y_petri 2.1.26 → 2.1.30

checksums.yaml

@@ -1,7 +1,7 @@
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data/lib/y_petri/core/timed/gillespie.rb

@@ -21,16 +21,16 @@ module YPetri::Core::Timed::Gillespie
   def step! Δt=simulation.step
     @gillespie_time = curr_time = simulation.time
     target_time = curr_time + Δt
-    propensities = propensity_vector_TS
-    puts "Propensity vector TS is:"
-    Kernel::p propensities
+    propensities = propensity_vector_TS.column_to_a
     update_next_gillespie_time( propensities )
     until ( @next_gillespie_time > target_time )
       gillespie_step! propensities
-      note_state_change
-      propensities = propensity_vector_TS
+      simulation.recorder.alert
+      propensities = propensity_vector_TS.column_to_a
       update_next_gillespie_time( propensities )
     end
+    simulation.increment_time! Δt
+    print '.'
   end
 
   # Name of this method.
@@ -61,22 +61,33 @@ module YPetri::Core::Timed::Gillespie
     Distribution::Exponential.p_value( rng.rand, sum )
   end
 
+  # Given a discrete probability distributions, this function makes a random
+  # choice of a category.
+  # 
+  def choose_from_discrete_distribution( distribution )
+    sum = rng.rand * distribution.reduce( :+ )
+    distribution.index do |p|
+      sum -= p
+      sum <= 0
+    end
+  end
+
   # Chooses the transition to fire.
   # 
   def choose_TS_transition( propensities )
-    n = rng.rand * Σ( propensities )
-    transitions[ propensities.index do |propensity|
-                   n -= propensity
-                   n <= 0
-                 end ]
+    transitions.fetch choose_from_discrete_distribution( propensities )
   end
 
-  # Fires a transition.
+  # Fires a transitions. More precisely, performs a single transition event with
+  # certain stoichiometry, adding / subtracting the number of quanta to / from
+  # the codomain places as indicated by the stoichiometry.
   # 
   def fire!( transition )
-    transition.∇.map { |place, change|
-      mv = simulation.marking_vector
-      mv.set( place, mv.fetch( place ) + change )
+    cd, sto = transition.codomain, transition.stoichiometry
+    mv = simulation.m_vector
+    cd.zip( sto ).each { |pl, coeff|
+      mv.set( pl, mv.fetch( pl ) + pl.quantum * coeff )
     }
+    @gillespie_time = @next_gillespie_time
   end
 end # YPetri::Core::Timed::Euler

data/lib/y_petri/core/timed.rb

@@ -18,8 +18,8 @@ class YPetri::Core::Timed < YPetri::Core
   # 
   def step! Δt=simulation.step
     increment_marking_vector Δ( Δt )
-    increment_time! Δt
-    note_state_change
+    simulation.increment_time! Δt
+    simulation.recorder.alert
   end
 
   # Gradient for free places.

data/lib/y_petri/simulation/marking_vector/access.rb

@@ -8,8 +8,7 @@ class YPetri::Simulation::MarkingVector
     # 
     def m_vector ids=nil
       if ids.nil? then
-        msg = "Marking vector not established yet!"
-        @m_vector or fail TypeError, msg
+        @m_vector or fail TypeError, "Marking vector not established yet!"
       else
         m_vector.select( ids )
       end

data/lib/y_petri/simulation/place_representation.rb

@@ -4,6 +4,8 @@
 # 
 class YPetri::Simulation
   class PlaceRepresentation < ElementRepresentation
+    attr_reader :quantum
+
     # Index
     def m_vector_index
       places.index( self )
@@ -13,6 +15,7 @@ class YPetri::Simulation
     # 
     def initialize net_place
       super
+      @quantum = source.quantum
     end
 
