y_nelson 2.1.0 → 2.3.0

data/YNelson_-_Hands-on_Tutorial.lyx

@@ -1,3701 +0,0 @@
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-\end_header
-
-\begin_body
-
-\begin_layout Title
-YNelson: 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
-YNelson
-\family default
-\color inherit
-, 
-\emph on
-\color green
-Nelson nets
-\emph default
-\color inherit
- and, partially, 
-\color red
-Ruby
-\color inherit
- language.
- It is not assumed that the reader is familiar with any of these, though
- familiarity with Ruby syntax would be an advantage.
- If you have never heard about Nelson nets, do not wonder: it is a semi-novel
- concept based on 
-\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
-.
- If you follow this guide closely, you will receive a concise and efficient
- introduction to each of these three (remark:
-\emph on
- only the Petri net aspect is covered in this version of this guide.
- ZZ structure aspect will be covered in the future versions of this manual)
-\emph default
-.
- Newly introduced 
-\color red
-Ruby keywords and terms
-\color inherit
- are highlighted in red, 
-\color green
-Petri net terms
-\color inherit
- in green, and 
-\color blue
-YNelson keywords and terms
-\color inherit
- in blue throughout this document.
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-\color blue
-YNelson
-\family default
-\color inherit
- is a domain model and a simulator of 
-\emph on
-\color green
-functional
-\emph default
- 
-\emph on
-Petri nets
-\emph default
-\color inherit
- living in the 
-\emph on
-\color green
-ZZ space
-\emph default
-\color inherit
-.
- The Petri net flavor used in 
-\family typewriter
-YNelson
-\family default
- is similar, but not identical with 
-\emph on
-\color green
-hybrid functional Petri nets
-\emph default
- (HFPNs)
-\color inherit
- introduced by 
-\begin_inset CommandInset citation
-LatexCommand citet
-key "Matsuno2011brs"
-
-\end_inset
-
-.
- For a recent review of the various flavors of Petri nets, see eg.
- 
-\begin_inset CommandInset citation
-LatexCommand citet
-key "Bos2008mbs"
-
-\end_inset
-
-.
- 
-\family typewriter
-YNelson
-\family default
- is implemented in 
-\emph on
-\color red
-Ruby programming language
-\emph default
-\color inherit
-.
- It is publicly available as 
-\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
- (
-\emph on
-\color red
-gem
-\emph default
-\color inherit
- = Ruby library).
- 
-\family typewriter
-YNelson
-\family default
- is one of the series of Ruby gems (
-\family typewriter
-\color blue
-
-\begin_inset CommandInset href
-LatexCommand href
-name "YPetri"
-target "https://rubygems.org/gems/y_petri"
-
-\end_inset
-
-
-\family default
-\color inherit
-, 
-\family typewriter
-\color blue
-YChem
-\family default
-\color inherit
-, 
-\family typewriter
-\color blue
-YCell
-\family default
-\color inherit
-, 
-\family typewriter
-\color blue
-
-\begin_inset CommandInset href
-LatexCommand href
-name "Yzz"
-target "https://rubygems.org/gems/yzz"
-
-\end_inset
-
-
-\family default
-\color inherit
-, metrology library 
-\family typewriter
-\color blue
-
-\begin_inset CommandInset href
-LatexCommand href
-name "SY"
-target "https://rubygems.org/gems/sy"
-
-\end_inset
-
-
-\family default
-\color inherit
-...), whose design intent is to bring ergonomy to biochemical modeling.
- Note that 
-\family typewriter
-YNelson
-\family default
- depends on 
-\family typewriter
-YPetri
-\family default
- and 
-\family typewriter
-Yzz
-\family default
- gems, its usage together with 
-\family typewriter
-SY
-\family default
- might be desirable if you are dealing with physical units.
- Also, 
-\family typewriter
-YNelson
-\family default
- use is not limited to biochemistry, but for all the applications where
- Petri nets and/or relational databases are used.
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-YNelson
-\family default
- provides a 
-\emph on
-\color red
-domain-specific language
-\emph default
- (DSL)
-\color inherit
-, which you can use in scripts, or access interactively from 
-\color red
-inferior Ruby interpreter (
-\emph on
-irb
-\emph default
-)
-\color inherit
-.
