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-This file will provide an overview of the BNW code.
-
-At this point, BNW requires two packages that are not currently included in the BNW directory.
-These are Octave and dot/graphviz. The BNW code assumes:
-a) dot can be executed using /usr/bin/dot
-b) octave can be executed using /usr/bin/octave
-
-BNW is currently located at /var/www/html/compbio/BNW_x.xx
-(Current development version is BNW_1.12).
-
-It contains two basic files (index.html and home.php) and two directories.
-home.php can be modified/updated to use other versions of BNW
-
-downloads: This contains the downloadable version of the BNW structure learning package.
-
-sourcecodes: This contains the files and codes that are used by the webserver.
-The main purpose of this file is to provide an overview of the files that are contained in 'sourcecodes'.
-
-1. Directories within sourcecodes:
-a) bnt-master: This contains the code for BayesNetToolbox which is used in parameter learning in BNW.
-	It has been slightly modified to work with Octave instead of MATLAB.
-
-b) parameter_learning: This contains the MATLAB/Octave code that we have written for parameter_learning.
-        It also prepares data that has been uploaded to BNW for use with the structure learning code.
-
-c) k-best and localscore: These two directories contains the code used for structure learning.
-
-d) BNW_workflow_test_files, example_datasets, and examples: These three directories contain files that are used by the tutorials and examples on the BNW homepage.
-
-e) data: The data for files generated by using BNW is written to this directory. It also contains several sub-directories that contain example data and networks.
-
-
-2. Files within sourcecodes:
-a) Major BNW php files:
-Many of these will be described in more detail in another file.
-bn_file_load_gom.php: Used in uploading data to be used for structure learning.
-create_tiers_gom.php: Structural constraint interface.
-home_upload.php: Used in uploading a data file and a structure file when the structure is known. 
-layout_example.php: Main php file for displaying/making predictions with network using example data.
-layout.php: Main php file for displaying/making predictions with network using user uploaded data.
-net_structure.php: Used in uploading structure file when the network structure is known.
-upload_structure_file.php: Used in uploading structure file when the network structure is known.
-faq.php
-getting_started.php
-help.php
-home.php
-workflow.php
-
-b) Files related to the structure learning package:
-build.sh
-network_score
-structure
-
-c) Files related to home page, help files, example data sets, and tutorials:
-BNW_overview.png
-BNW_workflow_1.htm
-BNW_workflow_2.htm
-BNW_workflow_net1.htm
-BNW_workflow_sci.htm
-index.html
-example.php
-examplefilecopy.sh
-
-d) General html/css/inc files:
-header_batchsearch.inc
-header_new.inc
-js-graph-it.css
-js-graph-it.js
-my_new_style.css
-sf-homepage.css
-
-e) PHP files that support layout.php or layout_example.php:
-add_evd_example.php
-add_evd.php
-add_inv_example.php
-add_inv.php
-network_layout_evd_2_example.php
-network_layout_evd_2.php
-network_layout_evd_2xample.php
-network_layout_evd.php
-network_layout_inv_2_example.php
-network_layout_inv_2.php
-network_layout_inv_example.php
-network_layout_inv.php
-
-f) Scripts used in structure and parameter learning:
-run_octave: perform parameter learning with original data set and no evidence or intervention
-run_octave_evd: perform parameter learning when considering evidence
-run_octave_inv: perform parameter learning when considering intervention
-run_prep_input: perform prepare data uploaded to BNW for use with structure/parameter learning packages
-run.sh: perform structure learning
-
-g) Files that perform specific functions:
-tier_description_processing_gom.php
--Used by create_tiers_gom.php for the structure constraint interface.
-
-clear_example.php, clear.php, and filecopy.sh
--Used by layout.php to clear entered evidence/intervention 
-
-execute_bn_gom.php
--Runs the script (run.sh) that performs structure learning after uploading data/adding constraints
--It is actually called by executionprogress.php
-
-executionprogress.php, runtime_check.php, k_only_table.txt, and maxparent_table.txt
--Used to provide an estimate of how long structure learning will take.
-
-graphviz_structure.php
--Called by net_structure.php and used to generate files when users upload data with a known structure.
-
-mat_structure.php
--Called by add_inv.php and add_inv_example.php when making predictions after an intervention.
--Interventions can change the network structure and this file help account for these changes.
-
-matrix.php
--Allows for display of the structure matrix file.
-
-input_check.php
--Allows for display of the input file and variable description files.
-
-parameter_display.php
--Allows for display of the network parameters of the original data set and after entering evidence/intervention.
-
-
-
-
-