y_petri 2.4.8 → 2.4.9

data/Introduction_to_YPetri_and_YNelson.lyx

@@ -0,0 +1,3429 @@
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+\index Index
+\shortcut idx
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+
+\begin_body
+
+\begin_layout Title
+Introduction to YNelson and YPetri (hands-on tutorial)
+\end_layout
+
+\begin_layout Part*
+Introduction
+\end_layout
+
+\begin_layout Standard
+This document is a hands-on guide to 
+\family typewriter
+\color blue
+YPetri
+\family default
+\color inherit
+, 
+\family typewriter
+\color blue
+YNelson
+\family default
+\color inherit
+ and 
+\emph on
+\color green
+Nelson nets
+\emph default
+\color inherit
+, which in turn rely on 
+\color red
+Ruby
+\color inherit
+ language.
+ It is not assumed you are familiar with Ruby, you can follow this guide
+ even if you never heard about it (but you will have to install it).
+ You more than likely never heard about Nelson nets.
+ Nelson net is a novel concept of 
+\emph on
+\color green
+Petri nets
+\emph default
+\color inherit
+ crossed with Ted Nelson's 
+\emph on
+\color green
+ZZ structures
+\emph default
+\color inherit
+.
+ Do not worry about them: just follow the guide and you will learn everything
+ in time.
+ The text of this guide lets you know when new keywords and are introduced.
+ When mentioned for the first time, 
+\color red
+Ruby keywords and terms
+\color inherit
+ are highlighted in red, 
+\color green
+Petri net terms
+\color inherit
+ in green, and 
+\family typewriter
+\color blue
+YPetri / YNelson
+\family default
+ keywords and terms
+\color inherit
+ in blue throughout this document.
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+\color blue
+YNelson
+\family default
+\color inherit
+ serves to specify and simulate Nelson nets, a derivative of 
+\emph on
+\color green
+functional
+\emph default
+ 
+\emph on
+Petri nets
+\emph default
+\color inherit
+ that live in 
+\emph on
+\color green
+ZZ space
+\emph default
+\color inherit
+.
+ (You don't need to worry about ZZ space yet.) 
+\family typewriter
+\color blue
+YPetri
+\family default
+\color inherit
+ serves to specify and simulate Petri nets.
+ Petri nets are one of the basic formalisms in systems simulation.
+ I designed 
+\family typewriter
+YPetri
+\family default
+ and 
+\family typewriter
+YNelson
+\family default
+ because I needed to specify biochemical systems and I believed a Ruby DSL
+ would be ideal for that task.
+ Use of Petri nets for specifying biochemical systems is reviewed eg.
+ in 
+\begin_inset CommandInset citation
+LatexCommand citet
+key "Bos2008mbs"
+
+\end_inset
+
+ and 
+\begin_inset CommandInset citation
+LatexCommand citet
+key "Koch2015pns"
+
+\end_inset
+
+.
+ 
+\family typewriter
+YPetri
+\family default
+ provides a universal Petri net abstraction similar, but not identical with
+ 
+\emph on
+\color green
+hybrid functional Petri net (HFPN)
+\emph default
+\color inherit
+ introduced by 
+\begin_inset CommandInset citation
+LatexCommand citet
+key "Matsuno2011brs"
+
+\end_inset
+
+.
+ 
+\family typewriter
+YPetri
+\family default
+ / 
+\family typewriter
+YNelson
+\family default
+ serve equally well not just for biochemical systems, but for arbitrary
+ dynamical systems.
+\end_layout
+
+\begin_layout Standard
+Finally, please forgive me for taking your time with this guide.
+ If you want to seriously work with 
+\emph on
+complicated
+\emph default
+ Petri Nets, no tool can avoid taking you through the process of learning
+ the language and the tool's interface.
+ Visual Petri net modelling tools are nice for simple tasks, such as drawing
+ arcs between places and transitions, but you need text anyway to write
+ the mathematical functions that govern firing of transitions.
+ 
+\family typewriter
+YPetri
+\family default
+ / 
+\family typewriter
+YNelson
+\family default
+ are all textual without commiting the sin of introducing a new programming
+ language.
+ They are implemented as 
+\emph on
+\color red
+internal domain-specific languages (DSL)
+\emph default
+\color inherit
+ using Ruby as a host language.
+ You can run them interactively from 
+\color red
+Ruby interpreter (
+\emph on
+irb
+\emph default
+)
+\color inherit
+.
+ In this way, you can freely use the host language to automate your interaction
+ with Petri nets.
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+YPetri
+\family default
+ / 
+\family typewriter
+YNelson
+\family default
+ are publicly available as 
+\emph on
+\color blue
+
+\begin_inset CommandInset href
+LatexCommand href
+name "y_petri"
+target "https://rubygems.org/gems/y_petri"
+
+\end_inset
+
+
+\emph default
+\color inherit
+ and 
+\emph on
+\color blue
+
+\begin_inset CommandInset href
+LatexCommand href
+name "y_nelson gem"
+target "https://rubygems.org/gems/y_nelson"
+
+\end_inset
+
+
+\emph default
+\color inherit
+ gems (
+\emph on
+\color red
+gem
+\emph default
+\color inherit
+ = Ruby library).
+ 
+\family typewriter
+YNelson
+\family default
+ depends on 
+\family typewriter
+YPetri
+\family default
+ and 
+\family typewriter
+Yzz
+\family default
+ gems, which in turn depend on our 
+\family typewriter
+YSupport
+\family default
+ gem.
+ Splitting the more general concerns to multiple gem is a desirable feature
+ – separation of concerns is a maxim of good software engineering.
+ I also separated dealing with physical units in your models out into 
+\family typewriter
+SY
+\family default
+ gem (
+\emph on
+\color blue
+
+\begin_inset CommandInset href
+LatexCommand href
+name "sy"
+target "https://rubygems.org/gems/sy"
+
+\end_inset
+
+
+\emph default
+\color inherit
+).
+\end_layout
+
+\begin_layout Part*
+Using This Guide, or 
+\begin_inset Quotes eld
+\end_inset
+
+The Hard Way Is Easier
+\begin_inset Quotes erd
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+The phrase above is borrowed from the textbook by Zed Shaw named 
+\begin_inset Quotes eld
+\end_inset
+
+Learn Ruby the Hard Way
+\begin_inset Quotes erd
+\end_inset
+
+ (highly recommended, 
+\emph on
+\color magenta
+
+\begin_inset CommandInset href
+LatexCommand href
+name "hyperlink here"
+target "http://ruby.learncodethehardway.org/"
+
+\end_inset
+
+
+\emph default
+\color inherit
+).
+ Apart from being a great shark-jumper, Zed is a great teacher familiar
+ with many programming languages, and I will borrow his teaching method
+ here.
+ Citing Zed, 
+\begin_inset Quotes eld
+\end_inset
+
+The title says it's the hard way...
+ but actually it's not.
+\begin_inset Quotes erd
+\end_inset
+
+ It's only 
+\begin_inset Quotes eld
+\end_inset
+
+hard
+\begin_inset Quotes erd
+\end_inset
+
+ because of the way people 
+\emph on
+used
+\emph default
+ to teach things.
+ 
+\family typewriter
+YNelson
+\family default
+ is a language.
+ To learn it and see its usefulness, you will still need to do the incredibly
+ simple things that all language learners do:
+\end_layout
+
+\begin_layout Enumerate
+Go through each example.
+\end_layout
+
+\begin_layout Enumerate
+Type each sample code exactly.
+\end_layout
+
+\begin_layout Enumerate
+Make it run.
+\end_layout
+
+\begin_layout Standard
+\noindent
+That's it.
+ This might feel 
+\emph on
+very
+\emph default
+ difficult at first, but stick with it.
+ It seems stupidly obvious, but if you have a problem installing 
+\family typewriter
+YPetri
+\family default
+ and 
+\family typewriter
+YNelson
+\family default
+, running 
+\emph on
+irb
+\emph default
+ and typing, you will have a problem learning.
+ If you go through this document without actually doing the exercises, you
+ might as well just not even read it.
+ Do not skip and do not skim.
+ By typing each example 
+\emph on
+exactly
+\emph default
+, you will be training your brain to focus on the details of what you are
+ doing, as you are doing it.
+ While you do these examples, typing each one in, you will be making mistakes.
+ It's inevitable; humans do make mistakes.
+ By doing so, you will train yourself to notice mistakes and other problems.
+ Do not copy-paste.
+ Type each code sample in, manually.
+ The point is to train your hands, your brain, and your mind in how to read,
+ write and see Ruby and 
+\family typewriter
+YNelson
+\family default
+ code.
+ If you skip, skim and copy-paste, you are cheating yourself out of the
+ effectiveness of this guide.
+\end_layout
+
+\begin_layout Part*
+Prerequisites
+\end_layout
+
+\begin_layout Standard
+Firstly, you will need a working installation of Ruby 2.3 or later on your
+ computer.