     # Setter of clamp.

data/lib/y_petri/version.rb

@@ -1,4 +1,4 @@
 module YPetri
-  VERSION = "2.1.26"
+  VERSION = "2.1.30"
   DEBUG = false
 end

data/test/examples/gillespie.rb

@@ -0,0 +1,25 @@
+#! /usr/bin/ruby
+# coding: utf-8
+
+# ==============================================================================
+# 
+# encoding: utf-8
+
+require 'y_petri'
+require 'sy'       # This pathway model uses 'sy' metrology domain model.
+require 'mathn'    # Standard library 'mathn' is required.
+include YPetri     # pull in the DSL
+
+A = Place m!: 10
+B = Place m!: 10
+A2B = Transition s: { A: -1, B: 1 }, rate: 0.1
+B2A = Transition s: { A: 1, B: -1 }, rate: 0.05
+
+set_step 1 # in seconds
+set_target_time 100
+set_sampling 1
+set_simulation_method :gillespie
+sim = new_simulation guarded: false
+run!
+
+plot_state

data/test/simulation_test.rb

@@ -56,6 +56,7 @@ describe YPetri::Simulation do
         @s.net.places.names.must_equal [:A, :B]
         @s.pn.must_equal [:A, :B]
         @s.send( :places ).free.size.must_equal 1
+        @s.send( :places ).first.quantum.must_equal 1
         @s.send( :free_places ).names.must_equal [:A]
         @s.send( :places ).clamped.size.must_equal 1
         @s.send( :clamped_places ).names.must_equal [:B]

