BEST: a Shiny/R web-based application to easily retrieve cross-related enzyme functional parameters and information from BRENDA

2020 ◽  
Author(s):  
Juan Saez Hidalgo ◽  
Karen Y Oróstica ◽  
Anamaria Sanchez–Daza ◽  
Álvaro Olivera–Nappa
Keyword(s):  
Protein Engineering ◽  
Supplementary Information ◽  
Web Interface ◽  
Web Based ◽  
Related Information ◽  
Search Tool ◽  
Engineering Information ◽  
Related Enzyme ◽  
Enzyme Families ◽  
Cross Reference

Abstract Motivation BRENDA is the largest enzyme functional database, containing information of 84 000 experimentally characterized enzyme entries. This database is an invaluable resource for researchers in the biological field, which classifies enzyme-related information in categories that are very useful to obtain specific functional and protein engineering information for enzyme families. However, the BRENDA web interface, the most used by researchers with a non-informatic background, does not allow the user to cross-reference data from different categories or sub-categories in the database. Obtaining information in an easy and fast way, in a friendly web interface, without the necessity to have a deep informatics knowledge, will facilitate and improve research in the enzymology and protein engineering field. Results We developed the Brenda Easy Search Tool (BEST), an interactive Shiny/R application that enables querying the BRENDA database for complex cross-tabulated characteristics, and retrieving enzyme-related parameters and information readily and efficiently, which can be used for the study of enzyme function or as an input for other bioinformatics tools. Availability and implementation BEST and its tutorial are freely available from https://pesb2.cl/best/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals GAPIN: Grouped and Aligned Protein Interface Networks

2019 ◽  
Author(s):  
Biharck M. Araújo ◽  
Aline L. Coelho ◽  
Sabrina A. Silveira ◽  
João P. R. Romanelli ◽  
Raquel C. de Melo-Minardi ◽  
...  
Keyword(s):  
Interaction Network ◽  
Supplementary Information ◽  
Protein Interface ◽  
Supplementary Data ◽  
Web Interface ◽  
Web Based ◽  
Structural Interaction ◽  
Peptidase Inhibitor ◽  
Supplementary Material ◽  
Hydrophobic Patterns

AbstractSummaryGAPIN is a web-based application for structural interaction network analysis among any type of PDB molecules, regardless of whether their interfaces are between chain-chain or chain-ligand. A special emphasis is given to graph clustering, allowing users to scrutinize target contexts for ligand candidates. We show how GAPIN can be used to unveil underlying hydrophobic patterns on a set of peptidase-inhibitor complexes. In another experiment, we show there is a positive correlation between cluster sizes and the presence of druggable spots, indicating that the clustering may discriminate the higher complexity of these hot subnetworks.Availability and implementationGAPIN is freely available as an easy-to-use web interface at https://[email protected], [email protected] informationSupplementary data are available online.

scholarly journals PharmaKU: A Web-Based Tool Aimed at Improving Outreach and Clinical Utility of Pharmacogenomics

2021 ◽  
Vol 11 (3) ◽  
pp. 210
Author(s):  
Sumi Elsa John ◽  
Arshad Mohamed Channanath ◽  
Prashantha Hebbar ◽  
Rasheeba Nizam ◽  
Thangavel Alphonse Thanaraj ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Clinical Utility ◽  
Reference Genome ◽  
Web Interface ◽  
Sequencing Technology ◽  
Web Based ◽  
Related Information ◽  
Clinical Reality ◽  
Reference Genome Assembly ◽  
User Friendly

With the tremendous advancements in genome sequencing technology in the field of pharmacogenomics, data have to be made accessible to be more efficiently utilized by broader clinical disciplines. Physicians who require the drug–genome interactome information, have been challenged by the complicated pharmacogenomic star-based classification system. We present here an end-to-end web-based pharmacogenomics tool, PharmaKU, which has a comprehensive interface easy-to-use interface. PharmaKU can help to overcome several hurdles posed by previous pharmacogenomics tools, including input in hg38 format only, while hg19/GRCh37 is now the most popular reference genome assembly among clinicians and geneticists, as well as the lack of clinical recommendations and other pertinent dosage-related information. This tool extracts genetic variants from nine well-annotated pharmacogenes (for which diplotype to phenotype information is available) from whole genome variant files and uses Stargazer software to assign diplotypes and apply prescribing recommendations from pharmacogenomic resources. The tool is wrapped with a user-friendly web interface, which allows for choosing hg19 or hg38 as the reference genome version and reports results as a comprehensive PDF document. PharmaKU is anticipated to enable bench to bedside implementation of pharmacogenomics knowledge by bringing precision medicine closer to a clinical reality.