+ Once this condition is met, basic 
+\family typewriter
+YNelson
+\family default
+ installation is as simple as typing 
+\begin_inset Quotes eld
+\end_inset
+
+
+\family typewriter
+gem install y_nelson
+\family default
+
+\begin_inset Quotes erd
+\end_inset
+
+ in the command prompt.
+ This will install most other dependencies, including 
+\family typewriter
+YPetri
+\family default
+.
+ However, 
+\family typewriter
+YPetri
+\family default
+ has other dependencies (gnuplot gem, graphviz gem), whose installation
+ may pose challenges.
+ Once
+\family typewriter
+ YNelson
+\family default
+ is installed, run 
+\emph on
+irb
+\emph default
+ command interpreter, and type:
+\end_layout
+
+\begin_layout LyX-Code
+
+\color red
+require
+\color inherit
+ 'y_nelson';
+\color red
+ include
+\color inherit
+ YNelson
+\end_layout
+
+\begin_layout Standard
+This will augment your irb command session with interactive 
+\family typewriter
+YNelson
+\family default
+ command interface (
+\family typewriter
+YNelson
+\family default
+ DSL CI).
+ You may also choose to work only with 
+\family typewriter
+YPetri
+\family default
+ alone, in which case the require line is:
+\end_layout
+
+\begin_layout LyX-Code
+
+\color red
+require
+\color inherit
+ 'y_petri';
+\color red
+ include
+\color inherit
+ YPetri
+\end_layout
+
+\begin_layout Standard
+You have to re-run 
+\emph on
+irb
+\emph default
+ from the scratch, and re-type '
+\family typewriter
+require
+\family default
+' and '
+\family typewriter
+include
+\family default
+' statements before each of the usage examples written below.
+ The nucleotide metabolism model in Example 3 is not realiscit (its kinetics
+ is not precise).
+ If something in this guide does not work, please do not hesitate to notify
+ me, I will appreciate your feedback.
+\end_layout
+
+\begin_layout Part*
+Example I: Basics
+\end_layout
+
+\begin_layout Standard
+This example is a gentle introduction to Petri net terminology, 
+\family typewriter
+YNelson
+\family default
+ DSL terminology, and Ruby syntax.
+ The most basic capability that 
+\family typewriter
+YNelson
+\family default
+ offers, is that of user-driven 
+\emph on
+\color green
+token game
+\emph default
+\color inherit
+.
+ We will thus create a small Petri net containing 2 
+\emph on
+\color green
+places
+\emph default
+\color inherit
+ and play token game with it.
+\end_layout
+
+\begin_layout Subsection*
+Places
+\end_layout
+
+\begin_layout Standard
+Type:
+\end_layout
+
+\begin_layout LyX-Code
+A = 
+\color blue
+Place
+\color inherit
+( marking: 2 )
+\end_layout
+
+\begin_layout Standard
+Syntactically, this will call 
+\emph on
+\color red
+method
+\emph default
+\color inherit
+ '
+\family typewriter
+Place
+\family default
+' of 
+\family typewriter
+YNelson
+\family default
+ DSL and assign its 
+\emph on
+\color red
+return value
+\emph default
+\color inherit
+ to the 
+\emph on
+\color red
+constant
+\emph default
+\color inherit
+ 
+\family typewriter
+A
+\family default
+.
+ In this case, the method is called with a single 
+\emph on
+\color red
+argument
+\emph default
+\color inherit
+, 
+\family typewriter
+marking
+\family default
+.
+ The return value is an 
+\emph on
+\color red
+object
+\emph default
+\color inherit
+, which is an 
+\emph on
+\color red
+instance
+\emph default
+\color inherit
+ of 
+\family typewriter
+\color blue
+YNelson::Place
+\family default
+\color inherit
+ 
+\emph on
+\color red
+class
+\emph default
+\color inherit
+.
+ We say that 
+\family typewriter
+YNelson::Place
+\family default
+ class 
+\emph on
+\color red
+represents
+\emph default
+\color inherit
+ the concept of Petri net places in 
+\family typewriter
+YNelson
+\family default
+ 
+\emph on
+domain model
+\emph default
+.
+ ('
+\family typewriter
+Place
+\family default
+' method is called a 
+\emph on
+\color red
+constructor
+\emph default
+\color inherit
+ of 
+\family typewriter
+YNelson::Place
+\family default
+, which is not important.) This newly created Petri net place has now been
+ assigned to 
+\family typewriter
+A
+\family default
+.
+ On the screen, you will see the output, which is simply the name of the
+ place – 
+\family typewriter
+A
+\family default
+.
+ In the following text, screen output will always be written immediately
+ under the code sample, preceded by sherocket (
+\family typewriter
+#=>)
+\family default
+:
+\end_layout
+
+\begin_layout LyX-Code
+B = Place( marking: 5 ) #=> B
+\end_layout
+
+\begin_layout Standard
+In the above, we have so far defined 2 Petri net places (named 
+\family typewriter
+A
+\family default
+, 
+\family typewriter
+B
+\family default
+).
+ You can check them by typing:
+\end_layout
+
+\begin_layout LyX-Code
+
+\color blue
+places
+\color inherit
+()                #=> [A, B]
+\end_layout
+
+\begin_layout LyX-Code
+A.
+\color blue
+name
+\color inherit
+()                #=> :A
+\end_layout
+
+\begin_layout Standard
+These have automatically become part of a default Petri net instance (of
+ 
+\family typewriter
+YNelson::Net
+\family default
+ class; object id may vary):
+\end_layout
+
+\begin_layout LyX-Code
+
+\color blue
+net
+\color inherit
+()                   #=> #<Net: name: Top, 2 places, 0 transitions>
+\end_layout
+
+\begin_layout Standard
+Of course, you have full power of Ruby at your disposal.
+ To eg.
+ list only place names as strings, you can use standard Ruby methods:
+\end_layout
+
+\begin_layout LyX-Code
+places.
+\color red
+map
+\color inherit
+( &:name )    #=> [:A, :B]
+\end_layout
+
+\begin_layout Standard
+Here, Ruby 
+\family typewriter
+map
+\family default
+ method transforms the 
+\emph on
+\color red
+array
+\emph default
+\color inherit
+ of places to the array of their names.
+ The advantage of internal DSLs is, that one retains full power of the language,
+ augmented with human-friendly, domain-specific commands.
+ GUI systems generally sandbox the user inside their interface, with no
+ way to overcome its limitations.
+ But let us go on.
+ You can notice that the 
+\emph on
+\color green
+marking
+\emph default
+\color inherit
+ of 
+\family typewriter
+A
+\family default
+, 
+\family typewriter
+B
+\family default
+ is one we gave them upon their creation:
+\end_layout
+
+\begin_layout LyX-Code
+places.map( &:marking ) #=> [2, 5]
+\end_layout
+
+\begin_layout Standard
+In classical Petri nets, marking is understood as the number of 
+\emph on
+\color green
+tokens
+\emph default
+\color inherit
+ in each place, which is always integer.
+ In this case, 
+\family typewriter
+A
+\family default
+ contains 2 tokens, while 
+\family typewriter
+B
+\family default
+ contains 5 tokens.
+ Tokens can represent anything: molecules, parts in the production line,
+ trains in the railway network...
+\end_layout
+
+\begin_layout Subsection*
+Transitions
+\end_layout
+
+\begin_layout Standard
+The behavior of a Petri net is defined by 
+\emph on
+\color green
+transitions
+\emph default
+\color inherit
+.
+ Each transition defines a single operation: Adding / subtracting some amount
+ of tokens to / from some places.
+ Transition operation can often be expressed by 
+\emph on
+stoichiometry
+\emph default
+ – pairs of places with a corresponding number of tokens to add / subtract
+ when the transition 
+\emph on
+\color green
+fires
+\emph default
+\color inherit
+.
+ For example, let us define:
+\end_layout
+
+\begin_layout LyX-Code
+A2B = 
+\color blue
+Transition
+\color inherit
+( stoichiometry: { A: -1, B: 1 } )
+\end_layout
+
+\begin_layout LyX-Code
+#=> A2B
+\end_layout
+
+\begin_layout Standard
+Stoichiometry of this transition is given by the 
+\emph on
+\color red
+hash
+\emph default
+\color inherit
+ 
+\family typewriter
+{ A: -1, B: 1 }
+\family default
+.
+ This hash is available from 
+\family typewriter
+A2B
+\family default
+ via '
+\family typewriter
+\color blue
+s
+\family default
+\color inherit
+' method:
+\end_layout
+
+\begin_layout LyX-Code
+A2B.
+\color blue
+s
+\color inherit
+()               #=> {:A=>-1, :B=>1}
+\end_layout
+
+\begin_layout Standard
+
+\emph on
+\color red
+Keys
+\emph default
+\color inherit
+ of this hash are place names, 
+\emph on
+\color red
+values
+\emph default
+\color inherit
+ are 
+\emph on
+\color green
+stoichiometry coefficients
+\emph default
+\color inherit
+.