- A DSLs can be thought of as APIs with user-friendly syntax.
- As a believer in robot equality, I dislike the distinction between API
- and UI (user interface), and prefer common textual command interface (CI)
- for humanoid as well as cybernetic users.
-\end_layout
-
-\begin_layout Standard
-And why bother learning Ruby syntax and 
-\family typewriter
-YNelson
-\family default
-? Half-jokingly, 
-\family typewriter
-YNelson
-\family default
- is 
-\emph on
-The Simplest Way To Work With Complicated Petri Nets
-\emph default
-™.
- Petri net software at higher development stage, or written for a different
- purpose than 
-\family typewriter
-YNelson
-\family default
-, does exist.
- But none of the programs written for the same purpose as 
-\family typewriter
-YNelson
-\family default
- can avoid taking the user through the process of learning the interface.
- Advantages of using textual DSL become apparent as soon as the user's models
- become less simple.
-\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
-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
-Most importantly, you will need a working installation of Ruby 1.9 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.
- However, 
-\family typewriter
-YNelson
-\family default
- currently uses 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'
-\end_layout
-
-\begin_layout Standard
-After succesful 
-\family typewriter
-require
-\family default
-, type:
-\end_layout
-
-\begin_layout LyX-Code
-
-\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 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.
- Please, also notice that this guide itself is alpha stage, so the actual
- 
-\family typewriter
-YNelson
-\family default
- version you will be using may somewhat differ from this guide.
- Also, the nucleotide metabolism model in Example 3 is yet to be tuned to
- be realistic.
- If something in this guide does not work, please do not hesitate to notify
- us, we 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
-()
-\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 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
- (and '
-\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.).
- Whole this object has now been assigned to 
-\family typewriter
-A
-\family default
-.
- On the screen, you will see the output: 
-\family typewriter
-#<Place: name: A, marking: nil, default_marking: ø>
-\family default
-.
- (This is the 
-\emph on
-\color red
-inspect string
-\emph default
-\color inherit
- of the object, created by 
-\family typewriter
-YNelson::Place#
-\color red
-inspect
-\family default
-\color inherit
- method, which is not important.) In the following, screen output will always
- be written immediately under the code sample, preceded by sherocket (
-\family typewriter
-#=>):
-\end_layout
-
-\begin_layout LyX-Code
-B = Place()
-\end_layout
-
-\begin_layout LyX-Code
-
-\family typewriter
-#=> #<Place: name: B, marking: nil, default_marking: ø>
-\end_layout
-
-\begin_layout Standard
-We have so far defined 2 Petri net places named 
-\family typewriter
-A
-\family default
-, 
-\family typewriter
-B
-\family default
-.
- You can check it by typing:
-\end_layout
-
-\begin_layout LyX-Code
-
-\color blue
-places
-\color inherit
-()
-\end_layout
-
-\begin_layout LyX-Code
-#=> [#<Place: name: A, marking: nil, default_marking: ø>,
-\end_layout
-
-\begin_layout LyX-Code
-     #<Place: name: B, marking: nil, default_marking: ø>]
-\end_layout
-
-\begin_layout LyX-Code
-A.
-\color blue
-name
-\color inherit
-()
-\end_layout
-
-\begin_layout LyX-Code
-#=> :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
-()
-\end_layout
-
-\begin_layout LyX-Code
-#=> #<Net: name: Top, 2 pp, 0 tt >
-\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 )
-\end_layout
-
-\begin_layout LyX-Code
-#=> [: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 CI.
- GUI systems generally sandbox the user inside their interface, with no
- way to overcome its limitations.
- But let us go on.
- Way above, you might have noticed '
-\family typewriter
-\color red
-nil
-\family default
-\color inherit
-' in the places' inspect strings.
- This is because we have specified no 
-\emph on
-\color green
-marking
-\emph default
-\color inherit
- for 
-\family typewriter
-A
-\family default
-, 
-\family typewriter
-B
-\family default
-:
-\end_layout
-
-\begin_layout LyX-Code
-A.
