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.

Improving Knowledge and Information Sharing to Promote Best Practices in Stroke Care

2013 ◽  
Vol 2 (1) ◽  
pp. 11-25 ◽  
Author(s):  
Elizabeth Sternke ◽  
Nicholas Burrus ◽  
Virginia Daggett ◽  
Laurie Plue ◽  
Katherine Carlson ◽  
...  
Keyword(s):  
Best Practices ◽  
Qualitative Interviews ◽  
Stroke Care ◽  
Care Quality ◽  
Veterans Health ◽  
Health Administration ◽  
Web Based ◽  
Geographically Dispersed ◽  
User Friendly

Despite many advances in stroke care treatment, there is substantial room for improvement in quality of care for stroke patients. In an attempt to disseminate up-to-date quality information and evidence-based best practices of stroke care, the Veterans Health Administration (VHA)and the VHA Stroke QUERI implemented an innovative web-based toolkit tailored for providers and program planners interested in improving stroke care quality. This study evaluated the VA Stroke QUERI Toolkit to determine its most useful aspects and those that require improvement. In-depth qualitative interviews (n = 48) were conducted with a geographically dispersed sample of clinicians and program planners throughout the VHA system. Findings suggest the Stroke QUERI toolkit was perceived as an effective, efficient and user-friendly site but knowledge of the toolkit continues to be initiated and shared mainly through individuals and small groups. To achieve greater impact a comprehensive set of strategies designed to encourage broader uptake is required.

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 G4Hunter web application: a web server for G-quadruplex prediction

2019 ◽  
Vol 35 (18) ◽  
pp. 3493-3495 ◽  
Author(s):  
Václav Brázda ◽  
Jan Kolomazník ◽  
Jiří Lýsek ◽  
Martin Bartas ◽  
Miroslav Fojta ◽  
...  
Keyword(s):  
Data Storage ◽  
Web Application ◽  
Data Representation ◽  
Complete Characterization ◽  
Supplementary Information ◽  
Web Based ◽  
Rna Molecules ◽  
Dna And Rna ◽  
Sorting Data ◽  
User Friendly

Abstract Motivation Expanding research highlights the importance of guanine quadruplex structures. Therefore, easy-accessible tools for quadruplex analyses in DNA and RNA molecules are important for the scientific community. Results We developed a web version of the G4Hunter application. This new web-based server is a platform-independent and user-friendly application for quadruplex analyses. It allows retrieval of gene/nucleotide sequence entries from NCBI databases and provides complete characterization of localization and quadruplex propensity of quadruplex-forming sequences. The G4Hunter web application includes an interactive graphical data representation with many useful options including visualization, sorting, data storage and export. Availability and implementation G4Hunter web application can be accessed at: http://bioinformatics.ibp.cz. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals COSIFER: a Python package for the consensus inference of molecular interaction networks

2020 ◽  
Author(s):  
Matteo Manica ◽  
Charlotte Bunne ◽  
Roland Mathis ◽  
Joris Cadow ◽  
Mehmet Eren Ahsen ◽  
...  
Keyword(s):  
High Throughput ◽  
Network Inference ◽  
State Of The Art ◽  
Interaction Network ◽  
Molecular Networks ◽  
Supplementary Information ◽  
Web Based ◽  
Molecular Interaction Networks ◽  
Inference Methods ◽  
User Friendly

Abstract Summary The advent of high-throughput technologies has provided researchers with measurements of thousands of molecular entities and enable the investigation of the internal regulatory apparatus of the cell. However, network inference from high-throughput data is far from being a solved problem. While a plethora of different inference methods have been proposed, they often lead to non-overlapping predictions, and many of them lack user-friendly implementations to enable their broad utilization. Here, we present Consensus Interaction Network Inference Service (COSIFER), a package and a companion web-based platform to infer molecular networks from expression data using state-of-the-art consensus approaches. COSIFER includes a selection of state-of-the-art methodologies for network inference and different consensus strategies to integrate the predictions of individual methods and generate robust networks. Availability and implementation COSIFER Python source code is available at https://github.com/PhosphorylatedRabbits/cosifer. The web service is accessible at https://ibm.biz/cosifer-aas. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Thyroid Cancer and Tumor Collaborative Registry (TCCR)

2016 ◽  
Vol 15 ◽  
pp. CIN.S32470 ◽  
Author(s):  
Oleg Shats ◽  
Whitney Goldner ◽  
Jianmin Feng ◽  
Alexander Sherman ◽  
Russell B. Smith ◽  
...  
Keyword(s):  
Thyroid Cancer ◽  
Dietary Habits ◽  
Distribution Model ◽  
End User ◽  
Web Based ◽  
Agile Methodology ◽  
Software Distribution ◽  
User Friendly ◽  
Collection And Management

A multicenter, web-based Thyroid Cancer and Tumor Collaborative Registry (TCCR, http://tccr.unmc.edu ) allows for the collection and management of various data on thyroid cancer (TC) and thyroid nodule (TN) patients. The TCCR is coupled with OpenSpecimen, an open-source biobank management system, to annotate biospecimens obtained from the TCCR subjects. The demographic, lifestyle, physical activity, dietary habits, family history, medical history, and quality of life data are provided and may be entered into the registry by subjects. Information on diagnosis, treatment, and outcome is entered by the clinical personnel. The TCCR uses advanced technical and organizational practices, such as (i) metadata-driven software architecture (design); (ii) modern standards and best practices for data sharing and interoperability (standardization); (iii) Agile methodology (project management); (iv) Software as a Service (SaaS) as a software distribution model (operation); and (v) the confederation principle as a business model (governance). This allowed us to create a secure, reliable, user-friendly, and self-sustainable system for TC and TN data collection and management that is compatible with various end-user devices and easily adaptable to a rapidly changing environment. Currently, the TCCR contains data on 2,261 subjects and data on more than 28,000 biospecimens. Data and biological samples collected by the TCCR are used in developing diagnostic, prevention, treatment, and survivorship strategies against TC.

