SciCombinator

Discover the most talked about and latest scientific content & concepts.

Concept: HTML

171

BACKGROUND: A molecule editor, i.e. a program facilitating graphical input and interactive editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. Today, when a web browser has become the universal scientific user interface, a tool to edit molecules directly within the web browser is essential. One of the most popular tools for molecular structure input on the web is the JME applet. Since its release nearly 15 years ago, however the web environment has changed and Java applets are facing increasing implementation hurdles due to their maintenance and support requirements, as well as security issues. This prompted us to update the JME editor and port it to a modern Internet programming language - JavaScript. SUMMARY: The actual molecule editing Java code of the JME editor was translated into JavaScript with help of the Google Web Toolkit compiler and a custom library that emulates a subset of the GUI features of the Java runtime environment. In this process, the editor was enhanced by additional functionalities including a substituent menu, copy/paste, drag and drop and undo/redo capabilities and an integrated help. In addition to desktop computers, the editor supports molecule editing on touch devices, including iPhone, iPad and Android phones and tablets. In analogy to JME the new editor is named JSME. This new molecule editor is compact, easy to use and easy to incorporate into web pages. CONCLUSIONS: A free molecule editor written in JavaScript was developed and is released under the terms of permissive BSD license. The editor is compatible with JME, has practically the same user interface as well as the web application programming interface. The JSME editor is available for download from the project web page http://peter-ertl.com/jsme/

Concepts: Java, World Wide Web, Programming language, Web browser, Web page, Google, Web server, HTML

155

JBrowse is a fast and full-featured genome browser built with JavaScript and HTML5. It is easily embedded into websites or apps but can also be served as a standalone web page.

Concepts: World Wide Web, Website, Web browser, Web page, Adobe Flash, Netscape, Web server, HTML

144

QIIME (Quantitative Insights Into Microbial Ecology) is one of the most popular open-source bioinformatics suite for performing metagenome, 16S rRNA amplicon and Internal Transcribed Spacer (ITS) data analysis. Although, it is very comprehensive and powerful tool, it lacks a method to provide publication ready taxonomic pie charts. The script plot_taxa_summary.py bundled with QIIME generate a html file and a folder containing taxonomic pie chart and legend as separate images. The images have randomly generated alphanumeric names. Therefore, it is difficult to associate the pie chart with the legend and the corresponding sample identifier. Even if the option to have the legend within the html file is selected while executing plot_taxa_summary.py, it is very tedious to crop a complete image (having both the pie chart and the legend) due to unequal image sizes. It requires a lot of time to manually prepare the pie charts for multiple samples for publication purpose. Moreover, there are chances of error while identifying the pie chart and legend pair due to random alphanumeric names of the images. To bypass all these bottlenecks and make this process efficient, we have developed a python based program, prepare_taxa_charts.py, to automate the renaming, cropping and merging of taxonomic pie chart and corresponding legend image into a single, good quality publication ready image. This program not only augments the functionality of plot_taxa_summary.py but is also very fast in terms of CPU time and user friendly.

Concepts: Ribosomal RNA, 16S ribosomal RNA, Central processing unit, Bar chart, Chart, Pie chart, HTML

34

heatmaply is an R package for easily creating interactive cluster heatmaps that can be shared online as a stand-alone HTML file. Interactivity includes a tooltip display of values when hovering over cells, as well as the ability to zoom in to specific sections of the figure from the data matrix, the side dendrograms, or annotated labels. Thanks to the synergistic relationship between heatmaply and other R packages, the user is empowered by a refined control over the statistical and visual aspects of the heatmap layout.