data/test/ttp_pathway.rb

@@ -0,0 +1,233 @@
+#! /usr/bin/ruby
+# coding: utf-8
+
+# ==============================================================================
+# 
+# Thymidine triphosphate pathway model.
+# 
+# Author: Boris Stitnicky
+# Affiliation:
+# ... etc etc same shit as in SBML
+# 
+# ==============================================================================
+
+# === Load the required libraries.
+require 'y_nelson' # This pathway model uses FPN domain model.
+require 'sy'       # This pathway model uses 'sy' metrology domain model.
+require 'mathn'    # Standard library 'mathn' is required.
+include YNelson    # pull in the DSL
+
+require "./ttp_pathway/version"             # version number
+require './ttp_pathway/michaelis_menten'    # basic function definitions
+require './ttp_pathway/general_assumptions' # general model assumptions
+
+# === Load the chosen cell cycle model.
+require "./ttp_pathway/simple_cell_cycle"
+
+# === Load the original version of the dTTP pathway based on the literature.
+require "./ttp_pathway/literature_model"
+
+# === Simulate it.
+set_step 1 # in seconds
+set_target_time 24.h.in :s
+set_sampling 5.min.in :s
+set_simulation_method :pseudo_euler
+sim = new_simulation guarded: false
+sim.guarded?
+sim.run! upto: 10
+sim.run! upto: 20
+sim.run! upto: 30
+sim.run! upto: 40
+# FIXME: Here it breaks if step is set to
+#     set_step 5 # seconds
+# it seems that the problem is actually caused by one of the closures
+# returning an incompatible result (imaginary number in this particular case),
+# which causes the whole marking vector become imaginary numbers and fail upon
+# comparison (#>) subsequently.
+#
+# The challenge here is to make it easy to debug the models. In execution, I am
+# against artificial constraints on place marking, and not just because it slows
+# things down, but mainly because such thing is not a part of the Petri net
+# business model as I understand it. But at debug time, I am for "type" checking
+# that identify the source of problem values. And that should be implemented in
+# simulation, in those several #create_*_closures at the end of the class. There
+# should be versions of these closures that check the values of the transition
+# functions as they are produced and pinpoint where the problem is coming from.
+#
+# Obviously, YNelson at its current shape has no problems simulating well-written
+# nets with good simulation settings
+#
+# I am not going to program this right now. I'll just look at the simulation
+# class, and that will be it for this week. Next programming session: Monday.
+sim.run! upto: 50
+sim.run! upto: 60
+sim.run! upto: 70
+sim.run! upto: 80
+sim.run! upto: 90
+sim.run! upto: 100
+sim.run! upto: 1000
+sim.run! upto: 10000
+sim.run!
+
+sim = new_timed_simulation( guarded: true )
+sim.run! upto: 1000
+sim.run! upto: 1000
+
+# It turns out that simply, the step was too big
+
+# === Load the acceptance tests for the dTTP pathway behavior.
+require_relative "ttp_pathway/acceptance_tests"
+
+# === Run those tests.
+test simulation
+
+# === Load the pathway updates according to human judgment.
+require_relative "ttp_pathway/model_correction"
+
+# === Rerun the simulation.
+run!
+
+# === Run those tests.
+test simulation
+
+# Now, having at our disposal a satisfactory dTTP pathway, we can simulate
+# its behavior throughout the cell cycle.
+
+# === Rerun the simulation.
+run!
+
+# === Visualization suggestions
+plot :all, except: Timer # marking of all the FPN places except Timer
+
+plot [ S_phase, A_phase, Cdc20A ] # cell-cycle places marking
+plot [ S_phase, A_phase, Cdc20A, TK1, TK1di, TK1tetra, TK1di_P, TMPK ] # TTP pathway concentrations
+plot [ S_phase, TK1, TK1di, TK1tetra, TK1di_P ] # TTP pathway enzyme concentrations
+plot [ S_phase, Thymidine, TMP, TDP, TTP, T23P ] # TTP patwhay concentrations simplified
+plot :flux, except: Clock # all flux except time flow
+plot :flux, except: [ Clock, T23P_flux_clamp, TMP_flux_clamp,
+                      Thymidine_flux_clamp ] # all except flux clamps
+plot :state, except: [ Timer, AMP, ADP, ATP, UTP, UDP, UMP, GMP, DeoxyATP,
+                       DeoxyADP, DeoxyAMP, DeoxyCytidine, DeoxyCMP, DeoxyCDP,
+                       DeoxyCTP, DeoxyGTP, DeoxyGMP, DeoxyUridine, DeoxyUMP,
+                       DeoxyUDP, DeoxyUTP, DeoxyT23P ] # cell cycle marking
+
+# Now let's look into the graph visualization.
+
+# Define function to display it with kioclient
+# 
+def showit( fɴ )
+  system "sleep 0.2; kioclient exec 'file:%s'" %
+    File.expand_path( '.', fɴ )
+end
+
+# Define enzyme places
+enzyme_places = {
+  TK1: "TK1",
+  TK1di: "TK1 dimer",
+  TK1di_P: "TK1 phosphorylated dimer",
+  TK1tetra: "TK1 tetramer",
+  TMPK: "TMPK"
+}
+
+# Define small molecule places
+small_molecule_places = {
+  Thymidine: "Thymidine",
+  TMP: "Thymidine monophosphate",
+  T23P: "Thymidine diphosphate / triphosphate pool",
+  TDP: "Thymidine diphosphate",
+  TTP: "Thymidine triphosphate"
+}
+
+# Define graphviz places
+def graphviz places
