Syed Abdul Mutalib Al Junid

Development of DNA sequencing accelerator based on Smith Waterman algorithm with heuristic divide and conquer technique for FPGA implementation

In this paper, a new approach is introduced to reduce the complexity of the Smith Waterman algorithm for FPGA implementation. We have developed the technique for the fastest comparison of the two DNA sequencing using Verilog on the Xilinx ISE 7.1. The Simulation has been running on the ModelSim XE III 6.0. The combinational delay for the proposed smith waterman algorithm based on divide and conquers technique sequencing is 10.214 ns while the original is 10.295 ns. We have proved that smith waterman algorithm based on divide and conquers technique gives better performance than existing technique.

An Intelligent Classification Model for Rubber Seed Clones Based on Shape Features through Imaging Techniques

This paper describes research work in developing an intelligent model for classifying selected rubber tree series clones based on shape features using image processing techniques. Sample of rubber tree seeds are captured using digital camera where the RGB color image are processed involving segmentation algorithm which includes thresholding and morphological technique. Shape features such as area, perimeter and radius are extracted from each image. Two models are being designed. Model 1 is represented by 38 input features while Model 2 is represented by a reduction of input size using Principle Component Analysis (PCA). The inputs for both models are then used to train a multi-layer perceptron Artificial Neural Network (ANN) using Levenberg-Marquardt algorithm. 160 samples are used as training set while another 100 samples are used for testing. The optimized ANN models are then evaluated and validated through analysis of performance indicators regularly applied in classification research work via pattern recognition. Findings in this work have shown that the optimized Model 2 has the best accuracy of 84% with more than 70% achievement for sensitivity and specificity.

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.

Comparative study for DNA data minimization technique on FPGA

Data minimization technique and existing DNA sequence data representation is compared and presented in this paper. The architecture of these two modules is compared and analyzed to study the complexity and performance characteristics of the system when dealing with large DNA sequences data on FPGA. These two technique is designed, synthesized and simulated using Altera Quartus II version 9.1 and targeted to Altera Cyclone II FPGA EP2C35 for determine the performance and complexity characteristic when running with DNA sequences data. Simulation results presented in this paper show it effects and feasibility when dealing with DNA sequences data on FPGA platform.

Real-Time Remote Monitoring with Data Acquisition System

The purpose of this system is to provide monitoring system for an electrical device and enable remote monitoring via web based application. This monitoring system allow the user to monitor the device condition from anywhere as the information will be synchronised to the website. The current and voltage reading of the monitored equipment, ambient temperature and humidity level are monitored and recorded. These parameters will be updated on the web page. All these sensor are connected to the microcontroller and the data will saved in micro secure digital (SD) card and send all the gathered information to a web page using the GPRS service connection synchronously. The collected data will be displayed on the website and the user enable to download the data directly from the website. The system will help user to monitor the devices condition and ambient changes with ease. The system is successfully developed, tested and has been installed at residential area in Taman Cahaya Alam, Section U12, Shah Alam, Selangor, Malaysia.

High-sensitivity gas detection and monitoring system for high-risk welding activity

This study attempted to investigate and design a new mechanism in monitoring safety by detecting gas concentration levels to prevent an explosion during welding activities at a high-risk site. The objective of this project was to design and develop a new safety precaution monitoring system during welding activity using a low-cost microcontroller to improve the current practice. The study was conducted by dividing the project into three stages: sensing, controlling, and notification. At the sensing stage, different gas concentration levels have been tested and analyzed to determine the safety range or level. However, the controller part managed the responses based on the detection of gas in the environment. Indicator and secure digital memory have been used to notify and record the activity during the operation. In the environment test, the system starts to trigger when sensing the level produced at 1.416 V, which represents 30% of the gas concentration. Nevertheless, the gas sensor required a 10-second initialized time to stabilize and produce the desired sensing level. At the end of this paper, the system has been successfully designed, developed, and tested at the prototype level.

Improved data minimization technique in reducing memory space complexity for DNA local alignment accelerator application

Improved data minimization technique to optimize the length of DNA sequence and alignment result characters representation is presented in this paper. The primary objective is to improve and optimize data representation for DNA sequences alignment and result character. The proposed design change in algorithm and architecture is presented in this paper. Algorithm design based on binary equivalent method is used to obtain the optimal size of characters representation. The code is written, compiled and simulated using Altera Quartus II Version 9.0 EDA tools. Verilog Hardware Description Language (HDL) and Altera Cyclone II EP2C35 FPGA are used as coding language and target device respectively. In addition, the structural modelling technique is used to reduce the design complexity. Simulation result showed that the improved data minimization technique takes 50% more memory compared to previous work, but it covers 6 DNA sequences and alignment result characters.

Sequence alignment using systolic array for an accelerator

Performance and large memory space are the most prominent issues highlighted for local DNA sequences alignment. Therefore, this study is an attempt to test the systolic array approach for Smith-Waterman (SW) algorithm for improving the performance of DNA sequence alignment accelerator. The design was developed using LabVIEW and targeted to Xilinx Spartan 3E while the original SW has been used as a benchmark for performance comparison. Systolic array SW has recorded better performance as compared to original SW. Thus, by applying systolic array concept, it will improve the alignment performance whilst minimize the complexity of the design.

Implementation of genetic algorithm for optimizing DNA sequence alignment

This paper presents potential of genetic algorithms (GA) for optimizing DNA sequences alignment based on dynamic programming or evolutionary programming. The ultimate objective of this paper is to accelerate the process of DNA sequences alignment towards reducing the time and space complexity. In addition, the theoretical study, design, compilation and simulation of the proposed GA were carried out using Xilinx ISE 12.3 EDA software by applying divide and conquer design technique towards finding the optimal solution. The proposed GA has shown that it can solve up to 10 DNA sequences base pair in three clock cycles with reduction time up to 84.21 % as compare to original Smith-Waterman algorithm. As a conclusion, the proposed GA has proved and able to optimize the existing DNA sequences alignment time complexity.

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.