comets toolbox  (MathWorks Inc)

Journal: Nature protocols

Article Title: A metabolic modeling platform for the Computation Of Microbial Ecosystems in Time and Space (COMETS)

doi: 10.1038/s41596-021-00593-3

Figure Lengend Snippet: Troubleshooting

Article Snippet: 4 4 4 4 Use the COMETS MATLAB toolbox commands as follows to create an empty COMETS layout and add the model to it: >> world = CometsLayout(); >> world = world.addModel(ecoli); This creates a default COMETS simulation spatial layout structure with one model in it: . models: {[1×1 struct]} xdim: 1 ydim: 1 mets: {20×1 cell} media_amt: [20×1 double] params: [1×1 CometsParams] diffusion_constants: [20×2 double] global_media_refresh: [20×1 double] media_refresh: [20×1 double] global_static_media: [20×2 double] static_media: [20×1 double] initial_media: 0 barrier: 0 initial_pop: 1.0000e-06 external_rxns: [0×0 table] external_rxn_mets: [0×0 table] .

Techniques: Combined Bisulfite Restriction Analysis Assay, Clone Assay, Software, Blocking Assay, Diffusion-based Assay

Journal: Nature protocols

Article Title: A metabolic modeling platform for the Computation Of Microbial Ecosystems in Time and Space (COMETS)

doi: 10.1038/s41596-021-00593-3

Figure Lengend Snippet: List of key COMETS capabilities and application examples.

Article Snippet: Here we simulate one such experiment with a genome-scale model of Prochlorococcus 84 , the most abundant marine photoautotroph. . Procedure 4: simulations including extracellular reactions This protocol demonstrates the capacity of COMETS to simulate reactions involving extracellular metabolites using the MATLAB toolbox.

Techniques: Diffusion-based Assay, Activation Assay, Concentration Assay, Activity Assay

Journal: Nature protocols

Article Title: A metabolic modeling platform for the Computation Of Microbial Ecosystems in Time and Space (COMETS)

doi: 10.1038/s41596-021-00593-3

Figure Lengend Snippet: Troubleshooting

Article Snippet: Here we simulate one such experiment with a genome-scale model of Prochlorococcus 84 , the most abundant marine photoautotroph. . Procedure 4: simulations including extracellular reactions This protocol demonstrates the capacity of COMETS to simulate reactions involving extracellular metabolites using the MATLAB toolbox.

Techniques: Combined Bisulfite Restriction Analysis Assay, Clone Assay, Software, Blocking Assay, Diffusion-based Assay

Journal: Nature protocols

Article Title: A metabolic modeling platform for the Computation Of Microbial Ecosystems in Time and Space (COMETS)

doi: 10.1038/s41596-021-00593-3

Figure Lengend Snippet: These figures show results obtained from the simulation described in Procedure 1. a) Plot of biomass vs. time. b) Plot of the key metabolites vs. time. The biomass growth stops when the glucose is completely depleted. The production of the typical products of fermentation also coincides with the growth of the biomass.

Article Snippet: Here we simulate one such experiment with a genome-scale model of Prochlorococcus 84 , the most abundant marine photoautotroph. . Procedure 4: simulations including extracellular reactions This protocol demonstrates the capacity of COMETS to simulate reactions involving extracellular metabolites using the MATLAB toolbox.

Techniques:

