Dataset Information

A Generic Framework and Library for Exploration of Small Multiples through Interactive Piling.

ABSTRACT: Small multiples are miniature representations of visual information used generically across many domains. Handling large numbers of small multiples imposes challenges on many analytic tasks like inspection, comparison, navigation, or annotation. To address these challenges, we developed a framework and implemented a library called PILlNG.JS for designing interactive piling interfaces. Based on the piling metaphor, such interfaces afford flexible organization, exploration, and comparison of large numbers of small multiples by interactively aggregating visual objects into piles. Based on a systematic analysis of previous work, we present a structured design space to guide the design of visual piling interfaces. To enable designers to efficiently build their own visual piling interfaces, PILlNG.JS provides a declarative interface to avoid having to write low-level code and implements common aspects of the design space. An accompanying GUI additionally supports the dynamic configuration of the piling interface. We demonstrate the expressiveness of PILlNG.JS with examples from machine learning, immunofluorescence microscopy, genomics, and public health.

SUBMITTER: Lekschas F

PROVIDER: S-EPMC10029706 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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A Generic Framework and Library for Exploration of Small Multiples through Interactive Piling.

Lekschas Fritz F Zhou Xinyi X Chen Wei W Gehlenborg Nils N Bach Benjamin B Pfister Hanspeter H

IEEE transactions on visualization and computer graphics 20210128 2

Small multiples are miniature representations of visual information used generically across many domains. Handling large numbers of small multiples imposes challenges on many analytic tasks like inspection, comparison, navigation, or annotation. To address these challenges, we developed a framework and implemented a library called PILlNG.JS for designing interactive piling interfaces. Based on the piling metaphor, such interfaces afford flexible organization, exploration, and comparison of large ...[more]

PMID: 33026994

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Project description:MotivationIt has been known that mature transfer RNAs (tRNAs) that are encoded in the nuclear genome give rise to short molecules, collectively known as tRNA fragments or tRFs. Recently, we reported that, in healthy individuals and in patients, tRFs are constitutive, arise from mitochondrial as well as from nuclear tRNAs, and have composition and abundances that depend on a person's sex, population origin and race as well as on tissue, disease and disease subtype. Our findings as well as similar work by other groups highlight the importance of tRFs and presage an increase in the community's interest in elucidating the roles of tRFs in health and disease.ResultsWe created MINTbase, a web-based framework that serves the dual-purpose of being a content repository for tRFs and a tool for the interactive exploration of these newly discovered molecules. A key feature of MINTbase is that it deterministically and exhaustively enumerates all possible genomic locations where a sequence fragment can be found and indicates which fragments are exclusive to tRNA space, and thus can be considered as tRFs: this is a very important consideration given that the genomes of higher organisms are riddled with partial tRNA sequences and with tRNA-lookalikes whose aberrant transcripts can be mistaken for tRFs. MINTbase is extremely flexible and integrates and presents tRF information from multiple yet interconnected vantage points ('vistas'). Vistas permit the user to interactively personalize the information that is returned and the manner in which it is displayed. MINTbase can report comparative information on how a tRF is distributed across all anticodon/amino acid combinations, provides alignments between a tRNA and multiple tRFs with which the user can interact, provides details on published studies that reported a tRF as expressed, etc. Importantly, we designed MINTbase to contain all possible tRFs that could ever be produced by mature tRNAs: this allows us to report on their genomic distributions, anticodon/amino acid properties, alignments, etc. while giving users the ability to at-will investigate candidate tRF molecules before embarking on focused experimental explorations. Lastly, we also introduce a new labeling scheme that is tRF-sequence-based and allows users to associate a tRF with a universally unique label ('tRF-license plate') that is independent of a genome assembly and does not require any brokering mechanism.Availability and implementationMINTbase is freely accessible at http://cm.jefferson.edu/MINTbase/. Dataset submissions to MINTbase can be initiated at http://cm.jefferson.edu/MINTsubmit/Contactisidore.rigoutsos@jefferson.eduSupplementary informationSupplementary data are available at Bioinformatics online.

Dataset Information

A Generic Framework and Library for Exploration of Small Multiples through Interactive Piling.

Publications

A Generic Framework and Library for Exploration of Small Multiples through Interactive Piling.

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