Simulation Results

ecoli_core_dfba

This simulation runs a dFBA (dynamic Flux Balance Analysis) model of E. coli core metabolism, tracking external concentrations and biomass.

Runtime: 0.51 seconds

ecoli_core_dfba.json

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ecoli core dFBA
inputs
substrates
glucose
[0]"fields"
[1]"glucose"
acetate
[0]"fields"
[1]"acetate"
biomass
[0]"fields"
[1]"ecoli core biomass"
outputs
substrates
glucose
[0]"fields"
[1]"glucose"
acetate
[0]"fields"
[1]"acetate"
biomass
[0]"fields"
[1]"ecoli core biomass"
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
fields
glucose"10.0"
acetate"0.0"
ecoli core biomass"0.1"

ecoli_core_dfba_viz.png

ecoli_core_dfba.png

ecoli_dfba

This simulation runs a dFBA of the large E. coli metabolic model, iAF1260

Runtime: 5.09 seconds

ecoli_dfba.json

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ecoli dFBA
inputs
substrates
glucose
[0]"fields"
[1]"glucose"
formate
[0]"fields"
[1]"formate"
biomass
[0]"fields"
[1]"ecoli biomass"
outputs
substrates
glucose
[0]"fields"
[1]"glucose"
formate
[0]"fields"
[1]"formate"
biomass
[0]"fields"
[1]"ecoli biomass"
interval1.0
address"local:DynamicFBA"
config
model_file"iAF1260.xml"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
formate
[0]"0.5"
[1]"1.0"
substrate_update_reactions
glucose"EX_glc__D_e"
formate"EX_for_e"
bounds
sharednull
fields
glucose"10.0"
formate"5.0"
ecoli biomass"0.1"

ecoli_dfba_viz.png

ecoli_dfba.png

cdiff_dfba

This simulation runs a dFBA model of Clostridioides difficile. iCN900

Runtime: 1.97 seconds

cdiff_dfba.json

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cdiff dFBA
inputs
substrates
glucose
[0]"fields"
[1]"glucose"
acetate
[0]"fields"
[1]"acetate"
biomass
[0]"fields"
[1]"cdiff biomass"
outputs
substrates
glucose
[0]"fields"
[1]"glucose"
acetate
[0]"fields"
[1]"acetate"
biomass
[0]"fields"
[1]"cdiff biomass"
interval1.0
address"local:DynamicFBA"
config
model_file"iCN900.xml"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
sharednull
fields
glucose"2.0"
acetate"10.0"
cdiff biomass"0.1"

cdiff_dfba_viz.png

cdiff_dfba.png

pputida_dfba

This simulation runs a dFBA model of Pseudomonas putida, iJN746

Runtime: 2.97 seconds

pputida_dfba.json

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pputida dFBA
inputs
substrates
glucose
[0]"fields"
[1]"glucose"
ammonium
[0]"fields"
[1]"ammonium"
glycolate
[0]"fields"
[1]"glycolate"
biomass
[0]"fields"
[1]"pputida biomass"
outputs
substrates
glucose
[0]"fields"
[1]"glucose"
ammonium
[0]"fields"
[1]"ammonium"
glycolate
[0]"fields"
[1]"glycolate"
biomass
[0]"fields"
[1]"pputida biomass"
interval1.0
address"local:DynamicFBA"
config
model_file"iJN746.xml"
kinetic_params
glucose
[0]"1.0"
[1]"2.0"
ammonium
[0]"2.0"
[1]"4.0"
glycolate
[0]"0.5"
[1]"1.0"
substrate_update_reactions
glucose"EX_glc__D_e"
ammonium"EX_nh4_e"
glycolate"EX_glyclt_e"
bounds
sharednull
fields
glucose"8.0"
ammonium"10.0"
glycolate"10.0"
pputida biomass"2.0"

pputida_dfba_viz.png

pputida_dfba.png

yeast_dfba

This simulation runs a dFBA model of Saccharomyces cerevisiae (yeast), iMM904

Runtime: 3.84 seconds

yeast_dfba.json

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yeast dFBA
inputs
substrates
glucose
[0]"fields"
[1]"glucose"
ammonium
[0]"fields"
[1]"ammonium"
biomass
[0]"fields"
[1]"yeast biomass"
outputs
substrates
glucose
[0]"fields"
[1]"glucose"
ammonium
[0]"fields"
[1]"ammonium"
biomass
[0]"fields"
[1]"yeast biomass"
interval1.0
address"local:DynamicFBA"
config
model_file"iMM904.xml"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
ammonium
[0]"0.5"
[1]"1.0"
substrate_update_reactions
glucose"EX_glc__D_e"
ammonium"EX_nh4_e"
bounds
sharednull
fields
glucose"5.0"
ammonium"10.0"
yeast biomass"0.1"

yeast_dfba_viz.png

yeast_dfba.png

llactis_dfba

This simulation runs a dFBA model of Lactococcus lactis, iNF517

Runtime: 1.63 seconds

llactis_dfba.json

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llactis dFBA
inputs
substrates
glucose
[0]"fields"
[1]"glucose"
glutatmate
[0]"fields"
[1]"glutatmate"
serine
[0]"fields"
[1]"serine"
biomass
[0]"fields"
[1]"llactis biomass"
outputs
substrates
glucose
[0]"fields"
[1]"glucose"
glutatmate
[0]"fields"
[1]"glutatmate"
serine
[0]"fields"
[1]"serine"
biomass
[0]"fields"
[1]"llactis biomass"
interval1.0
address"local:DynamicFBA"
config
model_file"iNF517.xml"
kinetic_params
glucose
[0]"0.5"
[1]"1.25"
glutatmate
[0]"0.05"
[1]"0.1"
serine
[0]"0.05"
[1]"0.1"
substrate_update_reactions
glucose"EX_glc__D_e"
glutatmate"EX_glu__L_e"
serine"EX_ser__L_e"
bounds
sharednull
fields
glucose"100.0"
glutatmate"10.0"
serine"10.0"
llactis biomass"2.0"

llactis_dfba_viz.png

llactis_dfba.png

multi_dfba

This simulation runs multiple dFBA processes in the same environment, each with its own model and parameters.

Runtime: 16.59 seconds

multi_dfba.json

View full JSON
dfba_ecoli core
inputs
substrates
glucose
[0]"fields"
[1]"glucose"
acetate
[0]"fields"
[1]"acetate"
biomass
[0]"fields"
[1]"ecoli core"
outputs
substrates
glucose
[0]"fields"
[1]"glucose"
acetate
[0]"fields"
[1]"acetate"
biomass
[0]"fields"
[1]"ecoli core"
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dfba_ecoli
inputs
substrates
glucose
[0]"fields"
[1]"glucose"
formate
[0]"fields"
[1]"formate"
biomass
[0]"fields"
[1]"ecoli"
outputs
substrates
glucose
[0]"fields"
[1]"glucose"
formate
[0]"fields"
[1]"formate"
biomass
[0]"fields"
[1]"ecoli"
interval1.0
address"local:DynamicFBA"
config
model_file"iAF1260.xml"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
formate
[0]"0.5"
[1]"1.0"
substrate_update_reactions
glucose"EX_glc__D_e"
formate"EX_for_e"
bounds
sharednull
dfba_cdiff
inputs
substrates
glucose
[0]"fields"
[1]"glucose"
acetate
[0]"fields"
[1]"acetate"
biomass
[0]"fields"
[1]"cdiff"
outputs
substrates
glucose
[0]"fields"
[1]"glucose"
acetate
[0]"fields"
[1]"acetate"
biomass
[0]"fields"
[1]"cdiff"
interval1.0
address"local:DynamicFBA"
config
model_file"iCN900.xml"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
sharednull
dfba_pputida
inputs
substrates
glucose
[0]"fields"
[1]"glucose"
ammonium
[0]"fields"
[1]"ammonium"
glycolate
[0]"fields"
[1]"glycolate"
biomass
[0]"fields"
[1]"pputida"
outputs
substrates
glucose
[0]"fields"
[1]"glucose"
ammonium
[0]"fields"
[1]"ammonium"
glycolate
[0]"fields"
[1]"glycolate"
biomass
[0]"fields"
[1]"pputida"
interval1.0
address"local:DynamicFBA"
config
model_file"iJN746.xml"
kinetic_params
glucose
[0]"1.0"
[1]"2.0"
ammonium
[0]"2.0"
[1]"4.0"
glycolate
[0]"0.5"
[1]"1.0"
substrate_update_reactions
glucose"EX_glc__D_e"
ammonium"EX_nh4_e"
glycolate"EX_glyclt_e"
bounds
sharednull
dfba_yeast
inputs
substrates
glucose
[0]"fields"
[1]"glucose"
ammonium
[0]"fields"
[1]"ammonium"
biomass
[0]"fields"
[1]"yeast"
outputs
substrates
glucose
[0]"fields"
[1]"glucose"
ammonium
[0]"fields"
[1]"ammonium"
biomass
[0]"fields"
[1]"yeast"
interval1.0
address"local:DynamicFBA"
config
model_file"iMM904.xml"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
ammonium
[0]"0.5"
[1]"1.0"
substrate_update_reactions
glucose"EX_glc__D_e"
ammonium"EX_nh4_e"
bounds
sharednull
dfba_llactis
inputs
substrates
glucose
[0]"fields"
[1]"glucose"
glutatmate
[0]"fields"
[1]"glutatmate"
serine
[0]"fields"
[1]"serine"
biomass
[0]"fields"
[1]"llactis"
outputs
substrates
glucose
[0]"fields"
[1]"glucose"
glutatmate
[0]"fields"
[1]"glutatmate"
serine
[0]"fields"
[1]"serine"
biomass
[0]"fields"
[1]"llactis"
interval1.0
address"local:DynamicFBA"
config
model_file"iNF517.xml"
kinetic_params
glucose
[0]"0.5"
[1]"1.25"
glutatmate
[0]"0.05"
[1]"0.1"
serine
[0]"0.05"
[1]"0.1"
substrate_update_reactions
glucose"EX_glc__D_e"
glutatmate"EX_glu__L_e"
serine"EX_ser__L_e"
bounds
sharednull
fields
glucose"10.0"
acetate"0.0"
ecoli core"0.1"
formate"0.0"
ecoli"0.1"
cdiff"0.1"
ammonium"0.0"
glycolate"0.0"
pputida"0.1"
yeast"0.1"
glutatmate"0.0"
serine"0.0"
llactis"0.1"

multi_dfba_viz.png

multi_dfba.png

spatial_many_dfba

This simulation introduces a spatial lattice, with a single dFBA process in each lattice site.

