+
+
This workflow will provide
+an overview of how to use BNW to:
+
+
1) Select
+a structure learning method and upload data into BNW
+
+
2) Use
+the BNW structural restraint interface
+
+
3) Make
+predictions with the network structure
+
+
+
+
1.
+Select structure learning method and uploading data into BNW
+
+
For this workflow, we are
+creating a network using a biological data set containing both continuous and
+discrete variables. The variables are a genotype (the discrete variable), three
+gene expression traits (Gene1, Gene2, Gene3), and a phenotype.
+
+
+
+
We do not know the network
+structure for this dataset, so we will first use BNW to learn the structure. Selecting
+Learn a network model from data on the BNW home page presents a list of the
+three structure learning methods that are currently implemented in BNW.
+
+
![]()
+
+
Because the network contains
+only 5 variables, we can use any of these structure learning methods. If more
+than 6 variables are present, using the global optimal search method would likely be necessary.
+We will use the exhaustive search with model averaging method in this workflow.
+More information about the structure learning methods can be found on the BNW
+help page.
+
+
+
+
After selecting the
+Exhaustive Search button, we are prompted to upload a file containing the data.
+
+
+
+![]()
+
+
The figure
+below shows BNW after we have uploaded the data file. The first line of the
+data contains the names of the variables included in the network, while the
+remaining lines are the variable values for individual samples. A description
+of how to format data files for use in BNW can be found on the BNW help page and can be accessed by the the Data formatting guidelines option in the left menu. Additionally, two additional options, Select additional constraints or Perform Bayesian network modeling with no restraints, appear in the left menu after loading the data file.
+
+
+![]()
+
+
2.
+Use the structural constraint interface
+
+
Here, we will use the
+structural constraint interface to help identify biologically meaningful
+network structures. Specifically, we want to investigate how the genotype
+impacts gene expression which then impacts the phenotype.
+
+
+
+
The first
+section of the structural constraint interface allows users to assign the variables
+(nodes) in the network to tiers. By default, three tiers are shown, but this
+can be changed by selecting a different number in the drop-down menu. The
+leftmost box of this section contains draggable boxes with the names of the
+variables in the network.
+
+
+![]()
+
+
For this
+network, we want to assign Genotype to Tier1, the gene expression traits to
+Tier2, and the Phenotype to Tier3.
+
+
+![]()
+
+
The second
+section in the structural constraint interface allows users to specify the
+types of interactions that are allowed both between and within tiers. In this
+case, we will keep the default settings, which will allow there to be edges
+between nodes within a tier, prevent nodes in Tier1 from being the child of
+Tier2 and Tier3 nodes, and prevent nodes in Tier2 from being the child of Tier2
+nodes.
+
+
![]()
+
+
The final
+section of the structural constraint interface would allow for the
+specification of particular edges that should be banned from the network or
+required to be in the network. Users can identify these edges by dragging the
+nodes to appropriate boxes. In this case, we do not want to ban or require any
+specific edges.
+
+
+![]()
+
+
After
+entering the structural constraints, BNW will perform structure learning from
+the data after clicking Perform Bayesin network modeling on the left menu and
+present the structure of the network as shown below. Genotype, the discrete
+node, is shown as a bar chart with the bars showing the fraction of samples
+with each genotype in the data, while the other nodes are shown as lines with
+the Gaussian distributions that best fit the data.
+
+
![]()
+
+
To further
+investigate the structure of the network, users can select Display Structure
+Matrix in the left menu. This will bring up a popup windoe containing a table
+showing the confidence of each directed edge in the network after model
+averaging. For this network, all of the nodes included in the network were
+present in almost all high scoring networks, as the values of the edges are all
+near 1. BNW displays all edges with a confidence greater than 0.5 in the
+network structure. A second table in the window shows the structure matrix with
+a 1 for edges included in the structure and 0 for edges that are not included. These
+tables can be downloaded by clicking the download link.
+
+
![]()
+
+
3) Make
+predictions with the network structure
+
+
BNW can be used to both
+predict the values of variables in a network given known evidence and to
+investigate how the network might change in response to interventions. Users
+can switch between evidence and intervention modes by selecting the proper
+button on the top of the page containing the network structure.
+
+
For example,
+suppose we want to use the model to make predictions for a new sample that was
+not in the original dataset. We know that this sample was from an individual
+with Genotype=2 and want to predict the values of the genes and phenotype for
+the individual. To enter this evidence in the network, we simply click on the
+Genotype node in the network and enter 2 in the popup window.
+
+
The figure below shows the
+changes in the network after entering this evidence.The node for which evidence was entered now contains a red outline and all of the nodes in the network now contain both blue and red lines. The blue lines show the original values of the distributions, while the red lines shown the predicted values given the
+evidence. In this case, knowing that the individual had Genotype=2 would cause
+us to predict that the expression of Gene1 and the value of the phenotype would
+be above average, while the expression of Gene2 and Gene3 would be decreases.
+The specific changes in the predicted values can be investigated by hovering
+over the nodes and observing the values at the peaks of the distribution.
+
+
![]()
+
+
Evidence
+can be entered in more than one node in the network. For example, the figure
+below shows predicted values for the network after entering evidence for both
+Genotype and Gene1.
+
+
![]()
+
+
To use the
+network to predict the results of intervention, select the proper button on the
+top of the window to enter intervention mode. While evidence simply changes the
+predicted values of the other nodes in the network, intervention has a larger
+effect, as it removes the dependence of the intervened network on its parents
+and changes the network structure.
+
+
![]()
+
+
The figure
+below shows the changes in the network in BNW after intervention on Gene1 that
+results Gene1 having a low value. The predictions of the network after this
+intervention could be compared with experiments that prevent Gene1 from being
+expressed. Intervention that decreases Gene1 is predicted to result in an increase
+in Gene2 and a decrease in the phenotype. Note that Genotype and Gene3, which
+are not descendents of Gene1, are not affected by the intervention.
+
+
![]()
+
+
+
+
+
+
+
+
This workflow contains examples of using the BNW structural constraint interface to help identify biologically meaningful genetic network models for two cases:
+
+
1) A genetic network linking genotype and phenotype
+
+
2) A genetic network with multiple genotypes and cis- and trans-regulated genes
+
+
+
+
+
1.
+A genetic network linking genotype and phenotype
+
+
In this example, we will use the structural constraint interface to create a genetic network linking a genotype with intermediated phenotypes (i.e., gene expression or other cellular level traits) and a higher-order phenotype. The figure below shows a screenshot of BNW after loading the data file and selecting Go to structure learning settings and the BNW structural constraint interface. There are 5 nodes in the network, Genotype, Int1, Int2, Int3, and a Phenotype.
+
![]()
+
+
+
We want to assign the nodes to three tiers in this example, so we will keep the number of tiers at the default setting, and drag the nodes to the proper tiers.
+
![]()
+
+
In this example, we do not want the genotype to be the direct parent of the phenotype, so we made some changes to the Define interactions allowed between tiers section of the structural constraint interface. Specifically, we have unchecked two boxes that are different from the default settings: (1) we have unchecked the box that allows the node(s) in Tier1 from being the parents of the node(s) in Tier3 and (2) we have unchecked the box that allows the node(s) in Tier3 from being the children of the node(s) in Tier1. Actually, unchecking either of these boxes would have been sufficient in preventing direct interactions between Genotype and Phenotype, but, there is no harm in unchecking both boxes. There are no additional specific edges that we want to ban or require in the network, so we do not have to add any edges to the Specify additional constraint section and we can proceed with structure learning.
+
![]()
+
+
+
2.
+A genetic network with multiple genotypes and cis- and trans-regulated genes.
+
+
In this example, we will add restrictions to a network containing 8 nodes: 2 genotype nodes (Geno1 and Geno2), 3 cis-regulated gene expression traits (cisGene1, cisGene2, and cisGene3), 2 trans-regulated gene expression traits (transGene1 and transGene2), and a phenotype (Pheno). We have four tiers of nodes (genotypes, cis-regulated genes, trans-regulated genes, and phenotype), so we have selected 4 from the dropdown menu at the top of the page and assigned the nodes to the correct tiers. We could make a more complex system of tiers that would allow us to specify which genes are regulated by which genotypes (for example, Geno1 regulates cisGene1 and transGene1, while Geno2 regulates cisGene2, cisGene3, and transGene2), but, for this example, we will use a simpler system of 4 tiers.
+
+
+![]()
+
+
+
We have made one change to the default setting in the Define interactions allowed between tiers section. For Tier1, which contains the genotypes, we have selected "No" for the "Are within tier interactions allowed?", as it does not make biological sense for one genotype variation to cause the variation in another genotype in this examples.
+
+
+![]()
+
+
Assume that a known regulatory relationship between cisGene1 and transGene1 has been established from previous experiments. We can require that this relationship is included in the network by adding the edge list of required edges in the Specify additional constraints section.
+
+
+![]()
+
";
@@ -167,17 +165,12 @@ if($searchID!="")
The uploaded data file has the following properties:
-
-
>Download cross-validation results
+
>Download cross-validation results
Perform leave-one-out cross-validation of another network variable
@@ -139,8 +132,7 @@ $table_text = json_encode(file("file://".$dir.$filename1));
} else {
?>
Perform leave-one-out cross-validation of network
-
-
+
Select the variable that you want to examine the predictions of below.
diff --git a/sourcecodes/cv_plotly.py b/sourcecodes/cv_plotly.py
index 05d0621d..c22e0dcc 100644
--- a/sourcecodes/cv_plotly.py
+++ b/sourcecodes/cv_plotly.py
@@ -1,7 +1,9 @@
-#!/var/www/html/compbio/BNW_1.3/bnw-env/bin/python3
+#!/home/jziebart/python/Python-2.7.15/python
import os
import sys
+#sys.path.append('/home/jziebart/.local/bin')
+#sys.path.append('/home/jziebart/.local/lib')
import plotly
import plotly.graph_objs as go
@@ -17,10 +19,9 @@ f=open(filename,"r")
lines=f.readlines()
#Read the last line to get the variable name
line = lines.pop()
-#line = map(string.strip,line.strip().split(" "))
-line = line.strip().split(" ")
+line = map(string.strip,line.strip().split(" "))
varName = line[3][:-1]
-plot_title = varName+" LOOCV"
+plot_title = "
"+varName+" LOOCV"
#remove header line
header = lines.pop(0)
@@ -28,11 +29,9 @@ header = lines.pop(0)
typefile = netID+"type.txt"
tf=open(typefile,"r")
line=tf.readline()
-#varnames = map(string.strip,line.strip().split("\t"))
-varnames = line.strip().split("\t")
+varnames = map(string.strip,line.strip().split("\t"))
line=tf.readline()
-#vartypes = map(string.strip,line.strip().split("\t"))
-vartypes = line.strip().split("\t")
+vartypes = map(string.strip,line.strip().split("\t"))
varindex = varnames.index(varName)
cd_type = int(vartypes[varindex])
@@ -48,8 +47,7 @@ if cd_type == 1:
# line = f.readline()
# while line:
for line in lines:
- #line = map(string.strip,line.strip().split("\t"))
- line = line.strip().split("\t")
+ line = map(string.strip,line.strip().split("\t"))
x.append(float(line[1]))
y.append(float(line[2]))
# line=f.readline()
@@ -62,11 +60,7 @@ if cd_type == 1:
size=24,
color='black'
),
- title_xref="paper",
- title_x=0.5,
- title_xanchor="center",
- title_yanchor="middle",
- xaxis=dict(
+ xaxis=dict(
autorange=True,
title='Actual values',
titlefont=dict(
@@ -92,8 +86,7 @@ if cd_type == 1:
else:
#Make bar chart for discrete data
#Get names of states
- #header = map(string.strip,header.strip().split("\t"))
- header = header.strip().split("\t")
+ header = map(string.strip,header.strip().split("\t"))
states = header[2:]
#Read the data
actual = []
@@ -101,8 +94,7 @@ else:
# line = f.readline()
# while line:
for line in lines:
- #line = map(string.strip,line.strip().split("\t"))
- line = line.strip().split("\t")
+ line = map(string.strip,line.strip().split("\t"))
actual.append(line[1])
predict_x = line[2:]
predict_x = [float(x) for x in predict_x]
@@ -153,10 +145,6 @@ else:
size=24,
color='black'
),
- title_xref="paper",
- title_x=0.5,
- title_xanchor="center",
- title_yanchor="middle",
xaxis=dict(
autorange=True,
title='State',
diff --git a/sourcecodes/cv_predictions.php b/sourcecodes/cv_predictions.php
index 65915534..54a565ed 100644
--- a/sourcecodes/cv_predictions.php
+++ b/sourcecodes/cv_predictions.php
@@ -32,8 +32,7 @@ $keyval=valid_keyval($_GET["My_key"]);
This feature has recently been added to BNW and is still being tested. Please inform us of any issues.
Its use is briefly described here.
k-fold cross-validation predictions are being calculated.
Click here to update status.
diff --git a/sourcecodes/data/LRlnetwork.json b/sourcecodes/data/LRlnetwork.json
deleted file mode 100644
index 7ee3b56f..00000000
--- a/sourcecodes/data/LRlnetwork.json
+++ /dev/null
@@ -1,10 +0,0 @@
-{
- "nodes": [
- {
- "data": {
- "id": "1",
- "label": "Node1"
- }
- }
- ]
-}
diff --git a/sourcecodes/data/old/Backupfiles/evidencemodified b/sourcecodes/data/old/Backupfiles/evidencemodified
deleted file mode 100644
index 9b3f7563..00000000
Binary files a/sourcecodes/data/old/Backupfiles/evidencemodified and /dev/null differ
diff --git a/sourcecodes/data/old/Backupfiles/initialstructure b/sourcecodes/data/old/Backupfiles/initialstructure
deleted file mode 100644
index 9ecf1bc7..00000000
Binary files a/sourcecodes/data/old/Backupfiles/initialstructure and /dev/null differ
diff --git a/sourcecodes/data/old/Backupfiles/newintervention b/sourcecodes/data/old/Backupfiles/newintervention
deleted file mode 100644
index d818a943..00000000
Binary files a/sourcecodes/data/old/Backupfiles/newintervention and /dev/null differ
diff --git a/sourcecodes/data/old/Backupfiles/temp_evidence_file b/sourcecodes/data/old/Backupfiles/temp_evidence_file
deleted file mode 100644
index b687ceaf..00000000
--- a/sourcecodes/data/old/Backupfiles/temp_evidence_file
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/bin/sh
-# script for execution of deployed applications
-#
-# Sets up the MCR environment for the current $ARCH and executes
-# the specified command.
-#
-exe_name=$0
-exe_dir=`dirname "$0"`
-echo "------------------------------------------"
-if [ "x$1" = "x" ]; then
- echo Usage:
- echo $0 \ args
-else
- echo Setting up environment variables
- MCRROOT="$1"
- echo ---
- LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64;
- MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ;
- XAPPLRESDIR=${MCRROOT}/X11/app-defaults ;
- export LD_LIBRARY_PATH;
- export XAPPLRESDIR;
- echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH};
- shift 1
- args=
- while [ $# -gt 0 ]; do
- token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank
- args="${args} ${token}"
- shift
- done
- "${exe_dir}"/evidencemodified
\ No newline at end of file
diff --git a/sourcecodes/data/old/Backupfiles/temp_intervention_file b/sourcecodes/data/old/Backupfiles/temp_intervention_file
deleted file mode 100644
index cdf5ce0f..00000000
--- a/sourcecodes/data/old/Backupfiles/temp_intervention_file
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/bin/sh
-# script for execution of deployed applications
-#
-# Sets up the MCR environment for the current $ARCH and executes
-# the specified command.
-#
-exe_name=$0
-exe_dir=`dirname "$0"`
-echo "------------------------------------------"
-if [ "x$1" = "x" ]; then
- echo Usage:
- echo $0 \ args
-else
- echo Setting up environment variables
- MCRROOT="$1"
- echo ---
- LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64;
- MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ;
- XAPPLRESDIR=${MCRROOT}/X11/app-defaults ;
- export LD_LIBRARY_PATH;
- export XAPPLRESDIR;
- echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH};
- shift 1
- args=
- while [ $# -gt 0 ]; do
- token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank
- args="${args} ${token}"
- shift
- done
- "${exe_dir}"/newintervention
\ No newline at end of file
diff --git a/sourcecodes/data/old/Backupfiles/temp_shell_file_initial_structure b/sourcecodes/data/old/Backupfiles/temp_shell_file_initial_structure
deleted file mode 100644
index 5d1c323d..00000000
--- a/sourcecodes/data/old/Backupfiles/temp_shell_file_initial_structure
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/bin/sh
-# script for execution of deployed applications
-#
-# Sets up the MCR environment for the current $ARCH and executes
-# the specified command.
