PANDA: Processing in Magnetic Random-Access Memory-Accelerated de Bruijn Graph-Based DNA Assembly
In this work, we present an efficient Processing in MRAM-Accelerated De Bruijn Graph-based DNA Assembly platform, named PANDA, based on an optimized and hardware-friendly genome assembly algorithm. PANDA is able to assemble large-scale DNA sequence datasets from all-pair overlaps. We first design a...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2024-02-01
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| Series: | Journal of Low Power Electronics and Applications |
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| Online Access: | https://www.mdpi.com/2079-9268/14/1/9 |
| _version_ | 1797240514028765184 |
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| author | Shaahin Angizi Naima Ahmed Fahmi Deniz Najafi Wei Zhang Deliang Fan |
| author_facet | Shaahin Angizi Naima Ahmed Fahmi Deniz Najafi Wei Zhang Deliang Fan |
| author_sort | Shaahin Angizi |
| collection | DOAJ |
| description | In this work, we present an efficient Processing in MRAM-Accelerated De Bruijn Graph-based DNA Assembly platform, named PANDA, based on an optimized and hardware-friendly genome assembly algorithm. PANDA is able to assemble large-scale DNA sequence datasets from all-pair overlaps. We first design a PANDA platform that exploits MRAM as computational memory and converts it to a potent processing unit for genome assembly. PANDA can not only execute efficient bulk bit-wise X(N)OR-based comparison/addition operations heavily required for the genome assembly task but also a full set of 2-/3-input logic operations inside the MRAM chip. We then develop a highly parallel and step-by-step hardware-friendly DNA assembly algorithm for PANDA that only requires the developed in-memory logic operations. The platform is then configured with a novel data partitioning and mapping technique that provides local storage and processing to utilize the algorithm level’s parallelism fully. The cross-layer simulation results demonstrate that PANDA reduces the run time and power by a factor of 18 and 11, respectively, compared with CPU. Moreover, speed-ups of up to 2.5 to 10× can be obtained over other recent processing in-memory platforms to perform the same task, like STT-MRAM, ReRAM, and DRAM. |
| first_indexed | 2024-04-24T18:08:38Z |
| format | Article |
| id | doaj.art-ed2d82633fb641e7addfdeb2ef98229e |
| institution | Directory Open Access Journal |
| issn | 2079-9268 |
| language | English |
| last_indexed | 2024-04-24T18:08:38Z |
| publishDate | 2024-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Journal of Low Power Electronics and Applications |
| spelling | doaj.art-ed2d82633fb641e7addfdeb2ef98229e2024-03-27T13:48:58ZengMDPI AGJournal of Low Power Electronics and Applications2079-92682024-02-01141910.3390/jlpea14010009PANDA: Processing in Magnetic Random-Access Memory-Accelerated de Bruijn Graph-Based DNA AssemblyShaahin Angizi0Naima Ahmed Fahmi1Deniz Najafi2Wei Zhang3Deliang Fan4Department of Electrical and Computer Engineering, New Jersey Institute of Technology, Newark, NJ 07103, USADepartment of Computer Science, University of Central Florida, Orlando, FL 32816, USADepartment of Electrical and Computer Engineering, New Jersey Institute of Technology, Newark, NJ 07103, USADepartment of Computer Science, University of Central Florida, Orlando, FL 32816, USADepartment of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, MD 21218, USAIn this work, we present an efficient Processing in MRAM-Accelerated De Bruijn Graph-based DNA Assembly platform, named PANDA, based on an optimized and hardware-friendly genome assembly algorithm. PANDA is able to assemble large-scale DNA sequence datasets from all-pair overlaps. We first design a PANDA platform that exploits MRAM as computational memory and converts it to a potent processing unit for genome assembly. PANDA can not only execute efficient bulk bit-wise X(N)OR-based comparison/addition operations heavily required for the genome assembly task but also a full set of 2-/3-input logic operations inside the MRAM chip. We then develop a highly parallel and step-by-step hardware-friendly DNA assembly algorithm for PANDA that only requires the developed in-memory logic operations. The platform is then configured with a novel data partitioning and mapping technique that provides local storage and processing to utilize the algorithm level’s parallelism fully. The cross-layer simulation results demonstrate that PANDA reduces the run time and power by a factor of 18 and 11, respectively, compared with CPU. Moreover, speed-ups of up to 2.5 to 10× can be obtained over other recent processing in-memory platforms to perform the same task, like STT-MRAM, ReRAM, and DRAM.https://www.mdpi.com/2079-9268/14/1/9processing in memoryDNA assemblySOT-MRAM |
| spellingShingle | Shaahin Angizi Naima Ahmed Fahmi Deniz Najafi Wei Zhang Deliang Fan PANDA: Processing in Magnetic Random-Access Memory-Accelerated de Bruijn Graph-Based DNA Assembly Journal of Low Power Electronics and Applications processing in memory DNA assembly SOT-MRAM |
| title | PANDA: Processing in Magnetic Random-Access Memory-Accelerated de Bruijn Graph-Based DNA Assembly |
| title_full | PANDA: Processing in Magnetic Random-Access Memory-Accelerated de Bruijn Graph-Based DNA Assembly |
| title_fullStr | PANDA: Processing in Magnetic Random-Access Memory-Accelerated de Bruijn Graph-Based DNA Assembly |
| title_full_unstemmed | PANDA: Processing in Magnetic Random-Access Memory-Accelerated de Bruijn Graph-Based DNA Assembly |
| title_short | PANDA: Processing in Magnetic Random-Access Memory-Accelerated de Bruijn Graph-Based DNA Assembly |
| title_sort | panda processing in magnetic random access memory accelerated de bruijn graph based dna assembly |
| topic | processing in memory DNA assembly SOT-MRAM |
| url | https://www.mdpi.com/2079-9268/14/1/9 |
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