Abstract
Applications in the biomedical sector have a rising demand for computational power due to the rapid growth 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 efficiency 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 can help to adapt similar algorithms from different domains to benefit from Cloud computing.
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References
Atallah, M., Pantazopoulos, K., Spafford, E.: Secure outsourcing of some computations. Computer pp. 1–24 (1996). http://docs.lib.purdue.edu/cgi/viewcontent.cgi?article=2327&context=cstech
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, p. 48. ACM Press, New York, New York, USA (2010). DOI 10.1145/1755688.1755695. http://dl.acm.org/citation.cfm?id=1755688.1755695
Atallah, M.J., Pantazopoulos, K.N., Rice, J.R., Spafford, E.H.: Secure outsourcing of scientific computations. ADVANCES IN COMPUTERS pp. 215 – 272 (1998).http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.158.9763
Beck, M., Kerschbaum, F.: Approximate two-party privacy-preserving string matching with linear complexity (2013)
Blass, E., Pietro, R.D., Molva, R., O¨ nen, M.: PRISM–Privacy-Preserving Search in MapReduce. Privacy Enhancing Technologies (2012). http://www.springerlink.com/index/0720TJP211W4Q6U7.pdf
Boneh, D., Goh, E.J., Nissim, K.: Evaluating 2-DNF formulas on ciphertexts. Theory of Cryptography (TCC) ’05 3378, 325–341 (2005). http://www.springerlink.com/index/wtt5caxkr94laxkg.pdf
Bonomi, L., Xiong, L., Chen, R., Fung, B.: Privacy Preserving Record Linkage via grams Projections. arXiv preprint arXiv:1208.2773 (2012). http://arxiv.org/abs/1208.2773
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), LNCS, vol. 7025. Springer (2011). http://thomaschneider.de/papers/BNSS11.pdf
Buyya, R., Ranjan, R., Calheiros, R.: InterCloud: Utility-Oriented Federation of Cloud Computing Environments for Scaling of Application Services. In: C.H. Hsu, L. Yang, J. Park, S.S. Yeo (eds.) Algorithms and Architectures for Parallel Processing, Lecture Notes in Computer Science, vol. 6081, pp. 13–31. Springer Berlin / Heidelberg (2010). http://dx.doi.org/10.1007/978-3-642-13119-6_2
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, pp. 352–361 (2011)
Chong, C.R., Sullivan, D.J.: New uses for old drugs. Nature 448(7154), 645–646 (2007). DOI 10.1038/448645a. http://dx.doi.org/10.1038/448645a
Chuang, H.Y., Lee, E., Liu, Y.T., Lee, D., Ideker, T.: Network-based classification of breast cancer metastasis. Mol Syst Biol 3, 140 (2007). DOI 10.1038/msb4100180. http://dx.doi.org/10.1038/msb4100180
Cloud Security Alliance: Top Threats to Cloud Computing (March), 1–14 (2010)
Daminelli, S., Haupt, V.J., Reimann, M., Schroeder, M.: Drug repositioning through incomplete bi-cliques in an integrated drug-target-disease network. Integr Biol (Camb) 4(7), 778–788 (2012). DOI 10.1039/c2ib00154c. http://dx.doi.org/10.1039/c2ib00154c
DiMasi, J.A., Feldman, L., Seckler, A., Wilson, A.: Trends in risks associated with new drug development: success rates for investigational drugs. Clin Pharmacol Ther 87(3), 272–277 (2010). DOI 10.1038/clpt.2009.295. http://dx.doi.org/10.1038/clpt.2009.295
Doms, A.: GoPubMed : Ontology-based literature search for the life sciences. Dresden, Techn. Univ., Diss., 2009 (2008). http://dx.doi.org/10.1073/pnas.0704422105 http://d-nb.info/992853664
Doms, A., Schroeder, M.: Gopubmed: exploring pubmed with the gene ontology. Nucleic Acids Res 33(Web Server issue), W783–W786 (2005). DOI 10.1093/nar/gki470. http://dx.doi.org/10.1093/nar/gki470
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), S3 (2013). DOI 10.1186/2041-1480-4-S1-S3. http://www.jbiomedsem.com/content/4/S1/S3
Fortney, K., Jurisica, I.: Integrative computational biology for cancer research. Hum Genet 130(4), 465–481 (2011). DOI 10.1007/s00439-011-0983-z. http://dx.doi.org/10.1007/s00439-011-0983-z
Franz, M., Deiseroth, B., Hamacher, K., Jha, S., Katzenbeisser, S., Schr¨oder, H.: Towards Secure Bioinformatics Services. Financial Cryptography and Data Security - Lecture Notes in Computer Science 7035, 276–283 (2012)
Gentry, C.: Fully homomorphic encryption using ideal lattices. In: Proceedings of the 41st annual ACM symposium on Theory of computing, STOC ’09, pp. 169–178. ACM, New York, NY, USA (2009). DOI http://doi.acm.org/10.1145/1536414.1536440. http://doi.acm.org/10.1145/1536414.1536440
Hakenberg, J., Plake, C., Royer, L., Strobelt, H., Leser, U., Schroeder, M., Group, A.B., Centre, B., Dresden, T.U., Knowledge, G.: Open Access Gene mention normalization and interaction extraction with 9(Suppl 2) (2008). DOI 10.1186/gb-2008-9-S2-S14
Haupt, V.J., Daminelli, S., Schroeder, M.: Drug promiscuity in PDB: Protein binding site similarity is key. PLoS One (2013)
Haupt, V.J., Schroeder, M.: Old friends in new guise: Repositioning of known drugs with structural bioinformatics. Brief Bioinform 12(4), 312–326 (2011). DOI 10.1093/bib/bbr011. http://dx.doi.org/10.1093/bib/bbr011