Concepts: Graphical user interface, Interactivity, Package, ZOOM, HTML, Java package

27

Targeted sequencing using next-generation sequencing technologies is currently being rapidly adopted for clinical sequencing and cancer marker tests. However, no existing bioinformatics tool is available for the analysis and visualization of multiple targeted sequencing datasets. In the present study, we use cancer panel targeted sequencing datasets generated by the Life Technologies Ion Personal Genome Machine (PGM) Sequencer as an example to illustrate how to develop an automated pipeline for the comparative analyses of multiple datasets. Cancer Panel Analysis Pipeline (CPAP) uses standard output files from variant calling software to generate a distribution map of SNPs among all of the samples in a circular diagram generated by Circos. The diagram is hyper-linked to a dynamic HTML table that allows the users to identify target SNPs by using different filters. CPAP also integrates additional information about the identified SNPs by linking to an integrated SQL database compiled from SNP-related databases, including dbSNP, 1000 Genomes Project, COSMIC and dbNSFP. CPAP only takes 17 minutes to complete a comparative analysis of 500 datasets. CPAP not only provides an automated platform for the analysis of multiple cancer panel datasets but can also serve as a model for any customized targeted sequencing project. This article is protected by copyright. All rights reserved.

Concepts: DNA, Bioinformatics, Molecular biology, Database, All rights reserved, Copyright, SQL, HTML

26

Does PubMed Central-a government-run digital archive of biomedical articles-compete with scientific society journals? A longitudinal, retrospective cohort analysis of 13,223 articles (5999 treatment, 7224 control) published in 14 society-run biomedical research journals in nutrition, experimental biology, physiology, and radiology between February 2008 and January 2011 reveals a 21.4% reduction in full-text hypertext markup language (HTML) article downloads and a 13.8% reduction in portable document format (PDF) article downloads from the journals' websites when U.S. National Institutes of Health-sponsored articles (treatment) become freely available from the PubMed Central repository. In addition, the effect of PubMed Central on reducing PDF article downloads is increasing over time, growing at a rate of 1.6% per year. There was no longitudinal effect for full-text HTML downloads. While PubMed Central may be providing complementary access to readers traditionally underserved by scientific journals, the loss of article readership from the journal website may weaken the ability of the journal to build communities of interest around research papers, impede the communication of news and events to scientific society members and journal readers, and reduce the perceived value of the journal to institutional subscribers.-Davis, P. M. Public accessibility of biomedical articles from PubMed Central reduces journal readership-retrospective cohort analysis.

Concepts: Cohort study, Open access, XML, Markup language, Wiki, HTML, XHTML, DocBook

24

The original version of this Article contained an error in the title, which was incorrectly given as ‘APRDX1 mutant allele causes a MMACHC secondary epimutation in cblC patients’. This has now been corrected in both the PDF and HTML versions of the Article to read ‘A PRDX1 mutant allele causes a MMACHC secondary epimutation in cblC patients’.

Concepts: Version, HTML

16

Nearly everyone in society uses the Internet in one form or another. The Internet is heralded as an efficient way of providing mental health treatments and services. However, some people are still excluded from using Internet-enabled technology through lack of resources, skills, and confidence.

Concepts: World Wide Web, Internet, History of the Internet, HTML, X Window System, ARPANET, World Summit on the Information Society, IPTV

15

The original version of this Article contained an error in Eq. 1. The arrows between the symbols “T” and “B”, and “B” and “T”, were written “↔” but should have been “→”, and incorrectly read: IEBIC=IEBAC+ISEE+I(e↔h)+IEBICT↔B+IESEEB↔T The correct from of the Eq. 1 is as follows:IEBIC=IEBAC+ISEE+I(e↔h)+IEBICT→B+IESEEB→T This has now been corrected in both the PDF and HTML versions of the article.

Concepts: Electron, Electric current, Writing, Version, HTML

6

Many studies have provided evidence for the effectiveness of Internet-based stand-alone interventions for mental disorders. A newer form of intervention combines the strengths of face-to-face (f2f) and Internet approaches (blended interventions).

Concepts: Mental disorder, Intervention, World Wide Web, Internet, History of the Internet, Freedom of information, HTML