+ ('Stoichiometry' is a word known from the domain of chemistry, but '
+\emph on
+stoicheion
+\emph default
+' means simply 'element' in Greek, so there is no problem with using it
+ in the domain of general Petri nets.) To see the stoichiometry coefficients
+ of 
+\family typewriter
+A2B
+\family default
+ as an array, type:
+\end_layout
+
+\begin_layout LyX-Code
+A2B.
+\color blue
+stoichiometry
+\color inherit
+()   #=> [-1, 1]
+\end_layout
+
+\begin_layout Standard
+Simply, 
+\family typewriter
+A2B
+\family default
+ subtracts 1 token from 
+\family typewriter
+A
+\family default
+, and adds 1 token to 
+\family typewriter
+B
+\family default
+.
+ This can represent conversion of 
+\family typewriter
+A
+\family default
+ to 
+\family typewriter
+B
+\family default
+.
+ In classical Petri nets, the arrows connecting places and transitions are
+ called 
+\emph on
+\color green
+arcs
+\emph default
+\color inherit
+.
+ (The term was borrowed from graph theory.) For example, at this moment,
+ our Petri net would contain one arc going from 
+\family typewriter
+A
+\family default
+ to 
+\family typewriter
+A2B
+\family default
+, and one arc going from 
+\family typewriter
+A2B
+\family default
+ to 
+\family typewriter
+B
+\family default
+.
+ In 
+\family typewriter
+YNelson
+\family default
+ domain model, 'arcs' are not first-class citizens.
+ The word is understood simply as a synonym for transitions' connectivity
+ – the list of places connected to each transition:
+\end_layout
+
+\begin_layout LyX-Code
+A2B.
+\color blue
+arcs
+\color inherit
+()            #=> [A, B]
+\end_layout
+
+\begin_layout Standard
+The transition 
+\family typewriter
+A2B
+\family default
+ is 
+\emph on
+\color blue
+timeless
+\emph default
+\color inherit
+:
+\end_layout
+
+\begin_layout LyX-Code
+A2B.
+\color blue
+timeless?
+\color inherit
+()       #=> true
+\end_layout
+
+\begin_layout Standard
+'Timeless' means that the transition's firing is not defined in time – it
+ can fire anytime, as long as it is 
+\emph on
+\color green
+enabled
+\emph default
+\color inherit
+.
+ Classical Petri nets are timeless.
+ In classical Petri nets, a transition is enabled whenever its 
+\emph on
+\color blue
+downstream arcs
+\emph default
+\color inherit
+ allow it to happen.
+ Downstream arcs, or 
+\emph on
+\color blue
+codomain
+\emph default
+\color inherit
+ of a transition (these two are synonyms) are those places, whose marking
+ can be directly affected by the transition's firing.
+ In this case, both 
+\family typewriter
+A
+\family default
+ and 
+\family typewriter
+B
+\family default
+ is affected:
+\end_layout
+
+\begin_layout LyX-Code
+A2B.
+\color blue
+downstream_arcs
+\color inherit
+() #=> [A, B]
+\end_layout
+
+\begin_layout LyX-Code
+A2B.
+\color blue
+codomain
+\color inherit
+()        #=> [A, B]
+\end_layout
+
+\begin_layout Standard
+Since 
+\family typewriter
+A2B
+\family default
+ subtracts tokens from 
+\family typewriter
+A
+\family default
+, it will be enabled so long, as there are any tokens left in 
+\family typewriter
+A
+\family default
+.
+\end_layout
+
+\begin_layout LyX-Code
+A2B.
+\color blue
+enabled?
+\color inherit
+()        #=> true
+\end_layout
+
+\begin_layout Subsection*
+Token game
+\end_layout
+
+\begin_layout Standard
+After 
+\family typewriter
+A2B
+\family default
+ fires, the marking will change:
+\end_layout
+
+\begin_layout LyX-Code
+A2B.
+\color blue
+fire!
+\color inherit
+()                 #=> nil
+\end_layout
+
+\begin_layout LyX-Code
+places.map( &:marking )     #=> [1, 6]
+\end_layout
+
+\begin_layout LyX-Code
+A2B.fire!()                 #=> nil
+\end_layout
+
+\begin_layout LyX-Code
+places.map( &:marking )     #=> [0, 7]
+\end_layout
+
+\begin_layout Standard
+At this point, there are no tokens left in 
+\family typewriter
+A
+\family default
+ and 
+\family typewriter
+A2B
+\family default
+ becomes 
+\emph on
+\color green
+disabled
+\emph default
+\color inherit
+:
+\end_layout
+
+\begin_layout LyX-Code
+A2B.enabled?                #=> false
+\end_layout
+
+\begin_layout Standard
+Attempt to fire a disabled transition 
+\emph on
+\color red
+raises
+\emph default
+\color inherit
+ an 
+\emph on
+\color red
+error
+\emph default
+\color inherit
+ (in Ruby, errors are friendly objects, who, like damsels in distress, are
+ meant to be rescued with a bonus outcome):
+\end_layout
+
+\begin_layout LyX-Code
+A2B.fire!
+\end_layout
+
+\begin_layout LyX-Code
+#=> YPetri::GuardError: Marking -1:Fixnum of A should not be negative!
+\end_layout
+
+\begin_layout Subsection*
+Functional transitions and non-integer marking
+\end_layout
+
+\begin_layout Standard
+So far, all the examples were compatible with classical Petri nets.
+ But 
+\family typewriter
+YNelson
+\family default
+ goes beyond – it represents 
+\emph on
+functional Petri nets
+\emph default
+, similar to 
+\emph on
+Hybrid Functional Petri Net (HFPN)
+\emph default
+ proposed by 
+\begin_inset CommandInset citation
+LatexCommand citet
+key "Matsuno2011brs"
+
+\end_inset
+
+, which I already mentioned in the introductory part of this document.
+ 
+\family typewriter
+YNelson
+\family default
+ domain model is similar, but not identical to HFPN.
+ On the side of similarities, 
+\family typewriter
+YNelson
+\family default
+ allows non-integer marking of places:
+\end_layout
+
+\begin_layout LyX-Code
+C = Place( 
+\color blue
+marking
+\color inherit
+: 7.77 )  #=> C
+\end_layout
+
+\begin_layout Standard
+Here, you can notice that marking of places can be specified already upon
+ initialization using '
+\family typewriter
+:marking
+\family default
+' 
+\emph on
+\color red
+named argument
+\emph default
+\color inherit
+.
+ Let us now define a 
+\emph on
+\color blue
+timed
+\emph default
+\color inherit
+ transition, representing logarithmic decay of 
+\family typewriter
+C
+\family default
+ with a rate constant of 0.05:
+\end_layout
+
+\begin_layout LyX-Code
+C_decay = Transition( stoichiometry: { C: -1 }, 
+\color blue
+rate
+\color inherit
+: 0.05 )
+\end_layout
+
+\begin_layout LyX-Code
+#=> C_decay
+\end_layout
+
+\begin_layout LyX-Code
+C_decay.
+\color blue
+timed?
+\color inherit
+              #=> true
+\end_layout
+
+\begin_layout Standard
+Here, in the 
+\family typewriter
+transition
+\family default
+ constructor method, apart from '
+\family typewriter
+stoichiometry:
+\family default
+' named argument, another named argument, '
+\family typewriter
+rate:
+\family default
+', is introduced.
+ Under '
+\family typewriter
+rate:
+\family default
+', it is possible to specify the transition's 
+\emph on
+\color green
+function
+\emph default
+\color inherit
+, which governs its rate.
+ Specifying a function in Ruby requires special syntax (called Ruby 
+\emph on
+\color red
+closures
+\emph default
+\color inherit
+), based on lambda calculus.
+ Ruby closures are easy to learn.
+ But for the moment, in 
+\family typewriter
+C_decay
+\family default
+ transition, we are taking use of the convenience, that allows us to pass
+ a numeric value under '
+\family typewriter
+rate:
+\family default
+' named argument, and have 
+\family typewriter
+YNelson
+\family default
+ create default mass action equation, using the supplied number as its rate
+ constant.
+ For 
+\family typewriter
+C_decay
+\family default
+ stoichiometry, 
+\family typewriter
+{ C: -1 }
+\family default
+, default mass action will be logarithmic decay with rate constant 0.05.
+ Naturally, when firing timed transitions, the time interval (
+\begin_inset Formula $\Delta$
+\end_inset
+
+time) must be specified, for which the transition should be active:
+\end_layout
+
+\begin_layout LyX-Code
+C_decay.fire!( 1 )          #=> nil
+\end_layout
+
+\begin_layout LyX-Code
+C.marking                   #=> 7.3815
+\end_layout
+
+\begin_layout LyX-Code
+C_decay.fire! 1             #=> nil
+\end_layout
+
+\begin_layout LyX-Code
+C.marking                   #=> 7.012425
+\end_layout
+
+\begin_layout LyX-Code
+C_decay.fire!( 0.1 )        #=> nil
+\end_layout
+
+\begin_layout LyX-Code
+C.marking                   #=> 6.977362875000001
+\end_layout
+
+\begin_layout LyX-Code
+100.
