cell_cycle 0.0.3 → 0.1.1
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- checksums.yaml +4 -4
- data/lib/cell_cycle/simple.rb +2 -3
- data/lib/cell_cycle/version.rb +3 -1
- data/lib/cell_cycle/virginia_tech.rb +26 -43
- data/lib/cell_cycle.rb +14 -3
- metadata +1 -1
checksums.yaml
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 16fa9dd102f38e28071366b53da9752f8e332785
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data.tar.gz: 49cc905bc4a42fcaef78c882d3082567ef3fa705
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 22047cc300354bc3a0f0c5f018dfd442ba53583069e9d3c34c1d0a78e181580d7ea54e8076d8f5b10496876577a9fb35c729d80e071cd840db1c1b596c5a4f18
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data.tar.gz: 4550945464c1112d256248333203cdbd46e6b2611ec84c61e6de3a98674120accf441944690ef276bf73b72ba0e8594ac7e240af22e6f7b134b4295216de4bec
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data/lib/cell_cycle/simple.rb
CHANGED
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# phase. Cdc20A represents the APC (Anaphase Promoting Complex). When present,
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# it degrades the cell cycle enzyme machinery.
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require '
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require 'sy'
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require 'cell_cycle'
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# Constants that control the cell cycle settings.
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S_phase_duration = 12.h
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@@ -50,7 +49,7 @@ S_phase = Place m!: 0
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Cdc20A = Place m!: 1
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# Include them in the CELL_CYCLE net.
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CELL_CYCLE
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CELL_CYCLE << Timer << Clock << A_phase << S_phase << Cdc20A
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# Assignment transitions that control the state of the places A_phase, S_phase
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# and Cdc20A.
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data/lib/cell_cycle/version.rb
CHANGED
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# Generic cell cycle published in Csikasznagy2006agm. Mammalian constants used.
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# Initial state was obtained as described in Csikasznagy2006agm.
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require '
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require 'cell_cycle'
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# == TRICKS =====================================================================
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@@ -419,52 +419,35 @@ finalize # YNelson command that finishes the net from the prescribed commands.
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# ==============================================================================
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CELL_CYCLE.merge! net # This is quite fragile, since it assumes that no places
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# and/or transitions have been created before requiring
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# the cell cycle gem.
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# Net that defines cell growth, to be used eg. for testing or separate use.
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CELL_GROWTH_NET = Net()
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CELL_GROWTH_NET << Mass << Cell_growth << CycD <<
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transition( :CycD_ϝ ) << CycB << ActCycB << # cyclin B
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Ck_license << Cytokinesis << License_cocking # cytokinesis
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# cell growth
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def CELL_CYCLE.default_simulation
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simulation time: 0..96.h.in( :s ),
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step: 5,
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sampling: 300
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# FIXME: This method #default_simulation doesn't work, and I don't know why,
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# while standard way of simulation works. I can just use the standard way
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# of simulation by simply calling run! command, and fix this later.
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end
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=begin
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# === Whole CELL_CYCLE Nelson net ===
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-
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CELL_CYCLE = Net() << A_phase << S_phase << Cdc20A
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# === Cell growh net ===
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CELL_GROWTH_NET = Net() <<
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Mass << Cell_growth << CycD << transition( :CycD_ϝ ) << # cell growth
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CycB << ActCycB << # cyclin B
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Ck_license << Cytokinesis << License_cocking # cytokinesis
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set_step 5 # simulation settings
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set_step 5
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set_target_time 96.h.in( :s )
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set_sampling 300
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set_target_time 3600 * 24 * 4
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new_simulation
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pm # prints marking of the newly created simulation
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simulation.step! # peforms a single simulation step
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pm # prints marking again
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# simulation.run! upto: 3600 # we can run 1 hour of this simulation
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recording.plot # and plot the recording
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#
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#
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#
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# I commented this out, I don't really want to run this lengthy simulation upon
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# requiring the gem.
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# run!
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# Note: Possible things to do with the recording, such as resampling, feature
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# extraction, saving to a file, reconstruction of a new simulation object at
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# a given time etc.
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data/lib/cell_cycle.rb
CHANGED
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# encoding: utf-8
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#
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#
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# Mammalian cell cycle model. 2 versions available at the moment,
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# 'cell_cycle/simple' and 'cell_cycle/virginia_tech'. This is the
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# common 'cell_cycle.rb' file.
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# Require dependencies.
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require 'sy'
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require 'y_nelson' and include YNelson
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# Define the empty CELL_CYCLE net (its contents is to be added by
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# the particular implemented cell cycle types).
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CELL_CYCLE = Net()
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# Cell cycle version.
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require_relative "cell_cycle/version"
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