y_petri 2.1.51 → 2.2.0
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- checksums.yaml +4 -4
- data/lib/y_petri/net.rb +65 -23
- data/lib/y_petri/version.rb +1 -1
- data/test/acceptance/simulation_with_physical_units_test.rb +1 -1
- data/test/acceptance/visualization_test.rb +1 -1
- data/test/agent_test.rb +1 -1
- data/test/net_test.rb +1 -1
- data/test/place_test.rb +1 -1
- data/test/simulation_test.rb +1 -1
- data/test/transition_test.rb +1 -1
- data/test/world_test.rb +1 -1
- data/test/y_petri_test.rb +1 -1
- metadata +2 -6
- data/test/sim_test +0 -565
- data/test/ttp_pathway.rb +0 -233
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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1
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---
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2
2
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SHA1:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: 83dcb590fe26b6d6bb33cf3294d36f3ec2e55739
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4
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+
data.tar.gz: 406058cde1b0a815b77dc4feedd0da86cd0613e6
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: 1aef6f5b2bee23dbfae95c73806633355dc83daa7af0f87a3384d7442f8128eaecfe53fcdef7a48864269ca59ac6449d7fc161bb4e6b66803736c8145bcbe430
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7
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+
data.tar.gz: 921a481415b9c45df393c46cc709eac71eaae664562e8c971aee49c07820426813aecdd1863b6b697fd5a5ab18dc208c8940850627bae2e6d9b3f63fab75a18a
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data/lib/y_petri/net.rb
CHANGED
@@ -44,8 +44,8 @@ class YPetri::Net
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|
44
44
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with: { net: self } )
|
45
45
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end
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46
46
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|
47
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-
# Includes a place in the
|
48
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-
# place is already included in the net.
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47
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+
# Includes a place in the receiver. Returns _true_ if successful, _false_ if
|
48
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+
# the place is already included in the receiver net.
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49
49
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#
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50
50
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def include_place id
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51
51
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pl = Place().instance( id )
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@@ -53,9 +53,9 @@ class YPetri::Net
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|
53
53
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true.tap { @places << pl }
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54
54
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end
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55
55
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56
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-
# Includes a transition in the
|
57
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-
# the transition is already included in the net. The arcs of the transition
|
58
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-
# being included may only connect to the places already in the net.
|
56
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+
# Includes a transition in the receiver. Returns _true_ if successful, _false_
|
57
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+
# if the transition is already included in the net. The arcs of the transition
|
58
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+
# being included may only connect to the places already in the receiver net.
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59
59
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#
|
60
60
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def include_transition id
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61
61
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tr = Transition().instance( id )
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@@ -65,9 +65,9 @@ class YPetri::Net
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65
65
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true.tap { @transitions << tr }
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66
66
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end
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67
67
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|
68
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-
# Excludes a place from the
|
69
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-
# place was not found in the net. A place may not be excluded
|
70
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-
# long as any transitions
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68
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+
# Excludes a place from the receiver. Returns _true_ if successful, _false_
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69
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+
# if the place was not found in the receiver net. A place may not be excluded
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70
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+
# from the receiver so long as any transitions therein connect to it.
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71
71
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#
|
72
72
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def exclude_place id
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73
73
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pl = Place().instance( id )
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@@ -76,33 +76,75 @@ class YPetri::Net
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|
76
76
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false.tap { return true if @places.delete( pl ) }
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77
77
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end
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78
78
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|
79
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-
# Excludes a transition from the
|
80
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-
# the transition was not found in the net.
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79
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+
# Excludes a transition from the receiver. Returns _true_ if successful,
|
80
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+
# _false_ if the transition was not found in the receiver net.
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81
81
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#
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82
82
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def exclude_transition id
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83
83
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tr = Transition().instance( id )
|
84
84
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false.tap { return true if @transitions.delete( tr ) }
|
85
85
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end
|
86
86
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|
87
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-
# Includes
|
87
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+
# Includes another net in the receiver net. Returns _true_ if successful
|
88
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+
# (ie. if there was any change to the receiver net), _false_ if the receiver
|
89
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+
# net already includes the argument net.
|
90
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+
#
|
91
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+
def include_net id
|
92
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+
net = Net().instance( id )
|
93
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+
p_rslt = net.pp.map { |p| include_place p }.reduce :|
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94
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+
t_rslt = net.tt.map { |t| include_transition t }.reduce :|
|
95
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+
p_rslt || t_rslt
|
96
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+
end
|
97
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+
alias merge! include_net
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98
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+
|
99
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+
# Excludes another net from the receiver net. Returns _true_ if successful
|
100
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# (ie. if there was any change to the receiver net), _false_ if the receiver
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101
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+
# net contained no element of the argument net.
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102
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#
|
103
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+
def exclude_net id
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104
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net = Net().instance( id )
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105
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+
t_rslt = net.tt.map { |t| exclude_transition t }.reduce :|
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106
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+
p_rslt = net.pp.map { |p| exclude_place p }.reduce :|
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107
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p_rslt || t_rslt
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108
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+
end
|
109
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+
|
110
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+
# Includes an element (place or transition) in the net.
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88
111
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#
|
89
112
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def << element_id
|
90
113
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begin
|
91
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-
element = self.class.place( element_id )
|
92
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-
type = :place
|
114
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+
type, element = :place, self.class.place( element_id )
|
93
115
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rescue NameError, TypeError
|
94
116
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begin
|
95
|
-
element = self.class.transition( element_id )
|
96
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-
type = :transition
|
117
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+
type, element = :transition, self.class.transition( element_id )
|
97
118
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rescue NameError, TypeError => err
|
98
119
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raise TypeError, "Current world contains no place or transition " +
|
99
120
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"identified by #{element_id}! (#{err})"
|
100
121
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end
|
101
122
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end
|
102
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-
#
|
103
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-
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104
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-
|
105
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-
else fail "Implementation error
|
123
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+
case type # Factored out to minimize the code inside the rescue clause.
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124
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+
when :place then include_place( element )
|
125
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+
when :transition then include_transition( element )
|
126
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+
else fail "Implementation error!" end
|
127
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+
return self # important to enable chaining, eg. foo_net << p1 << p2 << t1
|
128
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+
end
|
129
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+
|
130
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+
# Creates a new net that contains all the places and transitions of both
|
131
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+
# operands.
|
132
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+
#
|
133
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+
def + other
|
134
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+
self.class.send( :new ).tap do |net|
|
135
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+
net.merge! self
|
136
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+
net.merge! other
|
137
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+
end
|
138
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+
end
|
139
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+
|
140
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+
# Creates a new net that contains the places and transition of the receiver
|
141
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+
# after excluding the second operand.
|
142
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+
#
|
143
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+
def - other
|
144
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+
self.class.send( :new ).tap do |net|
|
145
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+
net.merge! self
|
146
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+
net.exclude_net other
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147
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+
end
|
106
148
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end
|
107
149
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|
108
150
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# Is the net _functional_?
|
@@ -133,10 +175,10 @@ class YPetri::Net
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|
133
175
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# Returns a string briefly describing the net.
|
134
176
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#
|
135
177
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def to_s
|
136
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-
"#<Net: "
|
137
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-
|
138
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-
"#{pp.size rescue '∅'} places, #{tt.size rescue '∅'} transitions"
|
139
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-
|
178
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+
form = "#<Net: %s>"
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179
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+
content = ( name.nil? ? "%s" : "name: #{name}, %s" ) %
|
180
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+
"#{pp.size rescue '∅'} places, #{tt.size rescue '∅'} transitions"
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181
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form % content
|
140
182
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end
|
141
183
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|
142
184
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# Inspect string of the instance.
