This is vast. Lots to do.

Small To Do:

• Email Abigail re: GROW program
• Submit back-log of reimbursements for Manchester & shellfish club
• Email re: Oly session @ NSA 2018 - deadline FRIDAY
• Register for Parasites once add code comes through
• Book return ferries @ 7am on Friday!
• Learn how to tag notebook posts
• Take geoduck proteomics poster to WA Co-op once location confirmed (I think SAFS somewhere)
• Submit geoduck project presentation for GSS
• Throw away some geoduck vials (D, E, autosampler vials) & organize others (original samples, quantified proteins, digested peptides)

Large To-Do:

Geoduck proteomics

• Clean up scripts from SRM analysis
• Figure out which vials to throw away from SRM run:
  • Throw away: “D”, “E”, Autosampler vials (highly unlikely we’ll use these again, since they sat around and not enough volume to re-run, and PRTC was messed up
  • KEEP: 1) other 1/2 of sample not digested, 2) protein in solution from quantification step, 3) completely digested peptides (“F”)
• More analysis for SRM:
  • Figure out how to calculate distances between tech reps, to numerically validate my removal of poor-quality reps
  • Generate Linear Response Plot, as per Emma: Peak area on the y, amount of peptide (moles) on the x. Don’t know absolute quantity of experimental peptides, could make the x-axis relative quantity or something. Can generate plots like these in MSstats.
  • Determine if abundance difference is “biologically relevant,” aka look to lit for abundance values to see what is low, normal, high (if possible!)
  • See if I can bring DIA results into SRM analysis (at very least, compare 3 proteins in DIA data)
  • Consider implications: HSP70 is not highly specific, since some interference w/ gigas in dilution curve
• Start drafting geoduck proteomics paper
  • Outline everything
  • SRM Methods detailed
  • DIA Methods detailed
  • Full lit review
• Document steps from Vantage -> Replicate Review. Write notebooks for:
  • How to create Skyline project file with .raw SRM data including PRTC
  • Calculating predicted RT
  • Pick peaks & adjust retention time ranges using predicted RT
  • Remove peaks, replicates, and transitions/peptides that are poor quality, as determined via: RT, dilution curve
  • Export abundance data as report & re-format slightly
  • Data analysis in R
• Document steps from Lumos -> selecting proteins for SRM
  • Download & convert .raw files to .mzML
  • Prep files for PECAN, including using Protein Digestion Simulator
  • Run PECAN (at least include PECAN input files, commands, and lessons learned)
  • Create Skyline Project & export report
  • Calculate error rate
  • Data analysis in R (not excel!)

Record podcast pilot with Megan

• Read Megan’s paper
• Rent mic from UW tech resources for this
• Where to record?

Oly genetics hatchery vs. wild

• Meet with Brent re: Oly genetics paper, see if he has scripts for calling loci
• Gather materials from 1st genetic testing
• Read Fischer et al. 2012

Application things

• Start drafting GROW application
• Get project description from Abigail
• NDSEG
• NSA travel grant, other?
• Dive grant: http://www.wdhof.org/wdhof-scholarshipDesc.aspx
• differed UW FINS for Vegas - Apply in January
• Coenv travel fund, due Oct. 27

Oly experiment:

• Transition Oly’s to ambient T
• Make screen envelopes and move olys to dock, affix to cage (move on Thursday 10/5).
• Make sure I’m organized
• Write-up 1-stop shopping list of Oly project including:
  • Experiment summary
  • Samples collected
  • Data collected
  • Treatments, populations, etc.
• Figure out how/when to transport Oly samples from Manchester/Rick’s -80
• Meet with STATS resource to figure out how to analyze Oly larval survival - parse out survival data to 224um, to juvenile, by time for reps

For Committee:

• Schedule 1st meeting - mid October
• Complete committee sheet for SAFS
• Complete academic timeline
• Presentation for committee meeting: 20-30 mins, to include:
  • Overall goals of PhD
    • Research interests
    • Motivation
    • Post-graduation ideals
  • Proposed timeline, travel, etc.
  • What I’ve done to date
    • Chapter 1 - Proteomics
    • Chapter 2 - Oly OA/T experiment Generation 1
  • What I plan to do
    • Chapter X - Oly OA/T experiment Generation 2
    • Chapter X - Oly OA/T experiment, wild generation OR hatchery-produced F1’s (repeat experiment, using silos only for larvae!)
    • Chapter X - Oly genetics wild vs. hatchery (?)
    • Chapter X - Project in Australia on reproductive peptides
    • Chapter X - Could I do a geoduck genetics wild vs. hatchery? (or, what is “baseline”?)
  • Grants & Fellowships
  • Extra curriculars

Scientific Diving

• Find local vendor that sells dry suits, try on to determine size
• Purchase gear
• Start weekly dives with Will beginning early-mid October - starting Nov. 8th