Yaamini’s Notebook: April Goals

I was so busy catching up on classes I forgot it was April!


March Goals Recap

NSA went well! I’m happy with my poster, and I learned a lot about the field and hashed out some future directions for my projects. It was also really flattering that people thought I was a late-career Ph.D student (I’m not sure if they thought I just looked old or if my work was at that level, but I’d like to think it was the latter). I still haven’t touched either Pubathon paper in a while, nor have I thought about future experiments. But hey, that’s what monthly goals are for, right?

April Goals

This month, I want to focus on my metaanalysis since I was so absorbed in the DNR project last quarter. I also need to think critically about the questions I want to address with the Manchester experiment.

Manchester Project:

  • Shut down OA experimenta and sample oysters: April 8
  • Develop heat shock plan: April 17
  • Develop in-depth spawning plan: April 30
  • Schedule labwork: April 30

Metaanalysis Paper:

  • Formulate question: April 11
  • Analysis plan/methods: April 13
  • Introduction: April 30

DNR Project:

  • Meet with all involved parties to discuss next step in analysis: April 20

DNR Paper:

  • Update methods: April 10
  • Introduction: April 20


  • Committee Ideas: When I met with Steven this week, we decided to think about the committee more in the summer. However, I now think it may be best for me to establish my committee this quarter so I can use my time over the summer to develop my proposal and have my committee provide feedback.
  • Brainstorm members + reasons why: April 10
  • Run ideas by Steven: April 13
  • Contact individuals: April 20
  • PCSGA Abstract: April 13
  • Shellfish Permitting White Paper
  • Readings: April 10
  • Contact experts for interviews: April 10
  • Draft 1: April 14
  • Draft 2: April 21
  • Final Draft: April 28
  • ASLO Science Communication Internship Application: April 28

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Yaamini’s Notebook: Manchester Day 44

What happened when Laura got stranded in the Midwest

A little fun backstory before I proceed:

Laura and I were on different flights out of the Knoxville Airport leaving NSA. My flight got delayed by more than an hour, so I had to run across the airport, poster tube in hand, to make my flight. Laura wasn’t so lucky, and got stuck in Chicago overnight. Today, I took on the responsibility for water chemistry sampling and system maintenance. My first time flying solo and it wasn’t so bad!

  • Water chemistry sampling: 1L grab samples and bottle samples
  • Took standard curve measurements first, everything looked consistent with previous iterations of this process
  • Quickly poisoned samples while waiting for Rick to get to the office
  • Used Rick’s probe to get salinity data
  • Cleaned filters
  • Bleached algal lines
  • Moved probes
  • This time I also recorded what time I moved the probes so we could match it to our data
  • Drained and vortexxed all tanks
  • Found more of that stringy stuff (see below) in Tanks 1 and 2 (the ones closest to the pH monitors). The other times we found this stuff, it was in the same two tank positions. Perhaps it’s something in those lines or valves? Laura and I are going to take microbial samples when we shut the system down.
  • Rinsed all oysters with freshwater
  • Pulled polychaetes from oyster shell if I saw any. I’m going to ask Chelsea Wood if she can help identify them.
  • Found one dead Oly in Tank 2. It was at the bottom of the tank instead of in an oyster bag, so I don’t know what population it came from.




Figures 1-3. That weird stringy stuff found in Tanks 1 and 2. It’s a little difficult to see, which is why I made a box around it.

3 31 data1

3 31 data2

Figures 4-5. Data collected.

Laura and I are letting the system run for one more week, and then we #shutitdown.

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PBJelly pt 2.

So I have PBJelly working! After trying a fork of the PBJelly project, which fixed the blasr compatibility issue but introduced other issues I went back to the original developer’s version and installed a legacy version.

Installation of legacy version of Blasr:

git clone git@github.com:PacificBiosciences/pitchfork.git pitchfork
git checkout legacy_blasr
cd ~/pitchfork
make init
make blasr 
source ~/pitchfork/deploymentssetup-env.sh

This takes a while

Next, we have to install networkx. This was tricky due to permission issues with pip being unwilling to install a package without sudo, but that resulting in borked permissions for my local python install.

I came across python -m pip install networkx as a method to install relative to a specific python install, and all seemed well after that.

First, I run the setup script for PBJelly via source ~/Documents/PBSuite2/PBSuite_15.8.24/setup.sh to set $PATH stuff for running. You have to do this every time unless you want to add this to your bash profile to auto-execute.

