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Microarchitecture of a MultiCore SoC for Data Analysis of a Lab-on-Chip Microarray

G. Kornaros, S. Blionas
2008 EURASIP Journal on Advances in Signal Processing  
This paper presents a reconfigurable architecture of a lab-on-chip (LoC) microarray device capable to process data either in genotyping or in gene expression applications in a fraction of the time that  ...  The proposed data processing and analysis electronic module are an embedded multicore reconfigurable systemon-chip designed to analyze data from the forthcoming high-density oligonucleotide microarrays  ...  Jiannis Ragoussis from the Genomics Lab of the Wellcome Trust Centre for Human Genetics of the Oxford University for their data to evaluate the performance of the proposed architecture.  ... 
doi:10.1155/2008/520641 fatcat:aou4oavdkbgajp56mwrlzl6ceu

Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application

Gaye Lightbody, Valeriia Haberland, Fiona Browne, Laura Taggart, Huiru Zheng, Eileen Parkes, Jaine K Blayney
2018 Briefings in Bioinformatics  
There has been an exponential growth in the performance and output of sequencing technologies (omics data) with full genome sequencing now producing gigabases of reads on a daily basis.  ...  such extensive omics data is exploited to its full potential, key factors, including sample sourcing, technology selection and computational expertise and resources, need to be considered, leading to an  ...  FPGA-based platforms FPGA devices (Figure 3, Supplementary Table S4 ) are programmable integrated circuits, which consist of an array of configurable logic blocks each comprising local memory and computational  ... 
doi:10.1093/bib/bby051 pmid:30084865 fatcat:q3mhy7s37jazdbi2kbekfzrmkq

Fine-grained parallelization of fitness functions in bioinformatics optimization problems: gene selection for cancer classification and biclustering of gene expression data

Juan A. Gomez-Pulido, Jose L. Cerrada-Barrios, Sebastian Trinidad-Amado, Jose M. Lanza-Gutierrez, Ramon A. Fernandez-Diaz, Broderick Crawford, Ricardo Soto
2016 BMC Bioinformatics  
These functions have been accelerated by means of FPGA devices in genetic programs for financial markets [25] , spatial image filters [26] , filtered image signals [27] , test cases [28] , and many  ...  Nevertheless, even these algorithms can be slow for complex problems, demanding more hardware resources based on current general-purpose processors or Central Processing Units (CPUs).  ...  In addition, JAGP implemented both bottom-level circuits on FPGA, measuring the speedups with regard to CPUs, whereas JLCB and STA did the same in multi-core CPUs for the biclustering of gene expression  ... 
doi:10.1186/s12859-016-1200-9 pmid:27581798 pmcid:PMC5007680 fatcat:i26tgdgnfvhrvhufxx7hfsuazm

Signal Processing for Applications in Healthcare Systems

Pau-Choo Chung, Chein-I Chang, Qi Tian, Chien-Cheng Lee
2008 EURASIP Journal on Advances in Signal Processing  
Accordingly, the quality of community and home healthcare has been significantly improved and many portable devices have also been developed for a wide variety of applications where signal processing-based  ...  The paper entitled "EEG-based subject-and sessionindependent drowsiness detection: an unsupervised approach" by Nikhil et al. develops an unsupervised subjectand session-independent approach for driver  ...  The 1D spline-based genetic algorithm can be executed in parallel and implemented into an FPGA to become a compact system.  ... 
doi:10.1155/2008/869364 fatcat:x6mgkrysrzegje7j6kdsst6ham

Real-time analysis and selection of methylated DNA by fluorescence-activated single molecule sorting in a nanofluidic channel

