scholarly journals Sequanix: A Dynamic Graphical Interface for Snakemake Workflows

2017 ◽  
Author(s):  
Dimitri Desvillechabrol ◽  
Rachel Legendre ◽  
Claire Rioualen ◽  
Christiane Bouchier ◽  
Jacques van Helden ◽  
...  
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Source Code ◽  
Graphical Interface ◽  
Link Type

AbstractSummaryWe designed a PyQt graphical user interface – Sequanix – aiming at democratizing the use of Snakemake pipelines. Although the primary goal of Sequanix was to facilitate the execution of NGS Snakemake pipelines available in the Sequana project (http://sequana.readthedocs.io), it can also handle any Snakemake pipelines. Therefore, Sequanix should be useful to all Snakemake developers willing to expose their pipelines to a wider audience.AvailabilitySource code available on http://github.com/sequana/sequana and standalone on http://bioconda.github.io (sequana package).

scholarly journals Knowledge.Bio: A Web Application for Exploring, Building and Sharing Webs of Biomedical Relationships Mined from PubMed

2016 ◽  
Author(s):  
Richard Bruskiewich ◽  
Kenneth Huellas-Bruskiewicz ◽  
Farzin Ahmed ◽  
Rajaram Kaliyaperumal ◽  
Mark Thompson ◽  
...  
Keyword(s):  
User Interface ◽  
Text Mining ◽  
Graphical User Interface ◽  
Biomedical Research ◽  
Web Application ◽  
Source Code ◽  
Research Literature ◽  
Knowledge Networks ◽  
Link Type ◽  
Web Platform

AbstractKnowledge.Bio is a web platform that enhances access and interpretation of knowledge networks extracted from biomedical research literature. The interaction is mediated through a collaborative graphical user interface for building and evaluating maps of concepts and their relationships, alongside associated evidence. In the first release of this platform, conceptual relations are drawn from the Semantic Medline Database and the Implicitome, two compleme ntary resources derived from text mining of PubMed abstracts.Availability— Knowledge.Bio is hosted at http://knowledge.bio/ and the open source code is available at http://bitbucket.org/sulab/kb1/.Contact— [email protected]; [email protected]

scholarly journals Varapp: A reactive web-application for variants filtering

2016 ◽  
Author(s):  
Julien Delafontaine ◽  
Alexandre Masselot ◽  
Robin Liechti ◽  
Dmitry Kuznetsov ◽  
Ioannis Xenarios ◽  
...  
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Web Application ◽  
De Novo ◽  
Source Code ◽  
Regions Of Interest ◽  
Mendelian Diseases ◽  
Link Type ◽  
Large Sets ◽  
Front End

AbstractSummary: Varapp is an open-source web application to filter variants from large sets of exome data stored in a relational database. Varapp offers a reactive graphical user interface, very fast data pro-cessing, security and facility to save, reproduce and shareresults. Typically, a few seconds suffice to apply non-trivial filters to a set of half a million variants and extract a handful of potential clinically relevant targets. Varapp implements different scenarios for Mendelian diseases (dominant, recessive, de novo, X-linked, andcompound heterozygous), and allows searching for variants in genes or chro-mosomal regions of interest.Availability: The application is made of a Javascript front-end and a Python back-end. Its source code is hosted at https://github.com/varapp. A demo version isavailable at https://varapp-demo.vital-it.ch. The full documentation can be found at https://varapp-demo.vital-it.ch/docs.Contact:[email protected]

Changing Technology in Control Room Design: Is One Graphical Interface Worth 1000 Indicators?

1995 ◽  
Vol 39 (21) ◽  
pp. 1435-1439 ◽  
Author(s):  
Leon D. Segal ◽  
Anthony D. Andre
Keyword(s):  
User Interface ◽  
Wind Tunnel ◽  
Graphical User Interface ◽  
Graphical Interface ◽  
Control Room ◽  
Analog To Digital ◽  
Room Design ◽  
Design Program ◽  
Actual Content ◽  
Different Levels

This paper presents a review of human factors (HF) efforts toward the introduction of a graphical user interface (GUI) designed for operators in the control room of the world's largest wind tunnel at NASA's Ames Research Center, located in Moffett Field, California. Design of GUIs for the control room of this facility involved application of HF principles at many different levels of the design program: the design process itself, the environmental context for design, and the actual content of the graphical interface. This paper presents the particular challenges associated with transforming a control room from analog to digital, as well as the specific advantages and drawbacks of using GUIs in the context of large, multi-operator, environments.

scholarly journals ShelXle: a Qt graphical user interface forSHELXL

2011 ◽  
Vol 44 (6) ◽  
pp. 1281-1284 ◽  
Author(s):  
Christian B. Hübschle ◽  
George M. Sheldrick ◽  
Birger Dittrich
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Structure Refinement ◽  
Source Code ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Graphical Display ◽  
Acta Cryst ◽  
Strongly Coupled ◽  
Difference Density

ShelXleis a graphical user interface forSHELXL[Sheldrick, G. M. (2008).Acta Cryst.A64, 112–122], currently the most widely used program for small-molecule structure refinement. It combines an editor with syntax highlighting for theSHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density (Fo–Fc) maps. Special features ofShelXleinclude intuitive atom (re-)naming, a strongly coupled editor, structure visualization in various mono and stereo modes, and a novel way of displaying disorder extending over special positions.ShelXleis completely compatible with all features ofSHELXLand is written entirely in C++ using the Qt4 and FFTW libraries. It is available at no cost for Windows, Linux and Mac-OS X and as source code.

scholarly journals MT-ComparEval: Graphical evaluation interface for Machine Translation development