-\color blue
-marking
-\color inherit
-()
-\end_layout
-
-\begin_layout LyX-Code
-#=> nil
-\end_layout
-
-\begin_layout LyX-Code
-places.map( &:marking )
-\end_layout
-
-\begin_layout LyX-Code
-#=> [nil, nil]
-\end_layout
-
-\begin_layout Standard
-Let us give these two places some marking:
-\end_layout
-
-\begin_layout LyX-Code
-A.
-\color blue
-marking =
-\color inherit
- 2
-\end_layout
-
-\begin_layout LyX-Code
-#=> 2
-\end_layout
-
-\begin_layout LyX-Code
-B.marking = 5
-\end_layout
-
-\begin_layout LyX-Code
-#=> 5
-\end_layout
-
-\begin_layout Standard
-The marking has indeed changed:
-\end_layout
-
-\begin_layout LyX-Code
-places.map( &:marking )
-\end_layout
-
-\begin_layout LyX-Code
-#=> [2, 5]
-\end_layout
-
-\begin_layout Standard
-In classical Petri nets, this marking is understood as the number of 
-\emph on
-\color green
-tokens
-\emph default
-\color inherit
- in each place, and is always an 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 the transition's 
-\emph on
-stoichiometry
-\emph default
- – a list of places together with the number of tokens added / subtracted
- 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
-#=> #<Transition: A2B (tS)>
-\end_layout
-
-\begin_layout Standard
-Stoichiometry of this transition is given by 
-\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
-()
-\end_layout
-
-\begin_layout LyX-Code
-#=> {: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
-()
-\end_layout
-
-\begin_layout LyX-Code
-#=> [-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
-()
-\end_layout
-
-\begin_layout LyX-Code
-#=> [#<Place: name: A, marking: 2, default_marking: ø >,
-\end_layout
-
-\begin_layout LyX-Code
-     #<Place: name: B, marking: 5, default_marking: ø >]
-\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
-()
-\end_layout
-
-\begin_layout LyX-Code
-#=> 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
-()
-\end_layout
-
-\begin_layout LyX-Code
-[#<Place: name: A, marking: 2, default_marking: ø>,
-\end_layout
-
-\begin_layout LyX-Code
- #<Place: name: B, marking: 5, default_marking: ø>]
-\end_layout
-
-\begin_layout LyX-Code
-A2B.
-\color blue
-codomain
-\color inherit
-()
-\end_layout
-
-\begin_layout LyX-Code
-[#<Place: name: A, marking: 2, default_marking: ø>,
-\end_layout
-
-\begin_layout LyX-Code
- #<Place: name: B, marking: 5, default_marking: ø>]
-\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
-()
-\end_layout
-
-\begin_layout LyX-Code
-#=> 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
-()
-\end_layout
-
-\begin_layout LyX-Code
-#=> nil
-\end_layout
-
-\begin_layout LyX-Code
-places.map( &:marking )
-\end_layout
-
-\begin_layout LyX-Code
-#=> [1, 6]
-\end_layout
-
-\begin_layout LyX-Code
-A2B.fire!()
-\end_layout
-
-\begin_layout LyX-Code
-#=> nil
-\end_layout
-
-\begin_layout LyX-Code
-places.map( &:marking )
-\end_layout
-
-\begin_layout LyX-Code
-#=> [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?
-\end_layout
-
-\begin_layout LyX-Code
-#=> 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
-#=> RuntimeError: Firing of #<Transition: A2B (tS)> would result in negative
- marking!
-\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 HFPNs proposed by 
-\begin_inset CommandInset citation
-LatexCommand citet
-key "Matsuno2011brs"
-
-\end_inset
-
-, which was already mentioned in the introduction.
- 
-\family typewriter
-YNelson
-\family default
- domain model is similar, but not identical.
- 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 )
-\end_layout
-
-\begin_layout LyX-Code
-#=> #<Place: name: C, marking: 7.77, default_marking: ø>
-\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
-#=> #<Transition: C_decay (TS)>
-\end_layout
-
-\begin_layout LyX-Code
-C_decay.
-\color blue
-timed?
