biobb-netprop 1.12.3

Biobb_NetProp is use case to build a prioritize PPI Network through Disc4All pre-process database REST API.

biobb_netprop

Introduction

BioBB formulated for the Disc4All EU project, containing functions for interrogating the DisGenet database, parsing the HIPPIE PPI database and using NetworkX to create basic nodes for a prioritized network based on the mentioned databases retrieval. new Biobbs by the community. Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools. The latest documentation of this package can be found in our readthedocs site: latest API documentation.

Version

v1.0.0 2022.4

Installation

If you have no experience with anaconda, please first take a look to the New with anaconda? section of the official documentation.

Download repository

Although the biobb_netprop repository is available at GitHub and thus you can clone it, we strongly recommend you to download it compressed and start your new project from scratch.

Create new conda environment

Once you have the project unzipped in your computer, please follow the next steps to create a new conda environment:

cd biobb_netprop
conda env create -f conda_env/environment.yml

Update environment paths

Edit conda_env/biobb_netprop.pth with the paths to your biobb_netprop folder. Example:

/home/user_name/projects/biobb_netprop/
/home/user_name/projects/biobb_netprop/biobb_netprop/netptrop

Copy the edited conda_env/biobb_netprop.pth file to the site-packages folder of your environment. This folder is in /[anaconda-path]/envs/biobb_netprop/lib/python3.7/site-packages, where /[anaconda-path] is usually /anaconda3 or /opt/conda.

cp conda_env/biobb_netprop.pth /[anaconda-path]/envs/biobb_netprop/lib/python3.7/site-packages

Activate environment

Then, activate the recently created biobb_netprop conda environment:

conda activate biobb_netprop

Create repository

This netprop includes some folders not standard for a biobb, such as biobb_netprop/adapters/, biobb_netprop/notebooks/ or conda_env/. For the sake of having a pure biobb structure, you should uncomment the three last lines of the .gitignore file before creating a new git repository:

biobb_netprop/adapters
biobb_netprop/notebooks
conda_env

Then, inialitize repository:

git init

WorkFlow example

In this directory, there is also a implemented Python version of the Static WorkFlow, but for it to run, it is mandatory to download and modify their paths in the YAML file, the DisGenet and the HIPPIE databases locally. You can find them here. Remember to unzip the files before using them, and remember also to modify the path of the directory/datasets in the YML file).

Binary paths configuration

Additionally, it's recommendable to configure binary paths in your environment in order to ease the command line execution. More info about this subject in the Binary path configuration section of the official documentation.

Documentation

Click here to find the API Documentation example for this BioBB and here for Command Line documentation.

And here you can find the full documentation about how to build a new BioExcel building block from scratch.

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728), Disc4All 955735.

• (c) 2015-2020 Barcelona Supercomputing Center
• (c) 2015-2020 Institute for Research in Biomedicine

Licensed under the Apache License 2.0, see the file LICENSE for details.