CarbonARA

Pick a StructRecon JSON file, define sources and targets, run the solver, watch the log stream, and inspect the reactions as plain text with common cofactors hidden by default.

Query

Model Sources

Targets

Status idle

No run yet.

Solution Summary

Run the solver to populate the summary table.

Reaction Text

Currently Hidden

Thermodynamic annotations will appear here after a result is loaded.

The formatted flow text will appear here after the solver finishes.

Storybook

Run or load a result to start the storybook.

Setup

These options are usually left alone once you have a good default workflow.

Solver Backend Choose between the original `mod` backend and the new mod-independent `gurobi` backend. Workspace StructRecon JSON Only usable StructRecon response JSONs are listed here. Mismatch reports and other auxiliary JSON files are hidden. Or Upload StructRecon JSON Upload a JSON file from elsewhere. This also does not trigger StructRecon. Number of Alternatives This means how many alternative flow files to enumerate. Objective Expression Available terms: `carbon_inflow`, `noncarbon_inflow`, `edge_use`, `vertex_use`, `edge_flow`. Supported operators: `+`, `-`, `*`, parentheses.

Thermodynamics

pH Ionic Strength (M) pMg Max Uphill Δ_rG'° (kJ/mol)

Reaction annotations use offline `equilibrator-api` with a persistent local cache. The first real calculation may trigger a one-time cache download and take noticeably longer.

Hidden Compounds These compounds are removed from the textual reaction view. Show mouse hover popup Show molecular structure in hover popup

Models are discovered from the solver repo on disk. When possible, CarbonARA auto-selects the matching `<model>/structrecon_response_complete.json` so structure previews have data to render.

Structure previews require a matching StructRecon JSON for the selected model. If none is available on disk, the hover popup will still show names and identifiers.

Cached Sessions

Same model + same JSON + same query + same objective + same thermodynamic conditions + same number of solutions means the result is reused from here.

