Related items
- People (273)
- Teams (178)
- Organizations (173)
- Data files (1+1)
- Publications (18)
- Presentations (4+1)
- Documents (5+5)
- Workflows (239+21)
Teams: CO2MICS Lab
Organizations: Biomedical Research Foundation (BRFAA) of the Academy of Athens
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
![](/assets/logos/orcid_16x16-2bdaa944d31633ca5dea4eee7d642234ec7ac150641a49dea324b86087116986.png)
Teams: BSC-CES
Organizations: Barcelona Supercomputing Center (BSC-CNS)
Teams: OME, Euro-BioImaging
Organizations: University of Dundee, Euro-BioImaging
![](/assets/logos/orcid_16x16-2bdaa944d31633ca5dea4eee7d642234ec7ac150641a49dea324b86087116986.png)
Teams: Edinburgh Genomics
Organizations: University of Edinburgh
![](/assets/logos/orcid_16x16-2bdaa944d31633ca5dea4eee7d642234ec7ac150641a49dea324b86087116986.png)
Teams: VIB Bioinformatics Core, Euro-BioImaging
Organizations: VIB, Euro-BioImaging
![](/assets/logos/orcid_16x16-2bdaa944d31633ca5dea4eee7d642234ec7ac150641a49dea324b86087116986.png)
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
Space: Independent Teams
Public web page: https://usegalaxy.eu
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
Space: Independent Teams
Public web page: https://ega-archive.org/
Organisms: Not specified
Space: Independent Teams
Public web page: Not specified
Organisms: Not specified
Laboratory of Microbial Genomics and Systems/Synthetic Biology
Space: Independent Teams
Public web page: http://www.microbiome.re.kr/
Organisms: Not specified
Mid-Ohio Regional Planning Commission (MORPC) is the Metropolitan Planning Organization and Regional Council of Governments for a 15-county region in Central Ohio (USA).
Space: Independent Teams
Public web page: https://morpc.org
Organisms: Not specified
team dedicated to the development of the deepdefense software
Space: Independent Teams
Public web page: Not specified
Organisms: Not specified
In the Cancer Therapeutics and Drug Safety research group, headed by Bob Van de Water, cell signaling programs that underlie adverse drug reactions as well as cancer development and progression are unraveled. Adverse drug reactions involve cell injury in critical target organ cells which leads to the activation of cellular stress response signaling pathways. We study the molecular mechanisms of cellular stress response activation and control of cell survival and cell death. In the context of ...
Space: Independent Teams
Public web page: https://www.universiteitleiden.nl/en/science/drug-research/cell-systems-and-drug-safety/cancer-therapeutics-and-drug-safety
Organisms: Not specified
The adult neurooncology team of the Division of Neuropathology and Neurochemistry of the Medical University of Vienna.
Space: Independent Teams
Public web page: https://neurologie.meduniwien.ac.at/en/our-departments/division-of-neuropathology-and-neurochemistry/
Organisms: Not specified
Space: Independent Teams
Public web page: https://schwartzlab.ca/
Organisms: Not specified
Space: Independent Teams
Public web page: Not specified
Organisms: Not specified
Country: Australia
City: Camperdown
Web page: https://www.centenary.org.au/research/programs/molecular-cardiology-program/
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
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.
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
Example Workflow of Tutorial "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.
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.
pod5_by_pore
A Snakemake workflow to take the POD5 files produced by an Oxford Nanopore sequencing run and re-batch them by pore (ie. by channel).
This is useful if you want to run duplex basecalling because you can meaningfully run "dorado duplex" on a single (or a subset of) the POD5 files.
Know issues
It is assumed all POD5 input files are from the same sequencing run, but this is not checked.
beacon-omop-worker-workflows
GBMatch_CNN
Work in progress... Predicting TS & risk from glioblastoma whole slide images
Reference
Upcoming paper: stay tuned...
Dependencies
python 3.7.7
randaugment by Khrystyna Faryna: https://github.com/tovaroe/pathology-he-auto-augment
tensorflow 2.1.0
scikit-survival 0.13.1
pandas 1.0.3
lifelines 0.25.0
Description
The pipeline implemented here predicts transcriptional subtypes and survival of glioblastoma patients based on H&E stained whole slide scans. Sample data is ...
A hecatomb is a great sacrifice or an extensive loss. Heactomb the software empowers an analyst to make data driven decisions to 'sacrifice' false-positive viral reads from metagenomes to enrich for true-positive viral reads. This process frequently results in a great loss of suspected viral sequences / contigs.
For information about installation, usage, tutorial etc please refer to the documentation: https://hecatomb.readthedocs.io/en/latest/
Quick start guide
Install Hecatomb from Bioconda ...
With this galaxy pipeline you can use Salmonella sp. next generation sequencing results to predict bacterial AMR phenotypes and compare the results against gold standard Salmonella sp. phenotypes obtained from food.
This pipeline is based on the work of the National Food Agency of Canada. Doi: 10.3389/fmicb.2020.00549
JAX NGS Operations Nextflow DSL2 Pipelines
This repository contains production bioinformatic analysis pipelines for a variety of bulk 'omics data analysis. Please see the Wiki documentation associated with this repository for all documentation and available analysis workflows.
Type: Nextflow
Creators: Michael Lloyd, Brian Sanderson, Barry Guglielmo, Sai Lek, Peter Fields, Harshpreet Chandok, Carolyn Paisie, Gabriel Rech, Ardian Ferraj, Anuj Srivastava
Submitter: Michael Lloyd
Complete workflow for TANGO as reported in Lecomte et al (2024), "Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling", Metabolic Eng. 83:24-38 https://doi.org/10.1016/j.ymben.2024.02.014
- Parameters for individual models are obtained by optimization
- Individual dynamics and community dynamics are simulated
- Figures for the manuscript are assembled from the results.