Bioinformatics tools and database resources for systems genetics analysis in mice-A short review and an evaluation of future needs

Caroline Durrant; Morris A. Swertz; Rudi Alberts; Danny Arends; Steffen Möller; Richard Mott; Pjotr Prins; K. Joeri van der Velde; Ritsert C. Jansen; Klaus Schughart

doi:10.1093/bib/bbr026

Bioinformatics tools and database resources for systems genetics analysis in mice-A short review and an evaluation of future needs

Caroline Durrant, Morris A. Swertz, Rudi Alberts, Danny Arends, Steffen Möller, Richard Mott, Pjotr Prins, K. Joeri van der Velde, Ritsert C. Jansen, Klaus Schughart^*

^*Corresponding author for this work

Research output: Contribution to journal › Short survey › peer-review

10 Citations (Scopus)

Abstract

During a meeting of the SYSGENET working group 'Bioinformatics', currently available software tools and databases for systems genetics in mice were reviewed and the needs for future developments discussed. The group evaluated interoperability and performed initial feasibility studies. To aid future compatibility of software and exchange of already developed software modules, a strong recommendation was made by the group to integrate HAPPY and R/qtl analysis toolboxes, GeneNetwork and XGAP database platforms, and TIQS and xQTL processing platforms. R should be used as the principal computer language for QTL data analysis in all platforms and a 'cloud' should be used for software dissemination to the community. Furthermore, the working group recommended that all data models and software source code should be made visible in public repositories to allow a coordinated effort on the use of common data structures and file formats.

Original language	English
Article number	bbr026
Pages (from-to)	135-142
Number of pages	8
Journal	Briefings in Bioinformatics
Volume	13
Issue number	2
DOIs	https://doi.org/10.1093/bib/bbr026
Publication status	Published - Mar 2012
Externally published	Yes

Keywords

Database
Mouse
QTL mapping
Systems genetics

Access to Document

10.1093/bib/bbr026

Cite this

Durrant, C., Swertz, M. A., Alberts, R., Arends, D., Möller, S., Mott, R., Prins, P., van der Velde, K. J., Jansen, R. C., & Schughart, K. (2012). Bioinformatics tools and database resources for systems genetics analysis in mice-A short review and an evaluation of future needs. Briefings in Bioinformatics, 13(2), 135-142. Article bbr026. https://doi.org/10.1093/bib/bbr026

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abstract = "During a meeting of the SYSGENET working group 'Bioinformatics', currently available software tools and databases for systems genetics in mice were reviewed and the needs for future developments discussed. The group evaluated interoperability and performed initial feasibility studies. To aid future compatibility of software and exchange of already developed software modules, a strong recommendation was made by the group to integrate HAPPY and R/qtl analysis toolboxes, GeneNetwork and XGAP database platforms, and TIQS and xQTL processing platforms. R should be used as the principal computer language for QTL data analysis in all platforms and a 'cloud' should be used for software dissemination to the community. Furthermore, the working group recommended that all data models and software source code should be made visible in public repositories to allow a coordinated effort on the use of common data structures and file formats.",

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AU - Durrant, Caroline

AU - Swertz, Morris A.

AU - Alberts, Rudi

AU - Arends, Danny

AU - Möller, Steffen

AU - Mott, Richard

AU - Prins, Pjotr

AU - van der Velde, K. Joeri

AU - Jansen, Ritsert C.

AU - Schughart, Klaus

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KW - Mouse

KW - QTL mapping

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Bioinformatics tools and database resources for systems genetics analysis in mice-A short review and an evaluation of future needs

Abstract

Keywords

Access to Document

Other files and links

Fingerprint

GeneNetwork: framework for web-based genetics

xQTL workbench: A scalable web environment for multi-level QTL analysis

The MOLGENIS toolkit: Rapid prototyping of biosoftware at the push of a button

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