GRNmap Testing Report 16 Test Files 2015-06-01: Difference between revisions

Latest revision as of 14:31, 2 June 2015

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

4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph
4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_no-graph
4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-1_graph
4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-1_no-graph
4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-0_graph
4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-0_no-graph
4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-1_graph
4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-1_no-graph
4-genes_6-edges_artificial-data_Sigmoidal_forward_graph
4-genes_6-edges_artificial-data_Sigmoidal_forward_no-graph
4-genes_6-edges_artificial-data_MM_estimation_fixP-1_graph
4-genes_6-edges_artificial-data_MM_estimation_fixP-1_no-graph
4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph
4-genes_6-edges_artificial-data_MM_estimation_fixP-0_no-graph
4-genes_6-edges_artificial-data_MM_forward_graph
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

GRNmap Testing Report 16 Test Files 2015-06-01: Difference between revisions

Latest revision as of 14:31, 2 June 2015

Contents

Test Conditions

Purpose

Results

Discussion

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@@ Line 1: / Line 1: @@
-==GRNmap Testing Report==
+==Test Conditions==
 *Date started: 2015-06-01
-*GRNmap code: GRNmap-beta branch downloaded from Github at 10:43 am 2015-06-01
+*Test Performed by: [[User:Tessa A. Morris| Tessa A. Morris]], [[Tessa A. Morris Electronic Lab Notebook| 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
-*Model was run computer (from door): Row#2 4
+*Computer on which the model was run: Row 2 4th from door
-==Input, Output, and Images==
+==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.
+*[https://github.com/kdahlquist/GRNmap/issues/74#issuecomment-108097323 Issue 74]
+==Results==
 #4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph
 #*[[Media:4-genes 6-edges artificial-data Sigmoidal estimation fixb-0 fixP-0 graph.xlsx|4-genes_6-edges_artificial-data Sigmoidal_estimation_fixb-0_fixP-0_graph.xlsx ]]
 #*[[Media:4-genes 6-edges artificial-data Sigmoidal estimation fixb-0 fixP-0 graph output.xlsx|4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph_output.xlsx]]
+#*[[Media:4-genes 6-edges artificial-data Sigmoidal estimation fixb-0 fixP-0 graph output.mat|4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph_output.mat]]
 #*[[Media:4-genes 6-edges artificial-data Sigmoidal estimation fixb-0 fixP-0 graph plots.zip| 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph_plots]]
 #4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_no-graph
 #*[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_no-graph.xlsx|4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_no-graph.xslx]]
-#*[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_no-graph.xlsx|4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_no-graph_output.xslx]]
+#*[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_no-graph_output.xlsx|4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_no-graph_output.xslx]]
+#*[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_no-graph_output.mat|4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_no-graph_output.mat]]
 #* No plots
 #4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-1_graph
 #*[[Media:4-genes 6-edges artificial-data Sigmoidal estimation fixb-0 fixP-1 graph.xlsx|4-genes_6-edges_artificial-data Sigmoidal_estimation_fixb-0_fixP-1_graph.xlsx ]]
 #*[[Media:4-genes 6-edges artificial-data Sigmoidal estimation fixb-0 fixP-1 graph output.xlsx|4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-1_graph_output.xlsx]]
+#*[[Media:4-genes 6-edges artificial-data Sigmoidal estimation fixb-0 fixP-1 graph output.mat|4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-1_graph_output.mat]]
 #*[[Media:4-genes 6-edges artificial-data Sigmoidal estimation fixb-0 fixP-1 graph plots.zip| 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-1_graph_plots]]
 #4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-1_no-graph
 #*[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-1_no-graph.xlsx|4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-1_no-graph.xslx]]
-#*[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-1_no-graph.xlsx|4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-1_no-graph_output.xslx]]
