Yaamini’s Notebook: May 2018 Goals

The meme has evolved

6b8

April Goals Recap:

DNR:

  • Got feedback from Alex and Micah at the end of April!
  • Didn’t finalize the repository or submit the paper because I was busy with the Manchester paper.

Manchester:

  • I SUCESSFULLY CHANNELED MY INNER MAC AND WROTE AN ENTIRE PAPER IN 15 DAYS AND SUBMITTED IT ON TIME!

Virginica:

Other:

May Goals

DNR:

  • Address Alex and Micah’s feedback
  • Send the draft to Steven, Emma, and Brent for final approval
  • Compile my supplemental material and repository
  • Submit the manuscript!

Virginica:

  • Understand methylkit and MACAU 2.0 for differential methylation analyses
  • Run a subset of samples through the pipeline for differential methylation analysis
  • Start the pipeline with all samples
  • Start writing methods and (maybe) results for Pubathon

Larval Mortality:

  • Start analyzing larval mortality data in a robust way
  • Prepare larvae and adults for MBDSeq and RNA analyses

Other:

  • Outline my next few chapters!

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Yaamini’s Notebook: In Situ Carbonate Chemistry Parameters

CCC: Carbonate Chemistry Calculations

After converting my pH values from mV to actual pH units, I needed to calculate the in situ pH. pH values can change based on the temperature and salinity at the time of measurement, so those variables need to be taken into account.

To calculate in situ pH (amongst other carbonate chemistry parameters), I needed total alkalinity, salinity, and temperature measurements. Therefore, I could only complete these calculations for the days I had TA measurements. I compiled all of the necessary inputs into this .csv file. Hollie shared the code I needed to calculate carbonate chemistry parameters in seacarb, which I modified in this R script. After running seacarb, I got my in situ carbonate chemistry parameters in this .csv file! Because the salinity of Tris buffer was extremely similar to that of my experimental tanks, my pH measurements did not change at all.

Although my JSR manuscript has already been submitted (YAY), Steven recommended that I do some work to bolster the water chemistry section, since that will be scrutinized the most. I now have scripts ready for all carbonate chemistry calculations, so that will be an easy fix. I just need to figure out if we need to run more TA samples.

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