Such tools should also enable users to display their data alongside canonical gene annotations, EST alignments and reference datasets harvested from the public domain. Web-based tools, because of their typically tight integration with back-end databases, often make it easy to display one's own data alongside reference datasets, but few match the interactivity and flexibility of desktop software.
The Integrated Genome Browser IGB, pronounced ig-bee aims to provide the best of both worlds, providing a highly interactive and user-friendly interface, while at the same time offering users the ability to load data from remote databases via web services middleware.
The IGB implements a flexible, highly interactive desktop software environment for viewing genome-scale datasets. IGB is the flagship product of the open source Genoviz project, which develops visualization software for bioinformatics and genomics.
The Genoviz SDK provides a framework for building visualization applications for genomics; it builds on work begun at the Berkeley Drosophila Genome Project Helt et al. Developers at Affymetrix created the first versions of IGB to support visualization of data from the Affymetrix tiling microarray platform. Since then, developers have streamlined the user interface and added new features, such as the ability to handle new data sources.
IGB can display data loaded from local files and web servers. Data providers can also embed links in web pages directing IGB to show a designated region. Examples appear in the web supplement of Cui and Loraine IGB can load data from multiple sources, allowing users to combine expression, genomic features, methylation, sequence similarity and sequence variation information for a given genome.
The DAS and Quickload mechanisms have complementary strengths. Quickload offers a simple way to load an entire data collection at once, such as the set of curated gene models from the Arabidopsis Information Resource TAIR. Quickload servers are easy to establish, consisting of web accessible or local directories with simple genome descriptor and annotation files. The DAS method works well for data collections that are too large to be viewed productively in their entirety, such as the set of all human ESTs.
IGB displays numerical data associated with base pair positions as highly customizable graphs. Users can also use IGB to display data saved to local files on their desktop.
When users load a new dataset or open a file, the new data appear in labeled tracks. Users can click-drag track labels to move tracks to new locations. Right- or control-clicking a track label activates a popup menu with multiple options. One option Make Annotation Depth Graph creates a new genome graph summarizing the number of annotations covering each base position, which users can save to a file Fig. Visualizing ESTs and tiling array data. ESTs blue are from a sequencing experiment Weber et al.
Data are from Arabidopsis seedlings. IGB supports dynamic zooming and panning through a genome, allowing users to navigate easily through a genome at multiple scales. Zooming focuses on the user's last click, indicated by a vertical stripe in the display. During zooming, the zoom stripe remains stationary as flanking regions expand or contract in an animated fashion as users operate the zoom controls.
The zoom stripe provides a base pair pointer in close-up views for inspecting residues at feature boundaries. The display contains several tabbed control panels and users can move into new windows using the View menu. The Graph Adjuster panel lets the users to fine-tune a graph's appearance and adjust the range of values it displays. It also offers options to add or subtract graphs from each other, providing a first-pass visual assessment of differential expression across sample types.
Refer to specific documentation, available on the same website, for information about downloading, installation and use of the Integrated Genome Browser. The browser must be open before you run the Affymetrix Integrated Genome Browser process. One Input Data Set is required for this process. This data set must contain either :. This information is used to create links to the genome browser. Priority: Major. Resolution: Done.
Labels: None. Sprint: Fall If I have the console open when I load them I get lots of instances of 'String index out of range' like this: java.
Issue Links. Hide Permalink. Code Review: Changes looks appropriate. New check for start is appropriately placed after a null check. This will avoid null pointer. Changes are well documented. Second level review: See comment added to the commit on AK's branch.
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