Abstract
BackgroundBioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process. Such efforts include the development of easy-to-use web interfaces to biomedical databases. Recent advancements in interactive web technologies require us to rethink the standard submit-and-wait paradigm, and craft bioinformatics web applications that share analytical and interactive power with their desktop relatives, while retaining simplicity and availability.ResultsWe have developed dictyExpress, a web application that features a graphical, highly interactive explorative interface to our database that consists of more than 1000 Dictyostelium discoideum gene expression experiments. In dictyExpress, the user can select experiments and genes, perform gene clustering, view gene expression profiles across time, view gene co-expression networks, perform analyses of Gene Ontology term enrichment, and simultaneously display expression profiles for a selected gene in various experiments. Most importantly, these tasks are achieved through web applications whose components are seamlessly interlinked and immediately respond to events triggered by the user, thus providing a powerful explorative data analysis environment.ConclusiondictyExpress is a precursor for a new generation of web-based bioinformatics applications with simple but powerful interactive interfaces that resemble that of the modern desktop. While dictyExpress serves mainly the Dictyostelium research community, it is relatively easy to adapt it to other datasets. We propose that the design ideas behind dictyExpress will influence the development of similar applications for other model organisms.
Highlights
Bioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process
We report on the development of a gene expression database and its corresponding web application, dictyExpress http://www.ailab.si/dictyExpress, that we consider to be a pioneering attempt at this change
Visual interaction is incorporated into data retrieval: a user can, for example, hand-draw an approximate gene expression profile and dictyExpress would find and display genes that match it
Summary
Bioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process Such efforts include the development of easy-to-use web interfaces to biomedical databases. Instead of the infamous "Submit" button and the corresponding switch from one web page to another, modern systems employ an interactive, single-screen interface, which adapts to the user's data and actions. Such interfaces are used in many popular applications, such as e-mail browsers, spreadsheets, words processors, and social networking websites, but the field of bioinformatics has yet to adopt these new technologies
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have