Related items
- People (284)
- Teams (182)
- Organizations (177)
- Data files (1+1)
- Publications (18)
- Presentations (4+1)
- Documents (5+5)
- Workflows (248+22)
Teams: CO2MICS Lab
Organizations: Biomedical Research Foundation (BRFAA) of the Academy of Athens
Teams: Medvedeva Lab
Organizations: Moscow Institute of Physics and Technology
Teams: MLme: Machine Learning Made Easy
Organizations: University of Bern
Teams: UX trial team
Organizations: The University of Manchester
Teams: IBISBA Workflows
Organizations: The University of Manchester
Teams: SKM3
Organizations: The Open University
Teams: Institute of Human Genetics
Organizations: Centre National de la Recherche Scientifique (CNRS)
Teams: IBISBA Workflows, nf-core viralrecon, Testing, Defragmentation TS, EuroScienceGateway, ELIXIR Training
Organizations: The University of Manchester
Expertise: Bioinformatics
Teams: EJPRD WP13 case-studies workflows
Organizations: EJP-RD
https://orcid.org/0000-0002-0637-9950Teams: BSC-CES
Organizations: Barcelona Supercomputing Center (BSC-CNS)
Teams: OME, Euro-BioImaging
Organizations: University of Dundee, Euro-BioImaging
https://orcid.org/0000-0001-8783-1429Teams: NBIS, ERGA Assembly
Organizations: NBIS – National Bioinformatics Infrastructure Sweden
https://orcid.org/0000-0003-1675-0677Expertise: Bioinformatics, Genomics, Scientific workflow developement, Workflows
I'm a bioinformatician for the National Bioinformatics Infrastrure Sweden. I specialise in de novo genome assembly and workflow development with Nextflow. I'm also a Nextflow ambassador and nf-core maintainer.
Teams: Edinburgh Genomics
Organizations: University of Edinburgh
https://orcid.org/0000-0003-2470-9519Teams: VIB Bioinformatics Core, Euro-BioImaging
Organizations: VIB, Euro-BioImaging
https://orcid.org/0000-0001-6691-4233Space: Independent Teams
Public web page: https://ega-archive.org/
Organisms: Not specified
Space: Independent Teams
Public web page: Not specified
Organisms: Not specified
Protein-protein and protein-nucleic acid binding site prediction via interpretable hierarchical geometric deep learning
Space: Independent Teams
Public web page: http://www.liulab.top/GraphRBF
Organisms: Not specified
Space: Independent Teams
Public web page: https://usegalaxy.eu
Organisms: Not specified
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.
Space: Independent Teams
Public web page: https://fairease.eu/
Organisms: Not specified
Space: Independent Teams
Public web page: Not specified
Organisms: Not specified
The Snakemake-Workflows team develops best practice workflows for Snakemake
Space: Independent Teams
Public web page: https://github.com/snakemake-workflows
Organisms: Not specified
Space: Independent Teams
Public web page: https://kircherlab.bihealth.org
Organisms: Not specified
Space: Independent Teams
Public web page: Not specified
Organisms: Not specified
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 ...
Space: Independent Teams
Public web page: https://www.bsc.es/discover-bsc/organisation/scientific-structure/computational-earth-sciences
Organisms: Not specified
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 ...
Space: Independent Teams
Public web page: https://crim.ca
Organisms: Not specified
Fungal Genomics and Industrial Applications Lab
Space: Independent Teams
Public web page: https://fungialab.iata.csic.es/
Organisms: Not specified
Scipion team located at the National Centre for Biotechnology (CNB, CSIC)
Space: Independent Teams
Public web page: https://scipion.i2pc.es/
Organisms: Not specified
Space: Independent Teams
Public web page: Not specified
Organisms: Not specified
This is a test WorkflowHub Account
Space: Independent Teams
Public web page: Not specified
Organisms: Not specified
Space: Independent Teams
Public web page: https://krauthammerlab.ch/
Organisms: Not specified
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.
Space: Independent Teams
Public web page: https://www.plantandfood.com
Organisms: Not specified
MOLGENIS team Genomics Coordination Center, Department of Genetics, University Medical Center Groningen (UMCG)
Space: Independent Teams
Public web page: http://molgenis.org
Organisms: Not specified
EJPRD WP13 case-studies workflows from phase 1.
