Workflows

What is a Workflow?

723 Workflows visible to you, out of a total of 775

Galaxy Amber Protein MD Setup tutorial

BioBB Building Blocks

Stable

AMBER Protein MD Setup tutorials using BioExcel Building Blocks (biobb)

This workflow must be run in biobb.usegalaxy.es. Please, click here to access.

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 ...

Type: Galaxy

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.297.3

Created: 25th Mar 2022 at 10:10, Last updated: 3rd May 2023 at 14:50

Galaxy Protein-ligand Docking tutorial (Fpocket)

BioBB Building Blocks

Stable

Protein-ligand Docking tutorials using BioExcel Building Blocks (biobb)

This workflow must be run in biobb.usegalaxy.es. Please, click here to access.

This tutorials aim to illustrate the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb). The particular examples used are based on the Mitogen-activated protein kinase 14 (p38-α) protein (PDB code ...

Type: Galaxy

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.296.3

Created: 24th Mar 2022 at 14:58, Last updated: 3rd May 2023 at 14:48

Galaxy GMX Automatic Ligand Parameterization tutorial

BioBB Building Blocks

Stable

Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb)

This workflow must be run in biobb.usegalaxy.es. Please, click here to access.

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), ...

Type: Galaxy

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.294.3

Created: 24th Mar 2022 at 14:09, Last updated: 3rd May 2023 at 14:44

Galaxy Protein MD Setup tutorial

BioBB Building Blocks

Stable

Protein MD Setup tutorial using BioExcel Building Blocks (biobb)

This workflow must be run in biobb.usegalaxy.es. Please, click here to access.

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 ...

Type: Galaxy

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.277.3

Created: 14th Mar 2022 at 10:15, Last updated: 3rd May 2023 at 14:41

Katdetectr

Stable

Introduction

katdetectr is an R package for the detection, characterization and visualization of localized hypermutated regions, often referred to as kataegis.

Please see the Application Note (under submission) for additional background, details and performance evaluations of katdetectr.

The general workflow of katdetectr can be summarized as follows:

Import of genomic variants; VCF, MAF or VRanges objects.
Detection ...

Type: Unrecognized workflow type

Creators: Daan Hazelaar, Job van Riet

Submitter: Daan Hazelaar

DOI: 10.48546/workflowhub.workflow.463.1

Created: 2nd May 2023 at 12:51, Last updated: 2nd May 2023 at 12:54

multiAffinity

iPC: individualizedPaediatricCure

Stable

MultiAffinity enables the study of how gene dysregulation propagates on a multilayer network on a disease of interest, uncovering key genes. Find the detailed documentation for the tool here.

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Type: Common Workflow Language

Creators: Laura Rodriguez-Navas, Mar Batlle

Submitter: Laura Rodriguez-Navas

Download

Created: 14th Dec 2021 at 10:01, Last updated: 21st Apr 2023 at 12:06

COSIFER

iPC: individualizedPaediatricCure

Stable

COnSensus Interaction Network InFErence Service

Inference framework for reconstructing networks using a consensus approach between multiple methods and data sources.

Reference

[Manica, Matteo, Charlotte, Bunne, Roland, Mathis, Joris, Cadow, Mehmet Eren, Ahsen, Gustavo A, Stolovitzky, and María Rodríguez, Martínez. "COSIFER: a python package for the consensus inference of molecular interaction ...

Type: Common Workflow Language

Creators: Laura Rodriguez-Navas, José Mª Fernández

Submitter: Laura Rodriguez-Navas

Download

Created: 5th May 2021 at 16:50, Last updated: 21st Apr 2023 at 11:50

Python Protein MD Analysis tutorial

BioBB Building Blocks

Stable

Protein MD Analysis tutorial using BioExcel Building Blocks (biobb)

This workflow computes a set of Quality Control (QC) analyses on top of an uploaded MD trajectory. QC analyses include positional divergence (RMSd), change of shape (Radius of Gyration), identification of flexible regions (atomic/residue fluctuations), and identification of different molecular conformations (trajectory clustering).

Copyright & Licensing

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

Type: Python

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.287.3

Created: 17th Mar 2022 at 13:13, Last updated: 14th Apr 2023 at 09:58

Python Protein MD Setup tutorial with mutations

BioBB Building Blocks

Stable

Mutations 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 ...

Type: Python

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.290.3

Created: 17th Mar 2022 at 13:25, Last updated: 14th Apr 2023 at 09:56

Python Structural DNA helical parameters tutorial

BioBB Building Blocks

Stable

Structural DNA helical parameters from MD trajectory tutorial using BioExcel Building Blocks (biobb)

Based on the NAFlex server and in particular in its Nucleic Acids Analysis section.

This tutorial aims to illustrate the process of extracting structural and dynamical properties from a DNA MD trajectory helical parameters, step by step, using the **BioExcel Building Blocks ...

Type: Python

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.286.4

Created: 17th Mar 2022 at 11:10, Last updated: 14th Apr 2023 at 09:48

Workflows

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AMBER Protein MD Setup tutorials using BioExcel Building Blocks (biobb)

This workflow must be run in biobb.usegalaxy.es. Please, click here to access.

Protein-ligand Docking tutorials using BioExcel Building Blocks (biobb)

This workflow must be run in biobb.usegalaxy.es. Please, click here to access.

Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb)

This workflow must be run in biobb.usegalaxy.es. Please, click here to access.

Protein MD Setup tutorial using BioExcel Building Blocks (biobb)

This workflow must be run in biobb.usegalaxy.es. Please, click here to access.

Introduction

COnSensus Interaction Network InFErence Service

Reference

Protein MD Analysis tutorial using BioExcel Building Blocks (biobb)

Copyright & Licensing

Mutations Protein MD Setup tutorial using BioExcel Building Blocks (biobb)

Copyright & Licensing

Structural DNA helical parameters from MD trajectory tutorial using BioExcel Building Blocks (biobb)

Filters