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Update 03_fba.md
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jcwang587 committed Dec 23, 2024
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Expand Up @@ -34,11 +34,9 @@ Within the cell, there are several reactions involving metabolites A, B, and C.

Conceptually, this is essentially a set of kinetic or, more specifically, mass balance equations. In an actual cell, there would be hundreds of such exchanges and reactions, and instead of just three metabolites, a large-scale metabolic model might include thousands. For example, in the iMM904 metabolic reconstruction, there are approximately 4,000 metabolites. This example provides only a simple illustration. A real model is typically much larger and more complex, but this basic scenario helps convey the general idea of how Flux Balance Analysis (FBA) works.


```{figure} _static/fig3-2.jpg
:height: 400px
:name: figure-fba
Methodology for flux balance analysis {cite:p}`kauffman2003fba`.
```

Expand All @@ -62,7 +60,7 @@ We can perform the same process for metabolites B and C as well. After writing t
- $x$ be the vector of metabolite concentrations,
- $v$ be the vector of reaction fluxes (or reaction rates).

Then the mass balances for all metabolites can be written in compact form as {eq}`label_1`, which was also depicted in {numref}`figure_fba` (b).
Then the mass balances for all metabolites can be written in compact form as {eq}`label_1`, which was also depicted in {numref}`figure_fba`(b).

```{math}
:label: label_2
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