Moneil5 Dahlquist Lab Notebook

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

February 26, 2016

• Mistakes in a couple input sheets, need to look into helping Grace fix those
  • Explanation behind this error may be connected to the weird weight parameters output in the file on 2/23
• Look into helping Grace redo run for largest network with alpha value of 0.002

March 10, 2016

• Helped Grace in putting graph outputs of interesting genes on the poster for the spring/symposium. Also helped in adding MSE/ANOVA values, and parameter comparisons as well as in degree and out degree figures.
• Helped re-run some of the networks to remedy for an error in the first run.

March 27, 2016

• Looked at/worked on editing the abstract for ASBMB conference with Grace
• Told how the random networks might work, better understand the principles behind these networks

April 15, 2016

• Only a few weeks left, will be working to help Grace compile a powerpoint containing the graphs, figures, and tables for the dHAP4 network analysis done for the semester.
• Focusing on in-degree and out-degree distribution, small networks and whatever else Grace needs help on

Fall 2016

August 30, 2016

Mathematically modeling networks - how will graph theory help?

• Mostly focusing on using gene regulatory networks in relation to graph theory
  • Are there papers that suggest you can determine what is happening in a system based on outputs of graph theory-based statistics?
  • What do strict numbers from stats tell you about what is happening in a system? Or is it a mostly visually based interpretation that’s needed?

Are the feed forward loops AND or OR type loops? (i.e. A and B needed for C activation, alternatively A or B is needed for C activation) How does suppression and activation play a role in these feed forward loops?

Cursory searches:

• Graph properties
• Feed forward loops

September 6, 2016

• Searched “graph theory and yeast”
  • [1]
• Network properties in “using graph theory to analyze biological networks” - don’t pay attention to clustering, probably doesn’t relate to what we’re doing
• Pay attention to paragraph on gene regulatory networks
• Documentation of model TRACE model, see dry lab protocols
  • Look at papers referenced in the model
  • Issue #170 - goal is to get words on a page to describe GRNmap

September 12, 2016

• Code of conduct:
  • Re-read, agree, post to issue saying read and agree
• Need way to check calculations
• Look for pre-packaged ways to compute betweenness centrality and shortest path
• Start into mode of what we can get done in MatLab
• Start googling MatLab documentation, implementation in MatLab and use as independent check for GRNsight team
• Systems biology package for matlab
• Values computed for weighted and unweighted networks
• Look for code to do analysis with, continue literature search
• Looking for way to do degree distribution quickly an easily
• Projection: mma deg rates, good random network -> proceed to run simulations

September 13, 2016

• Look up and complete matlab tutorials
• Do write-up of data
• Find articles that focus on betweenness centrality and and shortest distance models for graph theory
• Worked with Kristen to make powerpoint with quick summations of the articles we read
  • Can be found here
• Looked into using a systems biology toolbox for MATLAB can be found online

September 19, 2016

• R in degree out degree generator- random networks only?
• Use bibliographic software to format references zoterro- web and standalone. *Can type in DOI and get field with everything. Export to whatever format ( AP etc.), best thing to do
• Find betweenness centrality program in matlab
• First 4 points of TRACE documentation [2]
• Double check everything about 5 15 gene networks and do production runs, generate random networks and collect data
• Test same network on same computer twice, different computers, and other control experiments

September 20, 2016

• Spent most of time getting familiar with basic Matlab functions using the Matlab tutorial found at this link: [3]
• Reviewed matlab basic tutorials and looked into tutorials for systems biology package and graph theory. Nothing concrete found yet, but will look more into it at the next research session