SciCombinator

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

Concept: Google

172

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

60

Public awareness of water- and drought-related issues is an important yet relatively unexplored component of water use behavior. To examine this relationship, we first quantified news media coverage of drought in California from 2005 to 2015, a period with two distinct droughts; the later drought received unprecedentedly high media coverage, whereas the earlier drought did not, as the United States was experiencing an economic downturn coinciding with a historic presidential election. Comparing this coverage to Google search frequency confirmed that public attention followed news media trends. We then modeled single-family residential water consumption in 20 service areas in the San Francisco Bay Area during the same period using geospatially explicit data and including news media coverage as a covariate. Model outputs revealed the factors affecting water use for populations of varying demographics. Importantly, the models estimated that an increase of 100 drought-related articles in a bimonthly period was associated with an 11 to 18% reduction in water use. Then, we evaluated high-resolution water consumption data from smart meters, known as advanced metering infrastructure, in one of the previously modeled service areas to evaluate breakpoints in water use trends. Results demonstrated that whereas nonresidential commercial irrigation customers responded to changes in climate, single-family residential customers decreased water use at the fastest rate following heavy drought-related news media coverage. These results highlight the need for water resource planners and decision makers to further consider the importance of effective, internally and externally driven, public awareness and education in water demand behavior and management.

Concepts: United States, Hydrology, Irrigation, Water resources, Water crisis, Google, San Francisco Bay Area, San Francisco Bay

42

Recent research indicates a high recall in Google Scholar searches for systematic reviews. These reports raised high expectations of Google Scholar as a unified and easy to use search interface. However, studies on the coverage of Google Scholar rarely used the search interface in a realistic approach but instead merely checked for the existence of gold standard references. In addition, the severe limitations of the Google Search interface must be taken into consideration when comparing with professional literature retrieval tools.The objectives of this work are to measure the relative recall and precision of searches with Google Scholar under conditions which are derived from structured search procedures conventional in scientific literature retrieval; and to provide an overview of current advantages and disadvantages of the Google Scholar search interface in scientific literature retrieval.

Concepts: Google Scholar, Accuracy and precision, Web search engine, Statistical classification, Object-oriented programming, Searching, Google, Recall

34

Dryland biomes cover two-fifths of Earth’s land surface, but their forest area is poorly known. Here, we report an estimate of global forest extent in dryland biomes, based on analyzing more than 210,000 0.5-hectare sample plots through a photo-interpretation approach using large databases of satellite imagery at (i) very high spatial resolution and (ii) very high temporal resolution, which are available through the Google Earth platform. We show that in 2015, 1327 million hectares of drylands had more than 10% tree-cover, and 1079 million hectares comprised forest. Our estimate is 40 to 47% higher than previous estimates, corresponding to 467 million hectares of forest that have never been reported before. This increases current estimates of global forest cover by at least 9%.

Concepts: Logic, Google, Google Maps, Aerial photography, Google Earth, Virtual globe, NASA World Wind, Satellite imagery

28

Bioinformatics is challenged by the fact that traditional analysis tools have difficulty in processing large-scale data from high-throughput sequencing. The open source Apache Hadoop project, which adopts the MapReduce framework and a distributed file system, has recently given bioinformatics researchers an opportunity to achieve scalable, efficient and reliable computing performance on Linux clusters and on cloud computing services. In this article, we present MapReduce frame-based applications that can be employed in the next-generation sequencing and other biological domains. In addition, we discuss the challenges faced by this field as well as the future works on parallel computing in bioinformatics.

Concepts: Future, Hadoop, Cloud computing, Grid computing, Linux, Google, File system, MapReduce

27

We introduce HiPub, a seamless Chrome browser plug-in that automatically recognizes, annotates and translates biomedical entities from texts into networks for knowledge discovery. Using a combination of two different named-entity recognition resources, HiPub can recognize genes, proteins, diseases, drugs, mutations and cell lines in texts, and achieve high precision and recall. HiPub extracts biomedical entity-relationships from texts to construct context-specific networks, and integrates existing network data from external databases for knowledge discovery. It allows users to add additional entities from related articles, as well as user-defined entities for discovering new and unexpected entity-relationships. HiPub provides functional enrichment analysis on the biomedical entity network, and link-outs to external resources to assist users in learning new entities and relations.

Concepts: DNA, Cell, Learning, Accuracy and precision, Web browser, Google, Plug-in, Toolbar

27

Finding romance, love, and sexual intimacy is a central part of our life experience. Although people engage in romance in a variety of ways, alternatives to “the couple” are largely overlooked in relationship research. Scholars and the media have recently argued that the rules of romance are changing, suggesting that interest in consensual departures from monogamy may become popular as people navigate their long-term coupling. This study utilizes Google Trends to assess Americans' interest in seeking out information related to consensual nonmonogamous relationships across a 10-year period (2006-2015). Using anonymous Web queries from hundreds of thousands of Google search engine users, results show that searches for words related to polyamory and open relationships (but not swinging) have significantly increased over time. Moreover, the magnitude of the correlation between consensual nonmonogamy Web queries and time was significantly higher than popular Web queries over the same time period, indicating this pattern of increased interest in polyamory and open relationships is unique. Future research avenues for incorporating consensual nonmonogamous relationships into relationship science are discussed.

Concepts: Polyamory, Monogamy, Web search engine, Google, Non-monogamy, Google search, Swinging, Open relationship

26

Hi-C experiments study how genomes fold in 3D, generating contact maps containing features as small as 20 bp and as large as 200 Mb. Here we introduce Juicebox, a tool for exploring Hi-C and other contact map data. Juicebox allows users to zoom in and out of Hi-C maps interactively, just as a user of Google Earth might zoom in and out of a geographic map. Maps can be compared to one another, or to 1D tracks or 2D feature sets.

Concepts: Geography, Geographic information system, Computer graphics, Map, Google, Google Maps, Cartography, Google Earth

22

As e-cigarette use rapidly increases in popularity, data from online social systems (Twitter, Instagram, Google Web Search) can be used to capture and describe the social and environmental context in which individuals use, perceive, and are marketed this tobacco product. Social media data may serve as a massive focus group where people organically discuss e-cigarettes unprimed by a researcher, without instrument bias, captured in near real time and at low costs.

Concepts: Tobacco, Nicotine, Electronic cigarette, Web search engine, Google, Google search, PageRank, Bing

17

Widespread use of single-occupancy cars often leads to traffic congestion. Using anonymized traffic speed data from Android phones collected through Google Maps, we investigated whether high-occupancy vehicle (HOV) policies can combat congestion. We studied Jakarta’s “three-in-one” policy, which required all private cars on two major roads to carry at least three passengers during peak hours. After the policy was abruptly abandoned in April 2016, delays rose from 2.1 to 3.1 minutes per kilometer (min/km) in the morning peak and from 2.8 to 5.3 min/km in the evening peak. The lifting of the policy led to worse traffic throughout the city, even on roads that had never been restricted or at times when restrictions had never been in place. In short, we find that HOV policies can greatly improve traffic conditions.

Concepts: United Kingdom, New York City, São Paulo, Google, Rush hour, Traffic congestion, Traffic flow, Three phase traffic theory