Runtime: 9.06 seconds

spatial_many_dfba.json

View full JSON
fields
glucose
list
[0]
[0]4.111997574867148
[1]6.569004199302839
[2]13.781440881981137
[3]15.756766741475964
[4]13.964457101903792
[1]
[0]11.281220276824337
[1]5.082316325677844
[2]12.49634972013476
[3]6.550690737870017
[4]1.5187936907009614
[2]
[0]14.430279482154988
[1]12.884559215049316
[2]16.57793090264263
[3]11.787467265767742
[4]11.39052868518097
[3]
[0]9.857968330044411
[1]3.12850613862778
[2]9.806510596196922
[3]16.272288488981214
[4]11.935606943464883
[4]
[0]1.9501120787341786
[1]0.03886618014131482
[2]1.4282533022197907
[3]19.933693419615196
[4]0.5739876617537365
[5]
[0]3.2066020945183293
[1]10.424221017153501
[2]1.93234462690685
[3]15.43121859352288
[4]0.6579729406563262
[6]
[0]4.308840951602349
[1]10.834194622178387
[2]3.096412294929305
[3]17.074500228751216
[4]10.027430940329456
[7]
[0]18.7748017409718
[1]1.620891044227779
[2]8.814211676735518
[3]9.458675693485695
[4]8.940211009153563
[8]
[0]10.521992583802396
[1]4.596861203567473
[2]10.809248477198313
[3]14.627844094320267
[4]0.3724790828065183
[9]
[0]11.515288263513085
[1]8.548283812782076
[2]16.104446943771187
[3]7.902985883959368
[4]1.4562806746477586
data"float"
shape
[0]10
[1]5
acetate
list
[0]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[1]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[2]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[3]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[4]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[6]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[7]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[8]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[9]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
data"float"
shape
[0]10
[1]5
biomass
list
[0]
[0]0.09296366354652733
[1]0.05515314044583589
[2]0.03909116599591812
[3]0.07615490755659021
[4]0.06881346395522374
[1]
[0]0.09620274839261328
[1]0.019640084527316738
[2]0.035941774053058706
[3]0.05264038677437687
[4]0.05377237514702278
[2]
[0]0.008737438161619837
[1]0.07364580335774322
[2]0.03533822774747447
[3]0.041480280410022774
[4]0.08562944547666418
[3]
[0]0.00399873085660436
[1]0.011719728616622238
[2]0.0918548686299345
[3]0.059097830578169586
[4]0.07850678884679518
[4]
[0]0.04161222692317351
[1]0.09837163829608006
[2]0.07249018071865922
[3]0.08551132809448893
[4]0.01768498211762105
[5]
[0]0.05794026845023677
[1]0.0006931890553204201
[2]0.059066683154170775
[3]0.022067920870290293
[4]0.03047548289671096
[6]
[0]0.06307858700842149
[1]0.03571774329606619
[2]0.037515602339756066
[3]0.058400280264369955
[4]0.02661379791962213
[7]
[0]0.026435074163859706
[1]0.03405922834261208
[2]0.08674919020167916
[3]0.04760330042158163
[4]0.002341839938484458
[8]
[0]0.07186527295522349
[1]0.0011610426163855992
[2]0.07721013836246648
[3]0.06276769009507038
[4]0.019861037184205434
[9]
[0]0.030507898305718897
[1]0.06064413173407236
[2]0.07712800645996994
[3]0.0662925987040946
[4]0.02621590065752462
data"float"
shape
[0]10
[1]5
spatial_dfba
dFBA[0,0]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]0
[4]0
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]0
[4]0
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]0
[4]0
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]0
[4]0
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]0
[4]0
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]0
[4]0
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[0,1]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]0
[4]1
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]0
[4]1
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]0
[4]1
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]0
[4]1
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]0
[4]1
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]0
[4]1
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[0,2]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]0
[4]2
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]0
[4]2
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]0
[4]2
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]0
[4]2
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]0
[4]2
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]0
[4]2
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[0,3]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]0
[4]3
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]0
[4]3
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]0
[4]3
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]0
[4]3
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]0
[4]3
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]0
[4]3
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[0,4]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]0
[4]4
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]0
[4]4
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]0
[4]4
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]0
[4]4
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]0
[4]4
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]0
[4]4
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[1,0]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]1
[4]0
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]1
[4]0
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]1
[4]0
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]1
[4]0
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]1
[4]0
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]1
[4]0
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[1,1]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]1
[4]1
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]1
[4]1
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]1
[4]1
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]1
[4]1
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]1
[4]1
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]1
[4]1
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[1,2]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]1
[4]2
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]1
[4]2
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]1
[4]2
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]1
[4]2
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]1
[4]2
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]1
[4]2
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[1,3]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]1
[4]3
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]1
[4]3
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]1
[4]3
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]1
[4]3
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]1
[4]3
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]1
[4]3
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[1,4]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]1
[4]4
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]1
[4]4
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]1
[4]4
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]1
[4]4
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]1
[4]4
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]1
[4]4
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[2,0]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]2
[4]0
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]2
[4]0
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]2
[4]0
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]2
[4]0
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]2
[4]0
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]2
[4]0
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[2,1]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]2
[4]1
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]2
[4]1
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]2
[4]1
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]2
[4]1
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]2
[4]1
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]2
[4]1
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[2,2]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]2
[4]2
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]2
[4]2
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]2
[4]2
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]2
[4]2
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]2
[4]2
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]2
[4]2
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[2,3]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]2
[4]3
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]2
[4]3
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]2
[4]3
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]2
[4]3
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]2
[4]3
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]2
[4]3
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[2,4]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]2
[4]4
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]2
[4]4
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]2
[4]4
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]2
[4]4
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]2
[4]4
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]2
[4]4
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[3,0]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]3
[4]0
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]3
[4]0
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]3
[4]0
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]3
[4]0
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]3
[4]0
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]3
[4]0
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[3,1]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]3
[4]1
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]3
[4]1
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]3
[4]1
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]3
[4]1
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]3
[4]1
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]3
[4]1
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[3,2]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]3
[4]2
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]3
[4]2
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]3
[4]2
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]3
[4]2
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]3
[4]2
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]3
[4]2
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[3,3]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]3
[4]3
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]3
[4]3
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]3
[4]3
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]3
[4]3
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]3
[4]3
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]3
[4]3
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[3,4]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]3
[4]4
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]3
[4]4
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]3
[4]4
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]3
[4]4
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]3
[4]4
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]3
[4]4
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[4,0]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]4
[4]0
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]4
[4]0
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]4
[4]0
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]4
[4]0
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]4
[4]0
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]4
[4]0
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[4,1]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]4
[4]1
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]4
[4]1
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]4
[4]1
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]4
[4]1
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]4
[4]1
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]4
[4]1
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[4,2]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]4
[4]2
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]4
[4]2
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]4
[4]2
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]4
[4]2
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]4
[4]2
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]4
[4]2
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[4,3]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]4
[4]3
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]4
[4]3
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]4
[4]3
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]4
[4]3
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]4
[4]3
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]4
[4]3
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[4,4]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]4
[4]4
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]4
[4]4
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]4
[4]4
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]4
[4]4
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]4
[4]4
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]4
[4]4
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[5,0]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]5
[4]0
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]5
[4]0
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]5
[4]0
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]5
[4]0
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]5
[4]0
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]5
[4]0
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[5,1]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]5
[4]1
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]5
[4]1
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]5
[4]1
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]5
[4]1
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]5
[4]1
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]5
[4]1
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[5,2]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]5
[4]2
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]5
[4]2
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]5
[4]2
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]5
[4]2
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]5
[4]2
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]5
[4]2
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[5,3]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]5
[4]3
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]5
[4]3
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]5
[4]3
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]5
[4]3
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]5
[4]3
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]5
[4]3
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[5,4]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]5
[4]4
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]5
[4]4
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]5
[4]4
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]5
[4]4
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]5
[4]4
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]5
[4]4
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[6,0]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]6
[4]0
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]6
[4]0
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]6
[4]0
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]6
[4]0
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]6
[4]0
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]6
[4]0
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[6,1]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]6
[4]1
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]6
[4]1
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]6
[4]1
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]6
[4]1
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]6
[4]1
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]6
[4]1
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[6,2]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]6
[4]2
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]6
[4]2
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]6
[4]2
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]6
[4]2
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]6
[4]2
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]6
[4]2
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[6,3]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]6
[4]3
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]6
[4]3
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]6
[4]3
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]6
[4]3
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]6
[4]3
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]6
[4]3
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[6,4]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]6
[4]4
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]6
[4]4
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]6
[4]4
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]6
[4]4
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]6
[4]4
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]6
[4]4
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[7,0]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]7
[4]0
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]7
[4]0
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]7
[4]0
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]7
[4]0
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]7
[4]0
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]7
[4]0
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[7,1]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]7
[4]1
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]7
[4]1
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]7
[4]1
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]7
[4]1
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]7
[4]1
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]7
[4]1
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[7,2]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]7
[4]2
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]7
[4]2
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]7
[4]2
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]7
[4]2
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]7
[4]2
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]7
[4]2
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[7,3]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]7
[4]3
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]7
[4]3
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]7
[4]3
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]7
[4]3
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]7
[4]3
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]7
[4]3
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[7,4]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]7
[4]4
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]7
[4]4
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]7
[4]4
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]7
[4]4
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]7
[4]4
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]7
[4]4
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[8,0]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]8
[4]0
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]8
[4]0
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]8
[4]0
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]8
[4]0
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]8
[4]0
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]8
[4]0
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[8,1]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]8
[4]1
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]8
[4]1
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]8
[4]1
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]8
[4]1
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]8
[4]1
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]8
[4]1
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[8,2]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]8
[4]2
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]8
[4]2
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]8
[4]2
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]8
[4]2
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]8
[4]2
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]8
[4]2
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[8,3]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]8
[4]3
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]8
[4]3
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]8
[4]3
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]8
[4]3
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]8
[4]3
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]8
[4]3
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[8,4]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]8
[4]4
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]8
[4]4
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]8
[4]4
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]8
[4]4
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]8
[4]4
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]8
[4]4
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[9,0]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]9
[4]0
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]9
[4]0
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]9
[4]0
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]9
[4]0
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]9
[4]0
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]9
[4]0
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[9,1]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]9
[4]1
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]9
[4]1
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]9
[4]1
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]9
[4]1
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]9
[4]1
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]9
[4]1
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[9,2]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]9
[4]2
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]9
[4]2
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]9
[4]2
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]9
[4]2
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]9
[4]2
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]9
[4]2
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[9,3]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]9
[4]3
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]9
[4]3
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]9
[4]3
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]9
[4]3
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]9
[4]3
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]9
[4]3
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
dFBA[9,4]
inputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]9
[4]4
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]9
[4]4
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]9
[4]4
outputs
substrates
glucose
[0]".."
[1]"fields"
[2]"glucose"
[3]9
[4]4
acetate
[0]".."
[1]"fields"
[2]"acetate"
[3]9
[4]4
biomass
[0]".."
[1]"fields"
[2]"biomass"
[3]9
[4]4
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull

