Existing Building Blocks and Workflows

This section provides a list of available PerMedCoE building blocks (BB), existing workflows and links to further user documentation.

Building blocks are executed using the permedcoe base package. In PerMedCoE, a BB is considered a unit of work, like a black box that performs a particular computation. Consequently, it has inputs and outputs, and can be instantiated into applications and piped as required. Combinations of several building blocks can be used to execute different workflows.

The permedcoe package enables BB execution using a variety of workflow managers, such as PyCOMPSs, Snakemake or Nextflow.

Contents:

• Available Building Blocks
  • High-throughput Mutant Analysis
  • Meta-analysis of PhysiBoSS Output
  • Personalise Patient
  • PhysiBoSS
  • Single-cell Processing
  • Build Model from Genes
  • Print Drug Results
  • CARNIVAL
  • CARNIVALPy
  • CARNIVAL Feature Merger
  • CARNIVAL Gex Preprocess
  • Export Solver HDF5
  • JAX drug prediction
  • OmniPath
  • PROGENy
  • TF Enrichment
  • CellNOpt
  • Invasion Analysis
  • PhysiBoSS Invasion
  • COBREXA FVA
  • CLL Prepare Data
  • CLL Tf Activities
  • CLL Network Inference
  • CLL Personalize Boolean Models
  • CLL Run Boolean Model
  • CLL Combine Models
• Existing Workflows
  • Basic examples
  • COVID-19 Multiscale Modelling of the Virus and Patients’ Tissue
  • Drug Synergies Screening
  • Single drug prediction
  • Cancer invasion
  • Cancer diagnosis
• Tutorial
  • Local
  • Supercomputer