+  require 'graphviz'
+  γ = GraphViz.new :G, type: :digraph  # Create a new graph
+
+  # # set global node options
+  # γ.node[:color] = "#ddaa66"
+  # γ.node[:style] = "filled"
+  # γ.node[:shape] = "box"
+  # γ.node[:penwidth] = "1"
+  # γ.node[:fontname] = "Trebuchet MS"
+  # γ.node[:fontsize] = "8"
+  # γ.node[:fillcolor] = "#ffeecc"
+  # γ.node[:fontcolor] = "#775500"
+  # γ.node[:margin] = "0.0"
+
+  # # set global edge options
+  # γ.edge[:color] = "#999999"
+  # γ.edge[:weight] = "1"
+  # γ.edge[:fontsize] = "6"
+  # γ.edge[:fontcolor] = "#444444"
+  # γ.edge[:fontname] = "Verdana"
+  # γ.edge[:dir] = "forward"
+  # γ.edge[:arrowsize] = "0.5"
+
+  nodes = Hash[ places.map { |pɴ, label|         # make nodes
+                  [ pɴ, γ.add_nodes( label ) ]
+                } ]
+
+  places.each { |pɴ, label|                      # add edges
+    p = place pɴ
+    p.upstream_places.each { |up|
+      node = nodes[ pɴ ]
+      next unless places.map { |ɴ, _| ɴ }.include? up.name
+      next if up == p
+      upstream_node = nodes[ up.name ]
+      upstream_node << node
+    }
+  }
+
+  γ.output png: "enzymes.png"        # Generate output image
+  showit "enzymes.png"
+end
+
+[ enzyme_places, small_molecule_places ].each { |ꜧ|
+  ꜧ.define_singleton_method :+ do |o| merge o end }
+
+graphviz enzyme_places
+graphviz small_molecule_places
+graphviz enzyme_places + small_molecule_places # combining pathways
+
+net.visualize
+
+
+# ==============================================================================
+# 
+# 1. Please note that the script contained in this file does not constitute
+# programming in the sense of software development. It is simply scripted
+# user interaction with YPetri FPN simulator. This user interaction takes
+# place inside the interactive Ruby session (irb), or it can be saved and
+# run all at once as a script. The user has at her disposal the devices and
+# language constructs of full-fledged Ruby. The user is not sandboxed (the
+# problem of many GUI-based "applications"). In other words, the simulation
+# software does not wrap its host language. Rather, it extends Ruby, giving
+# its interactive session new, pathway-specific abilities. No constraints
+# are placed on how complicated or intelligent the user's use of the software
+# can be.
+#
+# 2. However, on this dTTP pathway model, it can be already noted, that there
+# would be certain actions, that the user will have to repeat in most of
+# her biological models usin YPetri. For example, Michaelis & Menten function
+# definitions are to be expected in many pathway models. More seriously, the
+# Petri net models of enzymes and signal proteins suffer exponential explosion
+# with number of eligible reactants, competitive inhibitors, and other
+# interacting molecules. In typical smaller pathway models, this explosion is
+# not deadly, because only few of these interacting molecules are considered.
+# But the amount of scripting the user is required to do would still be
+# reduced many times, if such enzymes and signal proteins can be expressed
+# declaratively, rather than by manual enumeration of their Petri net
+# transitions. All of this provides motivation towards developing even more
+# concise way of pathway encoding than that provided by plain FPN.
+#
+# 3. In the planned more concise pathway encoding (that would subsume the
+# functionality of the current standards such as SBML), there is one more
+# major concern – storing relations. I feel tempted to use Ted Nelson's zz
+# structure as an alternative to usual SQL and non-SQL relational databases.
+# The usability of zz structures in bioinformatics has already been noted.
+# However, I am aware of the advantage held by the existing database merely
+# by the virtue of its maturity. To account for the possibility, that my zz
+# domain model would become a bottleneck, I will leave the back door open on
+# the possibility of using existing database software later on.
+# 
+# ==============================================================================

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: y_petri
 version: !ruby/object:Gem::Version
-  version: 2.1.26
+  version: 2.1.30
 platform: ruby
 authors:
 - boris
@@ -178,12 +178,14 @@ files:
 - test/examples/demonstrator_3.rb
 - test/examples/demonstrator_4.rb
 - test/examples/example_2.rb
+- test/examples/gillespie.rb
 - test/examples/manual_examples.rb
 - test/net_test.rb
 - test/place_test.rb
 - test/sim_test
 - test/simulation_test.rb
 - test/transition_test.rb
+- test/ttp_pathway.rb
 - test/world_mock.rb
 - test/world_test.rb
 - test/y_petri_test.rb
@@ -224,12 +226,14 @@ test_files:
 - test/examples/demonstrator_3.rb
 - test/examples/demonstrator_4.rb
 - test/examples/example_2.rb
+- test/examples/gillespie.rb
 - test/examples/manual_examples.rb
 - test/net_test.rb
 - test/place_test.rb
 - test/sim_test
 - test/simulation_test.rb
 - test/transition_test.rb
+- test/ttp_pathway.rb
 - test/world_mock.rb
 - test/world_test.rb
 - test/y_petri_test.rb