scholarly journals EasyVS: a user-friendly web-based tool for molecule library selection and structure-based virtual screening

2020 ◽  
Vol 36 (14) ◽  
pp. 4200-4202 ◽  
Author(s):  
Douglas E V Pires ◽  
Wandré N P Veloso ◽  
YooChan Myung ◽  
Carlos H M Rodrigues ◽  
Michael Silk ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Web Interface ◽  
Web Based ◽  
Protein Target ◽  
User Friendly ◽  
Library Selection ◽  
Intuitive Interface

Abstract Summary EasyVS is a web-based platform built to simplify molecule library selection and virtual screening. With an intuitive interface, the tool allows users to go from selecting a protein target with a known structure and tailoring a purchasable molecule library to performing and visualizing docking in a few clicks. Our system also allows users to filter screening libraries based on molecule properties, cluster molecules by similarity and personalize docking parameters. Availability and implementation EasyVS is freely available as an easy-to-use web interface at http://biosig.unimelb.edu.au/easyvs. Contact [email protected] or [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

Using Popular Mobile Devices in Voice Therapy

2013 ◽  
Vol 23 (3) ◽  
pp. 82-87 ◽  
Author(s):  
Eva van Leer
Keyword(s):  
Exercise Behavior ◽  
Voice Therapy ◽  
Pure Oxygen ◽  
Mobile Platforms ◽  
Self Monitoring ◽  
Web Based ◽  
Motivational Messages ◽  
Related Information ◽  
Health Related ◽  
Tailored Approach

Mobile tools are increasingly available to help individuals monitor their progress toward health behavior goals. Commonly known commercial products for health and fitness self-monitoring include wearable devices such as the Fitbit© and Nike + Pedometer© that work independently or in conjunction with mobile platforms (e.g., smartphones, media players) as well as web-based interfaces. These tools track and graph exercise behavior, provide motivational messages, offer health-related information, and allow users to share their accomplishments via social media. Approximately 2 million software programs or “apps” have been designed for mobile platforms (Pure Oxygen Mobile, 2013), many of which are health-related. The development of mobile health devices and applications is advancing so quickly that the Food and Drug Administration issued a Guidance statement with the purpose of defining mobile medical applications and describing a tailored approach to their regulation.

scholarly journals ccNetViz: a WebGL-based JavaScript library for visualization of large networks

2020 ◽  
Vol 36 (16) ◽  
pp. 4527-4529
Author(s):  
Ales Saska ◽  
David Tichy ◽  
Robert Moore ◽  
Achilles Rasquinha ◽  
Caner Akdas ◽  
...  
Keyword(s):  
Systems Biology ◽  
Complex Networks ◽  
Open Source ◽  
High Speed ◽  
A Priori ◽  
Supplementary Information ◽  
Network Visualization ◽  
Supplementary Data ◽  
Web Based ◽  
Flow Of Information

Abstract Summary Visualizing a network provides a concise and practical understanding of the information it represents. Open-source web-based libraries help accelerate the creation of biologically based networks and their use. ccNetViz is an open-source, high speed and lightweight JavaScript library for visualization of large and complex networks. It implements customization and analytical features for easy network interpretation. These features include edge and node animations, which illustrate the flow of information through a network as well as node statistics. Properties can be defined a priori or dynamically imported from models and simulations. ccNetViz is thus a network visualization library particularly suited for systems biology. Availability and implementation The ccNetViz library, demos and documentation are freely available at http://helikarlab.github.io/ccNetViz/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals APPLICATION OF METADATA MODELING TO DISPUTE REVIEW REPORT MANAGEMENT

2010 ◽  
Vol 16 (4) ◽  
pp. 491-498
Author(s):  
Yimin Zhu ◽  
Mehmet Emre Bayraktar ◽  
Shu-Ching Chen
Keyword(s):  
Information Management ◽  
Information Search ◽  
Construction Projects ◽  
Portable Document Format ◽  
Heterogeneous Data ◽  
Web Based ◽  
Related Information ◽  
Management Processes ◽  
Florida Department ◽  
Efficiency And Effectiveness

