Past Two(ish) Weeks:
Feb. 3rd
Addressing results and methods edits Mac suggested for rphil:
- [x] protein domains – [pFAM database for uncharacterized genes (n=16)
- [x] add in meaningful definition of log2fold change in results
- [x] indicate how many annotated,
- [x] how many go terms,
- [x] and (lack of) enrichment in results
- [ ] include distribution of RNA type (stacked bar plot)
- [x] look at pvalue for rRNA between treatments
* will need to re run chi square for this
- [x] add in mito, rRNA, and protein coding (similar to stacked bar plot, but pie chart)
- [x] move enrichment info to results instead pof methods
- [ ] add in info on how mnay RNA egg samples we had egg size data for (will add in info about egg samples we did have to intro when summarizing / referencing Larken paper findings)
Feb. 4th
Continue addressing action items/feedback from mac above, as well as addressing Steven’s comments. Specifically, the chi square and t tests for RNA analysis
GIS class
Grading 270 lab assingments
Feb. 5th
Grading 270 lab assignments
lab prep and lab
Feb. 6th
finalizing results and methods edits as well as prepping/summarizing chi square output for meeting
meeting with Mac, Steven, and Emma to discuss results
Feb. 7th
Grading 270 lab assignments
lab prep and lab
Feb. 10th
Had some doctors appointments and was out first half of day.
Started presentation outline for AQ25 practice talk
Some admin work – emails, setting meetings, planning classes for next q.
Feb. 11th
Worked on presentation for AQ25, primarily going through each biological process gene and reviewing NCBI info, UniProt info, GO ancestry, and literature to parse out general ‘umbrella’ functions
Feb. 12th
Further presentation prep. Filling in content to outline I made Monday. Decided to scrap most of the individual gene slides and put instead just 1 example one and 1 summary slide due to time limits on how long the presentation is. Womp womp :/ Those slides were so pretty too.
Lab prep and lab. Incubator problems and 3 tears shed.
Feb. 13th
Finalizing presentation and presented to lab group. Not so bad
Feb. 14th
Light day. TA meeting and some more admin work (sorting out TA stuff for next Q)
Feb. 17th
Meeting prep for Phylo methods meeting with Luke tuesday. Reading R documentation for different packages and some use cases of Robinson foulds distance for identifying genes of interest. Rough procedure outlined here.
Feb. 18th
morning: finished meeting prep for methods meeting with Luke
noon: meeting with luke – ran long and we set a date for next week to finish up. balancing going in depth with the phylogenetics side of things without getting too into the weeds with it. going to create a plan on what methods will be best suited for my overall goal, and feasible for my timeline.
afternoon: 270 grading
Feb. 19th
270 grading and office hours
270 lab prep and lab
Anticipated Next Two Weeks:
2/20
finish 270 grading,
meeting with kerry,
lab meeting,
steven meeting,
and meeting with undergrad in Lukes lab to go over isotope protocols and show iso room in FSH
2/21
TA meeting
write letter of rec for Zoey (270 student)
fill out pre-authorization paperwork for AQ25 travel funding (WSU workday)
start working on presentation edits
2/22
presentation edits
2/24
doctors appointment
presentation edits
2/25
presentation edits and practice
practice talk with steven and mac
2/26
update/part 2 methods meeting with Luke
270 office hours
270 lab
2/27
rphil writing (intro and disc.)
GIS homework
2/28
TA meeting
rphil writing (intro and disc)
3/3
doctors appointment
more rphil writing (intro and disc)
3/4
practice presentation more
270 grading
3/5
270 grading and office hours
270 lab prep and lab
3/6
leave for AQ25!