Genome Projector: zoomable genome map with multiple views. Export

@article{citeulike:3935210, abstract = {BACKGROUND: Molecular biology data exist on diverse scales, from the level of molecules to -omics. At the same time, the data at each scale can be categorised into multiple layers, such as the genome, transcriptome, proteome, metabolome, and biochemical pathways. Due to the highly multi-layer and multi-dimensional nature of biological information, software interfaces for database browsing should provide an intuitive interface that allows for rapid migration across different views and scales. The Zoomable User Interface (ZUI) and tabbed browsing have proven successful for this purpose in other areas, especially to navigate the vast information in the World Wide Web. RESULTS: This paper presents Genome Projector, a Web-based gateway for genomics information with a zoomable user interface using Google Maps API, equipped with four seamlessly accessible and searchable views: a circular genome map, a traditional genome map, a biochemical pathways map, and a DNA walk map. The Web application for 320 bacterial genomes is available at http://www.g-language.org/GenomeProjector/. All data and software including the source code, documentations, and development API are freely available under the GNU General Public License. Zoomable maps can be easily created from any image file using the development API, and an online data mapping service for Genome Projector is also available at our Web site. CONCLUSION: Genome Projector is an intuitive Web application for browsing genomics information, implemented with a zoomable user interface and tabbed browsing utilising Google Maps API and Asynchronous JavaScript and XML (AJAX) technology.}, author = {Arakawa, Kazuharu and Tamaki, Satoshi and Kono, Nobuaki and Kido, Nobuhiro and Ikegami, Keita and Ogawa, Ryu and Tomita, Masaru}, citeulike-article-id = {3935210}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2105-10-31}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19166610}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19166610}, doi = {10.1186/1471-2105-10-31}, issn = {1471-2105}, journal = {BMC bioinformatics}, keywords = {ajax, api, bioinformatics, genomics, google, javascript, open-source, software, visualization}, number = {1}, posted-at = {2009-01-25 19:37:28}, priority = {2}, title = {Genome Projector: zoomable genome map with multiple views.}, url = {http://dx.doi.org/10.1186/1471-2105-10-31}, volume = {10}, year = {2009} }

TY - JOUR ID - citeulike:3935210 L3 - citeulike-article-id:3935210 N2 - BACKGROUND: Molecular biology data exist on diverse scales, from the level of molecules to -omics. At the same time, the data at each scale can be categorised into multiple layers, such as the genome, transcriptome, proteome, metabolome, and biochemical pathways. Due to the highly multi-layer and multi-dimensional nature of biological information, software interfaces for database browsing should provide an intuitive interface that allows for rapid migration across different views and scales. The Zoomable User Interface (ZUI) and tabbed browsing have proven successful for this purpose in other areas, especially to navigate the vast information in the World Wide Web. RESULTS: This paper presents Genome Projector, a Web-based gateway for genomics information with a zoomable user interface using Google Maps API, equipped with four seamlessly accessible and searchable views: a circular genome map, a traditional genome map, a biochemical pathways map, and a DNA walk map. The Web application for 320 bacterial genomes is available at http://www.g-language.org/GenomeProjector/. All data and software including the source code, documentations, and development API are freely available under the GNU General Public License. Zoomable maps can be easily created from any image file using the development API, and an online data mapping service for Genome Projector is also available at our Web site. CONCLUSION: Genome Projector is an intuitive Web application for browsing genomics information, implemented with a zoomable user interface and tabbed browsing utilising Google Maps API and Asynchronous JavaScript and XML (AJAX) technology. IS - 1 JF - BMC bioinformatics SN - 1471-2105 TI - Genome Projector: zoomable genome map with multiple views. VL - 10 KW - ajax KW - api KW - bioinformatics KW - genomics KW - google KW - javascript KW - open-source KW - software KW - visualization AU - Arakawa, Kazuharu AU - Tamaki, Satoshi AU - Kono, Nobuaki AU - Kido, Nobuhiro AU - Ikegami, Keita AU - Ogawa, Ryu AU - Tomita, Masaru PY - 2009/// UR - http://dx.doi.org/10.1186/1471-2105-10-31 ER -