M. F. M. Idros

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.

Quantitative Analysis of Spectroscopy's Study for Engine Oil Degradation Monitoring Due to Temperature Effect

This paper presents the quantitative analysis of spectroscopy measurement for engine oil degradation prediction due to the temperature effect. The main objective of this project is to study the behavior of engine oil if the continues high temperature are applied to the engine oil as compared to the effect of running condition. Two types of engine oil were used as samples in this project from grade SAE 10W40 and 20W50. The experiment was done by heating the engine oil with inductance coil at 100oC for 5 minutes and then cool it about half an hour before continue heating for other 5 minute. This process repeat continuously until 100 minutes and samples were taken at every 10 minutes after cooling process. A spectrometer is used to measure the percentage reflectance of the samples. Data was arranged and analyzed in order to predict the degradation of the engine oil. The data will be used to develop an optical sensor for signal processing in monitoring the engine oil degradation.

Potential of Graph Theory Algorithm Approach for DNA Sequence Alignment and Comparison

Today, the need for high performance computation method for align biological sequence has increased due to exponential growth of biological sequence databases. Therefore, this paper is an attempt to study and investigate the potential of graph theory algorithm approach for optimizing the alignment process of DNA sequences towards determines the region of common between two or more DNA sequences. This study will initially involve the modification of algorithms, mathematical formulation, logic design, simulation, verification and implementation of graph-theory algorithms in DNA sequences alignment context. The design and simulation was carried out using Altera Quartus II version 7.2 EDA software and targeted to Altera Cyclone II FPGA. As a result, the proposed DNA sequences alignment using graph theory algorithm able to determine the optimal path for four DNA sequences base-pair in two clock cycle with reduction 71.42% compare to Smith Waterman algorithm. Finally, the new proposed DNA sequences using graph theory algorithm alignment can accelerate the process of DNA sequences alignment faster than existing DNA sequences alignment on hardware accelerator.

Implementation of Real-Time Kinematic Data to Determine the Ionospheric Total Electron Content

Ionosphere layer is an important medium in communication system. At this layer where the total electron content exist because of ionization by the Suns extreme ultraviolet radiation, meanwhile the night side ionosphere electron content is reduced by chemical recombination. Maximum Total Electron Content (TEC) was detected at 0500 Local Time Clock (LTC) and will decrease gradually and reached its minimum at 2200 LTC. TEC during the day is higher than at night. The ultraviolet (UV) radiation from the sun ionizes fractions of the neutral atmosphere and forms the ionosphere. The elevation angle of satellite will also influence the TEC value. The higher elevation angle, the value of vertical TEC will also increase. The data from GPS Stations in RINEX format is supplied by Department of Survey and Mapping Malaysia (JUPEM). The data is taken from two different stations located at GPS Station Arau, Perlis and GPS Station Universiti Teknologi Malaysia Skudai, Johor.

A design of butterworth low pass filter's layout basideal filter approximation on the ideal filter approximation

This paper presents the study and analysis on Butterworth Low Pass filter, to discover the filters order effect on the ideal filter approximation. Theoretically, as the numbers of order increased, the filter will approximate ideal filter characteristics. The challenges are; by increasing the filters order, it will increase the circuit complexity and the cost. In order to reduce the circuit complexity, the Sallen-Key topology has been selected since the topology requires fewer components. This paper also presents the techniques and issues that should be considered while designing the schematic and layout of the filter.

Design, fabrication and characterization of conductivity sensor using printed circuit board

This paper described about design, fabrication and characterization of conductivity sensor using printed circuit board (PCB). The main objective is to sense the conductivity of aqua agriculture. A sensor was design by using interdigital capacitor concept where the term interdigital refers to pattern of fingers that is resembled by the shape and relative position of the electrodes. This sensor was fabricated by using PCB in order to minimize the cost than the existing conductivity sensor. Sensor performance was characterized by various test setups to check ability and accuracy of the sensor. From the result, it shown that the sensor has very good sensitivity with correlation coefficient R2 of 0.969.

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.

Mobile Carbon Monoxide Monitoring System Based on Arduino-Matlab for Environmental Monitoring Application

Nowadays, the increasing level of carbon monoxide globally has become a serious environmental issue which has been highlighted in most of the country globally. The monitoring of carbon monoxide content is one of the approaches to identify the level of carbon monoxide pollution towards providing the solution for control the level of carbon monoxide produced. Thus, this paper proposed a mobile carbon monoxide monitoring system for measuring the carbon monoxide content based on Arduino-Matlab General User Interface (GUI). The objective of this project is to design, develop and implement the real-time mobile carbon monoxide sensor system and interfacing for measuring the level of carbon monoxide contamination in real environment. Four phases or stages of work have been carried out for the accomplishment of the project, which classified as sensor development, controlling and integrating sensor, data collection and data analysis. As a result, a complete design and developed system has been verified with the handheld industrial standard carbon monoxide sensor for calibrating the sensor sensitivity and measurement in the laboratory. Moreover, the system has been tested in real environments by measuring the level of carbon monoxide in three different lands used location; industrial area; residential area and main road (commercial area). In this real environment test, the industrial area recorded the highest reading with 71.23 ppm and 82.59 ppm for sensor 1 and sensor 2 respectively. As a conclusion, the mobile realtime carbon monoxide system based on the Arduino-Matlab is the best approach to measure the carbon monoxide concentration in different land-used since it does not require a manual data collection and reduce the complexity of the existing carbon monoxide level concentration measurement practise at the same time with a complete data analysis facilities.