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data/lib/y_petri/version.rb
CHANGED
@@ -16,7 +16,7 @@ describe "Graphviz visualization" do
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16
16
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@m.Place name: :D, m!: 2.5
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17
17
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@m.Transition name: :A_pump, s: { A: -1 }, rate: proc { 0.005 }
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18
18
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@m.Transition name: :B_decay, s: { B: -1 }, rate: 0.05
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19
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-
@m.Transition name: :C_guard,
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19
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+
@m.Transition name: :C_guard, codomain: :C, assignment: -> { 2 }
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20
20
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end
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21
21
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22
22
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it "should work" do
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data/test/agent_test.rb
CHANGED
data/test/net_test.rb
CHANGED
data/test/place_test.rb
CHANGED
data/test/simulation_test.rb
CHANGED
data/test/transition_test.rb
CHANGED
data/test/world_test.rb
CHANGED
data/test/y_petri_test.rb
CHANGED
metadata
CHANGED
@@ -1,14 +1,14 @@
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1
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: y_petri
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3
3
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version: !ruby/object:Gem::Version
|
4
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-
version: 2.
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4
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+
version: 2.2.0
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5
5
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platform: ruby
|
6
6
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authors:
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7
7
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- boris
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8
8
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autorequire:
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9
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bindir: bin
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10
10
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cert_chain: []
|
11
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-
date: 2013-
|
11
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+
date: 2013-10-14 00:00:00.000000000 Z
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12
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dependencies:
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13
13
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- !ruby/object:Gem::Dependency
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14
14
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name: y_support
|
@@ -182,10 +182,8 @@ files:
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182
182
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- test/examples/manual_examples.rb
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183
183
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- test/net_test.rb
|
184
184
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- test/place_test.rb
|
185
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-
- test/sim_test
|
186
185
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- test/simulation_test.rb
|
187
186
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- test/transition_test.rb
|
188
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-
- test/ttp_pathway.rb
|
189
187
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- test/world_mock.rb
|
190
188
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- test/world_test.rb
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191
189
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- test/y_petri_test.rb
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@@ -230,10 +228,8 @@ test_files:
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230
228
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- test/examples/manual_examples.rb
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231
229
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- test/net_test.rb
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232
230
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- test/place_test.rb
|
233
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-
- test/sim_test
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234
231
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- test/simulation_test.rb
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235
232
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- test/transition_test.rb
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236
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-
- test/ttp_pathway.rb
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237
233
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- test/world_mock.rb
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238
234
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- test/world_test.rb
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239
235
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- test/y_petri_test.rb
