#Main Input:
Data_File	
Gene_Annotation_Source	User provided
Gene_Annotation_File	
Cross_Reference_Source	User provided
Cross_Reference_File	
Gene_Location_Source	User provided
Gene_Location_File	
Clustering_Method[STEM Clustering Method,K-means]	STEM Clustering Method
Maximum_Number_of_Model_Profiles	50
Maximum_Unit_Change_in_Model_Profiles_between_Time_Points	2
Number_of_Clusters_K	10
Number_of_Random_Starts	20
Normalize_Data[Log normalize data,Normalize data,No normalization/add 0]	Normalize data
Spot_IDs_included_in_the_data_file	false

#Repeat data
Repeat_Data_Files(comma delimited list)	
Repeat_Data_is_from[Different time periods,The same time period]	Different time periods

#Comparison Data:
Comparison_Data_File	
Comparison_Repeat_Data_Files(comma delimited list)	
Comparison_Repeat_Data_is_from[Different time periods,The same time period]	Different time periods
Comparison_Minimum_Number_of_genes_in_intersection	5
Comparison_Maximum_Uncorrected_Intersection_pvalue	0.0050

#Filtering:
Maximum_Number_of_Missing_Values	0
Minimum_Correlation_between_Repeats	0.0
Minimum_Absolute_Log_Ratio_Expression	1.0
Change_should_be_based_on[Maximum-Minimum,Difference From 0]	Maximum-Minimum
Pre-filtered_Gene_File	

#Model Profiles
Maximum_Correlation	1.0
Number_of_Permutations_per_Gene	50
Maximum_Number_of_Candidate_Model_Profiles	1000000
Significance_Level	0.05
Correction_Method[Bonferroni,False Discovery Rate,None]	Bonferroni
Permutation_Test_Should_Permute_Time_Point_0	true

#Clustering Profiles:
Clustering_Minimum_Correlation	0.7
Clustering_Minimum_Correlation_Percentile	0.0

#Gene Annotations:
Category_ID_File	
Include_Biological_Process	true
Include_Molecular_Function	true
Include_Cellular_Process	true
Only_include_annotations_with_these_evidence_codes	
Only_include_annotations_with_these_taxon_IDs	

#GO Analysis:
Multiple_hypothesis_correction_method_enrichment[Bonferroni,Randomization]	Randomization
Minimum_GO_level	3
GO_Minimum_number_of_genes	5
Number_of_samples_for_randomized_multiple_hypothesis_correction	500

#Interface Options
Gene_display_policy_on_main_interface[Do not display,Display only selected,Display all]	Do not display
Gene_Color(R,G,B)	204,51,0
Display_Model_Profile	true
Display_Profile_ID	true
Display_details_when_ordering	true
Show_Main_Y-axis_gene_tick_marks	false
Main_Y-axis_gene_tick_interval	1.0
Y-axis_scale_for_genes_on_main_interface_should_be[Gene specific,Profile specific,Global]	Profile specific
Scale_should_be_based_on_only_selected_genes	true
Y-axis_scale_on_details_windows_should_be[Determined automatically,Fixed]	Determined automatically
Y_Scale_Min	-3.0
Y_Scale_Max	3.0
Tick_interval	1.0
X-axis_scale_should_be[Uniform,Based on real time]	Uniform
