J-ICE: a newJmolinterface for handling and visualizing crystallographic and electronic properties

2010 ◽  
Vol 44 (1) ◽  
pp. 225-229 ◽  
Author(s):  
Pieremanuele Canepa ◽  
Robert M. Hanson ◽  
Piero Ugliengo ◽  
Maria Alfredsson
Keyword(s):  
Graphical User Interface ◽  
Condensed Matter ◽  
Quantum Mechanical ◽  
Molecular Graphics ◽  
Crystalline Materials ◽  
Java Language ◽  
Software Packages ◽  
Bug Fixing ◽  
Development Procedure ◽  
Graphics Engine

The growth in complexity of quantum mechanical software packages for modelling the physicochemical properties of crystalline materials may hinder their usability by the vast majority of non-specialized users. Consequently, a free operating-system-independent graphical user interface (GUI) has been developed to drive the most common simulation packages for treating both molecules and solids. In order to maintain maximum portability and graphical efficiency, the popular molecular graphics engineJmol, written in the portable Java language, has been combined with a specialized GUI encoded in HTML and JavaScript. This framework, calledJ-ICE, allows users to visualize, build and manipulate complex input or output results (derived from modelling) entirelyviaa web server,i.e.without the burden of installing complex packages. This solution also dramatically speeds up both the development procedure and bug fixing. Among the range of software appropriate for modelling condensed matter, the focus ofJ-ICEis currently only onCRYSTAL09andVASP.

scholarly journals Quantum-mechanical condensed matter simulations with CRYSTAL

2018 ◽  
Vol 8 (4) ◽  
pp. e1360 ◽  
Author(s):  
Roberto Dovesi ◽  
Alessandro Erba ◽  
Roberto Orlando ◽  
Claudio M. Zicovich-Wilson ◽  
Bartolomeo Civalleri ◽  
...  
Keyword(s):  
Condensed Matter ◽  
Quantum Mechanical

X-Seed 4: updates to a program for small-molecule supramolecular crystallography

2020 ◽  
Vol 53 (4) ◽  
pp. 1141-1146 ◽  
Author(s):  
Leonard J. Barbour
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Crystal Packing ◽  
Current Version ◽  
Molecular Graphics ◽  
High Quality ◽  
The Past ◽  
Structure Solution ◽  
User Friendly ◽  
Microsoft Windows

X-Seed is a native Microsoft Windows program with three primary functions: (i) to serve as a graphical user interface to the SHELX suite of programs, (ii) to facilitate exploration of crystal packing and intermolecular interactions, and (iii) to generate high-quality molecular graphics artwork suitable for publication and presentation. Development of X-Seed Version 1.0 began in 1998, when point-and-click crystallographic software was still limited in scope and power. Considerable enhancements have been implemented within X-Seed over the past two decades. Of particular importance are support for the SHELX2019 programs (SHELXS, SHELXD, SHELXT and SHELXL) for structure solution and refinement, and MSRoll for rendering void spaces in crystal structures. The current version (i.e. Version 4) of X-Seed has a new interface designed to be more interactive and user friendly, and the software can be downloaded and used free of charge.

scholarly journals Exact quasi-relativistic wavefunctions of Hydrogen-like atoms

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Luis Grave de Peralta
Keyword(s):  
Bound States ◽  
Relativistic Quantum ◽  
Quantum Mechanical ◽  
Solid State Physics ◽  
Mechanical Wave ◽  
Atomic Orbitals ◽  
Exact Analytical Expression ◽  
Quantum Particles ◽  
Software Packages ◽  
Analytical Expressions

Abstract Exact solutions of a novel quasi-relativistic quantum mechanical wave equation are found for Hydrogen-like atoms. This includes both, an exact analytical expression for the energies of the bound states, and exact analytical expressions for the wavefunctions, which successfully describe quantum particles with mass and spin-0 up to energies comparable to the energy associated to the mass of the particle. These quasi-relativistic atomic orbitals may be used for improving ab-initio software packages dedicated to numerical simulations in physical-chemistry and atomic and solid-state physics.

scholarly journals Anions in metallic matrices model: application to the aluminium crystal chemistry

2006 ◽  
Vol 62 (2) ◽  
pp. 220-227 ◽  
Author(s):  
Ángel Vegas ◽  
David Santamaría-Pérez ◽  
Miriam Marqués ◽  
Manuel Flórez ◽  
Valentín García Baonza ◽  
...  
Keyword(s):  
Electronic Structures ◽  
Metallic Matrix ◽  
Quantum Mechanical ◽  
Metallic Elements ◽  
Test Bed ◽  
Central Idea ◽  
Crystalline Materials ◽  
Direct Interpretation ◽  
Interpretative Model ◽  
Variable Coordination