-\end_layout
-
-\begin_layout LyX-Code
-#=> 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 )
-\end_layout
-
-\begin_layout LyX-Code
-#=> nil
-\end_layout
-
-\begin_layout LyX-Code
-C.marking
-\end_layout
-
-\begin_layout LyX-Code
-#=> 7.3815
-\end_layout
-
-\begin_layout LyX-Code
-C_decay.fire! 1
-\end_layout
-
-\begin_layout LyX-Code
-#=> nil
-\end_layout
-
-\begin_layout LyX-Code
-C.marking
-\end_layout
-
-\begin_layout LyX-Code
-#=> 7.012425
-\end_layout
-
-\begin_layout LyX-Code
-C_decay.fire!( 0.1 )
-\end_layout
-
-\begin_layout LyX-Code
-#=> nil
-\end_layout
-
-\begin_layout LyX-Code
-C.marking
-\end_layout
-
-\begin_layout LyX-Code
-#=> 6.977362875000001
-\end_layout
-
-\begin_layout LyX-Code
-100.
-\color red
-times
-\color inherit
- do C_decay.fire! 1 end
-\end_layout
-
-\begin_layout LyX-Code
-#=> 100
-\end_layout
-
-\begin_layout LyX-Code
-C.marking
-\end_layout
-
-\begin_layout LyX-Code
-#=> 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 }
-\end_layout
-
-\begin_layout LyX-Code
-#=> 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
-\end_layout
-
-\begin_layout LyX-Code
-#=> 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
-\end_layout
-
-\begin_layout LyX-Code
-#=> :tS
-\end_layout
-
-\begin_layout Standard
-Or investigate the type with inquirer methods:
-\end_layout
-
-\begin_layout LyX-Code
-A2B.
-\color blue
-t?
-\end_layout
-
-\begin_layout LyX-Code
-#=> true
-\end_layout
-
-\begin_layout LyX-Code
-A2B.
-\color blue
-T?
-\end_layout
-
-\begin_layout LyX-Code
-#=> false
-\end_layout
-
-\begin_layout LyX-Code
-A2B.
-\color blue
-s?
-\end_layout
-
-\begin_layout LyX-Code
-#=> false
-\end_layout
-
-\begin_layout LyX-Code
-A2B.
-\color blue
-S?
-\end_layout
-
-\begin_layout LyX-Code
-#=> true
-\end_layout
-
-\begin_layout LyX-Code
-A2B.
-\color blue
-TS?
-\end_layout
-
-\begin_layout LyX-Code
-#=> false
-\end_layout
-
-\begin_layout LyX-Code
-A2B.
-\color blue
-tS?
-\end_layout
-
-\begin_layout LyX-Code
-#=> true
-\end_layout
-
-\begin_layout LyX-Code
-A2B.
-\color blue
-Ts?
-\end_layout
-
-\begin_layout LyX-Code
-#=> false
-\end_layout
-
-\begin_layout LyX-Code
-A2B.
-\color blue
-ts?
-\end_layout
-
-\begin_layout LyX-Code
-#=> 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
-#=> #<Transition: A_to_42 (A Assign.)>
-\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!
-\end_layout
-
-\begin_layout LyX-Code
-#=> nil
-\end_layout
-
-\begin_layout LyX-Code
-A.marking
-\end_layout
-
-\begin_layout LyX-Code
-#=> 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
-\end_layout
-
-\begin_layout LyX-Code
-#=> :A
-\end_layout
-
-\begin_layout LyX-Code
-A_to_42.A?
-\end_layout
-
-\begin_layout LyX-Code
-#=> true
-\end_layout
-
-\begin_layout LyX-Code
-A_to_42.a?
-\end_layout
-
-\begin_layout LyX-Code
-#=> false
-\end_layout
-
-\begin_layout Part*
-Example II: Convenience
-\end_layout
-
-\begin_layout Standard
-So 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
-Use of whole words in the constructor method makes the 
-\family typewriter
-YNelson
-\family default
- DSL very explicit.
- But for the cases, where trading readability for brevity is desirable,
- these syntactic constructs can be shortened.
- Actually, we have already used this convenience in the earlier examples.
