Open-source Web Application Research Articles

Multi-disciplinary Peer-mark Moderation of Group Work

Self and peer assessment offers benefits for enhancing student learning. Peer moderation provides a convenient solution for awarding individual marks in group assignments. This paper provides a significant review of peer-mark moderation, and describes an award winning, web-based tool that was developed in the UK and is now spreading across the world as an open-source web application. It is available for use in any discipline. Qualitative research, at the home institution over several years, reinforces the evaluation of quantitative data extracted from the system and from an extensive user survey to confirm, update and strengthen the previous literature. The research also describes new insights into the thoughts of students, who appear to recognise the transparency that automated moderation offers. The statistics suggest few incidences of team-collusion when entering data, but indicate that peer-marking behaviour is influenced by group size, selection method and year of study. Students comment positively on the recognition of their levels of achievement within a team.

Crawling Ajax-Based Web Applications through Dynamic Analysis of User Interface State Changes

Using JavaScript and dynamic DOM manipulation on the client side of Web applications is becoming a widespread approach for achieving rich interactivity and responsiveness in modern Web applications. At the same time, such techniques---collectively known as Ajax ---shatter the concept of webpages with unique URLs, on which traditional Web crawlers are based. This article describes a novel technique for crawling Ajax -based applications through automatic dynamic analysis of user-interface-state changes in Web browsers. Our algorithm scans the DOM tree, spots candidate elements that are capable of changing the state, fires events on those candidate elements, and incrementally infers a state machine that models the various navigational paths and states within an Ajax application. This inferred model can be used in program comprehension and in analysis and testing of dynamic Web states, for instance, or for generating a static version of the application. In this article, we discuss our sequential and concurrent Ajax crawling algorithms. We present our open source tool called Crawljax , which implements the concepts and algorithms discussed in this article. Additionally, we report a number of empirical studies in which we apply our approach to a number of open-source and industrial Web applications and elaborate on the obtained results.

Development of a Web Based GIS Application for Spatial Natural Resources Information System Using Effective Open Source Software and Standards

There is growing needs for web based GIS for easy and fast dissemination, sharing, displaying and processing of spatial information which in turns helping in decision making for various natural resources based applications. In order to make a cost effective implementation, operation and maintenance of spatial information over the web, a cheaper yet feature rich alternative to commercial software is required which can be fulfilled by Open Source GIS software. This paper conveys an efficient approach to customize and integrate an open source web GIS system based on Mapserver as a web GIS server and PostgreSQL/PostGIS as an object oriented relational database management system (ORDBMS) for effective dissemination, sharing and management of spatial information over the internet. An open source web application tool built on top of MapScript using the PHP programming language has been used as for development of interactive user interface. The configurable Web Mapping Client Components (CWC2) tags have been added to HTML template pages in order to deploy the mapping contents to a web application. It is observed that the present system developed using open source software enables user to view, update, customized retrieval, query and analysis of natural resources information for specific needs.

Security Analysis System to Detect Threats on a SIP VoIP Infrasctructure Elements

SIP PBX is definitely the alpha and omega of any IP telephony infrastructure and frequently also provides other services than those related to VoIP traffic. These exchanges are, however, very often the target of attacks by external actors. The article describes a system that was developed on VSB-TU Ostrava as a testing tool to verify if the target VoIP PBX is adequately secured and protected against any real threats. The system tests the SIP element for several usually occurring attacks and it compiles evaluation of its overall security on the basis of successfully or unsuccessfully penetrations. The article describes the applications and algorithms that are used by system and the conclusion consists recommendations and guidelines to ensure effective protection against VoIP PBX threats. The system is designed as an open-source web application, thus allowing independent access and is fully extensible to other test modules.