B. R. Cipriany, P. J. Murphy, J. A. Hagarman, A. Cerf, D. Latulippe, S. L. Levy, J. J. Benitez, C. P. Tan, J. Topolancik, P. D. Soloway, H. G. Craighead
2012 Proceedings of the National Academy of Sciences of the United States of America  
Real-time photon counting and signal analysis was performed using an FPGA operating with an adjustable, 50 μs time base or bin.  ...  (C) An FPGA-based electrical circuit was used to evaluate photon count signals, X 1 ðtÞ and X 2 ðtÞ, each reporting a different fluorescence color.  ... 
doi:10.1073/pnas.1117549109 pmid:22586076 pmcid:PMC3365150 fatcat:gy4bxahwafc5fcxvvwsykntuay

ROI-based Compression on Radiological Image by Urdhva-Tiryagbhyam and DWT Over FPGA

Suma, V. Sridhar
2017 International Journal of Advanced Computer Science and Applications  
Hence, this paper presents an analytical modelling of ROI (Region of Interest)-based radiological image compression that applies Vedic Multiplier Urdhva-Tiryagbhyam to enhance the performance of coding  ...  The study outcome was implemented in Matlab and multiple test bed of FPGA devices (Virtex 4 FX100 -12 FF1152 and Spartan 3 XC400-5TQ144) and assessed using both visual and numerical outcomes to find that  ...  One of such form is DNA microarray, which is frequently used in genetic engineering. Cabronero et al.  ... 
doi:10.14569/ijacsa.2017.080228 fatcat:i77g7le7fzg3vfxsngwphammim

Dedicated hardware accelerators for the epistatic analysis of human genetic data

Fabio Cancare, Alessandro Marin, Donatella Sciuto
2011 2011 International Conference on Embedded Computer Systems: Architectures, Modeling and Simulation  
The recent advances in genomic microarrays design provide the possibility to retrieve hundreds of thousands of significative genetic features from patients at affordable costs.  ...  This paper presents three hardware-accelerated implementations of the MDR algorithm, tailored for many-core processors, Xilinx Virtex-5 FPGAs and generic GPUs respectively.  ...  FPGA results The FPGA-based implementation was tested using the previously mentioned Xilinx Virtex-5 XC5VFX70T FPGA.  ... 
doi:10.1109/samos.2011.6045450 dblp:conf/samos/CancareMS11 fatcat:k4wlxqs5znfghpydduowdabxiy

Custom Hardware Versus Cloud Computing in Big Data [chapter]

Gaye Lightbody, Fiona Browne, Valeriia Haberland
2017 Advanced Information and Knowledge Processing  
Then an overview is given of some of the high-performance computing options that are available, ranging from multiple Central Processing Unit (CPU) setups, Graphical Processing Units (GPUs), Field Programmable  ...  Gate Arrays (FPGAs) and cloud solutions.  ...  The Darwin Neural Processing Unit is another exciting example of an ASIC co-processer based on SNN [Shen et al., 2016] .  ... 
doi:10.1007/978-3-319-59090-5_9 fatcat:p74b7a42xvajvbghyugmfpwdga

An ISFET Microarray Sensor System for Detecting the DNA Base Pairing

Peng Sun, Yongxin Cong, Ming Xu, Huaqing Si, Dan Zhao, Dongping Wu
2021 Micromachines  
Deoxyribonucleic acid (DNA) sequencing technology provides important data for the disclosure of genetic information and plays an important role in gene diagnosis and gene therapy.  ...  DNA base pairing is successfully detected by the sensor system, which includes the ISFET microarray chip, microfluidic system, and test platform.  ...  (a) The sensor chip is processed on an 8-inch wafer according to the layout design; the wafer is cut into several microarray sensor chips, having the chip area of 15 × 15 mm.  ... 
doi:10.3390/mi12070731 fatcat:fxzeybcpt5fw5c6coynmeehavq

Comparing the performance of clusters, Hadoop, and Active Disks on microarray correlation computations

