scholarly journals piRNAdb: A piwi-interacting RNA database

2021 ◽  
Author(s):  
Ricardo Piuco ◽  
Pedro A.F. Galante
Keyword(s):  
Gene Ontology ◽  
Transposable Elements ◽  
Information Exchange ◽  
Feedback System ◽  
Data Repository ◽  
Web Tool ◽  
Genomic Location ◽  
Cellular Development ◽  
Location Clustering ◽  
User Friendly

Motivation: Found in several metazoan species, piwi-interacting RNAs (piRNAs) regulate the expression of a wide variety of transposable elements and genes associated with cellular development, differentiation, and growth. Despite their importance, piRNAs are not well known and are still underexplored. To facilitate piRNA research, a comprehensive and easy-to-use piRNA database is still needed. Results: Here, we present piRNAdb, an integrative and user-friendly database designed to encompass several aspects of piRNAs. We selected piRNAs from four reliable human RNA-sequencing datasets to start our database. After data processing, we displayed these sequences, their genomic location, clustering information, putative targets on known genes and transposable elements, as well as direct links to other databases. In this first release, piRNAdb catalogues 27,329 piRNAs, as well as 23,380 genes that are putative targets and 47,060 associated gene ontology terms, both of which are organized and linked to each respective piRNA. Finally, to improve information exchange and increase the confidence of sequences, a feedback system is provided to users of piRNAdb. Conclusion: The inclusion of new features to facilitate piRNA analyses, data visualization, and integration is the major pillar of piRNAdb. Our main goal was to make this database an easy interface between the data and the user. We believe that this web tool achieves this objective by providing a streamlined and well-organized data repository for piRNAs and that it will be extremely useful to those already studying piRNAs and to the broader community. Availability: piRNAdb is available freely and is compatible with smartphones and tablets: https://www.pirnadb.org/ .

scholarly journals Erratum to: InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology

BMC Genomics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Jiajie Peng ◽  
Hongxiang Li ◽  
Yongzhuang Liu ◽  
Liran Juan ◽  
Qinghua Jiang ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Web Tool

A Remote Synthetic Testbed For Human-Robot Teaming: An Iterative Design Process

2021 ◽  
Vol 65 (1) ◽  
pp. 781-785
Author(s):  
Margaret Wong ◽  
Akudasuo Ezenyilimba ◽  
Alexandra Wolff ◽  
Tyrell Anderson ◽  
Erin Chiou ◽  
...  
Keyword(s):  
Design Process ◽  
Information Exchange ◽  
Task Environment ◽  
Research Administration ◽  
Urban Search And Rescue ◽  
Pilot Studies ◽  
Iterative Design ◽  
Hazardous Environments ◽  
User Friendly ◽  
Real Time Information

Urban Search and Rescue (USAR) missions often involve a need to complete tasks in hazardous environments. In such situations, human-robot teams (HRT) may be essential tools for future USAR missions. Transparency and explanation are two information exchange processes where transparency is real-time information exchange and explanation is not. For effective HRTs, certain levels of transparency and explanation must be met, but how can these modes of team communication be operationalized? During the COVID-19 pandemic, our approach to answering this question involved an iterative design process that factored in our research objectives as inputs and pilot studies with remote participants. Our final research testbed design resulted in converting an in-person task environment to a completely remote study and task environment. Changes to the study environment included: utilizing user-friendly video conferencing tools such as Zoom and a custom-built application for research administration tasks and improved modes of HRT communication that helped us avoid confounding our performance measures.

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.

Transcriptomics Analysis using Galaxy and other Online Servers for Rheumatoid Arthritis

2021 ◽  
Vol 9 (VII) ◽  
pp. 459-466
Author(s):  
Sourabh Parmar
Keyword(s):  
Rheumatoid Arthritis ◽  
Data Mining ◽  
Gene Ontology ◽  
Complex Disease ◽  
Differential Expression Analysis ◽  
Biological Data ◽  
Systemic Autoimmune Disease ◽  
Transcriptomic Data ◽  
Pathway Enrichment ◽  
User Friendly

Researchers use transcriptomics analyses for biological data mining, interpretation, and presentation. Galaxy-based tools are utilized to analyze various complex disease transcriptomic data to understand the pathogenesis of the disease, which are user-friendly. This work provides simple methods for differential expression analysis and analysis of these results in gene ontology and pathway enrichment tools like David, WebGestalt. This method is very effective in better analysis and understanding the transcriptomic data. Transcriptomics analysis has been made on rheumatoid arthritis sra data. Rheumatoid arthritis (RA) is a systemic autoimmune disease. T cells and autoantibodies mediate the pathogenesis. This article discusses the genes which are differentially expressed between the healthy (n=50) and diseased (n=51) and the functions of those genes in the pathogenesis of RA.

