2DDB – a bioinformatics solution for analysis of quantitative proteomics data
Malmström, Lars LU ; Marko-Varga, György LU ; Westergren-Thorsson, Gunilla LU
; Laurell, Thomas
LU
and Malmström, Johan
LU
(2006)
In BMC Bioinformatics
7(158).
- Abstract
- Background
We present 2DDB, a bioinformatics solution for storage, integration and analysis of quantitative proteomics data. As the data complexity and the rate with which it is produced increases in the proteomics field, the need for flexible analysis software increases.
Results
2DDB is based on a core data model describing fundamentals such as experiment description and identified proteins. The extended data models are built on top of the core data model to capture more specific aspects of the data. A number of public databases and bioinformatical tools have been integrated giving the user access to large amounts of relevant data. A statistical and graphical package, R, is used for statistical and... (More) - Background
We present 2DDB, a bioinformatics solution for storage, integration and analysis of quantitative proteomics data. As the data complexity and the rate with which it is produced increases in the proteomics field, the need for flexible analysis software increases.
Results
2DDB is based on a core data model describing fundamentals such as experiment description and identified proteins. The extended data models are built on top of the core data model to capture more specific aspects of the data. A number of public databases and bioinformatical tools have been integrated giving the user access to large amounts of relevant data. A statistical and graphical package, R, is used for statistical and graphical analysis. The current implementation handles quantitative data from 2D gel electrophoresis and multidimensional liquid chromatography/mass spectrometry experiments.
Conclusion
The software has successfully been employed in a number of projects ranging from quantitative liquid-chromatography-mass spectrometry based analysis of transforming growth factor-beta stimulated fi-broblasts to 2D gel electrophoresis/mass spectrometry analysis of biopsies from human cervix. The software is available for download at SourceForge. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/749035
- author
- Malmström, Lars
LU
; Marko-Varga, György
LU
; Westergren-Thorsson, Gunilla
LU
; Laurell, Thomas
LU
and Malmström, Johan
LU
- organization
- publishing date
- 2006
- type
- Contribution to journal
- publication status
- published
- subject
- in
- BMC Bioinformatics
- volume
- 7
- issue
- 158
- publisher
- BioMed Central (BMC)
- external identifiers
-
- wos:000236762100001
- pmid:16549013
- scopus:33645801199
- ISSN
- 1471-2105
- DOI
- 10.1186/1471-2105-7-158
- language
- English
- LU publication?
- yes
- additional info
- The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Analytical Chemistry (S/LTH) (011001004), Lung Biology (013212002), Biomedical Engineering (011200011)
- id
- c48f32ff-0a51-49fe-ad8d-2732ed46ca3e (old id 749035)
- alternative location
- http://www.biomedcentral.com/1471-2105/7/158
- date added to LUP
- 2016-04-04 09:24:04
- date last changed
- 2024-01-12 13:00:34
@article{c48f32ff-0a51-49fe-ad8d-2732ed46ca3e,
abstract = {{Background<br/><br>
We present 2DDB, a bioinformatics solution for storage, integration and analysis of quantitative proteomics data. As the data complexity and the rate with which it is produced increases in the proteomics field, the need for flexible analysis software increases.<br/><br>
<br/><br>
Results<br/><br>
2DDB is based on a core data model describing fundamentals such as experiment description and identified proteins. The extended data models are built on top of the core data model to capture more specific aspects of the data. A number of public databases and bioinformatical tools have been integrated giving the user access to large amounts of relevant data. A statistical and graphical package, R, is used for statistical and graphical analysis. The current implementation handles quantitative data from 2D gel electrophoresis and multidimensional liquid chromatography/mass spectrometry experiments.<br/><br>
<br/><br>
Conclusion<br/><br>
The software has successfully been employed in a number of projects ranging from quantitative liquid-chromatography-mass spectrometry based analysis of transforming growth factor-beta stimulated fi-broblasts to 2D gel electrophoresis/mass spectrometry analysis of biopsies from human cervix. The software is available for download at SourceForge.}},
author = {{Malmström, Lars and Marko-Varga, György and Westergren-Thorsson, Gunilla and Laurell, Thomas and Malmström, Johan}},
issn = {{1471-2105}},
language = {{eng}},
number = {{158}},
publisher = {{BioMed Central (BMC)}},
series = {{BMC Bioinformatics}},
title = {{2DDB – a bioinformatics solution for analysis of quantitative proteomics data}},
url = {{http://dx.doi.org/10.1186/1471-2105-7-158}},
doi = {{10.1186/1471-2105-7-158}},
volume = {{7}},
year = {{2006}},
}