scholarly journals BioInfograph: An Online Tool to Design and Display Multi-Panel Scientific Figure Interactively

2022 ◽  
Vol 12 ◽  
Author(s):  
Kejie Li ◽  
Jessica Hurt ◽  
Christopher D. Whelan ◽  
Ravi Challa ◽  
Dongdong Lin ◽  
...  
Keyword(s):  
High Resolution ◽  
Biological Data ◽  
Web Based ◽  
Online Tool ◽  
Scalable Vector Graphics ◽  
High Resolution Images ◽  
Fit For Purpose ◽  
Programming Skills ◽  
User Friendly ◽  
Publication Quality

Many fit-for-purpose bioinformatics tools generate plots to interpret complex biological data and illustrate findings. However, assembling individual plots in different formats from various sources into one high-resolution figure in the desired layout requires mastery of commercial tools or even programming skills. In addition, it is a time-consuming and sometimes frustrating process even for a computationally savvy scientist who frequently takes a trial-and-error iterative approach to get satisfactory results. To address the challenge, we developed bioInfograph, a web-based tool that allows users to interactively arrange high-resolution images in diversified formats, mainly Scalable Vector Graphics (SVG), to produce one multi-panel publication-quality composite figure in both PDF and HTML formats in a user-friendly manner, requiring no programming skills. It solves stylesheet conflicts of coexisting SVG plots, integrates a rich-text editor, and allows creative design by providing advanced functionalities like image transparency, controlled vertical stacking of plots, versatile image formats, and layout templates. To highlight, the sharable interactive HTML output with zoom-in function is a unique feature not seen in any other similar tools. In the end, we make the online tool publicly available at https://baohongz.github.io/bioInfograph while releasing the source code at https://github.com/baohongz/bioInfograph under MIT open-source license.

scholarly journals figureComposer: A web-based interactive multi-panel bio-infographic designing tool

2020 ◽  
Author(s):  
Kejie Li ◽  
Jessica Hurt ◽  
Christopher D. Whelan ◽  
Ravi Challa ◽  
Dongdong Lin ◽  
...  
Keyword(s):  
High Resolution ◽  
Web Tool ◽  
Bioinformatics Tool ◽  
Web Based ◽  
Link Type ◽  
High Resolution Images ◽  
Fit For Purpose ◽  
Programming Skills ◽  
User Friendly ◽  
Publication Quality

AbstractBackgroundMany fit-for-purpose bioinformatics tools generate plots to investigate data quality and illustrate findings. However, assembling individual plots in different formats from various sources into one high-resolution figure requires mastery of commercial tools or even programming skills. In addition, it is a time-consuming and sometimes frustrating process even for scientists with modest computational skills.ResultsWe developed figureComposer, a web-based bioinformatics tool that interactively arranges high-resolution images in various formats, mainly SVG to produce one multi-panel publication-quality composite figure in both PDF and interactive HTML formats in a user-friendly matter, requiring no programming skills.ConclusionsfigureComposer is open-source and publicly available web tool that can be accessed online at https://baohongz.github.io/figureComposer while the source code is provided at https://github.com/baohongz/figureComposer.

scholarly journals Biblio-MetReS for user-friendly mining of genes and biological processes in scientific documents

2014 ◽  
Author(s):  
Anabel Usie ◽  
Hiren Karathia ◽  
Ivan Teixidó ◽  
Francesc Solsona ◽  
Rui Alves
Keyword(s):  
Text Mining ◽  
Network Reconstruction ◽  
Biological Processes ◽  
Web Based ◽  
New Strategy ◽  
Programming Skills ◽  
Run Time ◽  
Active Research ◽  
The Cost ◽  
User Friendly

