Workflows

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91 Workflows visible to you, out of a total of 94
Stable

Summary

This tutorial aims to illustrate how to compute a fast-growth mutation free energy calculation, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Staphylococcal nuclease protein (PDB code 1STN), a small, minimal protein, appropriate for a short tutorial.

Workflow engine is a jupyter notebook. Auxiliary libraries used are nb_conda_kernels, os, and plotly. Environment setup can be carried out using the environment.yml in the code

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Type: Unrecognized workflow type

Creators: Genís Bayarri, Adam Hospital

Submitter: Douglas Lowe

DOI: 10.48546/workflowhub.workflow.55.2

Stable

Summary

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 2-propylphenol small molecule (3-letter Code JZ4).

Workflow engine is a jupyter notebook. It can be run in binder, following the link given, or locally. Auxiliar libraries used are: nb_conda_kernels,

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Type: Unrecognized workflow type

Creators: Genís Bayarri, Adam Hospital

Submitter: Douglas Lowe

DOI: 10.48546/workflowhub.workflow.56.2

Stable

Summary

Jupyter Notebook containing a tutorial 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 minimize the structure, and generate parameters for the GROMACS package. With Generalized

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Type: Unrecognized workflow type

Creators: Genís Bayarri, Adam Hospital

Submitter: Robin Long

DOI: 10.48546/workflowhub.workflow.54.1

Stable

Summary

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).

Workflow engine is a jupyter notebook. It can be run in binder, following the link given, or locally. Auxiliar libraries used are: nb_conda_kernels, nglview, ipywidgets, plotly, and simpletraj. Environment can be setup using the included environment.yml

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Type: Unrecognized workflow type

Creators: Genís Bayarri, Adam Hospital

Submitter: Douglas Lowe

DOI: 10.48546/workflowhub.workflow.120.1

Stable

Common Workflow Language example that 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).

Type: Common Workflow Language

Creator: Genís Bayarri

Submitters: Robin Long, Douglas Lowe

DOI: 10.48546/workflowhub.workflow.29.2

Work-in-progress

Workflow for Metagenomics from raw reads to annotated bins.

Steps:

  • workflow_quality.cwl:

  • FastQC (control)

  • fastp (trimming)

  • Kraken2 (Taxonomic Read Classification

  • SPAdes (Assembly)

  • QUAST (Assembly quality report)

  • BBmap (Read mapping to assembly)

  • samtobam (sam to indexed bam)

  • metabatContigDepths (jgisummarizebamcontigdepths)

  • MetaBat2 (binning)

Type: Common Workflow Language

Creators: None

Submitter: Jasper Koehorst

Stable

COnSensus Interaction Network InFErence Service

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

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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

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