Scribl: An HTML5 Canvas-based graphics library for visualizing genomic data over the web.
- SourceAvailable from: Jianguo (Jeff) Xia[Show abstract] [Hide abstract]
ABSTRACT: Gene expression or metabolomics data generated from clinical settings is often associated with multiple metadata (i.e. diagnosis, genotype, gender, etc.). It is of great interest to analyze and to visualize the data in these contexts. Here, we introduce INVEX - a novel web-based tool that integrates the server-side capabilities for data analysis with the browse-based technology for data visualization. INVEX has two key features: 1) flexible differential expression analysis for a wide variety of experimental designs; and 2) interactive visualization within the context of metadata and biological annotations. INVEX has built-in support for gene / metabolite annotation, and a fully functional heatmap builder. Freely available at http://www.invex.ca. firstname.lastname@example.org.Bioinformatics 09/2013; 29(24). DOI:10.1093/bioinformatics/btt562 · 4.62 Impact Factor
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ABSTRACT: Nowadays virtual, remote and hybrid (with both virtual and real remote components) laboratories depend on a large stack of technologies, and are almost always webbased. However, still today those laboratories which require relatively advanced graphics (3D or even 2D graphics) often rely on non-standard components and browser plugins, such as Adobe Flash or Java Applets. These components were necessary because of the severe limitations that standard Web technologies have traditionally had in regard to graphics and RIAs (Rich Internet Applications). This paper analyzes two of the most common non-standard technologies that are still used today in remote laboratories. It also proposes two alternatives which make use of modern Web technologies (Canvas and WebGL). Additionally, it illustrates one of the proposed alternatives (WebGL) with an example: Weblab-FPGA-Watertank, a hybrid laboratory implemented at the University of Deusto under the WeblabDeusto RLMS (Remote Laboratory Management System), which lets users program a real FPGA device remotely to control a virtual environment. Users require only an up-todate browser and require no plugins whatsoever. The fullyfeatured virtual environment is rendered through WebGL. Finally, conclusions are drawn from the analysis and from the WebLab-FPGA-Watertank experience.2014 10th International Conference on Remote Engineering and Virtual Instrumentation (REV); 02/2014
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ABSTRACT: Approximately half the transcripts encoding ribosomal proteins in Escherichia coli include a structured RNA motif that interacts with a specific ribosomal protein to inhibit gene expression, thus allowing stoichiometric production of ribosome components. However, many of these RNA structures are not widely distributed across bacterial phyla. It is increasingly common for RNA motifs associated with ribosomal protein genes to be identified using comparative genomic methods, yet these are rarely experimentally validated. In this work, we characterize one such motif that precedes operons containing rpsF and rpsR, which encode ribosomal proteins S6 and S18. This RNA structure is widely distributed across many phyla of bacteria despite differences within the downstream operon, and examples are present in both E. coli and Bacillus subtilis. We demonstrate a direct interaction between an example of the RNA from B. subtilis and an S6:S18 complex using in vitro binding assays, verify our predicted secondary structure, and identify a putative protein-binding site. The proposed binding site bears a strong resemblance to the S18 binding site within the 16S rRNA, suggesting molecular mimicry. This interaction is a valuable addition to the canon of ribosomal protein mRNA interactions. This work shows how experimental verification translates computational results into concrete knowledge of biological systems.RNA 12/2013; 20(2). DOI:10.1261/rna.041285.113 · 4.62 Impact Factor