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Concept: JavaScript

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The original version of this Article omitted the following from the Acknowledgements:“This work was partly supported by the Research Council of Norway through its Centres of Excellence funding scheme, project number 262633, QuSpin."This has now been corrected in both the PDF and HTML versions of the article.

Concepts: JavaScript

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“Pro-ana” or Thinspiration websites are internet sites that support weight loss and eating disorders. Fitspiration websites are a newer type of site that supposedly advocates a fit and healthy lifestyle.

Concepts: Eating disorders, JavaScript, MySpace, Internet, World Wide Web, Nutrition, Website

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Application Programming Interfaces (APIs) are now widely used to distribute biological data. And many popular biological APIs developed by many different research teams have adopted Javascript Object Notation (JSON) as their primary data format. While usage of a common data format offers significant advantages, that alone is not sufficient for rich integrative queries across APIs.

Concepts: JavaScript, JSON, Computer program, Application programming interface

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Hadoop MapReduce-based approaches have become increasingly popular due to their scalability in processing large sequencing data sets. However, as these methods typically require in-depth expertise in Hadoop and Java, they are still out of reach of many bioinformaticians. In order to solve this problem, we have created SeqPig, a library and a collection of tools to manipulate, analyze and query sequencing data sets in a scalable and simple manner. SeqPig scripts use the Hadoop-based distributed scripting engine Apache Pig, which automatically parallelizes and distributes data processing tasks. We demonstrate SeqPig’s scalability over many computing nodes and illustrate its use with example scripts.Availability and Implementation: Available under the open source MIT license at http://sourceforge.net/projects/seqpig/ CONTACT: andre.schumacher@yahoo.com SUPPLEMENTARY INFORMATION: Instructions and examples for SeqPig.

Concepts: Python, JavaScript, Web server, JQuery, PHP, Lua, Scripting language, MIT License

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MOTIVATION: Biological analysis has shifted from identifying genes to mapping these genes to biological function. The ENCODE Project has generated hundreds of ChIP-Seq experiments spanning multiple transcription factors and cell lines for public use, but tools for a biomedical scientist to analyze these data are either non-existent or tailored to narrow biological questions. We present the ENCODE ChIP-Seq Significance Tool, a flexible web application leveraging public ENCODE data to identify enriched transcription factors in a gene or transcript list for comparative analyses.Implementation: The ENCODE ChIP-Seq Significance Tool is written in JavaScript on the client side and has been tested on Google Chrome, Apple Safari, and Mozilla Firefox browsers. Server-side scripts are written in PHP and leverage R and a MySQL database. The tool is available at http://encodeqt.stanford.edu.

Concepts: Web browser, Mozilla Firefox, JavaScript

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Web-based research is becoming ubiquitous in the behavioral sciences, facilitated by convenient, readily available participant pools and relatively straightforward ways of running experiments: most recently, through the development of the HTML5 standard. Although in most studies participants give untimed responses, there is a growing interest in being able to record response times online. Existing data on the accuracy and cross-machine variability of online timing measures are limited, and generally they have compared behavioral data gathered on the Web with similar data gathered in the lab. For this article, we took a more direct approach, examining two ways of running experiments online-Adobe Flash and HTML5 with CSS3 and JavaScript-across 19 different computer systems. We used specialist hardware to measure stimulus display durations and to generate precise response times to visual stimuli in order to assess measurement accuracy, examining effects of duration, browser, and system-to-system variability (such as across different Windows versions), as well as effects of processing power and graphics capability. We found that (a) Flash and JavaScript’s presentation and response time measurement accuracy are similar; (b) within-system variability is generally small, even in low-powered machines under high load; © the variability of measured response times across systems is somewhat larger; and (d) browser type and system hardware appear to have relatively small effects on measured response times. Modeling of the effects of this technical variability suggests that for most within- and between-subjects experiments, Flash and JavaScript can both be used to accurately detect differences in response times across conditions. Concerns are, however, noted about using some correlational or longitudinal designs online.

Concepts: World Wide Web, HTML5, Test method, JavaScript, Time, Web browser, Measurement, Adobe Flash

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This letter describes a simple way of using Adobe Acrobat Pro DC to help select and auto-extract data from Portable Document Format (PDFs) of randomised trials in order to assist swift early selection of trials for a systematic review.

Concepts: Interleaf, JavaScript, Ghostscript, Adobe Creative Suite, Randomized controlled trial, Adobe Acrobat, Portable Document Format

1

The selection of models of nucleotide substitution is one of the major steps of modern phylogenetic analysis. Different tools exist to accomplish this task, among which jModelTest 2 (jMT2) is one of the most popular. Still, in order to deal with large DNA alignments with hundreds or thousands of loci, users of jMT2 need to have access to High Performance Computing clusters, including installation and configuration capabilities, conditions not always met. Here we present jmodeltest.org, a novel web server for the transparent execution of jMT2 across different platforms and for a wide range of users. Its main benefit is straightforward execution, avoiding any configuration/execution issues, and reducing significantly in most cases the time required to complete the analysis.Availability and implementation: jmodeltest.org is accessible using modern browsers such as Firefox, Chrome, Opera, Safari and IE from http://jmodeltest.org. User registration is not mandatory, but users wanting to have additional functionalities, like access to previous analyses, have the possibility of opening a user account.

Concepts: Acid2, JavaScript, Web browser, Computer, Comparison of web browsers, Usage share of web browsers

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A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

Concepts: Gene expression, Diabetes mellitus, Portable Document Format, Hormone, Writing, JavaScript, Diabetes mellitus type 2

0

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

Concepts: Epidemiology, JavaScript, XML, Publication, Publishing, Diabetes mellitus type 1, Writing, Chronic kidney disease