One way to initiate the reconstruction of molecular circuits is by using automated text-mining techniques. Developing more efficient methods for such reconstruction is a topic of active research, and those methods are typically included by bioinformaticians in pipelines used to mine and curate large literature datasets. Nevertheless, experimental biologists have a limited number of available user-friendly tools that use text-mining for network reconstruction and require no programming skills to use. One of these tools is Biblio-MetReS. Originally, this tool permitted an on-the-fly analysis of documents contained in a number of web-based literature databases to identify co-occurrence of proteins/genes. This approach ensured results that were always up-to-date with the latest live version of the databases. However, this “up-to-dateness” came at the cost of large execution times. Here we report an evolution of the application Biblio-MetReS that permits constructing co-occurrence networks for genes, GO process, Pathways, or any combination of the three types of entities and graphically represent those entities. We show that the performance of Biblio-MetReS in identifying gene co-occurrence is as least as good as that of other comparable applications (STRING and iHOP). In addition, we also show that the identification of GO processes is on par to that reported in the latest BioCreAtIvE challenge. Finally, we also report the implementation of a new strategy that combines on-the-fly analysis of new documents with preprocessed information from documents that were encountered in previous analyses. This combination simultaneously decreases program run time and maintains “up-to-dateness” of the results. Availability: http://metres.udl.cat/index.php/downloads Contact: [email protected]

scholarly journals MeltingPlot: a user-friendly online tool for epidemiological investigation using High Resolution Melting data

2020 ◽  
Author(s):  
Matteo Perini ◽  
Gherard Batisti Biffignandi ◽  
Domenico Di Carlo ◽  
Ajay Ratan Pasala ◽  
Aurora Piazza ◽  
...  
Keyword(s):  
High Resolution ◽  
High Resolution Melting ◽  
Epidemiological Studies ◽  
Supplementary Information ◽  
Web Interface ◽  
Web Tool ◽  
Online Tool ◽  
Link Type ◽  
Surveillance Programs ◽  
User Friendly

AbstractSummaryMeltingPlot is an open source web tool for pathogen typing and epidemiological investigations using High Resolution Melting (HRM) data. The tool implements a graph-based algorithm designed to discriminate pathogen clones on the basis of HRM data, producing portable typing results. MeltingPlot also merges typing information with isolates and patients metadata to create graphical and tabular outputs useful in epidemiological studies. HRM technique allows pathogen typing in less than 5 hours with ~5 euros per sample. MeltingPlot is the first tool specifically designed for HRM-based epidemiological studies and it can analyse hundreds of isolates in a few seconds. Thus, the use of MeltingPlot makes HRM-based typing suitable for large surveillance programs as well as for rapid outbreak reconstructions.Availability and implementationMeltingPlot is implemented in R.The web interface is available at https://skynet.unimi.it/index.php/tools/meltingplot.The source code is also available at https://github.com/MatteoPS/[email protected] informationSupplementary data are available at Bioinformatics online.

Prolegomena do tagоwania frazemów w równoległym korpusie rosyjsko-polskim (literatura piękna) w aspekcie przekładoznawczym

2018 ◽  
Vol 2 (XXIII) ◽  
pp. 55-73
Author(s):  
Yury Fedorushkov
Keyword(s):  
Annotation Tool ◽  
Online Tool ◽  
Number Of Factors ◽  
The Status ◽  
Concurrent Objects ◽  
Programming Skills ◽  
User Friendly ◽  
Parallel Texts ◽  
Tagging Methods

This article considers tagging methods for parallel Russian-Polish phrasemathic objects. In particular, an opinion about the annotation tool brat v1.3.is given. This online tool offers a palette of possibilities for classifying words and phrases in parallel texts. Working with this software is largely simplified by a user-friendly interface, and therefore working with the corpus does not cause difficulties for philologists and translators who do not have programming skills. As an example of such a classification, the layout of the metadata system for tagging Russian and Polish parallel phrasemes is described. These resources allow experience to be gathered and concurrent objects to be categorized in the workshop of a translator. As an example, the article presents the tagging of Verb-Noun of the text classified as collocation phrasemes, for example, погасить свет. The status of Verb-Noun constructions is also discussed, which, according to a number of factors, relate to autonomous phrases, although with the status of “free compatibility”, for example, поехать в клуб. A number of recommendations is proposed for the configuration of parallel texts at the level of single sentences.