- We didn't type :
-\end_layout
-
-\begin_layout LyX-Code
-Transition( name: 
-\begin_inset Quotes eld
-\end_inset
-
-A2B
-\begin_inset Quotes erd
-\end_inset
-
-, codomain: [A, B], 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
-Even shorter way to express the same would be:
-\end_layout
-
-\begin_layout LyX-Code
-A2B = Transition s: { A: -1, B: 1 }
-\end_layout
-
-\begin_layout Standard
-The above is a timeless transition.
- But we could think eg.
- about a more complicated transition, that would transfer tokens from 
-\family typewriter
-B
-\family default
- to 
-\family typewriter
-A
-\family default
- with rate depending on the square root of the product of marking of 
-\family typewriter
-C
-\family default
- and 
-\family typewriter
-D
-\family default
-.
- 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( default_marking: 5 )
-\end_layout
-
-\begin_layout LyX-Code
-B = Place m!: 5 # notice 
-\begin_inset Quotes eld
-\end_inset
-
-m!
-\begin_inset Quotes erd
-\end_inset
-
- alias for 
-\begin_inset Quotes eld
-\end_inset
-
-default marking
-\begin_inset Quotes erd
-\end_inset
-
-
-\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 our work:
-\end_layout
-
-\begin_layout LyX-Code
-places.map &:m
-\end_layout
-
-\begin_layout LyX-Code
-#=> [5, 5, 1, 1]
-\end_layout
-
-\begin_layout Standard
-Indeed, the net state has been set according to the default markings of
- the places.
- 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 LyX-Code
-#=> #<Transition: B2A (TS)>
-\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
-\end_layout
-
-\begin_layout LyX-Code
-#=> nil
-\end_layout
-
-\begin_layout LyX-Code
-places.map &:m
-\end_layout
-
-\begin_layout LyX-Code
-#=> [5.1, 4.9, 1, 1]
-\end_layout
-
-\begin_layout Standard
-You can try to change marking of C and D to control the rate:
-\end_layout
-
-\begin_layout LyX-Code
-[A, B].each &:
-\color blue
-reset_marking
-\end_layout
-
-\begin_layout LyX-Code
-C.m = 4
-\end_layout
-
-\begin_layout LyX-Code
-D.m = 9
-\end_layout
-
-\begin_layout LyX-Code
-places.map &:m
-\end_layout
-
-\begin_layout LyX-Code
-#=> [5, 5, 4, 9]
-\end_layout
-
-\begin_layout LyX-Code
-B2A.fire! 0.1
-\end_layout
-
-\begin_layout LyX-Code
-places.map &:m
-\end_layout
-
-\begin_layout LyX-Code
-#=> [5.6, 4.4, 4, 9]
-\end_layout
-
-\begin_layout Standard
-We can see that the rate of 
-\family typewriter
-B2A
-\family default
- has risen 6 times as expected (4 * 9 is 36), so 
-\family typewriter
-B2A
-\family default
- works.
- The question is, could we have written 
-\family typewriter
-B2A
-\family default
- more concisely? For 
-\family typewriter
-TS
-\family default
- transitions (check 
-\family typewriter
-B2A.type
-\family default
- to make sure that it's a 
-\family typewriter
-TS
-\family default
- transition), 
-\family typewriter
-\color blue
-TS()
-\family default
-\color inherit
- constructor is available, allowing to express the same transition with
- a shorter syntactic construct:
-\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
-Restart the 
-\family typewriter
-irb
-\family default
- session again and use this shorter construct to see that the resulting
- transition behaves like before.
- Note the 
-\family typewriter
-\color red
-do ...
- end
-\family default
-\color inherit
- part of the construct: Using lambda syntax, it defines the rate function
- of the transition.
-\end_layout
-
-\begin_layout Standard
-One more convenience constructor I want to mention here is 
-\family typewriter
-\color blue
-AT()
-\family default
-\color inherit
- constructor 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
-This can be conveniently rewritten using 
-\family typewriter
-AT()
-\family default
- constructor as:
-\end_layout
-
-\begin_layout LyX-Code
-A_to_42 = AT A do 42 end
-\end_layout
-
-\begin_layout Standard
-In short, syntactic shorthands are less readable than full 
-\family typewriter
-Transition()
-\family default
- statements, but can save a lot of space and typing.
