November tasks
Geoduck proteomics
- Data analysis continued
- [ ] Finalize SRM tech. rep filter process
- [ ] 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.
- [ ] DIA error rate
- Notebooks
- [ ] DIA Skyline document, error rate checking
- [ ] DIA analysis
- [ ] SRM dilution curve notebook
- Researh
- [ ] Consider implications: HSP70 is not highly specific, since some interference w/ gigas in dilution curve
- [ ] More lit review – bioassays
- [ ] Determine if abundance difference is “biologically relevant.” If I can find SRM abundance good (haven’t found good references yet), OR find citable % diff.
- Writing Timeline:
Analysis | Writing | |
---|---|---|
Nov 1-5 | Additional SRM data analysis (follow-up to ANOSIM), dilution curve analysis notebook | More lit research & draft introduction |
Nov 6-12 | Re-do DIA analysis in R with notebook documentation | SRM results DIA results |
Nov 13-19 | DIA error rate, ROC curve, linear response plot | Edits to introduction, and start Discussion |
Nov 20-26 | Refine protein box plots | More discussion |
Nov 27-Dec 1 | Environmental data analysis & plots | Clean-up/edits |
Oly genetics hatchery vs. wild
- [ ] Read Fischer et al. 2012
- [ ] Get most current data set from Crystal
- [ ] ID best program to use
Application things
- [ ] GROW
- [ ] Finish NDSEG
- [ ] NSA travel grant, other?
- [ ] Dive grant: http://ift.tt/2hhG91E
- [ ] NSA travel award
- [ ] AA travel awards
Oly 2017 experiment:
- [ ] Organize data
- [ ] Analyze histology data
- [ ] Determine which samples to sequence
- [ ] 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
Oly 2018 experiment:
- [X] Help collect & clean FB
- [ ] Order histology supplies
- [ ] Sample broodstock for histology, send off
- [ ] Get broodstock into temp treatments
For Committee:
- [ ] Circulate proposal for approval
- [ ] Submit paperwork to office & proposal online
Scientific Diving
- [ ] Find local vendor that sells dry suits, try on to determine size
- [ ] Purchase gear
Record podcast pilot with Megan
- [ ] Read Megan’s paper
- [ ] Rent mic from UW tech resources for this
- [ ] Where to record?
Misc.
- [ ] Learn how to tag notebook posts
- [ ] Throw away some geoduck vials (D, E, autosampler vials) & organize others (original samples, quantified proteins, digested peptides)
- [ ] Create README.md for proteomics data on Owl
from LabNotebook http://ift.tt/2m1Mi49
via IFTTT
November Goals