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Data Management for High-Throughput Genomics [article]

Uwe Roehm
2009 arXiv   pre-print
In particular, we are interested in the storage management for high-throughput sequence data and in leveraging SQL and user-defined functions for data analysis inside a database system.  ...  This paper explores the potential and the limitations of using relational database systems as the data processing platform for high-throughput genomics.  ...  Acknowledgements We are grateful to Matt Wood and Roger Pettett from the Sanger Institute, UK, for their support, as well as to Todd Smith and Eric Olson from Geospiza, Inc., Seattle, for many fruitful  ... 
arXiv:0909.1764v1 fatcat:s6yzfx3pyjfcvf453qoxmwsckm

Node-Oriented Workflow (NOW): A Command Template Workflow Management Tool for High Throughput Data Analysis Pipelines

Gerard Tromp
2014 Journal of Data Mining in Genomics & Proteomics  
Next generation sequencing (NGS) systems produce vast quantities of data that require substantial computational resources for typical analysis tasks.  ...  We present Node-Oriented Workflow (NOW), a dynamic command template workflow engine for high performance distributed computing (HPC) systems.  ...  Citation: Lipsky EB, King BR, Tromp G (2014) Node-Oriented Workflow (NOW): A Command Template Workflow Management Tool for High Throughput Data Analysis Pipelines.  ... 
doi:10.4172/2153-0602.1000159 fatcat:vsgcb4r5wncfrm4qqxzwt5om2e

VCF‐Server: A web‐based visualization tool for high‐throughput variant data mining and management

Jianping Jiang, Jianlei Gu, Tingting Zhao, Hui Lu
2019 Molecular Genetics & Genomic Medicine  
Furthermore, as the mutation data are increasing exponentially, there is an urgent need to develop tools to manage these variant data in a centralized way.  ...  However, querying and filtering VCF files are extremely difficult for researchers without programming skills.  ...  HTSlib is a standard C library for quickly accessing high-throughput sequencing data and is also the core library of samtools (Li et al., 2009 ) and bcftools (Li, 2011) .  ... 
doi:10.1002/mgg3.641 pmid:31127704 pmcid:PMC6625089 fatcat:xezfxoz2inhvracjt24i23r56a

Introduction to the AMS Symposium "Phylogenomics of Mollusks," 82nd Annual Meeting of the American Malacological Society

Kevin M. Kocot
2017 American Malacological Bulletin  
and QC trending, troubleshooting, bioinformatics, data management, and IT infrastructure.  ...  Offering a fast, accurate solution to high-throughput WGS, HiSeq Analysis Software v2.0 processes data up to 6× faster than existing analysis methods.  ... 
doi:10.4003/006.035.0110 fatcat:7a7gfbzogrhcnnk3doldoe6elu

Genomics: Table of suppliers

2010 Nature  
National Center for Genome Resources High-throughput SNP genotyping, sequencing and analysis Santa Fe, New Mexico www.ncgr.org Oxford Gene Technology Genomic services, high-throughput microarray  ...  /Activity Location URL Accelrys Workflows for data management, analysis and reporting San Diego, California accelrys.com BC Platforms Data-management systems for genotyping and phenotyping Espoo  ... 
doi:10.1038/4671139a fatcat:rwfkmixaunf75b3qf3shkf5rxe

PREDA: an R-package to identify regional variations in genomic data

Francesco Ferrari, Aldo Solari, Cristina Battaglia, Silvio Bicciato
2011 Computer applications in the biosciences : CABIOS  
PREDA identifies relevant chromosomal patterns in high-throughput data using a smoothing approach that accounts for distance and density variability of genomics features.  ...  Thus, the integrative analysis of multiple sources of genomic data and information deepens the resolution and enhances the interpretation of stand-alone high-throughput data.  ...  Here, we describe PREDA, an R/Bioconductor package for detecting regional variations of genomic features from the integrative analysis of high-throughput data and genome local structural organization.  ... 
doi:10.1093/bioinformatics/btr404 pmid:21742634 fatcat:jkkmfincy5eobn2hjtexqkns3y

Molecular biorepositories and biomaterials management: enhancing the value of highthroughput molecular methodologies for the natural sciences

DL Distel
2007 Marine Ecology Progress Series  
I thank Debra Pittman, Nate Eckborg and Yvette Luyten for helpful comments on the text.  ...  This work was supported by the Ocean Genome Legacy, a nonprofit private research institution and genome resource biorepository dedicated to exploring and preserving the biological diversity of marine environments  ...  Ongoing development of high-throughput technologies for genomics, proteomics, etc. promises to further accelerate the rate at which we are able to obtain information from biological systems.  ... 
doi:10.3354/meps332307 fatcat:kmhjc4fm7ncfdbo633eadf3xfq

