Towards Graphical User Interface Redefinition without Source Code Access

2019 ◽  
Author(s):  
Rita Maia ◽  
J. C. Silva ◽  
José Luís Silva
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Source Code

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 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 PERANCANGAN PROGRAM PENENTUAN HISTOGRAM CITRA DENGAN GRAPHICAL USER INTERFACE (GUI)

2018 ◽  
Vol 1 (1) ◽  
pp. 11-17
Author(s):  
Ima Kurniastuti ◽  
Ary Andini
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Source Code ◽  
Testing Program

Dalam penelitian ini dilakukan perancangan program penentuan histogram citra yang dilengkapi dengan Graphical User Interface (GUI) sehingga pengguna lebih mudah dalam mengoperasikan program. Perancangan dilakukan dalam beberapa tahap yaitu tahap perancangan desain GUI, perancangan GUI, perancangan program dan testing program. Perancangan desain GUI bertujuan untuk menghasilkan desain GUI yang akan mempermudah programmer dalam merancang GUI program. GUI program merupakan tampilan yang akan muncul saat pengguna mengoperasikan program. Tahap perancangan program berfungsi untuk membuat source code yang berisi perintah-perintah dalam program. Tahap terakhir yang dilakukan dalam penelitian ini adalah testing program dengan menggunakan sebuah citra. Dari hasil testing program dapat disimpulkan bahwa program penentuan histogram citra berjalan dengan baik.

scholarly journals The GridCAT: A toolbox for automated analysis of human grid cell codes in fMRI

2017 ◽  
Author(s):  
Matthias Stangl ◽  
Jonathan Shine ◽  
Thomas Wolbers
Keyword(s):  
User Interface ◽  
Open Source ◽  
Graphical User Interface ◽  
Cognitive Processes ◽  
Source Code ◽  
Research Area ◽  
List Type ◽  
Grid Cells ◽  
Code Analysis ◽  
Open Source Code

AbstractHuman fMRI studies examining the putative firing of grid cells (i.e., the grid code) suggest that this cellular mechanism supports not only spatial navigation, but also more abstract cognitive processes. This research area, however, remains relatively unexplored, perhaps us to the complexities of data analysis. To overcome this, we have developed the Matlab-based Grid Code Analysis Toolbox (GridCAT), providing a graphical user interface, and open-source code, for the analysis of fMRI data. The GridCAT performs all analyses, from estimation and fitting of the grid code in the general linear model, to the generation of grid code metrics and plots. Moreover, it is flexible in allowing the specification of bespoke analysis pipelines; example data are provided to demonstrate the GridCAT’s main functionality. We believe the GridCAT is essential to opening this research area to the imaging community, and helping to elucidate the role of human grid codes in higher-order cognitive processes.HighlightsThe putative firing of grid cells (i.e., the grid code) can be examined using fMRINecessary steps for grid code analysis are reviewedThe Matlab-based grid code analysis toolbox (GridCAT) is introducedAutomated grid code analysis can be conducted either via a graphical user interface or open-source codeA detailed manual and an example dataset are provided

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]

Modelling and Simulating Complex Systems in Biology

2020 ◽  
pp. 898-929
Author(s):  
Pascal Ballet ◽  
Jérémy Rivière ◽  
Alain Pothet ◽  
Michaël Theron ◽  
Karine Pichavant ◽  
...  
Keyword(s):  
High Schools ◽  
User Interface ◽  
Middle Schools ◽  
Graphical User Interface ◽  
Source Code ◽  
Agent Based ◽  
Molecular Systems ◽  
Qualitative Survey ◽  
Multi Agent ◽  
Research And Education

Modelling and teaching complex biological systems is a difficult process. Multi-Agent Based Simulations (MABS) have proved to be an appropriate approach both in research and education when dealing with such systems including emergent, self-organizing phenomena. This chapter presents NetBioDyn, an original software aimed at biologists (students, teachers, researchers) to easily build and simulate complex biological mechanisms observed in multicellular and molecular systems. Thanks to its specific graphical user interface guided by the multi-agent paradigm, this software does not need any prerequisite in computer programming. It thus allows users to create in a simple way bottom-up models where unexpected behaviours can emerge from many interacting entities. This multi-platform software has been used in middle schools, high schools and universities since 2010. A qualitative survey is also presented, showing its ability to adapt to a wide and heterogeneous audience. The Java executable and the source code are available online at http://virtulab.univ-brest.fr.

