A taxonomy of tools and approaches for distributed genomic analyses

The amount of biomedical data collected and stored has grown significantly. Analyzing these extensive amounts of data cannot be done by individuals or single organizations anymore. Thus, the scientific community is creating global collaborative efforts to analyze these data. However, biomedical data...

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Autores:
Garzón, Wilmer
Benavides, Luis Alberto
Gignard, Alban
Südholt, Mario
Tipo de recurso:
Article of journal
Fecha de publicación:
2022
Institución:
Escuela Colombiana de Ingeniería Julio Garavito
Repositorio:
Repositorio Institucional ECI
Idioma:
eng
OAI Identifier:
oai:repositorio.escuelaing.edu.co:001/3156
Acceso en línea:
https://repositorio.escuelaing.edu.co/handle/001/3156
https://repositorio.escuelaing.edu.co/
Palabra clave:
Biometría
Biometry
Análisis de la información
Information analysis
Investigación biomédica
Biomedical research
Tecnología médica
Medical technology
Distributed biomedical analyses
Fully distributed collaborations
Reproducibility
Scalability Multi-site analyses
Distributed workflow analyses
Análisis biomédicos distribuidos
Colaboraciones totalmente distribuidas
Reproducibilidad
Análisis de escalabilidad multisitio
Análisis de flujo de trabajo distribuido
Rights
openAccess
License
http://purl.org/coar/access_right/c_abf2
id ESCUELAIG2_5d5f54a6d7c352f15aa23341e2ebbb11
oai_identifier_str oai:repositorio.escuelaing.edu.co:001/3156
network_acronym_str ESCUELAIG2
network_name_str Repositorio Institucional ECI
repository_id_str
dc.title.eng.fl_str_mv A taxonomy of tools and approaches for distributed genomic analyses
title A taxonomy of tools and approaches for distributed genomic analyses
spellingShingle A taxonomy of tools and approaches for distributed genomic analyses
Biometría
Biometry
Análisis de la información
Information analysis
Investigación biomédica
Biomedical research
Tecnología médica
Medical technology
Distributed biomedical analyses
Fully distributed collaborations
Reproducibility
Scalability Multi-site analyses
Distributed workflow analyses
Análisis biomédicos distribuidos
Colaboraciones totalmente distribuidas
Reproducibilidad
Análisis de escalabilidad multisitio
Análisis de flujo de trabajo distribuido
title_short A taxonomy of tools and approaches for distributed genomic analyses
title_full A taxonomy of tools and approaches for distributed genomic analyses
title_fullStr A taxonomy of tools and approaches for distributed genomic analyses
title_full_unstemmed A taxonomy of tools and approaches for distributed genomic analyses
title_sort A taxonomy of tools and approaches for distributed genomic analyses
dc.creator.fl_str_mv Garzón, Wilmer
Benavides, Luis Alberto
Gignard, Alban
Südholt, Mario
dc.contributor.author.none.fl_str_mv Garzón, Wilmer
Benavides, Luis Alberto
Gignard, Alban
Südholt, Mario
dc.contributor.researchgroup.spa.fl_str_mv CTG - Informática
dc.subject.armarc.none.fl_str_mv Biometría
Biometry
Análisis de la información
Information analysis
Investigación biomédica
Biomedical research
Tecnología médica
Medical technology
topic Biometría
Biometry
Análisis de la información
Information analysis
Investigación biomédica
Biomedical research
Tecnología médica
Medical technology
Distributed biomedical analyses
Fully distributed collaborations
Reproducibility
Scalability Multi-site analyses
Distributed workflow analyses
Análisis biomédicos distribuidos
Colaboraciones totalmente distribuidas
Reproducibilidad
Análisis de escalabilidad multisitio
Análisis de flujo de trabajo distribuido
dc.subject.proposal.eng.fl_str_mv Distributed biomedical analyses
Fully distributed collaborations
Reproducibility
Scalability Multi-site analyses
Distributed workflow analyses
dc.subject.proposal.spa.fl_str_mv Análisis biomédicos distribuidos
Colaboraciones totalmente distribuidas
Reproducibilidad
Análisis de escalabilidad multisitio
Análisis de flujo de trabajo distribuido
description The amount of biomedical data collected and stored has grown significantly. Analyzing these extensive amounts of data cannot be done by individuals or single organizations anymore. Thus, the scientific community is creating global collaborative efforts to analyze these data. However, biomedical data is subject to several legal and socio- economic restrictions hindering the possibilities for research collaboration. In this paper, we argue that researchers require new tools and techniques to address the restrictions and needs of global scientific collaborations over geo-distributed biomedical data. These tools and techniques must support what we call Fully Distributed Collaborations (FDC), which are research endeavors that harness means to exploit and analyze massive biomedical information collaboratively while respecting legal and socio-economical restrictions. This paper first motivates and discusses the requirements of FDCs in the context of a research collaboration on the development of diagnostic and predictive tools for the risk of intracranial aneurysm formation and rupture (the ICAN project). The paper then presents a taxonomy classifying the current tools and techniques for biomedical analysis with respect to the proposed requirements. The taxonomy considers three key architectural features to support FDC scenarios: data and computation placement, Privacy and Security, and Performance and Scalability. The review reveals new research opportunities to design tools and techniques for multi-site analyses encouraging scientific collaborations while mitigating technical and legal constraints.
