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      "description": "# COVID-19 Multiscale Modelling of the Virus and Patients’ Tissue Workflow\n\n## Table of Contents\n\n- [COVID-19 Multiscale Modelling of the Virus and Patients’ Tissue Workflow](#covid-19-multiscale-modelling-of-the-virus-and-patients-tissue-workflow)\n  - [Table of Contents](#table-of-contents)\n  - [Description](#description)\n  - [Contents](#contents)\n    - [Building Blocks](#building-blocks)\n    - [Workflows](#workflows)\n    - [Resources](#resources)\n    - [Tests](#tests)\n  - [Instructions](#instructions)\n    - [Local machine](#local-machine)\n      - [Requirements](#requirements)\n      - [Usage steps](#usage-steps)\n    - [MareNostrum 4](#marenostrum-4)\n      - [Requirements in MN4](#requirements-in-mn4)\n      - [Usage steps in MN4](#usage-steps-in-mn4)\n    - [Mahti or Puhti](#mahti-or-puhti)\n      - [Requirements](#requirements)\n      - [Steps](#steps)\n  - [License](#license)\n  - [Contact](#contact)\n\n## Description\n\nUses multiscale simulations to predict patient-specific SARS‑CoV‑2 severity subtypes\n(moderate, severe or control), using single-cell RNA-Seq data, MaBoSS and PhysiBoSS.\nBoolean models are used to determine the behaviour of individual agents as a function\nof extracellular conditions and the concentration of different  substrates, including\nthe number of virions. Predictions of severity subtypes are based on a meta-analysis of\npersonalised model outputs simulating cellular apoptosis regulation in epithelial cells\ninfected by SARS‑CoV‑2.\n\nThe workflow uses the following building blocks, described in order of execution:\n\n1. High-throughput mutant analysis\n2. Single-cell processing\n3. Personalise patient\n4. PhysiBoSS\n5. Analysis of all simulations\n\nFor details on individual workflow steps, see the user documentation for each building block.\n\n[`GitHub repository`]()\n\n\n## Contents\n\n### Building Blocks\n\nThe ``BuildingBlocks`` folder contains the script to install the\nBuilding Blocks used in the COVID-19 Workflow.\n\n### Workflows\n\nThe ``Workflow`` folder contains the workflows implementations.\n\nCurrently contains the implementation using PyCOMPSs and Snakemake (in progress).\n\n### Resources\n\nThe ``Resources`` folder contains dataset files.\n\n### Tests\n\nThe ``Tests`` folder contains the scripts that run each Building Block\nused in the workflow for the given small dataset.\nThey can be executed individually for testing purposes.\n\n## Instructions\n\n### Local machine\n\nThis section explains the requirements and usage for the COVID19 Workflow in a laptop or desktop computer.\n\n#### Requirements\n\n- [`permedcoe`](https://github.com/PerMedCoE/permedcoe) package\n- [PyCOMPSs](https://pycompss.readthedocs.io/en/stable/Sections/00_Quickstart.html) / [Snakemake](https://snakemake.readthedocs.io/en/stable/)\n- [Singularity](https://sylabs.io/guides/3.0/user-guide/installation.html)\n\n#### Usage steps\n\n1. Clone this repository:\n\n  ```bash\n  git clone https://github.com/PerMedCoE/covid-19-workflow.git\n  ```\n\n2. Install the Building Blocks required for the COVID19 Workflow:\n\n  ```bash\n  covid-19-workflow/BuildingBlocks/./install_BBs.sh\n  ```\n\n3. Get the required Building Block images from the project [B2DROP](https://b2drop.bsc.es/index.php/f/444350):\n\n  - Required images:\n      - MaBoSS.singularity\n      - meta_analysis.singularity\n      - PhysiCell-COVID19.singularity\n      - single_cell.singularity\n\n  The path where these files are stored **MUST be exported in the `PERMEDCOE_IMAGES`** environment variable.\n\n  &gt; :warning: **TIP**: These containers can be built manually as follows (be patient since some of them may take some time):\n  1. Clone the `BuildingBlocks` repository\n     ```bash\n     git clone https://github.com/PerMedCoE/BuildingBlocks.git\n     ```\n  2. Build the required Building Block images\n     ```bash\n     cd BuildingBlocks/Resources/images\n     sudo singularity build MaBoSS.sif MaBoSS.singularity\n     sudo singularity build meta_analysis.sif meta_analysis.singularity\n     sudo singularity build PhysiCell-COVID19.sif PhysiCell-COVID19.singularity\n     sudo singularity build single_cell.sif single_cell.singularity\n     cd ../../..\n     ```\n\n**If using PyCOMPSs in local PC** (make sure that PyCOMPSs in installed):\n\n4. Go to `Workflow/PyCOMPSs` folder\n\n   ```bash\n   cd Workflows/PyCOMPSs\n   ```\n\n5. Execute `./run.sh`\n\n**If using Snakemake in local PC** (make sure that SnakeMake is installed):\n\n4. Go to `Workflow/SnakeMake` folder\n\n   ```bash\n   cd Workflows/SnakeMake\n   ```\n\n5. Execute `./run.sh`\n  &gt; **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.