scholarly journals epiTAD: a web application for visualizing chromosome conformation capture data in the context of genetic epidemiology

2019 ◽  
Vol 35 (21) ◽  
pp. 4462-4464
Author(s):  
Jordan H Creed ◽  
Garrick Aden-Buie ◽  
Alvaro N Monteiro ◽  
Travis A Gerke
Keyword(s):  
Genetic Epidemiology ◽  
In Silico ◽  
Web Application ◽  
Large Scale ◽  
Source Code ◽  
Chromosome Conformation Capture ◽  
Chromosome Conformation ◽  
Web Based ◽  
Genome Wide ◽  
Public Data

Abstract Summary Complementary advances in genomic technology and public data resources have created opportunities for researchers to conduct multifaceted examination of the genome on a large scale. To meet the need for integrative genome wide exploration, we present epiTAD. This web-based tool enables researchers to compare genomic 3D organization and annotations across multiple databases in an interactive manner to facilitate in silico discovery. Availability and implementation epiTAD can be accessed at https://apps.gerkelab.com/epiTAD/ where we have additionally made publicly available the source code and a Docker containerized version of the application.

scholarly journals epiTAD: a web application for visualizing high throughput chromosome conformation capture data in the context of genetic epidemiology

2018 ◽  
Author(s):  
Jordan H. Creed ◽  
Garrick Aden-Buie ◽  
Alvaro N. Monteiro ◽  
Travis A. Gerke
Keyword(s):  
High Throughput ◽  
Genetic Epidemiology ◽  
In Silico ◽  
Web Application ◽  
Chromosome Conformation Capture ◽  
Chromosome Conformation ◽  
Web Based ◽  
Genome Wide ◽  
Public Data ◽  
Complex Scale

AbstractThe increasing availability of public data resources coupled with advancements in genomic technology has created greater opportunities for researchers to examine the genome on a large and complex scale. To meet the need for integrative genome wide exploration, we present epiTAD. This web-based tool enables researchers to compare genomic structures and annotations across multiple databases and platforms in an interactive manner in order to facilitate in silico discovery. epiTAD can be accessed at https://apps.gerkelab.com/epiTAD/.

scholarly journals Viewing RNA-seq data on the entire human genome

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 596 ◽  
Author(s):  
Eric M. Weitz ◽  
Lorena Pantano ◽  
Jingzhi Zhu ◽  
Bennett Upton ◽  
Ben Busby
Keyword(s):  
Web Application ◽  
Source Code ◽  
Gene Expression Omnibus ◽  
Expression Data ◽  
Rna Seq ◽  
Sequence Read Archive ◽  
Data Pipeline ◽  
Genome Wide ◽  
Small Team ◽  
Genome Wide Expression

RNA-Seq Viewer is a web application that enables users to visualize genome-wide expression data from NCBI’s Sequence Read Archive (SRA) and Gene Expression Omnibus (GEO) databases. The application prototype was created by a small team during a three-day hackathon facilitated by NCBI at Brandeis University. The backend data pipeline was developed and deployed on a shared AWS EC2 instance. Source code is available at https://github.com/NCBI-Hackathons/rnaseqview.

scholarly journals Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy

2019 ◽  
Author(s):  
Alessandro Bertero ◽  
Paul A. Fields ◽  
Alec S. T. Smith ◽  
Andrea Leonard ◽  
Kevin Beussman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Induced Pluripotent Stem Cell ◽  
Lamin A ◽  
Chromosome Conformation ◽  
Human Cardiomyocytes ◽  
Nuclear Lamins ◽  
Genome Wide ◽  
Induced Pluripotent ◽  
Gene Expression Alterations

AbstractPathogenic mutations in A-type nuclear lamins cause dilated cardiomyopathy, which is postulated to result from dysregulated gene expression due to changes in chromatin organization into active and inactive compartments. To test this, we performed genome-wide chromosome conformation analyses (Hi-C) in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) with a haploinsufficient mutation for lamin A/C. Compared to gene-corrected cells, mutant hiPSC-CMs have marked electrophysiological and contractile alterations, with modest gene expression changes. While large-scale changes in chromosomal topology are evident, differences in chromatin compartmentalization are limited to a few hotspots that escape inactivation during cardiogenesis. These regions exhibit upregulation of multiple non-cardiac genes including CACNA1A, encoding for neuronal P/Q-type calcium channels. Pharmacological inhibition of the resulting current partially mitigates the electrical alterations. On the other hand, A/B compartment changes do not explain most gene expression alterations in mutant hiPSC-CMs. We conclude that global errors in chromosomal compartmentation are not the primary pathogenic mechanism in heart failure due to lamin A/C haploinsufficiency.SummaryBertero et al. observe that lamin A/C haploinsufficiency in human cardiomyocytes markedly alters electrophysiology, contractility, gene expression, and chromosomal topology. Contrary to expectations, however, changes in chromatin compartments involve just few regions, and most dysregulated genes lie outside these hotspots.Condensed titleGenomic effects of lamin A/C haploinsufficiency

scholarly journals Pengembangan Sistem Informasi Industri Jasa Menjahit Online Berbasis Web Menggunakan Metode Waterfall

