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]

scholarly journals CLINE: a web-tool for the comparison of biological dendrogram structures

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Rodolfo S. Allendes Osorio ◽  
Lokesh P. Tripathi ◽  
Kenji Mizuguchi
Keyword(s):  
User Interface ◽  
Open Access ◽  
Special Interest ◽  
Web Application ◽  
Source Code ◽  
Visualization Tool ◽  
Web Tool ◽  
Link Type ◽  
Multiple Structures ◽  
Biological Interpretation

Abstract Background When visually comparing the results of hierarchical clustering, the differences in the arrangements of components are of special interest. However, in a biological setting, identifying such differences becomes less straightforward, as the changes in the dendrogram structure caused by permuting biological replicates, do not necessarily imply a different biological interpretation. Here, we introduce a visualization tool to help identify biologically similar topologies across different clustering results, even in the presence of replicates. Results Here we introduce CLINE, an open-access web application that allows users to visualize and compare multiple dendrogram structures, by visually displaying the links between areas of similarity across multiple structures. Through the use of a single page and a simple user interface, the user is able to load and remove structures form the visualization, change some aspects of their display and set the parameters used to match cluster topology across consecutive pairs of dendrograms. Conclusions We have implemented a web-tool that allows the users to visualize different dendrogram structures, showing not only the structures themselves, but also linking areas of similarity across multiple structures. The software is freely available at http://mizuguchilab.org/tools/cline/. Also, the source code, documentation and installation instructions are available on GitHub at https://github.com/RodolfoAllendes/cline/.

scholarly journals myCircos: Facilitating the Creation and Use of Circos Plots Online

2016 ◽  
Author(s):  
Caroline Labelle ◽  
Geneviève Boucher ◽  
Sébastien Lemieux
Keyword(s):  
User Interface ◽  
Web Application ◽  
Graphical Representation ◽  
Source Code ◽  
Command Line ◽  
Genomic Information ◽  
Link Type ◽  
Intuitive User Interface ◽  
The Creation

AbstractCircos plots were designed to display large amounts of processed genomic information on a single graphical representation. The creation of such plots remains challenging for less technical users as the leading tool requires command-line proficiency. Here, we introduce myCircos, a web application that facilitates the generation of Circos plots by providing an intuitive user interface, adding interactive functionalities to the representation and providing persistence of previous requests. myCircos is available at: http://mycircos.iric.ca. Non registered users can explore the application through the Guest user. Source code (for local server installation) is available upon request.

scholarly journals UROPA GUI: A web platform for genomic region annotation

2018 ◽  
Author(s):  
Hendrik Schultheis ◽  
Jens Preussner ◽  
Annika Fust ◽  
Mette Bentsen ◽  
Carsten Kuenne ◽  
...  
Keyword(s):  
Graphical User Interface ◽  
Bioinformatics Analysis ◽  
Source Code ◽  
Genomic Region ◽  
Command Line ◽  
Web Based ◽  
Link Type ◽  
R Shiny ◽  
Considerable Impact ◽  
Web Platform

AbstractThe annotation of genomic ranges such as peaks resulting from ChIP-seq/ATAC-seq or other techniques represents a fundamental task of bioinformatics analysis with considerable impact on many downstream analyses. In our previous work, we introduced the Universal Robust Peak Annotator (UROPA), a flexible command line based tool which improves upon the functionality of existing annotation software. In order to reduce the complexity for biologists and clinicians, we have implemented an intuitive web-based graphical user interface (GUI) and fully functional service platform for UROPA. This extension will empower all users to generate annotations for regions of interest interactively.Availability and ImplementationThe open source UROPA GUI server was implemented in R Shiny and Python and is available from http://loosolab.mpi-bn.mpg.de. The source code of our App can be downloaded at https://github.molgen.mpg.de/loosolab/UROPA_GUI under the MIT license.

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 GlycoGlyph: a glycan visualizing, drawing and naming application

2020 ◽  
Vol 36 (11) ◽  
pp. 3613-3614 ◽  
Author(s):  
Akul Y Mehta ◽  
Richard D Cummings
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Web Application ◽  
Web Browsers ◽  
Vector Graphic

Abstract Motivation Glycan structures are commonly represented using symbols or linear nomenclature such as that from the Consortium for Functional Glycomics (also known as modified IUPAC-condensed nomenclature). No current tool allows for writing the name in such format using a graphical user interface (GUI); thus, names are prone to errors or non-standardized representations. Results Here we present GlycoGlyph, a web application built using JavaScript, which is capable of drawing glycan structures using a GUI and providing the linear nomenclature as an output or using it as an input in a dynamic manner. GlycoGlyph also allows users to save the structures as an SVG vector graphic, and allows users to export the structure as condensed GlycoCT. Availability and implementation The application can be used at: https://glycotoolkit.com/Tools/GlycoGlyph/. The application is tested to work in modern web browsers such as Firefox or Chrome. Contact [email protected] or [email protected]

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 CoralP: Flexible visualization of the human phosphatome

2019 ◽  
Author(s):  
Amit Min ◽  
Erika Deoudes ◽  
Marielle L. Bond ◽  
Eric S. Davis ◽  
Douglas H. Phanstiel
Keyword(s):  
Web Application ◽  
Protein Phosphatases ◽  
Source Code ◽  
Protein Family ◽  
Biological Processes ◽  
Important Class ◽  
Pharmaceutical Development ◽  
Link Type ◽  
Phosphoryl Groups ◽  
Publication Quality

Protein phosphatases and kinases play critical roles in a host of biological processes and diseases via the removal and addition of phosphoryl groups. While kinases have been extensively studied for decades, recent findings regarding the specificity and activities of phosphatases have generated an increased interest in targeting phosphatases for pharmaceutical development. This increased focus has created a need for methods to visualize this important class of proteins within the context of the entire phosphatase protein family. Here, we present CoralP, an interactive web application for the generation of customizable, publication-quality representations of human phosphatome data. Phosphatase attributes can be encoded through edge colors, node colors, and node sizes. CoralP is the first and currently the only tool designed for phosphatome visualization and should be of great use to the signaling community. The source code and web application are available at https://github.com/PhanstielLab/coralp and http://phanstiel-lab.med.unc.edu/coralp respectively.

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