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segrelab / comets

Computation of Microbial Ecosystems in Time and Space
MIT License
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Death in COMETS #23

Open sulheim opened 4 years ago

sulheim commented 4 years ago

Summarizing our recent discussion on incorporating death in a more sophisticated manner. There are several level of detail, as given below:

Description of tasks

Death rate related to mainteinance reaction

If an organism can't fulfill the requirement for non-growth assosciated mainteinance (NGAM) the FBA-solution will in a normal case be infeasible. However, in this case we can relive the NGAM lower bound and then maximize this reaction. The death rate will then be a linear function of the difference between the NGAM original lower bound and the NGAM maximal flux (which is by by definition smaller or equal to the original lower bound).

Toxins

Toxins can be included as an organism specific death rate function (a hill function) dependent on the medium concentration of the toxic compound. We currently don't aim on taking into account interactions between several toxins, so the total death rate will be a sum of the individual contributions.

Spill of biomass

After a bactera dies (lysis) macromolecular compounds are spilled into the environment. The user should provide a lysis-function which details the content of these macromolecules. The default lysis-function can be the biomass components.

To Do

jeremymchacon commented 4 years ago

toxins are now present and working. I like the other ideas, maybe they should each get their own "issue" / feature request?

sulheim commented 4 years ago

Cool, so the death rate is now dependent on the concentration of the toxins? This is a part of the signalling feature? I don't have a strong opinion about dividing this issue into subtopics, so feel free to do that if you want 👍 However, I think all death-related features should have a consistent implementation, so I guess that is an argument for keeping this issue as is

liaochen1988 commented 11 months ago

Happy new year! Glad to see this feature will be added. I am wondering, will the new feature enable modeling antibiotic effect on microbes? Similar to toxins, this effect requires linking death rate to antibiotic concentration in space.