Abstract
Applications in the biomedical sector have a rising demand for computational power due to the growing amount of biological data. However, the setup and maintenance of a sufficient computational infrastructure is costly. Cloud computing allows distributed computing over a network and maximizes the effectiveness of the shared resources. Nevertheless, security concerns rise when valuable research data is transferred to a public Cloud. Herein, we describe – from the application and security perspective – three biomedical case studies from different domains: Patent annotation, cancer outcome prediction, and drug target prediction. We elaborate on different strategies to secure the data and results in the Cloud as well as on the infrastructure needed. The proposed Cloud solutions could help to adapt other similar algorithms from different domains to benefit from Cloud computing.
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References
Krishnan, A.: Gridblast: a globus-based high-throughput implementation of blastin a grid computing framework. Concurrency and Computation: Practice and Experience 17(13) (2005) 1607–1623
Morgan, J.C., Chapman, R.W., Anderson, P.E.: A next generation sequence processing and analysis platform with integrated cloud-storage and high performance computing resources. In: Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine. BCB ’12, New York, NY, USA, ACM (2012) 594–594
Ren, K., Wang, C., Wang, Q.: Security Challenges for the Public Cloud. IEEEInternet Computing 16(1) (January 2012) 69–73
Santos, N., Gummadi, K.P., Rodrigues, R.: Towards trusted cloud computing. In: Proceedings of the 2009 conference on Hot topics in cloud computing. HotCloud’09, Berkeley, CA, USA, USENIX Association (2009) 3
Bugiel, S., N¨urnberger, S., Sadeghi, A.R., Schneider, T.: Twin Clouds: Secure Cloud Computing with Low Latency. In: 12th Communications and Multimedia Security Conference (CMS’11). Volume 7025 of LNCS., Springer (2011)
Gentry, C.: Fully homomorphic encryption using ideal lattices. In: Proceedings ofthe 41st annual ACM symposium on Theory of computing. STOC ’09, New York, NY, USA, ACM (2009) 169–178
Yao, A.C.C.: How to generate and exchange secrets. In: Foundations of ComputerScience, 1986., 27th Annual Symposium on. (1986) 162–167
Beck, M., Kerschbaum, F.: Approximate two-party privacy-preserving string matching with linear complexity. (2013)
Open Grid Forum Working Group: OCCI – Open Cloud Computing Interface (2009)
Buyya, R., Ranjan, R., Calheiros, R.: InterCloud: Utility-Oriented Federation of Cloud Computing Environments for Scaling of Application Services. In Hsu, C.H., Yang, L., Park, J., Yeo, S.S., eds.: Algorithms and Architectures for Parallel Processing. Volume 6081 of Lecture Notes in Computer Science. Springer Berlin / Heidelberg (2010) 13–31
Rochwerger, B., Breitgand, D., Epstein, A., Hadas, D., Loy, I., Nagin, K., Tordsson,J., Ragusa, C., Villari, M., Clayman, S., Levy, E., Maraschini, A., Massonet, P., Mu andoz, H., Tofetti, G.: Reservoir - When One Cloud Is Not Enough. Computer 44(3) (March 2011) 44
Chakode, R., Yenke, B.O., Mehaut, J.F.: Resource Management of Virtual Infrastructure for On-demand SaaS Services. In: CLOSER2011: Proceedings of the 1st International conference on Cloud Computing and Service Science. (May 2011) 352–361
Eisinger, D., Tsatsaronis, G., Bundschus, M., Wieneke, U., Schroeder, M.: Automated patent categorization and guided patent search using ipc as inspired by mesh and pubmed. Journal of Biomedical Semantics 4(Suppl 1) (2013) S3