2020 ◽  
Vol 5 (2) ◽  
pp. 116
Author(s):  
Elsa Oktavia ◽  
Yulindon Yulindon ◽  
Rahmat Hidayat
Keyword(s):  
Information Systems ◽  
Web Application ◽  
Large Scale ◽  
Design Work ◽  
Financial Reports ◽  
Web Based ◽  
Work Systems ◽  
Face To Face ◽  
Service Information ◽  
Drastic Increase

Information systems are currently increasing very rapidly, but it is unfortunate if the utilization is not yet optimal. Reviewing the data from literature studies and observations that have been made, many people need sewing services. The drastic increase in demand makes competition in the convection industry. Most of the work systems in the convection industry are done manually and are not economical. Product development also lacks creativity. Therefore, this researcher will use IT as marketing and design work, this can make processing time shorter and more optimal. Thus, customers will be facilitated in ordering ready-made clothes or clothes that match the customer's wishes by using a web application that only sends data on the size of the clothes or clothing model that the customer wants. This web-based application system can make it easier for customers to transact with the owner and transactions do not have to meet face to face. In addition, clothing sales and large-scale orders can be neatly organized and financial reports can be well structured and organized clearly. The results of this research will be in the form of research reports and web-based online sewing service information systems using the waterfall method. 

scholarly journals EpiMetal: an open-source graphical web browser tool for easy statistical analyses in epidemiology and metabolomics

2020 ◽  
Vol 49 (4) ◽  
pp. 1075-1081
Author(s):  
Jussi Ekholm ◽  
Pauli Ohukainen ◽  
Antti J Kangas ◽  
Johannes Kettunen ◽  
Qin Wang ◽  
...  
Keyword(s):  
Web Application ◽  
Large Scale ◽  
Source Code ◽  
Statistical Analyses ◽  
Data Driven ◽  
Graphical Interface ◽  
Self Organizing Maps ◽  
Web Browser ◽  
Pilot Data ◽  
Molecular Measures

Abstract Motivation An intuitive graphical interface that allows statistical analyses and visualizations of extensive data without any knowledge of dedicated statistical software or programming. Implementation EpiMetal is a single-page web application written in JavaScript, to be used via a modern desktop web browser. General features Standard epidemiological analyses and self-organizing maps for data-driven metabolic profiling are included. Multiple extensive datasets with an arbitrary number of continuous and category variables can be integrated with the software. Any snapshot of the analyses can be saved and shared with others via a www-link. We demonstrate the usage of EpiMetal using pilot data with over 500 quantitative molecular measures for each sample as well as in two large-scale epidemiological cohorts (N >10 000). Availability The software usage exemplar and the pilot data are open access online at [http://EpiMetal.computationalmedicine.fi]. MIT licensed source code is available at the Github repository at [https://github.com/amergin/epimetal].

scholarly journals The Framework for Web-Based Automated Online Question Paper Generator through JEE

2018 ◽  
Vol 7 (3) ◽  
pp. 1415
Author(s):  
Vinayak Hegde ◽  
Lavanya V Rao ◽  
Shivali B S
Keyword(s):  
Web Application ◽  
Large Scale ◽  
Educational Institution ◽  
Faculty Members ◽  
Educational Institutions ◽  
Small Scale ◽  
Web Based ◽  
Educational Institute ◽  
User Friendly ◽  
Word Format

Examinations are an indispensable part of a student’s life. In the conventional mechanism, the question paper generation is time-consuming work for the faculty members of the educational institution. Every educational institute mandatorily expects exam setters to follow its own typesetting format. We have designed the automated question paper setting software to be user-friendly so that, paper setters can overcome from the typographic problem. Presently in most of the educational institutions question papers are set manually. It is time-consuming work and there may be chances of repetition of the same questions. So, in order to make the question paper generation more convenient to use, the web application is developed using Java Enterprise Edition (JEE) that can be accessed from LAN/Intranet.The application comes with the Admin Module and Teachers Module. The Admin grants access to the users by registering them. The faculty can access the system once they are registered. The faculty can enter questions in the database daily as per their free time. In this way, the question pool can be generated. The questions are approved by the chairperson and substandard questions are discarded. The question paper is then generated by selected course experts. The Fisher-Yates Shuffling algorithm used to choose questions randomly from the pool of questions from the database. Text Mining Algorithm aids in duplicity removal from the paper.  The generated question paper will be in Word Format. In our application, we assure better security, removal of duplicity, cost-effectiveness, and human intervention avoidance. It can be used by small-scale and large-scale institutions.  

