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A software framework for microarray and gene expression object model (MAGE-OM) array design annotation

Matloob Qureshi, Alasdair Ivens
2008 BMC Genomics  
The MIAME and MAGE-OM standards defined by the MGED society provide a specification and implementation of a software infrastructure to facilitate the submission and sharing of data from microarray studies  ...  Output of the application is fully compliant with the standards prescribed by the various public data repositories.  ...  We would like to thank the ArrayExpress curation team, particularly Helen Parkinson, Tim Rayner and Anna Farne for their help and guidance in validating MAGE-ML produced by the Adamant software.  ... 
doi:10.1186/1471-2164-9-133 pmid:18366695 pmcid:PMC2358904 fatcat:u25ith3hv5g6pekd4hsmxph2ry

Seqcrawler: biological data indexing and browsing platform

Olivier Sallou, Anthony Bretaudeau, Aurelien Roult
2012 BMC Bioinformatics  
Conclusions: Seqcrawler provides a complete open source search and store solution for labs or platforms needing to manage large amount of data/meta-data with a flexible and customizable web interface.  ...  All components (search engine, visualization and data storage), though independent, share a common and coherent data system that can be queried with a simple HTTP interface.  ...  Acknowledgements We would like to thank the GenOuest platform for hosting the software and the use of its cluster to index the data.  ... 
doi:10.1186/1471-2105-13-175 pmid:22827839 pmcid:PMC3481441 fatcat:vno6gfnms5b6pkebnuroohzz6y

The EBI SRS server--recent developments

E. M. Zdobnov, R. Lopez, R. Apweiler, T. Etzold
2002 Bioinformatics  
The SRS has become an integration system for both data retrieval and applications for data analysis.  ...  It provides capabilities to search multiple databases by shared attributes and to query across databases fast and efficiently.  ...  It provides capabilities to search multiple databases by shared attributes and to query across databases fast and efficiently.  ... 
doi:10.1093/bioinformatics/18.2.368 pmid:11847095 fatcat:gb2p2ulgpbaxnnkkklfuc6i4ra

CEBS object model for systems biology data, SysBio-OM

S. Xirasagar, S. Gustafson, B. A. Merrick, K. B. Tomer, S. Stasiewicz, D. D. Chan, K. J. Yost, J. R. Yates, S. Sumner, N. Xiao, M. D. Waters
2004 Bioinformatics  
Unified data representation via a single object model will greatly aid in integrating data storage and management, and facilitate reuse of software to analyze and display data resulting from diverse differential  ...  to house data from multiple complex data streams in a systems friendly manner that will accommodate extensive querying from users.  ...  ACKNOWLEDGEMENTS This project has been funded in whole or in part with Federal funds from the National Institute of Environmental Health Sciences, National Institutes of Health, under Contract No.  ... 
doi:10.1093/bioinformatics/bth189 pmid:15044233 fatcat:r5nao3ztmbf27evmhwjyx3uny4

Preliminary results in accelerating profile HMM search on FPGAs

Arpith C. Jacob, Joseph M. Lancaster, Jeremy D. Buhler, Roger D. Chamberlain
2007 2007 IEEE International Parallel and Distributed Processing Symposium  
Comparison between biosequences and probabilistic models is an increasingly important part of modern DNA and protein sequence analysis.  ...  of multiple sequences within one FPGA.  ...  The authors would like to thank Rahul Maddimsetty, Brandon Harris, and Eric Tyson for useful discussions during the development.  ... 
doi:10.1109/ipdps.2007.370447 dblp:conf/ipps/JacobLBC07 fatcat:vipf4z7jqvd7tg75zyvbexcxkm

Biosequence Similarity Search on the Mercury System

Praveen Krishnamurthy, Jeremy Buhler, Roger Chamberlain, Mark Franklin, Kwame Gyang, Arpith Jacob, Joseph Lancaster
2007 Journal of VLSI Signal Processing Systems for Signal, Image and Video Technology  
The most widely used similarity search tool for biosequences is BLAST, a program designed to compare query sequences to a database.  ...  Here, we present the design of BLASTN, the version of BLAST that searches DNA sequences, on the Mercury system, an architecture that supports high-volume, high-throughput data movement off a data store  ...  To keep track of the redundant w-mers, a record for every diagonal is stored in a data structure which contains the previous non-redundant database index.  ... 
doi:10.1007/s11265-007-0087-0 pmid:18846267 pmcid:PMC2564817 fatcat:6zsefgb7ubcrtaw5pmjy7u4tje

Scalable Softcore Vector Processor for Biosequence Applications

Arpith Jacob, Brandon Harris, Jeremy Buhler, Roger Chamberlain, Young Cho
2006 2006 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines  
Each functional unit includes an instruction controller, parallel processing elements with shared registers, and a memory unit which provides access to both local and streaming data.  ...  The SVP is a software programmable architecture constructed from predefined hardware building blocks. We leverage the flexibility and power of an FPGA to enhance a streaming vector processor design.  ...  Young Cho for valuable suggestions offered during the course of the project. We would like to thank our advisors Dr. Jeremy Buhler and Dr. Roger Chamberlain for their insight.  ... 
doi:10.1109/fccm.2006.62 dblp:conf/fccm/JacobHBCC06 fatcat:6gw4w4znlnhtllcc4k5gxlckbu

ALiCE: A Scalable Runtime Infrastructure for High Performance Grid Computing [chapter]