Session Key	Created	Model	Backend	Sources	Targets	Objective	Solutions	Flows
`2630e2c8cdec53c6`	1777388070.073836	iCGB21FR_nonbigg	gurobi	glc__D_c=1-3	gal_c=1-3	`carbon_inflow * 1000000 + edge_use * 1000 + noncarbon_inflow`	1	0
`765a1ebec5874e43`	1777387255.233103	iCGB21FR_nonbigg	gurobi	glc__D_c=1	gal_c=1	`carbon_inflow * 1000000 + edge_use * 1000 + noncarbon_inflow`	1	1
`255d74d91b6d0b49`	1777384555.347265	iCGB21FR_nonbigg	gurobi	glc__D_e=1	gal_c=1	`carbon_inflow * 1000000 + edge_use * 1000 + noncarbon_inflow`	1	1
`9cc440d89d27ccb2`	1777384331.8451588	iCGB21FR_nonbigg	gurobi	glc__D_e=1	gal_c=1	`carbon_inflow * 1000000 + edge_use * 1000 + noncarbon_inflow`	1	1
`836592972c1f4814`	1777383165.333753	iAF692	gurobi	glc__D_c=1	his__L_c=1	`carbon_inflow * 1000000 + edge_use * 1000 + noncarbon_inflow`	1	1
`792146ead3bfaf9d`	1777382981.234327	iAF692	gurobi	glc__D_c=1	his__L_c=1	`carbon_inflow * 1000000 + edge_use * 1000 + noncarbon_inflow`	1	1
`15577cf671e32e4f`	1777378896.431913	iCGB21FR_nonbigg	gurobi	glc__D_e=1-2	gal_c=1-2	`carbon_inflow * 1000000 + edge_use * 1000 + noncarbon_inflow`	1	0
`3da41214c5888993`	1777377928.1503701	iCGB21FR_nonbigg	gurobi	glc__D_e=1-3	gal_c=1-3	`carbon_inflow * 1000000 + edge_use * 1000 + noncarbon_inflow`	1	0
`70949e3475cb97b2`	1777377785.767756	iCGB21FR_nonbigg	gurobi	glc__D_e=1-6	gal_c=1-6	`carbon_inflow * 1000000 + edge_use * 1000 + noncarbon_inflow`	1	0
`3aeac1738be7f881`	1777377464.935606	iCGB21FR_nonbigg	gurobi	glc__D_e=1	gal_c=1	`carbon_inflow * 1000000 + edge_use * 1000 + noncarbon_inflow`	1	1
`3a4645c6944277f7`	1777377025.130079	iAF1260	gurobi	glc__D_c=1-2	his__L_c=1-2	`carbon_inflow * 1000000 + edge_use * 1000 + noncarbon_inflow`	3	0
`5713903056507d3c`	1777375863.755223	iCGB21FR_balanced	gurobi	gal1p_c=1	gal_c=1	`carbon_inflow + 0.001*edge_use`	1	1
`ae098714efa6c59c`	1777293946.107799	e_coli_core	gurobi	oaa_c=1-6	cit_c=1-4	`carbon_inflow * 1000000 + edge_use * 1000 + noncarbon_inflow`	3	0
`0160e24b66d72870`	1777293895.953086	e_coli_core	gurobi	oaa_c=1-6	cit_c=1-4	`carbon_inflow + 0.001*edge_use`	1	0
`2db6bc247ec66682`	1777200794.4234931	iAF692	gurobi	glc__D_c=1-6	his__L_c=1-6	`carbon_inflow * 1000000 + edge_use * 1000 + noncarbon_inflow`	3	0
`4b62d22a9c33aad4`	1777200551.879452	iAF692	gurobi	glc__D_c=1-3	his__L_c=1-4	`carbon_inflow * 1000000 + edge_use * 1000 + noncarbon_inflow`	3	0
`ab97a8f682b4cd5a`	1777200444.309314	iAF692	gurobi	glc__D_c=1-4	his__L_c=1-4	`carbon_inflow + 0.001*edge_use`	3	0
`42cc61f244b3252e`	1777200327.8169558	iAF692	gurobi	glc__D_c=1-3	his__L_c=1	`carbon_inflow * 1000000 + edge_use * 1000 + noncarbon_inflow`	3	0
`24b5f84dbd5eb284`	1777200120.275754	iAF692	gurobi	glc__D_c=1-3	his__L_c=1-3	`carbon_inflow * 1000000 + edge_use * 1000 + noncarbon_inflow`	3	0
`421c30baf9e9916d`	1777199406.498776	iAF692	gurobi	glc__D_c=1	his__L_c=1	`carbon_inflow + 0.001*edge_use`	1	1
`55f62cbb7f4e757f`	1777198893.949593	iAF692	gurobi	glc__D_c=1-2	his__L_c=1-2	`carbon_inflow * 1000000 + edge_use * 1000 + noncarbon_inflow`	3	0
`309141829de95420`	1777198545.647341	iAF692	gurobi	glc__D_c=1-4	his__L_c=1-4	`carbon_inflow * 1000000 + edge_use * 1000 + noncarbon_inflow`	3	0
`15303616c234fe21`	1777198381.529532	iAF692	gurobi	glc__D_c=1-3	his__L_c=1-3	`carbon_inflow + 0.001*edge_use`	3	0
`de739af149536487`	1776350358.736247	iAF692	gurobi	glc__D_c=1	his__L_c=1	`carbon_inflow * 1000000 + edge_use * 1000 + noncarbon_inflow`	3	3
`ac58aaf57d2157cf`	1776349675.301842	iJN746	gurobi	ccmuac_c=2	fum_c=2	`carbon_inflow * 1000000 + edge_use * 1000 + noncarbon_inflow`	3	3
`3932addfa65f1e2a`	1776349479.4511192	iJN746	gurobi	ccmuac_c=1	fum_c=3	`carbon_inflow * 1000000 + edge_use * 1000 + noncarbon_inflow`	1	1