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data/test/sim_test
DELETED
@@ -1,565 +0,0 @@
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1
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-
#! /usr/bin/ruby
|
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# -*- coding: utf-8 -*-
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3
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-
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4
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-
require 'minitest/spec'
|
5
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-
require 'minitest/autorun'
|
6
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-
require_relative '../lib/y_petri' # tested component itself
|
7
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-
# require 'y_petri'
|
8
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-
# require 'sy'
|
9
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-
require_relative 'workspace_mock'
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10
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-
|
11
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-
describe YPetri::Simulation::TransitionRepresentation do
|
12
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-
before do
|
13
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-
@pç, @tç, @nç = WORKSPACE_MOCK.()
|
14
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-
# Set up places:
|
15
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-
@p1 = @pç.nw "P1", 1
|
16
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-
@p2 = @pç.nw "P2", 2
|
17
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-
@p3 = @pç.nw "P3", 3
|
18
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-
@p4 = @pç.nw "P4", 4
|
19
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-
@p5 = @pç.nw "P5", 5
|
20
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-
# Set up transitions:
|
21
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-
@t1 = @tç.nw "T1", s: { @p1 => -1, @p2 => -1, @p4 => 1 },
|
22
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-
rate: 0.1
|
23
|
-
@t2 = @tç.nw "T2", s: { @p1 => -1, @p3 => 1 },
|
24
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-
rate: -> a { a * 0.5 }
|
25
|
-
@t3 = @tç.nw "T3", s: { @p1 => -1, @p2 => -1, @p4 => 1 },
|
26
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-
domain: @p3,
|
27
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-
rate: -> a { a * 0.5 }
|
28
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-
@net = @nç.new << @p1 << @p2 << @p3 << @p4 << @p5
|
29
|
-
@net.include_transition! @t1
|
30
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-
@net.include_transition! @t2
|
31
|
-
@net << @t3
|
32
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-
@s = YPetri::Simulation.new net: @net,
|
33
|
-
marking_clamps: { @p1 => 2.0, @p5 => 2.0 },
|
34
|
-
initial_marking: { @p2 => @p2.default_marking,
|
35
|
-
@p3 => @p3.default_marking,
|
36
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-
@p4 => @p4.default_marking }
|
37
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-
end
|
38
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-
|
39
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-
it "exposes the net" do
|
40
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-
@s.net.must_equal @net
|
41
|
-
@s.net.places.size.must_equal 5
|
42
|
-
@s.net.transitions.size.must_equal 3
|
43
|
-
assert @net.include? @t1
|
44
|
-
assert @s.net.include? @t1
|
45
|
-
assert @net.include? @t2
|
46
|
-
assert @s.net.include? @t2
|
47
|
-
assert @net.include? @t3
|
48
|
-
assert @s.net.include? @t3
|
49
|
-
@s.net.transitions.size.must_equal 3
|
50
|
-
end
|
51
|
-
|
52
|
-
it "exposes Petri net places" do
|
53
|
-
@s.places.map( &:source ).must_equal [ @p1, @p2, @p3, @p4, @p5 ]
|
54
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-
@s.pn.must_equal [ :P1, :P2, :P3, :P4, :P5 ]
|
55
|
-
end
|
56
|
-
|
57
|
-
it "exposes Petri net transitions" do
|
58
|
-
@s.transitions.map( &:source ).must_equal [ @t1, @t2, @t3 ]
|
59
|
-
@s.tn.must_equal [ :T1, :T2, :T3 ]
|
60
|
-
end
|
61
|
-
|
62
|
-
it "exposes place clamps" do
|
63
|
-
@s.marking_clamps.values.must_equal [2, 2]
|
64
|
-
@s.n_clamped.must_equal [:P1, :P5]
|
65
|
-
end
|
66
|
-
|
67
|
-
it "presents free places" do
|
68
|
-
@s.free_places.map( &:source ).must_equal [ @p2, @p3, @p4 ]
|
69
|
-
@s.n_free.must_equal [ :P2, :P3, :P4 ]
|
70
|
-
end
|
71
|
-
|
72
|
-
it "presents clamped places" do
|
73
|
-
@s.n_clamped.must_equal [ :P1, :P5 ]
|
74
|
-
@s.clamped_places.map( &:source ).must_equal [ @p1, @p5 ]
|
75
|
-
end
|
76
|
-
|
77
|
-
it "exposes initial marking" do
|
78
|
-
( @s.free_places.map( &:source ) >> @s.im( *@s.free_places ) )
|
79
|
-
.must_equal( { @p2 => 2, @p3 => 3, @p4 => 4 } )
|
80
|
-
( @s.n_free >> @s.im( *@s.free_places ) )
|
81
|
-
.must_equal( { P2: 2, P3: 3, P4: 4 } )
|
82
|
-
@s.im.must_equal [ 2, 3, 4 ]
|
83
|
-
@s.im_vector.must_equal Matrix[[2], [3], [4]]
|
84
|
-
@s.im_vector.must_equal @s.iᴍ
|
85
|
-
end
|
86
|
-
|
87
|
-
it "exposes marking (simulation state)" do
|
88
|
-
@s.marking.must_equal [2, 3, 4] # (we're after reset)
|
89
|
-
@s.free_places( :m ).must_equal( { @p2 => 2, @p3 => 3, @p4 => 4 } )
|
90
|
-
@s.free_pp( :m ).must_equal( { P2: 2, P3: 3, P4: 4 } )
|
91
|
-
@s.ᴍ.must_equal Matrix[[2], [3], [4]]
|
92
|
-
end
|
93
|
-
|
94
|
-
it "separately exposes marking of clamped places" do
|
95
|
-
@s.m( *@s.clamped_places ).must_equal [ 2, 2 ]
|
96
|
-
@s.clamped_places( :m_clamped ).must_equal( { @p1 => 2, @p5 => 2 } )
|
97
|
-
@s.clamped_pp( :m_clamped ).must_equal( { P1: 2, P5: 2 } )
|
98
|
-
@s.ᴍ_clamped.must_equal Matrix[[2], [2]]
|
99
|
-
end
|
100
|
-
|