scholarly journals Development of graphical user interface for open source VLSI digital synthesis tool Qflow

2018 ◽  
Vol 7 (2) ◽  
pp. 710
Author(s):  
K. Sripath Roy ◽  
K. Abhiram ◽  
M. Arun Sumanth ◽  
Jaishree Jaishankar ◽  
P. Abhishek ◽  
...  
Keyword(s):  
User Interface ◽  
Open Source ◽  
Graphical User Interface ◽  
Source Code ◽  
Command Line ◽  
Simulation Process ◽  
Vlsi Technology ◽  
Synthesis Tool ◽  
Digital Synthesis ◽  
User Friendly

There are many tools that are used for simulation in the domain of VLSI technology but none of them are easily accessible. There is a need for Free and open source tools in this stream so as to make them accessible to everyone. There are efficient tools that already exist in open source in VLSI stream but are not used widely because of their command line user interface. Hence, creating a user friendly interface will help many developers and users to work easily. This paper deals with the idea to solve the above issue by creating a Graphical User Interface for the open source VLSI tool called QFlow. Qflow is a tool used in synthesizing a VLSI circuit from the Verilog source code. There are multiple tools integrated with this tool to assure the simulation process. It is a combination of many dependencies that are used for synthesis, placement, layout viewing and routing in a fabrication process. All the independent tools used for the Verilog code simulation are integrated onto a single platform. Qt is used for creating the cross-stage application.

scholarly journals artMAP: a user-friendly tool for mapping EMS-induced mutations in Arabidopsis

2018 ◽  
Author(s):  
Peter Javorka ◽  
Vivek Raxwal ◽  
Jan Najvarek ◽  
Karel Riha
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Source Code ◽  
Ease Of Use ◽  
Sequencing Data ◽  
Induced Mutations ◽  
Mouse Click ◽  
User Friendly ◽  
Paired End Sequencing ◽  
Mapping By Sequencing

AbstractMapping-by-sequencing is a rapid method for identifying both natural as well as induced variations in the genome. However, it requires extensive bioinformatics expertise along with the computational infrastructure to analyze the sequencing data and these requirements have limited its widespread adoption. In the current study, we develop an easy to use tool, artMAP, to discover ethyl methanesulfonate (EMS) induced mutations in the Arabidopsis genome. The artMAP pipeline consists of well-established tools including TrimGalore, BWA, BEDTools, SAMtools, and SnpEff which were integrated in a Docker container. artMAP provides a graphical user interface and can be run on a regular laptop and desktop, thereby limiting the bioinformatics expertise required. artMAP can process input sequencing files generated from single or paired-end sequencing. The results of the analysis are presented in interactive graphs which display the annotation details of each mutation. Due to its ease of use, artMAP made the identification of EMS-induced mutations in Arabidopsis possible with only a few mouse click. The source code of artMAP is available on Github (https://github.com/RihaLab/artMAP).

scholarly journals Modelling and Simulating Complex Systems in Biology

2017 ◽  
pp. 128-158 ◽  
Author(s):  
Pascal Ballet ◽  
Jérémy Rivière ◽  
Alain Pothet ◽  
Michaël Theron ◽  
Karine Pichavant ◽  
...  
Keyword(s):  
High Schools ◽  
User Interface ◽  
Middle Schools ◽  
Graphical User Interface ◽  
Source Code ◽  
Agent Based ◽  
Molecular Systems ◽  
Qualitative Survey ◽  
Multi Agent ◽  
Research And Education

Modelling and teaching complex biological systems is a difficult process. Multi-Agent Based Simulations (MABS) have proved to be an appropriate approach both in research and education when dealing with such systems including emergent, self-organizing phenomena. This chapter presents NetBioDyn, an original software aimed at biologists (students, teachers, researchers) to easily build and simulate complex biological mechanisms observed in multicellular and molecular systems. Thanks to its specific graphical user interface guided by the multi-agent paradigm, this software does not need any prerequisite in computer programming. It thus allows users to create in a simple way bottom-up models where unexpected behaviours can emerge from many interacting entities. This multi-platform software has been used in middle schools, high schools and universities since 2010. A qualitative survey is also presented, showing its ability to adapt to a wide and heterogeneous audience. The Java executable and the source code are available online at http://virtulab.univ-brest.fr.

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).

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