+\color red
+times
+\color inherit
+ do C_decay.fire! 1 end #=> 100
+\end_layout
+
+\begin_layout LyX-Code
+C.marking                   #=> 0.04130968078231133
+\end_layout
+
+\begin_layout Standard
+The penultimate statement was a call of Ruby '
+\family typewriter
+times
+\family default
+' method with the integer 
+\family typewriter
+100
+\family default
+ as the receiver, which results in 100 time repetition of the statement
+ inside 
+\family typewriter
+\color red
+do ...
+ end 
+\family default
+\emph on
+block
+\emph default
+\color inherit
+.
+ Instead of 
+\family typewriter
+do ...
+ end
+\family default
+, it is possible to write a block using curly braces 
+\family typewriter
+\color red
+{ ...
+ }
+\family default
+\color inherit
+:
+\end_layout
+
+\begin_layout LyX-Code
+100.times { C_decay.fire! 1 } #=> 100
+\end_layout
+
+\begin_layout Standard
+This will cause another 100 time units of 
+\family typewriter
+C_decay
+\family default
+ firing.
+ This brings 
+\family typewriter
+C
+\family default
+ marking down to almost zero:
+\end_layout
+
+\begin_layout LyX-Code
+C.marking                   #=> 0.00024457517215434527
+\end_layout
+
+\begin_layout Subsection*
+Four transition types
+\end_layout
+
+\begin_layout Standard
+Thus far, we have demonstrated transitions with stoichiometry, which were
+ either 
+\emph on
+timed
+\emph default
+ or not timed (
+\emph on
+timeless
+\emph default
+).
+ Timed transitions are denoted by capital 
+\begin_inset Quotes eld
+\end_inset
+
+
+\family typewriter
+T
+\family default
+
+\begin_inset Quotes erd
+\end_inset
+
+, timeless transitions by small 
+\begin_inset Quotes eld
+\end_inset
+
+
+\family typewriter
+t
+\family default
+
+\begin_inset Quotes erd
+\end_inset
+
+.
+ Similarly, stoichiometric transitions are denoted by capital 
+\begin_inset Quotes eld
+\end_inset
+
+
+\family typewriter
+S
+\family default
+
+\begin_inset Quotes erd
+\end_inset
+
+, while transitions without stoichiometry (
+\emph on
+non-stoichiometric
+\emph default
+ transitions) by small 
+\begin_inset Quotes eld
+\end_inset
+
+
+\family typewriter
+s
+\family default
+
+\begin_inset Quotes erd
+\end_inset
+
+.
+ Together, this gives 4 basic types of transitions: 
+\family typewriter
+TS
+\family default
+, 
+\family typewriter
+tS
+\family default
+, 
+\family typewriter
+Ts
+\family default
+, and 
+\family typewriter
+ts
+\family default
+.
+\end_layout
+
+\begin_layout Standard
+The user can ask the type of a transition by calling the 
+\family typewriter
+\color blue
+type
+\family default
+\color inherit
+ method:
+\end_layout
+
+\begin_layout LyX-Code
+A2B.type                    #=> :tS
+\end_layout
+
+\begin_layout Standard
+Or investigate the type with inquirer methods:
+\end_layout
+
+\begin_layout LyX-Code
+A2B.
+\color blue
+t?
+\color inherit
+                      #=> true
+\end_layout
+
+\begin_layout LyX-Code
+A2B.
+\color blue
+T?
+\color inherit
+                      #=> false
+\end_layout
+
+\begin_layout LyX-Code
+A2B.
+\color blue
+s?
+\color inherit
+                      #=> false
+\end_layout
+
+\begin_layout LyX-Code
+A2B.
+\color blue
+S?
+\color inherit
+                      #=> true
+\end_layout
+
+\begin_layout LyX-Code
+A2B.
+\color blue
+TS?
+\color inherit
+                     #=> false
+\end_layout
+
+\begin_layout LyX-Code
+A2B.
+\color blue
+tS?
+\color inherit
+                     #=> true
+\end_layout
+
+\begin_layout LyX-Code
+A2B.
+\color blue
+Ts?
+\color inherit
+                     #=> false
+\end_layout
+
+\begin_layout LyX-Code
+A2B.
+\color blue
+ts?
+\color inherit
+                     #=> false
+\end_layout
+
+\begin_layout Subsection*
+Assignment transitions
+\end_layout
+
+\begin_layout Standard
+In 
+\family typewriter
+YNelson
+\family default
+, there is one more transition type: an assignment transition, denoted by
+ 
+\begin_inset Quotes eld
+\end_inset
+
+
+\family typewriter
+A
+\family default
+
+\begin_inset Quotes erd
+\end_inset
+
+.
+ Assignment transitions do not add or subtract tokens from their target,
+ but completely replace the codomain marking with their output.
+ (Again, in 
+\family typewriter
+YNelson
+\family default
+ transitions, 
+\emph on
+domain
+\emph default
+ and 
+\emph on
+codomain
+\emph default
+ mean respectively upstream and downstream places.) Transitions other than
+ 
+\family typewriter
+A
+\family default
+ transitions can be collectively called non-assignment transitions, denoted
+ by small 
+\begin_inset Quotes eld
+\end_inset
+
+
+\family typewriter
+a
+\family default
+
+\begin_inset Quotes erd
+\end_inset
+
+.
+ Note that assignment action is already achievable with plain 
+\family typewriter
+ts
+\family default
+ transitions (by subtracting away the previous codomain marking), so 
+\family typewriter
+A
+\family default
+ transitions are not strictly needed – their separate existence is just
+ a syntactic convenience.
+\end_layout
+
+\begin_layout Standard
+One way to construct assignment transitions is by setting 
+\family typewriter
+:assignment
+\family default
+ named argument to 
+\emph on
+true
+\emph default
+:
+\end_layout
+
+\begin_layout LyX-Code
+A_to_42 = Transition codomain: A, assignment: lambda { 42 }
+\end_layout
+
+\begin_layout LyX-Code
+#=> A_to_42
+\end_layout
+
+\begin_layout Standard
+Firing this transition results in marking of 
+\family typewriter
+A
+\family default
+ being set to 42:
+\end_layout
+
+\begin_layout LyX-Code
+A_to_42.fire!               #=> nil
+\end_layout
+
+\begin_layout LyX-Code
+A.marking                   #=> 42
+\end_layout
+
+\begin_layout Standard
+Assignment transitions are of special type 
+\family typewriter
+A
+\family default
+:
+\end_layout
+
+\begin_layout LyX-Code
+A_to_42.type                #=> :A
+\end_layout
+
+\begin_layout LyX-Code
+A_to_42.A?                  #=> true
+\end_layout
+
+\begin_layout LyX-Code
+A_to_42.a?                  #=> false
+\end_layout
+
+\begin_layout Part*
+Example II: Convenience
+\end_layout
+
+\begin_layout Standard
+So far, to avoid confusing you, I used fairly conservative syntax.
+ 
+\family typewriter
+YNelson
+\family default
+ can do better than that.
+ For convenience, many long keywords have short aliases.
+ Frequently used syntactic constructs usually have shorter way of expressing
+ the same.
+\end_layout
+
+\begin_layout Standard
+As you have seen, in 
+\family typewriter
+YNelson
+\family default
+ one often uses transition constructors.
+ Thus far, we have seen only one 
+\emph on
+constructor method
+\emph default
+ for transitions: 
+\family typewriter
+Transition()
+\family default
+.
+ 
+\family typewriter
+Transition()
+\family default
+ method accepts several different named arguments (
+\family typewriter
+:domain
+\family default
+, 
+\family typewriter
+:codomain
+\family default
+, 
+\family typewriter
+:stoichiometry
+\family default
+ 
+\family typewriter
+:assignment
+\family default
+, 
+\family typewriter
+:rate
+\family default
+, 
+\family typewriter
+:action
+\family default
+, 
+\family typewriter
+:name
+\family default
+...) and depending on their values, returns a 
+\family typewriter
+YNelson::Transition
+\family default
+ class object of required type and properties.
+\end_layout
+
+\begin_layout Standard
+Using long keywords in the constructor method makes the 
+\family typewriter
+YNelson
+\family default
+ code easy to read.
+ But for the cases where trading readability for brevity is desirable, such
+ as when you are playing with YNelson inside 
+\emph on
+irb
+\emph default
+ session, you will appreciate convenience.
+ Actually, we already used syntactic shorthands in the earlier examples.
+ We didn't type :
+\end_layout
+
+\begin_layout LyX-Code
+Transition( name: "A2B",
+\end_layout
+
+\begin_layout LyX-Code
+            codomain: [A, B],
+\end_layout
+
+\begin_layout LyX-Code
+            stoichiometry: [-1, 1] )
+\end_layout
+
+\begin_layout LyX-Code
+A2B = transition( :A2B )
+\end_layout
+
+\begin_layout Standard
+Instead, we just typed
+\end_layout
+
+\begin_layout LyX-Code
+A2B = Transition( stoichiometry: { A: -1, B: 1 } )
+\end_layout
+
+\begin_layout Standard
+Just so you know, the above shorthand is not easy to program in Ruby.