An open source web application for the surveillance and prevention of the impacts on public health of extreme meteorological events: the SUPREME system

BackgroundEvery year, many deaths or health problems are directly linked to heat waves. Consequently, numerous jurisdictions around the world have developed intervention plans that are employed during extreme heat events; beyond their emergency sections, these plans generally include preventive measures to be implemented each year. Over the last five years, local and regional information systems have been implemented in a few Canadian cities for surveillance purposes. However, until recently, no such systems existed at the provincial level. In the context of the Government of Quebec's 2006-2012 Action Plan on Climate Change, a real-time integrated system for the surveillance and monitoring of extreme heat events has been implemented on a provincial level. The system is a component of a broader approach that would also monitor the public health impacts of all types of extreme meteorological events.ResultsAfter conducting a detailed needs analysis, the Quebec National Institute for Public Health developed and implemented an integrated web application leveraging open source software for the real-time Surveillance and Prevention of the impacts of Extreme Meteorological Events on public health, called the SUPREME system. Its first field use involved heat waves. This decision-support system is based on open source software and is composed of four modules: (1) data acquisition and integration, (2) risk analysis and alerts, (3), cartographic application, and (4) information dissemination - climate change and health portal. The system is available to health specialists through a secure web information portal and provides access to weather forecasts, historic and real-time indicators (including deaths and hospital admissions), alerts and various cartographic data used for conducting prevention activities and launching emergency measures.ConclusionsThe SUPREME system was implemented and used during the summer of 2010. It served as an important decision-making tool during the July 2010 heat wave in the province of Quebec, Canada. Planned improvements for 2011 include the integration of data related to other risk factors for other extreme events to the system. The next steps will be to provide access to the application to other groups of specialists that are involved in the prevention, monitoring, or analysis of extreme meteorological events and their effects on community health and well-being.

Open Source Web Applications for Libraries

Open Source Web Applications for Libraries

Generating Effective Attacks for Efficient and Precise Penetration Testing against SQL Injection

An SQL injection attack is one of the most serious security threats to web applications. It allows an attacker to access the underlying database and execute arbitrary commands, which may lead to sensitive information disclosure. The primary way to prevent SQL injection attacks is to sanitize the user-supplied input. However, this is usually performed manually by developers and so is a laborious and error-prone task. Although security tools assist the developers in verifying the security of their web applications, they often generate a number of false positives/negatives. In this paper, we present our technique called Sania, which performs efficient and precise penetration testing by dynamically generating effective attacks through investigating SQL queries. Since Sania is designed to be used in the development phase of web applications, it can intercept SQL queries. By analyzing the SQL queries, Sania automatically generates precise attacks and assesses the security according to the context of the potentially vulnerable slots in the SQL queries. We evaluated our technique using real-world web applications and found that our solution is efficient. Sania generated more accurate attacks and less false positives than popular web application vulnerability scanners. We also found previously unknown vulnerabilities in a commercial product that was just about to be released and in open-source web applications.

Improving Health Literacy

The Internet is increasingly used as a medium for gathering and exchanging health information exchange. Healthcare professionals and organizations need to consider barriers that may exist within their patient-oriented Web applications. One approach to making the Web more accessible for those with lower health literacy may be to supplement textual content with audio annotation using text-to-speech engines, allowing for the creation of a virtual surrogate reader. One challenge is that with numerous text-to-speech engines on the market, objective measures of quality are difficult to obtain. To facilitate comparisons of text-to-speech engines, we developed an open-source Web application that measures user reaction times, subjective quality ratings, and accuracy in completing tasks across different audio files created by text-to-speech engines. Our research endeavor was successful in building and piloting this Web application; significant differences were found for subjective ratings of quality across three text-to-speech engines priced at different levels. However, no significant differences were found with reaction times or accuracy between these text-to-speech engines. Future avenues of research include exploring more complex tasks, usability issues related to implementing text-to-speech features, and applied health promotion and education opportunities among vulnerable populations.

