This workflows contains a pipeline in Scipion that performs the following steps:

1.1) Import small molecules: introduces a set of small molecular structures in the pipeline as prospective ligands

1.2) Import atomic structure: introduces a protein atomic structure in the pipeline as receptor.

2.1) Ligand preparation: uses RDKit to prepare the small molecules optimizing their 3D structure.

2.2) Receptor preparation: uses bioPython to prepare the receptor structure, removing waters, adding hydrogens ...

This workflow performs the most basic Virtual Drug Screening Pipeline to import a set of small molecules and dock them to an imported protein structure.

This workflow was built for the 2024 Bioinformatics Bootcamp at The Open University. It is meant to occur after the (universal) Filter, plot and explore tutorial to allow analysis of a single cluster.

BVSim: A Benchmarking Variation Simulator Mimicking Human Variation Spectrum

Table of Contents

• Getting Started
• Installation
• General Functions and Parameters
• Shared Parameters
• Output Naming Conventions
• [Write the Relative ...

CausalCoxMGM

Implementation of CausalCoxMGM algorithm and scripts for analysis of simulated and real-world biomedical datasets.

Installation

To install CoxMGM and CausalCoxMGM, run the following command in the terminal:

R CMD INSTALL rCausalMGM 

or alternatively:

R CMD INSTALL rCausalMGM/rCausalMGM_1.0.tar.gz 

Demonstration of CausalCoxMGM with the WHAS500 dataset

First, we begin by loading the necessray R packages for this analysis.

library(rCausalMGM) 
library(survival)
...

This workflow was developed for the 2024 Bioinformatics Bootcamp at The Open University. It imports datasets from the EBI SCXA, reformats then, and analyses them similar to the Filter, plot and explore Galaxy tutorial.

PVGA is a powerful virus-focused assembler that does both assembly and polishing. For virus genomes, small changes will lead to significant differences in terms of viral function and pathogenicity. Thus, for virus-focused assemblers, high-accuracy results are crucial. Our approach heavily depends on the input reads as evidence to produce the reported genome. It first adopts a reference genome to start with. We then align all the reads against the reference genome to get an alignment graph. After ...

Current version of this workflow: https://workflowhub.eu/workflows/1109. Please use only with the new version. KNIME workflow to gather ChEMBL permeability data is availbale: https://workflowhub.eu/workflows/1169.

gSpreadComp: Streamlining Microbial Community Analysis for Resistance, Virulence, and Plasmid-Mediated Spread

Overview

gSpreadComp is a UNIX-based, modular bioinformatics toolkit designed to streamline comparative genomics for analyzing microbial communities. It integrates genome annotation, gene spread calculation, plasmid-mediated horizontal gene transfer (HGT) detection and resistance-virulence ranking within the analysed microbial community to help researchers identify potential ...