Update BNW_file_overview.txt

1 files changed, 17 insertions, 15 deletions

diff --git a/BNW_file_overview.txt b/BNW_file_overview.txt
index 40528f49..881605ef 100644
--- a/BNW_file_overview.txt
+++ b/BNW_file_overview.txt
@@ -1,4 +1,4 @@
-This file will provide an overview of the BNW code.

+This file will provide an overview of the directory structure and files used by BNW.

 

 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:

@@ -6,9 +6,9 @@ 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).

+(The current development version is BNW_1.12).

 

-It contains two basic files (index.html and home.php) and two directories.

+The main directory 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.

@@ -17,13 +17,13 @@ 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.

+a) bnt-master: This contains the code for Bayes Net Toolbox which is used in parameter learning in BNW.

+	It has been slightly modified from its original version 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.

+        It also prepares data that has been uploaded to BNW so it can be used with the structure learning code.

 

-c) k-best and localscore: These two directories contains the code used for structure learning.

+c) k-best and localscore: These two directories contain the sourcecode 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.

 

@@ -32,14 +32,15 @@ e) data: The data for files generated by using BNW is written to this directory.
 

 2. Files within sourcecodes:

 a) Major BNW php files:

-Many of these will be described in more detail in another file.

+Many of these will be described in more detail in another file that I am working on.

 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.

+layout.php: Main php file for displaying a network and using it to make predictions.

+net_structure.php: Used in uploading the structure file when the network structure is known.

+upload_structure_file.php: Used in uploading the structure file when the network structure is known.

+The following are self-explanatory:

 faq.php

 getting_started.php

 help.php

@@ -70,6 +71,7 @@ my_new_style.css
 sf-homepage.css

 

 e) PHP files that support layout.php or layout_example.php:

+I will describe these further in another file.

 add_evd_example.php

 add_evd.php

 add_inv_example.php

@@ -109,16 +111,16 @@ graphviz_structure.php
 

 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.

+-Interventions can change the network structure and this file helps account for these changes.

 

 matrix.php

--Allows for display of the structure matrix file.

+-Allows for viewing the structure matrix file.

 

 input_check.php

--Allows for display of the input file and variable description files.

+-Allows for viewing the input file and variable description file after it is uploaded.

 

 parameter_display.php

--Allows for display of the network parameters of the original data set and after entering evidence/intervention.

+-Allows for viewing the network parameters of the original data set and after entering evidence/intervention.