+#*[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-1_no-graph_output.xlsx|4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-1_no-graph_output.xslx]]
+#*[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-1_no-graph_output.mat|4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-1_no-graph_output.mat]]
 #* No plots
 #4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-0_graph
 #*[[Media:4-genes 6-edges artificial-data Sigmoidal estimation fixb-1 fixP-0 graph.xlsx|4-genes_6-edges_artificial-data Sigmoidal_estimation_fixb-1_fixP-0_graph.xlsx ]]
 #*[[Media:4-genes 6-edges artificial-data Sigmoidal estimation fixb-1 fixP-0 graph output.xlsx|4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-9_graph_output.xlsx]]
+#*[[Media:4-genes 6-edges artificial-data Sigmoidal estimation fixb-1 fixP-0 graph output.mat|4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-9_graph_output.mat]]
 #*[[Media:4-genes 6-edges artificial-data Sigmoidal estimation fixb-1 fixP-0 graph plots.zip| 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-0_graph_plots]]
 #4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-0_no-graph
 #*[[Media:4-genes 6-edges artificial-data Sigmoidal estimation fixb-1 fixP-0 no-graph.xlsx|4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-0_no-graph.xslx]]
-#*[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-0_no-graph.xlsx|4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-0_no-graph_output.xslx]]
+#*[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-0_no-graph_output.xlsx|4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-0_no-graph_output.xslx]]
+#*[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-0_no-graph_output.mat|4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-0_no-graph_output.mat]]
 #* No plots
 #4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-1_graph
 #*[[Media:4-genes 6-edges artificial-data Sigmoidal estimation fixb-1 fixP-1 graph.xlsx|4-genes_6-edges_artificial-data Sigmoidal_estimation_fixb-1_fixP-1_graph.xlsx ]]
 #*[[Media:4-genes 6-edges artificial-data Sigmoidal estimation fixb-1 fixP-1 graph output.xlsx|4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-1_graph_output.xlsx]]
+#*[[Media:4-genes 6-edges artificial-data Sigmoidal estimation fixb-1 fixP-1 graph output.mat|4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-1_graph_output.mat]]
 #*[[Media:4-genes 6-edges artificial-data Sigmoidal estimation fixb-1 fixP-1 graph plots.zip| 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-1_graph_plots]]
 #4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-1_no-graph
 #*[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-1_no-graph.xlsx|4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-1_no-graph.xslx]]
-#*[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-1_no-graph.xlsx|4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-1_no-graph_output.xslx]]
+#*[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-1_no-graph_output.xlsx|4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-1_no-graph_output.xslx]]
+#*[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-1_no-graph_output.mat|4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-1_no-graph_output.mat]]
 #* No plots
 #4-genes_6-edges_artificial-data_Sigmoidal_forward_graph
 #*[[Media:4-genes_6-edges_artificial-data_Sigmoidal_forward_graph.xlsx|4-genes_6-edges_artificial-data_Sigmoidal_forward_graph.xlsx]]
 #*[[Media:4-genes_6-edges_artificial-data_Sigmoidal_forward_graph_output.xlsx|4-genes_6-edges_artificial-data_Sigmoidal_forward_graph_output.xlsx]]
+#*[[Media:4-genes_6-edges_artificial-data_Sigmoidal_forward_graph_output.mat|4-genes_6-edges_artificial-data_Sigmoidal_forward_graph_output.mat]]
 #*[[Media:4-genes_6-edges_artificial-data_Sigmoidal_forward_graph_plots.zip|4-genes_6-edges_artificial-data_Sigmoidal_forward_graph_plots]]
 #4-genes_6-edges_artificial-data_Sigmoidal_forward_no-graph
 #*[[Media:4-genes_6-edges_artificial-data_Sigmoidal_forward_no-graph.xlsx|4-genes_6-edges_artificial-data_Sigmoidal_forward_no-graph.xlsx]]
 #*[[Media:4-genes_6-edges_artificial-data_Sigmoidal_forward_no-graph_output.xlsx|4-genes_6-edges_artificial-data_Sigmoidal_forward_no-graph_output.xlsx]]
+#*[[Media:4-genes_6-edges_artificial-data_Sigmoidal_forward_no-graph_output.mat|4-genes_6-edges_artificial-data_Sigmoidal_forward_no-graph_output.mat]]
 #*No plots
 #4-genes_6-edges_artificial-data_MM_estimation_fixP-1_graph
 #*[[Media:4-genes_6-edges_artificial-data_MM_estimation_fixP-1_graph.xlsx|4-genes_6-edges_artificial-data_MM_estimation_fixP-1_graph.xlsx]]