-#
-exe_name=$0
-exe_dir=`dirname "$0"`
-echo "------------------------------------------"
-if [ "x$1" = "x" ]; then
- echo Usage:
- echo $0 \ args
-else
- echo Setting up environment variables
- MCRROOT="$1"
- echo ---
- LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64;
- MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ;
- XAPPLRESDIR=${MCRROOT}/X11/app-defaults ;
- export LD_LIBRARY_PATH;
- export XAPPLRESDIR;
- echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH};
- shift 1
- args=
- while [ $# -gt 0 ]; do
- token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank
- args="${args} ${token}"
- shift
- done
- "${exe_dir}"/initialstructure
\ No newline at end of file
diff --git a/sourcecodes/data/old/evidencemodified b/sourcecodes/data/old/evidencemodified
deleted file mode 100644
index 9b3f7563..00000000
Binary files a/sourcecodes/data/old/evidencemodified and /dev/null differ
diff --git a/sourcecodes/data/old/example_sci_bk/Lluban.txt b/sourcecodes/data/old/example_sci_bk/Lluban.txt
deleted file mode 100644
index 38108f00..00000000
--- a/sourcecodes/data/old/example_sci_bk/Lluban.txt
+++ /dev/null
@@ -1,15 +0,0 @@
-From To
-Gene1 Genotype
-Gene2 Genotype
-Gene3 Genotype
-Phenotype Genotype
-Gene1 Genotype
-Gene2 Genotype
-Gene3 Genotype
-Phenotype Gene1
-Phenotype Gene2
-Phenotype Gene3
-Phenotype Genotype
-Phenotype Gene1
-Phenotype Gene2
-Phenotype Gene3
diff --git a/sourcecodes/data/old/example_sci_bk/Llucontinuous_input.txt b/sourcecodes/data/old/example_sci_bk/Llucontinuous_input.txt
deleted file mode 100644
index 79295d7e..00000000
--- a/sourcecodes/data/old/example_sci_bk/Llucontinuous_input.txt
+++ /dev/null
@@ -1,503 +0,0 @@
-Genotype Gene3 Gene2 Phenotype Gene1
-2 1 1 1 1
-2 -1.0008 -0.44837 0.21808 -1.196
-1 -0.29368 -0.53043 -1.0893 -0.10136
-2 0.70835 0.72886 -0.18098 -0.42907
-1 0.63703 0.86428 1.7013 0.1425
-1 -1.2402 -0.69712 -1.7002 -0.71634
-1 -1.1952 0.27155 -0.79413 -1.0965
-2 0.62914 0.94265 1.8385 0.6135
-1 -1.91 -2.379 -3.1094 -1.0924
-2 -0.83436 -0.90968 -1.3598 1.335
-1 0.15685 0.4766 1.2891 -1.3309
-2 0.7047 1.0623 1.9811 1.2821
-1 0.59747 -0.023123 0.88555 -0.8844
-1 -1.0557 -1.5548 -1.3016 -0.77687
-2 1.5206 2.0289 0.90366 1.8089
-1 0.65525 -0.47226 -1.1824 0.41863
-2 -0.39262 0.382 -0.64829 0.40947
-2 0.14966 0.22972 0.33797 0.69647
-1 -1.8836 -0.68534 -0.99941 -0.78961
-1 0.48181 0.01241 1.2145 0.16835
-2 1.4673 2.0438 2.4674 2.5234
-1 -1.3242 -0.80218 -1.6446 -0.31044
-1 -1.2471 -2.0351 -1.0296 -1.937
-1 0.23695 -0.01724 -0.32851 -0.16484
-1 -0.13986 -0.6065 -0.8491 -0.95538
-2 0.90888 1.0365 2.7222 1.3507
-1 -0.30556 -1.1546 -0.86033 -2.2006
-2 0.5391 0.99532 0.96947 1.1575
-2 1.1235 0.37982 0.64439 0.94362
-2 1.7073 1.9303 2.8018 1.9158
-1 -0.20553 -0.074104 -0.50073 -1.0697
-1 -0.27415 0.23076 -0.27564 -0.11286
-1 -1.304 -1.1213 -0.71793 -1.3462
-2 0.54315 0.55846 0.87411 1.2432
-1 -1.0659 -0.38067 -1.4372 -2.0927
-1 0.21278 -1.0115 -1.0984 -0.72751
-1 -2.9061 -1.3118 -3.8372 -2.0448
-2 -0.69608 -0.61145 -1.0037 0.12181
-1 0.66835 0.018886 -1.0081 -1.4165
-1 0.32575 -0.51767 1.0187 -0.40914
-2 0.65837 1.2791 1.8388 2.2906
-2 0.37574 0.21618 -0.89435 1.2643
-1 0.13513 -0.31405 -0.16057 0.77712
-2 0.16054 0.40635 0.036165 1.6374
-1 1.9393 1.5717 2.6922 1.1933
-1 -0.59118 -0.47154 -0.20293 -1.5576
-1 -0.35938 -0.49565 -0.20837 0.61043
-2 -0.57133 0.15921 -0.44158 0.43312
-1 0.31835 0.49002 2.2029 0.17685
-1 -0.0093708 -0.85889 -1.0934 -1.6905
-1 -0.90501 -1.4637 -1.5526 -1.828
-2 0.11531 -0.022781 0.88843 0.8607
-1 0.34978 -0.34306 0.95301 -0.056177
-2 -0.22236 -0.13023 0.37608 0.18027
-1 -0.90103 -0.38393 -1.1513 -0.78153
-2 0.66848 0.81005 1.3945 3.3654
-2 0.10539 0.59781 0.77864 0.63865
-1 -1.15 -1.4531 -2.929 -1.6867
-1 0.20842 -0.0039076 -0.12879 -0.31459
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-2 0.17619 0.488 0.38575 0.19632
-1 0.79693 0.15328 -0.26972 -0.45147
-2 1.3618 1.6805 1.2152 2.1905
-2 -0.36075 1.0698 0.38569 2.5707
-1 -0.55325 -0.17572 -1.0232 -1.134
-2 0.9795 1.3777 0.26495 0.23258
-1 -0.92872 -1.2233 -2.1998 -1.9011
-1 0.47029 -0.06201 -0.34515 -0.57857
-1 -2.6597 -1.5144 -3.0038 -1.949
-2 -0.064474 -0.25394 -0.34794 0.76334
-2 0.52259 0.76325 0.93484 0.060827
-1 0.89037 0.68007 0.50459 -0.88464
-2 1.0031 1.3853 1.7313 0.75303
-2 0.6954 1.3692 0.19298 1.6174
-2 -0.14026 1.1774 0.39386 -0.25913
-2 -1.7796 -1.2709 -2.5775 -0.36996
-2 0.41557 1.9905 1.839 1.1327
-1 0.53878 -0.71974 -0.65395 -0.62597
-2 0.22326 1.3888 0.17221 1.2265
-1 -0.12667 -1.1336 -0.67 -3.6161
-2 1.0183 1.5883 2.2784 1.7509
-1 -2.0415 -2.2483 -2.8307 -3.1148
-2 -1.1513 -0.08575 -0.62876 2.164
-1 0.1961 0.075096 1.9551 0.039445
-2 -0.96925 0.12921 -1.2741 1.8371
-1 0.34137 0.086468 1.4716 0.55236
-1 -0.20756 -0.74846 0.65256 -0.7032
-2 1.1736 1.0214 1.258 1.0002
-2 0.48081 1.3275 0.54443 1.2194
-2 -0.45146 0.38298 0.64902 0.90395
-1 0.75519 -1.0627 -0.35778 -1.7689
-1 -1.4308 -1.0998 -1.0094 -0.66361
-1 -0.097019 0.18029 -9.0423e-07 0.59444
-2 1.3769 2.4872 3.2855 0.98727
-2 0.79201 0.76361 0.88459 3.119
-2 2.5125 2.4776 4.6119 3.966
-1 0.57129 -0.93689 -0.20516 -0.42323
-1 -0.91517 -0.25445 -1.3515 -0.99354
-1 0.17456 -0.98904 -0.49643 -0.8997
-1 -2.2724 -1.6869 -3.8034 -2.0882
-2 -1.8188 -0.57721 -2.4386 0.058963
-2 -0.19227 0.038901 -0.85065 0.6644
-1 -1.5517 -0.57182 -0.9874 -1.4081
-2 -0.47999 0.49667 0.27351 0.6261
-2 0.45041 0.48469 0.55808 2.0659
-1 -1.1302 -1.255 -2.7206 -1.2712
-1 -0.60672 -1.1008 -2.6889 -1.0078
-1 -1.0508 -0.99612 -1.555 -1.0463
-2 0.14434 0.97791 1.2498 1.7391
-2 0.21333 1.6686 1.219 1.8919
-2 -0.35461 -0.64694 -1.3312 -0.10481
-1 -2.0611 -2.1245 -3.6067 -1.6584
-2 -0.3534 0.45962 -0.39991 0.45667
-1 -0.37564 -0.63085 -1.2641 -1.3292
-1 0.30023 -0.20283 0.041852 -0.17139
-2 0.25089 1.0204 1.8084 1.0493
-1 -0.44041 -1.1143 -0.59224 -0.84288
-2 -0.11392 0.5681 -0.054604 0.88897
-1 0.41829 -1.042 -0.0042274 -1.9512
-2 1.4863 2.9227 3.0012 3.1253
-1 -0.60588 -1.1196 -1.4647 -0.92268
-1 -0.10497 -0.74629 -1.8353 -0.35425
-1 -1.2499 -0.83335 -2.4047 -1.4657
-1 -0.51414 -1.4602 -0.54649 -1.0475
-1 0.56956 0.79545 0.86494 -0.59471
-1 -0.64964 -0.78543 -1.9412 -2.2114
-2 1.0044 0.56431 1.2968 1.3807
-1 -1.1924 -0.69401 -0.72828 -1.7252
-2 0.15739 1.0449 0.3742 1.4303
-2 0.49582 1.4353 1.1652 1.5814
-
diff --git a/sourcecodes/data/old/example_sci_bk/Llugraphviz.txt b/sourcecodes/data/old/example_sci_bk/Llugraphviz.txt
deleted file mode 100644
index 88bbd3ba..00000000
--- a/sourcecodes/data/old/example_sci_bk/Llugraphviz.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-digraph G {
-size="10,10"; ratio = fill;
-node [shape=square,width=1.5];
-Genotype -> Gene3;
-Genotype -> Gene1;
-Gene3 -> Phenotype;
-Gene2 -> Gene3;
-Gene2 -> Phenotype;
-Gene1 -> Gene2;
-}
\ No newline at end of file
diff --git a/sourcecodes/data/old/example_sci_bk/Lluk.txt b/sourcecodes/data/old/example_sci_bk/Lluk.txt
deleted file mode 100644
index 83b33d23..00000000
--- a/sourcecodes/data/old/example_sci_bk/Lluk.txt
+++ /dev/null
@@ -1 +0,0 @@
-1000
diff --git a/sourcecodes/data/old/example_sci_bk/Llumap.txt b/sourcecodes/data/old/example_sci_bk/Llumap.txt
deleted file mode 100644
index 958281d5..00000000
--- a/sourcecodes/data/old/example_sci_bk/Llumap.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-Genotype 2 0.500305 1.514000
-Gene3 1 1.027261 -0.015284
-Gene2 1 1.160583 0.138097
-Phenotype 1 1.554104 0.069005
-Gene1 1 1.515414 0.174451
diff --git a/sourcecodes/data/old/example_sci_bk/Llumapdata.txt b/sourcecodes/data/old/example_sci_bk/Llumapdata.txt
deleted file mode 100644
index d684ea06..00000000
--- a/sourcecodes/data/old/example_sci_bk/Llumapdata.txt
+++ /dev/null
@@ -1 +0,0 @@
-Genotype Gene1 Gene2 Gene3 Phenotype
diff --git a/sourcecodes/data/old/example_sci_bk/Lluname.txt b/sourcecodes/data/old/example_sci_bk/Lluname.txt
deleted file mode 100644
index f3a1f5bf..00000000
--- a/sourcecodes/data/old/example_sci_bk/Lluname.txt
+++ /dev/null
@@ -1 +0,0 @@
-Genotype Gene3 Gene2 Phenotype Gene1
diff --git a/sourcecodes/data/old/example_sci_bk/Llunet_figure.txt b/sourcecodes/data/old/example_sci_bk/Llunet_figure.txt
deleted file mode 100644
index bdc07cbd..00000000
--- a/sourcecodes/data/old/example_sci_bk/Llunet_figure.txt
+++ /dev/null
@@ -1,433 +0,0 @@
-5
-1200 1200
-Genotype 0 0
-Gene1 120 200
-Gene2 0 400
-Gene3 120 600
-Phenotype 0 800
-Genotype 2
-250 150
-0
-2 2 4
-1 0.4860
-2 0.5140
-Gene1 1
-250 150
-1 1
-1 3
--3.5013 0.0009
--3.4313 0.0012
--3.3613 0.0015
--3.2912 0.0019
--3.2212 0.0024
--3.1512 0.0030
--3.0811 0.0037
--3.0111 0.0046
--2.9411 0.0056
--2.8710 0.0069
--2.8010 0.0083
--2.7310 0.0101
--2.6609 0.0121
--2.5909 0.0145
--2.5209 0.0174
--2.4508 0.0206
--2.3808 0.0243
--2.3108 0.0286
--2.2407 0.0335
--2.1707 0.0389
--2.1007 0.0451
--2.0306 0.0520
--1.9606 0.0597
--1.8906 0.0682
--1.8205 0.0775
--1.7505 0.0876
--1.6805 0.0986
--1.6104 0.1105
--1.5404 0.1231
--1.4704 0.1366
--1.4003 0.1508
--1.3303 0.1657
--1.2603 0.1811
--1.1902 0.1971
--1.1202 0.2134
--1.0502 0.2300
--0.9801 0.2467
--0.9101 0.2633
--0.8401 0.2797
--0.7700 0.2956
--0.7000 0.3110
--0.6300 0.3256
--0.5599 0.3392
--0.4899 0.3517
--0.4199 0.3629
--0.3498 0.3726
--0.2798 0.3808
--0.2098 0.3873
--0.1397 0.3920
--0.0697 0.3948
-0.0003 0.3958
-0.0704 0.3948
-0.1404 0.3920
-0.2104 0.3872
-0.2805 0.3807
-0.3505 0.3726
-0.4205 0.3628
-0.4906 0.3516
-0.5606 0.3391
-0.6306 0.3254
-0.7007 0.3108
-0.7707 0.2955
-0.8407 0.2795
-0.9108 0.2631
-0.9808 0.2465
-1.0508 0.2299
-1.1209 0.2133
-1.1909 0.1969
-1.2609 0.1810
-1.3310 0.1655
-1.4010 0.1507
-1.4710 0.1365
-1.5411 0.1230
-1.6111 0.1103
-1.6811 0.0985
-1.7512 0.0875
-1.8212 0.0774
-1.8912 0.0681
-1.9613 0.0596
-2.0313 0.0520
-2.1013 0.0451
-2.1714 0.0389
-2.2414 0.0334
-2.3114 0.0286
-2.3815 0.0243
-2.4515 0.0206
-2.5215 0.0173
-2.5916 0.0145
-2.6616 0.0121
-2.7316 0.0101
-2.8017 0.0083
-2.8717 0.0068
-2.9417 0.0056
-3.0118 0.0046
-3.0818 0.0037
-3.1518 0.0030
-3.2219 0.0024
-3.2919 0.0019
-3.3619 0.0015
-3.4320 0.0012
-3.5020 0.0009
-Gene2 1
-250 150
-1 2
-2 4 5
--3.5862 0.0008
--3.5124 0.0010
--3.4385 0.0013
--3.3647 0.0016
--3.2909 0.0020
--3.2171 0.0026