+ When designing 
+\family typewriter
+YNelson
+\family default
+, I took a lot of pain for your convenience.
+ Even shorter way to express the same would be:
+\end_layout
+
+\begin_layout LyX-Code
+A2B = Transition 
+\color blue
+s
+\color inherit
+: { A: -1, B: 1 }
+\end_layout
+
+\begin_layout Standard
+The above is a very simple timeless transition that just takes one token
+ from 
+\family typewriter
+A
+\family default
+ and puts it into 
+\family typewriter
+B
+\family default
+.
+ (Constructor convenience is even more powerful for complex transitions.)
+ Start a new 
+\family typewriter
+irb
+\family default
+ session and type:
+\end_layout
+
+\begin_layout LyX-Code
+require 'y_nelson'
+\end_layout
+
+\begin_layout LyX-Code
+include YNelson
+\end_layout
+
+\begin_layout LyX-Code
+A = Place 
+\color blue
+default_marking
+\color inherit
+: 5
+\end_layout
+
+\begin_layout Standard
+Constantly typing 
+\family typewriter
+default_marking
+\family default
+ is tiresome.
+ Shorter way to say the same is by using the alias 
+\family typewriter
+\color blue
+m!
+\family default
+\color inherit
+ of the same:
+\end_layout
+
+\begin_layout LyX-Code
+B = Place m!: 5
+\end_layout
+
+\begin_layout LyX-Code
+C = Place m!: 1
+\end_layout
+
+\begin_layout LyX-Code
+D = Place m!: 1
+\end_layout
+
+\begin_layout Standard
+Let's check the net's marking vector now:
+\end_layout
+
+\begin_layout LyX-Code
+places.map &:marking      #=> [5, 5, 1, 1]
+\end_layout
+
+\begin_layout Standard
+If you typed everything correctly, you should see the above result.
+ Shorter way to ask for the same information is:
+\end_layout
+
+\begin_layout LyX-Code
+net.marking               #=> "A: 5, B: 5, C: 1, D: 1"
+\end_layout
+
+\begin_layout Standard
+Even shorter way to ask is:
+\end_layout
+
+\begin_layout LyX-Code
+net.
+\color blue
+m
+\color inherit
+                     #=> [5, 5, 1, 1]
+\end_layout
+
+\begin_layout Standard
+Now let's define the transition we want:
+\end_layout
+
+\begin_layout LyX-Code
+B2A = Transition( stoichiometry: { B: -1, A: 1 },
+\end_layout
+
+\begin_layout LyX-Code
+                  domain: [C, D],
+\end_layout
+
+\begin_layout LyX-Code
+                  rate: lambda { |x, y| ( x * y ) ** 0.5 } )
+\end_layout
+
+\begin_layout Standard
+To prove that it works, let's fire it for 0.1 time units:
+\end_layout
+
+\begin_layout LyX-Code
+B2A.fire! 0.1             #=> nil
+\end_layout
+
+\begin_layout LyX-Code
+net.m                     #=> [5.1, 4.9, 1, 1]
+\end_layout
+
+\begin_layout Standard
+Can we express its constructor more concisely? The answer is yes.
+ 
+\family typewriter
+B2A
+\family default
+ is a 
+\family typewriter
+TS
+\family default
+ transition (check 
+\family typewriter
+B2A.type
+\family default
+ to make sure it is true), and for 
+\family typewriter
+TS
+\family default
+ transitions, 
+\family typewriter
+\color blue
+TS()
+\family default
+\color inherit
+ convenience constructor is available.
+ With 
+\family typewriter
+TS()
+\family default
+ constructor, the definition of B2A would be much shorter:
+\end_layout
+
+\begin_layout LyX-Code
+B2A = TS domain: [C, D], A: 1, B: -1 do |x, y| ( x * y ) ** 0.5 end
+\end_layout
+
+\begin_layout Standard
+Note the 
+\family typewriter
+\color red
+do ...
+ end
+\family default
+\color inherit
+ part in the above line: Using lambda syntax, it defines the rate function
+ of the transition.
+ Another convenience constructor worth mentioning is 
+\family typewriter
+\color blue
+AT()
+\family default
+\color inherit
+ for assignment transition.
+ Earlier, we defined:
+\end_layout
+
+\begin_layout LyX-Code
+A_to_42 = Transition codomain: A, assignment: lambda { 42 }
+\end_layout
+
+\begin_layout Standard
+Using 
+\family typewriter
+AT()
+\family default
+ constructor, we can shorten this to:
+\end_layout
+
+\begin_layout LyX-Code
+A_to_42 = AT A do 42 end
+\end_layout
+
+\begin_layout Standard
+In short, syntactic shorthands can save a lot of typing.
+ If you still miss some syntactic shorthand, feel free to define it on your
+ own.
+ For example, let us define a custom method named 
+\family typewriter
+Foo
+\family default
+ that acts as a constructor of places with default marking.
+\end_layout
+
+\begin_layout LyX-Code
+
+\color red
+def
+\color inherit
+ Foo( m )
+\end_layout
+
+\begin_layout LyX-Code
+  Place( default_marking: m )
+\end_layout
+
+\begin_layout LyX-Code
+end
+\end_layout
+
+\begin_layout Standard
+After this, you can define places with default marking with even less typing:
+\end_layout
+
+\begin_layout LyX-Code
+X = Foo 42
+\end_layout
+
+\begin_layout LyX-Code
+Y = Foo 43
+\end_layout
+
+\begin_layout Part*
+Example III: YNelson::Simulation
+\end_layout
+
+\begin_layout Standard
+So far, we have been defining Petri nets and playing the token game using
+ 
+\family typewriter
+#fire!
+\family default
+ method, let us now simulate a Petri net inside 
+\family typewriter
+YNelson
+\color blue
+::Simulation
+\family default
+\color inherit
+.
+ Restart your irb session as described in the 
+\series bold
+Prerequisites
+\series default
+ chapter.
+ We will now define 2 places.
+ Since we are going to use 
+\family typewriter
+TimedSimulation
+\family default
+, the marking owned by 
+\family typewriter
+YNelson::Place
+\family default
+ instances is irrelevant.
+ We just need to specify the initial state eg.
+ by specifying the default marking of the places:
+\end_layout
+
+\begin_layout LyX-Code
+require 'y_nelson'
+\end_layout
+
+\begin_layout LyX-Code
+include YNelson
+\end_layout
+
+\begin_layout LyX-Code
+A = Place 
+\color blue
+m!:
+\color inherit
+ 0.5
+\end_layout
+
+\begin_layout LyX-Code
+B = Place m!: 0.5
+\end_layout
+
+\begin_layout Standard
+Now let us define a transition corresponding to pumping 
+\family typewriter
+A
+\family default
+ out of the system at a constant rate 0.005 per time unit.
+\end_layout
+
+\begin_layout LyX-Code
+A_pump = Transition s: { A: -1 }, rate: 
+\color red
+proc
+\color inherit
+ { 0.005 }
+\end_layout
+
+\begin_layout Standard
+Here, 
+\family typewriter
+proc { 0.005 }
+\family default
+ is a closure, that defines the rate function.
+ Closure 
+\family typewriter
+proc { 0.005 }
+\family default
+ ensures fixed rate 0.005 per time unit regardless of the marking of 
+\family typewriter
+A
+\family default
+.
+ You can notice that this closure expects no arguments and always outputs
+ 0.005 as its return value.
+ It is the simplest possible way to write a constant function.
+ For comparison,
+\end_layout
+
+\begin_layout LyX-Code
+B_decay = Transition s: { B: -1 }, rate: 0.05
+\end_layout
+
+\begin_layout Standard
+will behind the scenes automatically create a slightly more complicated
+ mass action closure, which is logarithmic decay of 
+\family typewriter
+B
+\family default
+ in this case.
+ (You should remember this from 
+\series bold
+Example I
+\series default
+.) Now we have created a net of 2 places and 2 transitions:
+\end_layout
+
+\begin_layout LyX-Code
+net
+\end_layout
+
+\begin_layout LyX-Code
+#=> #<Net: name: Top, 2 places, 2 transitions>
+\end_layout
+
+\begin_layout Standard
+We can execute this Petri net as a 
+\family typewriter
+Simulation
+\family default
+ object simply by typing:
+\end_layout
+
+\begin_layout LyX-Code
+
+\color blue
+run!
+\color inherit
+                #=> 60
+\end_layout
+
+\begin_layout Standard
+At this point, 
+\family typewriter
+run!
+\family default
+ creates and executes a 
+\family typewriter
+Simulation
+\family default
+ instance.
+ The return value is the simulation instance itself (see the inspect string
+ above), which by now has already finished execution and holds the simulation
+ results.