\n\n\n### MareNostrum 4\n\nThis section explains the requirements and usage for the COVID19 Workflow in the MareNostrum 4 supercomputer.\n\n#### Requirements in MN4\n\n- Access to MN4\n\nAll Building Blocks are already installed in MN4, and the COVID19 Workflow available.\n\n#### Usage steps in MN4\n\n1. Load the `COMPSs`, `Singularity` and `permedcoe` modules\n\n   ```bash\n   export COMPSS_PYTHON_VERSION=3\n   module load COMPSs/3.1\n   module load singularity/3.5.2\n   module use /apps/modules/modulefiles/tools/COMPSs/libraries\n   module load permedcoe\n   ```\n\n   &gt; **TIP**: Include the loading into your `${HOME}/.bashrc` file to load it automatically on the session start.\n\n   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 (`COVID19WORKFLOW_DATASET` environment variable).\n\n2. Get a copy of the pilot workflow into your desired folder\n\n   ```bash\n   mkdir desired_folder\n   cd desired_folder\n   get_covid19workflow\n   ```\n\n3. Go to `Workflow/PyCOMPSs` folder\n\n   ```bash\n   cd Workflow/PyCOMPSs\n   ```\n\n4. Execute `./launch.sh`\n\n  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.\n\n  &gt; :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.\n\n  After the execution, a `results` folder will be available with with COVID19 Workflow results.\n\n### Mahti or Puhti\n\nThis section explains how to run the COVID19 workflow on CSC supercomputers using SnakeMake.\n\n#### Requirements\n\n- Install snakemake (or check if there is a version installed using `module spider snakemake`)\n- Install workflow, using the same steps as for the local machine. With the exception that containers have to be built elsewhere.\n\n#### Steps\n\n\n1. Go to `Workflow/SnakeMake` folder\n\n   ```bash\n   cd Workflow/SnakeMake\n   ```\n\n2. Edit `launch.sh` with the correct partition, account, and resource specifications.  \n\n3. Execute `./launch.sh`\n\n  &gt; :warning: Snakemake provides a `--cluster` flag, but this functionality should be avoided as it's really not suited for HPC systems.\n\n## License\n\n[Apache 2.0](https://www.apache.org/licenses/LICENSE-2.0)\n\n## Contact\n\n\n\nThis 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)).\n\n![](https://permedcoe.eu/wp-content/uploads/2020/11/logo_1.png \"PerMedCoE\")\n",
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      "description": "# COVID-19 Multiscale Modelling of the Virus and Patients’ Tissue Workflow\n\n## Table of Contents\n\n- [COVID-19 Multiscale Modelling of the Virus and Patients’ Tissue Workflow](#covid-19-multiscale-modelling-of-the-virus-and-patients-tissue-workflow)\n  - [Table of Contents](#table-of-contents)\n  - [Description](#description)\n  - [Contents](#contents)\n    - [Building Blocks](#building-blocks)\n    - [Workflows](#workflows)\n    - [Resources](#resources)\n    - [Tests](#tests)\n  - [Instructions](#instructions)\n    - [Local machine](#local-machine)\n      - [Requirements](#requirements)\n      - [Usage steps](#usage-steps)\n    - [MareNostrum 4](#marenostrum-4)\n      - [Requirements in MN4](#requirements-in-mn4)\n      - [Usage steps in MN4](#usage-steps-in-mn4)\n    - [Mahti or Puhti](#mahti-or-puhti)\n      - [Requirements](#requirements)\n      - [Steps](#steps)\n  - [License](#license)\n  - [Contact](#contact)\n\n## Description\n\nUses multiscale simulations to predict patient-specific SARS‑CoV‑2 severity subtypes\n(moderate, severe or control), using single-cell RNA-Seq data, MaBoSS and PhysiBoSS.\nBoolean models are used to determine the behaviour of individual agents as a function\nof extracellular conditions and the concentration of different  substrates, including\nthe number of virions. Predictions of severity subtypes are based on a meta-analysis of\npersonalised model outputs simulating cellular apoptosis regulation in epithelial cells\ninfected by SARS‑CoV‑2.\n\nThe workflow uses the following building blocks, described in order of execution:\n\n1. High-throughput mutant analysis\n2. Single-cell processing\n3. Personalise patient\n4. PhysiBoSS\n5. Analysis of all simulations\n\nFor details on individual workflow steps, see the user documentation for each building block.\n\n[`GitHub repository`]()\n\n\n## Contents\n\n### Building Blocks\n\nThe ``BuildingBlocks`` folder contains the script to install the\nBuilding Blocks used in the COVID-19 Workflow.\n\n### Workflows\n\nThe ``Workflow`` folder contains the workflows implementations.\n\nCurrently contains the implementation using PyCOMPSs and Snakemake (in progress).\n\n### Resources\n\nThe ``Resources`` folder contains dataset files.