Workflows
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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 ...
Type: Jupyter
Creators: Genís Bayarri, Adam Hospital, Douglas Lowe
Submitters: Robin Long, Genís Bayarri
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 ...
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 ...
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
- Includes a Galaxy Workflow Report
- Uses ...
demux_doublet_sim
Repository for Nextflow pipeline used in demuxSNP demultipelxing paper
Overall workflow
- 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
- 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
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:
- Nextflow. Installation guide: https://www.nextflow.io/docs/latest/getstarted.html
- Docker or Singularity. Installation guide: ...
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
...
From Obis data to Biodiversity indicators
Associated Tutorial
This workflows is part of the tutorial Obis marine indicators, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Marie Jossé
Tutorial Author(s): ...