+ This simulation instance is accessible via 
+\family typewriter
+simulation
+\family default
+ method.
+\end_layout
+
+\begin_layout LyX-Code
+
+\color blue
+simulation
+\end_layout
+
+\begin_layout LyX-Code
+#=> #<Simulation: time: 60, pp: 2, tt: 2, oid: 75530290>
+\end_layout
+
+\begin_layout Standard
+The simulation does not affect the net.
+ The simulation instance works with its own 
+\begin_inset Quotes eld
+\end_inset
+
+mental image
+\begin_inset Quotes erd
+\end_inset
+
+ of the net, therefore the marking owned by 
+\family typewriter
+YNelson::Place
+\family default
+ instances does not change:
+\end_layout
+
+\begin_layout LyX-Code
+net.marking         #=> "A: 0.5, B: 0.5"
+\end_layout
+
+\begin_layout Standard
+In a general case, it would be necessary to specify the simulation settings
+ (step size, sampling rate, simulation time etc.) before running the simulation.
+ Since we have not specified any, default settings were used:
+\end_layout
+
+\begin_layout LyX-Code
+simulation.
+\color blue
+settings
+\end_layout
+
+\begin_layout LyX-Code
+#=> {:method=>:basic, :guarded=>false, :step=>0.1, :sampling=>5, :time=>0..60}
+\end_layout
+
+\begin_layout Standard
+We can see sampling done by the simulation by typing:
+\end_layout
+
+\begin_layout LyX-Code
+
+\color blue
+print_recording
+\end_layout
+
+\begin_layout LyX-Code
+#=> :A      :B
+\end_layout
+
+\begin_layout LyX-Code
+    ----------------
+\end_layout
+
+\begin_layout LyX-Code
+    0.5000  0.5000
+\end_layout
+
+\begin_layout LyX-Code
+    0.4750  0.3892
+\end_layout
+
+\begin_layout LyX-Code
+    0.4500  0.3029
+\end_layout
+
+\begin_layout LyX-Code
+    0.4250  0.2357
+\end_layout
+
+\begin_layout LyX-Code
+    0.4000  0.1835
+\end_layout
+
+\begin_layout LyX-Code
+    0.3750  0.1428
+\end_layout
+
+\begin_layout LyX-Code
+    0.3500  0.1111
+\end_layout
+
+\begin_layout LyX-Code
+    0.3250  0.0865
+\end_layout
+
+\begin_layout LyX-Code
+    0.3000  0.0673
+\end_layout
+
+\begin_layout LyX-Code
+    0.2750  0.0524
+\end_layout
+
+\begin_layout LyX-Code
+    0.2500  0.0408
+\end_layout
+
+\begin_layout LyX-Code
+    0.2250  0.0317
+\end_layout
+
+\begin_layout LyX-Code
+    0.2000  0.0247
+\end_layout
+
+\begin_layout LyX-Code
+    nil
+\end_layout
+
+\begin_layout Standard
+Indeed, 
+\family typewriter
+A
+\family default
+ is decreasing at a constant rate, while 
+\family typewriter
+B
+\family default
+ undergoes logarithmic decay.
+ In a graphical desktop, we can plot a graph (requires 
+\emph on
+gnuplot
+\emph default
+ gem):
+\end_layout
+
+\begin_layout LyX-Code
+
+\color blue
+recording.plot    
+\color inherit
+ # plots a graph
+\end_layout
+
+\begin_layout Standard
+Previous command plots the default feature set, which is marking of the
+ places.
+ We can investigate also features of the recording (gradient or delta of
+ places, firing or flux of the transitions...):
+\end_layout
+
+\begin_layout LyX-Code
+recording.
+\color blue
+gradient
+\color inherit
+.plot
+\end_layout
+
+\begin_layout LyX-Code
+recording.
+\color blue
+flux
+\color inherit
+.plot
+\end_layout
+
+\begin_layout LyX-Code
+recording.
+\color blue
+delta
+\color inherit
+( 
+\color blue
+delta_time
+\color inherit
+: 0.1 ).plot
+\end_layout
+
+\begin_layout Standard
+The last feature set – delta – requires 
+\family typewriter
+delta_time
+\family default
+ named argument to extrapolate the changes (deltas) of the places in the
+ given delta time.
+ As for 
+\family typewriter
+\color blue
+firing
+\family default
+\color inherit
+, a feature of 
+\family typewriter
+tS
+\family default
+ transitions, the plot would show nothing here, as there ar no 
+\family typewriter
+tS
+\family default
+ transitions here.
+\end_layout
+
+\begin_layout Part*
+Example IV: A real system.
+\end_layout
+
+\begin_layout Standard
+A highly simplified cell-biological pathway.
+ Let's first define some assumptions.
+ Type in the following commands (output not shown):
+\end_layout
+
+\begin_layout LyX-Code
+require 'y_nelson'
+\end_layout
+
+\begin_layout LyX-Code
+include YNelson
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
+\begin_layout LyX-Code
+Pieces_per_microM = 100_000
+\end_layout
+
+\begin_layout LyX-Code
+
+\color blue
+set_step
+\color inherit
+ 10
+\end_layout
+
+\begin_layout LyX-Code
+
+\color blue
+set_sampling
+\color inherit
+ 30
+\end_layout
+
+\begin_layout LyX-Code
+
+\color blue
+set_target_time
+\color inherit
+ 30 * 60
+\end_layout
+
+\begin_layout Standard
+Let's define places corresponding to chemical species first (note that 
+\family typewriter
+:
+\color blue
+m!
+\family default
+\color inherit
+ is a synonym for 
+\family typewriter
+:default_marking)
+\end_layout
+
+\begin_layout LyX-Code
+AMP = Place 
+\color blue
+m!
+\color inherit
+: 8695.0
+\end_layout
+
+\begin_layout LyX-Code
+ADP = Place m!: 6521.0
+\end_layout
+
+\begin_layout LyX-Code
+ATP = Place m!: 3152.0
+\end_layout
+
+\begin_layout LyX-Code
+DeoxyCytidine = Place m!: 5.0
+\end_layout
+
+\begin_layout LyX-Code
+DeoxyCTP = Place m!: 20.0
+\end_layout
+
+\begin_layout LyX-Code
+DeoxyGMP = Place m!: 20.0
+\end_layout
+
+\begin_layout LyX-Code
+UMP_UDP_pool = Place m!: 2737.0
+\end_layout
+
+\begin_layout LyX-Code
+DeoxyUMP_DeoxyUDP_pool = Place m!: 10.0
+\end_layout
+
+\begin_layout LyX-Code
+DeoxyTMP = Place m!: 50.0
+\end_layout
+
+\begin_layout LyX-Code
+DeoxyTDP_DeoxyTTP_pool = Place m!: 100.0
+\end_layout
+
+\begin_layout LyX-Code
+Thymidine = Place m!: 10.0
+\end_layout
+
+\begin_layout Standard
+All the places above have their marking in micromolars.