Space: Independent Teams
Public web page: https://www.ejprarediseases.org/
Organisms: Not specified
Space: Independent Teams
Public web page: https://www.ukaachen.de/kliniken-institute/institut-fuer-humangenetik-und-genommedizin/institut/
Organisms: Not specified
Country: Australia
City: Camperdown
Web page: https://www.centenary.org.au/research/programs/molecular-cardiology-program/
Country: Switzerland
City: Lausanne
Web page: https://www.chuv.ch/en/microbiologie/imu-home/diagnostics/genomics-and-metagenomics
Download all genome from https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide with filter host:viridiplantae and Refseq on.
Creator: johan Rollin
Submitter: johan Rollin
Abstract (Expand)
Authors: W.T.K. Maassen, L.F. Johansson, B. Charbon, D. Hendriksen, S. van den Hoek, M.K. Slofstra, R. Mulder, M.T. Meems-Veldhuis, R. Sietsma, H.H. Lemmink, C.C. van Diemen, M.E. van Gijn, M.A. Swertz, K.J. van der Velde
Date Published: 15th Apr 2024
Publication Type: Unpublished
DOI: 10.1101/2024.04.11.24305656
Citation: medrxiv;2024.04.11.24305656v2,[Preprint]
Abstract (Expand)
Author: Yasmmin Martins
Date Published: 28th Sep 2023
Publication Type: Journal
DOI: 10.1101/2023.09.27.23296213
Citation: medrxiv;2023.09.27.23296213v1,[Preprint]
Abstract (Expand)
Authors: Yasmmin Côrtes Martins, Ronaldo Francisco da Silva
Date Published: 27th Sep 2023
Publication Type: Journal
DOI: 10.1101/2023.09.26.559599
Citation: biorxiv;2023.09.26.559599v1,[Preprint]
Abstract (Expand)
Authors: Yasmmin Martins, Ronaldo Francisco da Silva
Date Published: 22nd Jun 2023
Publication Type: Journal
DOI: 10.1101/2023.06.22.546079
Citation: biorxiv;2023.06.22.546079v1,[Preprint]
Abstract (Expand)
Author: Yasmmin C Martins
Date Published: 7th Jun 2023
Publication Type: Journal
DOI: 10.1101/2023.06.05.543725
Citation: biorxiv;2023.06.05.543725v1,[Preprint]
Abstract (Expand)
Authors: Yasmmin Côrtes Martins, Artur Ziviani, Maiana de Oliveira Cerqueira e Costa, Maria Cláudia Reis Cavalcanti, Marisa Fabiana Nicolás, Ana Tereza Ribeiro de Vasconcelos
Date Published: 2023
Publication Type: Journal
Citation: Bioinformatics Advances 3(1),vbad067
Abstract (Expand)
Authors: Rafael Terra, Kary Ocaña, Carla Osthoff, Lucas Cruz, Philippe Navaux, Diego Carvalho
Date Published: 19th Oct 2022
Publication Type: InProceedings
DOI: 10.5753/wscad.2022.226366
Citation: Anais do XXIII Simpósio em Sistemas Computacionais de Alto Desempenho (WSCAD 2022),pp.73-84,Sociedade Brasileira de Computação
Abstract (Expand)
Authors: Andrzej Oleksa, Eliza Căuia, Adrian Siceanu, Zlatko Puškadija, Marin Kovačić, M. Alice Pinto, Pedro João Rodrigues, Fani Hatjina, Leonidas Charistos, Maria Bouga, Janez Prešern, Irfan Kandemir, Slađan Rašić, Szilvia Kusza, Adam Tofilski
Date Published: 1st Oct 2022
Publication Type: Journal
Citation:
Abstract (Expand)
Authors: Rafael Terra, Kary Ocaña, Carla Osthoff, Diego Carvalho
Date Published: 18th Feb 2022
Publication Type: Master's Thesis
Citation: TERRA, R. S. Framework para execução de workflows de redes filogenéticas em ambientes de computação de alto desempenho. 2022. 71 f. Tese. (Programa de Pós-Graduação em Modelagem Computacional) - Laboratório Nacional de Computação Científica, Petrópolis, 2022.