--3.1432 0.0032
--3.0694 0.0041
--2.9956 0.0050
--2.9218 0.0062
--2.8479 0.0077
--2.7741 0.0094
--2.7003 0.0114
--2.6264 0.0138
--2.5526 0.0166
--2.4788 0.0199
--2.4050 0.0237
--2.3311 0.0281
--2.2573 0.0331
--2.1835 0.0388
--2.1097 0.0453
--2.0358 0.0526
--1.9620 0.0607
--1.8882 0.0696
--1.8143 0.0795
--1.7405 0.0903
--1.6667 0.1021
--1.5929 0.1147
--1.5190 0.1282
--1.4452 0.1426
--1.3714 0.1578
--1.2976 0.1736
--1.2237 0.1900
--1.1499 0.2069
--1.0761 0.2241
--1.0022 0.2414
--0.9284 0.2587
--0.8546 0.2758
--0.7808 0.2924
--0.7069 0.3084
--0.6331 0.3236
--0.5593 0.3377
--0.4855 0.3506
--0.4116 0.3621
--0.3378 0.3719
--0.2640 0.3800
--0.1901 0.3863
--0.1163 0.3905
--0.0425 0.3927
-0.0313 0.3929
-0.1052 0.3910
-0.1790 0.3870
-0.2528 0.3811
-0.3266 0.3732
-0.4005 0.3636
-0.4743 0.3524
-0.5481 0.3397
-0.6220 0.3258
-0.6958 0.3108
-0.7696 0.2949
-0.8434 0.2783
-0.9173 0.2613
-0.9911 0.2440
-1.0649 0.2267
-1.1387 0.2095
-1.2126 0.1925
-1.2864 0.1760
-1.3602 0.1601
-1.4341 0.1449
-1.5079 0.1304
-1.5817 0.1167
-1.6555 0.1039
-1.7294 0.0920
-1.8032 0.0811
-1.8770 0.0711
-1.9508 0.0620
-2.0247 0.0537
-2.0985 0.0464
-2.1723 0.0398
-2.2462 0.0340
-2.3200 0.0288
-2.3938 0.0243
-2.4676 0.0205
-2.5415 0.0171
-2.6153 0.0142
-2.6891 0.0117
-2.7629 0.0097
-2.8368 0.0079
-2.9106 0.0064
-2.9844 0.0052
-3.0583 0.0042
-3.1321 0.0034
-3.2059 0.0027
-3.2797 0.0021
-3.3536 0.0017
-3.4274 0.0013
-3.5012 0.0010
-3.5750 0.0008
-3.6489 0.0006
-3.7227 0.0005
-3.7965 0.0004
-Gene3 1
-250 150
-2 1 3
-1 5
--4.3571 0.0001
--4.2762 0.0001
--4.1954 0.0001
--4.1145 0.0001
--4.0336 0.0002
--3.9527 0.0002
--3.8719 0.0003
--3.7910 0.0004
--3.7101 0.0006
--3.6293 0.0008
--3.5484 0.0010
--3.4675 0.0013
--3.3866 0.0018
--3.3058 0.0023
--3.2249 0.0029
--3.1440 0.0037
--3.0632 0.0047
--2.9823 0.0059
--2.9014 0.0074
--2.8205 0.0092
--2.7397 0.0113
--2.6588 0.0139
--2.5779 0.0170
--2.4971 0.0206
--2.4162 0.0248
--2.3353 0.0297
--2.2544 0.0354
--2.1736 0.0419
--2.0927 0.0493
--2.0118 0.0576
--1.9310 0.0669
--1.8501 0.0773
--1.7692 0.0887
--1.6883 0.1012
--1.6075 0.1147
--1.5266 0.1292
--1.4457 0.1447
--1.3648 0.1610
--1.2840 0.1781
--1.2031 0.1958
--1.1222 0.2139
--1.0414 0.2323
--0.9605 0.2507
--0.8796 0.2688
--0.7987 0.2866
--0.7179 0.3036
--0.6370 0.3197
--0.5561 0.3345
--0.4753 0.3479
--0.3944 0.3597
--0.3135 0.3695
--0.2326 0.3773
--0.1518 0.3828
--0.0709 0.3861
-0.0100 0.3870
-0.0908 0.3855
-0.1717 0.3817
-0.2526 0.3756
-0.3335 0.3673
-0.4143 0.3570
-0.4952 0.3449
-0.5761 0.3311
-0.6569 0.3160
-0.7378 0.2996
-0.8187 0.2824
-0.8996 0.2645
-0.9804 0.2463
-1.0613 0.2279
-1.1422 0.2095
-1.2230 0.1915
-1.3039 0.1740
-1.3848 0.1570
-1.4657 0.1409
-1.5465 0.1256
-1.6274 0.1114
-1.7083 0.0981
-1.7891 0.0859
-1.8700 0.0747
-1.9509 0.0646
-2.0318 0.0555
-2.1126 0.0474
-2.1935 0.0402
-2.2744 0.0340
-2.3552 0.0285
-2.4361 0.0237
-2.5170 0.0197
-2.5979 0.0162
-2.6787 0.0132
-2.7596 0.0108
-2.8405 0.0087
-2.9213 0.0070
-3.0022 0.0056
-3.0831 0.0044
-3.1640 0.0035
-3.2448 0.0027
-3.3257 0.0021
-3.4066 0.0016
-3.4874 0.0013
-3.5683 0.0010
-3.6492 0.0007
-3.7301 0.0006
-Phenotype 1
-250 150
-2 3 4
-0
--3.5574 0.0010
--3.4806 0.0013
--3.4037 0.0016
--3.3268 0.0021
--3.2499 0.0026
--3.1731 0.0033
--3.0962 0.0042
--3.0193 0.0052
--2.9425 0.0065
--2.8656 0.0080
--2.7887 0.0098
--2.7118 0.0120
--2.6350 0.0146
--2.5581 0.0176
--2.4812 0.0212
--2.4044 0.0253
--2.3275 0.0300
--2.2506 0.0354
--2.1737 0.0416
--2.0969 0.0486
--2.0200 0.0564
--1.9431 0.0651
--1.8663 0.0748
--1.7894 0.0854
--1.7125 0.0970
--1.6356 0.1096
--1.5588 0.1230
--1.4819 0.1374
--1.4050 0.1526
--1.3282 0.1685
--1.2513 0.1850
--1.1744 0.2021
--1.0975 0.2195
--1.0207 0.2370
--0.9438 0.2545
--0.8669 0.2718
--0.7901 0.2887
--0.7132 0.3049
--0.6363 0.3202
--0.5594 0.3344
--0.4826 0.3473
--0.4057 0.3587
--0.3288 0.3684
--0.2520 0.3763
--0.1751 0.3822
--0.0982 0.3860
--0.0213 0.3877
-0.0555 0.3872
-0.1324 0.3846
-0.2093 0.3798
-0.2861 0.3731
-0.3630 0.3644
-0.4399 0.3539
-0.5168 0.3418
-0.5936 0.3283
-0.6705 0.3136
-0.7474 0.2979
-0.8242 0.2813
-0.9011 0.2643
-0.9780 0.2468
-1.0549 0.2293
-1.1317 0.2118
-1.2086 0.1945
-1.2855 0.1777
-1.3623 0.1614
-1.4392 0.1458
-1.5161 0.1310
-1.5930 0.1170
-1.6698 0.1039
-1.7467 0.0918
-1.8236 0.0806
-1.9004 0.0704
-1.9773 0.0612
-2.0542 0.0529
-2.1311 0.0454
-2.2079 0.0388
-2.2848 0.0329
-2.3617 0.0278
-2.4385 0.0234
-2.5154 0.0195
-2.5923 0.0162
-2.6692 0.0134
-2.7460 0.0110
-2.8229 0.0090
-2.8998 0.0073
-2.9766 0.0059
-3.0535 0.0047
-3.1304 0.0038
-3.2073 0.0030
-3.2841 0.0024
-3.3610 0.0019
-3.4379 0.0015
-3.5147 0.0011
-3.5916 0.0009
-3.6685 0.0007
-3.7454 0.0005
-3.8222 0.0004
-3.8991 0.0003
-3.9760 0.0002
-4.0528 0.0002
-4.1297 0.0001
diff --git a/sourcecodes/data/old/example_sci_bk/Llunet_figure_new.txt b/sourcecodes/data/old/example_sci_bk/Llunet_figure_new.txt
deleted file mode 100644
index 7e6f0d97..00000000
--- a/sourcecodes/data/old/example_sci_bk/Llunet_figure_new.txt
+++ /dev/null
@@ -1,433 +0,0 @@
-1
-5
-1200 1200
-Genotype 0 0
-Gene1 120 200
-Gene2 0 400
-Gene3 120 600
-Phenotype 0 800
-Genotype 2
-250 150
-0
-2 2 4
-1.0000 1.0000
-Gene1 1
-250 150
-1 1
-1 3
--3.5013 0.0000
--3.4313 0.0000
--3.3613 0.0000
--3.2912 0.0000
--3.2212 0.0000
--3.1512 0.0000
--3.0811 0.0000
--3.0111 0.0000
--2.9411 0.0000
--2.8710 0.0000
--2.8010 0.0000
--2.7310 0.0000
--2.6609 0.0000
--2.5909 0.0000
--2.5209 0.0001
--2.4508 0.0002
--2.3808 0.0004
--2.3108 0.0007
--2.2407 0.0014
--2.1707 0.0026
--2.1007 0.0046
--2.0306 0.0079
--1.9606 0.0133
--1.8906 0.0217
--1.8205 0.0344
--1.7505 0.0529
--1.6805 0.0791
--1.6104 0.1147
--1.5404 0.1615
--1.4704 0.2207
--1.4003 0.2928
--1.3303 0.3771
--1.2603 0.4715
--1.1902 0.5723
--1.1202 0.6743
--1.0502 0.7713
--0.9801 0.8564
--0.9101 0.9232
--0.8401 0.9660
--0.7700 0.9813
--0.7000 0.9676
--0.6300 0.9263
--0.5599 0.8608
--0.4899 0.7765
--0.4199 0.6800
--0.3498 0.5781
--0.2798 0.4771
--0.2098 0.3822
--0.1397 0.2973
--0.0697 0.2244
-0.0003 0.1645
-0.0704 0.1170
-0.1404 0.0808
-0.2104 0.0542
-0.2805 0.0353
-0.3505 0.0223
-0.4205 0.0137
-0.4906 0.0081
-0.5606 0.0047
-0.6306 0.0026
-0.7007 0.0014
-0.7707 0.0008
-0.8407 0.0004
-0.9108 0.0002
-0.9808 0.0001
-1.0508 0.0000
-1.1209 0.0000
-1.1909 0.0000
-1.2609 0.0000
-1.3310 0.0000
-1.4010 0.0000
-1.4710 0.0000
-1.5411 0.0000
-1.6111 0.0000
-1.6811 0.0000
-1.7512 0.0000
-1.8212 0.0000
-1.8912 0.0000
-1.9613 0.0000
-2.0313 0.0000
-2.1013 0.0000
-2.1714 0.0000
-2.2414 0.0000
-2.3114 0.0000
-2.3815 0.0000
-2.4515 0.0000
-2.5215 0.0000
-2.5916 0.0000
-2.6616 0.0000
-2.7316 0.0000
-2.8017 0.0000
-2.8717 0.0000
-2.9417 0.0000
-3.0118 0.0000
-3.0818 0.0000
-3.1518 0.0000
-3.2219 0.0000
-3.2919 0.0000
-3.3619 0.0000
-3.4320 0.0000
-3.5020 0.0000
-Gene2 1
-250 150
-1 2
-2 4 5
--3.5862 0.0000
--3.5124 0.0000
--3.4385 0.0000
--3.3647 0.0000
--3.2909 0.0000
--3.2171 0.0001
--3.1432 0.0001
--3.0694 0.0002
--2.9956 0.0003
--2.9218 0.0005
--2.8479 0.0008
--2.7741 0.0012
--2.7003 0.0018
--2.6264 0.0028
--2.5526 0.0041
--2.4788 0.0060
--2.4050 0.0087
--2.3311 0.0124
--2.2573 0.0175
--2.1835 0.0242
--2.1097 0.0329
--2.0358 0.0441
--1.9620 0.0583
--1.8882 0.0759
--1.8143 0.0974
--1.7405 0.1230
--1.6667 0.1530
--1.5929 0.1874
--1.5190 0.2262
--1.4452 0.2689
--1.3714 0.3148
--1.2976 0.3631
--1.2237 0.4126
--1.1499 0.4617
--1.0761 0.5089
--1.0022 0.5525
--0.9284 0.5908
--0.8546 0.6224
--0.7808 0.6458
--0.7069 0.6600
--0.6331 0.6644
--0.5593 0.6588
--0.4855 0.6434
--0.4116 0.6190
--0.3378 0.5866
--0.2640 0.5475
--0.1901 0.5034
--0.1163 0.4558
--0.0425 0.4066
-0.0313 0.3573
-0.1052 0.3092
-0.1790 0.2636
-0.2528 0.2213
-0.3266 0.1830
-0.4005 0.1491
-0.4743 0.1197
-0.5481 0.0946
-0.6220 0.0736
-0.6958 0.0565
-0.7696 0.0426
-0.8434 0.0317
-0.9173 0.0233
-0.9911 0.0168
-1.0649 0.0119
-1.1387 0.0084
-1.2126 0.0058
-1.2864 0.0039
-1.3602 0.0026
-1.4341 0.0017
-1.5079 0.0011
-1.5817 0.0007
-1.6555 0.0005
-1.7294 0.0003
-1.8032 0.0002
-1.8770 0.0001
-1.9508 0.0001
-2.0247 0.0000
-2.0985 0.0000
-2.1723 0.0000
-2.2462 0.0000
-2.3200 0.0000
-2.3938 0.0000
-2.4676 0.0000
-2.5415 0.0000
-2.6153 0.0000
-2.6891 0.0000
-2.7629 0.0000
-2.8368 0.0000
-2.9106 0.0000
-2.9844 0.0000
-3.0583 0.0000
-3.1321 0.0000
-3.2059 0.0000
-3.2797 0.0000
-3.3536 0.0000
-3.4274 0.0000
-3.5012 0.0000
-3.5750 0.0000
-3.6489 0.0000
-3.7227 0.0000
-3.7965 0.0000
-Gene3 1
-250 150
-2 1 3
-1 5
--4.3571 0.0002
--4.2762 0.0002
--4.1954 0.0003
--4.1145 0.0004
--4.0336 0.0005
--3.9527 0.0007
--3.8719 0.0010
--3.7910 0.0013
--3.7101 0.0017
--3.6293 0.0022
--3.5484 0.0028
--3.4675 0.0036
--3.3866 0.0046
--3.3058 0.0059
--3.2249 0.0074
--3.1440 0.0093
--3.0632 0.0115
--2.9823 0.0143
--2.9014 0.0175
--2.8205 0.0214
--2.7397 0.0260
--2.6588 0.0313
--2.5779 0.0374
--2.4971 0.0445
--2.4162 0.0526
--2.3353 0.0617
--2.2544 0.0719
--2.1736 0.0833
--2.0927 0.0958
--2.0118 0.1095
--1.9310 0.1243
--1.8501 0.1403
--1.7692 0.1572
--1.6883 0.1750
--1.6075 0.1936
--1.5266 0.2127
--1.4457 0.2322
--1.3648 0.2518
--1.2840 0.2713
--1.2031 0.2904
--1.1222 0.3088
--1.0414 0.3263
--0.9605 0.3424
--0.8796 0.3570
--0.7987 0.3698
--0.7179 0.3806
--0.6370 0.3890
--0.5561 0.3951
--0.4753 0.3987
--0.3944 0.3996
--0.3135 0.3980
--0.2326 0.3937
--0.1518 0.3869
--0.0709 0.3778
-0.0100 0.3665
-0.0908 0.3532
-0.1717 0.3381
-0.2526 0.3216
-0.3335 0.3039
-0.4143 0.2852
-0.4952 0.2660
-0.5761 0.2464
-0.6569 0.2268
-0.7378 0.2074
-0.8187 0.1884
-0.8996 0.1700
-0.9804 0.1524
-1.0613 0.1358
-1.1422 0.1201
-1.2230 0.1056
-1.3039 0.0922
-1.3848 0.0800
-1.4657 0.0690
-1.5465 0.0591
-1.6274 0.0502
-1.7083 0.0425
-1.7891 0.0357
-1.8700 0.0297
-1.9509 0.0246
-2.0318 0.0203
-2.1126 0.0166
-2.1935 0.0135
-2.2744 0.0109
-2.3552 0.0087
-2.4361 0.0070
-2.5170 0.0055
-2.5979 0.0043
-2.6787 0.0034
-2.7596 0.0026
-2.8405 0.0020
-2.9213 0.0015
-3.0022 0.0012
-3.0831 0.0009
-3.1640 0.0007
-3.2448 0.0005
-3.3257 0.0004
-3.4066 0.0003
-3.4874 0.0002
-3.5683 0.0001
-3.6492 0.0001
-3.7301 0.0001
-Phenotype 1
-250 150
-2 3 4
-0
--3.5574 0.0004
--3.4806 0.0006
--3.4037 0.0008
--3.3268 0.0012
--3.2499 0.0016
--3.1731 0.0022
--3.0962 0.0030
--3.0193 0.0040
--2.9425 0.0054
--2.8656 0.0071
--2.7887 0.0093
--2.7118 0.0121
--2.6350 0.0155
--2.5581 0.0198
--2.4812 0.0250