spatial_many_dfba_viz.png

spatial_many_dfba_timeseries.png

spatial_many_dfba.gif

spatial_dfba_process

This simulation introduces a spatial lattice, with a spatial dFBA process that runs all the lattice sites

Runtime: 12.71 seconds

spatial_dfba_process.json

View full JSON
spatial_dfba
inputs
fields
glucose
[0]"fields"
[1]"glucose"
acetate
[0]"fields"
[1]"acetate"
biomass
[0]"fields"
[1]"biomass"
outputs
fields
glucose
[0]"fields"
[1]"glucose"
acetate
[0]"fields"
[1]"acetate"
biomass
[0]"fields"
[1]"biomass"
interval1.0
address"local:SpatialDFBA"
config
n_bins
[0]"10"
[1]"5"
model_file"!nil"
models
model_grid
[0]
[0]"ecoli core"
[1]"ecoli core"
[2]"ecoli core"
[3]"ecoli core"
[4]"ecoli core"
[1]
[0]"ecoli"
[1]"ecoli"
[2]"ecoli"
[3]"ecoli"
[4]"ecoli"
[2]
[0]"cdiff"
[1]"cdiff"
[2]"cdiff"
[3]"cdiff"
[4]"cdiff"
[3]
[0]"pputida"
[1]"pputida"
[2]"pputida"
[3]"pputida"
[4]"pputida"
[4]
[0]"yeast"
[1]"yeast"
[2]"yeast"
[3]"yeast"
[4]"yeast"
[5]
[0]"llactis"
[1]"llactis"
[2]"llactis"
[3]"llactis"
[4]"llactis"
[6]
[0]""
[1]""
[2]""
[3]""
[4]""
[7]
[0]""
[1]""
[2]""
[3]""
[4]""
[8]
[0]""
[1]""
[2]""
[3]""
[4]""
[9]
[0]""
[1]""
[2]""
[3]""
[4]""
kinetic_params
substrate_update_reactions
bounds
sharednull
fields
glucose
list
[0]
[0]0.0
[1]5.0
[2]10.0
[3]15.0
[4]20.0
[1]
[0]0.0
[1]5.0
[2]10.0
[3]15.0
[4]20.0
[2]
[0]0.0
[1]5.0
[2]10.0
[3]15.0
[4]20.0
[3]
[0]0.0
[1]5.0
[2]10.0
[3]15.0
[4]20.0
[4]
[0]0.0
[1]5.0
[2]10.0
[3]15.0
[4]20.0
[5]
[0]0.0
[1]5.0
[2]10.0
[3]15.0
[4]20.0
[6]
[0]0.0
[1]5.0
[2]10.0
[3]15.0
[4]20.0
[7]
[0]0.0
[1]5.0
[2]10.0
[3]15.0
[4]20.0
[8]
[0]0.0
[1]5.0
[2]10.0
[3]15.0
[4]20.0
[9]
[0]0.0
[1]5.0
[2]10.0
[3]15.0
[4]20.0
data"float"
shape
[0]10
[1]5
acetate
list
[0]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[1]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[2]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[3]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[4]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[6]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[7]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[8]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[9]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
data"float"
shape
[0]10
[1]5
biomass
list
[0]
[0]0.01
[1]0.01
[2]0.01
[3]0.01
[4]0.01
[1]
[0]0.01
[1]0.01
[2]0.01
[3]0.01
[4]0.01
[2]
[0]0.01
[1]0.01
[2]0.01
[3]0.01
[4]0.01
[3]
[0]0.01
[1]0.01
[2]0.01
[3]0.01
[4]0.01
[4]
[0]0.01
[1]0.01
[2]0.01
[3]0.01
[4]0.01
[5]
[0]0.01
[1]0.01
[2]0.01
[3]0.01
[4]0.01
[6]
[0]0.01
[1]0.01
[2]0.01
[3]0.01
[4]0.01
[7]
[0]0.01
[1]0.01
[2]0.01
[3]0.01
[4]0.01
[8]
[0]0.01
[1]0.01
[2]0.01
[3]0.01
[4]0.01
[9]
[0]0.01
[1]0.01
[2]0.01
[3]0.01
[4]0.01
data"float"
shape
[0]10
[1]5

spatial_dfba_process_viz.png

spatial_dfba_process_model_grid.png

spatial_dfba_process_timeseries.png

spatial_dfba_process.gif

diffusion_process

This simulation includes finite volume method for diffusion and advection on a lattice.