101
|
-
it "exposes marking of all places (with capitalized M)" do
|
102
|
-
@s.pn.must_equal [:P1, :P2, :P3, :P4, :P5]
|
103
|
-
@s.m.must_equal [ 2, 2, 3, 4, 2 ]
|
104
|
-
( @s.places >> @s.m( *@s.places ) )
|
105
|
-
.must_equal( { @p1 => 2, @p2 => 2, @p3 => 3, @p4 => 4, @p5 => 2 } )
|
106
|
-
@s.marking_vector.must_equal Matrix[[2], [2], [3], [4], [2]]
|
107
|
-
end
|
108
|
-
|
109
|
-
it "has stoichiometry matrix for 3. tS transitions" do
|
110
|
-
@s.tS_stoichiometry_matrix.must_equal Matrix.empty( 3, 0 )
|
111
|
-
@s.tS_SM.must_equal Matrix.empty( 3, 0 )
|
112
|
-
end
|
113
|
-
|
114
|
-
it "has stoichiometry matrix for 6. TS transitions" do
|
115
|
-
@s.TS_SM.must_equal Matrix[[-1, 0, -1], [0, 1, 0], [1, 0, 1]]
|
116
|
-
@s.SM.must_equal @s.TS_SM
|
117
|
-
end
|
118
|
-
|
119
|
-
it "presents 1. TS transitions" do
|
120
|
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assert_equal [@t1, @t2, @t3], @s.TS_transitions.map( &:source )
|
121
|
-
assert_equal( { @t1 => :T1, @t2 => :T2, @t3 => :T3 },
|
122
|
-
@s.TS_transitions.map( &:source ) >> @s.n_TS )
|
123
|
-
assert_equal [:T1, :T2, :T3], @s.n_TS
|
124
|
-
end
|
125
|
-
|
126
|
-
it "presents 2. Ts transitions" do
|
127
|
-
assert_equal [], @s.Ts_transitions
|
128
|
-
assert_equal [], @s.n_Ts
|
129
|
-
end
|
130
|
-
|
131
|
-
it "presents 3. tS transitions" do
|
132
|
-
assert_equal [], @s.tS_transitions
|
133
|
-
assert_equal [], @s.n_tS
|
134
|
-
end
|
135
|
-
|
136
|
-
it "presents 4. ts transitions" do
|
137
|
-
assert_equal [], @s.ts_transitions
|
138
|
-
assert_equal [], @s.n_ts
|
139
|
-
end
|
140
|
-
|
141
|
-
it "presents A transitions" do
|
142
|
-
assert_equal [], @s.A_transitions
|
143
|
-
assert_equal [], @s.n_A
|
144
|
-
end
|
145
|
-
|
146
|
-
it "presents S transitions" do
|
147
|
-
assert_equal [@t1, @t2, @t3], @s.S_transitions.map( &:source )
|
148
|
-
assert_equal [:T1, :T2, :T3], @s.n_S
|
149
|
-
end
|
150
|
-
|
151
|
-
it "presents s transitions" do
|
152
|
-
assert_equal [], @s.s_transitions
|
153
|
-
assert_equal [], @s.n_s
|
154
|
-
end
|
155
|
-
|
156
|
-
it "1. handles TS transitions" do
|
157
|
-
@s.transitions.TS.rate_closures.size.must_equal 3
|
158
|
-
@s.transitions.TS.flux_vector.must_equal Matrix.column_vector( [ 0.4, 1.0, 1.5 ] )
|
159
|
-
@s.φ_for_SR.must_equal @s.flux_vector
|
160
|
-
@s.SR_tt( :φ_for_SR ).must_equal( { T1: 0.4, T2: 1.0, T3: 1.5 } )
|
161
|
-
@s.first_order_action_vector_for_SR( 1 )
|
162
|
-
.must_equal Matrix.column_vector [ 0.4, 1.0, 1.5 ]
|
163
|
-
@s.SR_tt( :first_order_action_for_SR, 1 ).must_equal( T1: 0.4, T2: 1.0, T3: 1.5 )
|
164
|
-
@s.Δ_SR( 1 ).must_equal Matrix[[-1.9], [1.0], [1.9]]
|
165
|
-
@s.free_pp( :Δ_SR, 1 ).must_equal( { P2: -1.9, P3: 1.0, P4: 1.9 } )
|
166
|
-
end
|
167
|
-
|
168
|
-
it "2. handles Ts transitions" do
|
169
|
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assert_equal [], @s.transitions.Ts.gradient_closures
|
170
|
-
@s.transitions.Ts.delta( 1.0 ).must_equal Matrix.zero( @s.n_free.size, 1 )
|
171
|
-
end
|
172
|
-
|
173
|
-
it "3. handles tS transitions" do
|
174
|
-
@s.transitions.tS.firing_closures.must_equal []
|
175
|
-
@s.transitions.tS.firing_vector.must_equal Matrix.column_vector( [] )
|
176
|
-
@s.transitions.tS.delta.must_equal Matrix.zero( @s.n_free.size, 1 )
|
177
|
-
end
|
178
|
-
|
179
|
-
it "1. handles ts transitions" do
|
180
|
-
@s.transitions.ts.delta_closures.must_equal []
|
181
|
-
end
|
182
|
-
|
183
|
-
it "presents sparse stoichiometry vectors for its transitions" do
|
184
|
-
@s.transition( @t1 ).sparse_sv.must_equal Matrix.cv( [-1, 0, 1] )
|
185
|
-
@s.sparse_stoichiometry_vector( of: @t1 )
|
186
|
-
.must_equal Matrix.cv( [-1, -1, 0, 1, 0] )
|
187
|
-
end
|
188
|
-
|
189
|
-
it "presents correspondence matrices free, clamped => all places" do
|
190
|
-
@s.f2a.must_equal Matrix[[0, 0, 0], [1, 0, 0], [0, 1, 0],
|
191
|
-
[0, 0, 1], [0, 0, 0]]
|
192
|
-
@s.c2a.must_equal Matrix[[1, 0], [0, 0], [0, 0], [0, 0], [0, 1]]
|
193
|
-
end
|
194
|
-
end
|
195
|
-
|
196
|
-
describe ::YPetri::Simulation do
|
197
|
-
before do
|
198
|
-
@pç, @tç, @nç = WORKSPACE_MOCK.()
|
199
|
-
# Set up places:
|
200
|
-
@p1 = @pç.nw "P1", 1
|
201
|
-
@p2 = @pç.nw "P2", 2
|
202
|
-
@p3 = @pç.nw "P3", 3
|
203
|
-
@p4 = @pç.nw "P4", 4
|
204
|
-
@p5 = @pç.nw "P5", 5
|
205
|
-
# Set up transitions:
|
206
|
-
@t1 = @tç.nw "T1", s: { @p1 => -1, @p2 => -1, @p4 => 1 },
|
207
|
-
rate: 0.1
|
208
|
-
@t2 = @tç.nw "T2", s: { @p1 => -1, @p3 => 1 },
|
209
|
-
rate: -> a { a * 0.5 }
|
210
|
-
@t3 = @tç.new "T3", s: { @p1 => -1, @p2 => -1, @p4 => 1 },
|
211
|
-
domain: @p3,
|
212
|
-
rate: -> a { a * 0.5 }
|
213
|
-
@net = @nç.new << @p1 << @p2 << @p3 << @p4 << @p5
|
214
|
-
@net.include_transition! @t1
|
215
|
-
@net.include_transition! @t2
|
216
|
-
@net << @t3
|
217
|
-
@s = YPetri::Simulation.new net: @net,
|
218
|
-
marking_clamps: { @p1 => 2.0, @p5 => 2.0 },
|
219
|
-
initial_marking: { @p2 => @p2.default_marking,
|
220
|
-
@p3 => @p3.default_marking,
|
221
|
-
@p4 => @p4.default_marking }
|
222
|
-
end
|
223
|
-
|
224
|
-
it "exposes the net" do
|
225
|
-
@s.net.must_equal @net
|
226
|
-
@s.net.places.size.must_equal 5
|
227
|
-
@s.net.transitions.size.must_equal 3
|
228
|
-
assert @net.include? @t1
|
229
|
-
assert @s.net.include? @t1
|
230
|
-
assert @net.include? @t2
|
231
|
-
assert @s.net.include? @t2
|
232
|
-
assert @net.include? @t3
|
233
|
-
assert @s.net.include? @t3
|
234
|
-
@s.net.transitions.size.must_equal 3
|
235
|
-
end
|
236
|
-
|
237
|
-
it "exposes Petri net places" do
|
238
|
-
@s.places.map( &:source ).must_equal [ @p1, @p2, @p3, @p4, @p5 ]
|
239
|
-
@s.pn.must_equal [ :P1, :P2, :P3, :P4, :P5 ]
|
240
|
-
end
|
241
|
-
|
242
|
-
it "exposes Petri net transitions" do
|
243