\n\n### Tests\n\nThe ``Tests`` folder contains the scripts that run each Building Block\nused in the workflow for the given small dataset.\nThey can be executed individually for testing purposes.\n\n## Instructions\n\n### Local machine\n\nThis section explains the requirements and usage for the COVID19 Workflow in a laptop or desktop computer.\n\n#### Requirements\n\n- [`permedcoe`](https://github.com/PerMedCoE/permedcoe) package\n- [PyCOMPSs](https://pycompss.readthedocs.io/en/stable/Sections/00_Quickstart.html) / [Snakemake](https://snakemake.readthedocs.io/en/stable/)\n- [Singularity](https://sylabs.io/guides/3.0/user-guide/installation.html)\n\n#### Usage steps\n\n1. Clone this repository:\n\n  ```bash\n  git clone https://github.com/PerMedCoE/covid-19-workflow.git\n  ```\n\n2. Install the Building Blocks required for the COVID19 Workflow:\n\n  ```bash\n  covid-19-workflow/BuildingBlocks/./install_BBs.sh\n  ```\n\n3. Get the required Building Block images from the project [B2DROP](https://b2drop.bsc.es/index.php/f/444350):\n\n  - Required images:\n      - MaBoSS.singularity\n      - meta_analysis.singularity\n      - PhysiCell-COVID19.singularity\n      - single_cell.singularity\n\n  The path where these files are stored **MUST be exported in the `PERMEDCOE_IMAGES`** environment variable.\n\n  &gt; :warning: **TIP**: These containers can be built manually as follows (be patient since some of them may take some time):\n  1. Clone the `BuildingBlocks` repository\n     ```bash\n     git clone https://github.com/PerMedCoE/BuildingBlocks.git\n     ```\n  2. Build the required Building Block images\n     ```bash\n     cd BuildingBlocks/Resources/images\n     sudo singularity build MaBoSS.sif MaBoSS.singularity\n     sudo singularity build meta_analysis.sif meta_analysis.singularity\n     sudo singularity build PhysiCell-COVID19.sif PhysiCell-COVID19.singularity\n     sudo singularity build single_cell.sif single_cell.singularity\n     cd ../../..\n     ```\n\n**If using PyCOMPSs in local PC** (make sure that PyCOMPSs in installed):\n\n4. Go to `Workflow/PyCOMPSs` folder\n\n   ```bash\n   cd Workflows/PyCOMPSs\n   ```\n\n5. Execute `./run.sh`\n\n**If using Snakemake in local PC** (make sure that SnakeMake is installed):\n\n4. Go to `Workflow/SnakeMake` folder\n\n   ```bash\n   cd Workflows/SnakeMake\n   ```\n\n5. Execute `./run.sh`\n  &gt; **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.\n\n\n### MareNostrum 4\n\nThis section explains the requirements and usage for the COVID19 Workflow in the MareNostrum 4 supercomputer.\n\n#### Requirements in MN4\n\n- Access to MN4\n\nAll Building Blocks are already installed in MN4, and the COVID19 Workflow available.\n\n#### Usage steps in MN4\n\n1. Load the `COMPSs`, `Singularity` and `permedcoe` modules\n\n   ```bash\n   export COMPSS_PYTHON_VERSION=3\n   module load COMPSs/3.1\n   module load singularity/3.5.2\n   module use /apps/modules/modulefiles/tools/COMPSs/libraries\n   module load permedcoe\n   ```\n\n   &gt; **TIP**: Include the loading into your `${HOME}/.bashrc` file to load it automatically on the session start.\n\n   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 (`COVID19WORKFLOW_DATASET` environment variable).\n\n2. Get a copy of the pilot workflow into your desired folder\n\n   ```bash\n   mkdir desired_folder\n   cd desired_folder\n   get_covid19workflow\n   ```\n\n3. Go to `Workflow/PyCOMPSs` folder\n\n   ```bash\n   cd Workflow/PyCOMPSs\n   ```\n\n4. Execute `./launch.sh`\n\n  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.\n\n  &gt; :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.\n\n  After the execution, a `results` folder will be available with with COVID19 Workflow results.\n\n### Mahti or Puhti\n\nThis section explains how to run the COVID19 workflow on CSC supercomputers using SnakeMake.\n\n#### Requirements\n\n- Install snakemake (or check if there is a version installed using `module spider snakemake`)\n- Install workflow, using the same steps as for the local machine. With the exception that containers have to be built elsewhere.\n\n#### Steps\n\n\n1. Go to `Workflow/SnakeMake` folder\n\n   ```bash\n   cd Workflow/SnakeMake\n   ```\n\n2. Edit `launch.sh` with the correct partition, account, and resource specifications.  \n\n3. Execute `./launch.sh`\n\n  &gt; :warning: Snakemake provides a `--cluster` flag, but this functionality should be avoided as it's really not suited for HPC systems.\n\n## License\n\n[Apache 2.0](https://www.apache.org/licenses/LICENSE-2.0)\n\n## Contact\n\n\n\nThis 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)).\n\n![](https://permedcoe.eu/wp-content/uploads/2020/11/logo_1.png \"PerMedCoE\")\n",
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