Workflows

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740 Workflows visible to you, out of a total of 795
Protein MD Setup tutorial using BioExcel Building Blocks (biobb) in KNIME
Work-in-progress

This is an experimental KNIME workflow of using the BioExcel building blocks to implement the Protein MD Setup tutorial for molecular dynamics with GROMACS.

Note that this workflow won't import in KNIME without the experimental KNIME nodes for BioBB - contact Adam Hospital for details.

Type: KNIME

Creator: Adam Hospital

Submitter: Stian Soiland-Reyes

DOI: 10.48546/workflowhub.workflow.201.1

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Protein MD Setup HPC tutorial using BioExcel Building Blocks (biobb) in PyCOMPSs
Stable

This PyCOMPSs workflow 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) in PyCOMPSs for execution on HPC. Three variants of the MD Setup workflows are included, supporting a list of structures, a list of mutations, or a cumulative set of mutations.

Type: COMPSs

Creators: Adam Hospital, Pau Andrio

Submitter: Stian Soiland-Reyes

DOI: 10.48546/workflowhub.workflow.200.1

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lncRNA
Stable

Analysis of RNA-seq data starting from BAM and focusing on mRNA, lncRNA and miRNA

Type: Galaxy

Creators: None

Submitter: Bianca Pasat

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Workflow of BioTranslator Comparative Analysis
Stable

This workflow is based on the idea of comparing different gene sets through their semantic interpretation. In many cases, the user studies a specific phenotype (e.g. disease) by analyzing lists of genes resulting from different samples or patients. Their pathway analysis could result in different semantic networks, revealing mechanistic and phenotypic divergence between these gene sets. The workflow of BioTranslator Comparative Analysis compares quantitatively the outputs of pathway analysis, ...

Type: Galaxy

Creators: None

Submitter: thodk

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BioTranslator Workflow
Stable

BioTranslator performs sequentially pathway analysis and gene prioritization: A specific operator is executed for each task to translate the input gene set into semantic terms and pinpoint the pivotal-role genes on the derived semantic network. The output consists of the set of statistically significant semantic terms and the associated hub genes (the gene signature), prioritized according to their involvement in the underlying semantic topology.

Type: Galaxy

Creators: None

Submitter: thodk

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entryTitleTest

Cryo-EM processing workflow

Type: Common Workflow Language

Creators: None

Submitter: Irene Sánchez

DOI: 10.48546/workflowhub.workflow.188.1

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testEntryTitleNew

Cryo-EM processing workflow

Type: Common Workflow Language

Creators: None

Submitter: Irene Sánchez

DOI: 10.48546/workflowhub.workflow.183.1

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Cryo electron microscopy of SARS-CoV-2 spike in prefusion state

Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures

Type: Common Workflow Language

Creators: None

Submitter: Irene Sánchez

DOI: 10.48546/workflowhub.workflow.160.1

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SAMBA: Standardized and Automated MetaBarcoding Analyses workflow
Stable

SAMBA is a FAIR scalable workflow integrating, into a unique tool, state-of-the-art bioinformatics and statistical methods to conduct reproducible eDNA analyses using Nextflow. SAMBA starts processing by verifying integrity of raw reads and metadata. Then all bioinformatics processing is done using commonly used procedure (QIIME 2 and DADA2) but adds new steps relying on dbOTU3 and microDecon to build high quality ASV count tables. Extended statistical analyses are also performed. Finally, SAMBA ...

Type: Nextflow

Creators: Cyril Noel, Alexandre Cormier, Laura Leroi, Patrick Durand, Laure Quintric

Submitter: Cyril Noel

DOI: 10.48546/workflowhub.workflow.156.1

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Germline-ShortV @ NCI-Gadi
Work-in-progress

Germline-ShortV @ NCI-Gadi is an implementation of the BROAD Institute's best practice workflow for germline short variant discovery. This implementation is optimised for the National Compute Infrastucture's Gadi HPC, utilising scatter-gather parallelism to enable use of multiple nodes with high CPU or memory efficiency. This workflow requires sample BAM files, which can be generated using the Fastq-to-bam @ NCI-Gadi pipeline. Germline-ShortV can be applied ...

Type: Shell Script

Creators: Rosemarie Sadsad, Georgina Samaha, Tracy Chew, Cali Willet

Submitter: Tracy Chew

DOI: 10.48546/workflowhub.workflow.143.1

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