Workflows

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422 Workflows visible to you, out of a total of 465
GADES reproducibility workflow
Stable

Article-GADES

This repository represents generating and benchmarking the results of the GADES package for Distance Matrix Calculation

Installation

git lfs install 
git clone https://github.com/lab-medvedeva/Article-GADES.git 
cd Article-GADES

Put the Real datasets in the MEX format to the folder Datasets/Real.

Running benchmark using Docker Deployment

docker run --gpus all \ 
-v $PWD/Datasets:/workspace/Article-GADES/Datasets
...

Type: Docker

Creator: Pavel Akhtyamov

Submitter: Pavel Akhtyamov

DOI: 10.48546/workflowhub.workflow.1125.1

Full Analyse Argo data

Process argo data with the Pangeo Ecosystem and visualise them with Ocean Data View (ODV)

Type: Galaxy

Creator: Marie Jossé

Submitter: Marie Jossé

Protein-protein and protein-nucleic acid binding site prediction via interpretable hierarchical geometric deep learning
Stable

GraphRBF is a state-of-the-art protein-protein/nucleic acid interaction site prediction model built by enhanced graph neural networks and prioritized radial basis function neural networks. This project serves users to use our software to directly predict protein binding sites or train our model on a new database. Identification of protein-protein and protein-nucleic acid binding sites provides insights into biological processes related to protein functions and technical guidance for disease ...

Type: BioCompute Object

Creator: 仕卓 张

Submitter: 仕卓 张

DOI: 10.48546/workflowhub.workflow.1107.1

Swedish Earth Biogenome Project Genome Assembly Workflow
Work-in-progress

Swedish Earth Biogenome Project - Genome Assembly Workflow

The primary genome assembly workflow for the Earth Biogenome Project at NBIS.

Workflow overview

General aim:

flowchart LR 
hifi[/ HiFi reads /] --> data_inspection 
ont[/ ONT reads /] --> data_inspection 
hic[/ Hi-C reads /] --> data_inspection 
data_inspection[[ Data inspection ]] --> preprocessing 
preprocessing[[ Preprocessing ]] --> assemble 
assemble[[ Assemble ]] --> validation 
validation[[ Assembly
...

Type: Nextflow

Creators: Mahesh Binzer-Panchal, Martin Pippel

Submitter: Mahesh Binzer-Panchal

Marine Omics identifying biosynthetic gene clusters

Secondary metabolite biosynthetic gene cluster (SMBGC) Annotation using Neural Networks Trained on Interpro Signatures

Type: Galaxy

Creator: Marie Jossé

Submitter: Marie Jossé

cocomico_wf_simulated

CoCoMiCo analyses on collections of simulated communities. Community: scatterplots and KW tests of cooperation and competition potentials, for each collection. Similarity: cooperation and competition potentials vs model similarity, defined as the Jaccard distance on sets of reactions. Added value: boxplots comparing the added value of models in communities.

Type: Common Workflow Language

Creators: None

Submitter: David James Sherman

CEITEC layer 1 workflow
Work-in-progress

The second-level complexity workflow is one among a collection of workflows designed to address tasks up to CTF estimation. In addition to the functionalities provided by the layer 0 workflow, this workflow aims to enhance the quality of acquisition images using quality protocols.

Quality control protocols

  • Movie max shift: automatic reject those movies whose frames move more than a given threshold. 

  • Tilt analysis: quality score based in the Power Spectrum Density (astigmatism and ...

Type: Scipion

Creators: None

Submitters: Daniel Marchan, Pablo Conesa

CRYOSPARC: acquire -> motionCorr -> ctf -> report
Work-in-progress

SPA workflow using cryosparc processing engine

Type: Unrecognized workflow type

Creators: None

Submitter: Radek Veverka

SCIPION: acquire -> motionCorr -> ctf -> report
Work-in-progress

The simplest workflow among a collection of workflows intended to solve tasks up to CTF estimation.

Type: Scipion

Creators: None

Submitter: Daniel Marchan

IMPaCT-Data quality control workflow implementation in nf-core/Sarek

IMPaCT program

IMPaCT IMPaCT-isciii IMPaCT-Data ...

Type: Nextflow

Creators: Arnau Soler Costa, Amy Curwin, Jordi Rambla, All the Sarek team, nf-core comunity and people in the IMPaCT-Data project.

Submitter: Arnau Soler Costa

DOI: 10.48546/workflowhub.workflow.1030.2

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