S. A. M. Al Junid

Development of Novel Data Compression Technique for Accelerate DNA Sequence Alignment Based on SmithWaterman Algorithm

This paper presents the development of high performance accelerating technique for DNA sequences alignment. The scope of the paper focuses on speed optimization and memory reduction of the existing technique on initialization module. The novel development of the optimization using data compression technique for accelerates the Smith-Waterman (SW) algorithm has been revealed through this paper. This technique has been implemented on hardware based acceleration device. The development is targeted to Altera Cyclone II 2C70 FPGA and using 50MHz oscillator. The code is written in verilog HDL syntax using Quartus 2 version 7.2 and the simulation is verified using Quartus 2 version 7.2 simulator tool. The theoretical analysis and simulation result based on implementation of the design using FPGA are presented and well organized in this paper. The comparative study based on theoretical and simulation results of this technique has been made to accomplish result of analysis. The compilation result for data compression technique development of SW algorithm consisting of 73 logic elements with 93.75% reduction in memory space requirement.

Optimization of DNA Sequences Data to Accelerate DNA Sequence Alignment on FPGA

This paper presents the design and development of high performance accelerating and optimization technique for accelerate the process of DNA sequences alignment. The scope of the paper focuses on memory and speed optimization by optimizing and mapping the DNA sequences data before alignment. This optimization technique is designed based on novel data compression technique in optimizing the numbers of data transmitted from computer to DNA sequences alignment accelerator. Consequently, the numbers of data per serial data transmission for alignment can be optimize and accelerate up to 400% greater than conventional DNA sequences alignment accelerator system. This technique has been design and implemented on hardware based acceleration device and targeted to Altera Cyclone II 2C70 FPGA and using 50MHz oscillator for clock source. The code is written in verilog HDL syntax using Quartus 2 version 7.2 and the simulation is verified using Quartus 2 version 7.2 simulator tools. As a result, the theoretical analysis, simulation and implementation result based on development and implementation of the proposed design on FPGA are presented and well organized in this paper. The comparative study based on theoretical, simulation and implementation results of this technique has been made to accomplish result of analysis.

Performance analysis of dual-axis solar tracking system

This paper presents the performance analysis of dualaxis solar tracking system using Arduino. The ultimate objective of this project is to investigate whether static solar panel is better than solar tracker, or the opposite. This project is divided into two stages namely, hardware and software development. In hardware development, five light dependent resistors (LDR) were utilized to capture the maximum light source from the sun. Two servo motors also were employed to move the solar panel to maximum light source location sensed by the LDRs. As for the software part, the code was constructed by using C programming language and was targeted to the Arduino UNO controller. The performance of the solar tracker was analyzed and compared with the static solar panel and the result showed that the solar tracker is better than the static solar panel in terms of voltage, current and power. Therefore, the solar tracker is proven more effective for capturing the maximum sunlight source for solar harvesting applications.

Classification of Rubber Tree Leaf Disease Using Spectrometer

In this paper, the classification of five types of rubber leaf disease by using the spectrometer and SPSS are presented. There are five of leaf disease that have been used as samples which are Oidium secondary leaf fall, Fusicoccum Leaf Blight, Bird eye’s spot and Anthracnose. The reflectance of the infected leaves sample is measured by using MCS600 Carl Zeiss spectrometer. Besides, Aspect Plus, a universal spectroscopy program from Zeiss manages to measure the spectral regions of the leaves sample. Further analysis and justification are completed by using approximate statistical tools from SPSS. The results obtained show that there are strong evidences that these diseases can be discriminated from each other using a spectrometer.

Design and Analysis of High Performance and Low Power Matrix Filling for DNA Sequence Alignment Accelerator Using ASIC Design Flow

Efficient sequence alignment is one of the most important and challenging activities in bioinformatics. Many algorithms have been proposed to perform and accelerate sequence alignment activities. Among them Smith-Waterman (S-W) is the most sensitive (accurate) algorithm. This paper presents a novel approach and analysis of High Performance and Low Power Matrix Filling for DNA Sequence Alignment Accelerator by using ASIC design flow. The objective of this paper is to improve the performance of the DNA sequence alignment and to optimize power reduction of the existing technique by using Smith Waterman (SW) algorithm. The scope of study is by using the matrix filling method which is in parallel implementation of the Smith-Waterman algorithm. This method provides more efficient speed up compared to the traditional sequential implementation but at the same time maintaining the level of sensitivity. The methodology of this paper is using FPGA and Synopsis. This technique is used to implement the massive parallelism. The design was developed in Verilog HDL coding and synthesized by using LINUX tools. Matrix Cells with a design area 8808.307mm2 at 40ns clock period is the best design. Thus the power required at this clock period also smaller, dynamic power 111.1415uW and leakage power 212.9538 Nw. This is a large improvement over existing designs and improves data throughput by using ASIC design flow.

