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Library curation BOLD
Work-in-progress

Perl CI DOI

Library curation BOLD

alt text

This repository contains scripts and synonymy data for pipelining the automated curation of BOLD data dumps in BCDM TSV ...

Type: Snakemake

Creators: Rutger Vos, Fabian Deister, Ben Price, Special thanks to Sujeevan Ratnasingham and the team at CBG for the creation of the BCDM data exchange format that this pipeline operates on

Submitter: Rutger Vos

DOI: 10.48546/workflowhub.workflow.833.1

Use Case 13: Novel Cell Surface Targets for Individual Cancer Patients Analyzed with Common Fund Datasets
Work-in-progress

The input to this workflow is a data matrix of gene expression that was collected from a pediatric patient tumor patient from the KidsFirst Common Fund program [1]. The RNA-seq samples are the columns of the matrix, and the rows are the raw expression gene count for all human coding genes (Table 1). This data matrix is fed into TargetRanger [2] to screen for targets which are highly expressed in the tumor but lowly expressed across most healthy human tissues based on gene expression data collected ...

Type: Common Workflow Language

Creators: None

Submitter: Daniel Clarke

SGWB model spectrum
Stable

This workflow provides a calculaiton of the power spectrum of Stochastic Gravitational Wave Backgorund (SGWB) from a first-order cosmological phase transition based on the parameterisations of Roper Pol et al. (2023). The power spectrum includes two components: from the sound waves excited by collisions of bubbles of the new phase and from the turbulence that is induced by these collisions.

The cosmological epoch of the phase transition is described by the temperature, T_star and by the number(s) ...

Type: Galaxy

Creators: Andrii Neronov, Théo Boyer

Submitter: Andrii Neronov

DOI: 10.48546/workflowhub.workflow.831.1

Scaffolding-Bionano-VGP7/main

Scaffolding with Bionano

Scaffolding using Bionano optical map data

Inputs

  1. Bionano data [cmap]
  2. Estimated genome size [txt]
  3. Phased assembly generated by Hifiasm [gfa1]

Outputs

  1. Scaffolds
  2. Non-scaffolded contigs
  3. QC: Assembly statistics
  4. QC: Nx plot
  5. QC: Size plot

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

Docker Protein-ligand Docking tutorial (Fpocket)
Stable

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

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 3HEC), a well-known Protein Kinase enzyme, in complex with the FDA-approved Imatinib (PDB Ligand code ...

Type: Docker

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.830.1

Docker 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: Docker

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.829.1

Docker Protein Ligand Complex MD Setup tutorial
Stable

Protein Ligand Complex 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 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 ...

Type: Docker

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.828.1

Docker Mutation Free Energy Calculations
Stable

Mutation Free Energy Calculations using BioExcel Building Blocks (biobb)

Based on the official pmx tutorial.

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. ...

Type: Docker

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.827.1

Docker Protein MD Setup tutorial
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 ...

Type: Docker

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.826.1

Docker GMX Notebook Automatic Ligand Parameterization tutorial
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 ...

Type: Docker

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.825.1

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