- In any case, in Ruby, the user can easily defined new aliases and routines
- that make the frequent tasks easier to type.
-\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.
- One way to do this is by specifying 
-\family typewriter
-\color blue
-:default_marking
-\family default
-\color inherit
- named argument:
-\end_layout
-
-\begin_layout LyX-Code
-A = Place( 
-\color blue
-default_marking:
-\color inherit
- 0.5 )
-\end_layout
-
-\begin_layout LyX-Code
-#=> #<Place: name: A, marking: 0.5, default_marking: 0.5>
-\end_layout
-
-\begin_layout LyX-Code
-B = Place( default_marking: 0.5 )
-\end_layout
-
-\begin_layout LyX-Code
-#=> #<Place: name: B, marking: 0.5, default_marking: 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( stoichiometry: { A: -1 }, rate: proc { 0.005 } )
-\end_layout
-
-\begin_layout LyX-Code
-#=> #<Transition: A_pump (TS)>
-\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( stoichiometry: { B: -1 }, rate: 0.05 )
-\end_layout
-
-\begin_layout LyX-Code
-#=> #<Transition: B_decay (TS)>
-\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 pp, 2 tt>
-\end_layout
-
-\begin_layout Standard
-We can execute this Petri net as 
-\family typewriter
-TimedSimulation
-\family default
- simply by typing:
-\end_layout
-
-\begin_layout LyX-Code
-
-\color blue
-run!
-\end_layout
-
-\begin_layout LyX-Code
-#=> 60
-\end_layout
-
-\begin_layout Standard
-At this point, 
-\family typewriter
-run!
-\family default
- creates and executes a 
-\family typewriter
-TimedSimulation
-\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
-places.map &:marking
-\end_layout
-
-\begin_layout LyX-Code
-#=> [0.5, 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
-#=> {: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 LyX-Code
-#=> ""
-\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.gradient.plot
-\end_layout
-
-\begin_layout LyX-Code
-recording.flux.plot
-\end_layout
-
-\begin_layout LyX-Code
-recording.delta( delta_time: 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
-firing
-\family default
-, 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 simulated with 
-\family typewriter
-YNelson::TimedSimulation
-\family default
-.
- Let's first define some assumptions.
- Type in the following commands (output not shown):
-\end_layout
-
-\begin_layout LyX-Code
-require 'y_nelson' and 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
-# require 'mathn' 
-\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
-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 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 in the heel 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
-\end_layout
-
-\begin_layout LyX-Code
-#=> #<±Magnitude: 1.m>
-\end_layout
-
-\begin_layout LyX-Code
-1.s
-\end_layout
-
-\begin_layout LyX-Code
-#=> #<±Magnitude: 1.s>
-\end_layout
-
-\begin_layout LyX-Code
-1.kg.m.s(-2)
-\end_layout
-
-\begin_layout LyX-Code
-#=> #<±Magnitude: 1.N>
-\end_layout
-
-\begin_layout LyX-Code
-1.cm + 1.mm
-\end_layout
-
-\begin_layout LyX-Code
-#=> #<±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
-\end_layout
-
-\begin_layout LyX-Code
-#=> #<Quantity:Length±>
-\end_layout
-
-\begin_layout LyX-Code
-1.cm.min⁻¹.quantity
-\end_layout
-
-\begin_layout LyX-Code
-#=> #<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
-\end_layout
-
-\begin_layout LyX-Code
-#=> 1000.0
-\end_layout
-
-\begin_layout LyX-Code
-1.cm.to_f
-\end_layout
-
-\begin_layout LyX-Code
-#=> 0.01
-\end_layout
-
-\begin_layout Subsection*
-Collaboration between 
-\family typewriter
-SY
-\family default
- and 
-\family typewriter
-YNelson
-\end_layout
-
-\begin_layout Standard
-Enter:
-\end_layout
-
-\begin_layout LyX-Code
-A = Place m!: 3.mM
-\end_layout
-
-\begin_layout LyX-Code
-#=> #<Place: name: A, marking: 0.003.M, default_marking: 0.003.M >
-\end_layout
-
-\begin_layout LyX-Code
-B = Place m!: 4.mM
-\end_layout
-
-\begin_layout LyX-Code
-#=> #<Place: name: B, marking: 0.004.M, default_marking: 0.004.M >
-\end_layout
-
-\begin_layout LyX-Code
-A2B = Transition s: { A: -1, B: 1 }, rate: 0.05.s⁻¹
-\end_layout
-
-\begin_layout LyX-Code
-#=> #<Transition: A2B (SR) >
-\end_layout
-
-\begin_layout LyX-Code
-B_decay = Transition s: { B: -1 }, rate: 0.002.s⁻¹
-\end_layout
-
-\begin_layout LyX-Code
-#=> 
-\family typewriter
-YNelson
-\family default
-::Transition[ B_decay: stoichiometric transition with rate ]
-\end_layout
-
-\begin_layout Standard
-Now we have created places and transitions, whose marking and rate closures
- are defined in physical units.
