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Privacy-Preserving Cloud Computing for Biomedical Research

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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

  1. 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

  2. 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

  3. 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

  4. Beck, M., Kerschbaum, F.: Approximate two-party privacy-preserving string matching with linear complexity (2013)

    Google Scholar 

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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)

    Google Scholar 

  11. 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

  12. 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

  13. Cloud Security Alliance: Top Threats to Cloud Computing (March), 1–14 (2010)

    Google Scholar 

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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)

    Google Scholar 

  21. 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

  22. 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

  23. Haupt, V.J., Daminelli, S., Schroeder, M.: Drug promiscuity in PDB: Protein binding site similarity is key. PLoS One (2013)

    Google Scholar 

  24. 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

  25. Jansen,W., Grance, T.: NIST Special Publication 800-144, Guidelines on Security and Privacy in Public Cloud Computing (2011)

    Google Scholar 

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. Open Grid Forum Working Group: OCCI – Open Cloud Computing Interface (2009)

    Google Scholar 

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. Verberne, S., D’hondt, E., Oostdijk, N.: Quantifying the Challenges in Parsing Patent Claims. 1st International Workshop on Advances in Patent Information Retrieval (2003)

    Google Scholar 

  43. 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

  44. 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

  45. 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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