|
-
@s.transitions.map( &:source ).must_equal [ @t1, @t2, @t3 ]
|
244
|
-
@s.tn.must_equal [ :T1, :T2, :T3 ]
|
245
|
-
end
|
246
|
-
|
247
|
-
it "exposes place clamps" do
|
248
|
-
@s.marking_clamps.values.must_equal [2, 2]
|
249
|
-
@s.n_clamped.must_equal [:P1, :P5]
|
250
|
-
end
|
251
|
-
|
252
|
-
it "presents free places" do
|
253
|
-
@s.free_places.map( &:source ).must_equal [ @p2, @p3, @p4 ]
|
254
|
-
@s.n_free.must_equal [ :P2, :P3, :P4 ]
|
255
|
-
end
|
256
|
-
|
257
|
-
it "presents clamped places" do
|
258
|
-
@s.n_clamped.must_equal [ :P1, :P5 ]
|
259
|
-
@s.clamped_places.map( &:source ).must_equal [ @p1, @p5 ]
|
260
|
-
end
|
261
|
-
|
262
|
-
it "exposes initial marking" do
|
263
|
-
( @s.free_places.map( &:source ) >> @s.im( *@s.free_places ) )
|
264
|
-
.must_equal( { @p2 => 2, @p3 => 3, @p4 => 4 } )
|
265
|
-
( @s.n_free >> @s.im( *@s.free_places ) )
|
266
|
-
.must_equal( { P2: 2, P3: 3, P4: 4 } )
|
267
|
-
@s.im.must_equal [ 2, 3, 4 ]
|
268
|
-
@s.im_vector.must_equal Matrix[[2], [3], [4]]
|
269
|
-
@s.im_vector.must_equal @s.iᴍ
|
270
|
-
end
|
271
|
-
|
272
|
-
it "exposes marking (simulation state)" do
|
273
|
-
@s.marking.must_equal [2, 3, 4] # (we're after reset)
|
274
|
-
@s.free_places( :m ).must_equal( { @p2 => 2, @p3 => 3, @p4 => 4 } )
|
275
|
-
@s.free_pp( :m ).must_equal( { P2: 2, P3: 3, P4: 4 } )
|
276
|
-
@s.ᴍ.must_equal Matrix[[2], [3], [4]]
|
277
|
-
end
|
278
|
-
|
279
|
-
it "separately exposes marking of clamped places" do
|
280
|
-
@s.m( *@s.clamped_places ).must_equal [ 2, 2 ]
|
281
|
-
@s.clamped_places( :m_clamped ).must_equal( { @p1 => 2, @p5 => 2 } )
|
282
|
-
@s.clamped_pp( :m_clamped ).must_equal( { P1: 2, P5: 2 } )
|
283
|
-
@s.ᴍ_clamped.must_equal Matrix[[2], [2]]
|
284
|
-
end
|
285
|
-
|
286
|
-
it "exposes marking of all places (with capitalized M)" do
|
287
|
-
@s.pn.must_equal [:P1, :P2, :P3, :P4, :P5]
|
288
|
-
@s.m.must_equal [ 2, 2, 3, 4, 2 ]
|
289
|
-
( @s.places >> @s.m( *@s.places ) )
|
290
|
-
.must_equal( { @p1 => 2, @p2 => 2, @p3 => 3, @p4 => 4, @p5 => 2 } )
|
291
|
-
@s.marking_vector.must_equal Matrix[[2], [2], [3], [4], [2]]
|
292
|
-
end
|
293
|
-
|
294
|
-
it "has stoichiometry matrix for 3. tS transitions" do
|
295
|
-
@s.tS_stoichiometry_matrix.must_equal Matrix.empty( 3, 0 )
|
296
|
-
@s.tS_SM.must_equal Matrix.empty( 3, 0 )
|
297
|
-
end
|
298
|
-
|
299
|
-
it "has stoichiometry matrix for 6. TS transitions" do
|
300
|
-
@s.TS_SM.must_equal Matrix[[-1, 0, -1], [0, 1, 0], [1, 0, 1]]
|
301
|
-
@s.SM.must_equal @s.TS_SM
|
302
|
-
end
|
303
|
-
|
304
|
-
it "presents 1. TS transitions" do
|
305
|
-
assert_equal [@t1, @t2, @t3], @s.TS_transitions.map( &:source )
|
306
|
-
assert_equal( { @t1 => :T1, @t2 => :T2, @t3 => :T3 },
|
307
|
-
@s.TS_transitions.map( &:source ) >> @s.n_TS )
|
308
|
-
assert_equal [:T1, :T2, :T3], @s.n_TS
|
309
|
-
end
|
310
|
-
|
311
|
-
it "presents 2. Ts transitions" do
|
312
|
-
assert_equal [], @s.Ts_transitions
|
313
|
-
assert_equal [], @s.n_Ts
|
314
|
-
end
|
315
|
-
|
316
|
-
it "presents 3. tS transitions" do
|
317
|
-
assert_equal [], @s.tS_transitions
|
318
|
-
assert_equal [], @s.n_tS
|
319
|
-
end
|
320
|
-
|
321
|
-
it "presents 4. ts transitions" do
|
322
|
-
assert_equal [], @s.ts_transitions
|
323
|
-
assert_equal [], @s.n_ts
|
324
|
-
end
|
325
|
-
|
326
|
-
it "presents A transitions" do
|
327
|
-
assert_equal [], @s.A_transitions
|
328
|
-
assert_equal [], @s.n_A
|
329
|
-
end
|
330
|
-
|
331
|
-
it "presents S transitions" do
|
332
|
-
assert_equal [@t1, @t2, @t3], @s.S_transitions.map( &:source )
|
333
|
-
assert_equal [:T1, :T2, :T3], @s.n_S
|
334
|
-
end
|
335
|
-
|
336
|
-
it "presents s transitions" do
|
337
|
-
assert_equal [], @s.s_transitions
|
338
|
-
assert_equal [], @s.n_s
|
339
|
-
end
|
340
|
-
|
341
|
-
it "1. handles TS transitions" do
|
342
|
-
@s.transitions.TS.rate_closures.size.must_equal 3
|
343
|
-
@s.transitions.TS.flux_vector.must_equal Matrix.column_vector( [ 0.4, 1.0, 1.5 ] )
|
344
|
-
@s.φ_for_SR.must_equal @s.flux_vector
|
345
|
-
@s.SR_tt( :φ_for_SR ).must_equal( { T1: 0.4, T2: 1.0, T3: 1.5 } )
|
346
|
-
@s.first_order_action_vector_for_SR( 1 )
|
347
|
-
.must_equal Matrix.column_vector [ 0.4, 1.0, 1.5 ]
|
348
|
-
@s.SR_tt( :first_order_action_for_SR, 1 ).must_equal( T1: 0.4, T2: 1.0, T3: 1.5 )
|
349
|
-
@s.Δ_SR( 1 ).must_equal Matrix[[-1.9], [1.0], [1.9]]
|
350
|
-
@s.free_pp( :Δ_SR, 1 ).must_equal( { P2: -1.9, P3: 1.0, P4: 1.9 } )
|
351
|
-
end
|
352
|
-
|
353
|
-
it "2. handles Ts transitions" do
|
354
|
-
assert_equal [], @s.transitions.Ts.gradient_closures
|
355
|
-
@s.transitions.Ts.delta( 1.0 ).must_equal Matrix.zero( @s.n_free.size, 1 )
|
356
|
-
end
|
357
|
-
|
358
|
-
it "3. handles tS transitions" do
|
359
|
-
@s.transitions.tS.firing_closures.must_equal []
|
360
|
-
@s.transitions.tS.firing_vector.must_equal Matrix.column_vector( [] )
|
361
|
-
@s.transitions.tS.delta.must_equal Matrix.zero( @s.n_free.size, 1 )
|
362
|
-
end
|
363
|
-
|
364
|
-
it "1. handles ts transitions" do
|
365
|
-
@s.transitions.ts.delta_closures.must_equal []
|
366
|
-
end
|
367
|
-
|
368
|
-
it "presents sparse stoichiometry vectors for its transitions" do
|
369
|
-
@s.transition( @t1 ).sparse_sv.must_equal Matrix.cv( [-1, 0, 1] )
|
370
|
-
@s.sparse_stoichiometry_vector( of: @t1 )
|
371
|
-
.must_equal Matrix.cv( [-1, -1, 0, 1, 0] )
|
372
|
-
end
|
373
|
-
|
374
|
-
it "presents correspondence matrices free, clamped => all places" do
|
375
|
-
@s.f2a.must_equal Matrix[[0, 0, 0], [1, 0, 0], [0, 1, 0],
|
376
|
-
[0, 0, 1], [0, 0, 0]]
|
377
|
-
@s.c2a.must_equal Matrix[[1, 0], [0, 0], [0, 0], [0, 0], [0, 1]]
|
378
|
-
end
|
379
|
-
end
|
380
|
-
|
381
|
-
|
382
|
-
describe ::YPetri::Simulation do
|
383
|
-
before do
