Dataset Information

ChromoZoom: a flexible, fluid, web-based genome browser.

ABSTRACT:

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Current web-based genome browsers require repetitious user input to scroll over long distances, alter the drawing density of elements or zoom through multiple orders of magnitude. Generally, either the server or the client is responsible for the majority of data processing, resulting in either servers having to receive and handle data relevant only to one user, or clients redundantly processing widely viewed data. ChromoZoom pre-renders and caches general-use tracks into tiled images on the server and serves them in an interactive web interface with inertial scrolling and precise, fluent zooming via the mouse wheel or trackpad. Custom tracks in several formats can be rendered by client-side code alongside the pre-rendered tracks, minimizing server load because of user-specific rendering and eliminating the need to transmit private data. ChromoZoom thereby enables rapid and simultaneous exploration of curated, experimental and personal genomic datasets.

Availability

Human and yeast genome researchers may browse recent assemblies within ChromoZoom at http://chromozoom.org/. Source code is available at http://github.com/rothlab/chromozoom/.

SUBMITTER: Pak TR

PROVIDER: S-EPMC3562068 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature

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Publications

ChromoZoom: a flexible, fluid, web-based genome browser.

Pak Theodore R TR Roth Frederick P FP

Bioinformatics (Oxford, England) 20121206 3

<h4>Unlabelled</h4>Current web-based genome browsers require repetitious user input to scroll over long distances, alter the drawing density of elements or zoom through multiple orders of magnitude. Generally, either the server or the client is responsible for the majority of data processing, resulting in either servers having to receive and handle data relevant only to one user, or clients redundantly processing widely viewed data. ChromoZoom pre-renders and caches general-use tracks into tiled ...[more]

PMID: 23220575

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Project description:BackgroundAcute lung injury and the acute respiratory distress syndrome are characterized by pulmonary inflammation, reduced endothelial barrier integrity and filling of the alveolar space with protein rich edema fluid and infiltrating leukocytes. Animal models are critical to uncovering the pathologic mechanisms of this devastating syndrome. Intravital imaging of the intact lung via two-photon intravital microscopy has proven a valuable method to investigate lung injury in small rodent models through characterization of inflammatory cells and vascular changes in real time. However, respiratory motion complicates the analysis of these time series images and requires selective data extraction to stabilize the image. Consequently, analysis of individual alveoli may not provide a complete picture of the integrated mechanical, vascular and inflammatory processes occurring simultaneously in the intact lung. To address these challenges, we developed a web browser-based visualization application named Alveolus Analysis to process, analyze and graphically display intravital lung microscopy data.ResultsThe designed tool takes raw temporal image data as input, performs image preprocessing and feature extraction offline, and visualizes the extracted information in a web browser-based interface. The interface allows users to explore multiple experiments in three panels corresponding to different levels of detail: summary statistics of alveolar/neutrophil behavior, characterization of alveolar dynamics including lung edema and inflammatory cells at specific time points, and cross-experiment analysis. We performed a case study on the utility of the visualization with two members or our research team and they found the tool useful because of its ability to preprocess data consistently and visualize information in a digestible and informative format.ConclusionsApplication of our software tool, Alveolus Analysis, to intravital lung microscopy data has the potential to enhance the information gained from these experiments and provide new insights into the pathologic mechanisms of inflammatory lung injury.

Dataset Information

ChromoZoom: a flexible, fluid, web-based genome browser.

Unlabelled

Availability

Publications

ChromoZoom: a flexible, fluid, web-based genome browser.

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