J.A. Delmerico, N.A. Byrnes, A.E. Bruno, M.D. Jones, S.M. Gallo, V. Chaudhary
2009 2009 International Conference on High Performance Computing (HiPC)  
Microarray-based comparative genomic hybridization (aCGH) offers an increasingly fine-grained method for detecting copy number variations in DNA.  ...  A useful analysis of the data produced from these microarray experiments is pairwise correlation.  ...  The implementation takes an N × M matrix of microarray sample data as input and subdivides the matrix row-wise based on the number of Map tasks.  ... 
doi:10.1109/hipc.2009.5433190 dblp:conf/hipc/DelmericoBBJGC09 fatcat:ftw5qcbi55dcfkj7xku5zfkoki

A hybrid architecture for bioinformatics

Bertil Schmidt, Heiko Schröder, Manfred Schimmler
2002 Future generations computer systems  
Cray XC40) Ź Intel CPUs and IBM Power processors By the time of this writing, not a single system contains FPGA-based computing devices.  ...  Furthermore, the alleles in question are replaced with fluorescent equivalent base pairs. Then, the material flows over a special chip called microarray.  ... 
doi:10.1016/s0167-739x(02)00058-4 fatcat:ktrtocmzh5hkzgdprusjxddmbi

Field Programmable Gate Array Applications—A Scientometric Review

Juan Ruiz-Rosero, Gustavo Ramirez-Gonzalez, Rahul Khanna
2019 Computation  
Field Programmable Gate Array (FPGA) is a general purpose programmable logic device that can be configured by a customer after manufacturing to perform from a simple logic gate operations to complex systems  ...  Also, we present an evolution and trend analysis of the related applications.  ...  Frequency relaying based on genetic algorithm using FPGAs.  ... 
doi:10.3390/computation7040063 fatcat:wxtatzsvvnfopghdfl25hcfc2a

Massive Parallel Digital Micro fluidic Biochip Architecture for Automating Large-Scale Biochemistry Assays

Abbas Haddad, Maryam Taajobian, Ali Jahanian
2018 Scientia Iranica. International Journal of Science and Technology  
In the new architecture, a FPGA-based structure is used, which increases exibility and parallelizing assay operations.  ...  Two main types of micro uidic-based biochips are used: continuous-ow-based and digital micro uidic biochips (DMFB).  ...  Figure 1 represents an EWOD-based micro uidic biochip and its basic unit cell. The detailed fabrication process of a basic unit cell in EWOD-based DMFB is described in [2, 7, 15] .  ... 
doi:10.24200/sci.2018.20797 fatcat:qcanixcxvbaqjkt2hv6pkzldlu

Label-Free DNA Detection Using a Charge Sensitive CMOS Microarray Sensor Chip

Javid Musayev, Yekbun Adlguzel, Haluk Kulah, Selim Eminoglu, Tayfun Akln
2014 IEEE Sensors Journal  
The microarray sensor, fabricated with a standard CMOS process, contains 1024 detector elements integrated together with their readout circuit in a single chip.  ...  The sensing part of the chip consists of an array of 7 µm × 7 µm capacitive metal electrodes arranged in 32 × 32 format with a pitch of 15 µm, which allows implementation of a portable and low-cost microarray  ...  Akar for the dicing and nitride coating of the microarray sensor chips.  ... 
doi:10.1109/jsen.2014.2301693 fatcat:j7ci5yx5x5dlvbsnoywdex4ozm

Recent advances in physical reservoir computing: A review

Gouhei Tanaka, Toshiyuki Yamane, Jean Benoit Héroux, Ryosho Nakane, Naoki Kanazawa, Seiji Takeda, Hidetoshi Numata, Daiju Nakano, Akira Hirose
2019 Neural Networks  
Reservoir computing is a computational framework suited for temporal/sequential data processing.  ...  The purpose of this review is to provide an overview of recent advances in physical reservoir computing by classifying them according to the type of the reservoir.  ...  The system without feedback was found to be capable of performing a cancer type classification task with genetic microarray data.  ... 
doi:10.1016/j.neunet.2019.03.005 fatcat:u4vjykpyxnch3n24kprqoi2tsy
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