--2.4044 0.0313
--2.3275 0.0389
--2.2506 0.0479
--2.1737 0.0584
--2.0969 0.0706
--2.0200 0.0846
--1.9431 0.1005
--1.8663 0.1184
--1.7894 0.1381
--1.7125 0.1597
--1.6356 0.1831
--1.5588 0.2081
--1.4819 0.2343
--1.4050 0.2615
--1.3282 0.2893
--1.2513 0.3173
--1.1744 0.3448
--1.0975 0.3714
--1.0207 0.3966
--0.9438 0.4197
--0.8669 0.4402
--0.7901 0.4576
--0.7132 0.4716
--0.6363 0.4816
--0.5594 0.4875
--0.4826 0.4891
--0.4057 0.4864
--0.3288 0.4794
--0.2520 0.4684
--0.1751 0.4535
--0.0982 0.4353
--0.0213 0.4140
-0.0555 0.3904
-0.1324 0.3648
-0.2093 0.3379
-0.2861 0.3102
-0.3630 0.2822
-0.4399 0.2545
-0.5168 0.2275
-0.5936 0.2016
-0.6705 0.1770
-0.7474 0.1541
-0.8242 0.1329
-0.9011 0.1136
-0.9780 0.0963
-1.0549 0.0809
-1.1317 0.0673
-1.2086 0.0556
-1.2855 0.0455
-1.3623 0.0368
-1.4392 0.0296
-1.5161 0.0236
-1.5930 0.0186
-1.6698 0.0146
-1.7467 0.0113
-1.8236 0.0087
-1.9004 0.0066
-1.9773 0.0050
-2.0542 0.0037
-2.1311 0.0028
-2.2079 0.0020
-2.2848 0.0015
-2.3617 0.0011
-2.4385 0.0008
-2.5154 0.0005
-2.5923 0.0004
-2.6692 0.0003
-2.7460 0.0002
-2.8229 0.0001
-2.8998 0.0001
-2.9766 0.0001
-3.0535 0.0000
-3.1304 0.0000
-3.2073 0.0000
-3.2841 0.0000
-3.3610 0.0000
-3.4379 0.0000
-3.5147 0.0000
-3.5916 0.0000
-3.6685 0.0000
-3.7454 0.0000
-3.8222 0.0000
-3.8991 0.0000
-3.9760 0.0000
-4.0528 0.0000
-4.1297 0.0000
diff --git a/sourcecodes/data/old/example_sci_bk/Llunlevels.txt b/sourcecodes/data/old/example_sci_bk/Llunlevels.txt
deleted file mode 100644
index 714e56bd..00000000
--- a/sourcecodes/data/old/example_sci_bk/Llunlevels.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-Genotype 1 2
-
diff --git a/sourcecodes/data/old/example_sci_bk/Llunnode.txt b/sourcecodes/data/old/example_sci_bk/Llunnode.txt
deleted file mode 100644
index 7ed6ff82..00000000
--- a/sourcecodes/data/old/example_sci_bk/Llunnode.txt
+++ /dev/null
@@ -1 +0,0 @@
-5
diff --git a/sourcecodes/data/old/example_sci_bk/Llunrows.txt b/sourcecodes/data/old/example_sci_bk/Llunrows.txt
deleted file mode 100644
index c15fb720..00000000
--- a/sourcecodes/data/old/example_sci_bk/Llunrows.txt
+++ /dev/null
@@ -1 +0,0 @@
-501
diff --git a/sourcecodes/data/old/example_sci_bk/Lluparent.txt b/sourcecodes/data/old/example_sci_bk/Lluparent.txt
deleted file mode 100644
index b8626c4c..00000000
--- a/sourcecodes/data/old/example_sci_bk/Lluparent.txt
+++ /dev/null
@@ -1 +0,0 @@
-4
diff --git a/sourcecodes/data/old/example_sci_bk/Llustructure_input.txt b/sourcecodes/data/old/example_sci_bk/Llustructure_input.txt
deleted file mode 100644
index bcf72d97..00000000
--- a/sourcecodes/data/old/example_sci_bk/Llustructure_input.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-Genotype Gene3 Gene2 Phenotype Gene1
-0 1 0 0 1
-0 0 0 1 0
-0 1 0 1 0
-0 0 0 0 0
-0 0 1 0 0
diff --git a/sourcecodes/data/old/example_sci_bk/Llustructure_input_temp.txt b/sourcecodes/data/old/example_sci_bk/Llustructure_input_temp.txt
deleted file mode 100644
index 95aa7a5d..00000000
--- a/sourcecodes/data/old/example_sci_bk/Llustructure_input_temp.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-Genotype Gene3 Gene2 Phenotype Gene1
-0.000000 0.999929 0.183248 0.000431 1.000000
-0.000000 0.000000 0.000000 1.000000 0.000000
-0.000000 0.935752 0.000000 1.000000 0.000000
-0.000000 0.000000 0.000000 0.000000 0.000000
-0.000000 0.053385 0.881001 0.156255 0.000000
diff --git a/sourcecodes/data/old/example_sci_bk/Llustructure_old.txt b/sourcecodes/data/old/example_sci_bk/Llustructure_old.txt
deleted file mode 100644
index 5b464577..00000000
--- a/sourcecodes/data/old/example_sci_bk/Llustructure_old.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-Genotype 0.4860 0.5140
-Gene3 0.0001 0.0001 0.0001 0.0001 0.0002 0.0002 0.0003 0.0004 0.0006 0.0008 0.0010 0.0013 0.0018 0.0023 0.0029 0.0037 0.0047 0.0059 0.0074 0.0092 0.0113 0.0139 0.0170 0.0206 0.0248 0.0297 0.0354 0.0419 0.0493 0.0576 0.0669 0.0773 0.0887 0.1012 0.1147 0.1292 0.1447 0.1610 0.1781 0.1958 0.2139 0.2323 0.2507 0.2688 0.2866 0.3036 0.3197 0.3345 0.3479 0.3597 0.3695 0.3773 0.3828 0.3861 0.3870 0.3855 0.3817 0.3756 0.3673 0.3570 0.3449 0.3311 0.3160 0.2996 0.2824 0.2645 0.2463 0.2279 0.2095 0.1915 0.1740 0.1570 0.1409 0.1256 0.1114 0.0981 0.0859 0.0747 0.0646 0.0555 0.0474 0.0402 0.0340 0.0285 0.0237 0.0197 0.0162 0.0132 0.0108 0.0087 0.0070 0.0056 0.0044 0.0035 0.0027 0.0021 0.0016 0.0013 0.0010 0.0007 0.0006
-Gene1 0.0009 0.0012 0.0015 0.0019 0.0024 0.0030 0.0037 0.0046 0.0056 0.0069 0.0083 0.0101 0.0121 0.0145 0.0174 0.0206 0.0243 0.0286 0.0335 0.0389 0.0451 0.0520 0.0597 0.0682 0.0775 0.0876 0.0986 0.1105 0.1231 0.1366 0.1508 0.1657 0.1811 0.1971 0.2134 0.2300 0.2467 0.2633 0.2797 0.2956 0.3110 0.3256 0.3392 0.3517 0.3629 0.3726 0.3808 0.3873 0.3920 0.3948 0.3958 0.3948 0.3920 0.3872 0.3807 0.3726 0.3628 0.3516 0.3391 0.3254 0.3108 0.2955 0.2795 0.2631 0.2465 0.2299 0.2133 0.1969 0.1810 0.1655 0.1507 0.1365 0.1230 0.1103 0.0985 0.0875 0.0774 0.0681 0.0596 0.0520 0.0451 0.0389 0.0334 0.0286 0.0243 0.0206 0.0173 0.0145 0.0121 0.0101 0.0083 0.0068 0.0056 0.0046 0.0037 0.0030 0.0024 0.0019 0.0015 0.0012 0.0009
-Phenotype 0.0010 0.0013 0.0016 0.0021 0.0026 0.0033 0.0042 0.0052 0.0065 0.0080 0.0098 0.0120 0.0146 0.0176 0.0212 0.0253 0.0300 0.0354 0.0416 0.0486 0.0564 0.0651 0.0748 0.0854 0.0970 0.1096 0.1230 0.1374 0.1526 0.1685 0.1850 0.2021 0.2195 0.2370 0.2545 0.2718 0.2887 0.3049 0.3202 0.3344 0.3473 0.3587 0.3684 0.3763 0.3822 0.3860 0.3877 0.3872 0.3846 0.3798 0.3731 0.3644 0.3539 0.3418 0.3283 0.3136 0.2979 0.2813 0.2643 0.2468 0.2293 0.2118 0.1945 0.1777 0.1614 0.1458 0.1310 0.1170 0.1039 0.0918 0.0806 0.0704 0.0612 0.0529 0.0454 0.0388 0.0329 0.0278 0.0234 0.0195 0.0162 0.0134 0.0110 0.0090 0.0073 0.0059 0.0047 0.0038 0.0030 0.0024 0.0019 0.0015 0.0011 0.0009 0.0007 0.0005 0.0004 0.0003 0.0002 0.0002 0.0001
-Gene2 0.0008 0.0010 0.0013 0.0016 0.0020 0.0026 0.0032 0.0041 0.0050 0.0062 0.0077 0.0094 0.0114 0.0138 0.0166 0.0199 0.0237 0.0281 0.0331 0.0388 0.0453 0.0526 0.0607 0.0696 0.0795 0.0903 0.1021 0.1147 0.1282 0.1426 0.1578 0.1736 0.1900 0.2069 0.2241 0.2414 0.2587 0.2758 0.2924 0.3084 0.3236 0.3377 0.3506 0.3621 0.3719 0.3800 0.3863 0.3905 0.3927 0.3929 0.3910 0.3870 0.3811 0.3732 0.3636 0.3524 0.3397 0.3258 0.3108 0.2949 0.2783 0.2613 0.2440 0.2267 0.2095 0.1925 0.1760 0.1601 0.1449 0.1304 0.1167 0.1039 0.0920 0.0811 0.0711 0.0620 0.0537 0.0464 0.0398 0.0340 0.0288 0.0243 0.0205 0.0171 0.0142 0.0117 0.0097 0.0079 0.0064 0.0052 0.0042 0.0034 0.0027 0.0021 0.0017 0.0013 0.0010 0.0008 0.0006 0.0005 0.0004
diff --git a/sourcecodes/data/old/example_sci_bk/Lluthr.txt b/sourcecodes/data/old/example_sci_bk/Lluthr.txt
deleted file mode 100644
index 2eb3c4fe..00000000
--- a/sourcecodes/data/old/example_sci_bk/Lluthr.txt
+++ /dev/null
@@ -1 +0,0 @@
-0.5
diff --git a/sourcecodes/data/old/example_sci_bk/Llutier.txt b/sourcecodes/data/old/example_sci_bk/Llutier.txt
deleted file mode 100644
index da7084fb..00000000
--- a/sourcecodes/data/old/example_sci_bk/Llutier.txt
+++ /dev/null
@@ -1 +0,0 @@
-3,Tier1,1,Genotype,Tier2,3,Gene1,Gene2,Gene3,Tier3,1,Phenotype,
\ No newline at end of file
diff --git a/sourcecodes/data/old/example_sci_bk/Llutype.txt b/sourcecodes/data/old/example_sci_bk/Llutype.txt
deleted file mode 100644
index 9ea66ce4..00000000
--- a/sourcecodes/data/old/example_sci_bk/Llutype.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-Genotype Gene3 Gene2 Phenotype Gene1
-2 1 1 1 1
diff --git a/sourcecodes/data/old/example_sci_bk/Lluvar.txt b/sourcecodes/data/old/example_sci_bk/Lluvar.txt
deleted file mode 100644
index 56a6051c..00000000
--- a/sourcecodes/data/old/example_sci_bk/Lluvar.txt
+++ /dev/null
@@ -1 +0,0 @@
-1
\ No newline at end of file
diff --git a/sourcecodes/data/old/example_sci_bk/Lluvardata.txt b/sourcecodes/data/old/example_sci_bk/Lluvardata.txt
deleted file mode 100644
index 56a6051c..00000000
--- a/sourcecodes/data/old/example_sci_bk/Lluvardata.txt
+++ /dev/null
@@ -1 +0,0 @@
-1
\ No newline at end of file
diff --git a/sourcecodes/data/old/example_sci_bk/Lluvarname.txt b/sourcecodes/data/old/example_sci_bk/Lluvarname.txt
deleted file mode 100644
index 3fe283bd..00000000
--- a/sourcecodes/data/old/example_sci_bk/Lluvarname.txt
+++ /dev/null
@@ -1 +0,0 @@
-Genotype
\ No newline at end of file
diff --git a/sourcecodes/data/old/example_sci_bk/Lluwhite.txt b/sourcecodes/data/old/example_sci_bk/Lluwhite.txt
deleted file mode 100644
index 83e81b8b..00000000
--- a/sourcecodes/data/old/example_sci_bk/Lluwhite.txt
+++ /dev/null
@@ -1 +0,0 @@
-From To
diff --git a/sourcecodes/data/old/example_sci_bk/old/Llurun_evidencemodified.sh b/sourcecodes/data/old/example_sci_bk/old/Llurun_evidencemodified.sh
deleted file mode 100644
index ee0dde13..00000000
--- a/sourcecodes/data/old/example_sci_bk/old/Llurun_evidencemodified.sh
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/bin/sh
-# script for execution of deployed applications
-#
-# Sets up the MCR environment for the current $ARCH and executes
-# the specified command.
-#
-exe_name=$0
-exe_dir=`dirname "$0"`
-echo "------------------------------------------"
-if [ "x$1" = "x" ]; then
- echo Usage:
- echo $0 \ args
-else
- echo Setting up environment variables
- MCRROOT="$1"
- echo ---
- LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64;
- MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ;
- XAPPLRESDIR=${MCRROOT}/X11/app-defaults ;
- export LD_LIBRARY_PATH;
- export XAPPLRESDIR;
- echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH};
- shift 1
- args=
- while [ $# -gt 0 ]; do
- token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank
- args="${args} ${token}"
- shift
- done
- "${exe_dir}"/evidencemodified Llu
-fi
-exit
diff --git a/sourcecodes/data/old/example_sci_bk/old/Llurun_initialstructure.sh b/sourcecodes/data/old/example_sci_bk/old/Llurun_initialstructure.sh
deleted file mode 100644
index adde14dd..00000000
--- a/sourcecodes/data/old/example_sci_bk/old/Llurun_initialstructure.sh
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/bin/sh
-# script for execution of deployed applications
-#
-# Sets up the MCR environment for the current $ARCH and executes
-# the specified command.
