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.

scholarly journals PathScore: a web tool for identifying altered pathways in cancer data

2016 ◽  
Author(s):  
Stephen G. Gaffney ◽  
Jeffrey P. Townsend
Keyword(s):  
Web Application ◽  
Somatic Mutations ◽  
Supplementary Information ◽  
Web Tool ◽  
Cancer Data ◽  
Link Type ◽  
Novel Approach ◽  
Supplementary Material ◽  
User Friendly ◽  
Pathway Effect

ABSTRACTSummaryPathScore quantifies the level of enrichment of somatic mutations within curated pathways, applying a novel approach that identifies pathways enriched across patients. The application provides several user-friendly, interactive graphic interfaces for data exploration, including tools for comparing pathway effect sizes, significance, gene-set overlap and enrichment differences between projects.Availability and ImplementationWeb application available at pathscore.publichealth.yale.edu. Site implemented in Python and MySQL, with all major browsers supported. Source code available at github.com/sggaffney/pathscore with a GPLv3 [email protected] InformationAdditional documentation can be found at http://pathscore.publichealth.yale.edu/faq.

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 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.

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

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Matteo Perini ◽  
Gherard Batisti Biffignandi ◽  
Domenico Di Carlo ◽  
Ajay Ratan Pasala ◽  
Aurora Piazza ◽  
...  
Keyword(s):  
High Resolution ◽  
Real Time ◽  
Large Scale ◽  
High Resolution Melting ◽  
Control Strategies ◽  
Rapid Identification ◽  
Clustering Methods ◽  
Molecular Biology Technique ◽  
Surveillance Programs ◽  
User Friendly

Abstract Background The rapid identification of pathogen clones is pivotal for effective epidemiological control strategies in hospital settings. High Resolution Melting (HRM) is a molecular biology technique suitable for fast and inexpensive pathogen typing protocols. Unfortunately, the mathematical/informatics skills required to analyse HRM data for pathogen typing likely limit the application of this promising technique in hospital settings. Results MeltingPlot is the first tool specifically designed for epidemiological investigations using HRM data, easing the application of HRM typing to large real-time surveillance and rapid outbreak reconstructions. MeltingPlot implements a graph-based algorithm designed to discriminate pathogen clones on the basis of HRM data, producing portable typing results. The tool also merges typing information with isolates and patients metadata to create graphical and tabular outputs useful in epidemiological investigations and it runs in a few seconds even with hundreds of isolates. Availability: https://skynet.unimi.it/index.php/tools/meltingplot/. Conclusions The analysis and result interpretation of HRM typing protocols can be not trivial and this likely limited its application in hospital settings. MeltingPlot is a web tool designed to help the user to reconstruct epidemiological events by combining HRM-based clustering methods and the isolate/patient metadata. The tool can be used for the implementation of HRM based real time large scale surveillance programs in hospital settings.

MetaADEDB 2.0: a comprehensive database on adverse drug events

2020 ◽  
Author(s):  
Zhuohang Yu ◽  
Zengrui Wu ◽  
Weihua Li ◽  
Guixia Liu ◽  
Yun Tang
Keyword(s):  
Safety Assessment ◽  
Adverse Drug Events ◽  
Adverse Event Reporting System ◽  
Adverse Event Reporting ◽  
Supplementary Information ◽  
Online Database ◽  
Web Interface ◽  
Drug Discovery And Development ◽  
Comprehensive Information ◽  
User Friendly

Abstract Summary MetaADEDB is an online database we developed to integrate comprehensive information on adverse drug events (ADEs). The first version of MetaADEDB was released in 2013 and has been widely used by researchers. However, it has not been updated for more than seven years. Here, we reported its second version by collecting more and newer data from the U.S. FDA Adverse Event Reporting System (FAERS) and Canada Vigilance Adverse Reaction Online Database, in addition to the original three sources. The new version consists of 744 709 drug–ADE associations between 8498 drugs and 13 193 ADEs, which has an over 40% increase in drug–ADE associations compared to the previous version. Meanwhile, we developed a new and user-friendly web interface for data search and analysis. We hope that MetaADEDB 2.0 could provide a useful tool for drug safety assessment and related studies in drug discovery and development. Availability and implementation The database is freely available at: http://lmmd.ecust.edu.cn/metaadedb/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals VIP-HL: Semi-automated ACMG/AMP variant interpretation platform for genetic hearing loss

