November Daily


Steven Roberts


November 1, 2023

November 1

Went to hatchery to clean oysters. A couple of pipes in control fell. Temperature was 13.9. Installed header heater to 16.

November 2

Non coding RNA meeting- followed by lab meeting- several appts

Insert date insert time date time. I spent a lot of time talking in different different meetings

Non-coding RNA

This meeting was a working group discussion on non-coding RNA. They began by discussing some issues Sam was having with workflows and output from programs like MirTrace. They determined that trimming reads to 25 bases led to more hits in the database, showing trimming has an impact. Steven shared some Markdown files documenting analysis steps and they discussed better ways to share these files. They agreed writing out methods sections ahead of time would help guide future work, even if all steps haven’t been completed yet. To wrap up, they decided tomorrow’s meeting should focus on working in breakout rooms to further develop introduction, methods, and other sections of their project.

Workflows and methods for genetic analysis. (0:02)

Analyzing audio transcript for microRNA analysis. (4:56)

Gene sequencing and merging code branches. (11:14)

Using GitHub to create documents and markdown files. (17:07)

Planning for tomorrow’s meeting. (39:37)

lab meeting

The meeting began with Grace presenting her research on modeling the immune response of sea stars to sea star wasting disease. Next, Maggie discussed her past research on the effects of temperature on metabolic rate in invasive blue catfish, and her current research using ROVs to study fish assemblages on artificial reefs. Then Aspen presented her chapter on modeling meta Dyneema infections in Tanner crab, showing patterns of infection correlated with temperature, shell condition, and black mat fungus infection. The group provided feedback on her analysis and suggestions for further exploring explanations for differences in infection patterns between sites. Finally, Steven Roberts reminded everyone about monthly reporting requirements and purchasing reimbursements.


The meeting discussed analyzing alternative splicing in oyster genes to determine if it occurs randomly or in a directed, non-random manner between control and treated samples. They debated different methods to quantify this, such as looking at exon counts and coefficients of variation. Zach agreed to generate exon expression data for all samples. Stephen said he would work on getting this exon count data into a matrix. They also agreed to read the methods section of a relevant paper to help inform their approach. Determining the next steps for analyzing Zach’s long non-coding RNA data was discussed, but the group felt it may not directly fit into the current manuscript.

November 3

Today started out with the Gugino paper meeting spent most of the time looking at the response to reviewers didn’t get too far. Need to deal with a figure. Also need to think of an interesting polite way to respond to crazy comments.

After that met with Zack to talk about the coral analysis and funding in the near term that transition directly into the five liquor meeting where we spent majority of the time coding for long, non-coding RNA discovery we actually broke out in the three breakout rooms, the other one group working on short RNA and another group working on the manuscript talking about bigger picture things, it was determined that definitely in the long term will be interested in looking at kind of the evolutionary relationship with cutting RNA.

This meeting was focused on analyzing long non-coding RNA sequences from multiple species. The group had been working on identifying these sequences and filtering them based on various parameters. For this meeting, Steven Roberts proposed focusing on finalizing the coding and discovery process. The group discussed their progress, with some working on refining the coding and others reviewing the manuscript. They discussed next steps of agreeing on a final list of long and short non-coding RNAs to present at the next meeting, as well as doing comparative analyses across species.

The next meeting was with Grace where we evaluated her long-term timeline to discuss projects finding courses, etc.

  • Grace presented a timeline and funding plan for her PhD research
  • She will be analyzing samples from summer 2022 experiments on disease resistance in sea stars
  • Her goals are to publish papers from each dataset as she analyzes them
  • Funding is secured for sequencing and analyses of the first two datasets
  • Drew will check on funding availability for the third dataset from Nature Conservancy
  • Grace will send Drew a budget estimate for sequencing the third dataset
  • They discussed applying for an NSF supplement to fund Grace’s stipend through an internship

Also met with Kathleen talked a little bit more about EI project and monthly goals and some background on the cod project and how we will need to identify samples for our analysis

November 4

This is dumb activating dictation from my Mac and recording a notebook post. So today been working on trying to grab a GTF of a long non-coding RNAs that is she seems to be dirty Heidi files from CPCR1 base off that you can’t do a query error substrate of original GTF.

November 6

E5 coding- submitted referenc letter.

November 7

E5 lnc coding, discussed timeline with Aspen - will follow up with credits.

November 8

E5 PI meeting: During the meeting, the group discussed their ongoing projects. Chema provided an update on their RNA analysis work. They also discussed progressing a manuscript on epigenetic simulation that has been in progress. Chema suggested dedicating focused weekly meetings to work on sections of this paper. The group agreed to an initial meeting on November 21st at 10am Pacific time to start working on outlining the paper.

LncRNA fail when removing splice sites, get no transcripts in merge. Will try repro… should have used separate notebook in hind sight

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