A Chinese Interactive Feedback System for a Virtual Campus

2010 ◽  
pp. 290-316
Author(s):  
Chen Jui-Fa ◽  
Lin Wei-Chuan ◽  
Jian Chih-Yu ◽  
Hung Ching-Chung
Keyword(s):  
Chinese Language ◽  
Feedback System ◽  
Feedback Mechanism ◽  
Lexical Database ◽  
Natural Languages ◽  
Virtual Campus ◽  
E Learning ◽  
User Friendly ◽  
Interactive Feedback ◽  
Proper Response

Considering the popularity of the Internet, an automatic interactive feedback system for E-learning websites is becoming increasingly desirable. However, computers still have problems understanding natural languages, especially the Chinese language, firstly because the Chinese language has no space to segment lexical entries (its segmentation method is more difficult than that of English) and secondly because of the lack of a complete grammar in the Chinese language, making parsing more difficult and complicated. Building an automated Chinese feedback system for special application domains could solve these problems. This paper proposes an interactive feedback mechanism in a virtual campus that can parse, understand and respond to Chinese sentences. This mechanism utilizes a specific lexical database according to the particular application. In this way, a virtual campus website can implement a special application domain that chooses the proper response in a user friendly, accurate and timely manner.

scholarly journals Mining human cancer datasets for kallikrein expression in cancer: the ‘KLK-CANMAP’ Shiny web tool

2018 ◽  
Vol 399 (9) ◽  
pp. 983-995
Author(s):  
Chenwei Wang ◽  
Leire Moya ◽  
Judith A. Clements ◽  
Colleen C. Nelson ◽  
Jyotsna Batra
Keyword(s):  
Web Application ◽  
Cancer Survival ◽  
Human Cancer ◽  
Web Tool ◽  
Significant Differential Expression ◽  
Box Plots ◽  
Kaplan Meier ◽  
R Shiny ◽  
Serine Protease Family ◽  
User Friendly

AbstractThe dysregulation of the serine-protease family kallikreins (KLKs), comprising 15 genes, has been reportedly associated with cancer. Their expression in several tissues and physiological fluids makes them potential candidates as biomarkers and therapeutic targets. There are several databases available to mine gene expression in cancer, which often include clinical and pathological data. However, these platforms present some limitations when comparing a specific set of genes and can generate considerable unwanted data. Here, several datasets that showed significant differential expression (p<0.01) in cancer vs. normal (n=118), metastasis vs. primary (n=15) and association with cancer survival (n=21) have been compiled in a user-friendly format from two open and/or publicly available databases Oncomine and OncoLnc for the 15 KLKs. The data have been included in a free web application tool: the KLK-CANMAP https://cancerbioinformatics.shinyapps.io/klk-canmap/. This tool integrates, analyses and visualises data and it was developed with the R Shiny framework. Using KLK-CANMAP box-plots, heatmaps and Kaplan-Meier graphs can be generated for the KLKs of interest. We believe this new cancer KLK focused web tool will benefit the KLK community by narrowing the data visualisation to only the genes of interest.

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.

Providing a user-friendly outlier analysis service implemented as open REST API

2020 ◽  
Author(s):  
Doron Goldfarb ◽  
Johannes Kobler ◽  
Johannes Peterseil
Keyword(s):  
Web Service ◽  
Data Retrieval ◽  
Environmental Data ◽  
Data Repository ◽  
Outlier Analysis ◽  
Data Set ◽  
Access Methods ◽  
Rest Api ◽  
Definition Of ◽  
User Friendly

&lt;p&gt;As outliers in any data set may have detrimental effects on further scientific analysis, the measurement of any environmental parameter and the detection of outliers within these data are closely linked. However, outlier analysis is complicated, as the definition of an outlier is controversially discussed and thus - until now - vague. Nonetheless, multiple methods have been implemented to detect outliers in data sets. The application of these methods often requires some statistical know-how.&lt;/p&gt;&lt;p&gt;The present use case, developed as proof-of-concept implementation within the EOSC-Hub project, is dedicated to providing a user-friendly outlier analysis web-service via an open REST API processing environmental data either provided via Sensor Observation Service (SOS) or stored as data files in a cloud-based data repository. It is driven by an R-script performing the different operation steps consisting of data retrieval,&amp;#160; outlier analysis and final data export. To cope with the vague definition of an outlier, the outlier analysis step applies numerous statistical methods implemented in various R-packages.&lt;/p&gt;&lt;p&gt;The web-service encapsulates the R-script behind a REST API which is decribed by a dedicated OpenAPI specification defining two distinct access methods (i.e. SOS- and file-based) and the required parameters to run the R-script. This formal specification is subsequently used to automatically generate a server stub based on the Python FLASK framework which is customized to execute the R-script on the server whenever an appropriate web request arrives. The output is currently collected in a ZIP file which is returned after each successful web request. The service prototype is designed to be operated using generic resources provided by the European Open Science Cloud (EOSC) and the European Grid Initiative (EGI) in order to ensure sustainability and scalability.&lt;/p&gt;&lt;p&gt;Due to its user-friendliness and open availability, the presented web-service will facilitate access to standardized and scientifically-based outlier analysis methods not only for individual scientists but also for networks and research infrastructures like eLTER. It will thus contribute to the standardization of quality control procedures for data provision in distributed networks of data providers.&lt;/p&gt;&lt;p&gt;&amp;#160;&lt;/p&gt;&lt;p&gt;Keywords: quality assessment, outlier detection, web service, REST-API, eLTER, EOSC, EGI, EOSC-Hub&lt;/p&gt;

scholarly journals InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology

BMC Genomics ◽  
2016 ◽  
Vol 17 (S5) ◽  
Author(s):  
Jiajie Peng ◽  
Hongxiang Li ◽  
Yongzhuang Liu ◽  
Liran Juan ◽  
Qinghua Jiang ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Web Tool

scholarly journals GOssTo: a stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology

2014 ◽  
Vol 30 (15) ◽  
pp. 2235-2236 ◽  
Author(s):  
H. Caniza ◽  
A. E. Romero ◽  
S. Heron ◽  
H. Yang ◽  
A. Devoto ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Web Tool
Sign in / Sign up

Export Citation Format

Share Document