SLIMS—a user-friendly sample operations and inventory management system for genotyping labs

Summary: We present the Sample-based Laboratory Information Management System (SLIMS), a powerful and user-friendly open source web application that provides all members of a laboratory with an interface to view, edit and create sample information. SLIMS aims to simplify common laboratory tasks with tools such as a user-friendly shopping cart for subjects, samples and containers that easily generates reports, shareable lists and plate designs for genotyping. Further key features include customizable data views, database change-logging and dynamically filled pre-formatted reports. Along with being feature-rich, SLIMS' power comes from being able to handle longitudinal data from multiple time-points and biological sources. This type of data is increasingly common from studies searching for susceptibility genes for common complex diseases that collect thousands of samples generating millions of genotypes and overwhelming amounts of data. LIMSs provide an efficient way to deal with this data while increasing accessibility and reducing laboratory errors; however, professional LIMS are often too costly to be practical. SLIMS gives labs a feasible alternative that is easily accessible, user-centrically designed and feature-rich. To facilitate system customization, and utilization for other groups, manuals have been written for users and developers.Availability: Documentation, source code and manuals are available at http://genapha.icapture.ubc.ca/SLIMS/index.jsp. SLIMS was developed using Java 1.6.0, JSPs, Hibernate 3.3.1.GA, DB2 and mySQL, Apache Tomcat 6.0.18, NetBeans IDE 6.5, Jasper Reports 3.5.1 and JasperSoft's iReport 3.5.1.Contact: denise.daley@hli.ubc.ca

An empirical investigation into open source web applications’ implementation vulnerabilities

Current web applications have many inherent vulnerabilities; in fact, in 2008, over 63% of all documented vulnerabilities are for web applications. While many approaches have been proposed to address various web application vulnerability issues, there has not been a study to investigate whether these vulnerabilities share any common properties. In this paper, we use an approach similar to the Goal-Question-Metric approach to empirically investigate four questions regarding open source web applications vulnerabilities: What proportion of security vulnerabilities in web applications can be considered as implementation vulnerabilities? Are these vulnerabilities the result of interactions between web applications and external systems? What is the proportion of vulnerable lines of code within a web application? Are implementation vulnerabilities caused by implicit or explicit data flows? The results from the investigation show that implementation vulnerabilities dominate. They are caused through interactions between web applications and external systems. Furthermore, these vulnerabilities only contain explicit data flows, and are limited to relatively small sections of the source code.

DraGnET: Software for storing, managing and analyzing annotated draft genome sequence data

BackgroundNew "next generation" DNA sequencing technologies offer individual researchers the ability to rapidly generate large amounts of genome sequence data at dramatically reduced costs. As a result, a need has arisen for new software tools for storage, management and analysis of genome sequence data. Although bioinformatic tools are available for the analysis and management of genome sequences, limitations still remain. For example, restrictions on the submission of data and use of these tools may be imposed, thereby making them unsuitable for sequencing projects that need to remain in-house or proprietary during their initial stages. Furthermore, the availability and use of next generation sequencing in industrial, governmental and academic environments requires biologist to have access to computational support for the curation and analysis of the data generated; however, this type of support is not always immediately available.ResultsTo address these limitations, we have developed DraGnET (Draft Genome Evaluation Tool). DraGnET is an open source web application which allows researchers, with no experience in programming and database management, to setup their own in-house projects for storing, retrieving, organizing and managing annotated draft and complete genome sequence data. The software provides a web interface for the use of BLAST, allowing users to perform preliminary comparative analysis among multiple genomes. We demonstrate the utility of DraGnET for performing comparative genomics on closely related bacterial strains. Furthermore, DraGnET can be further developed to incorporate additional tools for more sophisticated analyses.ConclusionsDraGnET is designed for use either by individual researchers or as a collaborative tool available through Internet (or Intranet) deployment. For genome projects that require genome sequencing data to initially remain proprietary, DraGnET provides the means for researchers to keep their data in-house for analysis using local programs or until it is made publicly available, at which point it may be uploaded to additional analysis software applications. The DraGnET home page is available at http://www.dragnet.cvm.iastate.edu and includes example files for examining the functionalities, a link for downloading the DraGnET setup package and a link to the DraGnET source code hosted with full documentation on SourceForge.

