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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

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 ...

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 ...

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 ...

Classification and visualization of SSU, LSU sequences.

Associated Tutorial

This workflows is part of the tutorial MGnify v5.0 Amplicon Pipeline, available in the GTN

Features

Type: Galaxy

Creators: None

Submitter: GTN Bot

GitHub Actions CI Status GitHub Actions Linting StatusAWS CI[![Cite ...

Type: Nextflow

Creators: None

Submitter: WorkflowHub Bot

Work-in-progress

demux_doublet_sim

Repository for Nextflow pipeline used in demuxSNP demultipelxing paper

Overall workflow

  1. Simulate doublets
  • Add per-sample suffix to barcodes in BAM
  • Merge per-sample BAMs
  • Generate lookup of barcodes to rename to reach a set % doublets
  • Rename barcodes in BAM as per lookup
  1. Benchmark methods
  • Experiments 1: Vary doublet rate
  • Experiment 2: Vary SNP subsetting

Inputs

Most inputs are specified in nextflow.config: container__souporcell: path to souporcell apptainer ...

Type: Nextflow

Creators: Michael Lynch, Leverages scripts developed by Weber et al (2021) DOI: https://doi.org/10.1093/gigascience/giab062

Submitter: Michael Lynch

DOI: 10.48546/workflowhub.workflow.1160.2

Work-in-progress

PaSTa is a nextflow-based end-to-end image analysis pipeline for decoding image-based spatial transcriptomics data. It performs imaging cycle registration, cell segmentation and transcripts peak decoding. It is currently supports analysis of three types of ST technology:

  • in-situ sequencing-like encoding
  • MERFISH-like encoding
  • RNAScope-like labelling

Prerequisites:

  1. Nextflow. Installation guide: https://www.nextflow.io/docs/latest/getstarted.html
  2. Docker or Singularity. Installation guide: ...

Type: Nextflow

Creator: Tong LI

Submitter: Tong LI

YOLO based tail analysis workflow for image segmentation and detection. The workflow is based on https://git.embl.org/grp-cba/tail-analysis/-/blob/main/analysis_workflow.md

Associated Tutorial

This workflows is part of the tutorial Training Custom YOLO Models for Object Detection and Segmentation in Bioimages, available in the GTN

...

Type: Galaxy

Creators: None

Submitter: GTN Bot

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