Moneil5 Dahlquist Lab Notebook
From OpenWetWare
Spring 2016
January 15, 2016
- branch
- date time downloaded
- name file link to download
- bug, functionality, priorities
- priority level
- 0-greatest priority
- 0.5- next up to work on
- 1- …
- 2- least priority
- data analysis- data not code
- question- asking people questions
- dont close issues on your own- write comment “resolved because…” and label review requested
- purely website ones
- assignments- assign issues to people (sparingly assign things to him)
- give updates when working in between meetings
- make electronic lab notebook that describes what was done each day- use as repository for files and such
- go through wiki checklist and edit user page to skills
- assignment for data bases class
- format like resume
- alphabetize the genes - gonna take some time
January 22, 2016
- p= production rate
- w=weight
- b=”threshold”
- Can control any of these parameters
- Production and threshold for every gene in network
- weight for every edge in network
- Number of timepoints vs number of parameters is out of whack
- trying to find overall set of values to closest set of values- might never converge on an answer
- LSE vs. penalty being plotted
- “sweet spot” for alpha value found in “elbow” of curve
- questions trying to answer:
- ex. what happens if ….?
- estimate w,p,b
- estimate just p
- estimate just w
- estimate just b
- compare sigmoid to mm
- want to look at just wild type or wild type plus mutant
- strain influence/ strain #
January 29th, 2016
- abstracts for undergrad symposium due by the 12th
- honors research grant also due by the 12th
- with grace on poster for symposium
- read trace paper
- not separating transcription and translation
- implementation verification
- output- tough because where we’d be making predictions
- change model to production_function in excel
- l-curve function call it 0
- put between production function and estimate_params
- run l curve analysis this week\
- Do 4 runs this week- do largest and smallest networks
- +/- deletion strains
- generates 4 l curves
- LSE on y-axis
- penalty on x-axis
- Should look like l (put labels for alpha values)
- make_graphs=0
February 5, 2016
- figure out how to run multi-core processor
- name of file- remove “dahlquist data” and put in initials of person running it instead
- make sure everyone deleted the same strains
- will be working with wild type data from beginning to understand process
February 11, 2016
- meet up with Brandon in Dahlquist’s lab to work on project on some day next week
- meeting next week is at 3:15
- plot data from LSE runs
- by next week- alpha selected, data collected
- replace 41998 #VALUE!
- 23 is correct # of data points wt
- t15=4
- t30=5
- t60=4
- t90=5
- t120=5
- total=23
- 20 is correct # data points dcin5
- t15=4
- t30=4
- t60=4
- t90=4
- t120=4
- total=20
February 17, 2016
- Quantitate the fluorescence signal in each spot (GenePix Pro)
- Calculate the ratio of red/green fluorescence (GenePix Pro)
- Log transform the ratios (GenePix Pro)
- Normalize the ratios on each microarray slide (within-chip normalization)
- Normalize the ratios for a set of slides in an experiment (between-chip normalization)
- Perform statistical analysis on the ratios
- Within-strain ANOVA
- Modified t test for each timepoint
- Between-strain ANOVA
- Benjamini & Hochberg and Bonferroni p value corrections for the above three tests
- "Sanity Check" on above three tests
- Determining candidate transcription factors and gene regulatory network (YEASTRACT)
- Dynamical modeling with GRNmap; visualization with GRNsight
February 19, 2016
- Grace to finish honors ambassadorial grant for Experimental Biology Conference in April
- Output parameter comparison for largest network with added strains for alpha values:
- 0.01
- 0.008
- 0.005
- 0.002
- 0.001
- To complete for the poster (two weeks after spring break)
- Stick with subfamily with strains_added
- "Production runs:" Evaluate (with graphs) the networks of 15, 34, 25, 20, and 30 genes.
- Help Grace run these networks