Robust Application with RoR

This paper describes the advantages of using Ruby on Rails in commercial and enterprise class web application development. This paper also describes the power and advantages of Open source in the field of web development. Rails is an open source web application framework for the Ruby programming language which is typically integrated with database server such as MySQL and a web server such as Apache. This paper includes the overview and features of rails. Some useful rails plugins are also discussed. Keywords: database, open source, web application framework, web server.

EmPAI Calc—for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry

emPAI Calc is an open-source web application for the estimation of protein abundance. It uses the correlation between the number of identified peptides and protein abundance in mass spectrometry-based proteomic experiments. The program is the first implementation of our previously reported emPAI algorithm; it calculates the emPAI from the protein identification results obtained by database search engines such as Mascot.

ANEXdb: an integrated animal ANnotation and microarray EXpression database.

To determine annotations of the sequence elements on microarrays used for transcriptional profiling experiments in livestock species, currently researchers must either use the sparse direct annotations available for these species or create their own annotations. ANEXdb ( http://www.anexdb.org ) is an open-source web application that supports integrated access of two databases that house microarray expression (ExpressDB) and EST annotation (AnnotDB) data. The expression database currently supports storage and querying of Affymetrix-based expression data as well as retrieval of experiments in a form ready for NCBI-GEO submission; these services are available online. AnnotDB currently houses a novel assembly of approximately 1.6 million unique porcine-expressed sequence reads called the Iowa Porcine Assembly (IPA), which consists of 140,087 consensus sequences, the Iowa Tentative Consensus (ITC) sequences, and 103,888 singletons. The IPA has been annotated via transfer of information from homologs identified through sequence alignment to NCBI RefSeq. These annotated sequences have been mapped to the Affymetrix porcine array elements, providing annotation for 22,569 of the 23,937 (94%) porcine-specific probe sets, of which 19,253 (80%) are linked to an NCBI RefSeq entry. The ITC has also been mined for sequence variation, providing evidence for up to 202,383 SNPs, 62,048 deletions, and 958 insertions in porcine-expressed sequence. These results create a single location to obtain porcine annotation of and sequence variation in differently expressed genes in expression experiments, thus permitting possible identification of causal variants in such genes of interest. The ANEXdb application is open source and available from SourceForge.net.

PathBuilder--open source software for annotating and developing pathway resources.

We have developed PathBuilder, an open-source web application to annotate biological information pertaining to signaling pathways and to create web-based pathway resources. PathBuilder enables annotation of molecular events including protein-protein interactions, enzyme-substrate relationships and protein translocation events either manually or through automated importing of data from other databases. Salient features of PathBuilder include automatic validation of data formats, built-in modules for visualization of pathways, automated import of data from other pathway resources, export of data in several standard data exchange formats and an application programming interface for retrieving existing pathway datasets. PathBuilder is freely available for download at http://pathbuilder.sourceforge.net/ under the terms of GNU lesser general public license (LGPL: http://www.gnu.org/copyleft/lesser.html). The software is platform independent and has been tested on Windows and Linux platforms. pandey@jhmi.edu Supplementary data are available at Bioinformatics online.

A-MADMAN: Annotation-based microarray data meta-analysis tool

BackgroundPublicly available datasets of microarray gene expression signals represent an unprecedented opportunity for extracting genomic relevant information and validating biological hypotheses. However, the exploitation of this exceptionally rich mine of information is still hampered by the lack of appropriate computational tools, able to overcome the critical issues raised by meta-analysis.ResultsThis work presents A-MADMAN, an open source web application which allows the retrieval, annotation, organization and meta-analysis of gene expression datasets obtained from Gene Expression Omnibus. A-MADMAN addresses and resolves several open issues in the meta-analysis of gene expression data.ConclusionA-MADMAN allows i) the batch retrieval from Gene Expression Omnibus and the local organization of raw data files and of any related meta-information, ii) the re-annotation of samples to fix incomplete, or otherwise inadequate, metadata and to create user-defined batches of data, iii) the integrative analysis of data obtained from different Affymetrix platforms through custom chip definition files and meta-normalization. Software and documentation are available on-line at .