Genome-wide analysis and characterization of an online sarcoma cohort.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 10097-10097
Author(s):  
Kimberly E Barnholt ◽  
Chuong B Do ◽  
Amy K Kiefer ◽  
Marisa Nelson ◽  
Judy Ellen Garber ◽  
...  
Keyword(s):  
Rare Diseases ◽  
Large Scale ◽  
Online Survey ◽  
Genome Wide Association Study ◽  
Research Participation ◽  
Research Progress ◽  
European Ancestry ◽  
Web Based ◽  
Genome Wide ◽  
Patient Reported

10097 Background: Recruitment of an adequately sized cohort for genome-wide studies presents a serious challenge for rare diseases such as sarcoma. Traditional barriers to participation include proximity of clinical centers and motivation or ability to travel. 23andMe’s web-based platform provides increased accessibility to research participation, facilitating rapid recruitment of patients (pts) and enabling a large-scale genome-wide association study (GWAS) of sarcoma. Methods: Sarcoma pts were recruited through web and email campaigns, patient advocacy groups, physician offices, and events. Pts provide IRB-approved consent, complete surveys, and receive updates about research progress through an online account. In collaboration with an uncompensated panel of academic experts, an online survey was developed to collect patient-reported data on diagnosis, family history, symptoms and treatment. Results: This web-based approach has accrued the largest genotyped, recontactable sarcoma cohort to date. In 20 months, 772 sarcoma pts have enrolled, 683 have been genotyped and 611 have provided data online. The cohort is primarily of European ancestry (92%), disproportionately female (72%), with an average age of 51 (± 15 years). More than 88% of pts indicated a soft tissue sarcoma diagnosis, with leiomyosarcoma, liposarcoma and “malignant fibrous histiocytoma” being the most commonly reported subtypes. Over 36% of pts report undergoing active treatment of some type. Association scans were conducted across a set of 8,058,452 imputed SNPs, using 568 unrelated sarcoma cases of European ancestry and >70,000 unrelated population controls from the 23andMe database. Initial results have identified no significant genome-wide associations for general sarcoma risk, despite having >90% power to detect risk variants with >5% minor allele frequency and odds ratio >2.5, suggesting the absence of common variants with strong shared effects across sarcoma subtypes. Conclusions: This pilot study demonstrates feasibility of rapid recruitment and longitudinal engagement of pts through online technology. Such techniques may significantly accelerate, and in some cases fully enable, large-scale genomic studies of sarcoma and other rare diseases.

Web Engineering

2011 ◽  
pp. 1-24 ◽  
Author(s):  
San Murugesan ◽  
Athula Ginige
Keyword(s):  
Web Application ◽  
Large Scale ◽  
Web Applications ◽  
Web Development ◽  
Application Development ◽  
Web Engineering ◽  
Web Based ◽  
Large Complex ◽  
Diverse Groups ◽  
Web Developers

Web-based systems and applications now deliver a complex array of functionality to a large number of diverse groups of users. As our dependence and reliance on the Web has increased dramatically over the years, their performance, reliability and quality have become paramount importance. As a result, the development of Web applications has become more complex and challenging than most of us think. In many ways, it is also different and more complex than traditional software development. But, currently, the development and maintenance of most Web applications is chaotic and far from satisfactory. To successfully build and maintain large, complex Web-based systems and applications, Web developers need to adopt a disciplined development process and a sound methodology. The emerging discipline of Web engineering advocates a holistic, disciplined approach to successful Web development. In this chapter, we articulate and raise awareness of the issues and considerations in large, complex Web application development, and introduce Web engineering as a way of managing complexity and diversity of large-scale Web development.

DAEH: A Tool for Specifying and Monitoring the Exception Handling Policy

2015 ◽  
Vol 25 (09n10) ◽  
pp. 1515-1530
Author(s):  
Joilson Abrantes ◽  
Roberta Coelho ◽  
Rodrigo Bonifácio
Keyword(s):  
Large Scale ◽  
Source Code ◽  
Exception Handling ◽  
Runtime Monitoring ◽  
Domain Specific Language ◽  
Monitoring Tool ◽  
Web Based ◽  
Domain Specific ◽  
Lack Of Information ◽  
Contract Language

The exception handling policy of a system comprises the set of design rules that specify its exception handling behavior (how exceptions should be handled and thrown). Such policy is usually undocumented and implicitly defined by the system architect. For this reason, developers often consider that by just including catch-blocks in the code they are dealing with exceptional conditions. This lack of information may turn the exception handling into a generalized “goto” mechanism making the program more complex and less reliable. This work presents a domain-specific language called ECL (Exception Contract Language) to specify the exception handling policy and a runtime monitoring tool which dynamically checks this policy. The monitoring tool is implemented in the form of an aspect library, which can be added to any Java system without the need to change the application source code. We applied this approach to two large-scale web-based systems and to a set of versions of the well-known JUnit framework. The results indicate that this approach can be used to express and to automatically check the exception handling policy of a system, and consequently support the development of more robust Java systems.

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