 #*[[Media:4-genes_6-edges_artificial-data_MM_estimation_fixP-1_graph_output.xlsx|4-genes_6-edges_artificial-data_MM_estimation_fixP-1_graph_output.xlsx]]
+#*[[Media:4-genes_6-edges_artificial-data_MM_estimation_fixP-1_graph_output.mat|4-genes_6-edges_artificial-data_MM_estimation_fixP-1_graph_output.mat]]
 #*[[Media:4-genes_6-edges_artificial-data_MM_estimation_fixP-1_graph_plots.zip|4-genes_6-edges_artificial-data_MM_estimation_fixP-1_graph_plots]]
 #4-genes_6-edges_artificial-data_MM_estimation_fixP-1_no-graph
 #*[[Media:4-genes_6-edges_artificial-data_MM_estimation_fixP-1_no-graph.xlsx|4-genes_6-edges_artificial-data_MM_estimation_fixP-1_no-graph.xlsx]]
 #*[[Media:4-genes_6-edges_artificial-data_MM_estimation_fixP-1_no-graph_output.xlsx|4-genes_6-edges_artificial-data_MM_estimation_fixP-1_no-graph_output.xlsx]]
+#*[[Media:4-genes_6-edges_artificial-data_MM_estimation_fixP-1_no-graph_output.mat|4-genes_6-edges_artificial-data_MM_estimation_fixP-1_no-graph_output.mat]]
 #*No plots
 #4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph
 #*[[Media:4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph.xlsx|4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph.xlsx]]
 #*[[Media:4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph_output.xlsx|4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph_output.xlsx]]
+#*[[Media:4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph_output.mat|4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph_output.mat]]
 #*[[Media:4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph_plots.zip|4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph_plots]]
 #4-genes_6-edges_artificial-data_MM_estimation_fixP-0_no-graph
 #*[[Media:4-genes_6-edges_artificial-data_MM_estimation_fixP-0_no-graph.xlsx|4-genes_6-edges_artificial-data_MM_estimation_fixP-0_no-graph.xlsx]]
 #*[[Media:4-genes_6-edges_artificial-data_MM_estimation_fixP-0_no-graph_output.xlsx|4-genes_6-edges_artificial-data_MM_estimation_fixP-0_no-graph_output.xlsx]]
+#*[[Media:4-genes_6-edges_artificial-data_MM_estimation_fixP-0_no-graph_output.mat|4-genes_6-edges_artificial-data_MM_estimation_fixP-0_no-graph_output.mat]]
 #*No plots
 #4-genes_6-edges_artificial-data_MM_forward_graph
 #*[[Media:4-genes_6-edges_artificial-data_MM_forward_graph.xlsx|4-genes_6-edges_artificial-data_MM_forward_graph.xlsx]]
 #*[[Media:4-genes_6-edges_artificial-data_MM_forward_graph_output.xlsx|4-genes_6-edges_artificial-data_MM_forward_graph_output.xlsx]]
+#*[[Media:4-genes_6-edges_artificial-data_MM_forward_graph_output.mat|4-genes_6-edges_artificial-data_MM_forward_graph_output.mat]]
 #*[[Media:4-genes_6-edges_artificial-data_MM_forward_graph_plots.zip|4-genes_6-edges_artificial-data_MM_forward_graph_plots]]
 #4-genes_6-edges_artificial-data_MM_forward_no-graph
 #*[[Media:4-genes_6-edges_artificial-data_MM_forward_no-graph.xlsx|4-genes_6-edges_artificial-data_MM_forward_no-graph.xlsx]]
 #*[[Media:4-genes_6-edges_artificial-data_MM_forward_no-graph_output.xlsx|4-genes_6-edges_artificial-data_MM_forward_no-graph_output.xlsx]]
+#*[[Media:4-genes_6-edges_artificial-data_MM_forward_no-graph_output.mat|4-genes_6-edges_artificial-data_MM_forward_no-graph_output.mat]]
 #*No plots
-==Methods==
+*Checklist for the output sheet is [[Media:Output sheet checklist 20150602 TM.xlsx| here]].
-===Selecting the GRNmap Version and Base Input Sheet===
+==Discussion==
-# Download the GRNmap-beta branch version from Github by downloading the zip file.
+*For Sigmoidal_estimation:
-# Move it to the desktop and unzip by right-clicking on it and choosing 7-zip > Extract here.
+**When fixP-0 the optimized_production_rates sheet was produced; fixP-1 no production rates sheet was produced.
-# Open the unzipped "GRNmap-beta branch" folder and find the folder "test_files" then navigate to "estimation_tests" and open the file "4-genes_6-edges_artificial-data_Sigmoid_estimation.xls"
+**When fixb-0 the optimized_threshold_b sheet was produced; fixb-1 no optimized_threshold_b sheet was produced
-#* We compared "4-genes_6-edges_artificial-data_Sigmoid_estimation.xls" and "4-genes_6-edges_artificial-data_Sigmoid_forward.xlsx" and found them to contain different data points and different time points, so the "4-genes_6-edges_artificial-data_Sigmoid_estimation.xls" was chosen as the base for the 16 test files.
+*For Sigmoidal_forward:
+**optimized_production_rates sheet was produced; optimized_threshold_b sheet was not
-===Editing the Optimization Parameters for each Input===