2020 ◽  
Author(s):  
Jiguang Peng ◽  
Jiale Xiang ◽  
Xiangqian Jin ◽  
Junhua Meng ◽  
Nana Song ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Expert Panel ◽  
Sequence Variant ◽  
Variant Interpretation ◽  
Web Interface ◽  
Online Tool ◽  
Genetic Hearing Loss ◽  
Genetics And Genomics ◽  
Evidence Based Guidelines ◽  
User Friendly

The American College of Medical Genetics and Genomics, and the Association for Molecular Pathology (ACMG/AMP) have proposed a set of evidence-based guidelines to support sequence variant interpretation. The ClinGen hearing loss expert panel (HL-EP) introduced further specifications into the ACMG/AMP framework for genetic hearing loss. This study developed a tool named VIP-HL, aiming to semi-automate the HL ACMG/AMP rules. VIP-HL aggregates information from external databases to automate 13 out of 24 ACMG/AMP rules specified by HL-EP, namely PVS1, PS1, PM1, PM2, PM4, PM5, PP3, BA1, BS1, BS2, BP3, BP4, and BP7. We benchmarked VIP-HL using 50 variants where 83 rules were activated by the ClinGen HL-EP. VIP-HL concordantly activated 96% (80/83) rules, significantly higher than that of by InterVar (47%; 39/83). Of 4948 ClinVar star 2+ variants from 142 deafness-related genes, VIP-HL achieved an overall variant interpretation concordance in 88.0% (4353/4948). VIP-HL is an integrated online tool for reliable automated variant classification in hearing loss genes. It assists curators in variant interpretation and provides a platform for users to share classifications with each other. VIP-HL is available with a user-friendly web interface at http://hearing.genetics.bgi.com/.

scholarly journals COVID-Align: Accurate online alignment of hCoV-19 genomes using a profile HMM

2020 ◽  
Author(s):  
Frédéric Lemoine ◽  
Luc Blassel ◽  
Jakub Voznica ◽  
Olivier Gascuel
Keyword(s):  
Daily Basis ◽  
Supplementary Information ◽  
Summary Statistics ◽  
Evolutionary Novelty ◽  
Bioinformatics Analyses ◽  
Link Type ◽  
Sequencing Quality ◽  
User Friendly ◽  
Profile Hmm ◽  
New Mutations

AbstractMotivationThe first cases of the COVID-19 pandemic emerged in December 2019. Until the end of February 2020, the number of available genomes was below 1,000, and their multiple alignment was easily achieved using standard approaches. Subsequently, the availability of genomes has grown dramatically. Moreover, some genomes are of low quality with sequencing/assembly errors, making accurate re-alignment of all genomes nearly impossible on a daily basis. A more efficient, yet accurate approach was clearly required to pursue all subsequent bioinformatics analyses of this crucial data.ResultshCoV-19 genomes are highly conserved, with very few indels and no recombination. This makes the profile HMM approach particularly well suited to align new genomes, add them to an existing alignment and filter problematic ones. Using a core of ∼2,500 high quality genomes, we estimated a profile using HMMER, and implemented this profile in COVID-Align, a user-friendly interface to be used online or as standalone via Docker. The alignment of 1,000 genomes requires less than 20mn on our cluster. Moreover, COVID-Align provides summary statistics, which can be used to determine the sequencing quality and evolutionary novelty of input genomes (e.g. number of new mutations and indels).Availabilityhttps://covalign.pasteur.cloud, hub.docker.com/r/evolbioinfo/[email protected], [email protected] informationSupplementary information is available at Bioinformatics online.

scholarly journals G4Killer web application: a tool to design G-quadruplex mutations