|
384
|
-
@pç, @tç, @nç = WORKSPACE_MOCK.()
|
385
|
-
# Set up places:
|
386
|
-
@p1 = @pç.nw "P1", 1
|
387
|
-
@p2 = @pç.nw "P2", 2
|
388
|
-
@p3 = @pç.nw "P3", 3
|
389
|
-
@p4 = @pç.nw "P4", 4
|
390
|
-
@p5 = @pç.nw "P5", 5
|
391
|
-
# Set up transitions:
|
392
|
-
@t1 = @tç.nw "T1", s: { @p1 => -1, @p2 => -1, @p4 => 1 },
|
393
|
-
rate: 0.1
|
394
|
-
@t2 = @tç.nw "T2", s: { @p1 => -1, @p3 => 1 },
|
395
|
-
rate: -> a { a * 0.5 }
|
396
|
-
@t3 = @tç.new "T3", s: { @p1 => -1, @p2 => -1, @p4 => 1 },
|
397
|
-
domain: @p3,
|
398
|
-
rate: -> a { a * 0.5 }
|
399
|
-
@net = @nç.new << @p1 << @p2 << @p3 << @p4 << @p5
|
400
|
-
@net.include_transition! @t1
|
401
|
-
@net.include_transition! @t2
|
402
|
-
@net << @t3
|
403
|
-
@s = YPetri::Simulation.new net: @net,
|
404
|
-
marking_clamps: { @p1 => 2.0, @p5 => 2.0 },
|
405
|
-
initial_marking: { @p2 => @p2.default_marking,
|
406
|
-
@p3 => @p3.default_marking,
|
407
|
-
@p4 => @p4.default_marking }
|
408
|
-
end
|
409
|
-
|
410
|
-
it "exposes the net" do
|
411
|
-
@s.net.must_equal @net
|
412
|
-
@s.net.places.size.must_equal 5
|
413
|
-
@s.net.transitions.size.must_equal 3
|
414
|
-
assert @net.include? @t1
|
415
|
-
assert @s.net.include? @t1
|
416
|
-
assert @net.include? @t2
|
417
|
-
assert @s.net.include? @t2
|
418
|
-
assert @net.include? @t3
|
419
|
-
assert @s.net.include? @t3
|
420
|
-
@s.net.transitions.size.must_equal 3
|
421
|
-
end
|
422
|
-
|
423
|
-
it "exposes Petri net places" do
|
424
|
-
@s.places.map( &:source ).must_equal [ @p1, @p2, @p3, @p4, @p5 ]
|
425
|
-
@s.pn.must_equal [ :P1, :P2, :P3, :P4, :P5 ]
|
426
|
-
end
|
427
|
-
|
428
|
-
it "exposes Petri net transitions" do
|
429
|
-
@s.transitions.map( &:source ).must_equal [ @t1, @t2, @t3 ]
|
430
|
-
@s.tn.must_equal [ :T1, :T2, :T3 ]
|
431
|
-
end
|
432
|
-
|
433
|
-
it "exposes place clamps" do
|
434
|
-
@s.marking_clamps.values.must_equal [2, 2]
|
435
|
-
@s.n_clamped.must_equal [:P1, :P5]
|
436
|
-
end
|
437
|
-
|
438
|
-
it "presents free places" do
|
439
|
-
@s.free_places.map( &:source ).must_equal [ @p2, @p3, @p4 ]
|
440
|
-
@s.n_free.must_equal [ :P2, :P3, :P4 ]
|
441
|
-
end
|
442
|
-
|
443
|
-
it "presents clamped places" do
|
444
|
-
@s.n_clamped.must_equal [ :P1, :P5 ]
|
445
|
-
@s.clamped_places.map( &:source ).must_equal [ @p1, @p5 ]
|
446
|
-
end
|
447
|
-
|
448
|
-
it "exposes initial marking" do
|
449
|
-
( @s.free_places.map( &:source ) >> @s.im( *@s.free_places ) )
|
450
|
-
.must_equal( { @p2 => 2, @p3 => 3, @p4 => 4 } )
|
451
|
-
( @s.n_free >> @s.im( *@s.free_places ) )
|
452
|
-
.must_equal( { P2: 2, P3: 3, P4: 4 } )
|
453
|
-
@s.im.must_equal [ 2, 3, 4 ]
|
454
|
-
@s.im_vector.must_equal Matrix[[2], [3], [4]]
|
455
|
-
@s.im_vector.must_equal @s.iᴍ
|
456
|
-
end
|
457
|
-
|
458
|
-
it "exposes marking (simulation state)" do
|
459
|
-
@s.marking.must_equal [2, 3, 4] # (we're after reset)
|
460
|
-
@s.free_places( :m ).must_equal( { @p2 => 2, @p3 => 3, @p4 => 4 } )
|
461
|
-
@s.free_pp( :m ).must_equal( { P2: 2, P3: 3, P4: 4 } )
|
462
|
-
@s.ᴍ.must_equal Matrix[[2], [3], [4]]
|
463
|
-
end
|
464
|
-
|
465
|
-
it "separately exposes marking of clamped places" do
|
466
|
-
@s.m( *@s.clamped_places ).must_equal [ 2, 2 ]
|
467
|
-
@s.clamped_places( :m_clamped ).must_equal( { @p1 => 2, @p5 => 2 } )
|
468
|
-
@s.clamped_pp( :m_clamped ).must_equal( { P1: 2, P5: 2 } )
|
469
|
-
@s.ᴍ_clamped.must_equal Matrix[[2], [2]]
|
470
|
-
end
|
471
|
-
|
472
|
-
it "exposes marking of all places (with capitalized M)" do
|
473
|
-
@s.pn.must_equal [:P1, :P2, :P3, :P4, :P5]
|
474
|
-
@s.m.must_equal [ 2, 2, 3, 4, 2 ]
|
475
|
-
( @s.places >> @s.m( *@s.places ) )
|
476
|
-
.must_equal( { @p1 => 2, @p2 => 2, @p3 => 3, @p4 => 4, @p5 => 2 } )
|
477
|
-
@s.marking_vector.must_equal Matrix[[2], [2], [3], [4], [2]]
|
478
|
-
end
|
479
|
-
|
480
|
-
it "has stoichiometry matrix for 3. tS transitions" do
|
481
|
-
@s.tS_stoichiometry_matrix.must_equal Matrix.empty( 3, 0 )
|
482
|
-
@s.tS_SM.must_equal Matrix.empty( 3, 0 )
|
483
|
-
end
|
484
|
-
|
485
|
-
it "has stoichiometry matrix for 6. TS transitions" do
|
486
|
-
@s.TS_SM.must_equal Matrix[[-1, 0, -1], [0, 1, 0], [1, 0, 1]]
|
487
|
-
@s.SM.must_equal @s.TS_SM
|
488
|
-
end
|
489
|
-
|
490
|
-
it "presents 1. TS transitions" do
|
491
|
-
assert_equal [@t1, @t2, @t3], @s.TS_transitions.map( &:source )
|
492
|
-
assert_equal( { @t1 => :T1, @t2 => :T2, @t3 => :T3 },
|
493
|
-
@s.TS_transitions.map( &:source ) >> @s.n_TS )
|
494
|
-
assert_equal [:T1, :T2, :T3], @s.n_TS
|
495
|
-
end
|
496
|
-
|
497
|
-
it "presents 2. Ts transitions" do
|
498
|
-
assert_equal [], @s.Ts_transitions
|
499
|
-
assert_equal [], @s.n_Ts
|
500
|
-
end
|
501
|
-
|
502
|
-
it "presents 3. tS transitions" do
|
503
|
-
assert_equal [], @s.tS_transitions
|
504
|
-
assert_equal [], @s.n_tS
|
505
|
-
end
|
506
|
-
|
507
|
-
it "presents 4. ts transitions" do
|
508
|
-
assert_equal [], @s.ts_transitions
|
509
|
-
assert_equal [], @s.n_ts
|
510
|
-
end
|
511
|
-
|
512
|
-
it "presents A transitions" do
|
513
|
-
assert_equal [], @s.A_transitions
|
514
|
-
assert_equal [], @s.n_A
|
515
|
-
end
|
516
|
-
|
517
|
-
it "presents S transitions" do
|
518
|
-
assert_equal [@t1, @t2, @t3], @s.S_transitions.map( &:source )
|
519
|
-
assert_equal [:T1, :T2, :T3], @s.n_S
|
520
|
-
end
|
521
|
-
|
522
|
-
it "presents s transitions" do
|
523
|
-
assert_equal [], @s.s_transitions
|
524
|
-
assert_equal [], @s.n_s
|
525
|
-
end
|
526
|
-
|
527
|
-
it "1. handles TS transitions" do
|
528
|
-
@s.transitions.TS.rate_closures.size.must_equal 3
|
529
|
-
@s.transitions.TS.flux_vector.must_equal Matrix.column_vector( [ 0.4, 1.0, 1.5 ] )
|
530
|
-
@s.φ_for_SR.must_equal @s.flux_vector
|
531
|
-