+ The enzyme places below will have their marking in molecules per cell:
+\end_layout
+
+\begin_layout LyX-Code
+TK1 = Place m!: 100_000 / Pieces_per_microM
+\end_layout
+
+\begin_layout LyX-Code
+TYMS = Place m!: 100_000 / Pieces_per_microM
+\end_layout
+
+\begin_layout LyX-Code
+RNR = Place m!: 100_000 / Pieces_per_microM
+\end_layout
+
+\begin_layout LyX-Code
+TMPK = Place m!: 100_000 / Pieces_per_microM
+\end_layout
+
+\begin_layout Standard
+Enzyme molecular weights:
+\end_layout
+
+\begin_layout LyX-Code
+TK1_kDa = 24.8
+\end_layout
+
+\begin_layout LyX-Code
+TYMS_kDa = 66.0
+\end_layout
+
+\begin_layout LyX-Code
+RNR_kDa = 140.0
+\end_layout
+
+\begin_layout LyX-Code
+TMPK_kDa = 50.0
+\end_layout
+
+\begin_layout Standard
+Enzyme specific activities (in 
+\emph on
+micromolar
+\emph default
+ / 
+\emph on
+minute
+\emph default
+ / 
+\emph on
+mg
+\emph default
+ ):
+\end_layout
+
+\begin_layout LyX-Code
+TK1_a = 5.40
+\end_layout
+
+\begin_layout LyX-Code
+TYMS_a = 3.80
+\end_layout
+
+\begin_layout LyX-Code
+RNR_a = 1.00
+\end_layout
+
+\begin_layout LyX-Code
+TMPK_a = 0.83
+\end_layout
+
+\begin_layout Standard
+Some species are kept fixed (as simulation-level clamps):
+\end_layout
+
+\begin_layout LyX-Code
+
+\color blue
+clamp
+\color inherit
+ AMP: 8695.0, ADP: 6521.0, ATP: 3152.0
+\end_layout
+
+\begin_layout LyX-Code
+clamp DeoxyCytidine: 0.5, DeoxyCTP: 1.0, DeoxyGMP: 1.0
+\end_layout
+
+\begin_layout LyX-Code
+clamp Thymidine: 0.5
+\end_layout
+
+\begin_layout LyX-Code
+clamp UMP_UDP_pool: 2737.0
+\end_layout
+
+\begin_layout Standard
+Before defining transitions, let's define some functions first:
+\end_layout
+
+\begin_layout LyX-Code
+Vmax_per_min_per_enz_molecule =
+\end_layout
+
+\begin_layout LyX-Code
+  lambda { |spec_act_microM_per_min_per_mg, kDa|
+\end_layout
+
+\begin_layout LyX-Code
+             spec_act_microM_per_min_per_mg * kDa }
+\end_layout
+
+\begin_layout LyX-Code
+Vmax_per_min =
+\end_layout
+
+\begin_layout LyX-Code
+  lambda { |spec_act, kDa, enz_molecules_per_cell|
+\end_layout
+
+\begin_layout LyX-Code
+           Vmax_per_min_per_enz_molecule.( spec_act, kDa ) *
+\end_layout
+
+\begin_layout LyX-Code
+             enz_molecules_per_cell }
+\end_layout
+
+\begin_layout LyX-Code
+Vmax_per_s =
+\end_layout
+
+\begin_layout LyX-Code
+  lambda { |spec_act, kDa, enz_mol_per_cell|
+\end_layout
+
+\begin_layout LyX-Code
+           Vmax_per_min.( spec_act, kDa, enz_mol_per_cell ) / 60 }
+\end_layout
+
+\begin_layout LyX-Code
+Km_reduced =
+\end_layout
+
+\begin_layout LyX-Code
+  lambda { |km, ki_hash={}|
+\end_layout
+
+\begin_layout LyX-Code
+           ki_hash.map { |c, ki| c / ki }.reduce( 1, :+ ) * km }
+\end_layout
+
+\begin_layout LyX-Code
+Occupancy =
+\end_layout
+
+\begin_layout LyX-Code
+  lambda { |c, km, compet_inh_w_Ki_hash={}|
+\end_layout
+
+\begin_layout LyX-Code
+           c / ( c + Km_reduced.( km, compet_inh_w_Ki_hash ) ) }
+\end_layout
+
+\begin_layout LyX-Code
+MM_with_inh_microM_per_second =
+\end_layout
+
+\begin_layout LyX-Code
+  lambda { |c, spec_act, kDa, enz_mol_per_cell, km, ki_hash={}|
+\end_layout
+
+\begin_layout LyX-Code
+            Vmax_per_s.( spec_act, kDa, enz_mol_per_cell ) *
+\end_layout
+
+\begin_layout LyX-Code
+              Occupancy.( c, km, ki_hash ) }
+\end_layout
+
+\begin_layout LyX-Code
+MMi = MM_with_inh_microM_per_second
+\end_layout
+
+\begin_layout Standard
+Michaelis constants:
+\end_layout
+
+\begin_layout LyX-Code
+TK1_Thymidine_Km = 5.0
+\end_layout
+
+\begin_layout LyX-Code
+TYMS_DeoxyUMP_Km = 2.0
+\end_layout
+
+\begin_layout LyX-Code
+RNR_UDP_Km = 1.0
+\end_layout
+
+\begin_layout LyX-Code
+DNA_creation_speed = 3_000_000_000 / ( 12 * 3600 )
+\end_layout
+
+\begin_layout LyX-Code
+TMPK_DeoxyTMP_Km = 12.0
+\end_layout
+
+\begin_layout Standard
+And finally, let us define the transitions:
+\end_layout
+
+\begin_layout LyX-Code
+Transition name: :TK1_Thymidine_DeoxyTMP,
+\end_layout
+
+\begin_layout LyX-Code
+           
+\color blue
+domain:
+\color inherit
+ [ Thymidine, TK1, DeoxyTDP_DeoxyTTP_pool, DeoxyCTP,
+\end_layout
+
+\begin_layout LyX-Code
+                     DeoxyCytidine, AMP, ADP, ATP ],
+\end_layout
+
+\begin_layout LyX-Code
+           stoichiometry: { Thymidine: -1, DeoxyTMP: 1 },
+\end_layout
+
+\begin_layout LyX-Code
+           rate: proc { |c, e, pool1, ci2, ci3, master1, master2, master3|
+\end_layout
+
+\begin_layout LyX-Code
+                        ci1 = pool1 * master3 / ( master2 + master3 )
+\end_layout
+
+\begin_layout LyX-Code
+                        MMi.( c, TK1_a, TK1_kDa, e, TK1_Thymidine_Km,
+\end_layout
+
+\begin_layout LyX-Code
+                              ci1 => 13.5, ci2 => 0.8, ci3 => 40.0 ) }
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
+\begin_layout LyX-Code
+Transition name: :TYMS_DeoxyUMP_DeoxyTMP,
+\end_layout
+
+\begin_layout LyX-Code
+           domain: [ DeoxyUMP_DeoxyUDP_pool, TYMS, AMP, ADP, ATP ],
+\end_layout
+
+\begin_layout LyX-Code
+           stoichiometry: { DeoxyUMP_DeoxyUDP_pool: -1, DeoxyTMP: 1 },
+\end_layout
+
+\begin_layout LyX-Code
+           rate: proc { |pool, e, mono, di, tri|
+\end_layout
+
+\begin_layout LyX-Code
+                        c = pool * di / ( mono + di )
+\end_layout
+
+\begin_layout LyX-Code
+                          MMi.( c, TYMS_a, TYMS_kDa, e, TYMS_DeoxyUMP_Km
+ ) }
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
+\begin_layout LyX-Code
+Transition name: :RNR_UDP_DeoxyUDP,
+\end_layout
+
+\begin_layout LyX-Code
+           domain: [ UMP_UDP_pool, RNR, DeoxyUMP_DeoxyUDP_pool, AMP, ADP,
+ ATP ],
+\end_layout
+
+\begin_layout LyX-Code
+           stoichiometry: { UMP_UDP_pool: -1, DeoxyUMP_DeoxyUDP_pool: 1
+ },
+\end_layout
+
+\begin_layout LyX-Code
+           rate: proc { |pool, e, mono, di, tri|
+\end_layout
+
+\begin_layout LyX-Code
+                        c = pool * di / ( mono + di )
+\end_layout
+
+\begin_layout LyX-Code
+                        MMi.( c, RNR_a, RNR_kDa, e, RNR_UDP_Km ) }
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
+\begin_layout LyX-Code
+Transition name: :DNA_polymerase_consumption_of_DeoxyTTP,
+\end_layout
+
+\begin_layout LyX-Code
+           stoichiometry: { DeoxyTDP_DeoxyTTP_pool: -1 },
+\end_layout
+
+\begin_layout LyX-Code
+           rate: proc { DNA_creation_speed / 4 }
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
+\begin_layout LyX-Code
+Transition name: :TMPK_DeoxyTMP_DeoxyTDP,
+\end_layout
+
+\begin_layout LyX-Code
+           domain: [ DeoxyTMP, TMPK, DeoxyTDP_DeoxyTTP_pool, DeoxyGMP, AMP,
+ ADP, ATP ],
+\end_layout
+
+\begin_layout LyX-Code
+           stoichiometry: { DeoxyTMP: -1, TMPK: 0, DeoxyTDP_DeoxyTTP_pool:
+ 1 },
+\end_layout
+
+\begin_layout LyX-Code
+           rate: proc { |c, e, pool, ci4, mono, di, tri|
+\end_layout
+
+\begin_layout LyX-Code
+                        ci1 = di
+\end_layout
+
+\begin_layout LyX-Code
+                        ci2 = pool * di / ( di + tri )
+\end_layout
+
+\begin_layout LyX-Code
+                        ci3 = pool * tri / ( di + tri )
+\end_layout
+
+\begin_layout LyX-Code
+                        MMi.( c, TMPK_a, TMPK_kDa, e, TMPK_DeoxyTMP_Km,
+\end_layout
+
+\begin_layout LyX-Code
+                              ci1 => 250.0, ci2 => 30.0, ci3 => 750, ci4 =>
+ 117 ) }
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
+\begin_layout LyX-Code
+Transition name: :PhosphataseI,
+\end_layout
+
+\begin_layout LyX-Code
+           stoichiometry: { DeoxyTMP: -1, Thymidine: 1 },
+\end_layout
+
+\begin_layout LyX-Code
+           rate: 0.04
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
+\begin_layout LyX-Code
+Transition name: :PhosphataseII,
+\end_layout
+
+\begin_layout LyX-Code
+           stoichiometry: { DeoxyTDP_DeoxyTTP_pool: -1, DeoxyTMP: 1 },
+\end_layout
+
+\begin_layout LyX-Code
+           rate: 0.01
+\end_layout
+
+\begin_layout Standard
+The created net can be visualized by:
+\end_layout
+
+\begin_layout LyX-Code
+net.visualize
+\end_layout
+
+\begin_layout Standard
+After executing the above command, you should see a file named 
+\family typewriter
+y_petri_graph.png
+\family default
+ in your working directory.
