@article{GARZON2022101024,
abstract = {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.},
author = {Wilmer Garz{\'o}n and Luis Benavides and Alban Gaignard and Richard Redon and Mario S{\"u}dholt},
doi = {https://doi.org/10.1016/j.imu.2022.101024},
issn = {2352-9148},
journal = {Informatics in Medicine Unlocked},
keywords = {Distributed biomedical analyses, Fully distributed collaborations, Reproducibility, Scalability, Multi-site analyses, Distributed workflow analyses},
pages = {101024},
title = {A taxonomy of tools and approaches for distributed genomic analyses},
url = {https://www.sciencedirect.com/science/article/pii/S2352914822001666},
volume = {32},
year = {2022},
bdsk-url-1 = {https://www.sciencedirect.com/science/article/pii/S2352914822001666},
bdsk-url-2 = {https://doi.org/10.1016/j.imu.2022.101024}
}
@inproceedings{ICEGOV2020,
address = {New York},
author = {Andrea Ceballos and Luis Daniel Benavides-Navarro and Victoria Eugenia Ospina},
booktitle = {Proceedings of the 13th International Conference on Theory and Practice of Electronic Governance (ICEGOV2020) 23-25 September 2020, Athens, Greece.},
date-added = {2020-10-15 10:34:15 -0500},
date-modified = {2020-10-15 10:40:22 -0500},
editor = {Charalabidis, Yannis and Cunha, Maria Alexandra and Sarantis, Demetrios},
month = {September},
publisher = {ACM Press},
title = {Towards a measuring framework for knowledge creation in smart cities},
year = {2020}
}
@article{IEEE-Access-2020,
author = {M. {Sanabria-Ardila} and Luis Daniel {Benavides-Navarro} and D. {D{\'\i}az-L{\'o}pez} and W. {Garz{\'o}n-Alfonso}},
journal = {IEEE Access},
pages = {143862-143880},
title = {A Semantic Framework for the Design of Distributed Reactive Real-Time Languages and Applications},
volume = {8},
year = {2020}
}
@inproceedings{CCGrid2019,
author = {F. {Boujdad} and A. {Gaignard} and M. {S{\"u}dholt} and W. {Garz{\'o}n-Alfonso} and L. D. {Benavides Navarro} and R. {Redon}},
booktitle = {2019 19th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGRID)},
pages = {611-620},
title = {On Distributed Collaboration for Biomedical Analyses},
year = {2019}
}
@inproceedings{10.1007/978-3-030-02852-7_20,
address = {Cham},
author = {Sanabria, Mateo and Alfonso, Wilmer Garz{\'o}n and Benavides Navarro, Luis Daniel},
booktitle = {New Trends in Model and Data Engineering},
editor = {Abdelwahed, El Hassan and Bellatreche, Ladjel and Benslimane, Djamal and Golfarelli, Matteo and Jean, St{\'e}phane and Mery, Dominique and Nakamatsu, Kazumi and Ordonez, Carlos},
pages = {231--243},
publisher = {Springer International Publishing},
title = {Towards Real-Time Semantics for a Distributed Event-Based MOP Language},
year = {2018}
}
@inproceedings{ccc2018,
abstract = {In this paper, we propose REAL-T, a distributed event-based language with explicit support for time manipulation. The language introduces automata for operational time manipulation, causality constructs and Linear Temporal Logic for declarative time predicates, and a distributed-time aware event model. We have developed a compiler for the language and a dynamic run-time framework. To validate the proposal we study detection of complex patterns of security vulnerabilities in IoT scenarios.},
address = {Cham},
author = {Benavides Navarro, Luis Daniel and Pimienta, Camilo and Sanabria, Mateo and D{\'\i}az, Daniel and Garz{\'o}n, Wilmer and Melo, Willson and Arboleda, Hugo},
booktitle = {Advances in Computing},
