Workflows

What is a Workflow?
1298 Workflows visible to you, out of a total of 1381
ont-assembly-snake
Stable

ont-assembly-snake

A Snakemake wrapper for easily creating de novo bacterial genome assemblies from Oxford Nanopore (ONT) sequencing data, and optionally Illumina data, using any combination of read filtering, assembly, long and short read polishing, and reference-based polishing.

Included programs

read filtering assembly long read polishing short read polishing reference-based polishing
Filtlong
...

Type: Snakemake

Creator: Peter Menzel

Submitter: Peter Menzel

DOI: 10.48546/workflowhub.workflow.787.1

Wound Healing Scrath Assay Image Analysis
Work-in-progress

This project is about the automated quantification of wound healing in high-throughput microscopy scratch assays.

Type: Galaxy

Creator: Christian Tischer

Submitter: Yi Sun

Lysozyme in water full version, using REMOTE dataset, two workers, data_persistence False

Lysozyme in water full COMPSs application run at MareNostrum IV, using full dataset with two workers

Type: COMPSs

Creator: Rosa M Badia

Submitter: Raül Sirvent

PyCOMPSs Probabilistic Tsunami Forecast (PTF) - Kos-Bodrum 2017 earthquake and tsunami test-case

PyCOMPSs implementation of Probabilistic Tsunami Forecast (PTF). PTF explicitly treats data- and forecast-uncertainties, enabling alert level definitions according to any predefined level of conservatism, which is connected to the average balance of missed-vs-false-alarms. Run of the Kos-Bodrum 2017 event test-case with 1000 scenarios, 8h tsunami simulation for each and forecast calculations for partial and full ensembles with focal mechanism and tsunami data updates.

Type: COMPSs

Creators: Louise Cordrie, Jorge Ejarque, Carlos Sánchez Linares, Jacopo Selva, Jorge Macías, Steven J. Gibbons, Fabrizio Bernardi, Roberto Tonini, Rosa M. Badia, Sonia Scardigno, Stefano Lorito, Finn Løvholt, Fabrizio Romano, Manuela Volpe, Alessandro D'Anca, Marc de la Asunción, Manuel J. Castro

Submitter: Jorge Ejarque

DOI: 10.48546/workflowhub.workflow.781.1

PyCOMPSs Probabilistic Tsunami Forecast (PTF) - Boumerdes-2003 earthquake and tsunami test-case

PyCOMPSs implementation of Probabilistic Tsunami Forecast (PTF). PTF explicitly treats data- and forecast-uncertainties, enabling alert level definitions according to any predefined level of conservatism, which is connected to the average balance of missed-vs-false-alarms. Run of the Boumerdes-2003 event test-case with 1000 scenarios, 8h tsunami simulation for each and forecast calculations for partial and full ensembles with focal mechanism and tsunami data updates.

Type: COMPSs

Creators: Louise Cordrie, Jorge Ejarque, Carlos Sánchez Linares, Jacopo Selva, Jorge Macías, Steven J. Gibbons, Fabrizio Bernardi, Roberto Tonini, Rosa M. Badia, Sonia Scardigno, Stefano Lorito, Finn Løvholt, Fabrizio Romano, Manuela Volpe, Alessandro D'Anca, Marc de la Asunción, Manuel J. Castro

Submitter: Jorge Ejarque

DOI: 10.48546/workflowhub.workflow.779.1

Galaxy Molecular Structure Checking
Stable

Molecular Structure Checking using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of checking a molecular structure before using it as an input for a Molecular Dynamics simulation. The workflow uses the BioExcel Building Blocks library (biobb). The particular structure used is the crystal structure of human Adenylate Kinase 1A (AK1A), in complex with the AP5A inhibitor (PDB code 1Z83).

**Structure ...

Type: Galaxy

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.778.1

CWL Molecular Structure Checking
Stable

Molecular Structure Checking using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of checking a molecular structure before using it as an input for a Molecular Dynamics simulation. The workflow uses the BioExcel Building Blocks library (biobb). The particular structure used is the crystal structure of human Adenylate Kinase 1A (AK1A), in complex with the AP5A inhibitor (PDB code 1Z83).

**Structure ...

Type: Common Workflow Language

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.776.1

fluorescence-nuclei-segmentation-and-counting/main

This workflow performs segmentation and counting of cell nuclei using fluorescence microscopy images. The segmentation step is performed using Otsu thresholding (Otsu, 1979). The workflow is based on the tutorial: https://training.galaxyproject.org/training-material/topics/imaging/tutorials/imaging-introduction/tutorial.html

Type: Galaxy

Creator: Leonid Kostrykin

Submitter: WorkflowHub Bot

flavivirushelicase_apo

This is a Galaxy workflow for performing molecular dynamics simulations and analysis with flavivirus helicases in the Apo or unbound state. The associated input files can be found at: https://zenodo.org/records/7493015 The associated output files can be found at: https://zenodo.org/records/7850935

Type: Galaxy

Creator: Bryan Raubenolt

Submitter: Bryan Raubenolt

DOI: 10.48546/workflowhub.workflow.762.1

coronavirushelicase_proteindrugcomplex

This is a Galaxy workflow for performing molecular dynamics simulations and analysis with coronavirus helicases bound to a ligand/drug molecule. The associated input files can be found at: https://zenodo.org/records/7492987. The associated output files can be found at: https://zenodo.org/records/7851000.

Type: Galaxy

Creator: Bryan Raubenolt

Submitter: Bryan Raubenolt

DOI: 10.48546/workflowhub.workflow.763.1

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