biobb/biobb_wf_pmx_tutorial repository overview

⁠Mutation Free Energy Calculations workflow using BioExcel Building Blocks (biobb)⁠

Based on the official pmx tutorial: https://pmx.mpibpc.mpg.de/sardinia2018_tutorial1/index.html⁠

This workflow aims to illustrate how to compute a fast-growth mutation free energy calculation, step by step, using the BioExcel Building Blocks library (biobb).

⁠Installation

docker pull biobb/biobb_wf_pmx_tutorial

⁠Workflow files

Below you can find the list of all the needed files for executing this workflow:

• workflow.yml: the configuration file with the I/O dependencies and settings for each step of the workflow. Download example⁠

Please put all these files in the same folder. In this execution folder, create a new folder named pmx_tutorial and put inside the following files:

• stateA.tpr: WT protein topology (GROMACS tpr format). Download example⁠
• stateA_1ns.xtc: Equilibrium trajectory for the WT protein. Download example⁠
• stateB.tpr: Mutated protein topology (GROMACS tpr format). Download example⁠
• stateB_1ns.xtc: Equilibrium trajectory for the Mutated protein. Download example⁠
• dhdlA.zip: Forward work values required to illustrate how to perform the last step of the pmx workflow with real values, to extract the free energy. Download example⁠
• dhdlB.zip: Reverse work values required to illustrate how to perform the last step of the pmx workflow with real values, to extract the free energy. Download example⁠
• schema.png: Tutorial graphic schema. Download example⁠

⁠Run workflow

The BioBB workflows containers can be executed either interactively via Jupyter Notebook or sequentially in python.

⁠Run in Jupyter Notebook

For running the container in Jupyter Notebook, please type the following instruction in your terminal:

docker run --name <container_name> -d -e MODE=jupyter -p <port>:8888 -v /path/to/inputs:/data biobb/biobb_wf_pmx_tutorial

Where:

• container_name is the name of the container (optional).
• port is the port of your computer where the output of the container will be redirected (ie 3000).
• /path/to/inputs is the path to the folder where the input(s) and workflow.yml files are located (all of them must be in the same folder).

This instruction will run the container in detached (or background) mode, so once it's running, you should go to your browser and type:

http://localhost:3000/notebooks/notebook.ipynb⁠

Note that the port can change depending on the value provided in the previous step.

⁠Run in Python

Below you can find the list of all the needed files for executing this workflow in python:

• workflow.yml: the configuration file with the I/O dependencies and settings for each step of the workflow.
• inputs: the inputs vary depending on the workflow, all the needed files are available in this same repository, just be sure to have them in the same folder where workflow.yml is.

For running the container in python, please type the following instruction in your terminal:

docker run --name <container_name> -v /path/to/inputs:/data biobb/biobb_wf_pmx_tutorial

Where:

• container_name is the name of the container (optional).
• /path/to/inputs is the path to the folder where the input(s) and workflow.yml files are located (all of them must be in the same folder).

⁠Time of execution

Take into account that depending on the number of steps, the tools executed and the settings provided, along with the power of your computer, the execution of the workflow can take from a few minutes to several hours. The workflow progress will be shown in your terminal if you execute the workflow via python.

⁠Get output results

⁠Jupyter Notebook

Once the workflow is finished, you just should enter the new wf_notebook/biobb_wf_pmx_tutorial folder and, inside it, you will find all the outputs generated by the workflow.

⁠Python

Once the workflow is finished, you just should enter the new wf_python/biobb_wf_pmx_tutorial folder and, inside it, you will find a folder for each step of the workflow with all the files generated in every step.