An approach to high-throughput genotyping

J M Hall, C A LeDuc, A R Watson, A H Roter
1996 Genome Research  
Data Management A number of data management issues are encountered in high-throughput genotyping for a large disease mapping project.  ...  The Sybase Database Management System has become a standard in the genome community for public data bases, such as the Genome Data Base, the Genome Sequence Data Base, and the National Center for Biotechnology  ... 
doi:10.1101/gr.6.9.781 pmid:8889547 fatcat:sfaeyrqudjcktmxzlzgpwdvccy

Structure determination of a novel protein of unknown function synthesized using a cell-free system

T. Wada, M. Shirouzu, T. Terada, T. Kigawa, S. Kuramitsu, S.-Y. Park, J. Tame, S. Yokoyama
2002 Acta Crystallographica Section A Foundations of Crystallography  
A management system for a large number of data is also indispensable.  ...  The system can make it easy to manage score record and the date and time of crystallization setup. The plasmids for the protein expression were provided by the RIKEN Structurome Project.  ...  We are developing the sample management system, which composed of the sample auto-changer and the database system, for high-throughput data collection.  ... 
doi:10.1107/s0108767302097064 fatcat:g7ou2drkebgbpc53mo4du7vqfi

Trends in life science grid: from computing grid to knowledge grid

Akihiko Konagaya
2006 BMC Bioinformatics  
Computing grid technologies have been matured enough to solve high-throughput real-world life scientific problems.  ...  Data grid technologies are strong candidates for realizing "resourceome" for bioinformatics.  ...  Acknowledgements The authors express special thanks for the member of the Open Bioinformatics Grid project and anonymous reviewers for their valuable discussion and useful comments for this manuscript.  ... 
doi:10.1186/1471-2105-7-s5-s10 pmid:17254294 pmcid:PMC1764466 fatcat:tlemqfzeljfdbaxa6gw5mid7f4

The High-Throughput Analyses Era: Are We Ready for the Data Struggle?

Valeria D'Argenio
2018 High-Throughput  
Recent and rapid technological advances in molecular sciences have dramatically increased the ability to carry out high-throughput studies characterized by big data production.  ...  Indeed, big data management is becoming an increasingly important aspect of many fields of molecular research including the study of human diseases.  ...  In addition, the increasing throughput of the sequencers imposes the need for tools that are able to manage a huge amount of data.  ... 
doi:10.3390/ht7010008 pmid:29498666 pmcid:PMC5876534 fatcat:rpmbxxrnmfbuvpi4cn36mlbe4i

Sequencing Complex Genomes with PromethION Technology in a Core Setting

Sara Goodwin, W Richard McCombie
2019 Journal of Biomolecular Techniques  
Basic data management methods like basecalling and data transmission can quickly overwhelm many data management systems.  ...  Another factor that much be considered is data management; as ~2Tb of data can be generated per flowcell.  ...  Basic data management methods like basecalling and data transmission can quickly overwhelm many data management systems.  ... 
pmid:31892909 pmcid:PMC6936911 fatcat:jsnqonc37zdbreqj3aqjgavrgq

Communication-Efficient Cluster Scalable Genomics Data Processing Using Apache Arrow Flight [article]

Tanveer Ahmad
2022 bioRxiv   pre-print
Current cluster scaled genomics data processing solutions rely on big data frameworks like Apache Spark, Hadoop and HDFS for data scheduling, processing and storage.  ...  Our solution is publicly available on GitHub at https://github.com/abs-tudelft/time-to-fly-high/tree/main/genomics  ...  high throughput data transfer and compute capabilities.  ... 
doi:10.1101/2022.04.01.486780 fatcat:6w4yxg3cx5gp7kwxyklxq5jxq4

Improving Genomic Selection with High-Throughput Phenotyping

John Doe
2018 CSA News  
Combining high-throughput Soil cores were placed in insulated racks to mimic surface soil temperatures and to provide a system for ready collection of leachate. Photo by P. Moore.  ...  Using high-throughput measurements of plant temperature and light reflectance combined with genomic information, they were able to increase accuracy of yield predictions by up to 7% over standard genomic  ... 
doi:10.2134/csa2018.63.0512 fatcat:rsmdrat3cvdollkhdhg325l32m

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

H. Parkinson, U. Sarkans, N. Kolesnikov, N. Abeygunawardena, T. Burdett, M. Dylag, I. Emam, A. Farne, E. Hastings, E. Holloway, N. Kurbatova, M. Lukk (+10 others)
2010 Nucleic Acids Research  
The ArrayExpress Archive (http://www.ebi.ac.uk/ arrayexpress) is one of the three international public repositories of functional genomics data supporting publications.  ...  It includes data generated by sequencing or array-based technologies. Data are submitted by users and imported directly from the NCBI Gene Expression Omnibus.  ...  INTRODUCTION The ArrayExpress Archive of Functional Genomics Data is one of the major international repositories for functional genomics high-throughput data.  ... 
doi:10.1093/nar/gkq1040 pmid:21071405 pmcid:PMC3013660 fatcat:4rn24k5lvzhajj4huiufljvsgy
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