Then, I test the Jelly install.

Screen Shot 2017-04-06 at 10.27.46 AM

Then I get to working my way though the different steps.

Screen Shot 2017-04-06 at 10.27.55 AM

Screen Shot 2017-04-06 at 10.28.04 AM

Screen Shot 2017-04-06 at 10.28.23 AM

Screen Shot 2017-04-06 at 10.28.35 AM

Screen Shot 2017-04-06 at 10.28.51 AM

and finally, Output:
Screen Shot 2017-04-06 at 10.29.03 AM

Which results in a bunch of files, most of interest is the .fasta file with our newly gap filled sequence
Screen Shot 2017-04-06 at 10.29.57 AM

Looks like everything worked! Now I just need to get some spare time on Emu to run the O. lurida stuff. Hopefully soon. Or maybe on Hyak if the new emails are to believed.

Laura’s Notebook: April 2017 Goals

Let’s review March goals to see how I did:

Completed goals:

  • Solidify personnel schedule for OA experiment through March, particularly HgCl injections during NSA conference
  • Formulate plan/timeline for post-OA conditioning, spawning, setting, and rearing Oly’s. Need to do this ASAP!
  • Poster – draft background/methods by 3/10, add data and have full draft by 3/17. Complete by 3/24, then attend conference!
  • Draft & complete article for ComSciCon PNW, then attend
  • Finalize proposal for Proposal Writing Class, study for Invert Zoology etc., also Qsci 482.

Started, but not fully completed:

  • Finish Pecan run! (ETA: Monday, March 6th)
  • Figure out how to use Skyline
  • Run files through Skyline, then figure out what to do next!

Not Started:

  • Research background/context for DNR paper; begin writing.
  • Develop rough draft of Results section for DNR project

April Goals: lots to accomplish this month!

  • NSF:
    • Complete activites report
    • Determine if I should go “on tenure” next year – what are the alternatives?
    • Consider appropriate timeline for applying for GRIP or GROW
    • Follow up with Marilyn about accepting Hyman & FHL funding for the Comparative Embryology course
  • Proteomic project:
    • Meet with Proteomics project collaborators to discuss next steps
    • De-multiplex .raw files
    • Re-run Pecan on more powerful computer to generate full .blib file
    • Perform lit review, focus on geoduck/clams
    • Begin drafting background section
    • Develop rough draft of Geoduck Results section for DNR project
  • Oly OA project:
    • Sample Oly’s post-OA on April 8th – also hold the Ladies of the Lab night out
    • Clean OA system
    • Condition Oly’s, raising temperature 1degC/day to 18deg, hold there there until 4 days before PSRF needs to reduce to 14deg, then decrease 1degC/day to 14.
    • Inventory existing spawning & rearing materials to determine what’s left to make/buy. Need: insulated 5 gal bucket, 2 gal bucket, mini banjos, air stones, blue lines, drippers (what rate?)
    • Figure out how/where to tap into heated line; can we tap in after the filtration system for PSRF’s conicals?
    • Send 4/8 histology casettes off for processing
    • Image histology slides
    • Process histology slide images with … ImageJ(?)
    • Use histology images to inform tissue sample processing
    • Research best method to use for DNA Methylation analysis; what other analyses should I consider?
    • Finalize spawning/rearing plan
    • Build system! – need to start week of 4/20
    • Augment Methods draft with Dec -> April activities
    • Get all water sampling & feeding data digitized

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Laura’s Notebook: Day 48 Activities

Upon arrival, pH & temp looked good, all tanks were flowing.

pH 04-04-2017

One note: every morning that I have been at Manchester the algae header tank has been empty, and PSRF usually refills it at the end of the day (~4pm). They have stated that the feed level lasts ~18 hours.

Collected water samples, below is a photo of the data sheet. Again, I used Rick’s Sond (?) for the salinity measurement, as well as recorded uS/cm from our salinity probe.

data sheet 04-04-2017


Changed the 1um filter, rinsed the 10um and 20um filters

PSRF has been keeping track of the Reed’s shellfish diet used for our experiment. Here are the data sheets:

algae fed 1

algae fed 2

I downloaded the HOBO data from March, here’s a sneak peak at the tank temperatures: HOBO-Data-March2017.pdf

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