34,359 research outputs found
Applications and Challenges of Real-time Mobile DNA Analysis
The DNA sequencing is the process of identifying the exact order of
nucleotides within a given DNA molecule. The new portable and relatively
inexpensive DNA sequencers, such as Oxford Nanopore MinION, have the potential
to move DNA sequencing outside of laboratory, leading to faster and more
accessible DNA-based diagnostics. However, portable DNA sequencing and analysis
are challenging for mobile systems, owing to high data throughputs and
computationally intensive processing performed in environments with unreliable
connectivity and power.
In this paper, we provide an analysis of the challenges that mobile systems
and mobile computing must address to maximize the potential of portable DNA
sequencing, and in situ DNA analysis. We explain the DNA sequencing process and
highlight the main differences between traditional and portable DNA sequencing
in the context of the actual and envisioned applications. We look at the
identified challenges from the perspective of both algorithms and systems
design, showing the need for careful co-design
Nanopore Sequencing Technology and Tools for Genome Assembly: Computational Analysis of the Current State, Bottlenecks and Future Directions
Nanopore sequencing technology has the potential to render other sequencing
technologies obsolete with its ability to generate long reads and provide
portability. However, high error rates of the technology pose a challenge while
generating accurate genome assemblies. The tools used for nanopore sequence
analysis are of critical importance as they should overcome the high error
rates of the technology. Our goal in this work is to comprehensively analyze
current publicly available tools for nanopore sequence analysis to understand
their advantages, disadvantages, and performance bottlenecks. It is important
to understand where the current tools do not perform well to develop better
tools. To this end, we 1) analyze the multiple steps and the associated tools
in the genome assembly pipeline using nanopore sequence data, and 2) provide
guidelines for determining the appropriate tools for each step. We analyze
various combinations of different tools and expose the tradeoffs between
accuracy, performance, memory usage and scalability. We conclude that our
observations can guide researchers and practitioners in making conscious and
effective choices for each step of the genome assembly pipeline using nanopore
sequence data. Also, with the help of bottlenecks we have found, developers can
improve the current tools or build new ones that are both accurate and fast, in
order to overcome the high error rates of the nanopore sequencing technology.Comment: To appear in Briefings in Bioinformatics (BIB), 201
An Approximately Optimal Algorithm for Scheduling Phasor Data Transmissions in Smart Grid Networks
In this paper, we devise a scheduling algorithm for ordering transmission of
synchrophasor data from the substation to the control center in as short a time
frame as possible, within the realtime hierarchical communications
infrastructure in the electric grid. The problem is cast in the framework of
the classic job scheduling with precedence constraints. The optimization setup
comprises the number of phasor measurement units (PMUs) to be installed on the
grid, a weight associated with each PMU, processing time at the control center
for the PMUs, and precedence constraints between the PMUs. The solution to the
PMU placement problem yields the optimum number of PMUs to be installed on the
grid, while the processing times are picked uniformly at random from a
predefined set. The weight associated with each PMU and the precedence
constraints are both assumed known. The scheduling problem is provably NP-hard,
so we resort to approximation algorithms which provide solutions that are
suboptimal yet possessing polynomial time complexity. A lower bound on the
optimal schedule is derived using branch and bound techniques, and its
performance evaluated using standard IEEE test bus systems. The scheduling
policy is power grid-centric, since it takes into account the electrical
properties of the network under consideration.Comment: 8 pages, published in IEEE Transactions on Smart Grid, October 201
A Case Study in Coordination Programming: Performance Evaluation of S-Net vs Intel's Concurrent Collections
We present a programming methodology and runtime performance case study
comparing the declarative data flow coordination language S-Net with Intel's
Concurrent Collections (CnC). As a coordination language S-Net achieves a
near-complete separation of concerns between sequential software components
implemented in a separate algorithmic language and their parallel orchestration
in an asynchronous data flow streaming network. We investigate the merits of
S-Net and CnC with the help of a relevant and non-trivial linear algebra
problem: tiled Cholesky decomposition. We describe two alternative S-Net
implementations of tiled Cholesky factorization and compare them with two CnC
implementations, one with explicit performance tuning and one without, that
have previously been used to illustrate Intel CnC. Our experiments on a 48-core
machine demonstrate that S-Net manages to outperform CnC on this problem.Comment: 9 pages, 8 figures, 1 table, accepted for PLC 2014 worksho
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