GRNmap Testing Report 16 Test Files 2015-06-01

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Contents

Test Conditions

  • Date started: 2015-06-01
  • Test Performed by: Tessa A. Morris, Electronic Notebook
  • Code Version: GRNmap-beta branch downloaded from Github at 10:43 am 2015-06-01
    • Changes were made to the GRNmap-beta branch which was downloaded at 4:39 pm 2015-06-01
    • version at 9:37 am 2016-06-02
  • MATLAB Version: 2014b
  • Computer on which the model was run: Row 2 4th from door

Purpose

  • The purpose was to create the sixteen different variations of the input sheet with a manageable number of genes and edges to use to test various versions of GRNmap.
  • Issue 74

Results

  1. 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph
  2. 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_no-graph
  3. 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-1_graph
  4. 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-1_no-graph
  5. 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-0_graph
  6. 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-0_no-graph
  7. 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-1_graph
  8. 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-1_no-graph
  9. 4-genes_6-edges_artificial-data_Sigmoidal_forward_graph
  10. 4-genes_6-edges_artificial-data_Sigmoidal_forward_no-graph
  11. 4-genes_6-edges_artificial-data_MM_estimation_fixP-1_graph
  12. 4-genes_6-edges_artificial-data_MM_estimation_fixP-1_no-graph
  13. 4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph
  14. 4-genes_6-edges_artificial-data_MM_estimation_fixP-0_no-graph
  15. 4-genes_6-edges_artificial-data_MM_forward_graph
  16. 4-genes_6-edges_artificial-data_MM_forward_no-graph
  • Checklist for the output sheet is here.

Discussion

  • For Sigmoidal_estimation:
    • When fixP-0 the optimized_production_rates sheet was produced; fixP-1 no production rates sheet was produced.
    • When fixb-0 the optimized_threshold_b sheet was produced; fixb-1 no optimized_threshold_b sheet was produced
  • For Sigmoidal_forward:
    • optimized_production_rates sheet was produced; optimized_threshold_b sheet was not
  • For Michaelis Menten
    • No optimized_threshold_b
    • optimized_production_rates sheet was produced only when fixP-0
  • The wt_log2_optimized_expression, wt_sigmas, dcin5_log2_optimized_expression, and dcin5_sigmas were produced for all inputs
  • optimization_diagnostics was not produced for any of the inputs
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