scholarly journals MG2C: a user-friendly online tool for drawing genetic maps

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Jiangtao Chao ◽  
Zhiyuan Li ◽  
Yuhe Sun ◽  
Oluwaseun Olayemi Aluko ◽  
Xinru Wu ◽  
...  
Keyword(s):  
Genetic Map ◽  
Recombination Frequency ◽  
Genetic Maps ◽  
Linear Arrangement ◽  
Time Saving ◽  
Online Tool ◽  
Data Output ◽  
Programming Skills ◽  
User Friendly ◽  
Important Basis

AbstractGenetic map is a linear arrangement of the relative positions of sites in the chromosome or genome based on the recombination frequency between genetic markers. It is the important basis for genetic analysis. Several kinds of software have been designed for genetic mapping, but all these tools require users to write or edit code, making it time-costing and difficult for researchers without programming skills to handle with. Here, MG2C, a new online tool was designed, based on PERL and SVG languages.Users can get a standard genetic map, only by providing the location of genes (or quantitative trait loci) and the length of the chromosome, without writing additional code. The operation interface of MG2C contains three sections: data input, data output and parameters. There are 33 attribute parameters in MG2C, which are further divided into 8 modules. Values of the parameters can be changed according to the users’ requirements. The information submitted by users will be transformed into the genetic map in SVG file, which can be further modified by other image processing tools.MG2C is a user-friendly and time-saving online tool for drawing genetic maps, especially for those without programming skills. The tool has been running smoothly since 2015, and updated to version 2.1. It significantly lowers the technical barriers for the users, and provides great convenience for the researchers.

scholarly journals OUTBREAK: a user-friendly georeferencing online tool for disease surveillance

2021 ◽  
Vol 54 (1) ◽  
Author(s):  
Raúl Arias-Carrasco ◽  
Jeevan Giddaluru ◽  
Lucas E. Cardozo ◽  
Felipe Martins ◽  
Vinicius Maracaja-Coutinho ◽  
...  
Keyword(s):  
Real Time ◽  
Disease Surveillance ◽  
Input Data ◽  
Policy Decisions ◽  
Web Tool ◽  
Web Based ◽  
Online Tool ◽  
Link Type ◽  
Health Authorities ◽  
User Friendly

AbstractThe current COVID-19 pandemic has already claimed more than 3.7 million victims and it will cause more deaths in the coming months. Tools that track the number and locations of cases are critical for surveillance and help in making policy decisions for controlling the outbreak. However, the current surveillance web-based dashboards run on proprietary platforms, which are often expensive and require specific computational knowledge. We developed a user-friendly web tool, named OUTBREAK, that facilitates epidemic surveillance by showing in an animated graph the timeline and geolocations of cases of an outbreak. It permits even non-specialist users to input data most conveniently and track outbreaks in real-time. We applied our tool to visualize the SARS 2003, MERS, and COVID19 epidemics, and provided them as examples on the website. Through the zoom feature, it is also possible to visualize cases at city and even neighborhood levels. We made the tool freely available at https://outbreak.sysbio.tools/. OUTBREAK has the potential to guide and help health authorities to intervene and minimize the effects of outbreaks.

Colonial America Revisited

2020 ◽  
Vol 21 (4) ◽  
pp. 23-26
Author(s):  
Jason Martin
Keyword(s):  
High Resolution ◽  
North America ◽  
Colonial America ◽  
Primary Source ◽  
Source Database ◽  
Research Collection ◽  
High Resolution Images ◽  
The Caribbean ◽  
User Friendly ◽  
British Colonies

Colonial America, a primary source database from Adam Matthew, features the entire archive of documents, contained in 1,450 volumes, from the agencies that oversaw the British colonies in North America and the Caribbean. The database has rich metadata that allows for powerful searching, high resolution images, and user friendly functionality. This database is a superb addition to any research collection.

scholarly journals LocusExplorer: a user-friendly tool for integrated visualization of human genetic association data and biological annotations