-#
-exe_name=$0
-exe_dir=`dirname "$0"`
-echo "------------------------------------------"
-if [ "x$1" = "x" ]; then
- echo Usage:
- echo $0 \ args
-else
- echo Setting up environment variables
- MCRROOT="$1"
- echo ---
- LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64;
- MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ;
- XAPPLRESDIR=${MCRROOT}/X11/app-defaults ;
- export LD_LIBRARY_PATH;
- export XAPPLRESDIR;
- echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH};
- shift 1
- args=
- while [ $# -gt 0 ]; do
- token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank
- args="${args} ${token}"
- shift
- done
- "${exe_dir}"/initialstructure Llu
-fi
-exit
diff --git a/sourcecodes/data/old/examplecar/OVIban.txt b/sourcecodes/data/old/examplecar/OVIban.txt
deleted file mode 100644
index 83e81b8b..00000000
--- a/sourcecodes/data/old/examplecar/OVIban.txt
+++ /dev/null
@@ -1 +0,0 @@
-From To
diff --git a/sourcecodes/data/old/examplecar/OVIcontinuous_input.txt b/sourcecodes/data/old/examplecar/OVIcontinuous_input.txt
deleted file mode 100644
index 3a2846cf..00000000
--- a/sourcecodes/data/old/examplecar/OVIcontinuous_input.txt
+++ /dev/null
@@ -1,1004 +0,0 @@
-Starts Dist SpkQual MFuse Alter Starter StMotor BatAge Charging PlugVolt BatVolt Timing Cranks Plugs AirFilter Air Fuel GasTank GasFilter
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-2 1 2 1 1 1 1 5.34859 1 3 1 1 1 3 1 1 1 1 1
-1 1 2 1 1 1 1 4.14217 2 2 2 1 1 1 1 1 1 1 1
-1 1 1 1 1 1 1 4.68854 1 1 1 1 1 1 1 1 1 1 1
-2 1 1 1 1 1 1 2.47433 1 1 1 1 2 1 1 1 2 1 1
-2 1 2 1 1 1 1 4.04289 2 3 3 1 2 1 1 1 1 1 1
-1 1 2 1 1 1 1 4.64514 2 2 2 1 1 1 1 2 1 1 1
-2 1 1 1 1 1 1 3.52575 1 1 1 2 1 1 1 1 2 2 1
-2 1 2 1 1 2 1 0.0085396 2 3 3 1 2 1 1 1 2 2 1
-2 1 2 1 1 2 1 3.75628 2 3 3 1 2 1 1 1 1 1 1
-2 1 2 1 1 2 1 4.46408 2 3 3 1 2 1 2 2 1 1 1
-1 1 2 1 1 1 1 4.407 1 2 2 1 1 1 2 1 1 1 1
-2 1 2 1 1 2 1 12.9879 2 3 3 1 2 1 1 1 2 1 1
-2 1 2 1 1 2 1 5.42745 2 3 3 1 2 1 1 1 1 1 1
-2 1 2 1 1 2 1 2.27077 2 3 3 1 2 1 1 1 2 1 1
-1 1 1 1 1 1 1 4.19191 1 1 1 1 1 1 1 1 1 1 1
-1 1 1 1 1 1 1 1.43925 1 1 1 1 1 1 1 2 1 1 1
-1 1 1 1 1 1 1 4.98537 1 1 1 1 1 1 1 1 1 1 1
-2 1 2 1 1 2 1 1.71189 2 3 3 1 2 1 1 1 1 1 1
-2 1 2 1 1 2 1 4.91003 2 3 3 1 2 1 1 1 1 1 1
-2 1 2 1 2 2 1 0.809663 2 3 3 1 2 1 1 1 1 1 1
-2 1 2 1 1 2 1 3.78373 2 3 3 1 2 1 1 1 1 1 1
-2 1 1 1 1 1 1 1.64728 1 1 1 1 2 1 1 2 2 1 1
-2 1 2 1 1 2 1 0.977114 2 3 3 1 2 2 1 1 1 1 1
-2 1 2 1 1 2 1 4.78619 2 3 3 1 2 1 1 1 1 1 1
-2 1 1 1 1 2 1 4.88483 1 1 1 2 2 1 1 1 2 1 1
-1 1 1 1 1 1 1 0.0447191 1 1 1 1 1 1 1 1 1 1 1
-2 1 2 1 1 2 1 6.22958 2 3 3 1 2 1 1 1 1 1 1
-1 1 1 1 1 1 1 4.02524 1 1 1 1 1 1 1 1 1 1 1
-2 1 2 1 1 1 1 5.10729 1 3 2 1 1 1 1 1 2 2 1
-2 1 2 1 1 2 1 8.97099 2 3 3 1 2 3 1 1 1 1 1
-2 1 2 1 1 2 1 5.59486 2 3 3 1 2 1 1 1 1 1 1
-1 1 1 1 1 1 1 1.13786 1 1 1 1 1 1 1 1 1 1 1
-2 1 2 1 1 1 1 11.3795 1 2 2 1 1 1 1 1 1 1 1
-
diff --git a/sourcecodes/data/old/examplecar/OVIgraphviz.txt b/sourcecodes/data/old/examplecar/OVIgraphviz.txt
deleted file mode 100644
index 2aaaecb2..00000000
--- a/sourcecodes/data/old/examplecar/OVIgraphviz.txt
+++ /dev/null
@@ -1,70 +0,0 @@
-digraph G {
-size="10,10"; ratio = fill;
-node [shape=square,width=1.5];
-Dist -> BatAge;
-Dist -> Timing;
-Dist -> Plugs;
-Dist -> AirFilter;
-Dist -> GasTank;
-Dist -> GasFilter;
-SpkQual -> Starts;
-MFuse -> Starts;
-MFuse -> Dist;
-MFuse -> SpkQual;
-MFuse -> Starter;
-MFuse -> BatAge;
-MFuse -> Charging;
-MFuse -> Timing;
-MFuse -> Cranks;
-MFuse -> Plugs;
-MFuse -> AirFilter;
-MFuse -> Air;
-MFuse -> Fuel;
-MFuse -> GasTank;
-MFuse -> GasFilter;
-Alter -> Dist;
-Alter -> MFuse;
-Alter -> BatAge;
-Alter -> Charging;
-Alter -> Timing;
-Alter -> Plugs;
-Alter -> AirFilter;
-Alter -> Air;
-Alter -> GasTank;
-Alter -> GasFilter;
-Starter -> Cranks;
-StMotor -> MFuse;
-StMotor -> Alter;
-StMotor -> Starter;
-StMotor -> BatAge;
-StMotor -> Timing;
-StMotor -> Plugs;
-StMotor -> AirFilter;
-StMotor -> Air;
-StMotor -> Fuel;
-StMotor -> GasTank;
-StMotor -> GasFilter;
-PlugVolt -> Starts;
-PlugVolt -> Dist;
-PlugVolt -> SpkQual;
-PlugVolt -> MFuse;
-PlugVolt -> Alter;
-PlugVolt -> Starter;
-PlugVolt -> StMotor;
-PlugVolt -> Charging;
-PlugVolt -> Cranks;
-BatVolt -> Starts;
-BatVolt -> Dist;
-BatVolt -> SpkQual;
-BatVolt -> MFuse;
-BatVolt -> Alter;
-BatVolt -> Starter;
-BatVolt -> StMotor;
-BatVolt -> Charging;
-BatVolt -> PlugVolt;
-BatVolt -> Cranks;
-Plugs -> SpkQual;
-AirFilter -> Air;
-GasTank -> Fuel;
-GasFilter -> Fuel;
-}
\ No newline at end of file
diff --git a/sourcecodes/data/old/examplecar/OVIk.txt b/sourcecodes/data/old/examplecar/OVIk.txt
deleted file mode 100644
index d00491fd..00000000
--- a/sourcecodes/data/old/examplecar/OVIk.txt
+++ /dev/null
@@ -1 +0,0 @@
-1
diff --git a/sourcecodes/data/old/examplecar/OVImap.txt b/sourcecodes/data/old/examplecar/OVImap.txt
deleted file mode 100644
index eda717d2..00000000
--- a/sourcecodes/data/old/examplecar/OVImap.txt
+++ /dev/null
@@ -1,19 +0,0 @@
-Starts 3 0.432505 1.751249
-Dist 3 0.094441 1.008991
-SpkQual 2 0.434234 1.748252
-MFuse 2 0.031607 1.000999
-Alter 2 0.054690 1.002997
-Starter 2 0.490666 1.402597
-StMotor 2 0.070534 1.004995
-BatAge 2 2.948418 3.295892
-Charging 2 0.500244 1.497502
-PlugVolt 2 0.908145 2.090909
-BatVolt 2 0.914876 1.999001
-Timing 2 0.293230 1.094905
-Cranks 2 0.500010 1.515485
-Plugs 2 0.819700 1.518482
-AirFilter 3 0.294607 1.095904
-Air 2 0.375671 1.169830
-Fuel 2 0.416982 1.223776
-GasTank 2 0.295974 1.096903
-GasFilter 1 0.164975 1.027972
diff --git a/sourcecodes/data/old/examplecar/OVImapdata.txt b/sourcecodes/data/old/examplecar/OVImapdata.txt
deleted file mode 100644
index d1eac895..00000000
--- a/sourcecodes/data/old/examplecar/OVImapdata.txt
+++ /dev/null
@@ -1 +0,0 @@
-BatVolt PlugVolt StMotor Alter MFuse Charging Starter Cranks Dist GasFilter GasTank Fuel AirFilter Air Plugs SpkQual Starts Timing BatAge
diff --git a/sourcecodes/data/old/examplecar/OVIname.txt b/sourcecodes/data/old/examplecar/OVIname.txt
deleted file mode 100644
index e7901e87..00000000
--- a/sourcecodes/data/old/examplecar/OVIname.txt
+++ /dev/null
@@ -1 +0,0 @@
-Starts Dist SpkQual MFuse Alter Starter StMotor BatAge Charging PlugVolt BatVolt Timing Cranks Plugs AirFilter Air Fuel GasTank GasFilter
diff --git a/sourcecodes/data/old/examplecar/OVInet_figure.txt b/sourcecodes/data/old/examplecar/OVInet_figure.txt
deleted file mode 100644
index ceed746e..00000000
--- a/sourcecodes/data/old/examplecar/OVInet_figure.txt
+++ /dev/null
@@ -1,237 +0,0 @@
-19
-2100 1800
-BatVolt 788 0
-PlugVolt 998 180
-StMotor 788 360
-Alter 998 540
-MFuse 788 720
-Charging 472 900
-Starter 998 900
-Cranks 0 1080
-Dist 1523 900
-GasFilter 263 1080
-GasTank 525 1080
-Fuel 472 1260
-AirFilter 788 1080
-Air 998 1260
-Plugs 1050 1080
-SpkQual 1523 1260
-Starts 788 1440
-Timing 1313 1080
-BatAge 1575 1080
-BatVolt 3
-250 150
-0
-10 2 3 4 5 6 7 8 9 16 17
-1 0.4184
-2 0.1639
-3 0.4177
-PlugVolt 3
-250 150
-1 1
-9 3 4 5 6 7 8 9 16 17
-1 0.3706
-2 0.1678
-3 0.4616
-StMotor 2
-250 150
-2 1 2
-11 4 5 7 10 11 12 13 14 15 18 19
-1 0.9955
-2 0.0045
-Alter 2
-250 150
-3 1 2 3
-10 5 6 9 10 11 13 14 15 18 19
-1 0.9970
-2 0.0030
-MFuse 2
-250 150
-4 1 2 3 4
-14 6 7 8 9 10 11 12 13 14 15 16 17 18 19
-1 0.9990
-2 0.0010
-Charging 2
-250 150
-4 1 2 4 5
-0
-1 0.5024
-2 0.4976
-Starter 2
-250 150
-4 1 2 3 5
-1 8
-1 0.5977
-2 0.4023
-Cranks 2
-250 150
-4 1 2 5 7
-0
-1 0.4848
-2 0.5152
-Dist 2
-250 150
-4 1 2 4 5
-6 10 11 13 15 18 19
-1 0.9910
-2 0.0090
-GasFilter 2
-250 150
-4 3 4 5 9
-1 12
-1 0.9725
-2 0.0275
-GasTank 2
-250 150
-4 3 4 5 9
-1 12
-1 0.9031
-2 0.0969
-Fuel 2
-250 150
-4 3 5 10 11
-0
-1 0.7756
-2 0.2244
-AirFilter 2
-250 150
-4 3 4 5 9
-1 14
-1 0.9040
-2 0.0960
-Air 2
-250 150
-4 3 4 5 13
-0
-1 0.8301
-2 0.1699
-Plugs 3
-250 150
-4 3 4 5 9
-1 16
-1 0.6922
-2 0.0970
-3 0.2109
-SpkQual 2
-250 150
-4 1 2 5 15
-1 17
-1 0.2568
-2 0.7432
-Starts 2
-250 150
-4 1 2 5 16
-0
-1 0.2497
-2 0.7503
-Timing 2
-250 150
-4 3 4 5 9
-0
-1 0.9053
-2 0.0947
-BatAge 1
-250 150
-4 3 4 5 9
-0
--2.1178 0.0437
--2.0287 0.0524
--1.9396 0.0623
--1.8505 0.0736
--1.7614 0.0862
--1.6723 0.1001
--1.5832 0.1155
--1.4941 0.1321
--1.4050 0.1499
--1.3159 0.1689
--1.2268 0.1888
--1.1377 0.2093
--1.0486 0.2303
--0.9595 0.2515
--0.8704 0.2725
--0.7813 0.2929
--0.6922 0.3124
--0.6031 0.3306
--0.5140 0.3471
--0.4249 0.3617
--0.3358 0.3740
--0.2467 0.3836
--0.1576 0.3905
--0.0685 0.3944
-0.0206 0.3952
-0.1097 0.3930
-0.1988 0.3877
-0.2879 0.3795
-0.3770 0.3687
-0.4661 0.3553
-0.5552 0.3398
-0.6443 0.3225
-0.7334 0.3036
-0.8225 0.2837
-0.9116 0.2629
-1.0007 0.2419
-1.0898 0.2207
-1.1789 0.1999
-1.2680 0.1796
-1.3571 0.1601
-1.4462 0.1417
-1.5353 0.1243
-1.6244 0.1083
-1.7135 0.0936
-1.8026 0.0803
-1.8917 0.0683
-1.9808 0.0576
-2.0699 0.0483
-2.1590 0.0401
-2.2481 0.0331
-2.3372 0.0271
-2.4263 0.0220
-2.5154 0.0177
-2.6045 0.0142
-2.6936 0.0112
-2.7827 0.0088
-2.8718 0.0069
-2.9609 0.0054
-3.0500 0.0041
-3.1391 0.0031
-3.2282 0.0024
-3.3173 0.0018
-3.4064 0.0013
-3.4954 0.0010
-3.5845 0.0007
-3.6736 0.0005
-3.7627 0.0004
-3.8518 0.0003
-3.9409 0.0002
-4.0300 0.0001
-4.1191 0.0001
-4.2082 0.0001
-4.2973 0.0000
-4.3864 0.0000
-4.4755 0.0000
-4.5646 0.0000
-4.6537 0.0000
-4.7428 0.0000
-4.8319 0.0000
-4.9210 0.0000
-5.0101 0.0000
-5.0992 0.0000
-5.1883 0.0000
-5.2774 0.0000
-5.3665 0.0000
-5.4556 0.0000
-5.5447 0.0000
-5.6338 0.0000
-5.7229 0.0000
-5.8120 0.0000
-5.9011 0.0000
-5.9902 0.0000
-6.0793 0.0000
-6.1684 0.0000
-6.2575 0.0000
-6.3466 0.0000
-6.4357 0.0000
-6.5248 0.0000
-6.6139 0.0000
-6.7030 0.0000
-6.7921 0.0000
diff --git a/sourcecodes/data/old/examplecar/OVInet_figure_new.txt b/sourcecodes/data/old/examplecar/OVInet_figure_new.txt
deleted file mode 100644
index bd2ec975..00000000
--- a/sourcecodes/data/old/examplecar/OVInet_figure_new.txt
+++ /dev/null
@@ -1,138 +0,0 @@
-19
-19
-2100 1800
-BatVolt 788 0
-PlugVolt 998 180
-StMotor 788 360
-Alter 998 540
-MFuse 788 720
-Charging 472 900
-Starter 998 900
-Cranks 0 1080
-Dist 1523 900
-GasFilter 263 1080
-GasTank 525 1080
-Fuel 472 1260
-AirFilter 788 1080
-Air 998 1260
-Plugs 1050 1080
-SpkQual 1523 1260
-Starts 788 1440
-Timing 1313 1080
-BatAge 1575 1080
-BatVolt 3
-250 150
-0
-10 2 3 4 5 6 7 8 9 16 17
-1 0.4186
-2 0.1642
-3 0.4172
-PlugVolt 3
-250 150
-1 1
-9 3 4 5 6 7 8 9 16 17
-1 0.3716
-2 0.1684
-3 0.4600
-StMotor 2
-250 150
-2 1 2
-11 4 5 7 10 11 12 13 14 15 18 19
-1 0.9982
-2 0.0018
-Alter 2
-250 150
-3 1 2 3
-10 5 6 9 10 11 13 14 15 18 19
-1 0.9985
-2 0.0015
-MFuse 2
-250 150
-4 1 2 3 4
-14 6 7 8 9 10 11 12 13 14 15 16 17 18 19
-1 1.0000
-2 0.0000
-Charging 2
-250 150
-4 1 2 4 5
-0
-1 0.5027
-2 0.4973
-Starter 2
-250 150
-4 1 2 3 5
-1 8
-1 0.5996
-2 0.4004
-Cranks 2
-250 150
-4 1 2 5 7
-0
-1 0.4861
-2 0.5139
-Dist 2
-250 150
-4 1 2 4 5
-6 10 11 13 15 18 19
-1 0.9948
-2 0.0052
-GasFilter 2
-250 150
-4 3 4 5 9
-1 12
-1 0.9736
-2 0.0264
-GasTank 2
-250 150
-4 3 4 5 9
-1 12
-1 0.9048
-2 0.0952
-Fuel 2
-250 150
-4 3 5 10 11
-0
-1 0.7770
-2 0.2230
-AirFilter 2
-250 150
-4 3 4 5 9
-1 14
-1 0.9045
-2 0.0955
-Air 2
-250 150
-4 3 4 5 13
-0
-1 0.8304
-2 0.1696
-Plugs 3
-250 150
-4 3 4 5 9
-1 16
-1 0.6923
-2 0.0968
-3 0.2108
-SpkQual 2
-250 150
-4 1 2 5 15
-1 17
-1 0.2573
-2 0.7427
-Starts 2
-250 150
-4 1 2 5 16
-0
-1 0.2504
-2 0.7496
-Timing 2
-250 150
-4 3 4 5 9
-0
-1 0.9080
-2 0.0920
-BatAge 1
-250 150
-4 3 4 5 9
-0
--1.3159 1.0000
diff --git a/sourcecodes/data/old/examplecar/OVInnode.txt b/sourcecodes/data/old/examplecar/OVInnode.txt
deleted file mode 100644
index d6b24041..00000000
--- a/sourcecodes/data/old/examplecar/OVInnode.txt
+++ /dev/null
@@ -1 +0,0 @@
-19
diff --git a/sourcecodes/data/old/examplecar/OVInrows.txt b/sourcecodes/data/old/examplecar/OVInrows.txt
deleted file mode 100644
index 7d802a3e..00000000
--- a/sourcecodes/data/old/examplecar/OVInrows.txt
+++ /dev/null
@@ -1 +0,0 @@
-1002
diff --git a/sourcecodes/data/old/examplecar/OVIparent.txt b/sourcecodes/data/old/examplecar/OVIparent.txt
deleted file mode 100644
index b8626c4c..00000000
--- a/sourcecodes/data/old/examplecar/OVIparent.txt
+++ /dev/null
@@ -1 +0,0 @@
-4
diff --git a/sourcecodes/data/old/examplecar/OVIstructure_input.txt b/sourcecodes/data/old/examplecar/OVIstructure_input.txt
deleted file mode 100644
index cad732f3..00000000
--- a/sourcecodes/data/old/examplecar/OVIstructure_input.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-Starts Dist SpkQual MFuse Alter Starter StMotor BatAge Charging PlugVolt BatVolt Timing Cranks Plugs AirFilter Air Fuel GasTank GasFilter
-0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 1 0 0 0 1 0 1 1 0 0 1 1
-1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-1 1 1 0 0 1 0 1 1 0 0 1 1 1 1 1 1 1 1
-0 1 0 1 0 0 0 1 1 0 0 1 0 1 1 1 0 1 1
-0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
-0 0 0 1 1 1 0 1 0 0 0 1 0 1 1 1 1 1 1
-0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-1 1 1 1 1 1 1 0 1 0 0 0 1 0 0 0 0 0 0
-1 1 1 1 1 1 1 0 1 1 0 0 1 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