Runtime: 0.15 seconds

diffusion_process.json

View full JSON
diffusion
inputs
fields
[0]"fields"
outputs
fields
[0]"fields"
interval1.0
address"local:DiffusionAdvection"
config
n_bins
[0]"20"
[1]"10"
bounds
[0]"10.0"
[1]"5.0"
default_diffusion_rate"0.1"
default_diffusion_dt"0.1"
diffusion_coeffs
glucose"0.01"
biomass"0.01"
advection_coeffs
glucose
[0]"0.0"
[1]"0.0"
biomass
[0]"0.0"
[1]"0.1"
sharednull
fields
biomass
list
[0]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[1]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[2]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[3]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[4]
[0]10.0
[1]10.0
[2]10.0
[3]10.0
[4]10.0
[5]10.0
[6]10.0
[7]10.0
[8]10.0
[9]10.0
[5]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[6]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[7]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[8]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[9]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[10]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[11]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[12]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[13]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[14]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[15]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[16]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[17]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[18]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[19]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
data"float"
shape
[0]20
[1]10
glucose
list
[0]
[0]1.3470310975673885
[1]1.4547463492481545
[2]1.5484067966054809
[3]1.6402657646117662
[4]1.419335586911848
[5]1.497104664271067
[6]0.6286667691494635
[7]0.8940246076714331
[8]1.8583032827310764
[9]1.2811345456820213
[1]
[0]1.4261949835965064
[1]0.3187160703697021
[2]0.30640385251978075
[3]0.1625131614370315
[4]0.35699695829894107
[5]0.8119180118637012
[6]0.6839351252055365
[7]0.7346479932133836
[8]1.7674992977811386
[9]0.6852589783068254
[2]
[0]1.6367961893051093
[1]0.4029092140068382
[2]0.17019163831673656
[3]1.2201304247434117
[4]0.8400732642960158
[5]1.3023508425666634
[6]0.1598826854292931
[7]1.4359557236364118
[8]0.9981647999614607
[9]1.6804301126114227
[3]
[0]0.6826214210833971
[1]1.2711842909379647
[2]0.7852144001641604
[3]0.5797924077439804
[4]1.2394702606680978
[5]0.7391609014753076
[6]1.3803400568861148
[7]1.9828787525422154
[8]1.7763800051716805
[9]1.2158330944354534
[4]
[0]0.15395086772244937
[1]1.6255076234600971
[2]1.5677563988373735
[3]1.3177220116765516
[4]1.1281503072228354
[5]0.8822228634885174
[6]1.8646589818546426
[7]1.2419009461016712
[8]0.20252742962480727
[9]0.8391571537825389
[5]
[0]0.6500840878957821
[1]1.16807966666847
[2]1.3365434971818266
[3]1.4943414484557624
[4]0.7289227291671186
[5]1.7632311294450658
[6]1.0466351838582866
[7]1.6403145562879917
[8]1.120911107934182
[9]1.5068226874617514
[6]
[0]0.5461493403516823
[1]1.8595908959506409
[2]0.18929963800502336
[3]1.5742929411689914
[4]1.7138590559109066
[5]0.44018684600318414
[6]1.9181609243935092
[7]1.4711429127068227
[8]0.6966792606952751
[9]1.3619121839434634
[7]
[0]1.259252018753447
[1]0.7353904525256124
[2]1.7621106387639038
[3]1.7184151417160636
[4]1.8052166278028594
[5]0.11493052292740988
[6]1.4982190459688283
[7]0.28906728115689084
[8]1.868482031854699
[9]1.2132862600780632
[8]
[0]1.7440122604120514
[1]0.7423469090328375
[2]1.4304123237920503
[3]0.7748189780390428
[4]1.2720939677184484
[5]0.23520009765099806
[6]1.4050185674137234
[7]0.3125762130787889
[8]1.472892850883099
[9]0.8200181607375361
[9]
[0]0.593652211294531
[1]1.5595098195536077
[2]0.16336150386142684
[3]1.0285831538575236
[4]0.8260158152833994
[5]1.8716885719174465
[6]1.6112705303631907
[7]1.0783648010368867
[8]1.4371182217817617
[9]0.22025313403752078
[10]
[0]1.772145029671162
[1]0.6994770308737497
[2]0.11400743725627463
[3]1.7771917535170494
[4]0.544416753958477
[5]0.49728731113669034
[6]0.9753839200221326
[7]1.534535523639727
[8]0.28589544711048376
[9]0.8818405158268667
[11]
[0]1.9073799332788013
[1]1.1282074559946862
[2]0.911593137856175
[3]0.7299114932253252
[4]1.6879275515625394
[5]0.9185533837454796
[6]0.77204134194887
[7]0.42872154754695513
[8]1.2267861405732068
[9]1.534946136177575
[12]
[0]1.1390543667004116
[1]1.4340304262985697
[2]0.4997677176380847
[3]0.38624859468210615
[4]1.21980482160504
[5]0.2996337443330502
[6]0.37785659621968104
[7]0.18232475167688555
[8]1.2801371413052167
[9]1.142572582295576
[13]
[0]1.9687135920117835
[1]1.933265383913449
[2]1.1572180931041787
[3]1.387273002051814
[4]1.2990957527220424
[5]0.19742066911623293
[6]0.5831406889342854
[7]0.5024760692595387
[8]0.3255451589460101
[9]1.9359699176236416
[14]
[0]1.776174763142884
[1]1.3095132558024967
[2]1.7110292024765237
[3]0.2578928988220153
[4]0.4863197304476894
[5]1.025681281089448
[6]1.300896740944118
[7]0.23928040566222525
[8]1.1295794078966919
[9]0.7317212312010265
[15]
[0]1.3250568778048482
[1]1.633900281309964
[2]0.13359139446241614
[3]1.2679686180110665
[4]1.3733050931542916
[5]0.4215552166643959
[6]0.7392960943674778
[7]1.6672729167404545
[8]0.8819625475194166
[9]1.5121167611085873
[16]
[0]0.3216998605109226
[1]1.988292086017162
[2]0.7968158853455974
[3]1.8829221718413165
[4]0.335801330297693
[5]1.5969478760023081
[6]0.9301677945989238
[7]1.7111940379266655
[8]0.18468883818588178
[9]1.043757252503573
[17]
[0]0.8913869779544082
[1]0.286913175252425
[2]1.0599047916176785
[3]1.3149943890227724
[4]0.2299759945746353
[5]0.6493930390834561
[6]1.1275847070987968
[7]1.8987085385391418
[8]0.22777716962968753
[9]1.3537781604714791
[18]
[0]1.152369026583515
[1]1.3378350126563747
[2]0.2554186974791622
[3]1.0281513112216563
[4]0.6417960526904138
[5]1.8095980774707474
[6]0.6721394606976487
[7]0.56907477950815
[8]1.1654007471549594
[9]0.10588318237011589
[19]
[0]0.5514637847123882
[1]0.8549505698008317
[2]0.34665400271726243
[3]1.6146804825791772
[4]0.20269691051505712
[5]0.837796467759821
[6]1.6024539476261945
[7]0.8758981926659956
[8]0.5677785556620263
[9]1.3457125884345345
data"float"
shape
[0]20
[1]10

diffusion_process_viz.png

diffusion_process.gif

comets

This simulation combines dFBA at each lattice site with diffusion/advection to make a spatio-temporal FBA.

Runtime: 17.87 seconds

comets.json

View full JSON
fields
biomass
list
[0]
[0]0.0
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[10]
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[11]
[0]0.0
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[12]
[0]0.0
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[13]
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[15]
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[16]
[0]0.0
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[17]
[0]0.0
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[18]
[0]0.0
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[19]
[0]0.0
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[5]0.0
[6]0.0
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[8]0.0
[9]0.0
data"float"
shape
[0]20
[1]10
glucose
list
[0]
[0]0.01
[1]0.01
[2]0.01
[3]0.01
[4]0.01
[5]0.01
[6]0.01
[7]0.01
[8]0.01
[9]0.01
[1]
[0]0.5357894736842106
[1]0.5357894736842106
[2]0.5357894736842106
[3]0.5357894736842106
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[6]0.5357894736842106
[7]0.5357894736842106
[8]0.5357894736842106
[9]0.5357894736842106
[2]
[0]1.0615789473684212
[1]1.0615789473684212
[2]1.0615789473684212
[3]1.0615789473684212
[4]1.0615789473684212
[5]1.0615789473684212
[6]1.0615789473684212
[7]1.0615789473684212
[8]1.0615789473684212
[9]1.0615789473684212
[3]
[0]1.5873684210526318
[1]1.5873684210526318
[2]1.5873684210526318
[3]1.5873684210526318
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[4]
[0]2.113157894736842
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[6]
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[7]
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[9]
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[14]
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[15]
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[16]
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[17]
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[1]8.948421052631579
[2]8.948421052631579
[3]8.948421052631579
[4]8.948421052631579
[5]8.948421052631579
[6]8.948421052631579
[7]8.948421052631579
[8]8.948421052631579
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[18]
[0]9.47421052631579
[1]9.47421052631579
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[3]9.47421052631579
[4]9.47421052631579
[5]9.47421052631579
[6]9.47421052631579
[7]9.47421052631579
[8]9.47421052631579
[9]9.47421052631579
[19]
[0]10.0
[1]10.0
[2]10.0
[3]10.0
[4]10.0
[5]10.0
[6]10.0
[7]10.0
[8]10.0
[9]10.0
data"float"
shape
[0]20
[1]10
acetate
list
[0]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
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[9]0.0
[1]
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[2]
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[5]
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[9]
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[10]
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[11]
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[12]
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[13]
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[14]
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[15]
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[16]
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[17]
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[18]
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[19]
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data"float"
shape
[0]20
[1]10
spatial_dfba
inputs
fields
glucose
[0]"fields"
[1]"glucose"
acetate
[0]"fields"
[1]"acetate"
biomass
[0]"fields"
[1]"biomass"
outputs
fields
glucose
[0]"fields"
[1]"glucose"
acetate
[0]"fields"
[1]"acetate"
biomass
[0]"fields"
[1]"biomass"
interval1.0
address"local:SpatialDFBA"
config
n_bins
[0]"20"
[1]"10"
model_file"textbook"
models
model_grid
[0]
[0]"ecoli core"
[1]"ecoli core"
[2]"ecoli core"
[3]"ecoli core"
[4]"ecoli core"
[5]"ecoli core"
[6]"ecoli core"
[7]"ecoli core"
[8]"ecoli core"
[9]"ecoli core"
[1]
[0]"ecoli core"
[1]"ecoli core"
[2]"ecoli core"
[3]"ecoli core"
[4]"ecoli core"
[5]"ecoli core"
[6]"ecoli core"
[7]"ecoli core"
[8]"ecoli core"
[9]"ecoli core"
[2]
[0]"ecoli core"
[1]"ecoli core"
[2]"ecoli core"
[3]"ecoli core"
[4]"ecoli core"
[5]"ecoli core"
[6]"ecoli core"
[7]"ecoli core"
[8]"ecoli core"
[9]"ecoli core"
[3]
[0]"ecoli core"
[1]"ecoli core"
[2]"ecoli core"
[3]"ecoli core"
[4]"ecoli core"
[5]"ecoli core"
[6]"ecoli core"
[7]"ecoli core"
[8]"ecoli core"
[9]"ecoli core"
[4]
[0]"ecoli core"
[1]"ecoli core"
[2]"ecoli core"
[3]"ecoli core"
[4]"ecoli core"
[5]"ecoli core"
[6]"ecoli core"
[7]"ecoli core"
[8]"ecoli core"
[9]"ecoli core"
[5]
[0]"ecoli core"
[1]"ecoli core"
[2]"ecoli core"
[3]"ecoli core"
[4]"ecoli core"
[5]"ecoli core"
[6]"ecoli core"
[7]"ecoli core"
[8]"ecoli core"
[9]"ecoli core"
[6]
[0]"ecoli core"
[1]"ecoli core"
[2]"ecoli core"
[3]"ecoli core"
[4]"ecoli core"
[5]"ecoli core"
[6]"ecoli core"
[7]"ecoli core"
[8]"ecoli core"
[9]"ecoli core"
[7]
[0]"ecoli core"
[1]"ecoli core"
[2]"ecoli core"
[3]"ecoli core"
[4]"ecoli core"
[5]"ecoli core"
[6]"ecoli core"
[7]"ecoli core"
[8]"ecoli core"
[9]"ecoli core"
[8]
[0]"ecoli core"
[1]"ecoli core"
[2]"ecoli core"
[3]"ecoli core"
[4]"ecoli core"
[5]"ecoli core"
[6]"ecoli core"
[7]"ecoli core"
[8]"ecoli core"
[9]"ecoli core"
[9]
[0]"ecoli core"
[1]"ecoli core"
[2]"ecoli core"
[3]"ecoli core"
[4]"ecoli core"
[5]"ecoli core"
[6]"ecoli core"
[7]"ecoli core"
[8]"ecoli core"
[9]"ecoli core"
[10]
[0]"ecoli core"
[1]"ecoli core"
[2]"ecoli core"
[3]"ecoli core"
[4]"ecoli core"
[5]"ecoli core"
[6]"ecoli core"
[7]"ecoli core"
[8]"ecoli core"
[9]"ecoli core"
[11]
[0]"ecoli core"
[1]"ecoli core"
[2]"ecoli core"
[3]"ecoli core"
[4]"ecoli core"
[5]"ecoli core"
[6]"ecoli core"
[7]"ecoli core"
[8]"ecoli core"
[9]"ecoli core"
[12]
[0]"ecoli core"
[1]"ecoli core"
[2]"ecoli core"
[3]"ecoli core"
[4]"ecoli core"
[5]"ecoli core"
[6]"ecoli core"
[7]"ecoli core"
[8]"ecoli core"
[9]"ecoli core"
[13]
[0]"ecoli core"
[1]"ecoli core"
[2]"ecoli core"
[3]"ecoli core"
[4]"ecoli core"
[5]"ecoli core"
[6]"ecoli core"
[7]"ecoli core"
[8]"ecoli core"
[9]"ecoli core"
[14]
[0]"ecoli core"
[1]"ecoli core"
[2]"ecoli core"
[3]"ecoli core"
[4]"ecoli core"
[5]"ecoli core"
[6]"ecoli core"
[7]"ecoli core"
[8]"ecoli core"
[9]"ecoli core"
[15]
[0]"ecoli core"
[1]"ecoli core"
[2]"ecoli core"
[3]"ecoli core"
[4]"ecoli core"
[5]"ecoli core"
[6]"ecoli core"
[7]"ecoli core"
[8]"ecoli core"
[9]"ecoli core"
[16]
[0]"ecoli core"
[1]"ecoli core"
[2]"ecoli core"
[3]"ecoli core"
[4]"ecoli core"
[5]"ecoli core"
[6]"ecoli core"
[7]"ecoli core"
[8]"ecoli core"
[9]"ecoli core"
[17]
[0]"ecoli core"
[1]"ecoli core"
[2]"ecoli core"
[3]"ecoli core"
[4]"ecoli core"
[5]"ecoli core"
[6]"ecoli core"
[7]"ecoli core"
[8]"ecoli core"
[9]"ecoli core"
[18]
[0]"ecoli core"
[1]"ecoli core"
[2]"ecoli core"
[3]"ecoli core"
[4]"ecoli core"
[5]"ecoli core"
[6]"ecoli core"
[7]"ecoli core"
[8]"ecoli core"
[9]"ecoli core"
[19]
[0]"ecoli core"
[1]"ecoli core"
[2]"ecoli core"
[3]"ecoli core"
[4]"ecoli core"
[5]"ecoli core"
[6]"ecoli core"
[7]"ecoli core"
[8]"ecoli core"
[9]"ecoli core"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
diffusion
inputs
fields
[0]"fields"
outputs
fields
[0]"fields"
interval1.0
address"local:DiffusionAdvection"
config
n_bins
[0]"20"
[1]"10"
bounds
[0]"10.0"
[1]"5.0"
default_diffusion_rate"0.1"
default_diffusion_dt"0.1"
diffusion_coeffs
glucose"0.0"
acetate"0.1"
advection_coeffs
glucose
[0]"0.0"
[1]"0.0"
acetate
[0]"0.0"
[1]"0.0"
sharednull

