Update BNW_file_overview.txt

1 files changed, 16 insertions, 23 deletions

diff --git a/info_files/BNW_file_overview.txt b/info_files/BNW_file_overview.txt
index a3c2fad7..b2d191f2 100644
--- a/info_files/BNW_file_overview.txt
+++ b/info_files/BNW_file_overview.txt
@@ -1,18 +1,17 @@
-This file will provide an overview of the BNW code.
+This file will provide an overview of the BNW code. It is not completely up to date. The information should be correct, but some files might be missing.
 
 At this point, BNW requires three packages that are not currently included in the BNW directory.
 These are dot/graphviz; octave; and plotly. The BNW code assumes:
 a) dot can be executed using /usr/bin/dot
 b) octave can be executed using /usr/bin/octave
 c) plotly: 
-    The version of python on the current server is too old for plotly. I installed an newer version of python in my home directory:
-     python2.7 is currently installed in /home/jziebart/python/Python-2.7.15/python
-    Then, to use plotly, I modified files.py in:
-      /home/jziebart/python/lib/python2.7/site-packages/plotly to use absolute paths for PLOTLY_DIR and TEST_DIR
-    The files that need plotly are:  cv_plotly.py, kfold_plotly.py, and ts_plotly.py
+    Plotly runs through a python environment for BNW. The python version is 3.6.8 and the plotly version is 4.13.0.
+    The python environment files are in bnw-env.
     
-BNW is currently located at /var/www/html/compbio/BNW_x.xx
-(The current development version is BNW_1.22).
+    The files that need plotly are:  cv_plotly.py, kfold_plotly.py, ts_plotly.py, violin_plotly.py, violin_ev_plotly.py, and violin_int_plotly.py.
+    
+BNW is currently located at /var/www/html/compbio/BNW_x.x
+(The current development version is BNW_1.3).
 
 The main BNW directory contains two basic files (index.html and home.php) and two directories.
 A couple of lines in home.php should be modified/updated to point to the correct BNW directory.
@@ -22,6 +21,8 @@ downloads: This contains the downloadable version of the BNW structure learning
 sourcecodes: This contains the files and codes that are used by the webserver.
 The main purpose of this file is to provide a brief overview of the files that are contained in 'sourcecodes'.
 
+bnw-env: The python environment for BNW.
+
 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.
@@ -30,19 +31,19 @@ a) bnt-master: This contains the code for BayesNetToolbox which is used in param
 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 C code used for structure learning.
+c) 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.
 
-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.
+d) 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.
 
-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.
+e) run_scripts: Scripts that run Octave calculations.
 
-f) run_scripts: Scripts that run Octave calculations.
+f) scripts: Javascript libraries and associated files. 
 
 2. Files within sourcecodes:
 a) Major BNW php files:
 Many of these will be described in BNW_data_flow.txt.
 bn_file_load_gom.php: Used in uploading data to be used for structure learning.
-create_tiers_gom.php: Structural constraint interface.
+create_tiers_gom_part1.php and create_tiers_gom_part2.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.
@@ -64,9 +65,7 @@ structure
 run.sh
 
 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_overview_new.png
 BNW_workflow_net1.htm
 BNW_workflow_sci.htm
 index.html
@@ -83,18 +82,12 @@ sf-homepage.css
 graph-creator.css
 graph-creator.js
 
-e) PHP files that support layout.php or layout_example.php:
-add_evd_example.php
+e) PHP files that support layout.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_example.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) Files used for cross-validation/making predictions using a test set: