13c-metabolic-flux

1# Carbon-13 metabolic flux inference
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3Turn reviewed carbon maps, explicit tracer mixtures, and corrected labeling measurements
4into feasible flux estimates and evidence about which fluxes the experiment constrains.
5Use the bundled solver rather than reconstructing isotope balances or fitting each
6reaction independently. It runs mfapy's EMU forward simulator and fits fluxes in the
7mass-balanced feasible space with SciPy. It does not use an FBA objective.
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9## Scope and required evidence
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11This implementation supports **metabolic and isotopic steady state**, a single shared
12flux state across one or more tracer experiments, nonnegative one-way reaction fluxes,
13and carbon-subset mass distributions. Reversible reactions are two separately mapped
14directions. Measurement error is Gaussian with a supplied covariance or a disclosed
15diagonal approximation.
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17Before fitting, obtain:
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19- The carbon network and the source of each atom assignment. Stoichiometry alone does
20  not specify where labeled atoms go. Record compartments as separate metabolite IDs.
21- Evidence for both steady-state assumptions. Stable metabolite abundance does not
22  establish isotopic steady state. Time-course labeling requires INST-MFA with pool
23  sizes and initial labeling; do not average it into this solver.
24- Every carbon input's positional isotopomer distribution, including unlabeled
25  supplements, bicarbonate/CO2 when assimilated, and tracer impurity.
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