A Grid-based solution for management and analysis of microarrays in distributed experiments

BMC Bioinformatics

Volumn 8, Issue SUPPL. 1, 2007, Pages

  Porro, Ivan ^a   Torterolo, Livia ^a   Corradi, Luca ^a   Fato, Marco ^a   Papadimitropoulos, Adam ^a   Scaglione, Silvia ^a   Schenone, Andrea ^a   Viti, Federica ^a  

^a UNIVERSITY OF GENOA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

AFFYMETRIX GENECHIP; BIOLOGICAL STUDIES; COMPUTATIONAL PERFORMANCE; DISTRIBUTED COMPUTATIONAL RESOURCES; FUNCTIONAL ARCHITECTURE; GENE EXPRESSION ANALYSIS; GRID-BASED APPROACH; MICROARRAY EXPERIMENTS;

COMPUTER OPERATING SYSTEMS; DIGITAL STORAGE; EXPERIMENTS; GENE EXPRESSION; GRID COMPUTING; MICROARRAYS; MIDDLEWARE; STATISTICAL TESTS;

SOFTWARE TESTING;

ARTICLE; DATA ANALYSIS; GENE EXPRESSION; INFORMATION PROCESSING; MATHEMATICAL COMPUTING; MICROARRAY ANALYSIS; RELIABILITY; SEQUENCE ANALYSIS; STANDARDIZATION; ALGORITHM; BIOLOGICAL MODEL; COMPUTER INTERFACE; COMPUTER PROGRAM; COMPUTER SIMULATION; DATA BASE; DNA MICROARRAY; EVALUATION; GENE EXPRESSION PROFILING; GENETIC DATABASE; INFORMATION RETRIEVAL; METHODOLOGY;

RATTUS;

ALGORITHMS; COMPUTER SIMULATION; DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; INFORMATION STORAGE AND RETRIEVAL; MODELS, BIOLOGICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 34248221983     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-S1-S7     Document Type: Article

References (19)

1. Brazma A On the importance of standardization in life sciences Bioinformatics 2001, 17(2):113-114. 11238066
2. Brody JP Williams BA Wold BJ Quake SR Significance and statistical errors in the analysis of DNA microarray data Proc Natl Acad Sci USA 2002, 99(20):12975-12978. 130571 12235357
3. Butte A The use and analysis of microarray data Nat Rev Drug Discov 2002, 1(12):951-60. Review 12461517
4. Armstrong NJ van de Wiel MA Microarray data analysis: From hypotheses to conclusions using gene expression data Cell Oncol 2004, 26:279-290. 15623938
5. Maurer M Molidor R Sturn A Hartler J Hackl H Stocker G Prokesch A Scheideler M Trajanoski Z MARS: Microarray analysis, retrieval, and storage system BMC Bioinformatics 2005, 6(1):101. 1090551 15836795
6. Romano P Bertolini G De Paoli F Fattore M Marra D Mauri G Merelli E Porro I Scaglione S Milanesi L Oncology over Internet: Integrating data and analysis of oncology interest on the net by means of workflows Journal of Integrative Bioinformatics 2006, 3(1):21. http://journal.imbio.de/index.php?paper_id=21
7. Stratowa C XPS, a Novel Framework for Distributed Storage and Analysis of Microarray Data in the Terabyte Range: An Alternative to BioConductor Proceedings of the 3rd International Workshop on Distributed Statistical Computing 2003.
8. Brun R Rademakers F ROOT - An Object Oriented Data Analysis Framework Proceedings AIHENP'96 Workshop, Lausanne, Sep Nucl Inst & Meth in Phys Res A 1996, 389:81-86.
9. Thorsten F ODD Genes - From Microarray Data to Discovery, Using the Grid and High Performance Computing Scottish Center for Genomics Technology and Informatics (SC-GTI) 3rd E-BioSci/ORIEL Annual Workshop 12-15 October 2004 Hinxton Hall Conference Centre, Hinxton, England
10. Alfieri R Barbera R Belluomo P Cavalli A Cecchini R Chierici A Fiaschini V Dell'Agnello L Donno F Ferro E The INFN-Grid Testbed Future Generation Computer Systems 2005, 21(2):249-258.
11. Tuecke S Welch V Engert D Pearlman L Thompson M Internet X.509 public key infrastructure (PKI) proxy certificate profile IETF RFC 2004, 3820.
12. http://www.adaptivepath.com/publications/essays/archives/000385.php
13. Li C Wong WH Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection Proc Natl Acad Sci USA 2001, 98:31-36. 14539 11134512
14. Gentleman RC Carey VJ Bates DJ Bolstad BM Dettling M Dudoit S Ellis B Gautier L Ge Y Gentry J Hornik K Hothorn T Huber W lacus S Irizarry R Leisch F Li C Maechler M Rossini AJ Sawitzki G Smith C Smyth GK Tierney L Yang YH Zhang J Bioconductor: Open software development for computational biology and bioinformatics Genome Biol 2004, 5(10):R80. 545600 15461798
15. Pfeffer LM Dinarello CA Herberman RB Williams BR Borden EC Bordens R Walter MR Nagabhushan TL Trotta PP Pestka S Biological properties of recombinant alpha-interferons: 40th anniversary of the discovery of interferons Cancer Res 1998, 58(12):2489-99. Review 9635566
16. Scaglione S Braccini A Wendt D Jaquiery C Beltrame F Quarto R Martin I Engineering of osteoinductive grafts by isolation and expansion of ovine bone marrow stromal cells directly on 3D ceramic scaffolds Biotechnol Bioeng 2006, 93(1):181-7. 16245346
17. Braccini A Wendt D Jaquiery C Jakob M Heberer M Kenins L Wodnar-Filipowicz A Quarto R Martin I Three-dimensional perfusion culture of human bone marrow cells and generation of osteoinductive grafts Stem Cells 2005, 23(8):1066-72. 16002780
18. http://egee-na4.ct.infn.it/biomed/
19. Andronico G Ardizzone V Barbera R Catania R Carrieri A Falzone A Giorgio E La Rocca G Monforte S Pappalardo M Passaro G Platania G GILDA: The Grid INFN Virtual Laboratory for Dissemination Activities First International Conference on Testbeds and Research Infrastructures for the DEvelopment of NeTworks and COMmunities (TRIDENTCOM'05) 2005, 304-305.