--- !ruby/object:Gem::Specification
name: y_petri
version: !ruby/object:Gem::Version
  version: 2.3.8
platform: ruby
authors:
- boris
autorequire: 
bindir: bin
cert_chain: []
date: 2014-12-03 00:00:00.000000000 Z
dependencies:
- !ruby/object:Gem::Dependency
  name: bundler
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '1.6'
  type: :development
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '1.6'
- !ruby/object:Gem::Dependency
  name: rake
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
  type: :development
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
- !ruby/object:Gem::Dependency
  name: y_support
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
- !ruby/object:Gem::Dependency
  name: gnuplot
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
- !ruby/object:Gem::Dependency
  name: ruby-graphviz
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
- !ruby/object:Gem::Dependency
  name: distribution
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
description: 'YPetri is a gem for modelling of dynamical systems. It is biologically
  inspired, but concerns of biology and chemistry have been purposely separated away
  from it. YPetri caters solely to the two main concerns of modelling, model specification
  and simulation, and it excels in the first one. Dynamical systems are described
  under a Petri net paradigm. YPetri implements a universal Petri net abstraction
  that integrates discrete/continous, deterministic/stochastic, timed/timeless and
  stoichiometric/nonstoichiometric dichotomies of the extended Petri nets, and allows
  efficient specification of any kind of dynamical system. Like Petri nets themselves,
  YPetri was inspired by problems from the domain of chemistry (biochemical pathway
  modelling), but is not specific to it. Other gems, YChem and YCell are planned to
  cater to the concerns specific to chemistry and cell biochemistry. A lower-level
  extension of YPetri is currently under development under the name YNelson. Its usage
  is practically identical to YPetri, so any YPetri user can now consider using YNelson
  instead. YNelson covers additional concerns: it allows relations among nodes and
  parameters to be specified under a zz structure paradigm (developed by Ted Nelson)
  and it is also aimed towards providing a higher level of abstraction in Petri net
  specification by providing commands that create more than one Petri net node per
  command. YPetri documentation is avalable online, but due to formatting issues,
  you may prefer to generate the documentation on your own by running rdoc in the
  gem directory. As for the user manuals, there are currently 3 documents applicable
  for both YPetri and YNelson, which are stored in the YNelson source directory: 1.
  Introduction to YNelson and YPetri (hands-on tutorial), 2. Object model of YNelson
  and YPetri, 3. Introduction to Ruby for YNelson users. These manuals will are written
  so that any would-be user, including those unfamiliar with Ruby, can start using
  YPetri and/or YNelson. For an example of how YPetri can be used to model complex
  dynamical systems, see the eukaryotic cell cycle model which I released as "cell_cycle"
  gem.'
email:
- '"boris@iis.sinica.edu.tw"'
executables: []
extensions: []
extra_rdoc_files: []
files:
- ".gitignore"
- ACKNOWLEDGMENT.txt
- Gemfile
- Introduction_to_Ruby_for_YNelson_Users.pdf
- Introduction_to_YNelson_and_YPetri.pdf
- LICENSE.txt
- Object_model_of_YNelson_and_YPetri.pdf
- README.md
- Rakefile
- lib/y_petri.rb
- lib/y_petri/agent.rb
- lib/y_petri/agent/hash_key_pointer.rb
- lib/y_petri/agent/petri_net_aspect.rb
- lib/y_petri/agent/selection.rb
- lib/y_petri/agent/simulation_aspect.rb
- lib/y_petri/core.rb
- lib/y_petri/core/guarded.rb
- lib/y_petri/core/timed.rb
- lib/y_petri/core/timed/euler.rb
- lib/y_petri/core/timed/gillespie.rb
- lib/y_petri/core/timed/methods.rb
- lib/y_petri/core/timed/pseudo_euler.rb
- lib/y_petri/core/timed/quasi_euler.rb
- lib/y_petri/core/timed/runge_kutta.rb
- lib/y_petri/core/timeless.rb
- lib/y_petri/core/timeless/methods.rb
- lib/y_petri/core/timeless/pseudo_euler.rb
- lib/y_petri/dsl.rb
- lib/y_petri/fixed_assets.rb
- lib/y_petri/net.rb
- lib/y_petri/net/data_set.rb
- lib/y_petri/net/node_access.rb
- lib/y_petri/net/own_state.rb
- lib/y_petri/net/state.rb
- lib/y_petri/net/state/feature.rb
- lib/y_petri/net/state/feature/assignment.rb
- lib/y_petri/net/state/feature/delta.rb
- lib/y_petri/net/state/feature/firing.rb
- lib/y_petri/net/state/feature/flux.rb
- lib/y_petri/net/state/feature/gradient.rb
- lib/y_petri/net/state/feature/marking.rb
- lib/y_petri/net/state/features.rb
- lib/y_petri/net/state/features/record.rb
- lib/y_petri/net/timed.rb
- lib/y_petri/net/visualization.rb
- lib/y_petri/place.rb
- lib/y_petri/place/arcs.rb
- lib/y_petri/place/features.rb
- lib/y_petri/place/guard.rb
- lib/y_petri/place/guarded.rb
- lib/y_petri/simulation.rb
