y_nelson 2.3.7 → 2.3.8

data/Introduction_to_YPetri_and_YNelson.lyx

@@ -1,3593 +0,0 @@
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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, such as 
-\family typewriter
-YPetri
-\family default
-.
- 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' and
-\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' and
-\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()
-\end_layout
-
-\begin_layout LyX-Code
-#=> 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
-()
-\end_layout
-
-\begin_layout LyX-Code
-#=> [A, B]
-\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 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 )
-\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 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 )
-\end_layout
-
-\begin_layout LyX-Code
-#=> [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
-()
-\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
-#=> [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
-()
-\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
-[A, B]
-\end_layout
-
-\begin_layout LyX-Code
-A2B.
-\color blue
-codomain
-\color inherit
-()
-\end_layout
-
-\begin_layout LyX-Code
-[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
-()
-\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
-#=> YPetri::GuardError: When trying call #fire method, adding action node
- no.
- 0 to A, marking change being -1, YPetri::GuardError occurred: 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 )
-\end_layout
-
-\begin_layout LyX-Code
-#=> 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?
-\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
-#=> 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!
-\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, 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: 
-\begin_inset Quotes eld
-\end_inset
-
-A2B
-\begin_inset Quotes erd
-\end_inset
-
-,
-\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               #=> [5, 5, 1, 1]
-\end_layout
-
-\begin_layout Standard
-Even shorter way to say the same 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         #=> [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
-#=> {: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
-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