+*For Michaelis Menten
-*There are sixteen different input sheets that need to be tested. The "optimization parameters" worksheet is adjusted for each type. For all inputs, the following optimization parameters will be left as they were originally entered
+**No optimized_threshold_b
-#* "alpha" should be 1.00E-10
+**optimized_production_rates sheet was produced only when fixP-0
-#* "kk_max" should be 1
+*The wt_log2_optimized_expression, wt_sigmas, dcin5_log2_optimized_expression, and dcin5_sigmas were produced for all inputs
-#* "MaxIter" should be 1e08
+*optimization_diagnostics was not produced for any of the inputs
-#* "TolFun" should be 1e-10
+[[Category:Dahlquist Lab]]
-#* "MaxFunEval" should be 1e08
+[[Category: GRNmap]]
-#* "TolX" should be 1e-10
-#* For the parameter "time" (Cell A13), should have "0.4", "0.8", "1.2", and "1.4"
-#* For the parameter "Strain" (Cell A14), make sure it says "dcin5", making sure that the capitalization and spelling is the same as the worksheet containing that strain's expression data.
-#* For the parameter "Sheet" (Cell A15), give the number of the worksheet from left to right that your "Strain" log2 expression data is in. This should be the fourth sheet.
-#*  For the parameter "Deletion", leave the zero in cell B15 (corresponding to wt).  In cell C15, put a number corresponding to the position in the list of gene names that the gene that was deleted appears. This should be the number three in the list (disregard the column header in this count and only consider the actual gene names themselves).
-#* For the parameter, "simtime", the row should read: 0, 0.1, 0.2, 0.3 <...fill by steps of 0.1...>, 2, each number in a different cell.
-*The parameters "Sigmoid","estimateParams", "makeGraphs","fix_P", and "fix_b" will be different for each input sheet.
-#4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph
-#* "Sigmoid" should be 1
-#* "estimateParams" should be 1
-#* "makeGraphs" should be 1
-#* "fix_P" should be 0
-#* "fix_b" should be 0
-#4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_no-graph
-#* "Sigmoid" should be 1
-#* "estimateParams" should be 1
-#* "makeGraphs" should be 0
-#* "fix_P" should be 0
-#* "fix_b" should be 0
-#4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-1_graph
-#* "Sigmoid" should be 1
-#* "estimateParams" should be 1
-#* "makeGraphs" should be 1
-#* "fix_P" should be 1
-#* "fix_b" should be 0
-#4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-1_no-graph
-#* "Sigmoid" should be 1
-#* "estimateParams" should be 1
-#* "makeGraphs" should be 0
-#* "fix_P" should be 1
-#* "fix_b" should be 0
-#4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-0_graph
-#* "Sigmoid" should be 1
-#* "estimateParams" should be 1
-#* "makeGraphs" should be 1
-#* "fix_P" should be 0
-#* "fix_b" should be 1
-#4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-0_no-graph
-#* "Sigmoid" should be 1
-#* "estimateParams" should be 1
-#* "makeGraphs" should be 0
-#* "fix_P" should be 0
-#* "fix_b" should be 1
-#4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-1_graph
-#* "Sigmoid" should be 1
-#* "estimateParams" should be 1
-#* "makeGraphs" should be 1
-#* "fix_P" should be 1
-#* "fix_b" should be 1
-#4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-1_no-graph
-#* "Sigmoid" should be 1
-#* "estimateParams" should be 1
-#* "makeGraphs" should be 0
-#* "fix_P" should be 1
-#* "fix_b" should be 1
-#4-genes_6-edges_artificial-data_Sigmoidal_forward_graph
-#* "Sigmoid" should be 1
-#* "estimateParams" should be 0
-#* "makeGraphs" should be 1
-#* "fix_P" should be 0
-#* "fix_b" should be 1
-#4-genes_6-edges_artificial-data_Sigmoidal_forward_no-graph
-#* "Sigmoid" should be 1
-#* "estimateParams" should be 0
-#* "makeGraphs" should be 0
-#* "fix_P" should be 0
-#* "fix_b" should be 1
-#4-genes_6-edges_artificial-data_MM_estimation_fixP-1_graph
-#* "Sigmoid" should be 0
-#* "estimateParams" should be 1
-#* "makeGraphs" should be 1
-#* "fix_P" should be 1
-#* "fix_b" should be 0
-#4-genes_6-edges_artificial-data_MM_estimation_fixP-1_no-graph
-#* "Sigmoid" should be 0
-#* "estimateParams" should be 1
-#* "makeGraphs" should be 0
-#* "fix_P" should be 1
-#* "fix_b" should be 0
-#4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph
-#* "Sigmoid" should be 0
-#* "estimateParams" should be 1
-#* "makeGraphs" should be 1
-#* "fix_P" should be 0
-#* "fix_b" should be 0
-#4-genes_6-edges_artificial-data_MM_estimation_fixP-0_no-graph
-#* "Sigmoid" should be 0
-#* "estimateParams" should be 1
