Language workbench user interfaces for data analysis

PeerJ
Victoria M Benson, Fabien Campagne

Abstract

Biological data analysis is frequently performed with command line software. While this practice provides considerable flexibility for computationally savy individuals, such as investigators trained in bioinformatics, this also creates a barrier to the widespread use of data analysis software by investigators trained as biologists and/or clinicians. Workflow systems such as Galaxy and Taverna have been developed to try and provide generic user interfaces that can wrap command line analysis software. These solutions are useful for problems that can be solved with workflows, and that do not require specialized user interfaces. However, some types of analyses can benefit from custom user interfaces. For instance, developing biomarker models from high-throughput data is a type of analysis that can be expressed more succinctly with specialized user interfaces. Here, we show how Language Workbench (LW) technology can be used to model the biomarker development and validation process. We developed a language that models the concepts of Dataset, Endpoint, Feature Selection Method and Classifier. These high-level language concepts map directly to abstractions that analysts who develop biomarker models are familiar with. We found that use...Continue Reading

References

Dec 26, 2001·Nucleic Acids Research·Ron EdgarAlex E Lash
Mar 1, 2006·BMC Bioinformatics·Sudhir Varma, Richard Simon
May 29, 2008·Journal of the National Cancer Institute·Sunita R SetlurMark A Rubin
May 4, 2010·Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology·Ludmila VelkovaPavlina Dolashka-Angelova
Feb 1, 2014·PeerJ·Manuele Simi, Fabien Campagne
Jul 9, 2014·Genome Biology·Daniel BlankenbergAnton Nekrutenko

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Methods Mentioned

BETA
FeatureSelection
Chip

Software Mentioned

Ant build scripts
MetaR
Linux
Java
libSVM
Clustal
LANG
GobyWeb
BDVal
pugin

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