doi = {https://doi.org/10.1007/978-3-319-98998-3_9},
editor = {Serrano C., Jairo E. and Mart{\'\i}nez-Santos, Juan Carlos},
isbn = {978-3-319-98998-3},
issn = {1865-0929},
pages = {113--127},
publisher = {Springer International Publishing},
title = {REAL-T: Time Modularization in Reactive Distributed Applications},
url = {https://link.springer.com/book/10.1007/978-3-319-98998-3},
volume = {885},
year = {2018},
bdsk-url-1 = {https://link.springer.com/book/10.1007/978-3-319-98998-3},
bdsk-url-2 = {https://doi.org/10.1007/978-3-319-98998-3_9}
}
@article{entcc2011,
author = {Benavides Navarro, Luis Daniel and Andr{\'e}s Barrera and Kiyoshige Garc{\'e}s and Hugo Arboleda},
doi = {10.1016/j.entcs.2011.11.030},
issn = {1571-0661},
journal = {Electronic Notes in Theoretical Computer Science},
keywords = {automata},
number = 0,
pages = {127 - 141},
title = {Detecting and Coordinating Complex Patterns of Distributed Events with KETAL},
url = {http://www.sciencedirect.com/science/article/pii/S1571066111001794},
volume = 281,
year = 2011,
bdsk-url-1 = {http://www.sciencedirect.com/science/article/pii/S1571066111001794},
bdsk-url-2 = {http://dx.doi.org/10.1016/j.entcs.2011.11.030}
}
@inproceedings{aosd11,
acmid = 1961362,
address = {New York, NY, USA},
author = {Mej\'{\i}a, Ismael and S\"{u}dholt, Mario and Benavides Navarro, Luis Daniel},
booktitle = {Proceedings of the 2nd international workshop on Variability and composition},
doi = {http://doi.acm.org/10.1145/1961359.1961362},
isbn = {978-1-4503-0646-1},
keywords = {aspect-oriented programming, distributed systems, health information systems, invasive software composition},
location = {Porto de Galinhas, Brazil},
numpages = 5,
pages = {7--11},
publisher = {ACM},
series = {VariComp '11},
title = {A study of invasive composition for the evolution of a health information system},
url = {http://doi.acm.org/10.1145/1961359.1961362},
year = 2011,
bdsk-url-1 = {http://doi.acm.org/10.1145/1961359.1961362}
}
@inproceedings{middleware08,
address = {Leuven, Belgium},
author = {Benavides Navarro, Luis Daniel and R{\'e}mi Douence, Mario S{\"u}dholt},
booktitle = {In proceedings of the {ACM}-{IFIP}-{USENIX} 9th International Middleware Conference},
month = dec,
publisher = {Springer-Verlag},
title = {Debugging and testing middleware with aspect-based control-flow and causal patterns},
year = 2008
}
@inproceedings{adi2008,
author = {Benavides Navarro, Luis Daniel and R{\'e}mi Douence and Angel Nu{\~n}ez and Mario S{\"u}dholt},
booktitle = {3rd International Workshop on Aspects, Dependencies and Interactions at the 22nd European Conference on Object-Oriented Programming ECOOP'08},
month = {July},
title = {{LTS}-based Semantics and Property Analysis of Distributed Aspects and Invasive Patterns},
url = {./publications/SemanticsAWED-InvPattCR-ADI07-ECOOP07.pdf},
year = 2008,
bdsk-url-1 = {./publications/SemanticsAWED-InvPattCR-ADI07-ECOOP07.pdf}
}
@inproceedings{sbac-pad08,
address = {Campo Grande,{MS}, Brasil},
author = {Benavides Navarro, Luis Daniel and R{\'e}mi Douence, Mario S{\"u}dholt},
booktitle = {In proceedings of the 20th International Symposium on Computer Architecture and High Performance Computing},
month = oct,
publisher = {{IEEE} Computer Society},
title = {Aspect-based patterns for grid programming},
year = 2008
}
@inproceedings{wcat07,
author = {Benavides Navarro, Luis Daniel and Mario S{\"u}dholt and R{\'e}mi Douence and Jean-Marc Menaud},
