scholarly journals Pixel: a content management platform for quantitative omics data

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6623 ◽  
Author(s):  
Thomas Denecker ◽  
William Durand ◽  
Julien Maupetit ◽  
Charles Hébert ◽  
Jean-Michel Camadro ◽  
...  
Keyword(s):  
Web Application ◽  
Content Management ◽  
Biological Information ◽  
Functional Tests ◽  
Single Experiment ◽  
Code Coverage ◽  
Development Platform ◽  
Management Platform ◽  
Strategic Position ◽  
Web App

Background In biology, high-throughput experimental technologies, also referred as “omics” technologies, are increasingly used in research laboratories. Several thousands of gene expression measurements can be obtained in a single experiment. Researchers are routinely facing the challenge to annotate, store, explore and mine all the biological information they have at their disposal. We present here the Pixel web application (Pixel Web App), an original content management platform to help people involved in a multi-omics biological project. Methods The Pixel Web App is built with open source technologies and hosted on the collaborative development platform GitHub (https://github.com/Candihub/pixel). It is written in Python using the Django framework and stores all the data in a PostgreSQL database. It is developed in the open and licensed under the BSD 3-clause license. The Pixel Web App is also heavily tested with both unit and functional tests, a strong code coverage and continuous integration provided by CircleCI. To ease the development and the deployment of the Pixel Web App, Docker and Docker Compose are used to bundle the application as well as its dependencies. Results The Pixel Web App offers researchers an intuitive way to annotate, store, explore and mine their multi-omics results. It can be installed on a personal computer or on a server to fit the needs of many users. In addition, anyone can enhance the application to better suit their needs, either by contributing directly on GitHub (encouraged) or by extending Pixel on their own. The Pixel Web App does not provide any computational programs to analyze the data. Still, it helps to rapidly explore and mine existing results and holds a strategic position in the management of research data.

scholarly journals Pixel: a content management platform for quantitative omics data

2018 ◽  
Author(s):  
Thomas Denecker ◽  
William Durand ◽  
Julien Maupetit ◽  
Charles Hébert ◽  
Jean-Michel Camadro ◽  
...  
Keyword(s):  
Web Application ◽  
Content Management ◽  
Biological Information ◽  
Functional Tests ◽  
Single Experiment ◽  
Code Coverage ◽  
Development Platform ◽  
Management Platform ◽  
Strategic Position ◽  
Web App

ABSTRACTBackgroundIn biology, high-throughput experimental technologies, also referred as “omics” technologies, are increasingly used in research laboratories. Several thousands of gene expression measurements can be obtained in a single experiment. Researchers are routinely facing the challenge to annotate, store, explore and mine all the biological information they have at their disposal. We present here the Pixel web application (Pixel Web App), an original content management platform to help people involved in a multi-omics biological project.MethodsThe Pixel Web App is built with open source technologies and hosted on the collaborative development platform GitHub (https://github.com/Candihub/pixel). It is written in Python using the Django framework and stores all the data in a PostgreSQL database. It is developed in the open and licensed under the BSD 3-clause license. The Pixel Web App is also heavily tested with both unit and functional tests, a strong code coverage and continuous integration provided by CircleCI. To ease the development and the deployment of the Pixel Web App, Docker and Docker Compose are used to bundle the application as well as its dependencies.ResultsThe Pixel Web App offers researchers an intuitive way to annotate, store, explore and mine their multi-omics results. It can be installed on a personal computer or on a server to fit the needs of many users. In addition, anyone can enhance the application to better suit their needs, either by contributing directly on GitHub (encouraged) or by extending Pixel on their own. The Pixel Web App does not provide any computational programs to analyze the data. Still, it helps to rapidly explore and mine existing results and holds a strategic position in the management of research data.

scholarly journals NCR-PCOPGene: An Exploratory Tool for Analysis of Sample-Classes Effect on Gene-Expression Relationships

2008 ◽  
Vol 2008 ◽  
pp. 1-7
Author(s):  
Juan Cedano ◽  
Mario Huerta ◽  
Enrique Querol
Keyword(s):  
Gene Expression ◽  
Web Application ◽  
Biological Information ◽  
Microarray Technology ◽  
Previous Knowledge ◽  
Type B ◽  
Gene Expressions ◽  
Microarray Experiments ◽  
Maximum Value ◽  
Class Definition