-0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
-0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
diff --git a/sourcecodes/data/old/examplecar/OVIstructure_input_temp.txt b/sourcecodes/data/old/examplecar/OVIstructure_input_temp.txt
deleted file mode 100644
index 09d40aa3..00000000
--- a/sourcecodes/data/old/examplecar/OVIstructure_input_temp.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-Starts Dist SpkQual MFuse Alter Starter StMotor BatAge Charging PlugVolt BatVolt Timing Cranks Plugs AirFilter Air Fuel GasTank GasFilter
-0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
-0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 1.000000 0.000000 0.000000 1.000000 1.000000
-1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
-1.000000 1.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 1.000000 0.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000
-0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000
-0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
-0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000
-0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
-0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
-1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
-1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
-0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
-0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
-0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
-0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000
-0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
-0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
-0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000
-0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000
diff --git a/sourcecodes/data/old/examplecar/OVIstructure_old.txt b/sourcecodes/data/old/examplecar/OVIstructure_old.txt
deleted file mode 100644
index 22f14ba3..00000000
--- a/sourcecodes/data/old/examplecar/OVIstructure_old.txt
+++ /dev/null
@@ -1,19 +0,0 @@
-Dist 0.9910 0.0090
-BatAge 0.0437 0.0524 0.0623 0.0736 0.0862 0.1001 0.1155 0.1321 0.1499 0.1689 0.1888 0.2093 0.2303 0.2515 0.2725 0.2929 0.3124 0.3306 0.3471 0.3617 0.3740 0.3836 0.3905 0.3944 0.3952 0.3930 0.3877 0.3795 0.3687 0.3553 0.3398 0.3225 0.3036 0.2837 0.2629 0.2419 0.2207 0.1999 0.1796 0.1601 0.1417 0.1243 0.1083 0.0936 0.0803 0.0683 0.0576 0.0483 0.0401 0.0331 0.0271 0.0220 0.0177 0.0142 0.0112 0.0088 0.0069 0.0054 0.0041 0.0031 0.0024 0.0018 0.0013 0.0010 0.0007 0.0005 0.0004 0.0003 0.0002 0.0001 0.0001 0.0001 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
-Timing 0.9053 0.0947
-Plugs 0.6922 0.0970 0.2109
-AirFilter 0.9040 0.0960
-GasTank 0.9031 0.0969
-GasFilter 0.9725 0.0275
-SpkQual 0.2568 0.7432
-Starts 0.2497 0.7503
-MFuse 0.9990 0.0010
-Starter 0.5977 0.4023
-Charging 0.5024 0.4976
-Cranks 0.4848 0.5152
-Air 0.8301 0.1699
-Fuel 0.7756 0.2244
-Alter 0.9970 0.0030
-StMotor 0.9955 0.0045
-PlugVolt 0.3706 0.1678 0.4616
-BatVolt 0.4184 0.1639 0.4177
diff --git a/sourcecodes/data/old/examplecar/OVIthr.txt b/sourcecodes/data/old/examplecar/OVIthr.txt
deleted file mode 100644
index 2eb3c4fe..00000000
--- a/sourcecodes/data/old/examplecar/OVIthr.txt
+++ /dev/null
@@ -1 +0,0 @@
-0.5
diff --git a/sourcecodes/data/old/examplecar/OVItype.txt b/sourcecodes/data/old/examplecar/OVItype.txt
deleted file mode 100644
index 0b76081c..00000000
--- a/sourcecodes/data/old/examplecar/OVItype.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-Starts Dist SpkQual MFuse Alter Starter StMotor BatAge Charging PlugVolt BatVolt Timing Cranks Plugs AirFilter Air Fuel GasTank GasFilter
-2 2 2 2 2 2 2 1 2 3 3 2 2 3 2 2 2 2 2
diff --git a/sourcecodes/data/old/examplecar/OVIvar.txt b/sourcecodes/data/old/examplecar/OVIvar.txt
deleted file mode 100644
index dec2bf5d..00000000
--- a/sourcecodes/data/old/examplecar/OVIvar.txt
+++ /dev/null
@@ -1 +0,0 @@
-19
\ No newline at end of file
diff --git a/sourcecodes/data/old/examplecar/OVIvardata.txt b/sourcecodes/data/old/examplecar/OVIvardata.txt
deleted file mode 100644
index e595bf94..00000000
--- a/sourcecodes/data/old/examplecar/OVIvardata.txt
+++ /dev/null
@@ -1 +0,0 @@
--1.3159
\ No newline at end of file
diff --git a/sourcecodes/data/old/examplecar/OVIvarname.txt b/sourcecodes/data/old/examplecar/OVIvarname.txt
deleted file mode 100644
index 2453221d..00000000
--- a/sourcecodes/data/old/examplecar/OVIvarname.txt
+++ /dev/null
@@ -1 +0,0 @@
-BatAge
\ No newline at end of file
diff --git a/sourcecodes/data/old/examplecar/OVIwhite.txt b/sourcecodes/data/old/examplecar/OVIwhite.txt
deleted file mode 100644
index 83e81b8b..00000000
--- a/sourcecodes/data/old/examplecar/OVIwhite.txt
+++ /dev/null
@@ -1 +0,0 @@
-From To
diff --git a/sourcecodes/data/old/examplecar/old/OVIrun_evidencemodified.sh b/sourcecodes/data/old/examplecar/old/OVIrun_evidencemodified.sh
deleted file mode 100644
index dab5c39a..00000000
--- a/sourcecodes/data/old/examplecar/old/OVIrun_evidencemodified.sh
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/bin/sh
-# script for execution of deployed applications
-#
-# Sets up the MCR environment for the current $ARCH and executes
-# the specified command.
-#
-exe_name=$0
-exe_dir=`dirname "$0"`
-echo "------------------------------------------"
-if [ "x$1" = "x" ]; then
- echo Usage:
- echo $0 \ args
-else
- echo Setting up environment variables
- MCRROOT="$1"
- echo ---
- LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64;
- MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ;
- XAPPLRESDIR=${MCRROOT}/X11/app-defaults ;
- export LD_LIBRARY_PATH;
- export XAPPLRESDIR;
- echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH};
- shift 1
- args=
- while [ $# -gt 0 ]; do
- token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank
- args="${args} ${token}"
- shift
- done
- "${exe_dir}"/evidencemodified OVI
-fi
-exit
diff --git a/sourcecodes/data/old/examplecar/old/OVIrun_initialstructure.sh b/sourcecodes/data/old/examplecar/old/OVIrun_initialstructure.sh
deleted file mode 100644
index d47ae324..00000000
--- a/sourcecodes/data/old/examplecar/old/OVIrun_initialstructure.sh
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/bin/sh
-# script for execution of deployed applications
-#
-# Sets up the MCR environment for the current $ARCH and executes
-# the specified command.
-#
-exe_name=$0
-exe_dir=`dirname "$0"`
-echo "------------------------------------------"
-if [ "x$1" = "x" ]; then
- echo Usage:
- echo $0 \ args
-else
- echo Setting up environment variables
- MCRROOT="$1"
- echo ---
- LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64;
- MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ;
- XAPPLRESDIR=${MCRROOT}/X11/app-defaults ;
- export LD_LIBRARY_PATH;
- export XAPPLRESDIR;
- echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH};
- shift 1
- args=
- while [ $# -gt 0 ]; do
- token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank
- args="${args} ${token}"
- shift
- done
- "${exe_dir}"/initialstructure OVI
-fi
-exit
diff --git a/sourcecodes/data/old/examplezoo/fSfban.txt b/sourcecodes/data/old/examplezoo/fSfban.txt
deleted file mode 100644
index 9197eeec..00000000
--- a/sourcecodes/data/old/examplezoo/fSfban.txt
+++ /dev/null
@@ -1,261 +0,0 @@
-From To
-aquatic airborne
-aquatic venomous
-aquatic predator
-aquatic domestic
-airborne aquatic
-airborne venomous
-airborne predator
-airborne domestic
-venomous aquatic
-venomous airborne
-venomous predator
-venomous domestic
-predator aquatic
-predator airborne
-predator venomous
-predator domestic
-domestic aquatic
-domestic airborne
-domestic venomous
-domestic predator
-eggs aquatic
-eggs airborne
-eggs venomous
-eggs predator
-eggs domestic
-milk aquatic
-milk airborne
-milk venomous
-milk predator
-milk domestic
-backbone aquatic
-backbone airborne
-backbone venomous
-backbone predator
-backbone domestic
-breathes aquatic
-breathes airborne
-breathes venomous
-breathes predator
-breathes domestic
-catsize aquatic
-catsize airborne
-catsize venomous
-catsize predator
-catsize domestic
-tail aquatic
-tail airborne
-tail venomous
-tail predator
-tail domestic
-toothed aquatic
-toothed airborne
-toothed venomous
-toothed predator
-toothed domestic
-hair aquatic
-hair airborne
-hair venomous
-hair predator
-hair domestic
-feathers aquatic
-feathers airborne
-feathers venomous
-feathers predator
-feathers domestic
-fins aquatic
-fins airborne
-fins venomous
-fins predator
-fins domestic
-legs aquatic
-legs airborne
-legs venomous
-legs predator
-legs domestic
-type aquatic
-type airborne
-type venomous
-type predator
-type domestic
-eggs aquatic
-eggs airborne
-eggs venomous
-eggs predator
-eggs domestic
-milk aquatic
-milk airborne
-milk venomous
-milk predator
-milk domestic
-backbone aquatic
-backbone airborne
-backbone venomous
-backbone predator
-backbone domestic
-breathes aquatic
-breathes airborne
-breathes venomous
-breathes predator
-breathes domestic
-catsize eggs
-catsize milk
-catsize backbone
-catsize breathes
-tail eggs
-tail milk
-tail backbone
-tail breathes
-toothed eggs
-toothed milk
-toothed backbone
-toothed breathes
-hair eggs
-hair milk
-hair backbone
-hair breathes
-feathers eggs
-feathers milk
-feathers backbone
-feathers breathes
-fins eggs
-fins milk
-fins backbone
-fins breathes
-legs eggs
-legs milk
-legs backbone
-legs breathes
-type eggs
-type milk
-type backbone
-type breathes
-catsize tail
-catsize toothed
-catsize hair
-catsize feathers
-catsize fins
-catsize legs
-tail catsize
-tail toothed
-tail hair
-tail feathers
-tail fins
-tail legs
-toothed catsize
-toothed tail
-toothed hair
-toothed feathers
-toothed fins
-toothed legs
-hair catsize
-hair tail
-hair toothed
-hair feathers
-hair fins
-hair legs
-feathers catsize
-feathers tail
-feathers toothed
-feathers hair
-feathers fins
-feathers legs
-fins catsize
-fins tail
-fins toothed
-fins hair
-fins feathers
-fins legs
-legs catsize
-legs tail
-legs toothed
-legs hair
-legs feathers
-legs fins
-catsize aquatic
-catsize airborne
-catsize venomous
-catsize predator
-catsize domestic
-tail aquatic
-tail airborne
-tail venomous
-tail predator
-tail domestic
-toothed aquatic
-toothed airborne
-toothed venomous
-toothed predator
-toothed domestic
-hair aquatic
-hair airborne
-hair venomous
-hair predator
-hair domestic
-feathers aquatic
-feathers airborne
-feathers venomous
-feathers predator
-feathers domestic
-fins aquatic
-fins airborne
-fins venomous
-fins predator
-fins domestic
-legs aquatic
-legs airborne
-legs venomous
-legs predator
-legs domestic
-catsize eggs
-catsize milk
-catsize backbone
-catsize breathes
-tail eggs
-tail milk
-tail backbone
-tail breathes
-toothed eggs
-toothed milk
-toothed backbone
-toothed breathes
-hair eggs
-hair milk
-hair backbone
-hair breathes
-feathers eggs
-feathers milk
-feathers backbone
-feathers breathes
-fins eggs
-fins milk
-fins backbone
-fins breathes
-legs eggs
-legs milk
-legs backbone
-legs breathes
-type catsize
-type tail
-type toothed
-type hair
-type feathers
-type fins
-type legs
-type aquatic
-type airborne
-type venomous
-type predator
-type domestic
-type eggs
-type milk
-type backbone
-type breathes
-type catsize
-type tail
-type toothed
-type hair
-type feathers
-type fins
-type legs
diff --git a/sourcecodes/data/old/examplezoo/fSfcontinuous_input.txt b/sourcecodes/data/old/examplezoo/fSfcontinuous_input.txt
deleted file mode 100644
index 340ad4f6..00000000
--- a/sourcecodes/data/old/examplezoo/fSfcontinuous_input.txt
+++ /dev/null
@@ -1,104 +0,0 @@
-hair feathers eggs milk airborne aquatic predator toothed backbone breathes venomous fins legs tail domestic catsize type
-2 2 2 2 2 2 2 2 2 2 2 2 6 2 2 2 7
-1 1 2 1 1 2 2 2 2 1 1 2 1 2 1 1 4
-1 1 2 1 1 2 1 2 2 1 1 2 1 2 2 1 4
-1 1 2 1 1 2 2 2 2 1 1 2 1 2 1 1 4
-1 1 2 1 1 2 2 2 2 1 1 2 1 2 1 1 4
-1 1 2 1 1 1 2 1 1 1 1 1 1 1 1 1 7
-1 1 2 1 1 2 2 2 2 1 1 2 1 2 1 2 4
-1 1 1 2 1 2 2 2 2 2 1 2 1 2 1 2 1
-1 1 2 1 1 2 1 2 2 1 1 2 1 2 1 1 4
-1 1 2 1 1 2 2 2 2 1 1 2 1 2 1 1 4
-1 1 2 1 1 2 2 2 2 1 1 2 1 2 1 2 4
-1 1 2 1 1 2 2 2 2 1 1 2 1 2 1 1 4
-1 1 2 1 1 1 2 2 2 2 2 1 1 2 1 1 3
-1 1 1 2 1 2 2 2 2 2 1 2 1 2 1 2 1
-1 1 2 1 1 2 1 2 2 1 1 2 1 2 1 1 4
-2 1 1 2 1 2 2 2 2 2 1 2 1 1 1 2 1
-1 1 1 1 1 2 2 2 2 1 2 1 1 2 1 1 3
-1 1 2 1 1 2 2 1 1 1 2 1 1 1 1 1 7
-1 1 2 1 1 1 2 2 2 2 1 1 1 2 1 1 3
-1 1 2 1 1 1 1 1 1 2 1 1 1 1 1 1 7
-1 1 2 1 1 2 1 2 2 1 1 2 1 2 1 1 4
-1 1 2 1 1 2 2 2 2 1 2 2 1 2 1 2 4
-1 1 2 1 1 2 2 2 2 1 1 2 1 2 1 2 4
-1 1 2 1 1 1 1 1 1 2 1 1 1 1 1 1 7
-1 2 2 1 2 1 1 1 2 2 1 1 2 2 2 1 2
-1 2 2 1 2 1 2 1 2 2 1 1 2 2 1 1 2
-1 2 2 1 2 1 1 1 2 2 1 1 2 2 2 1 2
-1 2 2 1 2 2 1 1 2 2 1 1 2 2 1 1 2
-1 2 2 1 2 1 1 1 2 2 1 1 2 2 1 2 2
-2 1 1 2 2 1 1 2 2 2 1 1 2 2 1 1 1
-2 1 1 2 1 1 2 2 2 2 1 1 2 1 2 2 1
-2 1 1 2 1 1 1 2 2 2 1 1 2 1 1 2 1
-1 2 2 1 2 2 2 1 2 2 1 1 2 2 1 1 2
-1 2 2 1 2 1 2 1 2 2 1 1 2 2 1 1 2
-1 2 2 1 1 1 2 1 2 2 1 1 2 2 1 1 2
-1 2 2 1 2 1 1 1 2 2 1 1 2 2 1 1 2
-1 2 2 1 1 1 1 1 2 2 1 1 2 2 1 2 2
-1 2 2 1 2 1 1 1 2 2 1 1 2 2 2 1 2
-1 2 2 1 1 2 2 1 2 2 1 1 2 2 1 2 2
-1 2 2 1 2 1 1 1 2 2 1 1 2 2 1 1 2
