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Reconfigurable acceleration of genetic sequence alignment: A survey of two decades of efforts

Ho-Cheung Ng, Shuanglong Liu, Wayne Luk
2017 2017 27th International Conference on Field Programmable Logic and Applications (FPL)  
Genetic sequence alignment has always been a computational challenge in bioinformatics.  ...  Therefore, this paper aims to provide a thorough survey of the proposed accelerators by giving a qualitative categorization based on their algorithms and speedup.  ...  ACKNOWLEDGMENT The support of the Lee Family Scholarship, the EU Horizon 2020 Research and Innovation Programme under grant agreement number 671653 and the UK EPSRC (EP/L00058X/1, EP/L016796/1, EP/N031768  ... 
doi:10.23919/fpl.2017.8056838 dblp:conf/fpl/NgLL17 fatcat:3nqeo75ysbfdrar2qx75yvw3ba

Dynamic Alignment of Digital Supply Chain Business Models

Jochen Nürk
2019 European Journal of Business Science and Technology  
A model for assessing the impact of Information System (IS) capabilities on the degree of strategic alignment within SCM domains has developed by qualitative research.  ...  changes and reduce complexity as key enablers of SC performance as well as its adoption to digital business models for autonomous alignment.  ...  The case study at SAP has been conducted by session sequences with each of 12 experts.  ... 
doi:10.11118/ejobsat.v5i1.161 fatcat:3qqcn2xzcndqrpi2bwd3lj7wdu

Hardware accelerators for biocomputing: A survey

Souradip Sarkar, Turbo Majumder, Ananth Kalyanaraman, Partha Pratim Pande
2010 Proceedings of 2010 IEEE International Symposium on Circuits and Systems  
In this paper, we present a survey of hardware accelerators for biocomputing by choosing a representative set of each. I.  ...  An emerging area is the investigation of hardware accelerators for speeding up the massive scale of computation needed in large-scale biocomputing applications.  ...  A simple search operation against a database of known sequences involves computing an unprecedented number of sequence alignment operations.  ... 
doi:10.1109/iscas.2010.5537736 dblp:conf/iscas/SarkarMKP10 fatcat:abxldburrvcgxe2rs4uhgqr2ka

Survey on Near-Data Processing: Applications and Architectures

Paulo Cesar Santos, Francis Birck Moreira, Aline Santana Cordeiro, Sairo Raoní Santos, Tiago Rodrigo Kepe, Luigi Carro, Marco Antonio Zanata Alves
2021 Journal of Integrated Circuits and Systems  
This survey presents a brief history of these accelerators, focusing on the applications domains migrated to near-data and the proposed architectures.  ...  In this context, Near-Data Processing (NDP) proposals have started to gain acceptance as an accelerator device.  ...  Angizi et al. propose the AlignS [60] using Spin-Orbit Torque Magnetoresistive Random-Access Memory (SOT-MRAM) and an assembler [61] using DRAM NCA accelerators to aid DNA sequence alignment and assembly  ... 
doi:10.29292/jics.v16i2.502 fatcat:3uiswd6z65djpjgvsxclutthxu

Basics of Reconfigurable Computing [chapter]

Reiner Hartenstein, Tu Kaiserslautern
2007 Designing Embedded Processors  
Xilinx released the first FPGA in 1985, the XC2064 chip with a 1,000 gate size. Two decades later, in the year 2004 the size of an FPGA was 10,000 times larger.  ...  Flow techniques can be used to align a set of nanowires into a single orientation, close pack them, and then transfer them onto a surface [176] [177] .  ... 
doi:10.1007/978-1-4020-5869-1_20 fatcat:2uyk5ixupfdorl4ou7apk2q4ra

fpgaConvNet: Mapping Regular and Irregular Convolutional Neural Networks on FPGAs

Stylianos I. Venieris, Christos-Savvas Bouganis
2018 IEEE Transactions on Neural Networks and Learning Systems  
Index Terms-Convolutional neural networks, design space exploration, FPGAs, parallel reconfigurable architectures.  ...  The proposed framework comprises an automated design methodology based on the Synchronous Dataflow (SDF) paradigm and defines a set of SDF transformation in order to efficiently navigate the architectural  ...  Finally, [12] provides a detailed survey of ConvNet-to-FPGA toolflows. fpgaConvNet differs from existing efforts by proposing a ConvNet-to-FPGA automated framework that combines systematic design space  ... 
doi:10.1109/tnnls.2018.2844093 pmid:29994725 fatcat:jp45bvjfhne7te2hi337x7ccne

Accelerating the Understanding of Life's Code Through Better Algorithms and Hardware Design [article]

Mohammed H K Alser
2019 arXiv   pre-print
The first key idea of our pre-alignment filters is to provide high filtering accuracy by correctly detecting all similar segments shared between two sequences.  ...  Calculating the similarities between a pair of genomic sequences is one of the most fundamental computational steps in genomic analysis.  ...  We describe next each of these three acceleration efforts in detail.  ... 
arXiv:1910.03936v1 fatcat:f2sw22g2sndc5b3jasnaoizw7i

Children's rare disease cohorts: an integrative research and clinical genomics initiative