Background. Microarray technology is so expensive and powerful that it is essential to extract maximum value from microarray data. Our tools allow researchers to test and formulate from a hypothesis to entire models. Results. The objective of the NCRPCOPGene is to study the relationships among gene expressions under different conditions, to classify these conditions, and to study their effect on the different relationships. The web application makes it easier to define the sample classes, grouping the microarray experiments either by using (a) biological, statistical, or any other previous knowledge or (b) their effect on the expression relationship maintained among specific genes of interest. By means of the type (a) class definition, the researcher can add biological information to the gene-expression relationships. The type (b) class definition allows for linking genes correlated neither linearly nor nonlinearly. Conclusions. The PCOPGene tools are especially suitable for microarrays with large sample series. This application helps to identify cellular states and the genes involved in it in a flexible way. The application takes advantage of the ability of our system to relate gene expressions; even when these relationships are noncontinuous and cannot be found using linear or nonlinear analytical methods.

scholarly journals Developing Web-Application’s Automated Testing Technique

2019 ◽  
Vol 17 (3) ◽  
pp. 93-110
Author(s):  
A. V. Tkachev ◽  
D. V. Irtegov
Keyword(s):  
Web Application ◽  
Development Process ◽  
Web Applications ◽  
Assessment System ◽  
Automated Testing ◽  
Automatic Assessment ◽  
Testing Technique ◽  
Code Coverage ◽  
Client Side ◽  
User Actions

The article is devoted to the technique of automated testing of NSUts – automatic assessment system for programming tasks developed at NSU. The main priority for this technique is to test both the old and the new versions of the application, so that the same or minimally modified tests could be executed on two versions of the system with different architectures. This could be useful while organizing the development process for other applications with a long life cycle. To test not only the server but also the client side of the web application, we suggest using tools like Selenium WebDriver to simulate user actions by sending commands to real browsers. We use the well-known Page Object design pattern to handle differences in HTML layout and functionality, and describe a number of ways to make developed tests less fragile and easily adapt those to work with the new version of the system. The article also describes the use of this technique to organize automated testing of the NSUts system and analyzes its effectiveness. The analysis shows that the estimated code coverage by these tests is quite high, and therefore the technique can be considered effective and applied to other similar web applications.

Design of Portal for Improvement Controlling Sales Channel

2014 ◽  
Vol 693 ◽  
pp. 445-450
Author(s):  
Matus Peci ◽  
Pavel Vazan ◽  
Vladimir Surka
Keyword(s):  
Performance Indicators ◽  
Web Application ◽  
Business Processes ◽  
Initial Conditions ◽  
Content Management ◽  
Appropriate Technology ◽  
Content Management System ◽  
Sales Channel ◽  
Advantages And Disadvantages ◽  
Financial Costs

This paper presents design of portal that improves controlling of sales channel at initial conditions. The customer needed to display key performance indicators on the portal and thus significantly improve the efficiency of business processes after the deployment of Microsoft Dynamics CRM 2011. The aim of this paper is to choose appropriate technology to create a portal and design possible architecture of solution. Microsoft Dynamics CRM 2011 with Web Application Microsoft SharePoint platform provide a solution for process control of business processes in company that is primarily offered like as the best solution. On the other hand, we found the possibility of open source content management system DotNetNuke, which meets customer's requirements and therefore, there is a possibility to reduce financial costs when selecting this system. Finally, we evaluated considered technologies, prepared more price variations of architecture and compared advantages and disadvantages of these variations.

Morpheus Web Testing: A Tool for Generating Test Cases for Widget Based Web Applications

2021 ◽  
Author(s):  
Romulo de Almeida Neves ◽  
Willian Massami Watanabe ◽  
Rafael Oliveira
Keyword(s):  
User Interfaces ◽  
Web Application ◽  
Web Applications ◽  
Test Cases ◽  
Code Coverage ◽  
Web Testing ◽  
The Cost ◽  
Software Lifecycle ◽  
The Web

Context: Widgets are reusable User Interfaces (UIs) components frequently delivered in Web applications.In the web application, widgets implement different interaction scenarios, such as buttons, menus, and text input.Problem: Tests are performed manually, so the cost associated with preparing and executing test cases is high.Objective: Automate the process of generating functional test cases for web applications, using intermediate artifacts of the web development process that structure widgets in the web application. The goal of this process is to ensure the quality of the software, reduce overall software lifecycle time and the costs associated with tests.Method:We elaborated a test generation strategy and implemented this strategy in a tool, Morpheus Web Testing. Morpheus Web Testing extracts widget information from Java Server Faces artifacts to generate test cases for JSF web applications. We conducted a case study for comparing Morpheus Web Testing with a state of the art tool (CrawlJax).Results: The results indicate evidence that the approach Morpheus Web Testing managed to reach greater code coverage compared to a CrawlJax.Conclusion: The achieved coverage values represent evidence that the results obtained from the proposed approach contribute to the process of automated test software engineering in the industry.

