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BASE--2nd generation software for microarray data management and analysis.

Vallon-Christersson, Johan LU ; Nordborg, Nicklas LU ; Svensson, Martin LU and Häkkinen, Jari LU (2009) In BMC Bioinformatics 10(Oct 12).
Abstract
BACKGROUND: Microarray experiments are increasing in size and samples are collected asynchronously over long time. Available data are re-analysed as more samples are hybridized. Systematic use of collected data requires tracking of biomaterials, array information, raw data, and assembly of annotations. To meet the information tracking and data analysis challenges in microarray experiments we reimplemented and improved BASE version 1.2. RESULTS: The new BASE presented in this report is a comprehensive annotable local microarray data repository and analysis application providing researchers with an efficient information management and analysis tool. The information management system tracks all material from biosource, via sample and through... (More)
BACKGROUND: Microarray experiments are increasing in size and samples are collected asynchronously over long time. Available data are re-analysed as more samples are hybridized. Systematic use of collected data requires tracking of biomaterials, array information, raw data, and assembly of annotations. To meet the information tracking and data analysis challenges in microarray experiments we reimplemented and improved BASE version 1.2. RESULTS: The new BASE presented in this report is a comprehensive annotable local microarray data repository and analysis application providing researchers with an efficient information management and analysis tool. The information management system tracks all material from biosource, via sample and through extraction and labelling to raw data and analysis. All items in BASE can be annotated and the annotations can be used as experimental factors in downstream analysis. BASE stores all microarray experiment related data regardless if analysis tools for specific techniques or data formats are readily available. The BASE team is committed to continue improving and extending BASE to make it usable for even more experimental setups and techniques, and we encourage other groups to target their specific needs leveraging on the infrastructure provided by BASE. CONCLUSION: BASE is a comprehensive management application for information, data, and analysis of microarray experiments, available as free open source software at http://base.thep.lu.se under the terms of the GPLv3 license. (Less)
Please use this url to cite or link to this publication:
author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
BMC Bioinformatics
volume
10
issue
Oct 12
publisher
BioMed Central
external identifiers
  • WOS:000271763000002
  • PMID:19822003
  • Scopus:70449732423
ISSN
1471-2105
DOI
10.1186/1471-2105-10-330
project
CREATE Health
language
English
LU publication?
yes
id
0619764a-b126-48b7-8b8a-2777efff08f9 (old id 1500411)
alternative location
http://www.ncbi.nlm.nih.gov/pubmed/19822003?dopt=Abstract
date added to LUP
2009-11-03 14:52:30
date last changed
2016-10-13 04:28:39
@misc{0619764a-b126-48b7-8b8a-2777efff08f9,
  abstract     = {BACKGROUND: Microarray experiments are increasing in size and samples are collected asynchronously over long time. Available data are re-analysed as more samples are hybridized. Systematic use of collected data requires tracking of biomaterials, array information, raw data, and assembly of annotations. To meet the information tracking and data analysis challenges in microarray experiments we reimplemented and improved BASE version 1.2. RESULTS: The new BASE presented in this report is a comprehensive annotable local microarray data repository and analysis application providing researchers with an efficient information management and analysis tool. The information management system tracks all material from biosource, via sample and through extraction and labelling to raw data and analysis. All items in BASE can be annotated and the annotations can be used as experimental factors in downstream analysis. BASE stores all microarray experiment related data regardless if analysis tools for specific techniques or data formats are readily available. The BASE team is committed to continue improving and extending BASE to make it usable for even more experimental setups and techniques, and we encourage other groups to target their specific needs leveraging on the infrastructure provided by BASE. CONCLUSION: BASE is a comprehensive management application for information, data, and analysis of microarray experiments, available as free open source software at http://base.thep.lu.se under the terms of the GPLv3 license.},
  author       = {Vallon-Christersson, Johan and Nordborg, Nicklas and Svensson, Martin and Häkkinen, Jari},
  issn         = {1471-2105},
  language     = {eng},
  number       = {Oct 12},
  publisher    = {ARRAY(0xb157b70)},
  series       = {BMC Bioinformatics},
  title        = {BASE--2nd generation software for microarray data management and analysis.},
  url          = {http://dx.doi.org/10.1186/1471-2105-10-330},
  volume       = {10},
  year         = {2009},
}