scholarly journals G-OnRamp: a Galaxy-based platform for collaborative annotation of eukaryotic genomes

2019 ◽  
Vol 35 (21) ◽  
pp. 4422-4423 ◽  
Author(s):  
Yating Liu ◽  
Luke Sargent ◽  
Wilson Leung ◽  
Sarah C R Elgin ◽  
Jeremy Goecks
Keyword(s):  
Genome Annotation ◽  
Source Code ◽  
Supplementary Information ◽  
Rna Seq ◽  
Sequence Alignments ◽  
Web Based ◽  
Collaborative Annotation ◽  
Genome Browsers ◽  
User Friendly ◽  
Eukaryotic Genomes

Abstract Summary G-OnRamp provides a user-friendly, web-based platform for collaborative, end-to-end annotation of eukaryotic genomes using UCSC Assembly Hubs and JBrowse/Apollo genome browsers with evidence tracks derived from sequence alignments, ab initio gene predictors, RNA-Seq data and repeat finders. G-OnRamp can be used to visualize large genomics datasets and to perform collaborative genome annotation projects in both research and educational settings. Availability and implementation The virtual machine images and tutorials are available on the G-OnRamp web site (http://g-onramp.org/deployments). The source code is available under an Academic Free License version 3.0 through the goeckslab GitHub repository (https://github.com/goeckslab). Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals RANCANG BANGUN APLIKASI PENGADAAN BARANG DAN JASA BERBASIS WEB PADA BMKG

2020 ◽  
Vol 4 (2) ◽  
pp. 97
Author(s):  
Shendyko Wicaksono ◽  
Martua Hami Siregar ◽  
Maysaroh Maysaroh
Keyword(s):  
Human Error ◽  
Document Management ◽  
Report Generation ◽  
Human Errors ◽  
Web Based ◽  
Goods And Services ◽  
Speed Up ◽  
Access Rights ◽  
User Friendly

Dalam proses pengelolaan dokumentasi surat perintah kerja pengadaan BMKG masih belum maksimal salah satunya banyak yang tercecer atau terjadinya duplikasi data dan sering terjadi human error. Hal ini menjadi sebuah kendala atau masalah dalam hal peningkatan kualitas pengelolaan dokumen surat perintah kerja pengadaan terutama didalam era teknologi dan informasi. Aplikasi Pengadaan Barang dan Jasa berbasis web ini, dapat mempermudah Pejabat Pengadaan (PP) dan Pejabat Pembuat Komitmen (PPK) dalam proses manajemen dokumen pengadaan dan pembuatan laporan dengan menggunakan bahasa pemrograman PHP dan MySQL sebagai database. Desain Aplikasi Pengadaan Barang dan Jasa berbasis web ini terlihat user friendly. Dapat mempercepat proses pengadaan barang dan jasa. Dapat mempercepat proses pembuatan laporan bulanan. Sistem yang dirancang menggunakan 2 hak akses yang diberikan kepada Admin, dan User.   Kata Kunci: Pengadaan Barang dan Jasa, PHP, MySQL, User Friendly Abstract: In the process of managing the documentation for the work order for BMKG procurement, it is still not optimal, one of which is that there are many scattered or duplication of data and frequent human errors. This becomes an obstacle or problem in terms of improving the quality of document management for procurement work orders, especially in the era of technology and information. This web-based application for procurement of goods and services can make it easier for Procurement Officers (PP) and Commitment Making Officers (PPK) in the process of procurement document management and report generation using the PHP programming language and MySQL as the database. This web-based application design for procurement of goods and services looks user friendly. Can speed up the process of procuring goods and services. Can speed up the process of making monthly reports. The system is designed using 2 access rights given to Admin and User. Keywords: Procurement of Goods and Services, PHP, MySQL, User Friendly

scholarly journals Metabolite-Investigator: an integrated user-friendly workflow for metabolomics multi-study analysis

2020 ◽  
Author(s):  
Carl Beuchel ◽  
Holger Kirsten ◽  
Uta Ceglarek ◽  
Markus Scholz
Keyword(s):  
Measurement Techniques ◽  
Supplementary Information ◽  
Metabolomics Data ◽  
Factors Affecting ◽  
Quantitative Metabolomics ◽  
Covariate Model ◽  
Shiny App ◽  
Analysis Workflow ◽  
Scalable Analysis ◽  
User Friendly

Abstract Motivation Many diseases have a metabolic background, which is increasingly investigated due to improved measurement techniques allowing high-throughput assessment of metabolic features in several body fluids. Integrating data from multiple cohorts is of high importance to obtain robust and reproducible results. However, considerable variability across studies due to differences in sampling, measurement techniques and study populations needs to be accounted for. Results We present Metabolite-Investigator, a scalable analysis workflow for quantitative metabolomics data from multiple studies. Our tool supports all aspects of data pre-processing including data integration, cleaning, transformation, batch analysis as well as multiple analysis methods including uni- and multivariable factor-metabolite associations, network analysis and factor prioritization in one or more cohorts. Moreover, it allows identifying critical interactions between cohorts and factors affecting metabolite levels and inferring a common covariate model, all via a graphical user interface. Availability and implementation We constructed Metabolite-Investigator as a free and open web-tool and stand-alone Shiny-app. It is hosted at https://apps.health-atlas.de/metabolite-investigator/, the source code is freely available at https://github.com/cfbeuchel/Metabolite-Investigator. Supplementary information Supplementary data are available at Bioinformatics online.

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