microarray data storage submission retrieval and analysis

... effectively and greatly improves the speed of data retrieval We introduce two types of indexes: content index and node index Blob Data Storage Beside the nonblob data storage problem, the blob data storage ... the data storage problem into two subproblems: nonblob data storage and blob data storage Nonblob data is stored in a graph database system which will be introduced in Section 3.1, while blob data ... we focus on the storage design and indexing In this thesis, the data storage problem is divided into two subproblems, nonblob data storage problem and blob data storage problem 1.3 Contribution...

Ngày tải lên: 04/10/2015, 10:24

... Saarela 34 DNA microarray data analysis Overview of data analysis In this book, we emphasize to microarray data analysis after the microarrays have been hybridized, scanned and the images have ... The following schematic workflow outlines the basic analysis steps of exploratory data analysis 4.1 cDNA microarray data analysis We start data analysis from the results of scanned images At this ... 31 32 33 Overview of data analysis 4.1 cDNA microarray data analysis 4.2 Affymetrix data analysis 4.3 Data analysis pipeline 34 34...

Ngày tải lên: 11/04/2014, 09:40

Ngày tải lên: 17/04/2014, 09:16

... optimization Figure 6: Vectorized data storage with bank optimization Figure 7: Data mapping and read commands needed for any MC data retrieval: (a) Image plane pixel map and the minimum required reference ... retrieving useful data; • increased number of read commands on the address bus toward the memory The vectorized data storage scheme is further described in next section Vectorized data storage The ... standard decoder faces with regard to its most demanding algorithm Section comes with the proposed solution for the previously presented problems and describes data mapping, reorganization, and...

Ngày tải lên: 18/06/2014, 22:20

... Workgroup We have established an international workgroup for the collection and analysis of RT and protease sequences and data from persons infected with non-B HIV-1 subtypes Currently, the workgroup ... 13 countries The goal of the workgroup is to collect and analyze a robust database of sequences and clinical data to identify similarities and differences among HIV-1 subtypes with respect to ... subtypes.[15] The collected data are intended to be publicly available, and can serve as a reference dataset and as a watch list for resistance surveillance programs and epidemiologic studies (see...

Ngày tải lên: 20/06/2014, 08:20

... retrieving useful data; • increased number of read commands on the address bus toward the memory The vectorized data storage scheme is further described in next section Vectorized data storage The ... standard decoder faces with regard to its most demanding algorithm Section comes with the proposed solution for the previously presented problems and describes data mapping, reorganization, and ... proposed data organization and addressing scheme The proposed data vectorization and the specific addressing scheme presented in this article not only provide a faster access to all the requested data, ...

Ngày tải lên: 20/06/2014, 21:20

... [10] L Klebanov, A Gordon, Y Xiao, H Land, and A Yakovlev, “A permutation test motivated by microarray data analysis, ” Computational Statistics and Data Analysis, vol 50, no 12, pp 3619–3628, ... “Goodness-of-fit tests for univariate and multivariate normal models,” in Handbook of Statistics, R Khattree and C R Rao, Eds., vol 22, pp 869– 906, Elsevier, North-Holland, The Netherlands, 2003 [8] R R Wilcox, ... study as follows (1) In each sample, data are generated from a normal distribution N(μ, σ ) with mean μ and variance σ In the context of microarray data analysis, this design implies that the...

Ngày tải lên: 22/06/2014, 22:20

... Matlab and tested it on the yeast gene microarray data that can be found at [15] The data consists of 2884 genes and 17 conditions We have obtained the following first results Initially, the data ... Maron-Katz, and R Shamir, “CLICK and EXPANDER: a system for clustering and visualizing gene expression data, ” Bioinformatics, vol 19, no 14, pp 1787–1799, 2003 [8] Y Kluger, R Basri, J T Chang, and M ... interests are in genomics and proteomics, programmable wireless networks, brain computing interfaces, healthcare safety, and data- nomic and pervasive computing and storage He is a Fellow of the...

Ngày tải lên: 22/06/2014, 23:20

Ngày tải lên: 29/06/2014, 11:20

... and Analysis (CAMERA, http://camera.calit2 net/) and Visualization and Analysis of Microbial Popu­ lation Structures (VAMPS, http://vamps.mbl.edu/) Other communities probably have their own databases ... changing formats for digital storage DNA won’t change, but computer disks will RK: The EBI’s SRA has a better data submission pipe­ line than NCBI’s, and I understand the EBI is keen to involve ... different data in different places, perhaps with duplications, with each database having different formats or policies for data access, different reliabilities and so on GenBank, ENA and DDBJ...

