BBC: BioBankCloud
From Navigators
- Research Line(s): Fault and Intrusion Tolerance in Open Distributed Systems (FIT)
- Coordinator: Kungliga Tekniska högskolan
- Partners: FCUL, Kungliga Tekniska högskolan, Karolinska Institutet, Humboldt - Universität zu Berlin, Charité - Universitätsmedizin Berlin
- Start Date: Nov. 2012
- Duration: 36 months
- Team at FCUL: Researchers including Alysson Bessani, Vinicius Vielmo Cogo, Fernando Ramos, Nuno Ferreira Neves, Tiago Oliveira
Summary
Big data is coming to Biobanks, driven by the decreasing cost of sequencing genomic data, which has been halving every 4 months since 2004. Biobanks, used to store and catalogue human biological material, are not prepared to handle this wave of data - there is a Biobank bottleneck: a lack of platform support for the storage and analysis of the coming wave of human genomic data. In this project, we will develop a cloud-computing platform as a service (PaaS) for Biobanking. The platform will provide security, storage, data-intensive tools and algorithms, and support for allowing Biobanks to share data with one another, all within the existing regulatory frameworks for Biobanking. Our research challenges include:
- the definition of the regulatory framework and data model for Biobank data sharing; the development of a scalable, highly available storage infrastructure;
- data-intensive tools and workflows for aligning, clustering, aggregating, compressing and anonymizing sequence data;
- a security platform that ensures data confidentiality, data integrity, and data access auditing;
- the inter-connection of Biobanks, while also leveraging the storage and processing capacity of public clouds ensuring security, dependability and privacy of the stored information; and
- the integration of these components as a PaaS.
The project will require focused inter-disciplinary research. In this way, the consortium comprises several teams with complementary competencies, from developers and users of Biobanks to systems researchers with deep expertise in building dependable and scalable software platforms. Our platform will be evaluated and disseminated at existing Biobanks in Sweden and Germany. Our project goal is to have BiobankCloud remove the Biobank bottleneck, enabling global leadership for European Biobanks, with improved support for preventing diseases, spotting trends, and advancing our understanding of clinical and molecular pathology.
Publications
- Ricardo Mendes, Tiago Oliveira, Vinicius Vielmo Cogo, Nuno Ferreira Neves, Alysson Bessani, “CHARON: A Secure Cloud-of-Clouds System for Storing and Sharing Big Data”, IEEE Transactions on Cloud Computing, vol. 9, no. 4, pp. 1349–1361, Oct. 2021. 10.1109/TCC.2019.2916856
- Vinicius Vielmo Cogo, Alysson Bessani, “Enabling the Efficient, Dependable Cloud-based Storage of Human Genomes”, in 1st Workshop on Distributed and Reliable Storage Systems (DRSS'19), Oct. 2019.
- Vinicius Vielmo Cogo, Alysson Bessani, Francisco M. Couto, Margarida Gama-Carvalho, Maria Fernandes, Paulo Esteves-Verissimo, “How can photo sharing inspire sharing genomes?”, in Proceedings of the 11th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB'17), Porto, Portugal, Jun. 2017.
- Vinicius Vielmo Cogo, Alysson Bessani, “From Data Islands to Sharing Data in the Cloud: the Evolution of Data Integration in Biological Data Repositories”, Communications and Innovations Gazette (ComInG), vol. 1, no. 1, pp. 1–11, Jan. 2016.
- Vinicius Vielmo Cogo, Alysson Bessani, Francisco M. Couto, Paulo Verissimo, “A High-Throughput Method to Detect Privacy-Sensitive Human Genomic Data”, in Proceedings of the Workshop on Privacy in the Electronic Society (WPES 2015), Denver, CO, US, Oct. 2015.
- Alysson Bessani, Jörgen Brandt, Marc Bux, Vinicius Vielmo Cogo, Lora Dimitrova, Jim Dowling, Ali Gholami, Kamal Hakimzadeh, Michael Hummel, Mahmoud Ismail, Erwin Laure, Ulf Leser, Jan-Eric Litton, Roxanna Martinez, Jane Reichel, Salman Niazi, Karin Zimmermann, “BiobankCloud: a Platform for the Secure Storage, Sharing, and Processing of Large Biomedical Data Sets”, in Proceedings of the 1st Int. Workshop on Data Management and Analytics for Medicine and Healthcare (DMAH 2015), Hawaii, US, Sept. 2015.
- Fernando Alves, Vinicius Vielmo Cogo, Sebastian Wandelt, Ulf Leser, Alysson Bessani, “On-Demand Indexing for Referential Compression of DNA Sequences”, PLoS ONE, vol. 10, no. 7, pp. e0132460, Jul. 2015. DOI: 10.1371/journal.pone.0132460
- Tobias Distler, Christopher Bahn, Alysson Bessani, Frank Fischer, Flavio Junqueira, “Extensible Distributed Coordination”, in Proceedings of the 10th ACM European Conference on Computer Systems (EuroSys), Bordeux, France, Apr. 2015.
- Fernando Alves, Vinicius Vielmo Cogo, Alysson Bessani, “Indexação sob Demanda para a Compressão Referencial de Ficheiros de ADN”, in Proceedings of the 6th Simpósio de Informática (INFORUM), Porto, Portugal, Sept. 2014, pp. 5–16.
- Fabio Botelho, Alysson Bessani, Fernando Ramos, Paulo Ferreira, “On the Design of Practical Fault-Tolerant SDN Controllers”, in Proceedings of the 3rd European Workshop on Software Defined Networks (EWSDN), Budapest, Hungary, Sept. 2014.
- Tiago Oliveira, Ricardo Mendes, Alysson Bessani, “Sharing Files Using Cloud Storage Services”, in Proceedings of the 2nd Workshop on Dependability and Interoperability in Heterogeneous Clouds (DIHC), co-located with Euro-Par, Aug. 2014.
- Alysson Bessani, Ricardo Mendes, Tiago Oliveira, Nuno Ferreira Neves, Miguel Correia, Marcelo Pasin, Paulo Verissimo, “SCFS: A Shared Cloud-backed File System”, in Proceedings of the 2014 USENIX Annual Technical Conference (USENIX-ATC), Philadelphia, PA, US, Jun. 2014.
- Vinicius Vielmo Cogo, Alysson Bessani, “BiobankCloud - Platform as a Service for Biobanking”, in Poster in the 2nd Annual Next Generation Sequencing Data Congress, London, UK, May 2014.
- Paulo Verissimo, Alysson Bessani, “E-biobanking: What Have You Done to My Cell Samples?”, IEEE Security & Privacy, vol. 11, no. 6, pp. 62–65, Dec. 2013.
BibTeX
Navigators - BBC project| Current projects: | VEDLIoT, SATO, ADMORPH, SEAL, AQUAMON, UPVN, REDBOOK, ThreatAdapt, SEL, Xivt |
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| Past projects: | TCLOUDS, MASSIF, MAFTIA, RESIST NoE, DiSIEM, KARYON, HIDENETS, CORTEX, CRUTIAL, TRONE, SITAN, ReD, IRCoC, DIVERSE, CloudFIT, READAPT, REGENESYS, RC-Clouds, TACID, DARIO, RITAS, AJECT, MICRA, DEAR-COTS, COPE, DEFEATS, MOOSCO, TOPCOM, RE:DY, NORTH, Abyss, SUPERCLOUD, COST Action IC1402, SEGRID, BioBankCloud, PROPHECY, SAPIENT, SecFuNet, FTH-Grid, AIR-II, AIR, ESFORS, CaberNet, GODC, BROADCAST, CoDiCom, Delta-4, RAPTOR |
