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245 Workflows visible to you, out of a total of 260
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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. ...

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: Python

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

Work-in-progress

Shotgun Metagenomics Analysis

Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more

Description

The input for this analysis is paired end next generation sequencing data from metagenomic samples. The workflow is designed to be modular, so that individual modules can be run depending on the nature of the metagenomics project at hand. More modules will be added as we develop them - this repo is a work in progress!

These scripts have been written ...

Type: Shell Script

Creators: Cali Willet, Rosemarie Sadsad, Tracy Chew, Smitha Sukumar, Elena Martinez, Christina Adler, Henry Lydecker, Fang Wang

Submitter: Tracy Chew

Work-in-progress

BridgeDb tutorial: Gene HGNC name to Ensembl identifier

This tutorial explains how to use the BridgeDb identifier mapping service to translate HGNC names to Ensembl identifiers. This step is part of the OpenRiskNet use case to link Adverse Outcome Pathways to WikiPathways.

First we need to load the Python library to allow calls to the BridgeDb REST webservice:

import requests 

Let's assume we're interested ...

Type: Jupyter

Creators: Marvin Martens, Egon Willighagen

Submitter: Marvin Martens

Performs Long Read assembly using PacBio data and Hifiasm. Part of VGP assembly pipeline. This workflow generate a phased assembly.

Type: Galaxy

Creator: Delphine Lariviere

Submitter: Cristóbal Gallardo

Work-in-progress

Performs scaffolding using HiC Data. Part of VGP assembly pipeline. The scaffolding can be performed on long read assembly contigs or on scaffolds (e.g.: Bionano scaffolds).

Type: Galaxy

Creator: Delphine Lariviere

Submitter: Cristóbal Gallardo

Performs scaffolding using Bionano Data. Part of VGP assembly pipeline.

Type: Galaxy

Creator: Delphine Lariviere

Submitter: Cristóbal Gallardo

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