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XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments.

Swertz MA, Velde KJ, Tesson BM, Scheltema RA, Arends D, Vera G, Alberts R, Dijkstra M, Schofield P, Schughart K, Hancock JM, Smedley D, Wolstencroft K, Goble C, de Brock EO, Jones AR, Parkinson HE, Coordination of Mouse Informatics Resources (CASIMIR)Genotype-To-Phenotype (GEN2PHEN) ConsortiumsJansen RC - Genome Biol. (2010)

Bottom Line: We present an extensible software model for the genotype and phenotype community, XGAP.XGAP has simple load formats for any type of genotype, epigenotype, transcript, protein, metabolite or other phenotype data.Current functionality includes tools ranging from eQTL analysis in mouse to genome-wide association studies in humans.

View Article: PubMed Central - HTML - PubMed

Affiliation: Genomics Coordination Center, Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands. m.a.swertz@rug.nl

ABSTRACT
We present an extensible software model for the genotype and phenotype community, XGAP. Readers can download a standard XGAP (http://www.xgap.org) or auto-generate a custom version using MOLGENIS with programming interfaces to R-software and web-services or user interfaces for biologists. XGAP has simple load formats for any type of genotype, epigenotype, transcript, protein, metabolite or other phenotype data. Current functionality includes tools ranging from eQTL analysis in mouse to genome-wide association studies in humans.

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Customizing XGAP. A file in MOLGENIS domain-specific language is used to describe and customize the XGAP database infrastructure in a few lines. (a) Shows how the addition of a Metabolite data entity as a new variant of Trait takes only a few lines in this DSL. (b) Shows how the GUI can be customized to suit a particular experimental process. (c) Shows how programmers can add a 'plug-in' program that is not generated by MOLGENIS but written by hand in Java.
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Figure 5: Customizing XGAP. A file in MOLGENIS domain-specific language is used to describe and customize the XGAP database infrastructure in a few lines. (a) Shows how the addition of a Metabolite data entity as a new variant of Trait takes only a few lines in this DSL. (b) Shows how the GUI can be customized to suit a particular experimental process. (c) Shows how programmers can add a 'plug-in' program that is not generated by MOLGENIS but written by hand in Java.

Mentions: Customizations and extensions of the XGAP object model can be described in a single text file using MOLGENIS [37,56] DSL. On the push of a button, the MOLGENIS generator instantly produces an extended version of the XGAP database software from this DSL file. A regression test procedure assists XGAP developers to ensure their extensions do not break the XGAP exchange format. Figure 5a shows how the addition of a Metabolite data entity as a new variant of Trait takes only a few lines in this DSL. Figure 5b shows how the GUI can be customized to suit a particular experimental process. Figure 5c shows how programmers can add a 'plug-in' program that is not generated by MOLGENIS but written by hand in Java (for example, a viewer that plots QTL profiles interactively). Moreover, use of Cascading Style Sheets (CSS) enables research projects to completely customize the look and feel of their XGAP.


XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments.

Swertz MA, Velde KJ, Tesson BM, Scheltema RA, Arends D, Vera G, Alberts R, Dijkstra M, Schofield P, Schughart K, Hancock JM, Smedley D, Wolstencroft K, Goble C, de Brock EO, Jones AR, Parkinson HE, Coordination of Mouse Informatics Resources (CASIMIR)Genotype-To-Phenotype (GEN2PHEN) ConsortiumsJansen RC - Genome Biol. (2010)

Customizing XGAP. A file in MOLGENIS domain-specific language is used to describe and customize the XGAP database infrastructure in a few lines. (a) Shows how the addition of a Metabolite data entity as a new variant of Trait takes only a few lines in this DSL. (b) Shows how the GUI can be customized to suit a particular experimental process. (c) Shows how programmers can add a 'plug-in' program that is not generated by MOLGENIS but written by hand in Java.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2864567&req=5

Figure 5: Customizing XGAP. A file in MOLGENIS domain-specific language is used to describe and customize the XGAP database infrastructure in a few lines. (a) Shows how the addition of a Metabolite data entity as a new variant of Trait takes only a few lines in this DSL. (b) Shows how the GUI can be customized to suit a particular experimental process. (c) Shows how programmers can add a 'plug-in' program that is not generated by MOLGENIS but written by hand in Java.
Mentions: Customizations and extensions of the XGAP object model can be described in a single text file using MOLGENIS [37,56] DSL. On the push of a button, the MOLGENIS generator instantly produces an extended version of the XGAP database software from this DSL file. A regression test procedure assists XGAP developers to ensure their extensions do not break the XGAP exchange format. Figure 5a shows how the addition of a Metabolite data entity as a new variant of Trait takes only a few lines in this DSL. Figure 5b shows how the GUI can be customized to suit a particular experimental process. Figure 5c shows how programmers can add a 'plug-in' program that is not generated by MOLGENIS but written by hand in Java (for example, a viewer that plots QTL profiles interactively). Moreover, use of Cascading Style Sheets (CSS) enables research projects to completely customize the look and feel of their XGAP.

Bottom Line: We present an extensible software model for the genotype and phenotype community, XGAP.XGAP has simple load formats for any type of genotype, epigenotype, transcript, protein, metabolite or other phenotype data.Current functionality includes tools ranging from eQTL analysis in mouse to genome-wide association studies in humans.

View Article: PubMed Central - HTML - PubMed

Affiliation: Genomics Coordination Center, Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands. m.a.swertz@rug.nl

ABSTRACT
We present an extensible software model for the genotype and phenotype community, XGAP. Readers can download a standard XGAP (http://www.xgap.org) or auto-generate a custom version using MOLGENIS with programming interfaces to R-software and web-services or user interfaces for biologists. XGAP has simple load formats for any type of genotype, epigenotype, transcript, protein, metabolite or other phenotype data. Current functionality includes tools ranging from eQTL analysis in mouse to genome-wide association studies in humans.

Show MeSH