Data Mining in Gene Expression Analysis

2008 ◽  
pp. 1643-1673
Author(s):  
Jilin Han ◽  
Le Gruenwald ◽  
Tyrrell Conway
Keyword(s):  
Gene Expression ◽  
Data Mining ◽  
Biological Information ◽  
Future Research ◽  
Gene Expression Data Analysis ◽  
Experimental Conditions ◽  
Single Experiment ◽  
Important Approach ◽  
Future Research Directions ◽  
Gene Expression Levels

The study of gene expression levels under defined experimental conditions is an important approach to understand how a living cell works. High-throughput microarray technology is a very powerful tool for simultaneously studying thousands of genes in a single experiment. This revolutionary technology results in an extensive amount of data, which raises an important question: how to extract meaningful biological information from these data? In this chapter, we survey data mining techniques that have been used for clustering, classification and association rules for gene expression data analysis. In addition, we provide a comprehensive list of currently available commercial and academic data mining software together with their features. Lastly, we suggest future research directions.

Methodology for ISO/IEC 29110 Profile Implementation in EPF Composer

2017 ◽  
Vol 10 (1) ◽  
pp. 61-74
Author(s):  
Alena Buchalcevova
Keyword(s):  
Czech Republic ◽  
Web Application ◽  
Implementation Process ◽  
Content Management ◽  
Management Tool ◽  
The Czech Republic ◽  
Process Framework ◽  
Profile Element ◽  
Implementation Methodology ◽  
Element Mapping

The article presents the ISO/IEC 29110 Profile Implementation Methodology that was developed to manage consistent implementation of individual ISO/IEC 29110 Profiles in the open-source content management tool Eclipse Process Framework Composer. Such an implementation enables effective managing of the standard and its publishing in the form of a web application that can be easily and efficiently used. This methodology represents an example of the usable outputs of the ISO/IEC 29110 standard being utilized in education and research in the Czech Republic. Its main elements described in this article can be also used for implementation purposes in other countries. First, the methodology structure is presented, followed by its individual elements, i.e. General Principles, Profile Structure, Profile Element Mapping, Implementation Conventions, EPF Composer Usage Guidelines, and Implementation Process. The evaluation of this methodology was performed during the implementation of the Entry Profile.

scholarly journals An Efficient Functional Test Generation Method For Processors Using Genetic Algorithms

2015 ◽  
Vol 66 (4) ◽  
pp. 185-193 ◽  
Author(s):  
Ján Hudec ◽  
Elena Gramatová
Keyword(s):  
Genetic Algorithms ◽  
Test Generation ◽  
Functional Test ◽  
Evolutionary Strategies ◽  
Instruction Set ◽  
Functional Tests ◽  
Automatic Test Generation ◽  
Code Coverage ◽  
Fitness Functions

Abstract The paper presents a new functional test generation method for processors testing based on genetic algorithms and evolutionary strategies. The tests are generated over an instruction set architecture and a processor description. Such functional tests belong to the software-oriented testing. Quality of the tests is evaluated by code coverage of the processor description using simulation. The presented test generation method uses VHDL models of processors and the professional simulator ModelSim. The rules, parameters and fitness functions were defined for various genetic algorithms used in automatic test generation. Functionality and effectiveness were evaluated using the RISC type processor DP32.

scholarly journals A Wireless Internet of Things Architecture Based on Mobile Internet

2017 ◽  
Vol 13 (10) ◽  
pp. 132
Author(s):  
Bing Zhou
Keyword(s):  
Internet Of Things ◽  
Database System ◽  
Content Management ◽  
Mobile Internet ◽  
System Response ◽  
The Internet ◽  
Wireless Internet ◽  
Management Platform ◽  
Internet Of Things Technology ◽  
The Internet Of Things

<p><span style="font-size: small;"><span style="font-family: Times New Roman;">In order to develop a valid wireless Internet of things system, a wireless Internet of things framework based on mobile Internet is designed. The architecture of the Internet of things determines the architecture of the Internet of things business platform. There is no uniform standard for the architecture of the Internet of things service platform. The Internet of things business platform is mostly in an isolated state. The platform uses the common information management platform of Internet websites to manage mobile internet. Combined with the technologies of perception, identification and network transmission in the Internet of things technology, it is a content management Web management information system with both B/S (Browser/Server) and C/S structure (Client/Server). The platform can operate anywhere, and can give full play to the processing capacity of the client PC, and greatly reduce the application server running data load. The experimental results show that compared with the centralized database system, in the same piece of redundant condition, when the test table data is greater than the 1 million and the concurrent number is 100, the distributed database system has shorter concurrent query time and faster system response rate. Based on the above finding, it is concluded that wireless Internet of things technology based on mobile Internet will promote the development of the whole logistics industry and other related industries.</span></span></p>

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