-1 2 2 1 1 1 2 1 2 2 1 1 2 2 1 2 2
-2 1 1 2 1 2 2 2 2 2 1 2 2 2 1 2 1
-1 2 2 1 2 2 2 1 2 2 1 1 2 2 1 1 2
-1 2 2 1 2 2 2 1 2 2 1 1 2 2 1 1 2
-1 2 2 1 2 1 1 1 2 2 1 1 2 2 1 1 2
-2 1 1 2 1 1 1 2 2 2 1 1 2 2 1 1 1
-1 2 2 1 2 2 1 1 2 2 1 1 2 2 1 2 2
-2 1 1 2 2 1 1 2 2 2 1 1 2 2 1 1 1
-1 2 2 1 2 1 2 1 2 2 1 1 2 2 1 2 2
-2 1 1 2 1 1 1 2 2 2 1 1 2 2 1 2 1
-1 2 2 1 2 1 1 1 2 2 1 1 2 2 1 1 2
-2 1 1 2 1 1 2 2 2 2 1 1 3 1 1 2 1
-2 1 1 2 1 1 1 2 2 2 1 1 3 2 1 2 1
-2 1 1 2 1 1 2 2 2 2 1 1 3 1 1 2 1
-2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1
-2 1 1 2 1 1 1 2 2 2 1 1 3 2 1 2 1
-2 1 1 2 1 1 1 2 2 2 1 1 3 2 2 2 1
-2 1 1 2 1 1 1 2 2 2 1 1 3 1 2 1 1
-2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1
-1 1 2 1 1 2 2 1 1 1 1 1 3 1 1 1 7
-2 1 1 2 1 1 1 2 2 2 1 1 3 2 1 2 1
-2 1 1 2 1 1 1 2 2 2 1 1 3 2 1 2 1
-1 1 2 1 1 2 2 2 2 2 1 1 3 1 1 1 5
-1 1 2 1 1 2 2 2 2 2 2 1 3 1 1 1 5
-2 1 1 2 1 1 1 2 2 2 1 1 3 2 1 2 1
-2 1 1 2 1 1 1 2 2 2 1 1 3 2 2 2 1
-2 1 1 2 1 1 1 2 2 2 1 1 3 2 2 1 1
-2 1 1 2 1 1 1 2 2 2 1 1 3 2 1 1 1
-2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1
-2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1
-2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1
-2 1 1 2 1 2 2 2 2 2 1 1 3 2 1 2 1
-2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 1 1
-2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1
-1 1 2 1 1 2 2 2 2 2 1 1 3 2 1 1 5
-2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 1 1
-2 1 1 2 1 1 1 2 2 2 1 1 3 2 1 2 1
-2 1 2 2 1 2 2 1 2 2 1 1 3 2 1 2 1
-2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1
-2 1 1 2 1 1 1 2 2 2 1 1 3 2 2 2 1
-2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1
-2 1 1 2 1 1 2 2 2 2 1 1 3 2 2 2 1
-2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1
-2 1 1 2 1 1 1 2 2 2 1 1 3 2 2 2 1
-1 1 2 1 1 2 1 2 2 2 1 1 3 1 1 1 5
-1 1 2 1 1 1 1 1 2 2 1 1 3 2 1 2 3
-1 1 2 1 1 1 2 2 2 2 1 1 3 2 1 1 3
-2 1 1 2 1 1 1 2 2 2 1 1 3 2 1 1 1
-2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1
-1 1 2 1 1 2 2 1 1 1 1 1 4 1 1 1 7
-1 1 2 1 1 2 2 1 1 1 1 1 5 1 1 1 7
-1 1 2 1 1 1 1 1 1 2 1 1 5 1 1 1 6
-1 1 2 1 2 1 1 1 1 2 1 1 5 1 1 1 6
-2 1 2 1 2 1 1 1 1 2 2 1 5 1 2 1 6
-2 1 2 1 2 1 1 1 1 2 1 1 5 1 1 1 6
-1 1 2 1 2 1 2 1 1 2 1 1 5 1 1 1 6
-1 1 2 1 1 2 2 1 1 1 1 1 5 1 1 1 7
-2 1 2 1 2 1 1 1 1 2 1 1 5 1 1 1 6
-1 1 2 1 1 1 1 1 1 2 1 1 5 1 1 1 6
-2 1 2 1 2 1 1 1 1 2 2 1 5 1 1 1 6
-1 1 2 1 1 2 2 1 1 1 1 1 6 1 1 2 7
-1 1 1 1 1 1 2 1 1 2 2 1 6 2 1 1 7
-
diff --git a/sourcecodes/data/old/examplezoo/fSfgraphviz.txt b/sourcecodes/data/old/examplezoo/fSfgraphviz.txt
deleted file mode 100644
index 701801c6..00000000
--- a/sourcecodes/data/old/examplezoo/fSfgraphviz.txt
+++ /dev/null
@@ -1,61 +0,0 @@
-digraph G {
-size="10,10"; ratio = fill;
-node [shape=square,width=1.5];
-feathers -> type;
-eggs -> hair;
-eggs -> feathers;
-eggs -> toothed;
-eggs -> backbone;
-eggs -> breathes;
-eggs -> legs;
-eggs -> tail;
-eggs -> catsize;
-milk -> hair;
-milk -> feathers;
-milk -> toothed;
-milk -> backbone;
-milk -> breathes;
-milk -> legs;
-milk -> tail;
-milk -> catsize;
-milk -> type;
-airborne -> eggs;
-airborne -> milk;
-airborne -> backbone;
-airborne -> breathes;
-airborne -> catsize;
-aquatic -> eggs;
-aquatic -> milk;
-aquatic -> breathes;
-aquatic -> fins;
-backbone -> hair;
-backbone -> feathers;
-backbone -> toothed;
-backbone -> fins;
-backbone -> legs;
-backbone -> tail;
-backbone -> type;
-breathes -> hair;
-breathes -> toothed;
-breathes -> backbone;
-breathes -> fins;
-breathes -> legs;
-breathes -> catsize;
-breathes -> type;
-venomous -> hair;
-venomous -> feathers;
-venomous -> eggs;
-venomous -> milk;
-venomous -> toothed;
-venomous -> backbone;
-venomous -> breathes;
-venomous -> fins;
-venomous -> legs;
-venomous -> tail;
-venomous -> catsize;
-legs -> type;
-domestic -> eggs;
-domestic -> milk;
-domestic -> fins;
-domestic -> tail;
-}
\ No newline at end of file
diff --git a/sourcecodes/data/old/examplezoo/fSfk.txt b/sourcecodes/data/old/examplezoo/fSfk.txt
deleted file mode 100644
index f599e28b..00000000
--- a/sourcecodes/data/old/examplezoo/fSfk.txt
+++ /dev/null
@@ -1 +0,0 @@
-10
diff --git a/sourcecodes/data/old/examplezoo/fSfmap.txt b/sourcecodes/data/old/examplezoo/fSfmap.txt
deleted file mode 100644
index 4a123441..00000000
--- a/sourcecodes/data/old/examplezoo/fSfmap.txt
+++ /dev/null
@@ -1,17 +0,0 @@
-hair 2 0.496921 1.425743
-feathers 2 0.400495 1.198020
-eggs 2 0.495325 1.584158
-milk 2 0.493522 1.405941
-airborne 2 0.427750 1.237624
-aquatic 2 0.481335 1.356436
-predator 2 0.499505 1.554455
-toothed 2 0.491512 1.603960
-backbone 2 0.384605 1.821782
-breathes 2 0.407844 1.792079
-venomous 2 0.271410 1.079208
-fins 6 0.376013 1.168317
-legs 2 1.253194 2.544554
-tail 2 0.439397 1.742574
-domestic 2 0.336552 1.128713
-catsize 7 0.498314 1.435644
-type 2 2.102709 2.831683
diff --git a/sourcecodes/data/old/examplezoo/fSfmapdata.txt b/sourcecodes/data/old/examplezoo/fSfmapdata.txt
deleted file mode 100644
index 19d91997..00000000
--- a/sourcecodes/data/old/examplezoo/fSfmapdata.txt
+++ /dev/null
@@ -1 +0,0 @@
-domestic venomous predator aquatic airborne milk eggs breathes catsize backbone tail legs fins toothed feathers type hair
diff --git a/sourcecodes/data/old/examplezoo/fSfname.txt b/sourcecodes/data/old/examplezoo/fSfname.txt
deleted file mode 100644
index c68267c4..00000000
--- a/sourcecodes/data/old/examplezoo/fSfname.txt
+++ /dev/null
@@ -1 +0,0 @@
-hair feathers eggs milk airborne aquatic predator toothed backbone breathes venomous fins legs tail domestic catsize type
diff --git a/sourcecodes/data/old/examplezoo/fSfnet_figure.txt b/sourcecodes/data/old/examplezoo/fSfnet_figure.txt
deleted file mode 100644
index 0c8f9428..00000000
--- a/sourcecodes/data/old/examplezoo/fSfnet_figure.txt
+++ /dev/null
@@ -1,130 +0,0 @@
-17
-1800 1200
-domestic 43 0
-venomous 343 0
-predator 643 0
-aquatic 943 0
-airborne 1243 0
-milk 523 171
-eggs 1123 171
-breathes 643 343
-catsize 523 514
-backbone 1123 514
-tail 0 686
-legs 257 686
-fins 514 686
-toothed 771 686
-feathers 1029 686
-type 823 857
-hair 1286 686
-domestic 2
-250 150
-0
-4 6 7 11 13
-1 0.8672
-2 0.1328
-venomous 2
-250 150
-0
-11 6 7 8 9 10 11 12 13 14 15 17
-1 0.8860
-2 0.1140
-predator 2
-250 150
-0
-0
-1 0.4455
-2 0.5545
-aquatic 2
-250 150
-0
-4 6 7 8 13
-1 0.6726
-2 0.3274
-airborne 2
-250 150
-0
-5 6 7 8 9 10
-1 0.8149
-2 0.1851
-milk 2
-250 150
-4 1 2 4 5
-9 8 9 10 11 12 14 15 16 17
-1 0.4703
-2 0.5297
-eggs 2
-250 150
-4 1 2 4 5
-8 8 9 10 11 12 14 15 17
-1 0.4962
-2 0.5038
-breathes 2
-250 150
-5 2 4 5 6 7
-7 9 10 12 13 14 16 17
-1 0.1666
-2 0.8334
-catsize 2
-250 150
-5 2 5 6 7 8
-0
-1 0.4789
-2 0.5211
-backbone 2
-250 150
-5 2 5 6 7 8
-7 11 12 13 14 15 16 17
-1 0.1743
-2 0.8257
-tail 2
-250 150
-5 1 2 6 7 10
-0
-1 0.2426
-2 0.7574
-legs 6
-250 150
-5 2 6 7 8 10
-1 16
-1 0.1827
-2 0.2108
-3 0.4747
-4 0.0111
-5 0.0799
-6 0.0409
-fins 2
-250 150
-5 1 2 4 8 10
-0
-1 0.8751
-2 0.1249
-toothed 2
-250 150
-5 2 6 7 8 10
-0
-1 0.3799
-2 0.6201
-feathers 2
-250 150
-4 2 6 7 10
-1 16
-1 0.8693
-2 0.1307
-type 7
-250 150
-5 6 8 10 12 15
-0
-1 0.5297
-2 0.1307
-3 0.0476
-4 0.0854
-5 0.0323
-6 0.0578
-7 0.1165
-hair 2
-250 150
-5 2 6 7 8 10
-0
-1 0.4597
-2 0.5403
diff --git a/sourcecodes/data/old/examplezoo/fSfnnode.txt b/sourcecodes/data/old/examplezoo/fSfnnode.txt
deleted file mode 100644
index 98d9bcb7..00000000
--- a/sourcecodes/data/old/examplezoo/fSfnnode.txt
+++ /dev/null
@@ -1 +0,0 @@
-17
diff --git a/sourcecodes/data/old/examplezoo/fSfnrows.txt b/sourcecodes/data/old/examplezoo/fSfnrows.txt
deleted file mode 100644
index 257e5632..00000000
--- a/sourcecodes/data/old/examplezoo/fSfnrows.txt
+++ /dev/null
@@ -1 +0,0 @@
-102
diff --git a/sourcecodes/data/old/examplezoo/fSfparent.txt b/sourcecodes/data/old/examplezoo/fSfparent.txt
deleted file mode 100644
index 7ed6ff82..00000000
--- a/sourcecodes/data/old/examplezoo/fSfparent.txt
+++ /dev/null
@@ -1 +0,0 @@
-5
diff --git a/sourcecodes/data/old/examplezoo/fSfstructure_input.txt b/sourcecodes/data/old/examplezoo/fSfstructure_input.txt
deleted file mode 100644
index c49d600b..00000000
--- a/sourcecodes/data/old/examplezoo/fSfstructure_input.txt
+++ /dev/null
@@ -1,18 +0,0 @@
-hair feathers eggs milk airborne aquatic predator toothed backbone breathes venomous fins legs tail domestic catsize type
-0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
-1 1 0 0 0 0 0 1 1 1 0 0 1 1 0 1 0
-1 1 0 0 0 0 0 1 1 1 0 0 1 1 0 1 1
-0 0 1 1 0 0 0 0 1 1 0 0 0 0 0 1 0
-0 0 1 1 0 0 0 0 0 1 0 1 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-1 1 0 0 0 0 0 1 0 0 0 1 1 1 0 0 1
-1 0 0 0 0 0 0 1 1 0 0 1 1 0 0 1 1
-1 1 1 1 0 0 0 1 1 1 0 1 1 1 0 1 0
-0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
-0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-0 0 1 1 0 0 0 0 0 0 0 1 0 1 0 0 0
-0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
diff --git a/sourcecodes/data/old/examplezoo/fSfstructure_input_temp.txt b/sourcecodes/data/old/examplezoo/fSfstructure_input_temp.txt
deleted file mode 100644
index 8910aaee..00000000
--- a/sourcecodes/data/old/examplezoo/fSfstructure_input_temp.txt
+++ /dev/null
@@ -1,18 +0,0 @@
-hair feathers eggs milk airborne aquatic predator toothed backbone breathes venomous fins legs tail domestic catsize type
-0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
-0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000
-1.000000 0.800011 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 0.000000 0.000000 1.000000 1.000000 0.000000 1.000000 0.000000
-1.000000 1.000000 0.500003 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 0.000000 0.000000 1.000000 1.000000 0.000000 1.000000 1.000000
-0.000000 0.400004 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000
-0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000
-0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
-0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
-1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 0.000000 0.000000 1.000000
-0.800018 0.799985 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 1.000000 1.000000
-1.000000 1.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 0.000000 1.000000 0.000000
-0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
-0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000
-0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
-0.199982 0.000000 0.900015 0.900010 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000
-0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
-0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
diff --git a/sourcecodes/data/old/examplezoo/fSfstructure_old.txt b/sourcecodes/data/old/examplezoo/fSfstructure_old.txt
deleted file mode 100644
index bf00f5d5..00000000
--- a/sourcecodes/data/old/examplezoo/fSfstructure_old.txt
+++ /dev/null
@@ -1,16 +0,0 @@
-feathers 0.8693 0.1307
-type 0.5297 0.1307 0.0476 0.0854 0.0323 0.0578 0.1165
-eggs 0.4962 0.5038
-hair 0.4597 0.5403
-toothed 0.3799 0.6201
-backbone 0.1743 0.8257
-breathes 0.1666 0.8334
-legs 0.1827 0.2108 0.4747 0.0111 0.0799 0.0409
-tail 0.2426 0.7574
-catsize 0.4789 0.5211
-milk 0.4703 0.5297
-airborne 0.8149 0.1851
-aquatic 0.6726 0.3274
-fins 0.8751 0.1249
-venomous 0.8860 0.1140
-domestic 0.8672 0.1328
diff --git a/sourcecodes/data/old/examplezoo/fSfthr.txt b/sourcecodes/data/old/examplezoo/fSfthr.txt
deleted file mode 100644
index aec258df..00000000
--- a/sourcecodes/data/old/examplezoo/fSfthr.txt
+++ /dev/null
@@ -1 +0,0 @@
-0.8
diff --git a/sourcecodes/data/old/examplezoo/fSftier.txt b/sourcecodes/data/old/examplezoo/fSftier.txt
deleted file mode 100644
index ca417b31..00000000
--- a/sourcecodes/data/old/examplezoo/fSftier.txt
+++ /dev/null
@@ -1 +0,0 @@
-4,Tier1,5,aquatic,airborne,venomous,predator,domestic,Tier2,4,eggs,milk,backbone,breathes,Tier3,7,catsize,tail,toothed,hair,feathers,fins,legs,Tier4,1,type,
\ No newline at end of file
diff --git a/sourcecodes/data/old/examplezoo/fSftype.txt b/sourcecodes/data/old/examplezoo/fSftype.txt
deleted file mode 100644
index 41c0f73e..00000000
--- a/sourcecodes/data/old/examplezoo/fSftype.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-hair feathers eggs milk airborne aquatic predator toothed backbone breathes venomous fins legs tail domestic catsize type
-2 2 2 2 2 2 2 2 2 2 2 2 6 2 2 2 7
diff --git a/sourcecodes/data/old/examplezoo/fSfwhite.txt b/sourcecodes/data/old/examplezoo/fSfwhite.txt
deleted file mode 100644
index 83e81b8b..00000000
--- a/sourcecodes/data/old/examplezoo/fSfwhite.txt
+++ /dev/null
@@ -1 +0,0 @@
-From To
diff --git a/sourcecodes/data/old/examplezoo/old/fSfrun_initialstructure.sh b/sourcecodes/data/old/examplezoo/old/fSfrun_initialstructure.sh
deleted file mode 100644
index f20a9a29..00000000
--- a/sourcecodes/data/old/examplezoo/old/fSfrun_initialstructure.sh
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/bin/sh
-# script for execution of deployed applications
-#
-# Sets up the MCR environment for the current $ARCH and executes
-# the specified command.
