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:

September 6, 2016

Searched “graph theory and yeast”
- | Results here
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 [1]
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: [2]
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

Moneil5 Dahlquist Lab Notebook

Contents