y_petri 2.1.30 → 2.1.31
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- checksums.yaml +4 -4
- data/README.md +31 -0
- data/lib/y_petri/version.rb +1 -1
- data/test/examples/gillespie.rb +13 -12
- metadata +1 -1
checksums.yaml
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SHA1:
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metadata.gz:
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metadata.gz: 4c98edfb8140dbc62e7012bd0ce4d25978451e22
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data.tar.gz: 6c3d695901347b8bf8deac87999bc588c21ed503
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metadata.gz: 78e6c1c2aa034e7e893411600381d3e4bad5cd4ec3e5a12f5dbc1a10fb938d7c90c0258a252474391b7f3092994f8b6b28e74bc17c26d61c8a6d7721871e30c6
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data.tar.gz: bec532ac1b9c25649a75e34d6e7806a774d231e6cdefc990c555559324ebc92a98cc460ac28004bba5f3f357a66a9191fcf1475c76c272ac26caaff20fb43997
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data/README.md
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@@ -85,6 +85,37 @@ If you have `gnuplot` gem installed properly, you can view plots:
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plot_state
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plot_flux
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```
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88
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## Gillespie method
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89
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90
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To try out another simulation method, Gillespie algorithm, open a fresh session
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and type:
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```ruby
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require 'y_petri'
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require 'sy'
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require 'mathn'
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include YPetri
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A = Place m!: 10
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B = Place m!: 10
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AB = Place m!: 0
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AB_association = Transition s: { A: -1, B: -1, AB: 1 }, rate: 0.1
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AB_dissociation = Transition s: { AB: -1, A: 1, B: 1 }, rate: 0.1
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A2B = Transition s: { A: -1, B: 1 }, rate: 0.05
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B2A = Transition s: { A: 1, B: -1 }, rate: 0.07
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set_step 1
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set_target_time 50
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set_sampling 1
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set_simulation_method :gillespie
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run!
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print_recording
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```
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Again, you can visualize the results using `gnuplot` gem:
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```ruby
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117
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plot_state
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```
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So much for the demo for now! Thanks for trying YPetri!
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## Contributing
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data/lib/y_petri/version.rb
CHANGED
data/test/examples/gillespie.rb
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@@ -1,25 +1,26 @@
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#! /usr/bin/ruby
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# coding: utf-8
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-
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# ==============================================================================
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#
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# encoding: utf-8
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require 'y_petri'
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require 'sy'
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require 'mathn'
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include YPetri
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require 'sy'
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require 'mathn'
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include YPetri
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A = Place m!: 10
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B = Place m!: 10
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-
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-
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11
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AB = Place m!: 0
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12
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AB_association = Transition s: { A: -1, B: -1, AB: 1 }, rate: 0.1
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13
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AB_dissociation = Transition s: { AB: -1, A: 1, B: 1 }, rate: 0.1
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14
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A2B = Transition s: { A: -1, B: 1 }, rate: 0.05
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B2A = Transition s: { A: 1, B: -1 }, rate: 0.07
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18
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set_step 1
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set_target_time
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set_step 1
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set_target_time 50
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set_sampling 1
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set_simulation_method :gillespie
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-
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run!
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print_recording
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plot_state
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