Welcome to PerMedCoE documentation!

This is the HPC/Exascale Centre of Excellence for Personalised Medicine in Europe (PerMedCoE) artifacts documentation.

The target audiences for this documentation are:

• Developers (Python) aiming at contributing to the Personalized Medicine project environment with Building Blocks or Workflows.

• Researchers aiming at conducting investigations using the available Building Blocks and Workflows.

This documentation is aimed at showing:

• How to use the permedcoe package:

  • Python API

  • Command Line Interface

• How to develop new Building Blocks

• How to execute Building Blocks individually

• How to develop Workflows using Building Blocks

• How to execute Workflows using:

  • PyCOMPSs

  • Croupier

• A step-by-step guide from creating a building block to execute a workflow

• A step-by-step tutorial for deploying and executing the existing Building Blocks and Workflows

• A sample application

The current status of the project is WORK IN PROGRESS.

Contents:

• Base Package Installation
  • Introduction
  • Requirements
  • Installation from Pypi
  • Installation from source code
  • Uninstall from Pypi
  • Uninstall from source code
• Base Package Components
  • Python API
  • Command line
    • Execution
      • Building Block execution
      • Application execution
    • Template creation
    • Automatic Deployment
      • Building Block Deployment
      • Workflow Deployment
• Existing Building Blocks and Workflows
  • 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
      • Requirements
      • Deployment
      • Usage
    • Supercomputer
      • SCs
• Creating Building Blocks
  • Building Block Templates
    • Building Block template creation
    • Package structure
    • Building Block structure
    • Deployment
      • Installation
      • Usage
      • Uninstall
    • Best practices
  • Application Templates
    • Application template creation
    • Folder structure
    • Execution
    • Best practices
  • Application Execution with Croupier
    • Introduction
    • Prerequisites
    • Croupier’s framework
      • Croupier plugin installation
    • Application definition (Blueprint)
    • Application installation (Rol: application provider)
    • Application instance deployment (Rol: application consumer)
    • Application instance execution
  • Tutorial
    • Requirements
    • Step-by-step
• Acknowledgements
  • Partners
  • Funding