booktitle = {4th International Workshop on Coordination and Adaptation Techniques for Software Entities (WCAT07) at the 21st European Conference on Object-Oriented Programming ECOOP'07},
month = jul,
title = {Invasive patterns: aspect-based adaptation of distributed applications},
url = {./publications/benavides-InvPatt-WCAT07.pdf},
year = 2007,
bdsk-url-1 = {./publications/benavides-InvPatt-WCAT07.pdf}
}
@inproceedings{doa07,
author = {Benavides Navarro, Luis Daniel and Mario S{\"u}dholt and R{\'e}mi Douence and Jean-Marc Menaud},
booktitle = {Proc. of the 9th International Symposium on Distributed Objects, Middleware, and Applications ({DOA}'07)},
doct = yes,
month = nov,
note = {ISSN: 0302-9743},
publisher = {Springer Verlag},
series = {LNCS},
title = {Invasive patterns for distributed programs},
url = {./publications/invasive-patterns-DOA07.pdf},
year = 2007,
bdsk-url-1 = {./publications/invasive-patterns-DOA07.pdf}
}
@inproceedings{acp4is07,
address = {New York, NY, USA},
author = {Benavides Navarro, Luis Daniel and Christa Schwanninger and Robert Sobotzik and Mario S{\"u}dholt},
booktitle = {ACP4IS '07: Proceedings of the 6th workshop on Aspects, components, and patterns for infrastructure software},
doi = {10.1145/1233901.1233908},
isbn = {1-59593-657-8},
location = {Vancouver, British Columbia, Canada},
month = mar,
pages = 7,
publisher = {ACM Press},
title = {ATOLL: aspect-oriented toll system},
url = {./publications/benavides-atoll-ACP4IS-aosd07.pdf},
year = 2007,
bdsk-url-1 = {./publications/benavides-atoll-ACP4IS-aosd07.pdf},
bdsk-url-2 = {http://dx.doi.org/10.1145/1233901.1233908}
}
@inproceedings{aosd06,
address = {New York, NY, USA},
author = {Benavides Navarro, Luis Daniel and Mario S{\"u}dholt and Wim Vanderperren and Bruno De Fraine and Davy Suv{\'e}e},
booktitle = {AOSD '06: Proceedings of the 5th international conference on Aspect-oriented software development},
doi = {10.1145/1119655.1119665},
isbn = {1-59593-300-X},
location = {Bonn, Germany},
month = mar,
pages = {51--62},
publisher = {ACM Press},
title = {Explicitly distributed AOP using AWED},
url = {./publications/benavides-awed-aosd06.pdf},
year = 2006,
bdsk-url-1 = {./publications/benavides-awed-aosd06.pdf},
bdsk-url-2 = {http://dx.doi.org/10.1145/1119655.1119665}
}
@inproceedings{doa06,
address = {Berlin, Germany},
author = {Benavides Navarro, Luis Daniel and Mario S{\"u}dholt and Wim Vanderperren and Bart Verheecke},
booktitle = {In Proceedings of On the Move to Meaningful Internet systems 2006: CoopIS, DOA,GADA, and ODBASE. 8th Int. Symposium on Distributed Objects and Applications (DOA'06)},
isbn = {1-540-48274-1},
issn = {0302-9743},
location = {Montpellier, France},
month = nov,
note = {ISSN: 0302-9743},
pages = {1449--1466},
publisher = {Springer Verlag},
series = {LNCS},
title = {Modularization of distributed web services using AWED},
url = {./publications/benavides-awed-doa06.pdf},
year = 2006,
bdsk-url-1 = {./publications/benavides-awed-doa06.pdf}
}
@techreport{inria2006,
author = {Benavides Navarro, Luis Daniel and Mario S{\"u}dholt and Wim Vanderperren and De Fraine, Bruno and Davy Suv{\'e}e},
institution = {INRIA},
month = {March},
note = {Slightly extended version of [Benavides et al., AOSD'06]},
number = {RR-5882},
title = {Explicitly distributed AOP using AWED},
type = {Research Report},
url = {./publications/benavides-awed-INRIA-TR-5882.pdf},
year = 2006,
bdsk-url-1 = {./publications/benavides-awed-INRIA-TR-5882.pdf}
}
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