IEEE Transactions on Computers
IEEE Transactions on Computers (TC) is a monthly publication that publishes research in such areas as computer organizations and architectures, digital devices, operating systems, and new and important applications and trends.
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From the January 2019 issue
Optimal Binning for Genomics
By Andrea Gulino, Abdulrahman Kaitoua, and Stefano CeriAdrian Garcia-Garcia, Juan Carlos Saez, and Manuel Prieto-Matias
Genome sequencing is expected to be the most prolific source of big data in the next decade; millions of whole genome datasets will open new opportunities for biological research and personalized medicine. Genome sequences are abstracted in the form of interesting regions, describing abnormalities of the genome. The parallel execution on the cloud of complex operations for joining and mapping billions of genomic regions is increasingly important. Genome binning, i.e., partitioning of the genome into small-size segments, adapts classic data partitioning methods to genomics; region distributions to bins must reflect operation-specific correctness rules. As a consequence, determining the optimal bin size for such operations is a complex mathematical problem, whose solution requires careful modeling. The main result of this paper is the mathematical formulation and solution of the optimal binning problem for join and map operations in the context of GMQL, a query language over genomic regions; the model is validated by experiments showing its accuracy and sensitivity to the variation of operations’ parameters. We also optimize sequences of operations by inheriting the binning between two consecutive operations and we show the deployment of GMQL and the tuning of the proposed model on different cloud computing systems.
Editorials and Announcements
- TC now offers authors access to Code Ocean. Code Ocean is a cloud-based executable research platform that allows authors to share their algorithms in an effort to make the world’s scientific code more open and reproducible. Learn more or sign up for free.
- Multimedia presentations of each monthly featured paper are now available in Chinese, English, and Spanish
- Thank-You State of the Journal Editorial from the Outgoing Editor in Chief (Jan 2019)
- Editorial from the Incoming Editor in Chief (Jan 2019)
- Guest Editors’ Introduction to the Special Issue on Cryptographic Engineering in a Post-Quantum World: State of the Art Advances (November 2018)
- Special Section on Secure Computer Architectures (March 2018)
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