-#* "makeGraphs" should be 0
-#* "fix_P" should be 0
-#* "fix_b" should be 0
-#4-genes_6-edges_artificial-data_MM_forward_graph
-#* "Sigmoid" should be 0
-#* "estimateParams" should be 0
-#* "makeGraphs" should be 1
-#* "fix_P" should be 1
-#* "fix_b" should be 0
-#4-genes_6-edges_artificial-data_MM_forward_no-graph
-#* "Sigmoid" should be 0
-#* "estimateParams" should be 0
-#* "makeGraphs" should be 0
-#* "fix_P" should be 1
-#* "fix_b" should be 0
-===Running GRNmap===
-You will now finally run the GRNmap model on each input workbook created above.
-# Open MATLAB and navigate to the "matlab" subfolder in the "GRNmap-beta" folder on the desktop
-# Move the input sheet that you would like to run into this folder.
-# In MATLAB type the command "GRNmodel" and select the input sheet of study
-# Once the model has finished running, plots showing the expression over time for all of the genes in the network will appear if "makeGraphs" was set to 1. The plots will automatically be saved as <code>*.jpg</code> files in the same folder as your input file.  Compile the figures into a folder following the naming convention described earlier. Compress this folder by right clicking then selecting "7-zip" and "Add to archive...". Make sure the archive format is "zip."
-# Upload the .xlsx output sheet and the zipped folder with the output plots onto openwetware.
-# In between each run type "close all" and "clear all" into MATLAB
-===Updating GRNmap on Github===
-#Download "Git" from this [https://git-scm.com/downloads link]
-#Go through the instillation process (no changes needed)
-#Once installed open "Git Bash" from the programs menu on the computer
-#To have the GRNmap folder to edit on the desktop type <code>cd Desktop</code> then press enter
-#To clone into GRNmap type <code>git clone https://github.com/kdahlquist/GRNmap.git</code> then press enter
-#To edit GRNmap, type <code>cd GRNmap</code> then press enter
-#To edit the Beta version, type <code>git checkout beta</code>
-#There will now be a file on the desktop titled "GRNmap" where you can put the updated test files and then upload them to github
-#Create two new folders in the "test_files" subfolder called "sixteen_tests" and "sixteen_tests_output"
-#*The "sixteen_tests" contains the input sheets and the "sixteen_tests_output" contains the output sheet.
-#To update the GRNmap on the web
-#* Type <code>git checkout beta</code> then press enter
-#* Type <code>git status</code> then press enter will show the changes that you made in red
-#* Type <code>git add test_files/s</code> then press enter
-#* Type <code>git add test_files/s</code> then press tab. The code should then read <code>git add test_files/sixteen_tests/</code> then press space and type <code>git add test_files/s</code> again then tab so it reads <code>git add test_files/sixteen_tests_output/</code> then type an underscore to indicate you're done.
-#*Type <code>git status</code> then press enter
-#*Type <code>git commit -m "add sixteen combinations of input files and their output files"</code> or a description of the change that was made then press enter
-#** I made a typo and wrote "coombinations instead of combinations", unfortunately
-#*In order to configure the computer to your user name Type <code>git config --global user.name "''github username''"</code> then press enter and then type <code>git config --global user.email "''email used for github''"</code> then press enter
-#*To update anything that was changed while you were working type <code>git pull</code> then press enter
-#*To update the website with your changes type <code>git push</code> then press enter and enter your username and password when prompted.
-#Comment on [https://github.com/kdahlquist/GRNmap/issues/74 Issue 74] on Github explaining what was done and change the label to "review requested" and select Dr. Dahlquist.
-==Data & Observations==
-*[[Media:GRNmap Testing Report 16 Test Files 2015-06-01.xlsx| Summary statistics]]
-*Every difference between graph and no graph was 0.
-*The optimized_production_rate sheet was only produced when fixP-0.
-*The optimized_threshold_b sheet was only produced when fixb-0 and the model with Sigmoidal.
-*The weights for the Sigmoidal were all about the same value. The MM was always larger, with the fixP-0 being much larger in the case of ACE2-->ACE2 and AFT2-->AFT2 and MM fixP-1 was much larger when CIN5-->FHL1. The MM fixP-1  had an opposite sign than all of the Sigmoidal, but the weight was of a small magnitude.
-{{Template:Tessa A. Morris ELN}}