January 2018

From OpenWetWare

Week 1: 1/8-1/12

  • Working with Maggie to systematically delete edges.
    • Run the model
  • Resurrect networks from class to work with.

Research Meeting

  • Apprentice Maggie and Brandon
    • Carve out some time to work with Brandon
  • Abstracts for the symposium due Feb. 9th
  • Outside Conferences
    • One at St. Mary's in the East Bay
    • Tri Beta Pacific District Convention - if SoCal, then probably this one. Saturday March 17th?
  • Priority levels: 0 > 0.5 > 1 > 2
  • Will be working on deleting db5 network edge by edge; 28 runs
    • LSE/minLSE to see what the effect of the deletions are
    • run models, get gephi stats
  • Brandon show me how to do post-hoc analysis
  • on team meeting issue, post schedule of when I will be working (4 hours)

Week 2: 1/16-1/19

  • running db5 with missing data and no missing data
    • start 1/16, figure out if there is some type of variation/different network weights between missing values and no missing values
    • if it works, make workbooks by next Tuesday.
  • db5 deletions
    • worried about deleting:
      • ZAP1-ACE2: delete ZAP1 (when you delete the edge you also have to delete the node.
      • GCR2-MSN2: delete GCR2
      • YHP1-GLN3: delete GLN3
    • db5 with and without missing values: graph looks the same in GRNsight
  • edge by edge
    • today
      • missing/non-missing
    • future
      • 28 model runs on GRNmap (next week)
      • 28 gephi stats (next 2 weeks)
      • LSE: min LSE ratios GRNmap output (1-3 weeks from now)
      • compile graph stats into a single excel file
        • compare each of the edge deletions and see if the overall network is statistically significant (sig. difference between original network and network with deletion, if there is a significant difference then the edge that was deleting is theoretically important)
  • started 3 runs
    • missing data, no missing data, and missing data on beta (no edge deletions, just db5)
  • met with Brandon on Wednesday, went over general things about what has happened in the project.

Research Meeting

  • Be sure to upload things to Github
  • missing data v1.8 did not generate minLSE (bug that should be fixed in beta)
  • Going Forward
    • Use the Beta code for now (so it computes minLSE)
    • download Beta code to whatever computer we do a run on (always be sure to be using the same exact code)
      • Maggie will get a flashdrive to keep the beta code on
    • Use missing data workbook on beta to do the 28 runs (edge by edge deletions)
    • clear to proceed

Week 3: 1/22-1/26

  • Generated Gephi .csv files
    • GRNsight
      • open file
      • export as an unweighted graphHML in to Gephi .csv folder
    • Gephi
      • open file that was exported from GRNsight
      • run eigenvector
      • run avg. path length
      • export table (remove "label", "integral", and "name")
      • save to Gephi .csv files folder

Research Meeting

  • Does a spreadsheet formula for LSE/minLSE exist?
  • Maggie and I ran the 28 iterations of GRNmap to conduct an edge deletion analysis, also ran generated output workbooks through Gephi
  • Metagraph?
  • Delete 2 edges to see if the LSE/minLSE ratio decreases more?
    • When we delete things, we delete uncertainty. Must make sure we have a good control
    • run a series of random networks with the same number of nodes and edges to make a comparison
  • Abstract deadline for LMU Symposium is the 9th
  • Using other databases from Biomathematical Modeling/other class?
  • Create a network that doesn't have any of the current genes in it?
  • For next week: finish up what we have been working on; not running any new models

Week 4: 1/29-2/2

  • Drafted abstracts
    • uploaded to GitHub
  • Will be doing ranked stats tests on the data next week
    • look at MSE|minMSE

Research Meeting

  • can't use a paired t-test to do the analysis - what type of ranked test can we do?
    • keep getting a divide by 0 error because in some cases the data are equal
      • transcription error, or deleting that edge did nothing