Keyword - Software

Federated privacy-protected meta- and mega-omics data analysis in multi-center studies with a fully open-source analytic platform.
Escriba-Montagut, Xavier; Marcon, Yannick; Anguita-Ruiz, Augusto; Avraam, Demetris; Urquiza, Jose; Morgan, Andrei S; Wilson, Rebecca C; Burton, Paul; Gonzalez, Juan R
PLoS Comput Biol, Volume 20, Issue 12 (2024)
PMID: 39652598 DOI: 10.1371/journal.pcbi.1012626 
Citations: 1 (Scopus)
Tags: Consortia: ATHLETE | Consortia: CERCA | Consortia: CINECA | Consortia: Consolidated Group on Health Analytics | Consortia: EUCAN-Connect | Consortia: IBEC | Consortia: PERIS | Type: software engineering

MOLGENIS Armadillo: a lightweight server for federated analysis using DataSHIELD.
Cadman, Tim; Slofstra, Mariska K; van der Geest, Marije A; Avraam, Demetris; Bishop, Tom R P; de Boer, Tommy; Duijts, Liesbeth; Haakma, Sido; Hyde, Eleanor; Jaddoe, Vincent; Karramass, Tarik; Kelpin, Fleur; Marcon, Yannick; Pinot de Moira, Angela; Postma, Dick; Tolboom, Clemens; Veenstra, Ruben L; Wheater, Stuart; Welten, Marieke; Wilson, Rebecca C; Zwart, Erik; Swertz, Morris
Bioinformatics, Volume 41, Issue 1 (2024)
PMID: 39673440 DOI: 10.1093/bioinformatics/btae726 
Citations: 1 (Scopus)
Tags: Consortia: ATHLETE | Consortia: EUCAN-Connect | Consortia: LifeCycle | Type: data systems | Type: software engineering

dsMTL: a computational framework for privacy-preserving, distributed multi-task machine learning.
Cao, Han; Zhang, Youcheng; Baumbach, Jan; Burton, Paul R; Dwyer, Dominic; Koutsouleris, Nikolaos; Matschinske, Julian; Marcon, Yannick; Rajan, Sivanesan; Rieg, Thilo; Ryser-Welch, Patricia; Späth, Julian; Herrmann, Carl; Schwarz, Emanuel
Bioinformatics, Volume 38, Issue 21 (2022)
PMID: 36073911 DOI: 10.1093/bioinformatics/btac616 
Citations: 8 (Scopus)
Tags: Study: GSE21138  | Study: GSE35977 | Study: GSE53987 | Study: phs000979.v3.p2 | Type: data systems | Type: proof of concept | Type: software engineering

Orchestrating privacy-protected big data analyses of data from different resources with R and DataSHIELD.
Marcon, Yannick; Bishop, Tom; Avraam, Demetris; Escriba-Montagut, Xavier; Ryser-Welch, Patricia; Wheater, Stuart; Burton, Paul; González, Juan R
PLoS Comput Biol, Volume 17, Issue 3 (2021)
PMID: 33784300 DOI: 10.1371/journal.pcbi.1008880 
Citations: 29 (Scopus)
Tags: Consortia: ATHLETE | Consortia: Connected Health Cities North East North Cumbria | Consortia: EUCAN-Connect | Consortia: VEIS: 001-P-001647 | Type: data systems | Type: software engineering

Deep generative models in DataSHIELD.
Lenz, Stefan; Hess, Moritz; Binder, Harald
BMC Med Res Methodol, Volume 21, Issue 1 (2021)
PMID: 33812380 DOI: 10.1186/s12874-021-01237-6 
Citations: 15 (Scopus)
Tags: Consortia: GEMOLS | Consortia: MIRACUM | Type: data systems | Type: proof of concept | Type: software engineering

A Queue-Poll Extension and DataSHIELD: Standardised, Monitored, Indirect and Secure Access to Sensitive Data.
Gruendner, Julian; Prokosch, Hans-Ulrich; Schindler, Sebastian; Lenz, Stefan; Binder, Harald
Stud Health Technol Inform, Volume 258 (2019)
PMID: 30942726 DOI: 10.3233/978-1-61499-959-1-115 
Citations: 5 (Scopus)
Tags: Consortia: MIRACUM | Study: Erlangen University Hospital | Study: Freiburg University Hospital | Study: Magdeburg University Hospital | Type: data governance | Type: software engineering

Software Application Profile: Opal and Mica: open-source software solutions for epidemiological data management, harmonization and dissemination.
Doiron, Dany; Marcon, Yannick; Fortier, Isabel; Burton, Paul; Ferretti, Vincent
Int J Epidemiol, Volume 46, Issue 5 (2017)
PMID: 29025122 DOI: 10.1093/ije/dyx180 
Citations: 69 (Scopus)
Tags: Consortia: BioSHaRE-EU | Consortia: InterConnect | Consortia: Maelstrom Research | Study: CLSA | Study: CPTP | Type: data harmonization | Type: software engineering

Genomic cloud computing: legal and ethical points to consider.
Dove, Edward S; Joly, Yann; Tassé, Anne-Marie; Knoppers, Bartha M
Eur J Hum Genet, Volume 23, Issue 10 (2015)
PMID: 25248396 DOI: 10.1038/ejhg.2014.196 
Citations: 76 (Scopus)
Tags: Consortia: International Cancer Genome Consortium | Consortia: P3G | Type: data governance | Type: software engineering