Disagreements in construction projects often result in litigation that is both time‐consuming and expensive. A dispute review board (DRB) provides a valuable and proven alternative method of dispute resolution. Currently, the Florida Department of Transportation (FDOT) stores DRB reports in portable document format (PDF) with limited search capability. Improving information retrieval of DRB documents and providing a certain level of integration of DRB reports with relevant but heterogeneous data and documents is the key to enhancing the current FDOT DRB system. This paper presents a web‐based data management framework to improve information management processes of the FDOT DRB system by providing key features such as metadata generation, an integrated review process, a simple issue description, member information management, and versatile information search. The new system not only allows DRB members and FDOT construction engineers to store and retrieve DRB reports but also provides more functionality to process those re‐ports. New functionalities include a structured search based on the metadata of DRB reports, an unstructured search using advanced computer technology, and the integration of DRB reports with other related information for analysis. This type of functionality improves the efficiency and effectiveness of the DRB system. Santrauka Del nesutarimu vykdant statybos projektus dažnai kyla teisminiu ginču, kurie yra brangūs ir trunka ilgai. Vertingas ir praktikoje prigijes alternatyvus ginču sprendimo metodas yra ginču nagrinejimo taryba (GNT). Šiuo metu Floridos transporto departamentas (FTD) yra sukaupes GNT ataskaitas PDF formatu su ribota paieškos galimybe. GNT dokumentu informacijos paieška ir tinkamo lygio GNT ataskaitu integravimas su reikalingais, bet heterogeniniais duomenimis yra esmine prielaida tobulinti dabartine FTD GNT sistema. Straipsnyje pristatoma internetine duomenu valdymo sistema, skirta patobulinti FTD GNT valdymo procesa remiantis šiomis esminemis savybemis: metaduomenu generavimo, integruoto peržiūros proceso, paprasto ginčo aprašymo, dalyvio informacijos valdymo, visapusiškos informacijos paieškos. Naujoji sistema ne tik leidžia FTD BNT nariams saugoti bei rasti GNT ataskaitas, bet ir sudaro galimybes funkcionaliau jas apdoroti. Naujos sistemos funkcijos apima struktūrizuota paieška GNT ataskaitu metaduomenu pagrindu, restruktūri‐zuota paieška naudojant pažangias kompiuteriu technologijas ir GNT ataskaitu integravima su kita susijusia analizuojama informacija. Šios funkcines savybes pagerina GNT sistemos efektyvuma.

scholarly journals Quantifying Media Effects, Its Content, and Role in Promoting Community Awareness of Chikungunya Epidemic in Bangladesh

Epidemiologia ◽  
2021 ◽  
Vol 2 (1) ◽  
pp. 84-94
Author(s):  
Mst. Marium Begum ◽  
Osman Ulvi ◽  
Ajlina Karamehic-Muratovic ◽  
Mallory R. Walsh ◽  
Hasan Tarek ◽  
...  
Keyword(s):  
Social Media ◽  
Web Based ◽  
Study Objective ◽  
The Public ◽  
Mainstream Media ◽  
Related Information ◽  
Vector Borne ◽  
Media Outlet ◽  
And Control

Background: Chikungunya is a vector-borne disease, mostly present in tropical and subtropical regions. The virus is spread by Ae. aegypti and Ae. albopictus mosquitos and symptoms include high fever to severe joint pain. Dhaka, Bangladesh, suffered an outbreak of chikungunya in 2017 lasting from April to September. With the goal of reducing cases, social media was at the forefront during this outbreak and educated the public about symptoms, prevention, and control of the virus. Popular web-based sources such as the top dailies in Bangladesh, local news outlets, and Facebook spread awareness of the outbreak. Objective: This study sought to investigate the role of social and mainstream media during the chikungunya epidemic. The study objective was to determine if social media can improve awareness of and practice associated with reducing cases of chikungunya. Methods: We collected chikungunya-related information circulated from the top nine television channels in Dhaka, Bangladesh, airing from 1st April–20th August 2017. All the news published in the top six dailies in Bangladesh were also compiled. The 50 most viewed chikungunya-related Bengali videos were manually coded and analyzed. Other social media outlets, such as Facebook, were also analyzed to determine the number of chikungunya-related posts and responses to these posts. Results: Our study showed that media outlets were associated with reducing cases of chikungunya, indicating that media has the potential to impact future outbreaks of these alpha viruses. Each media outlet (e.g., web, television) had an impact on the human response to an individual’s healthcare during this outbreak. Conclusions: To prevent future outbreaks of chikungunya, media outlets and social media can be used to educate the public regarding prevention strategies such as encouraging safe travel, removing stagnant water sources, and assisting with tracking cases globally to determine where future outbreaks may occur.

scholarly journals Epidemiological modeling in StochSS Live!

