Browsing by Subject "Data sharing"
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Item Open Access The BioPAX community standard for pathway data sharing(Nature Publishing Group, 2010-09) Demir, Emek; Cary, M. P.; Paley, S.; Fukuda, K.; Lemer, C.; Vastrik, I.; Wu, G.; D'Eustachio, P.; Schaefer, C.; Luciano, J.; Schacherer, F.; Martinez-Flores, I.; Hu, Z.; Jimenez-Jacinto, V.; Joshi-Tope, G.; Kandasamy, K.; Lopez-Fuentes, A. C.; Mi, H.; Pichler, E.; Rodchenkov, I.; Splendiani, A.; Tkachev, S.; Zucker, J.; Gopinath, G.; Rajasimha, H.; Ramakrishnan, R.; Shah, I.; Syed, M.; Anwar, N.; Babur, Özgün; Blinov, M.; Brauner, E.; Corwin, D.; Donaldson, S.; Gibbons, F.; Goldberg, R.; Hornbeck, P.; Luna, A.; Murray-Rust, P.; Neumann, E.; Reubenacker, O.; Samwald, M.; Iersel, Martijn van; Wimalaratne, S.; Allen, K.; Braun, B.; Whirl-Carrillo, M.; Cheung, Kei-Hoi; Dahlquist, K.; Finney, A.; Gillespie, M.; Glass, E.; Gong, L.; Haw, R.; Honig, M.; Hubaut, O.; Kane, D.; Krupa, S.; Kutmon, M.; Leonard, J.; Marks, D.; Merberg, D.; Petri, V.; Pico, A.; Ravenscroft, D.; Ren, L.; Shah, N.; Sunshine, M.; Tang R.; Whaley, R.; Letovksy, S.; Buetow, K. H.; Rzhetsky, A.; Schachter, V.; Sobral, B. S.; Doğrusöz, Uğur; McWeeney, S.; Aladjem, M.; Birney, E.; Collado-Vides, J.; Goto, S.; Hucka, M.; Novère, Nicolas Le; Maltsev, N.; Pandey, A.; Thomas, P.; Wingender, E.; Karp, P. D.; Sander, C.; Bader, G. D.Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery. © 2010 Nature America, Inc. All rights reserved.Item Open Access Collusion-secure watermarking for sequential data(Bilkent University, 2017-09) Yılmaz, ArifIn this work, we address the liability issues that may arise due to unauthorized sharing of personal data. We consider a scenario in which an individual shares his sequential data (such as genomic data or location patterns) with several service providers (SPs). In such a scenario, if his data is shared with other third parties without his consent, the individual wants to determine the service provider that is responsible for this unauthorized sharing. To provide this functionality, we propose a novel optimization-based watermarking scheme for sharing of sequential data. Thus, in the case of an unauthorized sharing of sensitive data, the proposed scheme can nd the source of the leakage by checking the watermark inside the leaked data. In particular, the proposed schemes guarantees with a high probability that (i) the SP that receives the data cannot understand the watermarked data points, (ii) when more than one SPs aggregate their data, they still cannot determine the watermarked data points, (iii) even if the unauthorized sharing involves only a portion of the original data, the corresponding SP can be kept responsible for the leakage, and (iv) the added watermark is compliant with the nature of the corresponding data. That is, if there are inherent correlations in the data, the added watermark still preserves such correlations. Watermarking typically means changing certain parts of the data, and hence it may have negative e ects on data utility. The proposed scheme also minimizes such utility loss while it provides the aforementioned security guarantees. Furthermore, we conduct a case study of the proposed scheme on genomic data and show the security and utility guarantees of the proposed scheme.Item Open Access On-chip memory space partitioning for chip multiprocessors using polyhedral algebra(The Institution of Engineering and Technology, 2010) Ozturk, O.; Kandemir, M.; Irwin, M. J.One of the most important issues in designing a chip multiprocessor is to decide its on-chip memory organisation. While it is possible to design an application-specific memory architecture, this may not necessarily be the best option, in particular when storage demands of individual processors and/or their data sharing patterns can change from one point in execution to another for the same application. Here, two problems are formulated. First, we show how a polyhedral method can be used to design, for array-based data-intensive embedded applications, an application-specific hybrid memory architecture that has both shared and private components. We evaluate the resulting memory configurations using a set of benchmarks and compare them to pure private and pure shared memory on-chip multiprocessor architectures. The second approach proposed consider dynamic configuration of software-managed on-chip memory space to adapt to the runtime variations in data storage demand and interprocessor sharing patterns. The proposed framework is fully implemented using an optimising compiler, a polyhedral tool, and a memory partitioner (based on integer linear programming), and is tested using a suite of eight data-intensive embedded applications. © 2010 © The Institution of Engineering and Technology.