Journal: Nature protocols

Article Title: A metabolic modeling platform for the Computation Of Microbial Ecosystems in Time and Space (COMETS)

doi: 10.1038/s41596-021-00593-3

Figure Lengend Snippet: Results from a chemostat simulation (Procedure 2), prepared with the Python toolbox, in which one strain unable to break down lactose (LCTStex_KO) receives galactose from a different strain (galE_KO) that can break lactose into glucose and galactose, but is unable to metabolize galactose. The medium environment was composed of a constant supply of lactose (lcts_e), ammonia, and trace nutrients. Galactose (gal_e) was not supplied externally but started being available in the environment as galE_KO grew. a) Biomass of the two strains over time (cycle indicates the current time step). b) Amounts of the key metabolites over time (ac_e = acetate, for_e = formate, gal_e = galactose, glyclt_e = glycolate, lcts_e = lactose, meoh_e = methanol, pppn_e = phenylpropanoate). Note that it is typical for limiting nutrients (here, lactose and galactose) to have near-zero concentrations in a chemostat. c) Fluxes of relevant exchange reactions in galE_KO, and d) LCTStex_KO (the prefix “EX_” indicates an exchange reaction, and the metabolites being exchanged with the environment are: ac_e = acetate, for_e = formate, gal_e = galactose, lcts_e = lactose, nh4_e = ammonia). Negative flux represents uptake, while positive flux is excretion.

Article Snippet: Here we simulate one such experiment with a genome-scale model of Prochlorococcus 84 , the most abundant marine photoautotroph. . Procedure 4: simulations including extracellular reactions This protocol demonstrates the capacity of COMETS to simulate reactions involving extracellular metabolites using the MATLAB toolbox.

Techniques:

Journal: Nature protocols

Article Title: A metabolic modeling platform for the Computation Of Microbial Ecosystems in Time and Space (COMETS)

doi: 10.1038/s41596-021-00593-3

Figure Lengend Snippet: A two-species community colonizes a soil microhabitat (Procedure 6). a) Schematic detailing common features of a soil microhabitat, which are set in COMETS using simple commands to specify metabolite concentrations, and different ways of maintaining or supplementing those concentrations, in specific spatial locations. b) The initial state of the COMETS simulation, showing impenetrable barriers (gray) and the founder locations of the iJN1463 model (green) and the iYO844 model (blue). c) Time series showing biomass of the two models over time, integrated over the whole spatially structured environment. d) Snapshots of biomass and three key metabolites (f) succinate, f) O2, g) NH4) from 100 hours into the simulation. In the biomass snapshot, green is the iJN1463 model and blue is the iYO844 model. In e-g, the color scale denotes relative metabolite concentration, with bright yellow the maximum and dull purple the minimum. The scale bar shows 2mm.

Article Snippet: Here we simulate one such experiment with a genome-scale model of Prochlorococcus 84 , the most abundant marine photoautotroph. . Procedure 4: simulations including extracellular reactions This protocol demonstrates the capacity of COMETS to simulate reactions involving extracellular metabolites using the MATLAB toolbox.

Techniques: Concentration Assay

Journal: Nature protocols

Article Title: A metabolic modeling platform for the Computation Of Microbial Ecosystems in Time and Space (COMETS)

doi: 10.1038/s41596-021-00593-3

Figure Lengend Snippet: List of key COMETS capabilities and application examples.

Article Snippet: For this procedure, we use the iJO1366 model provided as part of COBRApy 83 . . Procedure 3: periodic environments and light absorption; modeling the diurnal cycle using the MATLAB toolbox COMETS can simulate periodically changing environments, where the periodic function can be either a step function, a sine function or a half sine function (shown below).

Techniques: Diffusion-based Assay, Activation Assay, Concentration Assay, Activity Assay

Journal: Nature protocols

Article Title: A metabolic modeling platform for the Computation Of Microbial Ecosystems in Time and Space (COMETS)

doi: 10.1038/s41596-021-00593-3

Figure Lengend Snippet: Troubleshooting

Article Snippet: For this procedure, we use the iJO1366 model provided as part of COBRApy 83 . . Procedure 3: periodic environments and light absorption; modeling the diurnal cycle using the MATLAB toolbox COMETS can simulate periodically changing environments, where the periodic function can be either a step function, a sine function or a half sine function (shown below).

Techniques: Combined Bisulfite Restriction Analysis Assay, Clone Assay, Software, Blocking Assay, Diffusion-based Assay