+ The simulation should work.
+\end_layout
+
+\begin_layout LyX-Code
+run!
+\end_layout
+
+\begin_layout Standard
+State recording can be plotted by:
+\end_layout
+
+\begin_layout LyX-Code
+recording.plot
+\end_layout
+
+\begin_layout Standard
+Flux of the transitions can be plotted by:
+\end_layout
+
+\begin_layout LyX-Code
+recording.flux.plot
+\end_layout
+
+\begin_layout Standard
+Please note that although this system qualitatively represents part of the
+ deoxynucleotide metabolism network, its behavior is not realistic, because
+ the available kinetic constants are not precise.
+\end_layout
+
+\begin_layout Part*
+Example V: Using SY.
+\end_layout
+
+\begin_layout Standard
+Here, we'll take a look at using 
+\family typewriter
+YNelson
+\family default
+ with 
+\family typewriter
+\color blue
+SY
+\family default
+ metrology library
+\color inherit
+.
+ If you are experienced with biochemical modeling, then you surely know
+ how big pain the physical units are.
+ Also, in 
+\series bold
+Example III
+\series default
+, you might have noticed how much attention has been spent on units (in
+ the assumptions, variable names, constant names...) You could have noticed
+ messy unit conversion formulas.
+ The aim of 
+\family typewriter
+SY
+\family default
+ is to take care of all this, to relieve the modeler from the task of unit
+ conversion, to clean up the model code, and let the modeler concentrate
+ on the real issue.
+\end_layout
+
+\begin_layout Subsection*
+
+\family typewriter
+SY
+\family default
+ metrology library
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+SY
+\family default
+ is publicly available as a Ruby gem '
+\family typewriter
+sy
+\family default
+'.
+ After installing it (
+\family typewriter
+gem install sy
+\family default
+), type:
+\end_layout
+
+\begin_layout LyX-Code
+require 'sy'
+\end_layout
+
+\begin_layout Standard
+Afterwards, your 
+\family typewriter
+\color red
+Numeric
+\family default
+\color inherit
+ objects (that is, numbers) should respond to methods representing physical
+ units:
+\end_layout
+
+\begin_layout LyX-Code
+1.m                    #=> #<±Magnitude: 1.m>
+\end_layout
+
+\begin_layout LyX-Code
+1.s                    #=> #<±Magnitude: 1.s>
+\end_layout
+
+\begin_layout LyX-Code
+1.kg.m.s(-2)           #=> #<±Magnitude: 1.N>
+\end_layout
+
+\begin_layout LyX-Code
+1.cm + 1.mm            #=> #<±Magnitude: 0.011.m>
+\end_layout
+
+\begin_layout Standard
+The core of the trick is that instead of naked numbers, numbers become magnitude
+s (
+\family typewriter
+SY::Magnitude
+\family default
+) of specified physical quantities:
+\end_layout
+
+\begin_layout LyX-Code
+1.m.quantity           #=> #<Quantity:Length>
+\end_layout
+
+\begin_layout LyX-Code
+1.cm.min⁻¹.quantity    #=> #<Quantity:Speed>
+\end_layout
+
+\begin_layout Standard
+(You can type 
+\family typewriter
+1.cm.min(-1)
+\family default
+ if you find it difficult to type Unicode superscript characters "
+\family typewriter
+⁻¹
+\family default
+".) Magnitudes can be converted back to numbers with 
+\family typewriter
+\color blue
+amount
+\family default
+\color inherit
+ (alias 
+\family typewriter
+\color blue
+to_f)
+\family default
+\color inherit
+ method:
+\end_layout
+
+\begin_layout LyX-Code
+1.km.amount            #=> 1000.0
+\end_layout
+
+\begin_layout LyX-Code
+1.cm.to_f              #=> 0.01
+\end_layout
+
+\begin_layout Subsection*
+Collaboration between 
+\family typewriter
+SY
+\family default
+ and 
+\family typewriter
+YNelson
+\end_layout
+
+\begin_layout Standard
+In a fresh 
+\family typewriter
+irb
+\family default
+ session, enter:
+\end_layout
+
+\begin_layout LyX-Code
+require 'sy'
+\end_layout
+
+\begin_layout LyX-Code
+require 'y_nelson'
+\end_layout
+
+\begin_layout LyX-Code
+include YNelson
+\end_layout
+
+\begin_layout LyX-Code
+A = Place m!: 3.mM
+\end_layout
+
+\begin_layout LyX-Code
+B = Place m!: 4.mM
+\end_layout
+
+\begin_layout LyX-Code
+A2B = Transition s: { A: -1, B: 1 }, rate: 0.05.s⁻¹
+\end_layout
+
+\begin_layout LyX-Code
+B_decay = Transition s: { B: -1 }, rate: 0.002.s⁻¹
+\end_layout
+
+\begin_layout Standard
+We hereby specified marking and rate in physical units.
+ Presently, 
+\family typewriter
+YNelson
+\family default
+ is not able to simulate such nets, but we can play token game with it:
+\end_layout
+
+\begin_layout LyX-Code
+net.m    #=> [#<±Magnitude: 0.003.M>, #<±Magnitude: 0.004.M>]
+\end_layout
+
+\begin_layout LyX-Code
+A2B.fire! 1.s
+\end_layout
+
+\begin_layout LyX-Code
+B_decay.fire! 1.s
+\end_layout
+
+\begin_layout LyX-Code
+net.m    #=> [#<±Magnitude: 0.00285.M>, #<±Magnitude: 0.00414.M>]
+\end_layout
+
+\begin_layout Standard
+Let us fire the 2 defined transitions for 100 seconds:
+\end_layout
+
+\begin_layout LyX-Code
+100.times do
+\end_layout
+
+\begin_layout LyX-Code
+  A2B.fire! 1.s
+\end_layout
+
+\begin_layout LyX-Code
+  B_decay.fire! 1.s
+\end_layout
+
+\begin_layout LyX-Code
+end
+\end_layout
+
+\begin_layout LyX-Code
+net.m    #=> [#<±Magnitude: 1.69e-05.M>, #<±Magnitude: 0.0058.M>]
+\end_layout
+
+\begin_layout Standard
+Finally, let us inspect the resulting marking of 
+\family typewriter
+A
+\family default
+ and 
+\family typewriter
+B
+\family default
+ expressed in micromolars:
+\end_layout
+
+\begin_layout LyX-Code
+A.marking.
+\color blue
+in
+\color inherit
+ :µM       #=> 16.873508277951963
+\end_layout
+
+\begin_layout LyX-Code
+B.marking.in :µM       #=> 5797.976678013365
+\end_layout
+
+\begin_layout Part*
+Example VI: Other simulation methods
+\end_layout
+
+\begin_layout Standard
+At this moment, the default simulation method 
+\family typewriter
+basic
+\family default
+ method.
+ This method is also called is implicit Euler, because when simulating timed
+ nets, it implies first-order Euler method.
+ For timed nets, YNelson provides two other methods: Runge-Kutta 4th order
+ method and Gillespie stochastic method.
+ Demonstrating Gillespie method:
+\end_layout
+
+\begin_layout LyX-Code
+require 'y_nelson'
+\end_layout
+
+\begin_layout LyX-Code
+include YNelson
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
+\begin_layout LyX-Code
+A = Place m!: 10
+\end_layout
+
+\begin_layout LyX-Code
+B = Place m!: 10
+\end_layout
+
+\begin_layout LyX-Code
+AB = Place m!: 0
+\end_layout
+
+\begin_layout LyX-Code
+AB_association = TS A: -1, B: -1, AB: 1, rate: 0.1
+\end_layout
+
+\begin_layout LyX-Code
+AB_dissociation = TS AB: -1, A: 1, B: 1, rate: 0.1
+\end_layout
+
+\begin_layout LyX-Code
+A2B = TS A: -1, B: 1, rate: 0.05
+\end_layout
+
+\begin_layout LyX-Code
+B2A = TS A: 1, B: -1, rate: 0.07
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
+\begin_layout LyX-Code
+set_step 1
+\end_layout
+
+\begin_layout LyX-Code
+set_target_time 50
+\end_layout
+
+\begin_layout LyX-Code
+set_sampling 1
+\end_layout
+
+\begin_layout LyX-Code
+set_simulation_method :gillespie
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
+\begin_layout LyX-Code
+run!
+\end_layout
+
+\begin_layout LyX-Code
+print_recording
+\end_layout
+
+\begin_layout LyX-Code
+plot_state
+\end_layout
+
+\begin_layout Standard
+The state recording should show a random walk of the system state over the
+ period of 50 time units.
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
+\begin_layout LyX-Code
+\begin_inset CommandInset bibtex
+LatexCommand bibtex
+bibfiles "/home/boris/b/8oav/ptn/ptn"
+options "plainnat"
+
+\end_inset
+
+
+\end_layout
+
+\end_body
+\end_document