Design and Analysis of 8-bit Smith Waterman based DNA Sequence Alignment Accelerator's Core on ASIC Design Flow

This paper present the design and analysis of 8-bit Smith Waterman (SW) based DNA sequence alignment accelerators core on ASIC design flow. The objective of the project is to construct and analyse the core module that can perform the Smith Waterman algorithms operations, which are comparing, scoring and back tracing, using the technique used in (1,2) on ASIC design flow. Nowadays, the DNA and protein databases are increasing rapidly and these add new challenges to the current computing resources. New techniques, algorithms, designs, hardware and software that can maximize the computational speed, minimize the power and energy consumption, and boost the throughput need to be developed in order to meet the current and future requirements. In DNA sequence alignment process, the DNA sequences are compared using different alignment requirement techniques such as global alignment, local alignment, motif alignment and multiple sequence alignment. Moreover, there are several algorithms used to perform the sequence alignment process such as Needleman- Wunch algorithm, Smith Waterman algorithm, FASTA, BLAST and so on. For this paper, the focus is on local alignment using Smith Waterman algorithm. The design was modelled using Verilog and the functionality was verified using Xilinx and VCS. The RTL codes was mapped and synthesized to technology based logics using Design Compiler (DC). The cores layout was implemented using Place and Route tool, IC Compiler (ICC). Based on the results, the core design area was 2108.937620 um 2 .The maximum time constraints were 6.85 ns and 6.93 ns in ICC and PT. The minimum time constraints were 0.28 ns and 0.30 ns in ICC and PT respectively. In conclusion, the design had been successfully implemented on ASIC design flow. Moreover, the results showed that the design can be further optimized to work at faster speeds.

Artificial Neural Networks Based Algorithm for Identifying Engine Oil Parameters

Engine oil is an essential type of lubricant normally used by internal combustion engines. The main job is to lubricate moving part of the engine. Engine oil is also performed to clean, inhibits corrosion and cools the engine by sinking the heat away from the main structure of the engine. However, the viscosity of the engine oil varies with respect to changes in mileage and the change of lubricant on schedule is always inaccurate. As a result, engine oil becomes out of condition for after a period of usage, resulting poor performance and increase cost and maintenance. Viscosity is a parameter to measure resistance of a fluid to flow. Through the theoretical and experimental method, this paper verifies the measurement of transmittance percentages of viscosity in terms of infrared wavelength with respect to several classes’ mileage distances. The most robust networks are also identified to be applied in this study. Finally, this information can be used in designing sensor to detect the degree of viscosity and development of the decay of lubricant evaluation index.

Capability of Indium Tin Oxide as a sensing mechanism for engine oil degradation monitoring

This paper presents the capabilities of glass Indium Tin Oxide (ITO) for engine oil degradation sensing monitoring system with resistive application. The glass ITO is a resistive material which has the ability to measure oil samples in resistive. This material is ideal with its durability and heat resistant characteristics. The characteristics of Indium Tin Oxide will be measured in voltage and resistance with suitable ROIC circuit interface. Aim for this research is to classify the resistance value with the same type engine oil with different lifespans. It is believe that this new type bulk resistive material can improve the oil degradation sensing in automotive application and cheaper manufacturing. A simple innovation system is constructed to provide oil conditioning in vehicle with implementing the small glass ITO at the end of the dipstick. This innovation is more precise way to determine the oil degradation with conditioning method.

Design and Analysis of High Performance Matrix Filling for DNA Sequence Alignment Accelerator Using ASIC Design Flow

This paper presents the design and analysis high performance matrix filling for DNA sequence alignment accelerator using ASIC design flow. The objective of this paper is to design and analysis matrix module of DNA sequence alignment accelerator using clock cycle to get high performance. The scope of this paper is to optimize the DNA sequences alignment on the matrix filling module by implementing a parallel method of the Smith-Waterman algorithm. This method provides magnificent speed up over than traditional sequential implementation methods while it s e n s i t i v i t y detection is still remained. To optimize the performance of the algorithm by exploiting parallelism in the design several techniques have been developed. In the advanced engineering technology, the massive parallelism can be implemented by using the Field Programmable Logic Array (FPGA) and ASIC techniques. The design was developed in Verilog HDL coding, synthesis and implemented by using Synopsys EDA tools. Using the Synopsys EDA tools, the optimum combination o f parameters is manipulated i n or de r to produce the o p t i m i z e IC. The design produces an matrix filling IP that can work at 3.75 ns clock period before it start to show the negative slack . The technique proposed increased the performance of the module significantly by reducing the clock cycle needed by the matrix filling from 16 cycles initially to single clock cycle. It was successfully implemented on ASIC design flow.

Wireless Sensors Integration for Bend Angle and Distance Rate of Gait Measurement

This project describes the development of a gait shoe system thats capable to continuous monitoring the gait analysis by using the Internet of Things (IoT) or wireless system approach. The system consists of two bend sensors, one ultrasound sensor, Intel Edison, Minnow board, Bluetooth module, mobile application and a database system. Currently, gait analysis is carried out in a motion laboratory that provides a full analysis of the motion body segments using a super highly accurate computer. This method is expensive and not affordable for everyone, indeed it requires quite a lot of maintenances. Furthermore, gait analysis requires a specialist to conduct and examine the patients, which means patients have to pay a lot of visits to hospital just only to get a treatment and feedback from the doctor that resulted waste of time, energy and money. Thus, this project will introduce a new and advance ways solution in order to evaluate the gait parameters. In this project, it will focus on two types of gait parameters, which is plantar flexion and dorsiflexion. One of the bend sensors is intended to be place under the sole and another one is around the ankle. The ultrasound sensor it will be assembled at the side of the shoe. The advantages of the completed system are when both of these sensors recorded all the gait information the subject or the patient still can do the daily routine life without interruption. The designed gait shoe is also able to display results from the analysis and sent it directly to the medical specialist through database to the data center analysis or online monitoring and at the same time the patient also can monitor via mobile phone.