Jansen,W., Grance, T.: NIST Special Publication 800-144, Guidelines on Security and Privacy in Public Cloud Computing (2011)
Johannes, M., Brase, J.C., Fr¨ohlich, H., Gade, S., Gehrmann, M., F¨alth, M., S¨ultmann, H., Beißbarth, T.: Integration of pathway knowledge into a reweighted recursive feature elimination approach for risk stratification of cancer patients. Bioinformatics 26(17), 2136–2144 (2010). DOI 10.1093/bioinformatics/btq345. http://dx.doi.org/10.1093/bioinformatics/btq345
Kann, M.G.: Advances in translational bioinformatics: computational approaches for the hunting of disease genes. Brief Bioinform 11(1), 96–110 (2010). DOI 10.1093/bib/bbp048. http://dx.doi.org/10.1093/bib/bbp048
Katz, J.: Secure text processing with applications to private DNA matching. Proceedings of the 17th ACM conference on 1, 485–492 (2010). http://dl.acm.org/citation. cfm?id = 1866361
Krishnan, A.: Gridblast: a globus-based high-throughput implementation of blast in a grid computing framework. Concurrency and Computation: Practice and Experience 17(13), 1607–1623 (2005). DOI 10.1002/cpe.906. http://dx.doi.org/10.1002/cpe.906
Kwon, T., Lee, M.K., Kwon, D.: ML Confidential: Machine Learning on Encrypted Data. Information Security and Cryptology – ICISC 2012 Lecture Notes in Computer Science 7839, 1–21 (2013). DOI 10.1007/978-3-642-37682-5. http://link.springer.com/10.1007/978-3-642-37682-5
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, pp. 594–594. ACM, New York, NY, USA (2012). DOI 10.1145/ 2382936.2383033. http://doi.acm.org/10.1145/2382936.2383033
O’Boyle, N.M., Morley, C., Hutchison, G.R.: Pybel: a python wrapper for the openbabel cheminformatics toolkit. Chem Cent J 2, 5 (2008). DOI 10.1186/1752-153X-2-5. http://dx.doi.org/10.1186/1752-153X-2-5
Open Grid Forum Working Group: OCCI – Open Cloud Computing Interface (2009)
Paillier, P.: Public-Key Cryptosystems Based on Composite Degree Residuosity Classes. Advances in Cryptography - Eurocrypt ’99 1592, 223–238 (1999). DOI 10.1007/3-540-48910-X. http://www.springerlink.com/index/10.1007/3-540-48910-X
Rahman, S.A., Bashton, M., Holliday, G.L., Schrader, R., Thornton, J.M.: Small molecule subgraph detector (smsd) toolkit. J Cheminform 1(1), 12 (2009). DOI 10.1186/1758-2946-1-12. http://dx.doi.org/10.1186/1758-2946-1-12
Ren, K., Wang, C., Wang, Q.: Security Challenges for the Public Cloud. IEEE Internet Computing 16(1), 69–73 (2012). DOI 10.1109/MIC.2012.14. http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6123700
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˜n andoz, H., Tofetti, G.: Reservoir - When One Cloud Is Not Enough. Computer 44(3), 44 –51 (2011). DOI 10.1109/MC.2011.64
Roy, J., Winter, C., Isik, Z., Schroeder, M.: Network information improves cancer outcome prediction. Brief Bioinform (2012). DOI 10.1093/bib/bbs083. http://dx.doi.org/10.1093/bib/bbs083
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, p. 3. USENIX Association, Berkeley, CA, USA (2009). http://portal.acm.org/citation.cfm?id=1855533.1855536
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), W585–W591 (2012). DOI 10.1093/nar/gks563. http://dx.doi.org/10.1093/nar/gks563
Troncoso-Pastoriza, J.R., Katzenbeisser, S., Celik, M.: Privacy preserving error resilient dna searching through oblivious automata. In: Proceedings of the 14th ACM conference on Computer and communications security - CCS ’07, p. 519. ACM Press, New York, New York, USA (2007). DOI 10.1145/1315245.1315309. http://dl.acm.org/citation.cfm?id=1315245.1315309
Verberne, S., D’hondt, E., Oostdijk, N.: Quantifying the Challenges in Parsing Patent Claims. 1st International Workshop on Advances in Patent Information Retrieval (2003)
Winter, C., Kristiansen, G., Kersting, S., Roy, J., Aust, D., Kn¨osel, T., R¨ummele, P., Jahnke, B., Hentrich, V., R¨uckert, F., Niedergethmann, M., Weichert, W., Bahra, M., Schlitt, H.J., Settmacher, U., Friess, H., B¨uchler, M., Saeger, H.D., Schroeder, M., Pilarsky, C., Gr¨utzmann, R.: Google goes cancer: improving outcome prediction for cancer patients by network-based ranking of marker genes. PLoS Comput Biol 8(5), e1002,511 (2012). DOI 10.1371/journal.pcbi.1002511. http://dx.doi.org/10.1371/journal.pcbi.1002511
Xie, L., Bourne, P.E.: Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc Natl Acad Sci U S A 105(14), 5441–5446 (2008). DOI 10.1073/pnas.0704422105. http://dx.doi.org/10.1073/pnas.0704422105
Yao, A.C.C.: How to generate and exchange secrets. In: Foundations of Computer Science, 1986., 27th Annual Symposium on, pp. 162–167 (1986). DOI 10.1109/SFCS.1986.25
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Beck, M. et al. (2014). Privacy-Preserving 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_16
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DOI: https://doi.org/10.1007/978-3-319-12718-7_16
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