2015 ◽  
Vol 104 (1) ◽  
pp. 63-74 ◽  
Author(s):  
Ondřej Klejch ◽  
Eleftherios Avramidis ◽  
Aljoscha Burchardt ◽  
Martin Popel
Keyword(s):  
Comparative Analysis ◽  
User Interface ◽  
Machine Translation ◽  
Graphical User Interface ◽  
Statistical Significance ◽  
Web Based ◽  
Link Type ◽  
Evaluation Panel ◽  
N Gram

Abstract The tool described in this article has been designed to help MT developers by implementing a web-based graphical user interface that allows to systematically compare and evaluate various MT engines/experiments using comparative analysis via automatic measures and statistics. The evaluation panel provides graphs, tests for statistical significance and n-gram statistics. We also present a demo server http://wmt.ufal.cz with WMT14 and WMT15 translations.

scholarly journals Design y development of a graphical user interface in LabVIEW for acquisition and visualization of climatological data (temperature and relative humidity)

2020 ◽  
pp. 18-29
Author(s):  
Víctor PEREZ-GARCIA ◽  
Joel QUINTANILLA-DOMINGUEZ ◽  
Israel YAÑEZ-VARGAS ◽  
José AGUILERA-GONZALEZ
Keyword(s):  
User Interface ◽  
Relative Humidity ◽  
Graphical User Interface ◽  
Graphical Interface ◽  
Monitoring And Control ◽  
Virtual Instrumentation ◽  
Text Documents ◽  
Wireless Monitoring ◽  
And Control ◽  
Future Work

This paper describes the design and development of a Graphical User Interface through the virtual instrumentation software NI LabVIEW using the VISA function, to graphically visualize and storage the data of the climatological variables of temperature and relative humidity. The graphical interface offers the option to export the date, time and data of the two variables to text documents with extension “.txt”, which acquires the information of the electronic board wireless monitoring and control, which uses a main device PIC16F877A microcontroller. AMT1001 Precision Analog Sensor was used to sense temperature and relative humidity. The PIC16F877A was programmed using a C programming language in the CCS Compiler compiler, to the data acquisition, and send it via RS232 communication to the computer, using the PL2303 module USB to TTL converter. To check the GUI operation, the electronic wireless monitoring and control card was connected to the computer equipment by wire, however, the monitoring of the climate variables can be done wirelessly by XBEE technology. Future work aims to monitor the climate of a horticultural greenhouse with XBBE technology, so that the data is sent wirelessly to a computer that has the GUI, and is also connected to Ethernet or WIFI, which will have the LabVIEW graphical interface explained in this article, and the data will be displayed / analyzed through the internet.

scholarly journals LexOPS: An R package and user interface for the controlled generation of word stimuli

2020 ◽  
Vol 52 (6) ◽  
pp. 2372-2382
Author(s):  
Jack E. Taylor ◽  
Alistair Beith ◽  
Sara C. Sereno
Keyword(s):  
User Interface ◽  
Factorial Design ◽  
Graphical User Interface ◽  
R Package ◽  
Psycholinguistic Research ◽  
Link Type ◽  
Control Current ◽  
Word Lists ◽  
And Control ◽  
Manipulation And Control

AbstractLexOPS is an R package and user interface designed to facilitate the generation of word stimuli for use in research. Notably, the tool permits the generation of suitably controlled word lists for any user-specified factorial design and can be adapted for use with any language. It features an intuitive graphical user interface, including the visualization of both the distributions within and relationships among variables of interest. An inbuilt database of English words is also provided, including a range of lexical variables commonly used in psycholinguistic research. This article introduces LexOPS, outlining the features of the package and detailing the sources of the inbuilt dataset. We also report a validation analysis, showing that, in comparison to stimuli of existing studies, stimuli optimized with LexOPS generally demonstrate greater constraint and consistency in variable manipulation and control. Current instructions for installing and using LexOPS are available at https://JackEdTaylor.github.io/LexOPSdocs/.

scholarly journals FoldX 5.0: working with RNA, small molecules and a new graphical interface

2019 ◽  
Vol 35 (20) ◽  
pp. 4168-4169 ◽  
Author(s):  
Javier Delgado ◽  
Leandro G Radusky ◽  
Damiano Cianferoni ◽  
Luis Serrano
Keyword(s):  
User Interface ◽  
Small Molecules ◽  
Graphical User Interface ◽  
Graphical Interface ◽  
Rna Molecules ◽  
User Friendly

Abstract Summary A new version of FoldX, whose main new features allows running classic FoldX commands on structures containing RNA molecules and includes a module that allows parametrization of ligands or small molecules (ParamX) that were not previously recognized in old versions, has been released. An extended FoldX graphical user interface has also being developed (available as a python plugin for the YASARA molecular viewer) allowing user-friendly parametrization of new custom user molecules encoded using JSON format. Availability and implementation http://foldxsuite.crg.eu/

scholarly journals NanoPack: visualizing and processing long read sequencing data

2017 ◽  
Author(s):  
Wouter De Coster ◽  
Svenn D’Hert ◽  
Darrin T. Schultz ◽  
Marc Cruts ◽  
Christine Van Broeckhoven
Keyword(s):  
Web Service ◽  
Graphical User Interface ◽  
Source Code ◽  
Supplementary Information ◽  
Command Line ◽  
Sequencing Data ◽  
Link Type ◽  
Oxford Nanopore ◽  
Long Read ◽  
Oxford Nanopore Technologies

AbstractSummary: Here we describe NanoPack, a set of tools developed for visualization and processing of long read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences.Availability and Implementation: The NanoPack tools are written in Python3 and released under the GNU GPL3.0 Licence. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for linux and are available as a graphical user interface, a web service at http://nanoplot.bioinf.be and command line tools.Contact:[email protected] information: Supplementary tables and figures are available at Bioinformatics online.

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