2015 ◽  
Vol 32 (6) ◽  
pp. 949-951 ◽  
Author(s):  
Tokhir Dadaev ◽  
Daniel A. Leongamornlert ◽  
Edward J. Saunders ◽  
Rosalind Eeles ◽  
Zsofia Kote-Jarai
Keyword(s):  
Genetic Association ◽  
Source Code ◽  
Biological Data ◽  
Single Image ◽  
Web Browser ◽  
File Formats ◽  
Exploration Tool ◽  
Association Data ◽  
User Friendly ◽  
Publication Quality

Abstract Summary: In this article, we present LocusExplorer, a data visualization and exploration tool for genetic association data. LocusExplorer is written in R using the Shiny library, providing access to powerful R-based functions through a simple user interface. LocusExplorer allows users to simultaneously display genetic, statistical and biological data for humans in a single image and allows dynamic zooming and customization of the plot features. Publication quality plots may then be produced in a variety of file formats. Availability and implementation: LocusExplorer is open source and runs through R and a web browser. It is available at www.oncogenetics.icr.ac.uk/LocusExplorer/ or can be installed locally and the source code accessed from https://github.com/oncogenetics/LocusExplorer. Contact: [email protected]

scholarly journals Biblio-MetReS for user-friendly mining of genes and biological processes in scientific documents

2014 ◽  
Author(s):  
Anabel Usie ◽  
Hiren Karathia ◽  
Ivan Teixidó ◽  
Francesc Solsona ◽  
Rui Alves
Keyword(s):  
Text Mining ◽  
Network Reconstruction ◽  
Biological Processes ◽  
Web Based ◽  
New Strategy ◽  
Programming Skills ◽  
Run Time ◽  
Active Research ◽  
The Cost ◽  
User Friendly

One way to initiate the reconstruction of molecular circuits is by using automated text-mining techniques. Developing more efficient methods for such reconstruction is a topic of active research, and those methods are typically included by bioinformaticians in pipelines used to mine and curate large literature datasets. Nevertheless, experimental biologists have a limited number of available user-friendly tools that use text-mining for network reconstruction and require no programming skills to use. One of these tools is Biblio-MetReS. Originally, this tool permitted an on-the-fly analysis of documents contained in a number of web-based literature databases to identify co-occurrence of proteins/genes. This approach ensured results that were always up-to-date with the latest live version of the databases. However, this “up-to-dateness” came at the cost of large execution times. Here we report an evolution of the application Biblio-MetReS that permits constructing co-occurrence networks for genes, GO process, Pathways, or any combination of the three types of entities and graphically represent those entities. We show that the performance of Biblio-MetReS in identifying gene co-occurrence is as least as good as that of other comparable applications (STRING and iHOP). In addition, we also show that the identification of GO processes is on par to that reported in the latest BioCreAtIvE challenge. Finally, we also report the implementation of a new strategy that combines on-the-fly analysis of new documents with preprocessed information from documents that were encountered in previous analyses. This combination simultaneously decreases program run time and maintains “up-to-dateness” of the results. Availability: http://metres.udl.cat/index.php/downloads Contact: [email protected]

FeXIV Line Emission Polarization of the July 11, 1991 Solar Corona

1994 ◽  
Vol 144 ◽  
pp. 541-547
Author(s):  
J. Sýkora ◽  
J. Rybák ◽  
P. Ambrož
Keyword(s):  
High Resolution ◽  
Solar Corona ◽  
Emission Line ◽  
Solar Eclipse ◽  
White Light ◽  
Preliminary Analysis ◽  
Line Emission ◽  
Total Solar Eclipse ◽  
Degree Of Polarization ◽  
High Resolution Images

AbstractHigh resolution images, obtained during July 11, 1991 total solar eclipse, allowed us to estimate the degree of solar corona polarization in the light of FeXIV 530.3 nm emission line and in the white light, as well. Very preliminary analysis reveals remarkable differences in the degree of polarization for both sets of data, particularly as for level of polarization and its distribution around the Sun’s limb.

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