Retrospective Experiments

Below are commands to reproduce our retrospective experiments.

The input .screen.h5 files are available for download here:

Warning: These retrospective simulation experiments require a lot of computation time. We recommend these be run on a high performance computing cluster or cloud computing service. Use the appropriate -profile to specify the computing environment.

Merck

..code-block:: bash

python3 nextflow/scripts/batchie.py –mode retrospective

-c nextflow/config/merck_retrospective_simulation.config –batch-size 9 –screen merck_2016.screen.h5 –outdir merck_sim –max_memory 64G –max_cpus 1 –max_time 24h

NCI Almanac

..code-block:: bash

python3 nextflow/scripts/batchie.py –mode retrospective

-c nextflow/config/nci_almanac_retrospective_simulation.config –batch-size 18 –screen nci_almanac.screen.h5 –outdir merck_sim –max_memory 64G –max_cpus 1 –max_time 24h

GDSC^2

..code-block:: bash

python3 nextflow/scripts/batchie.py –mode retrospective

-c nextflow/config/gdsc_sq_retrospective_simulation.config –batch-size 36 –screen gdsc_sq.screen.h5 –outdir merck_sim –max_memory 64G –max_cpus 1 –max_time 24h