comets_viz.png

comets_timeseries.png

comets_results.gif

particles

This simulation uses Brownian particles with mass moving randomly in space, and with a minimal reaction process inside of each particle uptaking or secreting from the field.

Runtime: 0.74 seconds

particles.json

View full JSON
particles
kND2sx7n
id"kND2sx7n"
position
[0]"4.577604416974662"
[1]"1.5738361442933102"
mass"0.7918250127611848"
local
exchange
minimal_particle
inputs
mass
[0]"mass"
substrates
[0]"local"
outputs
mass
[0]"mass"
substrates
[0]"exchange"
interval1.0
address"local:MinimalParticle"
config
reactions
grow
reactant"glucose"
product"mass"
release
reactant"mass"
product"detritus"
kinetic_params
glucose
[0]"0.5"
[1]"0.01"
mass
[0]"1.0"
[1]"0.001"
shared
particle_movement
inputs
particles
[0]"particles"
fields
[0]"fields"
outputs
particles
[0]"particles"
fields
[0]"fields"
interval1.0
address"local:Particles"
config
bounds
[0]"5.0"
[1]"10.0"
n_bins
[0]"10"
[1]"20"
diffusion_rate"0.1"
advection_rate
[0]"0.0"
[1]"-0.1"
add_probability"0.4"
boundary_to_add
[0]"top"
boundary_to_remove
[0]"top"
[1]"bottom"
[2]"left"
[3]"right"
division_mass_threshold"5.0"
division_jitter"0.001"
sharednull
fields
glucose
list
[0]
[0]1.2034283714169298
[1]1.9097138008935453
[2]1.0462373973699308
[3]1.2412072320929028
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[6]0.804860122357087
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[8]0.9295767908328623
[9]0.7083609960220398
[10]0.8989173583440805
[11]1.105204521022583
[12]1.383227923978515
[13]1.5903575626336932
[14]0.5161903710950344
[15]1.9656506401585259
[16]1.9704570410336268
[17]0.9699555256604
[18]1.9488669037826014
[19]1.7407580571024426
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[0]0.6657980646018313
[1]1.2422709937817054
[2]0.8373398471185398
[3]1.0173232181208953
[4]1.957074812108542
[5]0.8768496669797465
[6]1.0964945957244803
[7]1.5300637444274665
[8]1.558090999457118
[9]1.8567076085349563
[10]0.5668757519242937
[11]1.2788367116376764
[12]1.3116829190947683
[13]1.7551347131873527
[14]1.4496580534027212
[15]1.5724439217302122
[16]1.6690917081460699
[17]0.6762818203448736
[18]1.410136876326366
[19]1.7164620761721094
[2]
[0]1.0892182670582176
[1]1.9600180935079798
[2]0.7412148140179591
[3]1.0569497916751218
[4]1.152915233052363
[5]1.1047161370749257
[6]1.0070198514571533
[7]0.6035111140189511
[8]1.8405206544410895
[9]1.215622934544228
[10]0.9287476774384633
[11]0.5939319031362253
[12]1.5879138740426721
[13]1.1672085605779001
[14]0.8750873848358183
[15]1.375831420731088
[16]1.7376373684335027
[17]1.8476236480266957
[18]1.6627190007122579
[19]1.0087442683256864
[3]
[0]0.6864477059549874
[1]1.426602959257596
[2]1.944389063721503
[3]1.6375908615542327
[4]1.463268297870105
[5]1.6604260901233951
[6]1.3735701692804403
[7]1.3589513831605837
[8]1.2921874500352657
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[0]0.8862158358051606
[1]1.6688639756066677
[2]1.2003444966756145
[3]1.276237188394529
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[19]1.2919980151725294
[5]
[0]0.8617281463534738
[1]1.9522571131919195
[2]1.721547579350783
[3]1.2193279950408036
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[17]1.5973482330491193
[18]1.5341956657508253
[19]1.9848384586219698
[6]
[0]0.9244774421533437
[1]0.9182534716554676
[2]0.6669441349122874
[3]0.8443834955205218
[4]1.5987051783678523
[5]1.4541600507245462
[6]1.596528890884773
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[8]1.5687920669072488
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[14]1.7717411242987606
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[17]1.1628512417252388
[18]1.5083615692845043
[19]1.0072117683677417
[7]
[0]0.9641989813366287
[1]1.2244315631459761
[2]1.677839066037219
[3]1.1903809850530498
[4]1.860858007632787
[5]0.7891338049516459
[6]1.5776829212931693
[7]1.5629043776224751
[8]0.6226593785296848
[9]1.1337982113590304
[10]1.9563507849540533
[11]0.8295422416956504
[12]1.893246040804618
[13]1.110640009505384
[14]1.8456353548242146
[15]0.9304957059937936
[16]1.4139986768691584
[17]0.9453896476566153
[18]1.3757929951351096
[19]1.3105079066530525
[8]
[0]1.453537007862122
[1]1.858556178689886
[2]0.6420441780605068
[3]1.6047604153807067
[4]1.1377345046676324
[5]1.0260224811334206
[6]1.3346978298839638
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[9]1.6328553456236021
[10]1.6879793748740874
[11]1.666705276724227
[12]1.0184140372771406
[13]0.71841547032041
[14]1.733055064302618
[15]0.9055454223572961
[16]1.2662727509778293
[17]1.3333823245715954
[18]0.6205717016891358
[19]0.9021758606407444
[9]
[0]0.7615524315856927
[1]1.4273006966670687
[2]1.458034911315207
[3]1.3041215708745257
[4]0.7933396935193717
[5]0.5236764157483749
[6]0.8538831380895471
[7]1.4655247986174564
[8]1.2358994452997094
[9]1.15142975822357
[10]0.531648109722426
[11]1.7939370850083591
[12]0.8507259975972492
[13]0.8092647791862955
[14]0.8244596741326644
[15]0.8495356617436243
[16]1.1903322038524713
[17]0.9255975348038068
[18]1.0706641935362173
[19]0.753751900029592
data"float"
shape
[0]10
[1]20
detritus
list
[0]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[10]0.0
[11]0.0
[12]0.0
[13]0.0
[14]0.0
[15]0.0
[16]0.0
[17]0.0
[18]0.0
[19]0.0
[1]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[10]0.0
[11]0.0
[12]0.0
[13]0.0
[14]0.0
[15]0.0
[16]0.0
[17]0.0
[18]0.0
[19]0.0
[2]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[10]0.0
[11]0.0
[12]0.0
[13]0.0
[14]0.0
[15]0.0
[16]0.0
[17]0.0
[18]0.0
[19]0.0
[3]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
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[11]0.0
[12]0.0
[13]0.0
[14]0.0
[15]0.0
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[17]0.0
[18]0.0
[19]0.0
[4]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[10]0.0
[11]0.0
[12]0.0
[13]0.0
[14]0.0
[15]0.0
[16]0.0
[17]0.0
[18]0.0
[19]0.0
[5]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[10]0.0
[11]0.0
[12]0.0
[13]0.0
[14]0.0
[15]0.0
[16]0.0
[17]0.0
[18]0.0
[19]0.0
[6]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[10]0.0
[11]0.0
[12]0.0
[13]0.0
[14]0.0
[15]0.0
[16]0.0
[17]0.0
[18]0.0
[19]0.0
[7]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[10]0.0
[11]0.0
[12]0.0
[13]0.0
[14]0.0
[15]0.0
[16]0.0
[17]0.0
[18]0.0
[19]0.0
[8]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
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[10]0.0
[11]0.0
[12]0.0
[13]0.0
[14]0.0
[15]0.0
[16]0.0
[17]0.0
[18]0.0
[19]0.0
[9]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
[7]0.0
[8]0.0
[9]0.0
[10]0.0
[11]0.0
[12]0.0
[13]0.0
[14]0.0
[15]0.0
[16]0.0
[17]0.0
[18]0.0
[19]0.0
data"float"
shape
[0]10
[1]20