Abstract (Expand)
Authors: Yasmmin Côrtes Martins, Artur Ziviani, Marisa Fabiana Nicolás, Ana Tereza Ribeiro de Vasconcelos
Date Published: 6th Sep 2021
Publication Type: Journal
DOI: 10.3389/fbinf.2021.731345
Citation: Front. Bioinform. 1,731345
Abstract (Expand)
Authors: Rafael Terra, Micaella Coelho, Lucas Cruz, Marco Garcia-Zapata, Luiz Gadelha, Carla Osthoff, Diego Carvalho, Kary Ocaña
Date Published: 18th Jul 2021
Publication Type: InProceedings
DOI: 10.5753/bresci.2021.15788
Citation: Anais do XV Brazilian e-Science Workshop (BRESCI 2021),pp.49-56,Sociedade Brasileira de Computação
Abstract (Expand)
Authors: Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić, Hervé Ménager, Stian Soiland-Reyes, Carole Goble
Date Published: 14th May 2021
Publication Type: Unpublished
Citation: arXiv 2105.07028 [cs.DC]
Abstract
Authors: Anna-Lena Lamprecht, Magnus Palmblad, Jon Ison, Veit Schwämmle, Mohammad Sadnan Al Manir, Ilkay Altintas, Christopher J. O. Baker, Ammar Ben Hadj Amor, Salvador Capella-Gutierrez, Paulos Charonyktakis, Michael R. Crusoe, Yolanda Gil, Carole Goble, Timothy J. Griffin, Paul Groth, Hans Ienasescu, Pratik Jagtap, Matúš Kalaš, Vedran Kasalica, Alireza Khanteymoori, Tobias Kuhn, Hailiang Mei, Hervé Ménager, Steffen Möller, Robin A. Richardson, Vincent Robert, Stian Soiland-Reyes, Robert Stevens, Szoke Szaniszlo, Suzan Verberne, Aswin Verhoeven, Katherine Wolstencroft
Date Published: 2021
Publication Type: Journal
DOI: 10.12688/f1000research.54159.1
Citation: F1000Res 10:897
Abstract (Expand)
Authors: Cristina S. Ferreira, Yasmmin C. Martins, Rangel Celso Souza, Ana Tereza R. Vasconcelos
Date Published: 2021
Publication Type: Journal
DOI: 10.7717/peerj.12548
Citation: PeerJ 9:e12548
Abstract
Authors: Carole Goble, Sarah Cohen-Boulakia, Stian Soiland-Reyes, Daniel Garijo, Yolanda Gil, Michael R. Crusoe, Kristian Peters, Daniel Schober
Date Published: 2020
Publication Type: Journal
DOI: 10.1162/dint_a_00033
Citation: Data Intellegence 2(1-2):108-121
Abstract (Expand)
Authors: Yasmmin Cortes Martins, Maria Cláudia Cavalcanti, Luis Willian Pacheco Arge, Artur Ziviani, Ana Tereza Ribeiro de Vasconcelos
Date Published: 2019
Publication Type: Journal
DOI: 10.1007/978-3-030-36599-8_23
Citation: Metadata and Semantic Research 1057:260-271,Springer International Publishing
Abstract (Expand)
Authors: Anna Nawrocka, Irfan Kandemir, Stefan Fuchs, Adam Tofilski
Date Published: 1st Apr 2018
Publication Type: Journal
Citation:
Abstract (Expand)
Authors: Yasmmin Cortes Martins, Fábio Faria da Mota, Maria Cláudia Cavalcanti
Date Published: 2016
Publication Type: Journal
DOI: 10.1007/978-3-319-49157-8_29
Citation: Metadata and Semantics Research 672:333-344,Springer International Publishing
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.
Creator: Daniel Marchan
Submitter: Daniel Marchan
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 ...
Creator: Mahnoor Zulfiqar
Submitter: Mahnoor Zulfiqar
Creator: Jasper Koehorst
Submitter: Jasper Koehorst
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 ...
Creators: Hrishikesh Dhondge, Isaure Chauvot de Beauchêne, Marie-Dominique Devignes
Submitter: Hrishikesh Dhondge
Creator: Jean-Marie Burel
Submitter: Jean-Marie Burel
Creator: panou@fleming.gr Panou
Submitter: panou@fleming.gr Panou
Creator: johan Rollin
Submitter: johan Rollin
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.
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
Type: Nextflow
Creators: Usman Rashid, Chen Wu, Jason Shiller, Ken Smith, Ross Crowhurst, Marcus Davy, Ting-Hsuan Chen, Susan Thomson, Cecilia Deng
Submitter: Usman Rashid
Workflow for gene set enrichment analsysis (GSEA) and co-expression analysis (WGCNA) on transcriptomics data to analyze pathways affected in Porto-Sinusoidal Vascular Disease.
Type: Common Workflow Language
Creators: Aishwarya Iyer, Friederike Ehrhart
Submitter: Aishwarya Iyer
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.