2018-12-16T22:57:08Z
http://jacr.iausari.ac.ir/?_action=export&rf=summon&issue=914
Journal of Advances in Computer Research
JACR
2345-606X
2345-606X
2014
5
2
Improved Alignment of Bisulfite Sequencing Data Using CpG Islands
Nadia
Barjaste
Reza
Nadimi
Majid
Alipour
<em>DNA methylation is an important biological process involving in human disease such as cancer Insomia and Diabetes. Bisulfite sequencing (BS-Seq) with next-generation technology is an accurate method for measuring DNA methylation. BS-seq data analysis is a considerable way to recognize methylated cytosines and several tools have been developed to analysis BS-Seq such as BS-Seeker, B-SOLANA, BRAT, BSMAP and etc. In this paper, we propose a novel idea to get more efficiency in the sequencing process, This idea will improve the rate of accuracy in the BSOLANA alignment tool using a new method in the preprocessing step. Our method is based on modification in some regions of DNA strand named CpG islands. CpG islands are significant regions in DNA strand which frequency of methylated cytosines is less than other CpG contexts. We compared our method with previous methods in the preprocessing of the original BSOLANA tool using on HG19 reads. The comparison shows that new method provides more ability to align read sequences in the BSOLANA.</em>
Bisulfite sequencing
DNA methylation
Alignment tools
2014
05
01
1
5
http://jacr.iausari.ac.ir/article_4431_f271fab0f420ee643645012b61e031db.pdf
Journal of Advances in Computer Research
JACR
2345-606X
2345-606X
2014
5
2
Data Steganography on VoIP through Combination of Residue Number System and DNA Sequences
Azin
Azizifard
Mohamad
Qermezkon
Tahereh
Postizadeh
Hamid
Barati
<em>Today, optimal performance and cost advantages of using Internet telephony are obvious. Despite current standardized techniques, voice transferring through protocol (VoIP) has lower security than traditional telephony. One of the most important security issues which should be noticed in using VoIP is end -to-end user<sup>2</sup> identity, i.e. whenÂ there is a connection between user A and B, user A should be assured of the identity of user B, and vice versa. The authentication of identity is one of so important information that could guarantee the security and integrity of information [1]. In this study, the security of VoIP and data steganography through the protocol has been investigated. Finally, a technique for data steganography<sup>4</sup> over this protocol will be proposed using the method of Residue Number System<sup>3</sup>. Also, using the combination of RNS, DNA sequences, and Huffman compressing algorithm, an algorithm is proposed for data steganography through VoIP. The algorithm improves security of the process of transmission of hidden text and can use the bandwidth effectively.</em>
Voice Over Internet Protocol
Steganography
Session Initiation Protocol (SIP)
Residue Number System
DNA String
Huffman Algorithm
2014
05
01
7
22
http://jacr.iausari.ac.ir/article_5676_ab8f6fefc223cff83cdfc73eac2c4b81.pdf
Journal of Advances in Computer Research
JACR
2345-606X
2345-606X
2014
5
2
Time-Distance Optimal Trajectory Planning For Mobile Robots On Straight And Circular Paths
Hossein
Barghi Jond
Adel
Akbarimajd
Nurhan Gursel
Ozmen
<em>Trajectories generally used to describe the space and time required to perform a desired motion task for a mobile robot or manipulator system. In this paper, we considered a cubic polynomial trajectory for the problem of moving a mobile robot from its initial position to a goal position in over a continuous set of time. Along the path, the robot requires to observe a certain acceleration profile. Then, we formulated an optimization approach to generate optimal trajectory profiles for the mobile robot in the cases of maximum-distance and minimum-time problems. The optimization problem presented to find the trajectory strategy that would give the robot time-distance optimality to move from a start point to an end point where the robot should stay inside its acceleration limits all the time. The problem solved analytically because as it is well known, numerical solutions and iterative methods are time-consuming, therefore, our closed-form solutions demand low computation time. Finally, the results are verified by simulations.</em>
Mobile Robots
Trajectory Planning
constrained optimization
Acceleration limits
2014
05
01
23
36
http://jacr.iausari.ac.ir/article_5677_0007b1cd551c8dbfb53bc344e7b385c7.pdf
Journal of Advances in Computer Research
JACR
2345-606X
2345-606X
2014
5
2
Improving Reliability through Selecting Data in Grid Distributed System and Comparing it with Other Presented Algorithms
Sedigheh
Navaezadeh
Iman
Zangeneh
Elham
Tavakol
