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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.
+
+
+
+
+