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Becksteinlab / kda

Python package used for the analysis of biochemical kinetic diagrams.
GNU General Public License v3.0
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TST: Add test for transition/cycle/operational flux relations #67

Open nawtrey opened 1 year ago

nawtrey commented 1 year ago

In T.L. Hill's book, "Free Energy Transduction and Biochemical Cycle Kinetics", he discusses simple relationships between transition fluxes, net cycle fluxes, and operational fluxes. Specifically, equations 3.3 and 3.4 show flux identities for a simple model. A test should be added that verifies these identities to further ensure consistency between various flux calculation types.

Test should be written to compare the output expressions, which can be compared with the normalization factor Sigma.

nawtrey commented 1 year ago

Additionally equations 3.5 and 3.6 show several relationships that should all hold if everything is internally consistent.

nawtrey commented 5 months ago

See the kda-examples PR #18 for example code comparing operational fluxes generated using both net cycle fluxes and net transition fluxes.

nawtrey commented 2 weeks ago

With GH-83 merged this is already more tractable, but I think we will wait until the net cycle fluxes are added (issue #57) to complete this.