particles_viz.png

particles_alone.gif

particles_with_fields.gif

particle_comets

This simulation extends COMETS with particles that have internal minimal reaction processes.

Runtime: 11.32 seconds

particle_comets.json

View full JSON
particles
THBr78Vz
id"THBr78Vz"
position
[0]"4.637925144282459"
[1]"2.7139787959930475"
mass"9.521920735310838"
local
glucose"10.0"
acetate"0.0"
detritus"0.0"
biomass"0.0"
exchange
glucose"0.0"
acetate"0.0"
detritus"0.0"
biomass"0.0"
minimal_particle
inputs
mass
[0]"mass"
substrates
[0]"local"
outputs
mass
[0]"mass"
substrates
[0]"exchange"
interval1.0
address"local:MinimalParticle"
config
reactions
grow
reactant"glucose"
product"mass"
release
reactant"mass"
product"detritus"
kinetic_params
glucose
[0]"0.5"
[1]"0.01"
mass
[0]"1.0"
[1]"0.001"
shared
8ILQBsph
id"8ILQBsph"
position
[0]"1.7719618272441378"
[1]"9.66718187486297"
mass"6.706425493871353"
local
glucose"10.0"
acetate"0.0"
detritus"0.0"
biomass"0.0"
exchange
glucose"0.0"
acetate"0.0"
detritus"0.0"
biomass"0.0"
minimal_particle
inputs
mass
[0]"mass"
substrates
[0]"local"
outputs
mass
[0]"mass"
substrates
[0]"exchange"
interval1.0
address"local:MinimalParticle"
config
reactions
grow
reactant"glucose"
product"mass"
release
reactant"mass"
product"detritus"
kinetic_params
glucose
[0]"0.5"
[1]"0.01"
mass
[0]"1.0"
[1]"0.001"
shared
VKzBCT2M
id"VKzBCT2M"
position
[0]"4.320571543934077"
[1]"9.896899677884301"
mass"2.2974415164335302"
local
glucose"10.0"
acetate"0.0"
detritus"0.0"
biomass"0.0"
exchange
glucose"0.0"
acetate"0.0"
detritus"0.0"
biomass"0.0"
minimal_particle
inputs
mass
[0]"mass"
substrates
[0]"local"
outputs
mass
[0]"mass"
substrates
[0]"exchange"
interval1.0
address"local:MinimalParticle"
config
reactions
grow
reactant"glucose"
product"mass"
release
reactant"mass"
product"detritus"
kinetic_params
glucose
[0]"0.5"
[1]"0.01"
mass
[0]"1.0"
[1]"0.001"
shared
CVdg_DSs
id"CVdg_DSs"
position
[0]"0.6555700831536304"
[1]"9.533617162893206"
mass"4.736381412075385"
local
glucose"10.0"
acetate"0.0"
detritus"0.0"
biomass"0.0"
exchange
glucose"0.0"
acetate"0.0"
detritus"0.0"
biomass"0.0"
minimal_particle
inputs
mass
[0]"mass"
substrates
[0]"local"
outputs
mass
[0]"mass"
substrates
[0]"exchange"
interval1.0
address"local:MinimalParticle"
config
reactions
grow
reactant"glucose"
product"mass"
release
reactant"mass"
product"detritus"
kinetic_params
glucose
[0]"0.5"
[1]"0.01"
mass
[0]"1.0"
[1]"0.001"
shared
un3OYv5I
id"un3OYv5I"
position
[0]"3.5142247446254316"
[1]"4.376035034337784"
mass"6.673952748082454"
local
glucose"10.0"
acetate"0.0"
detritus"0.0"
biomass"0.0"
exchange
glucose"0.0"
acetate"0.0"
detritus"0.0"
biomass"0.0"
minimal_particle
inputs
mass
[0]"mass"
substrates
[0]"local"
outputs
mass
[0]"mass"
substrates
[0]"exchange"
interval1.0
address"local:MinimalParticle"
config
reactions
grow
reactant"glucose"
product"mass"
release
reactant"mass"
product"detritus"
kinetic_params
glucose
[0]"0.5"
[1]"0.01"
mass
[0]"1.0"
[1]"0.001"
shared
pvpdmvyp
id"pvpdmvyp"
position
[0]"3.845992866233639"
[1]"1.616294237549829"
mass"8.340099694440148"
local
glucose"10.0"
acetate"0.0"
detritus"0.0"
biomass"0.0"
exchange
glucose"0.0"
acetate"0.0"
detritus"0.0"
biomass"0.0"
minimal_particle
inputs
mass
[0]"mass"
substrates
[0]"local"
outputs
mass
[0]"mass"
substrates
[0]"exchange"
interval1.0
address"local:MinimalParticle"
config
reactions
grow
reactant"glucose"
product"mass"
release
reactant"mass"
product"detritus"
kinetic_params
glucose
[0]"0.5"
[1]"0.01"
mass
[0]"1.0"
[1]"0.001"
shared
6FtQ4oh1
id"6FtQ4oh1"
position
[0]"0.23751813835932833"
[1]"6.731323771858333"
mass"2.3749409864954902"
local
glucose"10.0"
acetate"0.0"
detritus"0.0"
biomass"0.0"
exchange
glucose"0.0"
acetate"0.0"
detritus"0.0"
biomass"0.0"
minimal_particle
inputs
mass
[0]"mass"
substrates
[0]"local"
outputs
mass
[0]"mass"
substrates
[0]"exchange"
interval1.0
address"local:MinimalParticle"
config
reactions
grow
reactant"glucose"
product"mass"
release
reactant"mass"
product"detritus"
kinetic_params
glucose
[0]"0.5"
[1]"0.01"
mass
[0]"1.0"
[1]"0.001"
shared
k6Jz8IvN
id"k6Jz8IvN"
position
[0]"1.3709487155165334"
[1]"9.960283848526167"
mass"9.188062379720948"
local
glucose"10.0"
acetate"0.0"
detritus"0.0"
biomass"0.0"
exchange
glucose"0.0"
acetate"0.0"
detritus"0.0"
biomass"0.0"
minimal_particle
inputs
mass
[0]"mass"
substrates
[0]"local"
outputs
mass
[0]"mass"
substrates
[0]"exchange"
interval1.0
address"local:MinimalParticle"
config
reactions
grow
reactant"glucose"
product"mass"
release
reactant"mass"
product"detritus"
kinetic_params
glucose
[0]"0.5"
[1]"0.01"
mass
[0]"1.0"
[1]"0.001"
shared
XhL4QHTN
id"XhL4QHTN"
position
[0]"0.2358591028558238"
[1]"2.845105157220539"
mass"8.477161140028812"
local
glucose"10.0"
acetate"0.0"
detritus"0.0"
biomass"0.1"
exchange
glucose"0.0"
acetate"0.0"
detritus"0.0"
biomass"0.0"
minimal_particle
inputs
mass
[0]"mass"
substrates
[0]"local"
outputs
mass
[0]"mass"
substrates
[0]"exchange"
interval1.0
address"local:MinimalParticle"
config
reactions
grow
reactant"glucose"
product"mass"
release
reactant"mass"
product"detritus"
kinetic_params
glucose
[0]"0.5"
[1]"0.01"
mass
[0]"1.0"
[1]"0.001"
shared
LutKbk7A
id"LutKbk7A"
position
[0]"1.1361489558125326"
[1]"2.9800007363013603"
mass"7.193495023959923"
local
glucose"10.0"
acetate"0.0"
detritus"0.0"
biomass"0.0"
exchange
glucose"0.0"
acetate"0.0"
detritus"0.0"
biomass"0.0"
minimal_particle
inputs
mass
[0]"mass"
substrates
[0]"local"
outputs
mass
[0]"mass"
substrates
[0]"exchange"
interval1.0
address"local:MinimalParticle"
config
reactions
grow
reactant"glucose"
product"mass"
release
reactant"mass"
product"detritus"
kinetic_params
glucose
[0]"0.5"
[1]"0.01"
mass
[0]"1.0"
[1]"0.001"
shared
spatial_dfba
inputs
fields
glucose
[0]"fields"
[1]"glucose"
acetate
[0]"fields"
[1]"acetate"
detritus
[0]"fields"
[1]"detritus"
biomass
[0]"fields"
[1]"biomass"
outputs
fields
glucose
[0]"fields"
[1]"glucose"
acetate
[0]"fields"
[1]"acetate"
detritus
[0]"fields"
[1]"detritus"
biomass
[0]"fields"
[1]"biomass"
interval1.0
address"local:SpatialDFBA"
config
n_bins
[0]"10"
[1]"20"
model_file"textbook"
models
model_grid
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
diffusion
inputs
fields
[0]"fields"
outputs
fields
[0]"fields"
interval1.0
address"local:DiffusionAdvection"
config
n_bins
[0]"10"
[1]"20"
bounds
[0]"5.0"
[1]"10.0"
default_diffusion_rate"0.1"
default_diffusion_dt"0.1"
diffusion_coeffs
glucose"0.1"
acetate"0.1"
detritus"0.1"
advection_coeffs
glucose
[0]"0.0"
[1]"0.0"
acetate
[0]"0.0"
[1]"0.0"
detritus
[0]"0.0"
[1]"0.0"
sharednull
particle_movement
inputs
particles
[0]"particles"
fields
[0]"fields"
outputs
particles
[0]"particles"
fields
[0]"fields"
interval1.0
address"local:Particles"
config
bounds
[0]"5.0"
[1]"10.0"
n_bins
[0]"10"
[1]"20"
diffusion_rate"0.1"
advection_rate
[0]"0.0"
[1]"-0.1"
add_probability"0.1"
boundary_to_add
[0]"top"
boundary_to_remove
[0]"top"
[1]"bottom"
[2]"left"
[3]"right"
division_mass_threshold"5.0"
division_jitter"0.001"
sharednull
fields
glucose
list
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[2]
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[4]
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[5]
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[0]10.0
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[7]
[0]10.0
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[8]
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[9]
[0]10.0
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[15]10.0
[16]10.0
[17]10.0
[18]10.0
[19]10.0
data"float"
shape
[0]10
[1]20
acetate
list
[0]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
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[16]0.0
[17]0.0
[18]0.0
[19]0.0
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[12]0.0
[13]0.0
[14]0.0
[15]0.0
[16]0.0
[17]0.0
[18]0.0
[19]0.0
[2]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
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[11]0.0
[12]0.0
[13]0.0
[14]0.0
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[16]0.0
[17]0.0
[18]0.0
[19]0.0
[3]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
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[6]0.0
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[11]0.0
[12]0.0
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[14]0.0
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[17]0.0
[18]0.0
[19]0.0
[4]
[0]0.0
[1]0.0
[2]0.0
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[5]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
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[11]0.0
[12]0.0
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[16]0.0
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[19]0.0
[6]
[0]0.0
[1]0.0
[2]0.0
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[4]0.0
[5]0.0
[6]0.0
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[19]0.0
[7]
[0]0.0
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[6]0.0
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[8]
[0]0.0
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[6]0.0
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[9]
[0]0.0
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[13]0.0
[14]0.0
[15]0.0
[16]0.0
[17]0.0
[18]0.0
[19]0.0
data"float"
shape
[0]10
[1]20
detritus
list
[0]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
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[2]
[0]0.0
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[5]
[0]0.0
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[12]0.0
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[6]
[0]0.0
[1]0.0
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[7]
[0]0.0
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[10]0.0
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[17]0.0
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[8]
[0]0.0
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[9]
[0]0.0
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[14]0.0
[15]0.0
[16]0.0
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[19]0.0
data"float"
shape
[0]10
[1]20
biomass
list
[0]
[0]0.0
[1]0.0
[2]0.1
[3]0.1
[4]0.1
[5]0.1
[6]0.1
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[4]
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[5]
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[0]0.0
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[0]0.0
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[17]0.0
[18]0.0
[19]0.0
data"float"
shape
[0]10
[1]20