@s.SR_tt( :φ_for_SR ).must_equal( { T1: 0.4, T2: 1.0, T3: 1.5 } )
|
532
|
-
@s.first_order_action_vector_for_SR( 1 )
|
533
|
-
.must_equal Matrix.column_vector [ 0.4, 1.0, 1.5 ]
|
534
|
-
@s.SR_tt( :first_order_action_for_SR, 1 ).must_equal( T1: 0.4, T2: 1.0, T3: 1.5 )
|
535
|
-
@s.Δ_SR( 1 ).must_equal Matrix[[-1.9], [1.0], [1.9]]
|
536
|
-
@s.free_pp( :Δ_SR, 1 ).must_equal( { P2: -1.9, P3: 1.0, P4: 1.9 } )
|
537
|
-
end
|
538
|
-
|
539
|
-
it "2. handles Ts transitions" do
|
540
|
-
assert_equal [], @s.transitions.Ts.gradient_closures
|
541
|
-
@s.transitions.Ts.delta( 1.0 ).must_equal Matrix.zero( @s.n_free.size, 1 )
|
542
|
-
end
|
543
|
-
|
544
|
-
it "3. handles tS transitions" do
|
545
|
-
@s.transitions.tS.firing_closures.must_equal []
|
546
|
-
@s.transitions.tS.firing_vector.must_equal Matrix.column_vector( [] )
|
547
|
-
@s.transitions.tS.delta.must_equal Matrix.zero( @s.n_free.size, 1 )
|
548
|
-
end
|
549
|
-
|
550
|
-
it "1. handles ts transitions" do
|
551
|
-
@s.transitions.ts.delta_closures.must_equal []
|
552
|
-
end
|
553
|
-
|
554
|
-
it "presents sparse stoichiometry vectors for its transitions" do
|
555
|
-
@s.transition( @t1 ).sparse_sv.must_equal Matrix.cv( [-1, 0, 1] )
|
556
|
-
@s.sparse_stoichiometry_vector( of: @t1 )
|
557
|
-
.must_equal Matrix.cv( [-1, -1, 0, 1, 0] )
|
558
|
-
end
|
559
|
-
|
560
|
-
it "presents correspondence matrices free, clamped => all places" do
|
561
|
-
@s.f2a.must_equal Matrix[[0, 0, 0], [1, 0, 0], [0, 1, 0],
|
562
|
-
[0, 0, 1], [0, 0, 0]]
|
563
|
-
@s.c2a.must_equal Matrix[[1, 0], [0, 0], [0, 0], [0, 0], [0, 1]]
|
564
|
-
end
|
565
|
-
end
|
data/test/ttp_pathway.rb
DELETED
@@ -1,233 +0,0 @@
|
|
1
|
-
#! /usr/bin/ruby
|
2
|
-
# coding: utf-8
|
3
|
-
|
4
|
-
# ==============================================================================
|
5
|
-
#
|
6
|
-
# Thymidine triphosphate pathway model.
|
7
|
-
#
|
8
|
-
# Author: Boris Stitnicky
|
9
|
-
# Affiliation:
|
10
|
-
# ... etc etc same shit as in SBML
|
11
|
-
#
|
12
|
-
# ==============================================================================
|
13
|
-
|
14
|
-
# === Load the required libraries.
|
15
|
-
require 'y_nelson' # This pathway model uses FPN domain model.
|
16
|
-
require 'sy' # This pathway model uses 'sy' metrology domain model.
|
17
|
-
require 'mathn' # Standard library 'mathn' is required.
|
18
|
-
include YNelson # pull in the DSL
|
19
|
-
|
20
|
-
require "./ttp_pathway/version" # version number
|
21
|
-
require './ttp_pathway/michaelis_menten' # basic function definitions
|
22
|
-
require './ttp_pathway/general_assumptions' # general model assumptions
|
23
|
-
|
24
|
-
# === Load the chosen cell cycle model.
|
25
|
-
require "./ttp_pathway/simple_cell_cycle"
|
26
|
-
|
27
|
-
# === Load the original version of the dTTP pathway based on the literature.
|
28
|
-
require "./ttp_pathway/literature_model"
|
29
|
-
|
30
|
-
# === Simulate it.
|
31
|
-
set_step 1 # in seconds
|
32
|
-
set_target_time 24.h.in :s
|
33
|
-
set_sampling 5.min.in :s
|
34
|
-
set_simulation_method :pseudo_euler
|
35
|
-
sim = new_simulation guarded: false
|
36
|
-
sim.guarded?
|
37
|
-
sim.run! upto: 10
|
38
|
-
sim.run! upto: 20
|
39
|
-
sim.run! upto: 30
|
40
|
-
sim.run! upto: 40
|
41
|
-
# FIXME: Here it breaks if step is set to
|
42
|
-
# set_step 5 # seconds
|
43
|
-
# it seems that the problem is actually caused by one of the closures
|
44
|
-
# returning an incompatible result (imaginary number in this particular case),
|
45
|
-
# which causes the whole marking vector become imaginary numbers and fail upon
|
46
|
-
# comparison (#>) subsequently.
|
47
|
-
#
|
48
|
-
# The challenge here is to make it easy to debug the models. In execution, I am
|
49
|
-
# against artificial constraints on place marking, and not just because it slows
|
50
|
-
# things down, but mainly because such thing is not a part of the Petri net
|
51
|
-
# business model as I understand it. But at debug time, I am for "type" checking
|
52
|
-
# that identify the source of problem values. And that should be implemented in
|
53
|
-
# simulation, in those several #create_*_closures at the end of the class. There
|
54
|
-
# should be versions of these closures that check the values of the transition
|
55
|
-
# functions as they are produced and pinpoint where the problem is coming from.
|
56
|
-
#
|
57
|
-
# Obviously, YNelson at its current shape has no problems simulating well-written
|
58
|
-
# nets with good simulation settings
|
59
|
-
#
|
60
|
-
# I am not going to program this right now. I'll just look at the simulation
|
61
|
-
# class, and that will be it for this week. Next programming session: Monday.
|
62
|
-
sim.run! upto: 50
|
63
|
-
sim.run! upto: 60
|
64
|
-
sim.run! upto: 70
|
65
|
-
sim.run! upto: 80
|
66
|
-
sim.run! upto: 90
|
67
|
-
sim.run! upto: 100
|
68
|
-
sim.run! upto: 1000
|
69
|
-
sim.run! upto: 10000
|
70
|
-
sim.run!
|
71
|
-
|
72
|
-
sim = new_timed_simulation( guarded: true )
|
73
|
-
sim.run! upto: 1000
|
74
|
-
sim.run! upto: 1000
|
75
|
-
|
76
|
-
# It turns out that simply, the step was too big
|
77
|
-
|
78
|
-
# === Load the acceptance tests for the dTTP pathway behavior.
|
79
|
-
require_relative "ttp_pathway/acceptance_tests"
|
80
|
-
|
81
|
-
# === Run those tests.
|
82
|
-
test simulation
|
83
|
-
|
84
|
-
# === Load the pathway updates according to human judgment.
|
85
|
-
require_relative "ttp_pathway/model_correction"
|
86
|
-
|
87
|
-
# === Rerun the simulation.
|
88
|
-
run!
|
89
|
-
|
90
|
-
# === Run those tests.
|
91
|
-
test simulation
|
92
|
-
|
93
|
-
# Now, having at our disposal a satisfactory dTTP pathway, we can simulate
|
94
|
-
# its behavior throughout the cell cycle.
|
95
|
-
|
96
|
-
# === Rerun the simulation.
|
97
|
-
run!