We introduce and discuss an interpretative model of the structure and bonding of inorganic crystals containing metallic elements. The central idea is the conception of the crystal structure of such an inorganic compound as a metallic matrix whose geometric and electronic structures govern the formation and localization of the anions in the lattice. This is the reason for labelling the model anions in metallic matrices (AMM). Taking the AlX 3 crystal family (X = F, Cl, OH) as a suitable test-bed class of compounds, we illustrate how this approach gives a direct interpretation of the crystalline structures and explains the variable coordination that Al exhibits in crystalline materials. An exhaustive analysis of the topology of the electron density allows us to provide a quantum-mechanical assessment of the main hypotheses of the AMM model and to uncover, using microscopic arguments, the behavior of anions as chemical pressure agents.

scholarly journals omicplotR: visualizing omic datasets as compositions

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Daniel J. Giguere ◽  
Jean M. Macklaim ◽  
Brandon Y. Lieng ◽  
Gregory B. Gloor
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
High Throughput Sequencing ◽  
Principal Component ◽  
Visual Exploration ◽  
Command Line ◽  
Sequencing Data ◽  
Software Packages ◽  
High Throughput Sequencing Data ◽  
Differential Abundance Analysis

Abstract Background Differential abundance analysis is widely used with high-throughput sequencing data to compare gene abundance or expression between groups of samples. Many software packages exist for this purpose, but each uses a unique set of statistical assumptions to solve problems on a case-by-case basis. These software packages are typically difficult to use for researchers without command-line skills, and software that does offer a graphical user interface do not use a compositionally valid method. Results omicplotR facilitates visual exploration of omic datasets for researchers with and without prior scripting knowledge. Reproducible visualizations include principal component analysis, hierarchical clustering, MA plots and effect plots. We demonstrate the functionality of omicplotR using a publicly available metatranscriptome dataset. Conclusions omicplotR provides a graphical user interface to explore sequence count data using generalizable compositional methods, facilitating visualization for investigators without command-line experience.

scholarly journals Cyrface: An interface from Cytoscape to R that provides a user interface to R packages

F1000Research ◽  
2013 ◽  
Vol 2 ◽  
pp. 192 ◽  
Author(s):  
Emanuel Gonçalves ◽  
Julio Saez-Rodriguez
Keyword(s):  
Experimental Data ◽  
Data Analysis ◽  
User Interface ◽  
Graphical User Interface ◽  
Network Visualization ◽  
R Language ◽  
Software Packages ◽  
Graphical Interfaces ◽  
Basic Understanding ◽  
R Packages

There is an increasing number of software packages to analyse biological experimental data in the R environment. In particular, Bioconductor, a repository of curated R packages, is one of the most comprehensive resources for bioinformatics and biostatistics. The use of these packages is increasing, but it requires a basic understanding of the R language, as well as the syntax of the specific package used. The availability of user graphical interfaces for these packages would decrease the learning curve and broaden their application.   Here, we present a Cytoscape plug-in termed Cyrface that allows Cytoscape plug-ins to connect to any function and package developed in R. Cyrface can be used to run R packages from within the Cytoscape environment making use of a graphical user interface. Moreover, it links the R packages with the capabilities of Cytoscape and its plug-ins, in particular network visualization and analysis. Cyrface’s utility has been demonstrated for two Bioconductor packages (CellNOptR and DrugVsDisease), and here we further illustrate its usage by implementing a workflow of data analysis and visualization. Download links, installation instructions and user guides can be accessed from the Cyrface homepage (http://www.ebi.ac.uk/saezrodriguez/cyrface/).

scholarly journals Cyrface: An interface from Cytoscape to R that provides a user interface to R packages

F1000Research ◽  
2014 ◽  
Vol 2 ◽  
pp. 192
Author(s):  
Emanuel Gonçalves ◽  
Franz Mirlach ◽  
Julio Saez-Rodriguez
Keyword(s):  
Experimental Data ◽  
User Interface ◽  
Graphical User Interface ◽  
Network Visualization ◽  
R Language ◽  
Link Type ◽  
Software Packages ◽  
Graphical Interfaces ◽  
Basic Understanding ◽  
R Packages

There is an increasing number of software packages to analyse biological experimental data in the R environment. In particular, Bioconductor, a repository of curated R packages, is one of the most comprehensive resources for bioinformatics and biostatistics. The use of these packages is increasing, but it requires a basic understanding of the R language, as well as the syntax of the specific package used. The availability of user graphical interfaces for these packages would decrease the learning curve and broaden their application. Here, we present a Cytoscape app termed Cyrface that allows Cytoscape apps to connect to any function and package developed in R. Cyrface can be used to run R packages from within the Cytoscape environment making use of a graphical user interface. Moreover, it can link R packages with the capabilities of Cytoscape and its apps, in particular network visualization and analysis. Cyrface’s utility has been demonstrated for two Bioconductor packages (CellNOptR and DrugVsDisease), and here we further illustrate its usage by implementing a workflow of data analysis and visualization. Download links, installation instructions and user guides can be accessed from the Cyrface’s homepage (http://www.ebi.ac.uk/saezrodriguez/cyrface/) and from the Cytoscape app store (http://apps.cytoscape.org/apps/cyrface).

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