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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`](https://github.com/PerMedCoE/drug-synergies-workflow>) ## 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`](https://github.com/PerMedCoE/permedcoe) package - [PyCOMPSs](https://pycompss.readthedocs.io/en/stable/Sections/00_Quickstart.html) - [Singularity](https://sylabs.io/guides/3.0/user-guide/installation.html) #### Usage steps 1. Clone this repository: ```bash git clone https://github.com/PerMedCoE/drug-synergies-workflow.git ``` 2. Install the Building Blocks required for the COVID19 Workflow: ```bash drug-synergies-workflow/BuildingBlocks/./install_BBs.sh ``` 3. Get the required Building Block images from the project [B2DROP](https://b2drop.bsc.es/index.php/f/444350): - 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): 1. Clone the `BuildingBlocks` repository ```bash git clone https://github.com/PerMedCoE/BuildingBlocks.git ``` 2. Build the required Building Block images ```bash 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 ```bash 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 ```bash 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 ```bash mkdir desired_folder cd desired_folder get_drug_synergies_workflow ``` 3. Go to `Workflow/PyCOMPSs` folder ```bash 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. > :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 [Apache 2.0](https://www.apache.org/licenses/LICENSE-2.0) ## Contact This software has been developed for the [PerMedCoE project](https://permedcoe.eu/), funded by the European Commission (EU H2020 [951773](https://cordis.europa.eu/project/id/951773)).  https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/ http://schema.org/description # Drug Synergies Screening Workflow ## Table of Contents - [Drug Synergies Screening Workflow](#drug-synergies-screening-workflow) - [Table of Contents](#table-of-contents) - [Description](#description) - [Contents](#contents) - [Building Blocks](#building-blocks) - [Workflows](#workflows) - [Resources](#resources) - [Tests](#tests) - [Instructions](#instructions) - [Local machine](#local-machine) - [Requirements](#requirements) - [Usage steps](#usage-steps) - [MareNostrum 4](#marenostrum-4) - [Requirements in MN4](#requirements-in-mn4) - [Usage steps in MN4](#usage-steps-in-mn4) - [License](#license) - [Contact](#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`](https://github.com/PerMedCoE/drug-synergies-workflow>) ## 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`](https://github.com/PerMedCoE/permedcoe) package - [PyCOMPSs](https://pycompss.readthedocs.io/en/stable/Sections/00_Quickstart.html) - [Singularity](https://sylabs.io/guides/3.0/user-guide/installation.html) #### Usage steps 1. Clone this repository: ```bash git clone https://github.com/PerMedCoE/drug-synergies-workflow.git ``` 2. Install the Building Blocks required for the COVID19 Workflow: ```bash drug-synergies-workflow/BuildingBlocks/./install_BBs.sh ``` 3. Get the required Building Block images from the project [B2DROP](https://b2drop.bsc.es/index.php/f/444350): - 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): 1. Clone the `BuildingBlocks` repository ```bash git clone https://github.com/PerMedCoE/BuildingBlocks.git ``` 2. Build the required Building Block images ```bash 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 ```bash 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 ```bash 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 ```bash mkdir desired_folder cd desired_folder get_drug_synergies_workflow ``` 3. Go to `Workflow/PyCOMPSs` folder ```bash 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. > :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 [Apache 2.0](https://www.apache.org/licenses/LICENSE-2.0) ## Contact This software has been developed for the [PerMedCoE project](https://permedcoe.eu/), funded by the European Commission (EU H2020 [951773](https://cordis.europa.eu/project/id/951773)).  https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/ http://schema.org/encodingFormat application/ld+json https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/ http://schema.org/hasPart https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/folders/78e37aaa-926d-4a03-b835-9761e5c250d5 https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/ http://schema.org/hasPart https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/folders/8a0897c2-8eff-4790-bac4-6b29479dc217 https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/ http://schema.org/hasPart https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/folders/939d8834-ab5e-4dae-858f-4dc29464dca6 https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/ http://schema.org/hasPart