-#
-exe_name=$0
-exe_dir=`dirname "$0"`
-echo "------------------------------------------"
-if [ "x$1" = "x" ]; then
- echo Usage:
- echo $0 \ args
-else
- echo Setting up environment variables
- MCRROOT="$1"
- echo ---
- LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64;
- MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ;
- XAPPLRESDIR=${MCRROOT}/X11/app-defaults ;
- export LD_LIBRARY_PATH;
- export XAPPLRESDIR;
- echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH};
- shift 1
- args=
- while [ $# -gt 0 ]; do
- token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank
- args="${args} ${token}"
- shift
- done
- "${exe_dir}"/initialstructure fSf
-fi
-exit
diff --git a/sourcecodes/data/old/examplezoo/standardized_data.txt b/sourcecodes/data/old/examplezoo/standardized_data.txt
deleted file mode 100644
index 0975061e..00000000
--- a/sourcecodes/data/old/examplezoo/standardized_data.txt
+++ /dev/null
@@ -1,102 +0,0 @@
-domestic venomous predator aquatic airborne milk eggs breathes catsize backbone tail legs fins toothed feathers type hair
-1 1 2 2 1 1 2 1 1 2 2 1 2 2 1 4 1
-2 1 1 2 1 1 2 1 1 2 2 1 2 2 1 4 1
-1 1 2 2 1 1 2 1 1 2 2 1 2 2 1 4 1
-1 1 2 2 1 1 2 1 1 2 2 1 2 2 1 4 1
-1 1 2 1 1 1 2 1 1 1 1 1 1 1 1 7 1
-1 1 2 2 1 1 2 1 2 2 2 1 2 2 1 4 1
-1 1 2 2 1 2 1 2 2 2 2 1 2 2 1 1 1
-1 1 1 2 1 1 2 1 1 2 2 1 2 2 1 4 1
-1 1 2 2 1 1 2 1 1 2 2 1 2 2 1 4 1
-1 1 2 2 1 1 2 1 2 2 2 1 2 2 1 4 1
-1 1 2 2 1 1 2 1 1 2 2 1 2 2 1 4 1
-1 2 2 1 1 1 2 2 1 2 2 1 1 2 1 3 1
-1 1 2 2 1 2 1 2 2 2 2 1 2 2 1 1 1
-1 1 1 2 1 1 2 1 1 2 2 1 2 2 1 4 1
-1 1 2 2 1 2 1 2 2 2 1 1 2 2 1 1 2
-1 2 2 2 1 1 1 1 1 2 2 1 1 2 1 3 1
-1 2 2 2 1 1 2 1 1 1 1 1 1 1 1 7 1
-1 1 2 1 1 1 2 2 1 2 2 1 1 2 1 3 1
-1 1 1 1 1 1 2 2 1 1 1 1 1 1 1 7 1
-1 1 1 2 1 1 2 1 1 2 2 1 2 2 1 4 1
-1 2 2 2 1 1 2 1 2 2 2 1 2 2 1 4 1
-1 1 2 2 1 1 2 1 2 2 2 1 2 2 1 4 1
-1 1 1 1 1 1 2 2 1 1 1 1 1 1 1 7 1
-2 1 1 1 2 1 2 2 1 2 2 2 1 1 2 2 1
-1 1 2 1 2 1 2 2 1 2 2 2 1 1 2 2 1
-2 1 1 1 2 1 2 2 1 2 2 2 1 1 2 2 1
-1 1 1 2 2 1 2 2 1 2 2 2 1 1 2 2 1
-1 1 1 1 2 1 2 2 2 2 2 2 1 1 2 2 1
-1 1 1 1 2 2 1 2 1 2 2 2 1 2 1 1 2
-2 1 2 1 1 2 1 2 2 2 1 2 1 2 1 1 2
-1 1 1 1 1 2 1 2 2 2 1 2 1 2 1 1 2
-1 1 2 2 2 1 2 2 1 2 2 2 1 1 2 2 1
-1 1 2 1 2 1 2 2 1 2 2 2 1 1 2 2 1
-1 1 2 1 1 1 2 2 1 2 2 2 1 1 2 2 1
-1 1 1 1 2 1 2 2 1 2 2 2 1 1 2 2 1
-1 1 1 1 1 1 2 2 2 2 2 2 1 1 2 2 1
-2 1 1 1 2 1 2 2 1 2 2 2 1 1 2 2 1
-1 1 2 2 1 1 2 2 2 2 2 2 1 1 2 2 1
-1 1 1 1 2 1 2 2 1 2 2 2 1 1 2 2 1
-1 1 2 1 1 1 2 2 2 2 2 2 1 1 2 2 1
-1 1 2 2 1 2 1 2 2 2 2 2 2 2 1 1 2
-1 1 2 2 2 1 2 2 1 2 2 2 1 1 2 2 1
-1 1 2 2 2 1 2 2 1 2 2 2 1 1 2 2 1
-1 1 1 1 2 1 2 2 1 2 2 2 1 1 2 2 1
-1 1 1 1 1 2 1 2 1 2 2 2 1 2 1 1 2
-1 1 1 2 2 1 2 2 2 2 2 2 1 1 2 2 1
-1 1 1 1 2 2 1 2 1 2 2 2 1 2 1 1 2
-1 1 2 1 2 1 2 2 2 2 2 2 1 1 2 2 1
-1 1 1 1 1 2 1 2 2 2 2 2 1 2 1 1 2
-1 1 1 1 2 1 2 2 1 2 2 2 1 1 2 2 1
-1 1 2 1 1 2 1 2 2 2 1 3 1 2 1 1 2
-1 1 1 1 1 2 1 2 2 2 2 3 1 2 1 1 2
-1 1 2 1 1 2 1 2 2 2 1 3 1 2 1 1 2
-1 1 2 1 1 2 1 2 2 2 2 3 1 2 1 1 2
-1 1 1 1 1 2 1 2 2 2 2 3 1 2 1 1 2
-2 1 1 1 1 2 1 2 2 2 2 3 1 2 1 1 2
-2 1 1 1 1 2 1 2 1 2 1 3 1 2 1 1 2
-1 1 2 1 1 2 1 2 2 2 2 3 1 2 1 1 2
-1 1 2 2 1 1 2 1 1 1 1 3 1 1 1 7 1
-1 1 1 1 1 2 1 2 2 2 2 3 1 2 1 1 2
-1 1 1 1 1 2 1 2 2 2 2 3 1 2 1 1 2
-1 1 2 2 1 1 2 2 1 2 1 3 1 2 1 5 1
-1 2 2 2 1 1 2 2 1 2 1 3 1 2 1 5 1
-1 1 1 1 1 2 1 2 2 2 2 3 1 2 1 1 2
-2 1 1 1 1 2 1 2 2 2 2 3 1 2 1 1 2
-2 1 1 1 1 2 1 2 1 2 2 3 1 2 1 1 2
-1 1 1 1 1 2 1 2 1 2 2 3 1 2 1 1 2
-1 1 2 1 1 2 1 2 2 2 2 3 1 2 1 1 2
-1 1 2 1 1 2 1 2 2 2 2 3 1 2 1 1 2
-1 1 2 1 1 2 1 2 2 2 2 3 1 2 1 1 2
-1 1 2 2 1 2 1 2 2 2 2 3 1 2 1 1 2
-1 1 2 1 1 2 1 2 1 2 2 3 1 2 1 1 2
-1 1 2 1 1 2 1 2 2 2 2 3 1 2 1 1 2
-1 1 2 2 1 1 2 2 1 2 2 3 1 2 1 5 1
-1 1 2 1 1 2 1 2 1 2 2 3 1 2 1 1 2
-1 1 1 1 1 2 1 2 2 2 2 3 1 2 1 1 2
-1 1 2 2 1 2 2 2 2 2 2 3 1 1 1 1 2
-1 1 2 1 1 2 1 2 2 2 2 3 1 2 1 1 2
-2 1 1 1 1 2 1 2 2 2 2 3 1 2 1 1 2
-1 1 2 1 1 2 1 2 2 2 2 3 1 2 1 1 2
-2 1 2 1 1 2 1 2 2 2 2 3 1 2 1 1 2
-1 1 2 1 1 2 1 2 2 2 2 3 1 2 1 1 2
-2 1 1 1 1 2 1 2 2 2 2 3 1 2 1 1 2
-1 1 1 2 1 1 2 2 1 2 1 3 1 2 1 5 1
-1 1 1 1 1 1 2 2 2 2 2 3 1 1 1 3 1
-1 1 2 1 1 1 2 2 1 2 2 3 1 2 1 3 1
-1 1 1 1 1 2 1 2 1 2 2 3 1 2 1 1 2
-1 1 2 1 1 2 1 2 2 2 2 3 1 2 1 1 2
-1 1 2 2 1 1 2 1 1 1 1 4 1 1 1 7 1
-1 1 2 2 1 1 2 1 1 1 1 5 1 1 1 7 1
-1 1 1 1 1 1 2 2 1 1 1 5 1 1 1 6 1
-1 1 1 1 2 1 2 2 1 1 1 5 1 1 1 6 1
-2 2 1 1 2 1 2 2 1 1 1 5 1 1 1 6 2
-1 1 1 1 2 1 2 2 1 1 1 5 1 1 1 6 2
-1 1 2 1 2 1 2 2 1 1 1 5 1 1 1 6 1
-1 1 2 2 1 1 2 1 1 1 1 5 1 1 1 7 1
-1 1 1 1 2 1 2 2 1 1 1 5 1 1 1 6 2
-1 1 1 1 1 1 2 2 1 1 1 5 1 1 1 6 1
-1 2 1 1 2 1 2 2 1 1 1 5 1 1 1 6 2
-1 1 2 2 1 1 2 1 2 1 1 6 1 1 1 7 1
-1 2 2 1 1 1 1 2 1 1 2 6 1 1 1 7 1
diff --git a/sourcecodes/data/old/initialstructure b/sourcecodes/data/old/initialstructure
deleted file mode 100644
index 9ecf1bc7..00000000
Binary files a/sourcecodes/data/old/initialstructure and /dev/null differ
diff --git a/sourcecodes/data/old/newintervention b/sourcecodes/data/old/newintervention
deleted file mode 100644
index d818a943..00000000
Binary files a/sourcecodes/data/old/newintervention and /dev/null differ
diff --git a/sourcecodes/data/old/temp_evidence_file b/sourcecodes/data/old/temp_evidence_file
deleted file mode 100644
index b687ceaf..00000000
--- a/sourcecodes/data/old/temp_evidence_file
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/bin/sh
-# script for execution of deployed applications
-#
-# Sets up the MCR environment for the current $ARCH and executes
-# the specified command.
-#
-exe_name=$0
-exe_dir=`dirname "$0"`
-echo "------------------------------------------"
-if [ "x$1" = "x" ]; then
- echo Usage:
- echo $0 \ args
-else
- echo Setting up environment variables
- MCRROOT="$1"
- echo ---
- LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64;
- MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ;
- XAPPLRESDIR=${MCRROOT}/X11/app-defaults ;
- export LD_LIBRARY_PATH;
- export XAPPLRESDIR;
- echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH};
- shift 1
- args=
- while [ $# -gt 0 ]; do
- token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank
- args="${args} ${token}"
- shift
- done
- "${exe_dir}"/evidencemodified
\ No newline at end of file
diff --git a/sourcecodes/data/old/temp_intervention_file b/sourcecodes/data/old/temp_intervention_file
deleted file mode 100644
index cdf5ce0f..00000000
--- a/sourcecodes/data/old/temp_intervention_file
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/bin/sh
-# script for execution of deployed applications
-#
-# Sets up the MCR environment for the current $ARCH and executes
-# the specified command.
-#
-exe_name=$0
-exe_dir=`dirname "$0"`
-echo "------------------------------------------"
-if [ "x$1" = "x" ]; then
- echo Usage:
- echo $0 \ args
-else
- echo Setting up environment variables
- MCRROOT="$1"
- echo ---
- LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64;
- MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ;
- XAPPLRESDIR=${MCRROOT}/X11/app-defaults ;
- export LD_LIBRARY_PATH;
- export XAPPLRESDIR;
- echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH};
- shift 1
- args=
- while [ $# -gt 0 ]; do
- token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank
- args="${args} ${token}"
- shift
- done
- "${exe_dir}"/newintervention
\ No newline at end of file
diff --git a/sourcecodes/data/old/temp_shell_file_initial_structure b/sourcecodes/data/old/temp_shell_file_initial_structure
deleted file mode 100644
index 5d1c323d..00000000
--- a/sourcecodes/data/old/temp_shell_file_initial_structure
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/bin/sh
-# script for execution of deployed applications
-#
-# Sets up the MCR environment for the current $ARCH and executes
-# the specified command.
-#
-exe_name=$0
-exe_dir=`dirname "$0"`
-echo "------------------------------------------"
-if [ "x$1" = "x" ]; then
- echo Usage:
- echo $0 \ args
-else
- echo Setting up environment variables
- MCRROOT="$1"
- echo ---
- LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64;
- MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ;
- LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ;
- XAPPLRESDIR=${MCRROOT}/X11/app-defaults ;
- export LD_LIBRARY_PATH;
- export XAPPLRESDIR;
- echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH};
- shift 1
- args=
- while [ $# -gt 0 ]; do
- token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank
- args="${args} ${token}"
- shift
- done
- "${exe_dir}"/initialstructure
\ No newline at end of file
diff --git a/sourcecodes/data/sample_input.txt b/sourcecodes/data/sample_input.txt
deleted file mode 100644
index 5d900d3c..00000000
--- a/sourcecodes/data/sample_input.txt
+++ /dev/null
@@ -1,42 +0,0 @@
-Genotype Trait1 Trait2 Trait3 Phenotype
-A 0.969 3 3.25 1.0
-NA 0.925 1.6 2.46 1.03
-B 0.427 NA 4.20 0.83
-A 0.877 8.3 3.76 0.96
-A 0.914 4.4 3.69 1.04
-A 0.560 4.9 2.60 0.98
-B 0.383 13.1 4.27 0.81
-B 0.101 18.6 5.08 0.77
-B 0.106 18.9 4.91 0.80
-A 0.894 2.5 2.69 0.99
-B 0.067 19.8 4.87 0.84
-A 0.921 2.9 4.12 1.03
-A 0.938 0.7 4.36 0.98
-B 0.658 15.7 4.53 0.88
-A 0.9 4.8 2.60 0.91
-A 0.790 10.4 2.39 0.89
-B 0.295 8.6 4.24 0.85
-A 0.317 12.2 4.44 0.88
-B 0.032 20.2 5.05 0.81
-B 0.603 23.4 4.28 0.80
-A 0.939 3.6 2.34 0.95
-B 0.978 0.4 3.49 0.88
-B 0.1 23.2 4.67 0.76
-B 0.036 32.6 4.93 0.82
-B 0.660 9.2 3.82 0.92
-B 0.078 35.8 4.51 0.85
-B 0.186 20.7 5.04 0.77
-B 0.071 35.6 4.57 0.79
-B 0.239 15.4 4.33 0.94
-B 0.205 24.5 5.05 0.77
-B 0.062 13.4 4.59 0.83
-A 0.599 5 4.18 0.96
-B 0.324 13.2 4.25 0.85
-B 0.876 14.2 2.92 0.86
-B 0.146 15.6 4.57 0.9
-B 0.257 22.5 5.21 0.75
-B 0.033 31.1 4.63 0.71
-B 0.297 36.1 3.88 0.79
-A 0.872 4.2 4.09 0.85
-A 0.909 4.3 3.65 0.97
-B 0.100 28.3 4.46 0.75
diff --git a/sourcecodes/delete_cv_pred.sh b/sourcecodes/delete_cv_pred.sh
index b756e2b6..04bb0b77 100644
--- a/sourcecodes/delete_cv_pred.sh
+++ b/sourcecodes/delete_cv_pred.sh
@@ -1,22 +1,15 @@
#!/bin/bash
#cd ./data/
-#cd /tmp/bnw/
-cd /var/lib/genenet/bnw/
+cd /tmp/bnw/
temp='looCV_temp.txt'
rm $1$temp
temp='looCV.txt'
rm $1$temp
-rm $1$temp
-temp='loo_plotly.html'
temp='kfoldCV_temp.txt'
rm $1$temp
temp='kfoldCV.txt'
rm $1$temp
-temp='kfold_plotly.html'
-rm $1$temp
temp='ts_upload.txt'
rm $1$temp
temp='ts_output.txt'
rm $1$temp
-temp='ts_plotly.html'
-rm $1$temp
diff --git a/sourcecodes/enter_netID.php~ b/sourcecodes/enter_netID.php~
deleted file mode 100644
index c58e63f3..00000000
--- a/sourcecodes/enter_netID.php~
+++ /dev/null
@@ -1,74 +0,0 @@
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Enter network ID from previously used network
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Networks that have previously been generated in BNW can be accessed by entering the network ID in the input box below. The network ID is currently a three character string that can be found on the left hand menu of any network page. Network files are periodically deleted from BNW so it is possible that older networks may no longer be active.
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