- Presently, 
-\family typewriter
-YNelson::TimedSimulation
-\family default
- will not accept such Petri net, so the only thing we can do is play the
- token game ourselves:
-\end_layout
-
-\begin_layout LyX-Code
-fire_both_transitions = proc { |delta_t|
-\end_layout
-
-\begin_layout LyX-Code
-  A2B.fire! delta_t
-\end_layout
-
-\begin_layout LyX-Code
-  B_decay.fire! delta_t
-\end_layout
-
-\begin_layout LyX-Code
-}
-\end_layout
-
-\begin_layout LyX-Code
-#=> #<Proc:0x9b48f1c@(irb):19>
-\end_layout
-
-\begin_layout Standard
-Here, we have defined a closure accepting one argument 
-\begin_inset Formula $\Delta$
-\end_inset
-
-t, which it will use to 
-\family typewriter
-fire!
-\family default
- both 
-\family typewriter
-A2B
-\family default
- and 
-\family typewriter
-B_decay
-\family default
-.
- By calling this closure repeatedly, we can simulate the network without
- use of 
-\family typewriter
-TimedSimulation
-\family default
-:
-\end_layout
-
-\begin_layout LyX-Code
-places.map &:marking
-\end_layout
-
-\begin_layout LyX-Code
-#=> [#<±Magnitude: 0.003.M>, #<±Magnitude: 0.004.M>]
-\end_layout
-
-\begin_layout LyX-Code
-fire_both_transitions.( 1.s )
-\end_layout
-
-\begin_layout LyX-Code
-#=> nil
-\end_layout
-
-\begin_layout LyX-Code
-places.map &:marking
-\end_layout
-
-\begin_layout LyX-Code
-#=> [#<±Magnitude: 0.00285.M>, #<±Magnitude: 0.00414.M>]
-\end_layout
-
-\begin_layout LyX-Code
-100.times do fire_both_transitions.( 1.s ) end
-\end_layout
-
-\begin_layout LyX-Code
-#=> 100
-\end_layout
-
-\begin_layout LyX-Code
-places.map &:marking
-\end_layout
-
-\begin_layout LyX-Code
-#=> [#<±Magnitude: 1.69e-05.M>, #<±Magnitude: 0.0058.M>]
-\end_layout
-
-\begin_layout LyX-Code
-A.marking.
-\color blue
-in
-\color inherit
- :µM
-\end_layout
-
-\begin_layout LyX-Code
-#=> 16.873508277951963
-\end_layout
-
-\begin_layout LyX-Code
-B.marking.in :µM
-\end_layout
-
-\begin_layout LyX-Code
-#=> 5797.976678013365
-\end_layout
-
-\begin_layout Part*
-Example VI: Other simulation methods
-\end_layout
-
-\begin_layout Standard
-At this moment, the default simulation method is implicit Euler (or 
-\family typewriter
-pseudo_euler
-\family default
- – 
-\emph on
-pseudo
-\emph default
- because timeless transitions and assignment transtitions also fire at each
- step in time).
- From other simulation methods, Gillespie algorithm is available:
-\end_layout
-
-\begin_layout LyX-Code
-require 'y_nelson' and 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 the random walk of the system state over
- 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/1num/num,/home/boris/b/2prp/prp"
-options "plainnat"
-
-\end_inset
-
-
-\end_layout
-
-\end_body
-\end_document