scholarly journals Agnotology: learning from mistakes

2013 ◽  
Vol 4 (1) ◽  
pp. 451-505 ◽  
Author(s):  
R. E. Benestad ◽  
H. O. Hygen ◽  
R. van Dorland ◽  
J. Cook ◽  
D. Nuccitelli
Keyword(s):  
Open Source ◽  
Case Studies ◽  
Statistical Methods ◽  
Open Source Software ◽  
Scientific Literature ◽  
Set Up ◽  
Analytical Approaches

Abstract. Replication is an important part of science, and by repeating past analyses, we show that a number of papers in the scientific literature contain severe methodological flaws which can easily be identified through simple tests and demonstrations. In many cases, shortcomings are related to a lack of robustness, leading to results that are not universally valid but rather an artifact of a particular experimental set-up. Some examples presented here have ignored data that do not fit the conclusions, and in several other cases, inappropriate statistical methods have been adopted or conclusions have been based on misconceived physics. These papers may serve as educational case studies for why certain analytical approaches sometimes are unsuitable in providing reliable answers. They also highlight the merit of replication. A lack of common replication has repercussions for the quality of the scientific literature, and may be a reason why some controversial questions remain unanswered even when ignorance could be reduced. Agnotology is the study of such ignorance. A free and open-source software is provided for demonstration purposes.

scholarly journals Internal Quality Evolution of Open-Source Software Systems

2021 ◽  
Vol 11 (12) ◽  
pp. 5690
Author(s):  
Mamdouh Alenezi
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Software Evolution ◽  
Quality Metrics ◽  
Internal Quality ◽  
Software Systems ◽  
Software Metric ◽  
Significant Difference ◽  
The Relationship

The evolution of software is necessary for the success of software systems. Studying the evolution of software and understanding it is a vocal topic of study in software engineering. One of the primary concepts of software evolution is that the internal quality of a software system declines when it evolves. In this paper, the method of evolution of the internal quality of object-oriented open-source software systems has been examined by applying a software metric approach. More specifically, we analyze how software systems evolve over versions regarding size and the relationship between size and different internal quality metrics. The results and observations of this research include: (i) there is a significant difference between different systems concerning the LOC variable (ii) there is a significant correlation between all pairwise comparisons of internal quality metrics, and (iii) the effect of complexity and inheritance on the LOC was positive and significant, while the effect of Coupling and Cohesion was not significant.

scholarly journals Knowledge sharing in open source software communities: motivations and management

2015 ◽  
Vol 19 (4) ◽  
pp. 791-813 ◽  
Author(s):  
Zilia Iskoujina ◽  
Joanne Roberts
Keyword(s):  
Knowledge Sharing ◽  
Open Source ◽  
Open Source Software ◽  
Online Communities ◽  
Descriptive Analysis ◽  
Online Questionnaire ◽  
Content Type ◽  
The Individual ◽  
The Impact

Purpose – This paper aims to add to the understanding of knowledge sharing in online communities through an investigation of the relationship between individual participant’s motivations and management in open source software (OSS) communities. Drawing on a review of literature concerning knowledge sharing in organisations, the factors that motivate participants to share their knowledge in OSS communities, and the management of such communities, it is hypothesised that the quality of management influences the extent to which the motivations of members actually result in knowledge sharing. Design/methodology/approach – To test the hypothesis, quantitative data were collected through an online questionnaire survey of OSS web developers with the aim of gathering respondents’ opinions concerning knowledge sharing, motivations to share knowledge and satisfaction with the management of OSS projects. Factor analysis, descriptive analysis, correlation analysis and regression analysis were used to explore the survey data. Findings – The analysis of the data reveals that the individual participant’s satisfaction with the management of an OSS project is an important factor influencing the extent of their personal contribution to a community. Originality/value – Little attention has been devoted to understanding the impact of management in OSS communities. Focused on OSS developers specialising in web development, the findings of this paper offer an important original contribution to understanding the connections between individual members’ satisfaction with management and their motivations to contribute to an OSS project. The findings reveal that motivations to share knowledge in online communities are influenced by the quality of management. Consequently, the findings suggest that appropriate management can enhance knowledge sharing in OSS projects and online communities, and organisations more generally.

scholarly journals Macedonian Journal of Chemistry and Chemical Engineering: Open Journal Systems - Editor's Perspective

PRILOZI ◽  
2014 ◽  
Vol 35 (3) ◽  
pp. 51-55
Author(s):  
Zoran Zdravkovski
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Chemical Engineering ◽  
Profound Change ◽  
Online Submission ◽  
Limited Support ◽  
Computer Knowledge ◽  
Set Up ◽  
Printing Techniques ◽  
Open Journal Systems

