http://precedings.nature.com/tags/visualization Recently posted documents tagged with 'visualization' Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://dx.doi.org/10.1038/npre.2009.3167.1 So far researchers, web users were restricted to non-intuitive and visually poor text based databases every time they wanted to take a look on the mitochondrial DNA and find a region of interest. But with MitoWheel the situation is about to change. MitoWheel is a graphical representation of the circular human mitochondrial genome available on the web at http://mitowheel.org.The human mitochondrial DNA is a 16569 basepair long, circular molecule and this very circularity is the basic idea behind MitoWheel. The mitochondrial genome can be represented with a wheel and by spinning this wheel users can quickly scan through, browse and identify the particular regions. The spinning is via click-and-drag or by using the left and right arrows in the sequence bar.The sequence used is the standard Revised Cambridge Reference Sequence. The main components of the application are a search box, a sequence bar and the wheel itself.The most important feature of the MitoWheel is its versatile search function. As an output of a query the wheel and the sequence bar stops at the searched nucleotide position or sequence and additional information (whether the nucleotide or the sequence is part of a gene or other specific region) can be seen on a pop-up window. People can search for a nucleotide position or sequence in the search box with numbers (15450, 8366-8572), with nucleotides (ATGCTAAAA), search for an encoded gene or specific region by abbreviations (atp8), genes (complex III, cytochrome b) and sequence features, even mutations (12276A) with the possible functional effects of the mutation. Selected sequences or their reverse complementary sequences can be send to the clipboard and saved.MitoWheel incorporates data on fully sequenced human mitochondrial genomes that have been deposited in the GenBank nucleotide database by different research groups. The sequence bar contains information not only about the function of specific nucleotides, but also about allele frequencies at polymorphic positions.MitoWheel was developed by human mitochondrial geneticist Gábor Zsurka, the wheel was made with Flash Professional 8.0 and the code harnessed the power of Actionscript, a scripting language designed specially for Flash. Attila Csordás is the other member of the developer group. The web application can be useful for anybody interested in human mitochondrial genetics and its biological, medical consequences. http://dx.doi.org/10.1038/npre.2009.3167.1 Thu, 07 May 2009 15:03:08 UTC MitoWheel, visualizing the human mitochondrial genome doi:10.1038/npre.2009.3167.1 2009-05-07 Attila Csordás Nature Precedings 2009-05-07T15:03:08Z Poster Genetics & Genomics Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3141.1 In many cases, information from abstracts of biomedical publications is not sufficient for annotation of database entries. Therefore, text mining systems supporting curators of biodatabases should be able to process full text articles. Beside the technical problems arising from full text parsing, the representation of the annotated full text is an important issue. Journal articles are mostly electronically available in PDF or HTML format. Also with more easily manageable XML formats, readers would like to have a visualisation of annotations and semantic enrichment directly in the PDF or HTML. We summarize the technical problems arising from parsing of HTML and PDF journal full texts and show first results of visualisation in both formats. http://dx.doi.org/10.1038/npre.2009.3141.1 Wed, 22 Apr 2009 21:18:25 UTC Text Mining in Full Text Articles—Methodical and Represenation Issues doi:10.1038/npre.2009.3141.1 2009-04-22 Roman Klinger Nature Precedings 2009-04-22T21:18:25Z Poster Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3074/version/1 Results from multivariate molecular biological experiments become increasingly complex. Hence, the challenge of projecting high-dimensional data onto few dimensions for effective data visualization is becoming increasingly important in Systems Biology. Effective data visualization can summarize the activity of many variables over time as well as display relationships between variables. Dynamic interactive visualization tools can provide scientists with ways of visually identifying relationship and patterns, and improve communication of results on the web and in presentations. For this, interactive systems with animation have great potential since they add dimensions to static images limited to two dimensions. Interactivity and animation is particularly useful for showing time-series trends in multi-dimensional data. The Flash-based Motion Chart Google Gadget available through GoogleDocs is a recent advance in multi-dimensional data visualization. The Motion Chart Gadget is a component of the Trendalyzer software, which was developed for web-based animation of statistical results. Here we demonstrate the use of this Gadget to visualize molecular biological data, the phosphoproteomics results published on the Data Center of the Signaling Gateway web-site. http://precedings.nature.com/documents/3074/version/1 Thu, 16 Apr 2009 16:00:35 UTC Visualization of the Phosphoproteomic Data from AfCS with the Google Motion Chart Gadget hdl:10101/npre.2009.3074.1 2009-04-16 Avi Ma'ayan Nature Precedings 2009-04-16T16:00:35Z Manuscript Biotechnology Molecular Cell Biology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2007.50.1 Jmol is a free, open source molecule viewer for chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems. The software consists of three parts: the JmolApplet is a web browser applet that can be integrated into web pages; the Jmol application is a standalone Java application that runs on the desktop; and the JmolViewer is a development tool kit that can be integrated into other Java applications. http://dx.doi.org/10.1038/npre.2007.50.1 Thu, 14 Jun 2007 13:14:29 UTC Fast and Scriptable Molecular Graphics in Web Browsers without Java3D doi:10.1038/npre.2007.50.1 2007-06-14 Egon Willighagen Nature Precedings 2007-06-14T13:14:29Z Manuscript Chemistry Bioinformatics http://creativecommons.org/licenses/by/2.5/