz
../data/22-Apul-meth/ACR-140-TP2_R2.fastp-trim.fq.gz
Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!)
Output will be written into the directory: /home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/output/22-Apul-methylation/
Setting parallelization to single-threaded (default)

Summary of all aligner options: -q --score-min L,0,-1.0 -p 10 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Current working directory is: /home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/code

Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/data/

Single-core mode: setting pid to 1

Paired-end alignments will be performed
=======================================

---


253164476 reads; of these:
  253164476 (100.00%) were paired; of these:
    252724097 (99.83%) aligned concordantly 0 times
    215631 (0.09%) aligned concordantly exactly 1 time
    224748 (0.09%) aligned concordantly >1 times
0.17% overall alignment rate
253164476 reads; of these:
  253164476 (100.00%) were paired; of these:
    252721074 (99.82%) aligned concordantly 0 times
    210210 (0.08%) aligned concordantly exactly 1 time
    233192 (0.09%) aligned concordantly >1 times
0.18% overall alignment rate
Processed 253164476 sequences in total

December 6, 2024.

OK didn’t do much analysis today but did decide that the next focus is going to be to take Chris nutation samples. We run them hopefully with the new next flow pipeline, but that’ll be ready to see if unit directional alignment fixes the odd CG ratio thing

Relavant Species info

Based on the differences in life history, ecology, and biology between Acropora pulchra, Pocillopora meandrina, and Pocillopora tuahiniensis, we would expect differences in their gene regulatory mechanisms. Here’s why: • Different Symbiotic Strategies and Environmental Sensitivity: The sources highlight that these species have distinct symbiotic strategies, with A. pulchra being a horizontal transmitter and both Pocillopora species being vertical transmitters. Additionally, A. pulchra is generally considered more sensitive to environmental change. These differences likely require distinct gene regulatory mechanisms to manage the acquisition, maintenance, and potential stress responses associated with their symbionts. ◦ A. pulchra needs to regulate genes involved in recognizing and incorporating symbionts from the environment, while the Pocillopora species need to regulate genes for the inheritance of symbionts. ◦ The higher environmental sensitivity of A. pulchra suggests that its gene regulatory mechanisms may be more responsive to environmental stressors, leading to differential gene expression patterns compared to the Pocillopora species. • Symbiont Community Composition: Each species associates with different dominant Symbiodiniaceae species and profiles. This variation in symbiont partners is likely to influence host gene expression, as different symbionts may produce different signaling molecules or metabolites that interact with host gene regulatory pathways. ◦ For example, the sources found that symbiont community composition was significantly related to host physiology in Porites. This suggests that the specific types of symbionts present can influence host gene expression patterns. • Cryptic Diversity and Holobiont Identity: The sources emphasize the presence of cryptic diversity within the Pocillopora genus and the importance of considering holobiont identity. Even within the same species, different host haplotypes can exhibit distinct physiological responses and associate with different symbiont communities. This suggests potential genetic differences in gene regulatory mechanisms between holobionts. • Physiological Differences: The sources detail significant physiological differences between these species, indicating that their gene regulatory mechanisms must be tuned to support their distinct physiological needs. ◦ For example, the sources note that Porites corals, with their thicker tissues, have higher overall physiological rates compared to Acropora and Pocillopora. This would necessitate differences in the regulation of genes involved in metabolic processes, growth, and calcification. • Morphological Differences: The sources describe differences in tissue structure, with Acropora and Porites having perforate tissues and Pocillopora having imperforate tissues. These morphological differences could influence the microenvironment experienced by the coral host and its symbionts, potentially leading to differences in gene expression patterns. ◦ For example, perforate tissues might allow for greater exchange of nutrients and gases, which could affect metabolic processes and the regulation of related genes. Overall, the sources provide strong evidence that the different life histories, ecologies, symbiont communities, and physiologies of Acropora pulchra, Pocillopora meandrina, and Pocillopora tuahiniensis are likely associated with differences in their gene regulatory mechanisms. Further research, specifically focusing on gene expression analysis across these species, would be needed to confirm and explore the specific nature of these differences.

quarto render

find . -name "*.qmd" -mtime -1 -exec quarto render {} \;
November 21, 2024 18:47:09

Today in RStudio, I focused on several tasks related to my project “bestblogever.” I worked on rendering and saving files using Quarto for document preparation and management. I also engaged in coding activities, which included running shell scripts and managing directories and files for data processing. This involved setting up directories, creating checkpoint files, and running Bismark alignments, typically used for DNA methylation analysis. I ensured that the scripts executed successfully by checking command outputs and logging the results.

Additionally, I was involved in version control activities, such as staging, committing, and pushing changes to my Git repository. This included reviewing changes in various HTML and XML files related to my project documentation. I also managed my RStudio environment by loading workspaces and utilizing various RStudio features like the console, terminal, and background jobs.