Yong-Meng Teo, Xianbing Wang
2004 Lecture Notes in Computer Science  
The ALiCE layered grid architecture comprises of a core layer that provides the basic services for control and communication within a grid.  ...  Performance of a distributed Data Encryption Standard (DES) key search problem on two grid configurations are discussed.  ...  These resources can include supercomputers, storage systems, data sources and special classes of devices.  ... 
doi:10.1007/978-3-540-30141-7_16 fatcat:3lkqbbmrovgmvh2l4jtu7qsfre

Survey on index based homology search algorithms

Xianyang Jiang, Peiheng Zhang, Xinchun Liu, Stephen S.-T. Yau
2007 Journal of Supercomputing  
At the same time, several promising and new index techniques are also discussed. As a whole, the paper provides a survey on index based homology search algorithms.  ...  Up to now, there are many homology search algorithms that have been investigated and studied. However, a good classification method and a comprehensive comparison for these algorithms are absent.  ...  The authors thank Professor Dominique Lavenier for his valuable suggestions on this paper, and also thank anonymous reviewers for their comments to improve the readability of this paper.  ... 
doi:10.1007/s11227-006-0041-0 fatcat:hhijz2rah5a5jcbu4d6ecj3npi

Accessing and distributing EMBL data using CORBA (common object request broker architecture)

L Wang, P Rodriguez-Tomé, N Redaschi, P McNeil, A Robinson, P Lijnzaad
2000 Genome Biology  
A CORBA infrastructure developed by EMBL-EBI provides an efficient means of accessing and distributing EMBL data.  ...  The CORBA interfaces to the EMBL database address some of the problems of traditional flat-file formats and provide an efficient means for accessing and distributing EMBL data.  ...  When the structure of data changes at the database side as a result of the increasing complexity of biological data or the availability of new modeling capability in the database, we need only a change  ... 
doi:10.1186/gb-2000-1-5-research0010 pmid:11178259 pmcid:PMC15028 fatcat:isf37uzyvzbrxfnqgwo4bmotpi

Anatomy of a native XML base management system

T. Fiebig, S. Helmer, C.-C. Kanne, G. Moerkotte, J. Neumann, R. Schiele, T. Westmann
2002 The VLDB journal  
In this paper we give a tour of Natix, a database management system designed from scratch for storing and processing XML data.  ...  Contrary to the common belief that management of XML data is just another application for traditional databases like relational systems, we illustrate how almost every component in a database system is  ...  We also thank the anonymous referees for their comments and suggestions.  ... 
doi:10.1007/s00778-002-0080-y fatcat:mhtjrg4k7jatjdzlg6nlrmhlyy

Analysis of Parallel Algorithms on SMP Node and Cluster of Workstations Using Parallel Programming Models with New Tile-based Method for Large Biological Datasets

D. D. Shrimankar, S. R. Sathe
2016 Bioinformatics and Biology Insights  
CiTATioN: shrimankar and sathe. analysis of Parallel algorithms on smP node and cluster of Workstations Using Parallel Programming models with new tile-based method for large Biological datasets.  ...  We also demonstrate a communication model to approximate the overhead from communication in OpenMP loops. Our results are astonishing and inter esting to a large variety of input data files.  ...  Parallelism introduces a new set of concerns for the programmer: the scheduling of computations, placement of data, synchroni zation, and communication between processors.  ... 
doi:10.4137/bbi.s40744 pmid:27932868 pmcid:PMC5135121 fatcat:gs6tx25ujbcqzncxsgtpb4xqsu

Analyzing Proteomes and Protein Function Using Graphical Comparative Analysis of Tandem Mass Spectrometry Results

K. Jill McAfee, Dexter T. Duncan, Michael Assink, Andrew J. Link
2006 Molecular & Cellular Proteomics  
many data storage and dissemination issues.  ...  In addition, storage and dissemination of mass spectrometry-based proteomic data are problems facing the scientific community.  ...  The physical storage of these data is allocated among multiple table spaces and data files using the experiment ID.  ... 
doi:10.1074/mcp.t500027-mcp200 pmid:16707483 fatcat:orqf4pvq4rfvpgczejx3kaxofy

A health-care data model based on the HL7 Reference Information Model

T. J. Eggebraaten, J. W. Tenner, J. C. Dubbels
2007 IBM Systems Journal  
The integration of medical information from various sources is gaining in importance as hospitals and medical research centers attempt to gain new insights into existing data.  ...  Our approach, which combines elements of entity-relationship data modeling and entity-attribute-value data modeling, involves the modeling of base RIM classes, RIM inheritance, and RIM data types.  ...  This is because the data for a particular object are spread across multiple tables in the database; consequently, storing an object requires multiple inserts, and retrieving an object requires joining  ... 
doi:10.1147/sj.461.0005 fatcat:jc7jwuwd2re6hn2fgsu6twpoqm

Stress Fractures of the Tibia after Jogging

Steller EP Unlu C
2014 Journal of Trauma and Treatment  
and standards for database and network communication.  ...  Finally, the diversity and commonality of these initiatives suggest a comprehensive, unified language.  ...  The Hypertext Transfer Protocol Distribution and Replication Protocol (HTTP-DRP) provides a specification of a protocol for the efficient replication of data over HTTP.  ... 
doi:10.4172/2167-1222.s2-006 fatcat:73kmefkhtreindbb5grlmjlj4i
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