publishDate 2022
dc.date.issued.none.fl_str_mv 2022
dc.date.accessioned.none.fl_str_mv 2024-07-11T16:51:03Z
dc.date.available.none.fl_str_mv 2024-07-11T16:51:03Z
dc.type.spa.fl_str_mv Artículo de revista
dc.type.coar.fl_str_mv http://purl.org/coar/resource_type/c_2df8fbb1
dc.type.coarversion.fl_str_mv http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.version.spa.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.coar.spa.fl_str_mv http://purl.org/coar/resource_type/c_6501
dc.type.content.spa.fl_str_mv Text
dc.type.driver.spa.fl_str_mv info:eu-repo/semantics/article
format http://purl.org/coar/resource_type/c_6501
status_str publishedVersion
dc.identifier.uri.none.fl_str_mv https://repositorio.escuelaing.edu.co/handle/001/3156
dc.identifier.eissn.spa.fl_str_mv 2352-9148
dc.identifier.instname.spa.fl_str_mv Universidad Escuela Colombiana de Ingeniería Julio Garavito
dc.identifier.reponame.spa.fl_str_mv Repositorio Digital
dc.identifier.repourl.spa.fl_str_mv https://repositorio.escuelaing.edu.co/
url https://repositorio.escuelaing.edu.co/handle/001/3156
https://repositorio.escuelaing.edu.co/
identifier_str_mv 2352-9148
Universidad Escuela Colombiana de Ingeniería Julio Garavito
Repositorio Digital
dc.language.iso.spa.fl_str_mv eng
language eng
dc.relation.citationedition.spa.fl_str_mv Vol. 32 año 2022
dc.relation.citationendpage.spa.fl_str_mv 17
dc.relation.citationstartpage.spa.fl_str_mv 1
dc.relation.citationvolume.spa.fl_str_mv 32
dc.relation.ispartofjournal.eng.fl_str_mv Informatics in Medicine Unlocked
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spelling Garzón, Wilmer6b04a33a7db33dd5cc3491063fc48a95Benavides, Luis Albertof41ce80dc6191ec07a18f9540f4178a8Gignard, Alban6fbca16bc50d2c0b4dee4332f1d568c6Südholt, Mario0250aeec3f859c0b7205d04882c0260dCTG - Informática2024-07-11T16:51:03Z2024-07-11T16:51:03Z2022https://repositorio.escuelaing.edu.co/handle/001/31562352-9148Universidad Escuela Colombiana de Ingeniería Julio GaravitoRepositorio Digitalhttps://repositorio.escuelaing.edu.co/The amount of biomedical data collected and stored has grown significantly. Analyzing these extensive amounts of data cannot be done by individuals or single organizations anymore. Thus, the scientific community is creating global collaborative efforts to analyze these data. However, biomedical data is subject to several legal and socio- economic restrictions hindering the possibilities for research collaboration. In this paper, we argue that researchers require new tools and techniques to address the restrictions and needs of global scientific collaborations over geo-distributed biomedical data. These tools and techniques must support what we call Fully Distributed Collaborations (FDC), which are research endeavors that harness means to exploit and analyze massive biomedical information collaboratively while respecting legal and socio-economical restrictions. This paper first motivates and discusses the requirements of FDCs in the context of a research collaboration on the development of diagnostic and predictive tools for the risk of intracranial aneurysm formation and rupture (the ICAN project). The paper then presents a taxonomy classifying the current tools and techniques for biomedical analysis with respect to the proposed requirements. The taxonomy considers three key architectural features to support FDC scenarios: data and computation placement, Privacy and Security, and Performance and Scalability. The review reveals new research opportunities to design tools and techniques for multi-site analyses encouraging scientific collaborations while mitigating technical and legal constraints.La cantidad de datos biomédicos recopilados y almacenados ha aumentado significativamente. El análisis de estas grandes cantidades de datos ya no lo pueden realizar individuos ni organizaciones individuales. Así, la comunidad científica está creando esfuerzos colaborativos globales para analizar estos datos. Sin embargo, los datos biomédicos están sujetos a varias restricciones legales y socioeconómicas que obstaculizan las posibilidades de colaboración en investigación. En este artículo, sostenemos que los investigadores necesitan nuevas herramientas y técnicas para abordar las restricciones y necesidades de las colaboraciones