2021 ◽  
Author(s):  
Richard Jiang ◽  
Bruno Jacob ◽  
Matthew Geiger ◽  
Sean Matthew ◽  
Bryan Rumsey ◽  
...  
Keyword(s):  
Stochastic Model ◽  
Epidemiological Model ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Web Based ◽  
Epidemiological Modeling ◽  
Modeling Simulation ◽  
Wide Range ◽  
Biochemical Systems

Abstract Summary We present StochSS Live!, a web-based service for modeling, simulation and analysis of a wide range of mathematical, biological and biochemical systems. Using an epidemiological model of COVID-19, we demonstrate the power of StochSS Live! to enable researchers to quickly develop a deterministic or a discrete stochastic model, infer its parameters and analyze the results. Availability and implementation StochSS Live! is freely available at https://live.stochss.org/ Supplementary information Supplementary data are available at Bioinformatics online.

KEC: unique sequence search by K-mer exclusion

2021 ◽  
Author(s):  
Pavel Beran ◽  
Dagmar Stehlíková ◽  
Stephen P Cohen ◽  
Vladislav Čurn
Keyword(s):  
Amino Acid ◽  
Nucleic Acid ◽  
Source Code ◽  
Unique Sequence ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Laptop Computers ◽  
Sequence Search ◽  
Target Sequences ◽  
Cross Reference

Abstract Summary Searching for amino acid or nucleic acid sequences unique to one organism may be challenging depending on size of the available datasets. K-mer elimination by cross-reference (KEC) allows users to quickly and easily find unique sequences by providing target and non-target sequences. Due to its speed, it can be used for datasets of genomic size and can be run on desktop or laptop computers with modest specifications. Availability and implementation KEC is freely available for non-commercial purposes. Source code and executable binary files compiled for Linux, Mac and Windows can be downloaded from https://github.com/berybox/KEC. Supplementary information Supplementary data are available at Bioinformatics online.

CPVA: a web-based metabolomic tool for chromatographic peak visualization and annotation

2020 ◽  
Vol 36 (12) ◽  
pp. 3913-3915
Author(s):  
Hemi Luan ◽  
Xingen Jiang ◽  
Fenfen Ji ◽  
Zhangzhang Lan ◽  
Zongwei Cai ◽  
...  
Keyword(s):  
False Positive ◽  
Supplementary Information ◽  
Liquid Chromatography Mass Spectrometry ◽  
Targeted Metabolomics ◽  
Metabolomics Data ◽  
Web Based ◽  
Tremendous Amount ◽  
Chromatographic Peaks ◽  
User Friendly

Abstract Motivation Liquid chromatography–mass spectrometry-based non-targeted metabolomics is routinely performed to qualitatively and quantitatively analyze a tremendous amount of metabolite signals in complex biological samples. However, false-positive peaks in the datasets are commonly detected as metabolite signals by using many popular software, resulting in non-reliable measurement. Results To reduce false-positive calling, we developed an interactive web tool, termed CPVA, for visualization and accurate annotation of the detected peaks in non-targeted metabolomics data. We used a chromatogram-centric strategy to unfold the characteristics of chromatographic peaks through visualization of peak morphology metrics, with additional functions to annotate adducts, isotopes and contaminants. CPVA is a free, user-friendly tool to help users to identify peak background noises and contaminants, resulting in decrease of false-positive or redundant peak calling, thereby improving the data quality of non-targeted metabolomics studies. Availability and implementation The CPVA is freely available at http://cpva.eastus.cloudapp.azure.com. Source code and installation instructions are available on GitHub: https://github.com/13479776/cpva. Supplementary information Supplementary data are available at Bioinformatics online.

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