<em>In the past, one of the biggest problems requiring long and complicated computing was lack of appropriate software and hardware facilities in order to compute them in a proper and logical time. Due to this issue, sometimes, computing lasted for several days, months or years. Therefore, computer science pioneers tried to find a solution for this problem. One of the ways was to present Grid computing. In order to present high-quality service, Grid integrated separate organizations, and represented virtual organization. In this study, we improved reliability by using iteration feature as well as distributing and duplicating resources. We considered and used the first nearest resource of the second nearest resource for duplication in order to place data. In addition, in this study, we compared our proposed method with other algorithms.</em>
Grid
data propagation
firefly algorithm
2014
05
01
37
44
http://jacr.iausari.ac.ir/article_5453_1edc2c87f3a638b7a60f5e11499b80f6.pdf
Journal of Advances in Computer Research
JACR
2345-606X
2345-606X
2014
5
2
Cuckoo Optimization Algorithm in Cutting Conditions During Machining
Ahmad
Esfandiari
<em>Optimization of </em><em>cutting conditions </em><em>is a non-linear optimization with constraint and it is very important to the increase of productivity and the reduction of costs. In recent years, several evolutionary and meta-heuristic optimization algorithms were introduced. The Cuckoo Optimization Algorithm (COA) is one of several recent and powerful meta-heuristics which is inspired by the cuckoos and their lifestyle. </em><em>In this paper, COA, Simulated Annealing (SA), Genetic Algorithm (GA) and Imperialist Competitive Algorithm (ICA) are first applied to five test functions and the performance of these algorithms is compared. </em><em>These algorithms are then used to optimize the cutting conditions. The results showed that COA has more capabilities such as accuracy, faster convergence and better global optimum achievement than others.</em>
Cuckoo Optimization Algorithm (COA)
cutting conditions
Imperialist Competitive Algorithm (ICA)
Simulated Annealing (SA)
Genetic algorithm (GA)
2014
05
01
45
57
http://jacr.iausari.ac.ir/article_5951_2f1e9b27d9753b543eb6eeb63c3dcf88.pdf
Journal of Advances in Computer Research
JACR
2345-606X
2345-606X
2014
5
2
Presenting a Fault Tolerant Mechanism for Buffering Fault in Network on Chips
Sadeq
Lotfi
Ali
Afzali-kusha
Marzie
Saffari
<em>As technology scales deep into the nanometer regime, on-chip communication becomes more susceptible to transient noise sources, such as crosstalk, external radiation, and spurious voltage spikes. The Network on chip s modularity and reusability has brought about the use of error control methods to address transient errors in Network on chip links.In this work, we design a fault tolerance router with efficient area and power dissipated. Actually, we exploit the free virtual channel to store the redundant data. Virtual channel is used for deadlock avoidance it can be implement as 2, 4 or 8 channel. The almost time we can find a free channel that we can use in fault tolerance mechanism. We describe the proposed architecture with VHDL and implemented with synopsis compiler design. We use analytical model to evaluate the fault tolerance. The result shows that we improve the dynamic power dissipation, area, and reliability. </em>
Network on chip
Buffering
Virtual channel
Fault tolerance router
2014
05
01
59
68
http://jacr.iausari.ac.ir/article_6110_cb7596b5c6dfe1eb30b824d41e3f4876.pdf
Journal of Advances in Computer Research
JACR
2345-606X
2345-606X
2014
5
2
IPSO-SQP Algorithm for Solving Time Optimal Bang-Bang Control Problems and Its Application on Autonomous Underwater Vehicle
Tahereh
Taleshian
Abolfazl
Ranjbar Noei
Reza
Ghaderi
In this paper, an integration of Improve Particle Swarm Optimization (IPSO) in combination with Successive Quadratic programming (SQP) so called IPSO-SQP algorithm is proposed to solve time optimal bang-bang control problems. The procedure is found not sensitive to the initial guess of the solution. Due to random selection in the first stage of the search process, the chance of converging to the global optimum is significantly increased, without sticking in a local optimum. The combined technique gains both advantages of its original algorithms. The IPSO directly minimizes the cost function without the need for gradient-based techniques. The performance of the outcome will be increased when the SQP immediately undertakes the optimization task. This is shown via applying those on some other nonlinear systems. Consequently, the proposed algorithm is successfully applied on a time optimal bang-bang control of an autonomous underwater vehicle. A pitchprogramming task is also investigated for the autonomous underwater vehicle by designing an optimal PID controller .
