Abstract
BioPyramid is a Python package, which serves as a scaffold for building an online application for the exploration of gene expression data. It is designed for bioinformaticians wishing to quickly share transformed data and interactive analyses with collaborators. Current R-based tools similarly address the need to quickly share 'omics'-data in an exploratory format, but these are generally small-scale, single-dataset solutions. Biopyramid is written in Python pyramid framework and scalable to address longer-term or more complex projects. It contains a number of components designed to reduce the time and effort in building such an application from scratch, including gene annotation, dataset models and visualization tools. Freely available at http://github.com/jarny/biopyramid. Implemented in python and javascript.
Highlights
We have seen a huge increase in the number of high throughput genomics datasets produced, such as RNA-Seq datasets, primarily driven by cheaper and more accessible technologies
Some examples include Haemosphere [7], Immgen [8], Stemformatics [10] and GeneExpression Commons [9]. These applications contain a set of visualisation tools such as gene expression plots or heatmaps
We have developed BioPyramid as a python and javascript based framework for developing an online genomics application
Summary
We have seen a huge increase in the number of high throughput genomics datasets produced, such as RNA-Seq datasets, primarily driven by cheaper and more accessible technologies. Following this trend has been an increase in the number of applications which act as online portals to the datasets. Often designed for the bench biologists, these applications enable easy access and analyses of the datasets they host, enhancing their value and acting as hypothesis generators. These applications contain a set of visualisation tools such as gene expression plots or heatmaps.
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