particle_comets_viz.png

particle_comets_timeseries.png

particle_comets_with_fields.gif

particle_dfba_fields

This simulation puts dFBA inside of the particles, interacting with external fields and adding biomass into the particle mass, reflected by the particle size.

Runtime: 3.26 seconds

particle_dfba_fields.json

View full JSON
particles
8db8QoK5
id"8db8QoK5"
position
[0]"4.314317519928911"
[1]"0.9111322182559212"
mass"0.547692034571835"
local
glucose"2.1166971610362753"
acetate"0.0"
exchange
glucose"0.0"
acetate"0.0"
dFBA
inputs
substrates
[0]"local"
biomass
[0]"mass"
outputs
substrates
[0]"exchange"
biomass
[0]"mass"
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
shared
O1UwBTCK
id"O1UwBTCK"
position
[0]"4.069240648485398"
[1]"3.9166722489695927"
mass"0.9815756054100205"
local
glucose"4.89338883756241"
acetate"0.0"
exchange
glucose"0.0"
acetate"0.0"
dFBA
inputs
substrates
[0]"local"
biomass
[0]"mass"
outputs
substrates
[0]"exchange"
biomass
[0]"mass"
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
shared
diffusion
inputs
fields
[0]"fields"
outputs
fields
[0]"fields"
interval1.0
address"local:DiffusionAdvection"
config
n_bins
[0]"10"
[1]"20"
bounds
[0]"5.0"
[1]"10.0"
default_diffusion_rate"0.1"
default_diffusion_dt"0.1"
diffusion_coeffs
glucose"0.1"
acetate"0.1"
advection_coeffs
glucose
[0]"0.0"
[1]"0.0"
acetate
[0]"0.0"
[1]"0.0"
sharednull
particle_movement
inputs
particles
[0]"particles"
fields
[0]"fields"
outputs
particles
[0]"particles"
fields
[0]"fields"
interval1.0
address"local:Particles"
config
bounds
[0]"5.0"
[1]"10.0"
n_bins
[0]"10"
[1]"20"
diffusion_rate"0.1"
advection_rate
[0]"0.0"
[1]"-0.1"
add_probability"0.2"
boundary_to_add
[0]"top"
boundary_to_remove
[0]"top"
[1]"bottom"
[2]"left"
[3]"right"
division_mass_threshold"5.0"
division_jitter"0.001"
sharednull
fields
glucose
list
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[17]1.0897860606063445
[18]8.113362263541728
[19]8.714633969792985
data"float"
shape
[0]10
[1]20
acetate
list
[0]
[0]0.0
[1]0.0
[2]0.0
[3]0.0
[4]0.0
[5]0.0
[6]0.0
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[5]
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[6]
[0]0.0
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[7]
[0]0.0
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[8]
[0]0.0
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[9]
[0]0.0
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data"float"
shape
[0]10
[1]20

particle_dfba_fields_viz.png

particle_dfba_fields_mass.png

particle_dfba_fields_timeseries.png

particle_dfba_fields_with_fields.gif

particle_dfba_comets

This simulation combines dFBA inside of the particles with COMETS, allowing particles to uptake and secrete from the external fields.