AbstractThe development and availability of personal computers and software as well as printing techniques in the last twenty years have made a profound change in the publication of scientific journals. Additionally, the Internet in the last decade has revolutionized the publication process to the point of changing the basic paradigm of printed journals. The Macedonian Journal of Chemistry and Chemical Engineering in its 40-year history has adopted and adapted to all these transformations. In order to keep up with the inevitable changes, as editor-in-chief I felt my responsibility was to introduce an electronic editorial managing of the journal. The choice was between commercial and open source platforms, and because of the limited funding of the journal we chose the latter. We decided on Open Journal Systems, which provided online submission and management of all content, had flexible configuration - requirements, sections, review process, etc., had options for comprehensive indexing, offered various reading tools, had email notification and commenting ability for readers, had an option for thesis abstracts and was installed locally. However, since there is limited support it requires a moderate computer knowledge/skills and effort in order to set up. Overall, it is an excellent editorial platform and a convenient solution for journals with a low budget or journals that do not want to spend their resources on commercial platforms or simply support the idea of open source software.

Conquery: an Open Source Application to analyze High Content Healthcare Data (Preprint)

2021 ◽  
Author(s):  
Fabian Kovacs ◽  
Max Thonagel ◽  
Marion Ludwig ◽  
Alexander Albrecht ◽  
Manuel Hegner ◽  
...  
Keyword(s):  
Decision Making ◽  
Big Data ◽  
Data Analysis ◽  
Open Source ◽  
Open Source Software ◽  
Medical Records ◽  
Healthcare Sector ◽  
Study Cohort ◽  
Decision Making Processes ◽  
Analytical Approaches

BACKGROUND Big data in healthcare must be exploited to achieve a substantial increase in efficiency and competitiveness. Especially the analysis of patient-related data possesses huge potential to improve decision-making processes. However, most analytical approaches used today are highly time- and resource-consuming. OBJECTIVE The presented software solution Conquery is an open-source software tool providing advanced, but intuitive data analysis without the need for specialized statistical training. Conquery aims to simplify big data analysis for novice database users in the medical sector. METHODS Conquery is a document-oriented distributed timeseries database and analysis platform. Its main application is the analysis of per-person medical records by non-technical medical professionals. Complex analyses are realized in the Conquery frontend by dragging tree nodes into the query editor. Queries are evaluated by a bespoke distributed query-engine for medical records in a column-oriented fashion. We present a custom compression scheme to facilitate low response times that uses online calculated as well as precomputed metadata and data statistics. RESULTS Conquery allows for easy navigation through the hierarchy and enables complex study cohort construction whilst reducing the demand on time and resources. The UI of Conquery and a query output is exemplified by the construction of a relevant clinical cohort. CONCLUSIONS Conquery is an efficient and intuitive open-source software for performant and secure data analysis and aims at supporting decision-making processes in the healthcare sector.

Model to Estimate the Human Factor Quality in FLOSS Development

2015 ◽  
pp. 219-236
Author(s):  
Zulaima Chiquin ◽  
Kenyer Domínguez ◽  
Luis E. Mendoza ◽  
Edumilis Méndez
Keyword(s):  
Decision Making ◽  
Human Resources ◽  
Open Source ◽  
Open Source Software ◽  
Human Factor ◽  
Three Dimensions ◽  
Decision Making Process ◽  
Self Evaluation ◽  
Systemic Quality

This chapter presents a Model to Estimate the Human Factor Quality in Free/Libre Open Source Software (FLOSS) Development, or EHFQ-FLOSS. The model consists of three dimensions: Levels (individual, community, and foundation), Aspects (internal or contextual), and Forms of Evaluation (self-evaluation, co-evaluation, and hetero-evaluation). Furthermore, this model provides 145 metrics applicable to all three levels, as well as an algorithm that guides their proper application to estimate the systemic quality of human resources involved in the development of FLOSS, guide the decision-making process, and take possible corrective actions.

Open for Social

2011 ◽  
pp. 187-202
Author(s):  
James M. Laffey ◽  
Matthew Schmidt ◽  
Christopher J. Amelung
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Collaborative Work ◽  
Notification System ◽  
Education Experience ◽  
Social Nature ◽  
Narrow Framing ◽  
E Learning ◽  
K 12

Online learning in K-12 and higher education has been growing rapidly, and open source software has the potential to improve the quality of e-learning. This paper describes how FOSS enables turning e-learning from a potentially restrictive and narrow framing of the education experience to an emergent and social experience. The authors identify several key elements of the FOSS model that position open source initiatives to contribute to the emergent and social nature of experience in e-learning. The authors also describe several challenges to developing FOSS in a community of educators for e-learning. These elements and challenges are illustrated in a brief case report about the development of an open source software system called Context-aware Activity Notification System (CANS). CANS (http://cansaware.com) is a notification system that integrates with collaborative work and learning systems and is designed around the importance of awareness of user activity, a user’s social context and personal notification preferences.