|
98
|
-
|
99
|
-
# === Visualization suggestions
|
100
|
-
plot :all, except: Timer # marking of all the FPN places except Timer
|
101
|
-
|
102
|
-
plot [ S_phase, A_phase, Cdc20A ] # cell-cycle places marking
|
103
|
-
plot [ S_phase, A_phase, Cdc20A, TK1, TK1di, TK1tetra, TK1di_P, TMPK ] # TTP pathway concentrations
|
104
|
-
plot [ S_phase, TK1, TK1di, TK1tetra, TK1di_P ] # TTP pathway enzyme concentrations
|
105
|
-
plot [ S_phase, Thymidine, TMP, TDP, TTP, T23P ] # TTP patwhay concentrations simplified
|
106
|
-
plot :flux, except: Clock # all flux except time flow
|
107
|
-
plot :flux, except: [ Clock, T23P_flux_clamp, TMP_flux_clamp,
|
108
|
-
Thymidine_flux_clamp ] # all except flux clamps
|
109
|
-
plot :state, except: [ Timer, AMP, ADP, ATP, UTP, UDP, UMP, GMP, DeoxyATP,
|
110
|
-
DeoxyADP, DeoxyAMP, DeoxyCytidine, DeoxyCMP, DeoxyCDP,
|
111
|
-
DeoxyCTP, DeoxyGTP, DeoxyGMP, DeoxyUridine, DeoxyUMP,
|
112
|
-
DeoxyUDP, DeoxyUTP, DeoxyT23P ] # cell cycle marking
|
113
|
-
|
114
|
-
# Now let's look into the graph visualization.
|
115
|
-
|
116
|
-
# Define function to display it with kioclient
|
117
|
-
#
|
118
|
-
def showit( fɴ )
|
119
|
-
system "sleep 0.2; kioclient exec 'file:%s'" %
|
120
|
-
File.expand_path( '.', fɴ )
|
121
|
-
end
|
122
|
-
|
123
|
-
# Define enzyme places
|
124
|
-
enzyme_places = {
|
125
|
-
TK1: "TK1",
|
126
|
-
TK1di: "TK1 dimer",
|
127
|
-
TK1di_P: "TK1 phosphorylated dimer",
|
128
|
-
TK1tetra: "TK1 tetramer",
|
129
|
-
TMPK: "TMPK"
|
130
|
-
}
|
131
|
-
|
132
|
-
# Define small molecule places
|
133
|
-
small_molecule_places = {
|
134
|
-
Thymidine: "Thymidine",
|
135
|
-
TMP: "Thymidine monophosphate",
|
136
|
-
T23P: "Thymidine diphosphate / triphosphate pool",
|
137
|
-
TDP: "Thymidine diphosphate",
|
138
|
-
TTP: "Thymidine triphosphate"
|
139
|
-
}
|
140
|
-
|
141
|
-
# Define graphviz places
|
142
|
-
def graphviz places
|
143
|
-
require 'graphviz'
|
144
|
-
γ = GraphViz.new :G, type: :digraph # Create a new graph
|
145
|
-
|
146
|
-
# # set global node options
|
147
|
-
# γ.node[:color] = "#ddaa66"
|
148
|
-
# γ.node[:style] = "filled"
|
149
|
-
# γ.node[:shape] = "box"
|
150
|
-
# γ.node[:penwidth] = "1"
|
151
|
-
# γ.node[:fontname] = "Trebuchet MS"
|
152
|
-
# γ.node[:fontsize] = "8"
|
153
|
-
# γ.node[:fillcolor] = "#ffeecc"
|
154
|
-
# γ.node[:fontcolor] = "#775500"
|
155
|
-
# γ.node[:margin] = "0.0"
|
156
|
-
|
157
|
-
# # set global edge options
|
158
|
-
# γ.edge[:color] = "#999999"
|
159
|
-
# γ.edge[:weight] = "1"
|
160
|
-
# γ.edge[:fontsize] = "6"
|
161
|
-
# γ.edge[:fontcolor] = "#444444"
|
162
|
-
# γ.edge[:fontname] = "Verdana"
|
163
|
-
# γ.edge[:dir] = "forward"
|
164
|
-
# γ.edge[:arrowsize] = "0.5"
|
165
|
-
|
166
|
-
nodes = Hash[ places.map { |pɴ, label| # make nodes
|
167
|
-
[ pɴ, γ.add_nodes( label ) ]
|
168
|
-
} ]
|
169
|
-
|
170
|
-
places.each { |pɴ, label| # add edges
|
171
|
-
p = place pɴ
|
172
|
-
p.upstream_places.each { |up|
|
173
|
-
node = nodes[ pɴ ]
|
174
|
-
next unless places.map { |ɴ, _| ɴ }.include? up.name
|
175
|
-
next if up == p
|
176
|
-
upstream_node = nodes[ up.name ]
|
177
|
-
upstream_node << node
|
178
|
-
}
|
179
|
-
}
|
180
|
-
|
181
|
-
γ.output png: "enzymes.png" # Generate output image
|
182
|
-
showit "enzymes.png"
|
183
|
-
end
|
184
|
-
|
185
|
-
[ enzyme_places, small_molecule_places ].each { |ꜧ|
|
186
|
-
ꜧ.define_singleton_method :+ do |o| merge o end }
|
187
|
-
|
188
|
-
graphviz enzyme_places
|
189
|
-
graphviz small_molecule_places
|
190
|
-
graphviz enzyme_places + small_molecule_places # combining pathways
|
191
|
-
|
192
|
-
net.visualize
|
193
|
-
|
194
|
-
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# ==============================================================================
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#
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# 1. Please note that the script contained in this file does not constitute
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# programming in the sense of software development. It is simply scripted
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# user interaction with YPetri FPN simulator. This user interaction takes
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# place inside the interactive Ruby session (irb), or it can be saved and
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# run all at once as a script. The user has at her disposal the devices and
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# language constructs of full-fledged Ruby. The user is not sandboxed (the
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# problem of many GUI-based "applications"). In other words, the simulation
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# software does not wrap its host language. Rather, it extends Ruby, giving
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# its interactive session new, pathway-specific abilities. No constraints
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# are placed on how complicated or intelligent the user's use of the software
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# can be.
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#
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# 2. However, on this dTTP pathway model, it can be already noted, that there
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# would be certain actions, that the user will have to repeat in most of
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# her biological models usin YPetri. For example, Michaelis & Menten function
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# definitions are to be expected in many pathway models. More seriously, the
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# Petri net models of enzymes and signal proteins suffer exponential explosion
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# with number of eligible reactants, competitive inhibitors, and other
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# interacting molecules. In typical smaller pathway models, this explosion is
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# not deadly, because only few of these interacting molecules are considered.
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# But the amount of scripting the user is required to do would still be
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# reduced many times, if such enzymes and signal proteins can be expressed
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# declaratively, rather than by manual enumeration of their Petri net
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# transitions. All of this provides motivation towards developing even more
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# concise way of pathway encoding than that provided by plain FPN.
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#
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# 3. In the planned more concise pathway encoding (that would subsume the
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# functionality of the current standards such as SBML), there is one more
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# major concern – storing relations. I feel tempted to use Ted Nelson's zz
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# structure as an alternative to usual SQL and non-SQL relational databases.
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# The usability of zz structures in bioinformatics has already been noted.
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# However, I am aware of the advantage held by the existing database merely
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# by the virtue of its maturity. To account for the possibility, that my zz
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# domain model would become a bottleneck, I will leave the back door open on
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# the possibility of using existing database software later on.
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#
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# ==============================================================================
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