Activity Theory as a theoretical framework for the study of blended learning

Over the past decade we have witnessed the growing popularity of blended learning which provides opportunities to facilitate communication and collaboration, foster reflective thinking and promote discursive approaches to knowledge. However, the history of Educational Technology demonstrates that the opportunities afforded by technologies are not necessarily opportunities taken. E-learning does not appear to be an exception to this rule. Should the traditional pedagogical practices be adopted in e-learning then the conventional transmissionist practices are likely to replicated online, failing to support more active forms of learning. Novel pedagogical practices, activities, and tasks are required to make e-learning more effective. However, these novel approaches require a theoretical framework which will enable the systematic study of technological innovation. In this paper we employ Activity Theory (AT) as a theoretical tool for the study of blended learning. Activity Theory enables the study of tensions resulting from an innovation in an activity system such as a university course, allowing us to focus on what works and what does not work in an innovation. The data reported in this paper are derived from an ongoing design research project which focuses on how a Learning Management System (LMS) can be best integrated into conventional tertiary education practices. More specifically, the present study aims to (a) describe the patterns of use of online resources by undergraduate students and (b) explain those patterns through the use of AT. 22 students who attended an elective undergraduate course on participated in the study. Moodle, a free and open source web application, was used as the LMS which hosted the course. Three types of online resources were included: (a) course materials (lecture notes, papers, web links), (b) course assignments (instructions, examples, sample scripts, videotutorials), and (c) forum (for course news, questions, discussions and other activities). Data sources included surveys, group interviews, web server log files and field notes. Firstly, students completed an online questionnaire measuring their former ICT experience and attitudes towards ICT. Secondly, short semi-structured group interviews were conducted. Finally, the use of online resources was examined by looking at the log files which were recorded by Moodle. Information regarding the use of online resources was extracted from the server log files. This information was then combined with group interviews and other field notes to determine the students' perspective what on facilitated or hindered the use of the LMS. The analysis of the log files indicated only 1266 resource related views by all students while about one fifth of the online resources provided were not viewed at all. The analysis clearly suggested a pattern of minimal use: even though ample opportunities were offered in terms of online resources students have not taken these opportunities to enhance their learning. The analysis of the interviews suggested that four major tensions emerged from blended learning: within the object, the mediational means, the rules, and the division of labor. The implications of these tensions for blended learning are discussed. It turned out that students made minimal use of the LMS, treating it mostly as an online repository of materials which were required for passing the course. This minimal use clearly suggests low blended learning utilization and an overall “course survival strategy”. The paper is concluded with a discussion of the contribution that Activity Theory made to understanding the patterns of use of online resources by the students.

Replacing Proprietary Software on the Desktop

Open standards, open source software, and Web applications are causing a major shift in the way enterprises manage software. Whereas companies have traditionally been tied to a particular vendor and upgraded their software only when new versions became available, they are increasingly able to change software stacks with less fear of disruption due to incompatibilities or contractual hindrances. More businesses also have the choice of using Web applications that require only a browser instead of using software maintained on local PCs. Open source software and Web applications can be a cost-effective alternative for businesses. As enterprises become more familiar with the benefits that the open community approach and Internet computing offer, open source software and Web applications replace conventional software. The best strategy for our company depends on our particular circumstances

CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data

CoCo, ChIP-on-Chip online, is an open-source web application that supports the annotation and curation of regulatory regions and associated target genes discovered in ChIP-on-chip experiments. CoCo integrates ChIP-on-chip results with diverse types of gene expression data (expression profiling, in situ hybridization) and displays them within a genomic context. Regulatory relationships between the transcription factor-bound regions and putative target genes can be stored and expanded throughout different sessions. http://furlonglab.embl.de/methods/tools/coco.

CPath: open source software for collecting, storing, and querying biological pathways

BackgroundBiological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required.ResultsWe have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use.ConclusioncPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling.