Drug Synergies Screening Workflow
Table of Contents
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:
- Build model from species
- Personalise patient
- MaBoSS
- Print drug results
For details on individual workflow steps, see the user documentation for each building block.
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
- Clone this repository:
git clone https://github.com/PerMedCoE/drug-synergies-workflow.git
- Install the Building Blocks required for the COVID19 Workflow:
drug-synergies-workflow/BuildingBlocks/./install_BBs.sh
- 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.
:warning: TIP: These containers can be built manually as follows (be patient since some of them may take some time):
- Clone the
BuildingBlocks
repositorygit clone https://github.com/PerMedCoE/BuildingBlocks.git
- 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):
-
Go to
Workflow/PyCOMPSs
foldercd Workflows/PyCOMPSs
-
Execute
./run.sh
TIP: If you want to run the workflow with a different dataset, please update the
run.sh
script setting thedataset
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
-
Load the
COMPSs
,Singularity
andpermedcoe
modulesexport 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). -
Get a copy of the pilot workflow into your desired folder
mkdir desired_folder cd desired_folder get_drug_synergies_workflow
-
Go to
Workflow/PyCOMPSs
foldercd Workflow/PyCOMPSs
-
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.
:warning: 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
Contact
This software has been developed for the PerMedCoE project, funded by the European Commission (EU H2020 951773).
Version History
main @ 77403c9 (earliest) Created 23rd May 2023 at 13:36 by Miguel Vazquez
Merge pull request #4 from PerMedCoE/avoid-pycompss-disable
Removed pycompss disable from tests.
Frozen
main
77403c9
Creator
Submitter
Views: 1955 Downloads: 190
Created: 23rd May 2023 at 13:36
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