2020 ◽  
Vol 36 (10) ◽  
pp. 3246-3247
Author(s):  
Vaclav Brazda ◽  
Jan Kolomaznik ◽  
Jean-Louis Mergny ◽  
Jiri Stastny
Keyword(s):  
Dna Sequences ◽  
Web Application ◽  
Rational Design ◽  
Therapeutic Potential ◽  
Supplementary Information ◽  
Web Tool ◽  
Web Based ◽  
Dna Structures ◽  
G Quadruplex ◽  
User Friendly

Abstract Motivation G-quadruplexes (G4) are important regulatory non-B DNA structures with therapeutic potential. A tool for rational design of mutations leading to decreased propensity for G4 formation should be useful in studying G4 functions. Although tools exist for G4 prediction, no easily accessible tool for the rational design of G4 mutations has been available. Results We developed a web-based tool termed G4Killer that is based on the G4Hunter algorithm. This new tool is a platform-independent and user-friendly application to design mutations crippling G4 propensity in a parsimonious way (i.e., keeping the primary sequence as close as possible to the original one). The tool is integrated into our DNA analyzer server and allows for generating mutated DNA sequences having the desired lowered G4Hunter score with minimal mutation steps. Availability and implementation The G4Killer web tool can be accessed at: http://bioinformatics.ibp.cz. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals SWITCHES: Searchable Web Interface for Topologies of CHEmical Switches

2020 ◽  
Author(s):  
G.V. HarshaRani ◽  
S. Moza ◽  
N. Ramakrishnan ◽  
U.S. Bhalla
Keyword(s):  
Fixed Number ◽  
Parameter Analysis ◽  
Supplementary Information ◽  
Web Interface ◽  
Biochemical Reaction Networks ◽  
Chemical Systems ◽  
Link Type ◽  
Long Term Storage ◽  
Term Storage

ABSTRACTBistable biochemical switches are key motifs in cellular state decisions and long-term storage of cellular ‘memory’. There are a few known biological switches that have been well characterized, however these examples are insufficient for systematic surveys of properties of these important systems. Here we present a resource of all possible bistable biochemical reaction networks with up to 6 reactions between 3 molecules, and 3 reactions between 4 molecules. Over 35,000 reaction topologies were constructed by identifying unique combinations of reactions between a fixed number of molecules. Then, these topologies were populated with rates within a biologically realistic range. The Searchable Web Interface for Topologies of CHEmical Switches (SWITCHES, https://switches.ncbs.res.in) provides a bistability and parameter analysis of over 7 million models from this systematic survey of chemical reaction space. This database will be useful for theoreticians interested in analyzing stability in chemical systems and also experimentalists for creating robust synthetic biological switches.Availability and ImplementationFreely available on the web at https://switches.ncbs.res.in. Website implemented in PHP, MariaDB, Graphviz, and Apache, with all major browsers supported.Supplementary InformationNot applicable.

scholarly journals MOSGA: Modular Open-Source Genome Annotator

2020 ◽  
Author(s):  
Roman Martin ◽  
Thomas Hackl ◽  
Georges Hattab ◽  
Matthias G Fischer ◽  
Dominik Heider
Keyword(s):  
Open Source ◽  
Source Code ◽  
Supplementary Information ◽  
Web Interface ◽  
Fully Integrated ◽  
Sequencing Technologies ◽  
A Genome ◽  
Wide Range ◽  
User Friendly ◽  
Eukaryotic Genomes

Abstract Motivation The generation of high-quality assemblies, even for large eukaryotic genomes, has become a routine task for many biologists thanks to recent advances in sequencing technologies. However, the annotation of these assemblies—a crucial step toward unlocking the biology of the organism of interest—has remained a complex challenge that often requires advanced bioinformatics expertise. Results Here, we present MOSGA (Modular Open-Source Genome Annotator), a genome annotation framework for eukaryotic genomes with a user-friendly web-interface that generates and integrates annotations from various tools. The aggregated results can be analyzed with a fully integrated genome browser and are provided in a format ready for submission to NCBI. MOSGA is built on a portable, customizable and easily extendible Snakemake backend, and thus, can be tailored to a wide range of users and projects. Availability and implementation We provide MOSGA as a web service at https://mosga.mathematik.uni-marburg.de and as a docker container at registry.gitlab.com/mosga/mosga: latest. Source code can be found at https://gitlab.com/mosga/mosga Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

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