Ensure examples run on main

Change "clear all" to "clear" - this is technically only necessary for multiple SSIT runs where an input expression has been used, as "clear all" for some reason does not clear all symbolic expressions and therefore "formPropensitiesGeneral" will fail on subsequent runs.

Also, change "time_index" to "time" in example data.  TODO: add catch in SSIT - or the ability to tell SSIT what "time" has been called when using "loadData"

Author: alexpopinga

ExampleData/DUSP1_Dex_100nM_Rep1_Rep2.csv

@@ -1,4 +1,4 @@
-cell_number,time_index,RNA_nuc,RNA_cyto,RNA_total,Rep_num
+cell_number,time,RNA_nuc,RNA_cyto,RNA_total,Rep_num
 0,0,2,4,6,1
 1,0,2,9,11,1
 2,0,20,75,95,1

Examples/DUSP1SSAData50Expts.csv

@@ -2,7 +2,7 @@
 % Example script to show SSIT application to a simple bursting gene
 % expression model that ios being fit to smFISH data for DUSP1 upon
 % stimulation with Dexamethsone.
-clear all; clc; close all
+clear; clc; close all
 addpath(genpath('../src'));
 
 %% STEP1 == Define SSIT Model

Examples/ToggleSSAData50Expts.csv

@@ -1,8 +1,8 @@
 %% example_EscapeTimes
-% In this script, we demonstrate how to create and solve a fiorst passage
+% In this script, we demonstrate how to create and solve a first passage
 % time problem.
 close all
-clear all
+clear
 addpath(genpath('../src'));
 %% Example 1 - a simple transcription/translation model
 % First create a full model (e.g., for mRNA and protein)

Examples/example_DUSP1_Regulation.m

@@ -2,7 +2,7 @@
 % In this example, we show how to sample an FSM  model over intrinsic noise
 % in its various parameters. 
 close all 
-clear all
+clear
 addpath(genpath('../src'));
 %% Example 1 - transcription and translation
 % First create a full model (e.g., for mRNA and protein)

Examples/example_EscapeTimes.m

@@ -1,7 +1,7 @@
 %% fimExample
 % In this script, we show how to set up and solve the FSP-FIM matrix with
 % partial observations and probabilistic distortion.
-clear all
+clear
 close all
 addpath(genpath('../src'));
 

Examples/example_ExtrinsicNoiseModels.m

@@ -3,7 +3,7 @@
 % model to some single-cell smFISH data.  For this example, we will use
 % some data collected in Dr. Gregor Neuert's laboratory at Vanderbilt.
 close all
-clear all
+clear
 addpath(genpath('../src'));
 
 %% Create SSIT Model

Examples/example_FIMCalculation.m

@@ -2,7 +2,7 @@
 % In this script, we show how the SSIT can be used to identify a
 % time-inhomogeneous model for the activation of Dusp1 mRNA expression
 % under Dexamethasome stimulation of Glucocorticoid Receptors.
-clear all
+clear
 clc
 close all
 addpath(genpath('../src'));

Examples/example_Fit_STL1_mRNA_Data.m

@@ -4,7 +4,7 @@
 % other species (i.e., downstream species) evolving in a discrete
 % stochastic manner. 
 close all 
-clear all
+clear
 addpath(genpath('../src'));
 
 %% Example 1 - transcription and translation

Examples/example_FittingAndDesigningExperiments.m

@@ -1,5 +1,5 @@
 close all
-clear all
+clear
 addpath(genpath('../src'));
 
 rng(1)  % Set RNG seed for reproducibility.

Examples/example_HybridModel.m

@@ -1,7 +1,7 @@
 % In this example, we show how to create reduced FSP models using different
 % types of projectionbased transformations.
 close all 
-clear all
+clear
 addpath(genpath('../src'));
 
 %% First, choose a model on which to illustrate the reduction approximation,

Examples/example_IterativeBayesianExperimentDesign.m

@@ -7,7 +7,7 @@
 %   2) replica to replica variations are expected that would result in
 %   slightly different parameter combinations
 close all
-clear all
+clear
 addpath(genpath('../src'));
 
 %% Define SSIT Model

Examples/example_ModelReductionTool.m

@@ -1,4 +1,4 @@
-clear all
+clear
 close all
 addpath(genpath('../src'));
 

Examples/example_MultiModelTool.m

@@ -1,7 +1,7 @@
 %% example_toggleSwitch
 % Example script to show SSIT application to a simple two species genetic
 % toggle switch.
-clear all
+clear
 close all
 addpath(genpath('../src'));