Workflows

What is a Workflow?
536 Workflows visible to you, out of a total of 576
Stable

Protein Ligand Complex MD Setup tutorial using BioExcel Building Blocks (biobb)

Based on the official GROMACS tutorial.


This tutorial aims to illustrate the process of setting up a simulation system containing a protein in complex with a ligand, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the T4 lysozyme L99A/M102Q protein (PDB code 3HTB), in complex with the ...

Stable

Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb)


This tutorial aims to illustrate the process of ligand parameterization for a small molecule, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Sulfasalazine protein (3-letter code SAS), used to treat rheumatoid arthritis, ulcerative colitis, and Crohn's disease.

OpenBabel and ACPype packages are used to **add hydrogens, energetically ...

Stable

Protein MD Setup tutorial using BioExcel Building Blocks (biobb)

Based on the official GROMACS tutorial.


This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI).


Copyright & Licensing

This software has been developed in the [MMB ...

No description specified

Type: Pi

Creators: None

Submitter: Tina Tian

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Type: Python

Creators: None

Submitter: Tina Tian

Stable

Protein MD Setup tutorial using BioExcel Building Blocks (biobb)

Based on the official GROMACS tutorial.


This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI).


Copyright & Licensing

This software has been developed in the [MMB ...

Work-in-progress

WRF/EMEP Linear Workflow

Example Common Workflow Language (CWL) workflow and tool descriptors for running the Weather Research and Forecase (WRF) and EMEP models.

This workflow is designed for a single model domain. Example datasets for testing this workflow can be downloaded from Zenodo.

Requirements:

  • docker or singularity
  • conda
  • cwltool
  • Toil - optional, useful for running on HPC or distributed computing systems

CWL / Toil Installation:

The workflow runner (either cwltool, or ...

Type: Common Workflow Language

Creator: Douglas Lowe

Submitter: Douglas Lowe

Assembly and quantification metatranscriptome using metagenome data.

Version: see VERSION

Introduction

MetaGT is a bioinformatics analysis pipeline used for improving and quantification metatranscriptome assembly using metagenome data. The pipeline supports Illumina sequencing data and complete metagenome and metatranscriptome assemblies. The pipeline involves the alignment of metatranscriprome assembly to the metagenome assembly with further extracting CDSs, which are covered by ...

Type: Nextflow

Creators: Andrey Prjibelski, Varsha Kale, Anton Korobeynikov

Submitter: Varsha Kale

Work-in-progress

Workflow (hybrid) metagenomic assembly and binning + GEMs

Accepts both Illumina and Long reads (ONT/PacBio)

Workflow binnning https://workflowhub.eu/workflows/64?version=11 (optional)

  • Metabat2/MaxBin2/SemiBin
  • DAS Tool
  • CheckM ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

Work-in-progress

Workflow for LongRead Quality Control and Filtering

  • NanoPlot (read quality control) before and after filtering
  • Filtlong (read trimming)
  • Kraken2 taxonomic read classification before and after filtering
  • Minimap2 read filtering based on given references

Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default

All tool CWL files and other workflows can be found here: https://gitlab.com/m-unlock/cwl/workflows

**How to setup and use an UNLOCK ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst, Germán Royval

Submitter: Bart Nijsse

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