popsim-consortium / popsim-consortium/stdpopsim

modify SLiM engine to do bacterial species

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enhancement
Dominant language
Python
Stars
144
Forks
100
Avg merge
2h 44m
Merged PRs (30d)
2

Description

As discussed with @jeanrjc: how to do this is described in Cury et al:

  1. use a nonWF model
  2. have indviduals be haploid
  3. switch out the reproduction callback to do HGT

This might be pretty different to the existing SLiM engine because population regulation happens in a different way; for instance in the paper above it works as follows:

early()
{
 inds = p1.individuals;
 ages = inds.age;

 // kill off parental individuals; biologically they don’t even exist,
 // since they split by mitosis to generate their offspring
 inds[ages > 0].fitnessScaling = 0.0;

 // density-dependent population regulation on juveniles, toward Ne
 juvenileCount = sum(ages == 0);
 inds[ages == 0].fitnessScaling = Ne / juvenileCount;
}

However, probably a bunch of the same machinery from the existing implementation will be useful. I don't know if this should be a new engine, or just additional behavior of the same engine.

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reading the existing SLiM engine and the Cury et al. paper linked in the issue. Determine how nonWF models, haploid individuals, HGT reproduction, and juvenile population regulation should fit the current machinery, including whether this needs a new engine or additional behavior. Done means bacterial-species simulations support those behaviors.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
25/100

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