Resolved merge conflict

3 files changed, 27 insertions, 31 deletions

diff --git a/info_files/BNW_data_flow.txt b/info_files/BNW_data_flow.txt
index 0c9dabc4..faff6476 100644
--- a/info_files/BNW_data_flow.txt
+++ b/info_files/BNW_data_flow.txt
@@ -1,5 +1,5 @@
 This file will provide an overview of data flow within BNW and describe the output files that are created for the network. 
-These files are written to the /sourcecodes/data/ directory.
+Files created by BNW are now written to /var/lib/genenet/bnw.
 This discusses what happens after clicking on "Learn network model from data" on homepage (home.php) and focuses on the core functions of BNW.
 
 Step 1: Upload data
@@ -15,7 +15,7 @@ One additional note:
 BNW assigns each network a randomly generated 3 letter prefix when the file is uploaded.
 I will use ??? to signify this prefix.
 
-The following 13 files are written to /sourcecodes/data directory during this step:
+This writes many files to /var/lib/genenet/bnw directory during this step:
 1) ???continuous_input_orig.txt: This is an exact copy of the input file uploaded by the user.
 2) ???continuous_input.txt: Input file after processing by prepareInput.m.
    -A couple of notable changes are made that differentiate input.txt from input_orig.txt.
@@ -49,7 +49,7 @@ This is a link to executionprogress.php which just displays a "progress bar" and
 To start structure learning, it runs execute_bn_gom.php.
 execute_bn_gom.php starts structure learning using run.sh and, then, run_octave in the run_scripts directory discussed in Step 3.
 
-Output files from structure learning that are written to /sourcecodes/data:
+Output files from structure learning that are written to /var/lib/genenet/bnw:
 1) ???structure_input.txt: The structure matrix, containing the edges included in the network model.
    The format of this file is a header line containing the variable names.
    The rest is the strucure matrix where 1 indicates an edge is included in the network and a 2 is not.
@@ -66,14 +66,15 @@ Before the process described in Step 2a, additional constraints or changes to de
   can be added using the structural constraint interface.
 
 This can be accessed by clicking on "Go to structure learning settings and the BNW
-     structural constraint interface" which links to create_tiers_gom.php
+     structural constraint interface" which links to create_tiers_gom_part1.php
 
-The top section of create_tiers_gom.php is "Global structure learning settings"
-  Modifying this section will change the values in ???parent.txt, ???k.txt, and ???thr.txt.
+This page allows for modifying "Global structure learning settings"
+  This will change the values in ???parent.txt, ???k.txt, and ???thr.txt.
 
-The remaining sections will modify the ???ban.txt and ???white.txt files.
+Clicking "Continue assign variables to tiers" will go to create_tiers_gom_part2.php.
+  This page will modify the ???ban.txt and ???white.txt files.
 
-Clicking on "Perform Bayesian network modeling" goes to executionprogress.php and Step 2a is followed.
+Clicking on "Click here to perform Bayesian network modeling after creating tiers" goes to tier_description_processing_gom.php and Step 2a is followed.
 
 
 Step 3: Parameter learning of the original network.
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:
diff --git a/info_files/server_change_notes.txt b/info_files/old_server_change_notes.txt
index 849d6f84..e3638b60 100644
--- a/info_files/server_change_notes.txt
+++ b/info_files/old_server_change_notes.txt
@@ -1,3 +1,5 @@
+This is out of date, but I will leave it here until I can update it.
+
 This file will contain notes about changes that might need to be made on a new server:
 
 Required software: