scholarly journals Cafebr - Citation Amender/Formatter for Biological Research

2018 ◽  
Vol 4 ◽  
Author(s):  
Daisuke Tsugama
Keyword(s):  
User Interface ◽  
Biological Research ◽  
Reference List ◽  
Article Title ◽  
Web Browser ◽  
Change Orders ◽  
Final Output

A reference list is an essential part of a manuscript for an academic article. It is often necessary to reformat (i.e., change orders of pieces of article information such as authors, article title, publication year, and journal where the article was published) of a preformatted reference list when a manuscript is declined by one journal and submitted to another. EndNote, Zotero and Mendeley are examples of sophisticated reference management programs that help generate a reference list with less errors. However, their multifunctionality seems to have complicated the process of generating a reference list: they require many selection steps to obtain a final output, and also require to manually edit a file outside the execuiton program even to make small changes in the output. The author developed a program, Cafebr (Citation Amender/Formatter for Biological Research), to more simply generate a reference list for an article of biological research. It is written in HTML/JavaScript, and as such works on a web browser on any platform. On Cafebr, articles for a final reference list can be either given by a user or collected from PubMed. Pieces of article information are then extracted according to the format of these articles or to the delimiters designated by a user. Preset formats for output are currently only four, but all of them can be directly edited on the user interface, allowing to change output formats quickly and flexibly. All of the functions of Cafebr is available on its website (either http://stdtgm.itigo.jp/cafebr/cafebr.html (main) or http://studtsugama.s1006.xrea.com/cafebr/cafebr.xhtm (backup)) with aids of a CGI program. A stand-alone version of Cafebr is available at these websites or Zenodo (10.5281/zenodo.1404887).

Using Impenetrable Borders in a Graphical Web Browser: Are All Angles Equal?

2002 ◽  
Vol 46 (14) ◽  
pp. 1251-1255 ◽  
Author(s):  
J. Shawn Farris ◽  
Keith S. Jones ◽  
Brent A. Anders
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Ecological Validity ◽  
Past Research ◽  
Web Browser ◽  
Approach Angle

Impenetrable borders can be created by placing graphical user interface targets (e.g., buttons, scroll bars, etc.) on the edge of a computer display. Research demonstrated that targets with impenetrable borders (edge targets) are selected faster than targets of the same size that are not against the edge of the screen (non-edge targets). This paper discusses the reasons why edge targets are selected faster than non-edge target and points out a critical weakness in past research on impenetrable borders. Specifically, researchers have always placed targets at a 90° angle from the cursor's origin, thus forgoing any ecological validity. Accordingly, an experiment is reported that tests the effectiveness of impenetrable borders when approach angle varies on a graphical web browser interface. Results indicate that impenetrable borders are effective across all of the approach angles used. These results support the recommendation to place commonly used targets at the edge of the screen whenever possible.

Using Impenetrable Borders in a Graphical Web Browser: How Does Distance Influence Target Selection Speed?

2002 ◽  
Vol 46 (14) ◽  
pp. 1300-1304 ◽  
Author(s):  
J. Shawn Farris ◽  
Keith S. Jones ◽  
Brent A. Anders
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Target Selection ◽  
Past Research ◽  
Critical Distance ◽  
Web Browser ◽  
Detailed Design ◽  
Mouse Cursor ◽  
Design Recommendation

Impenetrable borders are edges of graphical user interface targets (e.g., buttons, scroll bars) that the mouse cursor cannot cross. Research has shown that targets with impenetrable borders (edge targets) are selected faster than targets without impenetrable borders (non-edge targets). In addition, prior research determined that the effectiveness of impenetrable borders is maximal between .50 and 11.75 cm distance from the cursor's origin to the target. However, this is a broad range and a more specific estimate of distance would be useful for designers wishing to maximize the effectiveness of impenetrable borders. Accordingly, the reported experiment searched for the critical distance where impenetrable border effectiveness asymptotes using a graphical web browser interface. Results indicate that impenetrable border effectiveness asymptotes between .50 cm and 3.50 cm distances. These results support past research and make a more detailed design recommendation. An example of a redesigned interface incorporating impenetrable borders is given.

scholarly journals Polyglot Programming in Applications Used for Genetic Data Analysis

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Robert M. Nowak
Keyword(s):  
Data Analysis ◽  
User Interface ◽  
Data Processing ◽  
Programming Languages ◽  
High Performance ◽  
Genetic Data ◽  
Web Browser ◽  
Data Process ◽  
Genetic Data Analysis

Applications used for the analysis of genetic data process large volumes of data with complex algorithms. High performance, flexibility, and a user interface with a web browser are required by these solutions, which can be achieved by using multiple programming languages. In this study, I developed a freely available framework for building software to analyze genetic data, which uses C++, Python, JavaScript, and several libraries. This system was used to build a number of genetic data processing applications and it reduced the time and costs of development.

scholarly journals The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes

2016 ◽  
Author(s):  
Luis M Rodriguez-R ◽  
Konstantinos T Konstantinidis
Keyword(s):  
User Interface ◽  
Case Studies ◽  
Graphical User Interface ◽  
Biological Research ◽  
Microbial Genomics ◽  
Online Analysis ◽  
Microbial Genomes ◽  
Novel Method ◽  
Over Dispersion ◽  
New Algorithms

Genomic and metagenomic analyses are increasingly becoming commonplace in several areas of biological research, but recurrent specialized analyses are frequently reported as in-house scripts rarely available after publication. We describe the enveomics collection, a growing set of actively maintained scripts for several recurrent and specialized tasks in microbial genomics and metagenomics, and present a graphical user interface and several case studies. Our resource includes previously described as well as new algorithms such as Transformed-space Resampling In Biased Sets (TRIBS), a novel method to evaluate phylogenetic under- or over-dispersion in reference sets with strong phylogenetic bias. The enveomics collection is freely available under the terms of the Artistic License 2.0 at https://github.com/lmrodriguezr/enveomics and for online analysis at http://enve-omics.ce.gatech.edu

