implement expression-limited fluxes (E-Flux like algorihm) #777
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PS let this be the final feature of the 1.x branch. I'll release 1.5, the rest of the 1.5 milestone will be applied as bugfixes to 1.5.x or better to 2.x directly. |
Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## master #777 +/- ##
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+ Coverage 91.34% 91.39% +0.05%
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Files 82 86 +4
Lines 2196 2209 +13
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+ Hits 2006 2019 +13
Misses 190 190
☔ View full report in Codecov by Sentry. |
stelmo
approved these changes
May 3, 2023
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| E-Flux algorithm is closer described by: *Colijn, Caroline, Aaron Brandes, | ||
| Jeremy Zucker, Desmond S. Lun, Brian Weiner, Maha R. Farhat, Tan-Yun Cheng, D. | ||
| Branch Moody, Megan Murray, and James E. Galagan. "Interpreting expression data | ||
| with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid | ||
| production." PLoS computational biology 5, no. 8 (2009): e1000489*. |
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People love making questionable cobra methods :/
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| Create E-Flux-like bounds for a reaction that requires gene products given by | ||
| `grr`, with expression "choke" data given by relative probabilities (between 0 | ||
| and 1) in `relative_expression`. |
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| isnothing(grr) && return 1.0 | ||
| lup(g) = get(relative_expression, g, 1.0) | ||
| 1 - prod(1 - prod(lup.(gr)) for gr in grr) |
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Ah, I thought this would have some stochasticity here
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Closes #552
I'll make a separate port to the 2.0 branch later.