A Memory Efficient Fast Distributed Real Time Commit Protocol

AbstractWith the emergence of portable DNA sequencers, such as Oxford Nanopore Technology MinION, metagenomic DNA sequencing can be performed in real-time and directly in the field. However, because metagenomic DNA analysis is computationally and memory intensive, and the current methods are designed for batch processing, the current metagenomic tools are not well suited for mobile devices.In this paper, we propose a new memory-efficient method to identify Operational Taxonomic Units (OTUs) in metagenomic DNA streams. Our method is based on finding connected components in overlap graphs constructed over a real-time stream of long DNA reads as produced by MinION platform. We propose an efficient algorithm to maintain connected components when an overlap graph is streamed, and show how redundant information can be removed from the stream by transitive closures. Through experiments on simulated and real-world metagenomic data, we demonstrate that the resulting solution is able to recover OTUs with high precision while remaining suitable for mobile computing devices.

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Real-time feature-based image morphing for memory-efficient impostor rendering and animation on GPU

The Visual Computer ◽

10.1007/s00371-012-0718-8 ◽

2012 ◽

Vol 29 (2) ◽

pp. 131-140 ◽

Cited By ~ 1

Author(s):

Kamer Ali Yuksel ◽

Alp Yucebilgin ◽

Selim Balcisoy ◽

Aytul Ercil

Keyword(s):

Real Time ◽

Image Morphing ◽

Feature Based ◽

Memory Efficient

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Shadow Sensitive SWIFT

Knowledge Discovery Practices and Emerging Applications of Data Mining - Advances in Data Mining and Database Management ◽

10.4018/978-1-60960-067-9.ch007 ◽

2010 ◽

pp. 130-150

Author(s):

Udai Shanker ◽

Abhay N. Singh ◽

Abhinav Anand ◽

Saurabh Agrawal

Keyword(s):

Real Time ◽

System Performance ◽

Database Systems ◽

Main Memory ◽

Communication Delay ◽

Data Item ◽

Commit Protocols ◽

Simulation Results ◽

Real Time Database ◽

Commit Protocol

This chapter proposes Shadow Sensitive SWIFT commit protocol for Distributed Real Time Database Systems (DRTDBS), where only abort dependent cohort having deadline beyond a specific value (Tshadow_creation_time) can forks off a replica of itself called a shadow, whenever it borrows dirty value of a data item. The new dependencies Commit-on-Termination external dependency between final commit operations of lender and shadow of its borrower and Begin-on-Abort internal dependency between shadow of borrower and borrower itself are defined. If there is serious problem in commitment of lender, execution of borrower is started with its shadow by sending YES-VOTE message piggy bagged with the new result to its coordinator after aborting it and abort dependency created between lender and borrower due to update-read conflict is reversed to commit dependency between shadow and lender with read-update conflict and commit operation governed by Commit-on-Termination dependency. The performance of Shadow Sensitive SWIFT is compared with shadow PROMPT, SWIFT and DSS-SWIFT commit protocols (Haritsa, Ramamritham, & Gupta, 2000; Shanker, Misra, & Sarje, 2006; Shanker, Misra, Sarje, & Shisondia, 2006) for both main memory resident and disk resident databases with and without communication delay. Simulation results show that the proposed protocol improves the system performance up to 5% as transaction miss percentage.

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PERDURABLE: A Real Time Commit Protocol

Recent Trends in Information Reuse and Integration ◽

10.1007/978-3-7091-0738-6_1 ◽

2011 ◽

pp. 1-17 ◽

Cited By ~ 7

Author(s):

Udai Shanker ◽

B. Vidyareddi ◽

Anupam Shukla

Keyword(s):

Real Time ◽

Commit Protocol

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