Drug Synergies Screening Workflow

Table of Contents

• Drug Synergies Screening Workflow
  • Table of Contents
  • Description
  • Contents
    • Building Blocks
    • Workflows
    • Resources
    • Tests
  • Instructions
    • Local machine
      • Requirements
      • Usage steps
    • MareNostrum 4
      • Requirements in MN4
      • Usage steps in MN4
  • License
  • Contact

Description

This pipeline simulates a drug screening on personalised cell line models. It automatically builds Boolean models of interest, then uses cell lines data (expression, mutations, copy number variations) to personalise them as MaBoSS models. Finally, this pipeline simulates multiple drug intervention on these MaBoSS models, and lists drug synergies of interest.

The workflow uses the following building blocks, described in order of execution:

1. Build model from species
2. Personalise patient
3. MaBoSS
4. Print drug results

For details on individual workflow steps, see the user documentation for each building block.

GitHub repository

Contents

Building Blocks

The BuildingBlocks folder contains the script to install the Building Blocks used in the Drug Synergies Workflow.

Workflows

The Workflow folder contains the workflows implementations.

Currently contains the implementation using PyCOMPSs.

Resources

The Resources folder contains a small dataset for testing purposes.

Tests

The Tests folder contains the scripts that run each Building Block used in the workflow for a small dataset. They can be executed individually without PyCOMPSs installed for testing purposes.

Instructions

Local machine

This section explains the requirements and usage for the Drug Synergies Workflow in a laptop or desktop computer.

Requirements

• permedcoe package
• PyCOMPSs
• Singularity

Usage steps

1. Clone this repository:

git clone https://github.com/PerMedCoE/drug-synergies-workflow.git

2. Install the Building Blocks required for the COVID19 Workflow:

drug-synergies-workflow/BuildingBlocks/./install_BBs.sh

3. Get the required Building Block images from the project B2DROP:

• Required images:
  • PhysiCell-COVID19.singularity
  • printResults.singularity
  • MaBoSS_sensitivity.singularity
  • FromSpeciesToMaBoSSModel.singularity

The path where these files are stored MUST be exported in the PERMEDCOE_IMAGES environment variable.

⚠️ TIP: These containers can be built manually as follows (be patient since some of them may take some time):

1. Clone the BuildingBlocks repository

   git clone https://github.com/PerMedCoE/BuildingBlocks.git
   

2. Build the required Building Block images

   cd BuildingBlocks/Resources/images
   sudo singularity build PhysiCell-COVID19.sif PhysiCell-COVID19.singularity
   sudo singularity build printResults.sif printResults.singularity
   sudo singularity build MaBoSS_sensitivity.sif MaBoSS_sensitivity.singularity
   sudo singularity build FromSpeciesToMaBoSSModel.sif FromSpeciesToMaBoSSModel.singularity
   cd ../../..
   

If using PyCOMPSs in local PC (make sure that PyCOMPSs in installed):

4. Go to Workflow/PyCOMPSs folder

   cd Workflows/PyCOMPSs
   

5. Execute ./run.sh

TIP: If you want to run the workflow with a different dataset, please update the run.sh script setting the dataset variable to the new dataset folder and their file names.

MareNostrum 4

This section explains the requirements and usage for the Drug Synergies Workflow in the MareNostrum 4 supercomputer.

Requirements in MN4

• Access to MN4

All Building Blocks are already installed in MN4, and the Drug Synergies Workflow available.

Usage steps in MN4

1. Load the COMPSs, Singularity and permedcoe modules

   export COMPSS_PYTHON_VERSION=3
   module load COMPSs/3.1
   module load singularity/3.5.2
   module use /apps/modules/modulefiles/tools/COMPSs/libraries
   module load permedcoe
   

   TIP: Include the loading into your ${HOME}/.bashrc file to load it automatically on the session start.

   This commands will load COMPSs and the permedcoe package which provides all necessary dependencies, as well as the path to the singularity container images (PERMEDCOE_IMAGES environment variable) and testing dataset (DRUG_SYNERGIES_WORKFLOW_DATASET environment variable).

2. Get a copy of the pilot workflow into your desired folder

   mkdir desired_folder
   cd desired_folder
   get_drug_synergies_workflow
   

3. Go to Workflow/PyCOMPSs folder

   cd Workflow/PyCOMPSs
   

4. Execute ./launch.sh

This command will launch a job into the job queuing system (SLURM) requesting 2 nodes (one node acting half master and half worker, and other full worker node) for 20 minutes, and is prepared to use the singularity images that are already deployed in MN4 (located into the PERMEDCOE_IMAGES environment variable). It uses the dataset located into ../../Resources/data folder.

⚠️ TIP: If you want to run the workflow with a different dataset, please edit the launch.sh script and define the appropriate dataset path.

After the execution, a results folder will be available with with Drug Synergies Workflow results.

License

Apache 2.0

Contact

This software has been developed for the PerMedCoE project, funded by the European Commission (EU H2020 951773).