Ngày tải lên: 09/08/2014, 22:23

... and Leukemia have been obtained by Dudoit and Fridlyand and Handl et al., respectively, via an accurate statistical screening of the three relevant microarray experiments that involved thousands ... assessed both in absolute and relative terms In order to partially fill the gap existing between the general data analysis literature and the special case of microarray data, Giancarlo et al [20] ... those designed for and tested on microarray data That class of measures assumes nothing about the structure of the dataset, which is inferred directly from the data In the general data mining literature,...

Ngày tải lên: 12/08/2014, 17:20

... pathogens and hosts, we have now developed a web-based PHI data integration and analysis system (PHIDIAS) that permits integration and analysis of genome sequences, curated literature data for ... other pathogens and PHI systems Finally, future plans for expanding PHIDIAS include development of a web-based database and an analysis pipeline that permit storage, processing, and modeling of ... that search and analyze annotated genome sequences, curated PHI data, and PHIrelated gene expression data (Figure 1a) Pathogen genomes are displayed and analyzed by PGBrowser, Pacodom, and BLAST...

Ngày tải lên: 14/08/2014, 08:20

... software and produced the data in GSE8746 Donald King and Paul Britton tested the software and helped produce the data in GSE8746 13 14 15 16 Additional data files The following additional data are ... Methods and data analysis The data used were downloaded from the Gene Expression Omnibus (GEO) [14], accession number GSE2228 The array platform for this data is GEO accession GPL1834, and top_fams ... normalization and significance testing functions for pathogen detection data DetectiV uses simple and well established visualization and statistical techniques to analyze data from pathogen detection microarrays...

Ngày tải lên: 14/08/2014, 08:20

... a workshop on the analysis of microarrays Conferences dealing with the statistical analyses of EADGENE Microarray Data Analysis Workshop 623 microarrays using common sets of data have been successfully ... Because the EADGENE Microarray Data Analysis Workshop 625 real data was from a mastitis experiment, some participants had a particular interest in this disease and its study via microarray analyses ... simulation of DNA -microarray gene expression data, BMC Bioinformatics (2006) 205 [2] Allison D.B., Cui X., Page G.P., Sabripour M., Microarray data analysis: from disarray to consolidation and consensus,...

Ngày tải lên: 14/08/2014, 13:22

... the real data set The groups are numbers 41 (top), 138 (middle) and 23 (bottom) Data has been scaled and centred Data from the E coli data set is shown on the left, and from the S aureus data set ... Kasprzyk A., Davis S., De M.B., Brazma A., Huber W., BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis, Bioinformatics 21 (2005) 3439–3440 [9] Eisen ... the data set and is based on an empirical Bayesian generalised linear model with the regression coefficients between expression data and the sample treatments (e.g time point or pathogen) as random...

Ngày tải lên: 14/08/2014, 13:22

... Article R37 Lemmens et al Materials and methods Microarray data The Spellman [12] and Gasch [12] datasets were used as microarray benchmark sets The Spellman dataset [12] contains 77 experiments ... al Gasch [13] dataset Additional data file and Additional data file consist of the extended modules identified in the Spellman [12] and Gasch [13] datasets, respectively Additional data file includes ... developed a procedure that learns modules from microarray and ChIP-chip data using a sequential analysis of the data In a first step, the ChIP-chip data is used to find a set of genes whose upstream...

Ngày tải lên: 14/08/2014, 16:21

... Analysis of high density microarrays and gene Applied Maths chips A Gene Expression Data Analysis and Management Tool Extracting and visualizing patterns in large multivariate data Analysis and ... array data storage, sharing and analysis It is not platform dependent We can analyze GPR datasets by uploading them directly 20 2.3 Stanford Microarray Database (SMD) The Stanford Microarray database ... different microarray datasets and a microarray data analysis tool for analyzing the stored data The repository currently allows datasets of GenepixPro format to be deposited, although it can be expanded...

Ngày tải lên: 30/10/2014, 20:10

... and their implementations Chapter provides a detailed analysis of the Microsphere Projection algorithm In Chapter we present an analysis and comparison of various 1D, 2D and 3D case studies and ... to address non-uniform data, this paper will restrict its discussion to the set of algorithms which are designed to handle non-uniform data This will exclude both Bilinear and Trilinear interpolations ... trend of the data, and is not guaranteed to pass through any of the data points exactly See Figure 1.1 However, if the primary loss of information (the primary difficulty) with the data is not...

Ngày tải lên: 30/10/2014, 20:12

... Summary Magnetic data storage has been an active and productive research field for several decades Targeted on the everlasting persuit of higher storage capacity, longer data retention, and lower energy ... nonvolatility and long data duration are also essential for the next-generation data storage devices As a supplement to the HDD, an idea of non-volatile magnetic storage, the magnetic random access ... materials and new physics In the following section, the trend in the development of magnetic data storage devices will be elucidated Chapter Introduction 1.1 The evolution of magnetic data storage and...

Ngày tải lên: 09/09/2015, 11:26