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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.

+

+

+

+

+