Shira Rockowitz, Nicholas LeCompte, Mary Carmack, Andrew Quitadamo, Lily Wang, Meredith Park, Devon Knight, Emma Sexton, Lacey Smith, Beth Sheidley, Michael Field, Ingrid A. Holm (+9 others)
2020 npj Genomic Medicine  
All sequencing data is integrated and combined with phenotypic and research data in a genomics learning system (GLS).  ...  Deployment of a genomically-ordered relational database allowed us to provide a modular and robust platform for centralized storage and analysis of research and clinical data, currently totaling 8516 exomes  ...  ACKNOWLEDGEMENTS A project of this breadth was possible due to the enthusiastic collaboration of numerous BCH investigators and their respective research teams.  ... 
doi:10.1038/s41525-020-0137-0 pmid:32655885 pmcid:PMC7338382 fatcat:wnhd6o6yq5erznyysdegxceriu

What RNA World? Why a Peptide/RNA Partnership Merits Renewed Experimental Attention

Charles Carter
2015 Life  
Sense/antisense coding affords a new bioinformatic metric for phylogenetic relationships much more distant than can be reconstructed from multiple sequence alignments of a single superfamily.  ...  A coherent structural basis for that scenario was articulated nearly a decade before the demonstration of catalytic RNA.  ...  Coding sequences in multiple alignments of such genes are aligned antiparallel to one another, using three-dimensional structures to align "anchors" containing the most conserved amino acids thought to  ... 
doi:10.3390/life5010294 pmid:25625599 pmcid:PMC4390853 fatcat:jcpzpeygtbhbvd4bfyytk56nbq

Genomics as a service: A joint computing and networking perspective

G. Reali, M. Femminella, E. Nunzi, D. Valocchi
2018 Computer Networks  
The second and main contribution of this survey consists of a methodological classification of computing and networking alternatives which can be used to offer what we call the Genomic-as-a-Service (GaaS  ...  A first contribution of this paper consists of identifying the still unexploited features of genomic data that could allow optimizing their networked management.  ...  STAR and Bowtie 2 are two examples of specialized tools for such purpose. A comprehensive survey of modern aligners and the relevant comparison can be found in [96] .  ... 
doi:10.1016/j.comnet.2018.08.005 fatcat:w562rwbavnax7pbtairhtnadje

A Middleware Framework for Maximum Likelihood Evaluation over Dynamic Grids

Wei-jen Wang, Kaoutar Maghraoui, John Cummings, Jim Napolitano, Boleslaw Szymanski, Carlos Varela
2006 2006 Second IEEE International Conference on e-Science and Grid Computing (e-Science'06)  
We have used our fitter to perform a partial wave analysis of particle physics data. Preliminary measurements have shown good performance and scalability.  ...  We have designed a maximum likelihood fitter using the actor model to distribute the computation over a heterogeneous network.  ...  Acknowledgements We would like to express our gratitude to Chris Kona, Heschi Kreinick, and Zack Goldstein for implementing the initial versions of the SALSA maximum likelihood programs.  ... 
doi:10.1109/e-science.2006.261189 dblp:conf/eScience/WangMCNSV06 fatcat:pvnty5j3xjhcvjpahncdmdwmn4

An Overview on Optimal Flocking [article]

Logan E. Beaver, Andreas A. Malikopoulos
2021 arXiv   pre-print
optimal flocking as a field.  ...  The study of robotic flocking has received considerable attention in the past twenty years.  ...  In general, these surveys have all considered flocking and optimal control to be two distinct problems.  ... 
arXiv:2009.14279v2 fatcat:iq7y5lpewfemzk4zer2ji4iozi

Biodefense Oriented Genomic-Based Pathogen Classification Systems: Challenges and Opportunities

Willy A Valdivia- Granda
2012 Journal of Bioterrorism & Biodefense  
A series of recommendations to promote genomics and bioinformatics as an effective form of deterrence and a valuable scientific platform for rapid technological insertion of detection, prophylactic, therapeutic  ...  Countermeasures that will effectively prevent or diminish the impact of a biological attack will depend on the rapid and accurate generation and analysis of genomic information.  ...  This project was partially funded by the Northeast Biodefense Center U54-AI057158-Lipkin, the Department of Homeland Security Center of Excellence for Emerging and Zoonotic Animal Disease (CEEZAD) under  ... 
doi:10.4172/2157-2526.1000113 pmid:25587492 pmcid:PMC4289626 fatcat:eh5kcx4mh5emzgcbavhiikabym

Vaccines for neglected and emerging diseases in Brazil by 2030: the "valley of death" and opportunities for RD&I in Vaccinology 4.0

Akira Homma, Marcos da Silva Freire, Cristina Possas
2020 Cadernos de Saúde Pública  
," with only two vaccines produced in a pipeline of 240 vaccines.  ...  Such constraints are aggravated by a global scenario of limited commercial interest from multinational companies in vaccines for neglected and emerging diseases, which are falling into a "valley of death  ...  The sustainability and competitiveness of this public manufacturer must be aligned with the reconfiguration of the global market.  ... 
doi:10.1590/0102-311x00128819 pmid:33111747 fatcat:pizqiz4dl5d3he2b76jgdqnty4

Introduction to Bioinformatics [article]

Sabu M. Thampi
2009 arXiv   pre-print
Bioinformatics is a new discipline that addresses the need to manage and interpret the data that in the past decade was massively generated by genomic research.  ...  of algorithms and statistics.  ...  How Do I Write a Program to Align Two Biological Sequences?  ... 
arXiv:0911.4230v1 fatcat:4trytpwrw5apvkiejbwhiqmp6m
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