https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/folders/bd9c36a5-1910-4e9c-a74d-6a16c0a4bec3 https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/ http://schema.org/hasPart https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/resources/1ec1efa3-054b-4cc6-b06b-a2d0326d7dfb https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/ http://schema.org/hasPart https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/resources/dab03da9-6f4d-4a21-bbec-439a907d7b97 https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/ http://schema.org/hasPart https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/resources/fa4dfed0-adf2-4c22-8b0d-f95e0efbec0b https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/ http://schema.org/identifier https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/ http://schema.org/isBasedOn https://github.com/PerMedCoE/drug-synergies-workflow https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/ http://schema.org/license https://choosealicense.com/no-permission/ https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/ http://schema.org/mainEntity Workflow/PyCOMPSs/run.sh https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/ http://schema.org/name Research Object Crate for PerMedCoE Drug Synergy https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/ http://schema.org/url https://workflowhub.eu/workflows/479/ro_crate?version=1 https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/ http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://purl.org/wf4ever/ro#ResearchObject https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/ http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://purl.org/wf4ever/roevo#LiveRO https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/ http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://schema.org/Dataset https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/ https://www.w3.org/ns/iana/link-relations/relation#cite-as Javier Conejero. 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[Table of Contents](#table-of-contents) - [Description](#description) - [Contents](#contents) - [Building Blocks](#building-blocks) - [Workflows](#workflows) - [Resources](#resources) - [Tests](#tests) - [Instructions](#instructions) - [Local machine](#local-machine) - [Requirements](#requirements) - [Usage steps](#usage-steps) - [MareNostrum 4](#marenostrum-4) - [Requirements in MN4](#requirements-in-mn4) - [Usage steps in MN4](#usage-steps-in-mn4) - [License](#license) - [Contact](#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`](https://github.com/PerMedCoE/drug-synergies-workflow>) ## 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`](https://github.com/PerMedCoE/permedcoe) package - [PyCOMPSs](https://pycompss.readthedocs.io/en/stable/Sections/00_Quickstart.html) - [Singularity](https://sylabs.io/guides/3.0/user-guide/installation.html) #### Usage steps 1. Clone this repository: ```bash git clone https://github.com/PerMedCoE/drug-synergies-workflow.git ``` 2. Install the Building Blocks required for the COVID19 Workflow: ```bash drug-synergies-workflow/BuildingBlocks/./install_BBs.sh ``` 3. Get the required Building Block images from the project [B2DROP](https://b2drop.bsc.es/index.php/f/444350): - 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): 1. Clone the `BuildingBlocks` repository ```bash git clone https://github.com/PerMedCoE/BuildingBlocks.git ``` 2. Build the required Building Block images ```bash 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 ```bash 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 ```bash 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 ```bash mkdir desired_folder cd desired_folder get_drug_synergies_workflow ``` 3. Go to `Workflow/PyCOMPSs` folder ```bash 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. > :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 [Apache 2.0](https://www.apache.org/licenses/LICENSE-2.0) ## Contact This software has been developed for the [PerMedCoE project](https://permedcoe.eu/), funded by the European Commission (EU H2020 [951773](https://cordis.europa.eu/project/id/951773)).  https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/resources/d9f38986-7753-486d-aa09-bacf33643dbb http://schema.org/encodingFormat text/x-sh https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/resources/d9f38986-7753-486d-aa09-bacf33643dbb http://schema.org/license https://choosealicense.com/no-permission/ https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/resources/d9f38986-7753-486d-aa09-bacf33643dbb http://schema.org/name PerMedCoE Drug Synergy https://w3id.org/ro-id/7ab8a5dd-8bc6-46c1-8ca9-a0c245a896ad/resources/d9f38986-7753-486d-aa09-bacf33643dbb http://schema.org/producer 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