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DIPSBC - data integration platform for systems biology collaborations
BACKGROUND: Modern biomedical research is often organized in collaborations involving labs worldwide. In particular in systems biology, complex molecular systems are analyzed that require the generation and interpretation of heterogeneous data for their explanation, for example ranging from gene exp...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3424966/ https://www.ncbi.nlm.nih.gov/pubmed/22568834 http://dx.doi.org/10.1186/1471-2105-13-85 |
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author | Dreher, Felix Kreitler, Thomas Hardt, Christopher Kamburov, Atanas Yildirimman, Reha Schellander, Karl Lehrach, Hans Lange, Bodo MH Herwig, Ralf |
author_facet | Dreher, Felix Kreitler, Thomas Hardt, Christopher Kamburov, Atanas Yildirimman, Reha Schellander, Karl Lehrach, Hans Lange, Bodo MH Herwig, Ralf |
author_sort | Dreher, Felix |
collection | PubMed |
description | BACKGROUND: Modern biomedical research is often organized in collaborations involving labs worldwide. In particular in systems biology, complex molecular systems are analyzed that require the generation and interpretation of heterogeneous data for their explanation, for example ranging from gene expression studies and mass spectrometry measurements to experimental techniques for detecting molecular interactions and functional assays. XML has become the most prominent format for representing and exchanging these data. However, besides the development of standards there is still a fundamental lack of data integration systems that are able to utilize these exchange formats, organize the data in an integrative way and link it with applications for data interpretation and analysis. RESULTS: We have developed DIPSBC, an interactive data integration platform supporting collaborative research projects, based on Foswiki, Solr/Lucene, and specific helper applications. We describe the main features of the implementation and highlight the performance of the system with several use cases. All components of the system are platform independent and open-source developments and thus can be easily adopted by researchers. An exemplary installation of the platform which also provides several helper applications and detailed instructions for system usage and setup is available at http://dipsbc.molgen.mpg.de. CONCLUSIONS: DIPSBC is a data integration platform for medium-scale collaboration projects that has been tested already within several research collaborations. Because of its modular design and the incorporation of XML data formats it is highly flexible and easy to use. |
format | Online Article Text |
id | pubmed-3424966 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-34249662012-08-23 DIPSBC - data integration platform for systems biology collaborations Dreher, Felix Kreitler, Thomas Hardt, Christopher Kamburov, Atanas Yildirimman, Reha Schellander, Karl Lehrach, Hans Lange, Bodo MH Herwig, Ralf BMC Bioinformatics Software BACKGROUND: Modern biomedical research is often organized in collaborations involving labs worldwide. In particular in systems biology, complex molecular systems are analyzed that require the generation and interpretation of heterogeneous data for their explanation, for example ranging from gene expression studies and mass spectrometry measurements to experimental techniques for detecting molecular interactions and functional assays. XML has become the most prominent format for representing and exchanging these data. However, besides the development of standards there is still a fundamental lack of data integration systems that are able to utilize these exchange formats, organize the data in an integrative way and link it with applications for data interpretation and analysis. RESULTS: We have developed DIPSBC, an interactive data integration platform supporting collaborative research projects, based on Foswiki, Solr/Lucene, and specific helper applications. We describe the main features of the implementation and highlight the performance of the system with several use cases. All components of the system are platform independent and open-source developments and thus can be easily adopted by researchers. An exemplary installation of the platform which also provides several helper applications and detailed instructions for system usage and setup is available at http://dipsbc.molgen.mpg.de. CONCLUSIONS: DIPSBC is a data integration platform for medium-scale collaboration projects that has been tested already within several research collaborations. Because of its modular design and the incorporation of XML data formats it is highly flexible and easy to use. BioMed Central 2012-05-08 /pmc/articles/PMC3424966/ /pubmed/22568834 http://dx.doi.org/10.1186/1471-2105-13-85 Text en Copyright ©2012 Dreher et al.; licensee BioMed Central Ltd http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Dreher, Felix Kreitler, Thomas Hardt, Christopher Kamburov, Atanas Yildirimman, Reha Schellander, Karl Lehrach, Hans Lange, Bodo MH Herwig, Ralf DIPSBC - data integration platform for systems biology collaborations |
title | DIPSBC - data integration platform for systems biology collaborations |
title_full | DIPSBC - data integration platform for systems biology collaborations |
title_fullStr | DIPSBC - data integration platform for systems biology collaborations |
title_full_unstemmed | DIPSBC - data integration platform for systems biology collaborations |
title_short | DIPSBC - data integration platform for systems biology collaborations |
title_sort | dipsbc - data integration platform for systems biology collaborations |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3424966/ https://www.ncbi.nlm.nih.gov/pubmed/22568834 http://dx.doi.org/10.1186/1471-2105-13-85 |
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