The impact of Docker containers on the performance of genomic pipelines

Autor: Paolo Di Tommaso, Emilio Palumbo, Maria Chatzou, Pablo Prieto, Michael L. Heuer, Cedric Notredame

Publikováno v: PeerJ, Vol 3, p e1273 (2015)

Genomic pipelines consist of several pieces of third party software and, because of their experimental nature, frequent changes and updates are commonly necessary thus raising serious deployment and reproducibility issues. Docker containers are emerg

Externí odkaz: https://doaj.org/article/0e8cf15c6a164b10b92cabc7f498a043

Multi-party trusted research environment federation: Establishing infrastructure for secure analysis across different clinical-genomic datasets

Autor: Nik-Zainal, Professor Serena, Seeger, Thorben, Fennessy, Rosanna, Hall, Eleanor, Moss, Parker, Coles, Geoff, Dunford, Maria Chatzou, Barja, Pablo Prieto, Avery, Mark, Raine, Keiran

Combining data assets for research has historically involved the movement of data between organisations. Trusted Research Environments (TREs) now offer an alternative to data sharing by providing secure environments for approved researchers to access

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cc1ea0ba6a2e8f3e610fbbc1d5b189e1

PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases

Autor: Evan Floden, Jia-Ming Chang, Cedrik Magis, Paolo Di Tommaso, Cedric Notredame, Maria Chatzou

Publikováno v: Nucleic Acids Research
Recercat. Dipósit de la Recerca de Catalunya
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The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches aga

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5e567ab8f052731206055766bb4d9514
http://europepmc.org/articles/PMC4987888

Using the Nextflow framework for reproducible in-silico omics analyses across clusters and clouds

Autor: Cedric Notredame, Maria Chatzou, Paolo Di Tommaso, Evan Floden

Reproducibility has become one of biology’s most pressing issues. This impasse has been fuelled by the combined reliance on increasingly complex data analysis methods and the exponential growth of biological datasets. Nextflow is a pipeline orchest

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3200b4e27c8de6c163f1fff85eff7bf7

Generalized Bootstrap Supports for Phylogenetic Analyses of Protein Sequences Incorporating Alignment Uncertainty

Autor: Olivier Gascuel, Maria Chatzou, Paolo Di Tommaso, Cedric Notredame, Evan Floden

Publikováno v: Systematic Biology
Systematic Biology, Oxford University Press (OUP), 2018, 67 (6), pp.997-1009. ⟨10.1093/sysbio/syx096⟩
Systematic Biology, 2018, 67 (6), pp.997-1009. ⟨10.1093/sysbio/syx096⟩

International audience; Phylogenetic reconstructions are essential in genomics data analyses and depend on accurate multiple sequence alignment (MSA) models. We show that all currently available large-scale progressive multiple alignment methods are

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::55c08448f453d12a6271bf9413b571d6
https://pubmed.ncbi.nlm.nih.gov/30295908