Autonomous Underwater Vehicle
IPSO-SQP Algorithm
Optimal PID Controller
Pitch Programming
Time Optimal Bang-Bang Control
2014
05
01
69
88
http://jacr.iausari.ac.ir/article_6144_2990a28a62eea5d0a712c13912744036.pdf
Journal of Advances in Computer Research
JACR
2345-606X
2345-606X
2014
5
2
Comparison of Conventional Salient-Pole Synchronous Generators and Permanent-Magnet-Assisted Salient-Pole Synchronous Generators based on Finite Element Analysis
Reza
Ilka
Yousef
Alinejad-Beromi
Hossein
Asgharpour-Alamdari
This paper presents a novel salient pole synchronous generator i.e. permanentmagnet- assisted salient-pole synchronous generator (PMa-SGs). Due to saturation of conventional synchronous generators (SGs), permanent-magnet-assisted salientpole synchronous generators (PMa-SGs) are presented. PMa-SGs are a new type of salient-pole synchronous machines with extra permanent magnets (PMs) between the adjacent pole shoes. Placing PMs between adjacent pole shoes leads to a reduction in flux saturation plus an increase in armature flux linkage. In other words, the generator can operate at higher capacity. In this paper, a comparative study is carried out between conventional SGs and PMa-SGs based on finite element analysis (FEA). This is done via simulation of a PMa-SG compared to a conventional SG. Simulation Results show superiority of PMa-SGs over SGs. In fact, in PMa-SG maximum flux density in stator core is increased and pole bodies are not saturated. Besides, PMa-SG has higher flux linkage compared to conventional SG. Therefore, higher voltage could be produced in the generator. In other words, the output performance of the PMa-SG is considerably better than that of a conventional SG.
Synchronous Generator (SG)
Magnetic Saturation
Permanent Magnet-assisted
salient-pole synchronous generators (PMa-SGs)
Finite Element Analysis
(FEA)
2014
05
01
89
96
http://jacr.iausari.ac.ir/article_6145_3f145cafe1f81ef997bf99dd91969418.pdf
Journal of Advances in Computer Research
JACR
2345-606X
2345-606X
2014
5
2
MAC Protocols in Underwater Wireless Sensor Networks: Issues and Simulations
Reza
Mohammadi
Seyyed Yahya
Nabavi
Reza
Javidan
Underwater Acoustic Wireless Sensor Network (UAWSN) use acoustic signals to transmit data. Acoustic signals in underwater environment have high bit error rate, long propagation delay and limited bandwidth. Another constraint in UWASN is energy. Due to these constraints, design of energy and bandwidth efficient and propagation delay aware MAC protocol is a great challenge in UWASN. Underwater sensor nodes have to share medium. The main role of the MAC layer protocol is to decide when a node accesses a shared medium and to resolve any conflicts between nodes. In this paper, we evaluate the performance of three famous underwater MAC protocols UWAN-MAC[1], R-MAC[2] and Slotted FAMA[3] in terms of packet drop rate, throughput and energy consumption. We have used Aquasim simulator to evaluate MAC protocols.
underwater MAC protocols
R-MAC
UWAN_MAC
Slotted FAMA
underwater acoustic wireless sensor networks
underwater simulation
2014
05
01
97
109
http://jacr.iausari.ac.ir/article_6146_b82a0eef329179d77b960f9d508620e4.pdf
Journal of Advances in Computer Research
JACR
2345-606X
2345-606X
2014
5
2
Chaotic Time Series Prediction by Auto Fuzzy Regression Model
Haleh
Nazari
Homayun
Motameni
Babak
Shirazi
Since the pioneering work of Zadeh, fuzzy set theory has been applied to a myriad of areas. Song and Chissom introduced the concept of fuzzy time series and applied some methods to the enrolments of the University of Alabama. Thereafter we apply fuzzy techniques for system identification and apply statistical techniques to modelling system. An automatic methodology framework that combines fuzzy techniques and statistical techniques for nonparametric residual variance estimation is proposed. The methodology framework is creating regression model by using fuzzy techniques. Identification is performed through learning from examples method introduced by Wang and Mendel algorithm. Delta test residual noise estimation is used in order to select the best subset of inputs as well as the number of linguistic labels for the inputs. An experimental result for chaotic time series prediction are compared with statistical model and shows the advantages of the proposed methodology in terms of approximation accuracy, generalization capability and linguistic interpretability.
fuzzy techniques
statistical techniques
chaotic time series
prediction
Regression
2014
05
01
111
116
http://jacr.iausari.ac.ir/article_6147_bd3c8a5f15cfebad7b2de2f0791cb0f6.pdf