tGD Drive-out

Expanding upon the ideas presented on: "A transcomplementing gene drive provides a flexible platform for laboratory investigation and potential field deployment"

Experiment Nomenclature

Folders and files follow this naming convention:

• E_fcs_fcb_fga_fgb_cut_hdr_ren_res
  • fcs: Fitness cost on the Cas9 allele (1e4)
  • fcb: Fitness cost on broken alleles at the Cas9 locus (1e4)
  • fga: Fitness cost on gRNA allele (1e4)
  • fgb: Fitness cost on broken alleles at the gRNA locus (1e4)
  • cut: Cutting rate (1e2)
  • hdr: Homing rate (1e2)
  • ren: Number of releases (1e0)
  • res: Size of releases (1e2)

For the breakdown of the AOI sets, look at the gene definitions:

• Linked Drive
• Split Drive
• tGD

Exported metrics (MOI) for the drive are:

• WOP: Total sum of time below the threshold
• TTI: First break below the threshold
• TTO: Last break below the threshold
• RAP: Fraction of the population with the genes at given points of time
• MNX: Minimum and maximum of genes in the population

Summary statistic files follow this naming convention:

• AOI_MOI_QNT_qnt.csv

Where the main AOI was HLT (presence of mosquitoes) and the outputs (labels) are:

• TTI, TTO, WOP: Fraction's threshold for the metric to be true
• RAP: Fraction of present genotypes at given points (days) of the simulation
• MNX: Min/Max and days at which these are achieved

Current Pipelines

The following lines should run the whole set of analysis for the current workflow:

./tGD_preCrunch.sh srv; \
./tGD_pstCrunch.sh srv 50 0.1; \
./tGD_clsCrunch.sh srv 50 0.1; \
./tGD_dtaTraces.sh srv 50 0.1 HLT HLT

./tGD_clsCrunch.sh srv2 50 0.1; ./tGD_clsCrunch.sh srv2 50 0.9; \
./tGD_clsCrunch.sh srv2 50 0.2; ./tGD_clsCrunch.sh srv2 50 0.8; \
./tGD_clsCrunch.sh srv2 50 0.25; ./tGD_clsCrunch.sh srv2 50 0.75; \
./tGD_clsCrunch.sh srv2 50 0.5;