- lib/y_petri/simulation/dependency.rb
- lib/y_petri/simulation/feature_set.rb
- lib/y_petri/simulation/initial_marking.rb
- lib/y_petri/simulation/initial_marking/access.rb
- lib/y_petri/simulation/marking_clamps.rb
- lib/y_petri/simulation/marking_clamps/access.rb
- lib/y_petri/simulation/marking_vector.rb
- lib/y_petri/simulation/marking_vector/access.rb
- lib/y_petri/simulation/matrix.rb
- lib/y_petri/simulation/node_representation.rb
- lib/y_petri/simulation/nodes.rb
- lib/y_petri/simulation/nodes/access.rb
- lib/y_petri/simulation/place_mapping.rb
- lib/y_petri/simulation/place_representation.rb
- lib/y_petri/simulation/places.rb
- lib/y_petri/simulation/places/access.rb
- lib/y_petri/simulation/places/clamped.rb
- lib/y_petri/simulation/places/free.rb
- lib/y_petri/simulation/places/types.rb
- lib/y_petri/simulation/recorder.rb
- lib/y_petri/simulation/timed.rb
- lib/y_petri/simulation/timed/recorder.rb
- lib/y_petri/simulation/timeless.rb
- lib/y_petri/simulation/timeless/recorder.rb
- lib/y_petri/simulation/transition_representation.rb
- lib/y_petri/simulation/transition_representation/A.rb
- lib/y_petri/simulation/transition_representation/S.rb
- lib/y_petri/simulation/transition_representation/T.rb
- lib/y_petri/simulation/transition_representation/TS.rb
- lib/y_petri/simulation/transition_representation/Ts.rb
- lib/y_petri/simulation/transition_representation/a.rb
- lib/y_petri/simulation/transition_representation/s.rb
- lib/y_petri/simulation/transition_representation/t.rb
- lib/y_petri/simulation/transition_representation/tS.rb
- lib/y_petri/simulation/transition_representation/ts.rb
- lib/y_petri/simulation/transition_representation/types.rb
- lib/y_petri/simulation/transitions.rb
- lib/y_petri/simulation/transitions/A.rb
- lib/y_petri/simulation/transitions/S.rb
- lib/y_petri/simulation/transitions/T.rb
- lib/y_petri/simulation/transitions/TS.rb
- lib/y_petri/simulation/transitions/Ts.rb
- lib/y_petri/simulation/transitions/a.rb
- lib/y_petri/simulation/transitions/access.rb
- lib/y_petri/simulation/transitions/s.rb
- lib/y_petri/simulation/transitions/t.rb
- lib/y_petri/simulation/transitions/tS.rb
- lib/y_petri/simulation/transitions/ts.rb
- lib/y_petri/simulation/transitions/types.rb
- lib/y_petri/transition.rb
- lib/y_petri/transition/A.rb
- lib/y_petri/transition/T.rb
- lib/y_petri/transition/arcs.rb
- lib/y_petri/transition/cocking.rb
- lib/y_petri/transition/construction_convenience.rb
- lib/y_petri/transition/t.rb
- lib/y_petri/transition/types.rb
- lib/y_petri/transition/usable_without_world.rb
- lib/y_petri/version.rb
- lib/y_petri/world.rb
- lib/y_petri/world/dependency.rb
- lib/y_petri/world/petri_net_aspect.rb
- lib/y_petri/world/simulation_aspect.rb
- test/acceptance/basic_usage_test.rb
- test/acceptance/simulation_test.rb
- test/acceptance/simulation_with_physical_units_test.rb
- test/acceptance/token_game_test.rb
- test/acceptance/visualization_test.rb
- test/acceptance_tests.rb
- test/agent_test.rb
- test/examples/demonstrator.rb
- test/examples/demonstrator_2.rb
- test/examples/demonstrator_4.rb
- test/examples/example_2.rb
- test/examples/example_IV.rb
- test/examples/example_VI_gillespie.rb
- test/examples/manual_examples.rb
- test/net_test.rb
- test/place_test.rb
- test/simulation_test.rb
- test/transition_test.rb
- test/world_mock.rb
- test/world_test.rb
- test/y_petri_test.rb
- y_petri.gemspec
homepage: ''
licenses:
- GPLv3
metadata: {}
post_install_message: 
rdoc_options: []
require_paths:
- lib
required_ruby_version: !ruby/object:Gem::Requirement
  requirements:
  - - ">="
    - !ruby/object:Gem::Version
      version: '2.0'
required_rubygems_version: !ruby/object:Gem::Requirement
  requirements:
  - - ">="
    - !ruby/object:Gem::Version
      version: '0'
requirements: []
rubyforge_project: 
rubygems_version: 2.2.2
signing_key: 
specification_version: 4
summary: Systems modelling and simulation gem. Biologically inspired, but concerns
  specific to biology and chemistry have been purposely separated away from it, so
  it is a general-purpose model specification and simulation DSL. Dynamical systems
  are specified by a specific universal type of a hybrid Petri net which YPetri implements
  and which allows description of any kind of dynamical system whatsoever.
test_files:
- test/acceptance/basic_usage_test.rb
- test/acceptance/simulation_test.rb
- test/acceptance/simulation_with_physical_units_test.rb
- test/acceptance/token_game_test.rb
- test/acceptance/visualization_test.rb
- test/acceptance_tests.rb
- test/agent_test.rb
- test/examples/demonstrator.rb
- test/examples/demonstrator_2.rb
- test/examples/demonstrator_4.rb
- test/examples/example_2.rb
- test/examples/example_IV.rb
- test/examples/example_VI_gillespie.rb
- test/examples/manual_examples.rb
- test/net_test.rb
- test/place_test.rb
- test/simulation_test.rb
- test/transition_test.rb
- test/world_mock.rb
- test/world_test.rb
- test/y_petri_test.rb