Runtime: 18.40 seconds

particle_dfba_comets.json

View full JSON
particles
U2QHjDXU
id"U2QHjDXU"
position
[0]"2.8987862211962034"
[1]"5.960048946559054"
mass"0.7437186096669489"
local
glucose"1.2872677938843293"
acetate"0.0"
biomass"0.07492284042920187"
exchange
glucose"0.0"
acetate"0.0"
biomass"0.0"
dFBA
inputs
substrates
[0]"local"
biomass
[0]"mass"
outputs
substrates
[0]"exchange"
biomass
[0]"mass"
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
shared
lUnKdbx2
id"lUnKdbx2"
position
[0]"3.9151223644826274"
[1]"7.744254682476489"
mass"0.3326748552057277"
local
glucose"4.148456437736626"
acetate"0.0"
biomass"0.01925442090843851"
exchange
glucose"0.0"
acetate"0.0"
biomass"0.0"
dFBA
inputs
substrates
[0]"local"
biomass
[0]"mass"
outputs
substrates
[0]"exchange"
biomass
[0]"mass"
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
shared
fS2716Zh
id"fS2716Zh"
position
[0]"1.1344566817362256"
[1]"3.9504928262531127"
mass"0.23870298709687662"
local
glucose"2.138480804729335"
acetate"0.0"
biomass"0.09364171921292688"
exchange
glucose"0.0"
acetate"0.0"
biomass"0.0"
dFBA
inputs
substrates
[0]"local"
biomass
[0]"mass"
outputs
substrates
[0]"exchange"
biomass
[0]"mass"
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
shared
Zr97LtTS
id"Zr97LtTS"
position
[0]"1.5157596922470573"
[1]"5.765271026549636"
mass"0.09099401996233615"
local
glucose"2.4601011516847837"
acetate"0.0"
biomass"0.07844046075603082"
exchange
glucose"0.0"
acetate"0.0"
biomass"0.0"
dFBA
inputs
substrates
[0]"local"
biomass
[0]"mass"
outputs
substrates
[0]"exchange"
biomass
[0]"mass"
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
shared
AcxMaywj
id"AcxMaywj"
position
[0]"0.11153131682965833"
[1]"6.998791374832104"
mass"0.45903105913214465"
local
glucose"4.166814604576521"
acetate"0.0"
biomass"0.03902874047106775"
exchange
glucose"0.0"
acetate"0.0"
biomass"0.0"
dFBA
inputs
substrates
[0]"local"
biomass
[0]"mass"
outputs
substrates
[0]"exchange"
biomass
[0]"mass"
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
shared
twCyLAJn
id"twCyLAJn"
position
[0]"2.9745574979242253"
[1]"6.7548455223582495"
mass"0.6497403649720788"
local
glucose"2.1545271376875372"
acetate"0.0"
biomass"0.013176648004487946"
exchange
glucose"0.0"
acetate"0.0"
biomass"0.0"
dFBA
inputs
substrates
[0]"local"
biomass
[0]"mass"
outputs
substrates
[0]"exchange"
biomass
[0]"mass"
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
shared
LjteiWFk
id"LjteiWFk"
position
[0]"3.468968896528624"
[1]"8.662031053818865"
mass"0.3205839647077567"
local
glucose"3.639896485717788"
acetate"0.0"
biomass"0.023221213761929718"
exchange
glucose"0.0"
acetate"0.0"
biomass"0.0"
dFBA
inputs
substrates
[0]"local"
biomass
[0]"mass"
outputs
substrates
[0]"exchange"
biomass
[0]"mass"
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
shared
ZIpEUzYZ
id"ZIpEUzYZ"
position
[0]"4.808922617451535"
[1]"6.103592314517574"
mass"0.8673340168760424"
local
glucose"1.0929945699596662"
acetate"0.0"
biomass"0.05315014676848965"
exchange
glucose"0.0"
acetate"0.0"
biomass"0.0"
dFBA
inputs
substrates
[0]"local"
biomass
[0]"mass"
outputs
substrates
[0]"exchange"
biomass
[0]"mass"
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
shared
DJcw8oVq
id"DJcw8oVq"
position
[0]"2.6187860271893237"
[1]"9.046091011156038"
mass"0.310080020423422"
local
glucose"1.7022714524039722"
acetate"0.0"
biomass"0.07983080652633757"
exchange
glucose"0.0"
acetate"0.0"
biomass"0.0"
dFBA
inputs
substrates
[0]"local"
biomass
[0]"mass"
outputs
substrates
[0]"exchange"
biomass
[0]"mass"
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
shared
czfznYfa
id"czfznYfa"
position
[0]"3.445898078316941"
[1]"1.8697193209133045"
mass"0.8189696560164677"
local
glucose"3.1837107875496646"
acetate"0.0"
biomass"0.09844798981828339"
exchange
glucose"0.0"
acetate"0.0"
biomass"0.0"
dFBA
inputs
substrates
[0]"local"
biomass
[0]"mass"
outputs
substrates
[0]"exchange"
biomass
[0]"mass"
interval1.0
address"local:DynamicFBA"
config
model_file"textbook"
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
shared
diffusion
inputs
fields
[0]"fields"
outputs
fields
[0]"fields"
interval1.0
address"local:DiffusionAdvection"
config
n_bins
[0]"10"
[1]"20"
bounds
[0]"5.0"
[1]"10.0"
default_diffusion_rate"0.1"
default_diffusion_dt"0.1"
diffusion_coeffs
glucose"0.1"
acetate"0.1"
biomass"0.1"
advection_coeffs
glucose
[0]"0.0"
[1]"0.0"
acetate
[0]"0.0"
[1]"0.0"
biomass
[0]"0.0"
[1]"0.1"
sharednull
spatial_dfba
inputs
fields
glucose
[0]"fields"
[1]"glucose"
acetate
[0]"fields"
[1]"acetate"
biomass
[0]"fields"
[1]"biomass"
outputs
fields
glucose
[0]"fields"
[1]"glucose"
acetate
[0]"fields"
[1]"acetate"
biomass
[0]"fields"
[1]"biomass"
interval1.0
address"local:SpatialDFBA"
config
n_bins
[0]"10"
[1]"20"
model_file"textbook"
models
model_grid
kinetic_params
glucose
[0]"0.5"
[1]"1.0"
acetate
[0]"0.5"
[1]"2.0"
substrate_update_reactions
glucose"EX_glc__D_e"
acetate"EX_ac_e"
bounds
EX_o2_e
lower"-2.0"
upper"!nil"
ATPM
lower"1.0"
upper"1.0"
sharednull
particle_movement
inputs
particles
[0]"particles"
fields
[0]"fields"
outputs
particles
[0]"particles"
fields
[0]"fields"
interval1.0
address"local:Particles"
config
bounds
[0]"5.0"
[1]"10.0"
n_bins
[0]"10"
[1]"20"
diffusion_rate"0.1"
advection_rate
[0]"0.0"
[1]"-0.1"
add_probability"0.2"
boundary_to_add
[0]"top"
boundary_to_remove
[0]"top"
[1]"bottom"
[2]"left"
[3]"right"
division_mass_threshold"5.0"
division_jitter"0.001"
sharednull
fields
glucose
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[16]0.03280786990386685
[17]0.04618379654474221
[18]0.05492956835898997
[19]0.06369456892989914
[4]
[0]0.06790692446212884
[1]0.050548965579443196
[2]0.054986499178995785
[3]0.012870149532029841
[4]0.02243292603830005
[5]0.0499565460268836
[6]0.09115393149306754
[7]0.0473565588465171
[8]0.07464174429506705
[9]0.0579889457642338
[10]0.027639834426020183
[11]0.01378711830491891
[12]0.07820325994388622
[13]0.04101621381922188
[14]0.07773918342478384
[15]0.03469959784459864
[16]0.0724556780306208
[17]0.0027395785044856628
[18]0.05023273869659228
[19]0.007039620510713296
[5]
[0]0.04793408691929185
[1]0.041967389472772246
[2]0.07549916112757116
[3]0.03217212884879761
[4]0.01314764946444188
[5]0.04008923081770802
[6]0.021012401217393197
[7]0.07484770436598291
[8]0.028034185433764437
[9]0.072368472529915
[10]0.030994619608371424
[11]0.07492284042920187
[12]0.007601266362206727
[13]0.013176648004487946
[14]0.021457534483555474
[15]0.07446758575232647
[16]0.08244604190328375
[17]0.015100254423352433
[18]0.07983080652633757
[19]0.02508045473663946
[6]
[0]0.06666614148579429
[1]0.051015603778591004
[2]0.020541518168837303
[3]0.09844798981828339
[4]0.040687887294181636
[5]0.037078114964843555
[6]0.05031061832576553
[7]0.06155236681922638
[8]0.007678728839129557
[9]0.07717980791009904
[10]0.01011076015070913
[11]0.060859879460946
[12]0.023102028507483052
[13]0.02958614762641807
[14]0.006836718495639083
[15]0.03883826736870404
[16]0.04541651086248305
[17]0.023221213761929718
[18]0.03146674612334893
[19]0.017406194162914567
[7]
[0]0.04033247534421017
[1]0.07414056781810692
[2]0.05462670466024558
[3]0.03568908349541881
[4]0.07544428191830505
[5]0.06379137664077761
[6]0.04022384606156997
[7]0.014764720240355123
[8]0.0739422061398907
[9]0.028752187327230283
[10]0.02351675138430386
[11]0.05860083339952954
[12]0.003077188983132262
[13]0.03645979068683743
[14]0.07825211606593015
[15]0.01925442090843851
[16]0.09913509100593575
[17]0.03418809188278639
[18]0.08881122786785121
[19]0.007032001200344973
[8]
[0]0.08051695163154733
[1]0.08767957688668843
[2]0.03126053929577586
[3]0.03894696987344096
[4]0.009967619383765303
[5]0.002221269622352584
[6]0.08044618773998503
[7]0.029091883577210754
[8]0.01865386131374566
[9]0.0205418290002797
[10]0.08081277187653457
[11]0.06653604813407951
[12]0.0012214173347145252
[13]0.05986469404320425
[14]0.05327406912467299
[15]0.09263569285541969
[16]0.04108543388511048
[17]0.05558692284510593
[18]0.08227776508717072
[19]0.015384056651760493
[9]
[0]0.08186220317087234
[1]0.0994229984445876
[2]0.028632464415451187
[3]0.049345475495220587
[4]0.08565466248463122
[5]0.031587575979573825
[6]0.09442757755547786
[7]0.052628011632335006
[8]0.006751881851317843
[9]0.002652190267816601
[10]0.034338131681372244
[11]0.058032112724165565
[12]0.05315014676848965
[13]0.025164966827576643
[14]0.06869051388924353
[15]0.002794851178589386
[16]0.05837953458395387
[17]0.058124916389147775
[18]0.068733064542279
[19]0.06522380111333928
data"float"
shape
[0]10
[1]20

particle_dfba_comets_viz.png

particle_dfba_comets_mass.png

particle_dfba_comets_timeseries.png

particle_dfba_comets_with_fields.gif

Total Simulation Time

106.12 seconds