Kinase similarity demo mode

[dominiquesydow]

Description

Make it easier to run the kinase similarity edition notebooks with a new set of kinases.

Todos

• Add kissim to environment
• Add demo mode:
  • Add a config file pipeline_config.csv next to kinase_selection.csv file with the following configurations
    • DEMO: True or False --- to run the notebooks exactly as displayed online; used in our CI)
    • N_STRUCTURES_PER_KINASE (has effect if DEMO == True) --- default is 3 (run KiSSim on 3 structures per kinase); if None use full dataset (this may take some time!)
    • N_CORES (has effect if DEMO == True) --- run KiSSim on user-specified number of cores (default is 1)
  • T25/KiSSim and T26/IFP: Add DEMO = True at the beginning of the notebooks; if False do not freeze the set of KLIFS structures
  • T25/KiSSim: Use N_STRUCTURES_PER_KINASE and N_CORES; add runtime warning for KiSSim
• Generalize examples in T24/Seq and T27/Ligands so that notebook runs on kinases other than EGFR and MET (generalize variables and text also where needed)
• Run notebooks on new dataset (problem 1 in this paper): RET, BRAF, SRC, S6K, MKNK1, TTK, ERK8, PDK, PAK3
  • Get KLIFS names for these kinases
  • Add this dataset to T23's quiz ("Rerun the notebooks on another kinase set, e.g. kinases XYZ)")
  • Pipeline runs? Yes :)

Questions

• T27/Ligands: Make ChEMBL version more prominent? Added to "Aim of this talktorial section"

Status

• Ready to go

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[dominiquesydow]

Failing CIs

• Ubuntu 3.7 - only timeouts in T17 and T18
• MacOS 3.7 - ERROR at setup of T20

Merging this to livecoms-review now since T23-28 are passing just fine.