Browsing by Author "Rastogi, P."

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GPU accelerated inexact matching for multiple patterns in DNA sequences
(2014) Rastogi, P.; Ram Mohana Reddy, Guddeti
DNA sequencing technology generates millions of patterns on Every run of the machine and it poses a challenge for matching these patterns to the reference genome effectively with high execution speed. The main idea here is inexact matching of patterns with mismatches and gaps (insertions and deletions). In Inexact match up pattern DNA sequence is to be matched with some allowed number of errors. Here we have considered 2 errors. Errors can be mismatches or gaps. Existing algorithm as SOAP3 performs inexact matching on GPU with mismatches only. SOAP3 doesn't consider gaps (insertion and deletion). General Purpose Graphical Processing Unit (GPGPU) is an effective solution in terms of the cost and speed and there by providing a high degree of parallelism. This paper presents a parallel implementation of multiple pattern inexact matching in genome reference using CUDA based on BWT. The algorithm incorporates DFS (Depth First Search) Strategy for For matching multiple patterns, each thread of GPGPU is provided with a different pattern and hence millions of patterns can be matched using only one CUDA kernel. Since the memory of the GPU is limited then memory management should handled carefully. Synchronization of multiple threads is provided in order to prevent illegal access to the shared memory. GPU results are compared with that of CPU execution Experimental results of the proposed methodology achieved an average speedup factor of seven as compared to that of CPU execution. � 2014 IEEE.
GPU accelerated inexact matching for multiple patterns in DNA sequences
(Institute of Electrical and Electronics Engineers Inc., 2014) Rastogi, P.; Guddeti, G.R.M.
DNA sequencing technology generates millions of patterns on Every run of the machine and it poses a challenge for matching these patterns to the reference genome effectively with high execution speed. The main idea here is inexact matching of patterns with mismatches and gaps (insertions and deletions). In Inexact match up pattern DNA sequence is to be matched with some allowed number of errors. Here we have considered 2 errors. Errors can be mismatches or gaps. Existing algorithm as SOAP3 performs inexact matching on GPU with mismatches only. SOAP3 doesn't consider gaps (insertion and deletion). General Purpose Graphical Processing Unit (GPGPU) is an effective solution in terms of the cost and speed and there by providing a high degree of parallelism. This paper presents a parallel implementation of multiple pattern inexact matching in genome reference using CUDA based on BWT. The algorithm incorporates DFS (Depth First Search) Strategy for For matching multiple patterns, each thread of GPGPU is provided with a different pattern and hence millions of patterns can be matched using only one CUDA kernel. Since the memory of the GPU is limited then memory management should handled carefully. Synchronization of multiple threads is provided in order to prevent illegal access to the shared memory. GPU results are compared with that of CPU execution Experimental results of the proposed methodology achieved an average speedup factor of seven as compared to that of CPU execution. Â© 2014 IEEE.
Learner centered design approach for E-learning using 3D virtual tutors
(2013) Mukherjee, S.; Singhal, H.; Jha, P.; Kokane, A.; Rastogi, P.; Mittal, R.; Ram Mohana Reddy, Guddeti
Most of the existing E-learning system designs have focused on the development of feature-rich, but usable systems with little effort in motivating students to develop interest in the teaching-learning process. This paper discusses the learner centered design approach for web-based tutoring to motivate young learners using 3D virtual tutors in a requirement-based, flexible pedagogical model. Students can choose course(s) and the study-mode. In the guided mode, the student is mentored by a human tutor, whereas a student in un-guided mode is tutored by 3D avatar. The student has access to study materials, educational videos and applets that are provided by the tutors, the student also has access to forums for doubt clearing and online assignments to be submitted for tutors' evaluation. Tutors can track students' progress using online quiz and reports modules. Further, tutors have access to teaching aids like online chat system and whiteboard-based teaching in a virtual classroom environment. � 2013 IEEE.
Learner centered design approach for E-learning using 3D virtual tutors
(IEEE Computer Society help@computer.org, 2013) Mukherjee, S.; Singhal, H.; Jha, P.; Kokane, A.; Rastogi, P.; Mittal, R.; Guddeti, G.
Most of the existing E-learning system designs have focused on the development of feature-rich, but usable systems with little effort in motivating students to develop interest in the teaching-learning process. This paper discusses the learner centered design approach for web-based tutoring to motivate young learners using 3D virtual tutors in a requirement-based, flexible pedagogical model. Students can choose course(s) and the study-mode. In the guided mode, the student is mentored by a human tutor, whereas a student in un-guided mode is tutored by 3D avatar. The student has access to study materials, educational videos and applets that are provided by the tutors, the student also has access to forums for doubt clearing and online assignments to be submitted for tutors' evaluation. Tutors can track students' progress using online quiz and reports modules. Further, tutors have access to teaching aids like online chat system and whiteboard-based teaching in a virtual classroom environment. Â© 2013 IEEE.