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- People (251)
- Teams (165)
- Organizations (160)
- Data files (1)
- Publications (17)
- Presentations (4+1)
- Documents (5+5)
- Workflows (229+18)
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
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: 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/0000-0001-6691-4233The 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
Space: Independent Teams
Public web page: https://github.com/oda-hub
Organisms: Not specified
Space: Independent Teams
Public web page: Not specified
Organisms: Not specified
Space: Independent Teams
Public web page: Not specified
Organisms: Not specified
Nextflow pipelines for metabolomics data
Space: Independent Teams
Public web page: https://github.com/Nextflow4Metabolomics
Organisms: Not specified
Space: Independent Teams
Public web page: https://www.kalbe.co.id/
Organisms: Not specified
The main goal of Ewoks is to automate data processing and experiments at large-scale facilities as well as making data processing more scientific (reproducible) and FAIR (traceable). Ewoks is not yet another workflow management system. To ensure the longevity of workflows and their implementation, Ewoks was designed to be a meta workflow system. This allows workflows to be isolated from the underlying software technologies used to execute and manage them.
Space: Independent Teams
Public web page: https://ewoks.esrf.fr/en/latest/
Organisms: Not specified
Bioinformatic pipelines generated as part of the Clark research group at the Natrual History Museum London.
Space: Independent Teams
Public web page: Not specified
Organisms: Not specified
Junk/test data
Space: Independent Teams
Public web page: Not specified
Organisms: Not specified
EMBL Centre for Bioimage Analysis
Space: Independent Teams
Public web page: Not specified
Organisms: Not specified
Space: Independent Teams
Public web page: Not specified
Organisms: Not specified
Quality critical distributed computing
Space: Independent Teams
Public web page: Not specified
Organisms: Not specified
Medical bioinformatics group of the Medical Proteome Center at the Ruhr University Bochum
Space: Independent Teams
Public web page: https://www.mpc.ruhr-uni-bochum.de/
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 repository contains the workflow files (.ga) for this project.
Space: Independent Teams
Public web page: Not specified
Organisms: Not specified
Space: Independent Teams
Public web page: https://openbioimageanalysis.org/
Organisms: Not specified
In view of the complexity in modeling phylogenetic network experiments, the present work introduces a workflow for phylogenetic network analyses coupled to be executed in High-Performance Computing (HPC) environments. The workflow aims to integrate well-established software, pipelines and scripts, implementing a challenging task since these tools do not consistently profit from the HPC environment, leading to an increase in the expected makespan and idle computing resources.
Space: Independent Teams
Public web page: https://github.com/rafaelstjf/biocomp
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)
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
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 ...
beacon-omop-worker-workflows
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.
ProGFASTAGen
The ProGFASTAGen (Protein-Graph-FASTA-Generator or ProtGraph-FASTA-Generator) repository contains workflows to generate so-called precursor-specific-FASTAs (using the precursors from MGF-files) including feature-peptides, like VARIANTs or CONFLICTs if desired, or global-FASTAs (as described in ProtGraph). The single workflow scripts have been implemented with Nextflow-DSL-2 ...
The input to this workflow is a data matrix of gene expression that was collected from a pediatric patient tumor patient from the KidsFirst Common Fund program [1]. The RNA-seq samples are the columns of the matrix, and the rows are the raw expression gene count for all human coding genes (Table 1). This data matrix is fed into TargetRanger [2] to screen for targets which are highly expressed in the tumor but lowly expressed across most healthy human tissues based on gene expression data collected ...
The tool provides a calculation of the power spectrum of Stochastic Gravitational Wave Backgorund (SGWB) from a first-order cosmological phase transition based on the parameterisations of Roper Pol et al. (2023). The power spectrum includes two components: from the sound waves excited by collisions of bubbles of the new phase and from the turbulence that is induced by these collisions.
The cosmological epoch of the phase transition is described by the temperature, T_star and by the number(s) of ...
Type: Galaxy
Creators: Andrii Neronov, Théo Boyer, Denys Savchenko, Volodymyr Savchenko
Submitter: Denys Savchenko
gene2phylo
gene2phylo is a snakemake pipeline for batch phylogenetic analysis of a given set of input genes.
Contents
Setup
The pipeline is written in Snakemake and uses conda to install the necessary tools.
It is strongly recommended to install conda using Mambaforge. See details here ...
skim2rrna
skim2rrna is a snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of ribosomal genes from low coverage genome skims. The pipeline was designed to work with sequence data from museum collections. However, it should also work with genome skims from recently collected samples.
Contents
- Setup
- Example data
- Input
- Output
- Filtering contaminants
- [Assembly and annotation ...
skim2mt
skim2mt is a snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes from low coverage genome skims. The pipeline was designed to work with sequence data from museum collections. However, it should also work with genome skims from recently collected samples.
Contents
- Setup
- Example data
- Input
- Output
- Filtering contaminants
- [Assembly and annotation ...
score-assemblies
A Snakemake-wrapper for evaluating de novo bacterial genome assemblies, e.g. from Oxford Nanopore (ONT) or Illumina sequencing.
The workflow includes the following programs:
...
ont-assembly-snake
A Snakemake wrapper for easily creating de novo bacterial genome assemblies from Oxford Nanopore (ONT) sequencing data, and optionally Illumina data, using any combination of read filtering, assembly, long and short read polishing, and reference-based polishing.
Included programs
read filtering | assembly | long read polishing | short read polishing | reference-based polishing |
---|---|---|---|---|
Filtlong | ||||
... |
This project is about the automated quantification of wound healing in high-throughput microscopy scratch assays.
This is a Galaxy workflow for performing molecular dynamics simulations and analysis with flavivirus helicases in the Apo or unbound state. The associated input files can be found at: https://zenodo.org/records/7493015 The associated output files can be found at: https://zenodo.org/records/7850935
This is a Galaxy workflow for performing molecular dynamics simulations and analysis with coronavirus helicases bound to a ligand/drug molecule. The associated input files can be found at: https://zenodo.org/records/7492987. The associated output files can be found at: https://zenodo.org/records/7851000.
This is a Galaxy workflow for performing molecular dynamics simulations and analysis with coronavirus helicases in the Apo or unbound state. The associated input files can be found at: https://zenodo.org/records/7492987. The associated output files can be found at: https://zenodo.org/records/7851000.