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

A new approach to observation and modelling of the Earth System, Environment and Biodiversity. An easy way to visualise, analyse and process environmental data on-demand.

The Snakemake-Workflows team develops best practice workflows for Snakemake

The Computational Earth Sciences (CES) group is a multidisciplinary team with different technical profiles that closely relates to all the other groups in the department. CES supports scientists in their daily work and provides a framework for the most efficient use of IT resources, specializing in HPC. At the same time, the group has different research lines related to profiling and optimization and porting Earth modeling codes toward Exascale computing. The group has links and collaborations ...

The Computer Research Institute of Montreal (CRIM) is a leading center for applied research and cutting-edge expertise in artificial intelligence and information technology. It generates concrete results and serves as a strategic partner for organizations focused on innovation.CRIM creates socio-economic value from scientific and technological advances through:- Support: providing companies access to experts who answer scientific and technological questions.- Applied research: contributing to ...

Fungal Genomics and Industrial Applications Lab

Scipion team located at the National Centre for Biotechnology (CNB, CSIC)

This is a test WorkflowHub Account

The New Zealand Institute for Plant and Food Research Limited is a New Zealand government-owned Crown Research Institute, subject to the Crown Entities Act 2004, the Crown Research Institutes Act 1992 and the Companies Act 1993.

MOLGENIS team Genomics Coordination Center, Department of Genetics, University Medical Center Groningen (UMCG)

EJPRD WP13 case-studies workflows from phase 1.

Download all genome from https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide with filter host:viridiplantae and Refseq on.

This document provides a detailed explanation of all the workflows, including their functionalities, problems they address, advantages, disadvantages, implementation requirements, and open points for future versions.

In the age of high-throughput data, computational workflows have made data processing tasks flexible, manageable, and automated. To administer different computational activities in a workflow, different workflow management systems (WMS) are used that necessitate a sophisticated level of standardisation. Standardisation and reproducibility can be achieved by using standard formats for specifying workflows, such as Common Workflow Language (CWL), and provenance gathering with the standard W3C PROV ...

Poster and presentation video by Ambarish Kumar

Protein domains can be viewed as building blocks, essential for understanding structure-function relationships in proteins. However, each domain database classifies protein domains using its own methodology. Thus, in many cases, boundaries between different domains or families differ from one domain database to the other, raising the question of domain definition and enumeration. The answer to this question cannot be found in a single database. Rather, expert integration and curation of various ...

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
...

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

EuCanImage FHIR ETL Implementation

This repository contains the ETL implementation for EuCanImage, encouraging semantic interoperability of the clinical data obtained in the studies by transforming it into a machine-readable format following FHIR standards. This parser uses FHIR Resources in order to create the dictionaries following a FHIR compliant structure.

• Code Language is written in Python 3.11. ...

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 ...

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
...

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

cfDNA UniFlow is a unified, standardized, and ready-to-use workflow for processing whole genome sequencing (WGS) cfDNA samples from liquid biopsies. It includes essential steps for pre-processing raw cfDNA samples, quality control and reporting. Additionally, several optional utility functions like GC bias correction and estimation of copy number state are included. Finally, we provide specialized methods for extracting coverage derived signals and visualizations comparing cases and controls. ...

This workflow takes a cell-type-annotated AnnData object (processed with SnapATAC2) and performs peak calling with MACS3 on the cell types. Next, a cell-by-peak matrix is constructed and differential accessibility tests are performed for comparison of either two cell types or one cell type with a background of all other cells. Lastly, differentially accessible marker regions for each cell type are identified.

This Workflow takes a dataset collection of single-cell ATAC-seq fragments and performs:

• preprocessing
• filtering
• concatenation
• dimension reduction
• batch correction (with Harmony and optionally Scanorama and MNC-correct)
• leiden clustering

• new SnapATAC2 version: from 2.5.3 to 2.6.4

Workflow for Single-cell ATAC-seq standard processing with SnapATAC2. This workflow takes a fragment file as input and performs the standard steps of scATAC-seq analysis: filtering, dimension reduction, embedding and visualization of marker genes with SnapATAC2. Finally, the clusters are manually annotated with the help of marker genes. In an alternative step, the fragment file can also be generated from a BAM file.

• newer Version: Updated SnapATAC2 version from 2.5.3 to 2.6.4

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.

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 ...

SPA workflow using cryosparc processing engine

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

...

...

Workflow for gene set enrichment analsysis (GSEA) and co-expression analysis (WGCNA) on transcriptomics data to analyze pathways affected in Porto-Sinusoidal Vascular Disease.

Predict variants and drug resistance from M. tuberculosis sequence samples (Illumina)

Variant Interpretation Pipeline (VIP) that annotates, filters and reports prioritized causal variants in humans, see https://github.com/molgenis/vip for more information.