Winter, C., Kristiansen, G., Kersting, S., Roy, J., Aust, D., Knösel, T., Rümmele, P., Jahnke, B., Hentrich, V., Rückert, F., Niedergethmann, M., Weichert, W., Bahra, M., Schlitt, H.J., Settmacher, U., Friess, H., Buühler, M., Saeger, H.D., Schroeder, M., Pilarsky, C., Grützmann, R.: Google goes cancer: improving outcome prediction for cancer patients by network-based ranking of marker genes. PLoS Comput Biol 8(5) (2012) e1002511
Roy, J., Winter, C., Isik, Z., Schroeder, M.: Network information improves canceroutcome prediction. Brief Bioinform (Dec 2012)
Haupt, V.J., Schroeder, M.: Old friends in new guise: Repositioning of knowndrugs with structural bioinformatics. Brief Bioinform 12(4) (Jul 2011) 312–326
Haupt, V.J., Daminelli, S., Schroeder, M.: Drug promiscuity in PDB: Protein binding site similarity is key. PLoS One (2013)
Doms, A., Schroeder, M.: Gopubmed: exploring pubmed with the gene ontology.Nucleic Acids Res 33(Web Server issue) (Jul 2005) W783–W786
Thomas, P., Starlinger, J., Vowinkel, A., Arzt, S., Leser, U.: Geneview: a comprehensive semantic search engine for pubmed. Nucleic Acids Res 40(Web Server issue) (Jul 2012) W585–W591
Verberne, S., D’hondt, E., Oostdijk, N.: Quantifying the Challenges in ParsingPatent Claims. 1st International Workshop on Advances in Patent Information Retrieval (2003)
Kwon, T., Lee, M.K., Kwon, D.: ML Confidential: Machine Learning on EncryptedData. Information Security and Cryptology ICISC 2012 Lecture Notes in Computer Science 7839 (2013) 1–21
Bonomi, L., Xiong, L., Chen, R., Fung, B.: Privacy Preserving Record Linkage viagrams Projections. arXiv preprint arXiv:1208.2773 (2012)
Katz, J.: Secure text processing with applications to private DNA matching. Proceedings of the 17th ACM conference on 1 (October 2010) 485–492
Blass, E., Pietro, R.D., Molva, R., Onen, M.: PRISMPrivacy-Preserving Search in MapReduce. Privacy Enhancing Technologies (2012)
Atallah, M.J., Frikken, K.B.: Securely outsourcing linear algebra computations. In: Proceedings of the 5th ACM Symposium on Information, Computer and Communications Security - ASIACCS ’10, New York, New York, USA, ACM Press (April 2010) 48
Atallah, M., Pantazopoulos, K., Spafford, E.: Secure outsourcing of some computations. Computer (1996) 1–24
Atallah, M.J., Pantazopoulos, K.N., Rice, J.R., Spafford, E.H.: Secure outsourcingof scientific computations. ADVANCES IN COMPUTERS (1998) 215 – 272
Paillier, P.: Public-Key Cryptosystems Based on Composite Degree ResiduosityClasses. Advances in Cryptography - Eurocrypt ’99 1592 (1999) 223–238
Boneh, D., Goh, E.J., Nissim, K.: Evaluating 2-DNF formulas on ciphertexts. Theory of Cryptography (TCC) ’05 3378 (2005) 325–341
DiMasi, J.A., Feldman, L., Seckler, A., Wilson, A.: Trends in risks associated withnew drug development: success rates for investigational drugs. Clin Pharmacol Ther 87(3) (Mar 2010) 272–277
Chong, C.R., Sullivan, D.J.: New uses for old drugs. Nature 448(7154) (Aug 2007) 645–646
Xie, L., Bourne, P.E.: Detecting evolutionary relationships across existing foldspace, using sequence order-independent profile-profile alignments. Proc Natl Acad Sci U S A 105(14) (Apr 2008) 5441–5446
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Funding by the German Federal Ministry of Economics and Technology is kindly acknowledged as GeneCloud is part of the Trusted Cloud Initiative.
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Beck, M. et al. (2014). GeneCloud: Secure Cloud Computing for Biomedical Research. In: Krcmar, H., Reussner, R., Rumpe, B. (eds) Trusted Cloud Computing. Springer, Cham. https://doi.org/10.1007/978-3-319-12718-7_1
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DOI: https://doi.org/10.1007/978-3-319-12718-7_1
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