World-Wide Web-Based Graphical User Interfaces for Laboratory Data

2002 ◽  
Vol 41 (05) ◽  
pp. 411-413 ◽  
Author(s):  
D. Keller ◽  
W. J. Schaller ◽  
J. S. K. Wong ◽  
P. C. de Groen
Keyword(s):  
Information System ◽  
User Interface ◽  
World Wide Web ◽  
Graphical User Interface ◽  
Mayo Clinic ◽  
World Wide ◽  
Laboratory Data ◽  
Laboratory Information System ◽  
Web Browser ◽  
Web Based

Summary Objectives: Electronic medical record systems permit collection of large amounts of medical information. Usually, information is presented in a fixed format, either as text or tables. Health care providers have to navigate this fixed format in order to find information useful for a specific patient-provider interaction. The main objective of this work was to allow the provider immediate access to specific laboratory information through the development of a highly customizable, graphical user interface to the Mayo Clinic laboratory information system. Methods – Results: Here we describe this platform-independent, World-Wide-Web-based graphical user interface that allows the provider to see all or a predetermined panel of essential laboratory data in graphical format. Advantages include availability at internet-based workstations, immediate recognition of trends over time, ability to zoom in and out of specific periods of time, and detailed analysis of patient values in relationship to normal values. Conclusions: Web browser-based user interface allowing graphical display of laboratory data using Java technology was described. The connection to the Mayo Clinic laboratory information system combines cross-platform support for use on virtually any networked machine, interaction through a Web browser for ease of use, and a combination of the Perl and Java languages for powerful data processing and interactivity.

scholarly journals A Framework for Effective User Interface Design for Web-Based Electronic Commerce Applications

10.28945/2357 ◽  
2001 ◽  
Author(s):  
Justyna Rudnicka ◽  
Gregory R. Madey
Keyword(s):  
User Interface ◽  
Electronic Commerce ◽  
Interface Design ◽  
Product Information ◽  
Central Component ◽  
Web Browser ◽  
Web Based ◽  
Design Attributes ◽  
Efficient Delivery ◽  
System Success

Efficient delivery of relevant product information is increasingly becoming the central basis of competition between firms. The interface design represents the central component for successful information delivery to consumers. However, interface design for web-based information systems is probably more an art than a science at this point in time. Much research is needed to understand properties of an effective interface for electronic commerce. This paper develops a framework identifying the relationship between user factors, the role of the user interface and overall system success for webbased electronic commerce. The paper argues that web-based systems for electronic commerce have some similar properties to decision support systems (DSS) and adapts an established DSS framework to the electronic commerce domain. Based on a limited amount of research studying web browser interface design, the framework identifies areas of research needed and outlines possible relationships between consumer characteristics, interface design attributes and measures of overall system success.

scholarly journals Sequenceserver: a modern graphical user interface for custom BLAST databases

2015 ◽  
Author(s):  
Anurag Priyam ◽  
Ben J Woodcroft ◽  
Vivek Rai ◽  
Alekhya Munagala ◽  
Ismail Moghul ◽  
...  
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Sequence Data ◽  
Biological Research ◽  
Work Patterns ◽  
User Input ◽  
Blast Analysis ◽  
Graphical Interfaces ◽  
User Centric ◽  
Computational Processes

The dramatic drop in DNA sequencing costs has created many opportunities for novel biological research. These opportunities largely rest upon the ability to effectively compare newly obtained and previously known sequences. This is commonly done with BLAST, yet using BLAST directly on new datasets requires substantial technical skills or helpful colleagues. Furthermore, graphical interfaces for BLAST are challenging to install and largely mimic underlying computational processes rather than work patterns of researchers. We combined a user-centric design philosophy with sustainable software development approaches to create Sequenceserver (http://sequenceserver.com), a modern graphical user interface for BLAST. Sequenceserver substantially increases the efficiency of researchers working with sequence data. This is due first to innovations at three levels. First, our software can be installed and used on custom datasets extremely rapidly for personal and shared applications. Second, based on analysis of user input and simple algorithms, Sequenceserver reduces the amount of decisions the user must make, provides interactive visual feedback, and prevents common potential errors that would otherwise cause erroneous results. Finally, Sequenceserver provides multiple highly visual and text-based output options that mirror the requirements and work patterns of researchers. Together, these features greatly facilitate BLAST analysis and interpretation and thus substantially enhance researcher productivity.

Learning Molecular Structures in a Tangible Augmented Reality Environment

2012 ◽  
pp. 1-18
Author(s):  
Kikuo Asai ◽  
Norio Takase
Keyword(s):  
User Interface ◽  
Augmented Reality ◽  
Performance Test ◽  
Three Dimensional ◽  
Preference Test ◽  
Molecular Structures ◽  
Web Browser ◽  
Usability Test ◽  
Sense Of Presence ◽  
Viewing Experience

This article presents the characteristics of using a tangible tabletop environment produced by augmented reality (AR), aimed at improving the environment in which learners observe three-dimensional molecular structures. The authors perform two evaluation experiments. A performance test for a user interface demonstrates that learners with a tangible AR environment were able to complete the task of identifying molecular structures more quickly and accurately than those with a typical desktop-PC environment using a Web browser. A usability test by participants who learned molecular structures and answered relevant questions demonstrates that the environments had no effect on their learning of molecular structures. However, a preference test reveals that learners preferred a more tangible AR environment to a Web-browser environment in terms of overall enjoyment, reality of manipulation, and sense of presence, and vice versa in terms of ease of viewing, experience, and durability.

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