científicas globales sobre datos biomédicos geodistribuidos. Estas herramientas y técnicas deben respaldar lo que llamamos Colaboraciones Totalmente Distribuidas (FDC), que son esfuerzos de investigación que aprovechan los medios para explotar y analizar información biomédica masiva de manera colaborativa respetando las restricciones legales y socioeconómicas. En primer lugar, este artículo motiva y analiza los requisitos de los CDF en el contexto de una colaboración de investigación sobre el desarrollo de herramientas de diagnóstico y predicción del riesgo de formación y rotura de aneurismas intracraneales (el proyecto ICAN). Luego, el artículo presenta una taxonomía que clasifica las herramientas y técnicas actuales para el análisis biomédico con respecto a los requisitos propuestos. La taxonomía considera tres características arquitectónicas clave para admitir escenarios FDC: ubicación de datos y cálculos, privacidad y seguridad, y rendimiento y escalabilidad. La revisión revela nuevas oportunidades de investigación para diseñar herramientas y técnicas para análisis multisitio que fomenten colaboraciones científicas y al mismo tiempo mitiguen las limitaciones técnicas y legales.17 páginasapplication/pdfengElsevier LtdBogotá (Colombia)www.elsevier.com/locate/imuA taxonomy of tools and approaches for distributed genomic analysesArtículo de revistainfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501http://purl.org/coar/resource_type/c_2df8fbb1Textinfo:eu-repo/semantics/articlehttp://purl.org/coar/version/c_970fb48d4fbd8a85Vol. 32 año 202217132Informatics in Medicine UnlockedAbouelhoda M, Issa SA, Ghanem M. Tavaxy: integrating taverna and galaxy workflows with cloud computing support. 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PLoS ONE 2011;6:e25988. https://doi.org/10.1371/journal. pone.0025988.info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2BiometríaBiometryAnálisis de la informaciónInformation analysisInvestigación biomédicaBiomedical researchTecnología médicaMedical technologyDistributed biomedical analysesFully distributed collaborationsReproducibilityScalability Multi-site analysesDistributed workflow analysesAnálisis biomédicos distribuidosColaboraciones totalmente distribuidasReproducibilidadAnálisis de escalabilidad multisitioAnálisis de flujo de trabajo distribuidoTEXTA taxonomy of tools and approaches for distributed genomic analyses.pdf.txtA taxonomy of tools and approaches for distributed genomic analyses.pdf.txtExtracted texttext/plain131146https://repositorio.escuelaing.edu.co/bitstream/001/3156/4/A%20taxonomy%20of%20tools%20and%20approaches%20for%20distributed%20genomic%20analyses.pdf.txteb26b4b320214d3ec325cd2e042520dbMD54open accessTHUMBNAILPortada A toxonomy of tools and aproaches for distributed genomic analyses.PNGPortada A toxonomy of tools and aproaches for distributed genomic analyses.PNGimage/png236507https://repositorio.escuelaing.edu.co/bitstream/001/3156/3/Portada%20A%20toxonomy%20of%20tools%20and%20aproaches%20for%20distributed%20genomic%20analyses.PNG2c10021a4b8daf155722e9f0326b3472MD53open accessA taxonomy of tools and approaches for distributed genomic analyses.pdf.jpgA taxonomy of tools and approaches for distributed genomic analyses.pdf.jpgGenerated Thumbnailimage/jpeg15578https://repositorio.escuelaing.edu.co/bitstream/001/3156/5/A%20taxonomy%20of%20tools%20and%20approaches%20for%20distributed%20genomic%20analyses.pdf.jpgadfb70997a6f9d9860a919c715d14321MD55open accessLICENSElicense.txtlicense.txttext/plain; charset=utf-81881https://repositorio.escuelaing.edu.co/bitstream/001/3156/2/license.txt5a7ca94c2e5326ee169f979d71d0f06eMD52open accessORIGINALA taxonomy of tools and approaches for distributed genomic analyses.pdfA taxonomy of tools and approaches for distributed genomic analyses.pdfapplication/pdf1871605https://repositorio.escuelaing.edu.co/bitstream/001/3156/1/A%20taxonomy%20of%20tools%20and%20approaches%20for%20distributed%20genomic%20analyses.pdf352bd361e8f413892b8b09b9617362ebMD51metadata only access001/3156oai:repositorio.escuelaing.edu.co:001/31562024-08-06 16:11:23.159metadata only accessRepositorio Escuela Colombiana de Ingeniería Julio Garavitorepositorio.eci@escuelaing.edu.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