Open Source Software Communities

2011 ◽  
pp. 363-367
Author(s):  
Kevin Carillo ◽  
Chitu Okoli
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Development Model ◽  
The People ◽  
Develop Software ◽  
Working Together ◽  
Software Development Model ◽  
Key Aspects ◽  
Open Source Communities

Open source software (OSS) development has continued to appear as a puzzling and enigmatic phenomenon and has drawn increasing attention as its importance has grown. Relying upon an alternative way to develop and to distribute software, open source communities have been able to challenge and often outperform proprietary software by enabling better reliability, lower costs, shorter development times, and a higher quality of code (Raymond, 2004). Behind the software is a mass of people working together in loose coordination, even portrayed as a rowdy marketplace (Raymond, 2001, p. 1): No quiet, reverent cathedral-building here—rather, the Linux community seemed to resemble a great babbling bazaar of differing agendas and approaches … out of which a coherent and stable system seemingly emerges only by a succession of miracles. More precisely, the people behind open source projects have been defined as: “Internet-based communities of software developers who voluntarily collaborate in order to develop software that they or their organizations need” (von Krogh, 2003, p. 14). In contrast to the sacred cathedral-like software development model that gave birth to most commercial and proprietary systems, such bazaar-like communities seem to have based their success on a pseudo-anarchic type of collaboration and developers’ interaction (Raymond, 2001). However, in spite of the apparent disorganization of these bazaars, a closer look distinguishes common values and norms that rule them, specific roles that can be identified, similar motives shared by people, and practices that follow patterns. This article highlights key aspects of what forms the communities that support these projects.

Evolution Impact on Architecture Stability in Open-Source Projects

2015 ◽  
Vol 5 (4) ◽  
pp. 24-35 ◽  
Author(s):  
Mamdouh Alenezi ◽  
Fakhry Khellah
Keyword(s):  
Software Architecture ◽  
Open Source ◽  
Open Source Software ◽  
Quality Standard ◽  
Management Style ◽  
Efficient Technique ◽  
Maintenance Cost ◽  
Software Systems ◽  
Architecture Evolution

Software systems usually evolve constantly, which requires constant development and maintenance. Subsequently, the architecture of these systems tends to degrade with time. Therefore, stability is a key measure for evaluating an architecture. Open-source software systems are becoming progressively vital these days. Since open-source software systems are usually developed in a different management style, the quality of their architectures needs to be studied. ISO/IEC SQuaRe quality standard characterized stability as one of the sub-characteristics of maintainability. Unstable software architecture could cause the software to require high maintenance cost and effort. In this work, the authors propose a simple, yet efficient, technique that is based on carefully aggregating the package level stability in order to measure the change in the architecture level stability as the architecture evolution happens. The proposed method can be used to further study the cause behind the positive or negative architecture stability changes.

scholarly journals A Case Report of Switching from Specific Vendor-Based to R-Based Pipelines for Untargeted LC-MS Metabolomics

Metabolites ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 28 ◽  
Author(s):  
Álvaro Fernández-Ochoa ◽  
Rosa Quirantes-Piné ◽  
Isabel Borrás-Linares ◽  
María de la Luz Cádiz-Gurrea ◽  
Marta E. Alarcón Riquelme ◽  
...  
Keyword(s):  
Case Report ◽  
Data Quality ◽  
Open Source ◽  
Open Source Software ◽  
Ease Of Use ◽  
Plasma Samples ◽  
Batch Effects ◽  
Multivariate Models ◽  
Metabolomic Study

Data pre-processing of the LC-MS data is a critical step in untargeted metabolomics studies in order to achieve correct biological interpretations. Several tools have been developed for pre-processing, and these can be classified into either commercial or open source software. This case report aims to compare two specific methodologies, Agilent Profinder vs. R pipeline, for a metabolomic study with a large number of samples. Specifically, 369 plasma samples were analyzed by HPLC-ESI-QTOF-MS. The collected data were pre-processed by both methodologies and later evaluated by several parameters (number of peaks, degree of missingness, quality of the peaks, degree of misalignments, and robustness in multivariate models). The vendor software was characterized by ease of use, friendly interface and good quality of the graphs. The open source methodology could more effectively correct the drifts due to between and within batch effects. In addition, the evaluated statistical methods achieved better classification results with higher parsimony for the open source methodology, indicating higher data quality. Although both methodologies have strengths and weaknesses, the open source methodology seems to be more appropriate for studies with a large number of samples mainly due to its higher capacity and versatility that allows combining different packages, functions, and methods in a single environment.

Virtual Reconstruction as Archaeological Observation: Embracing New Ways of Treating Sites, Places and Landscapes

2019 ◽  
Vol 7 (2) ◽  
pp. 127-139 ◽  
Author(s):  
Matthew J. Douglass ◽  
Zachary R. Day ◽  
Jeremy C. Brunette ◽  
Peter Bleed ◽  
Douglas Scott
Keyword(s):  
Open Source ◽  
Case Studies ◽  
Open Source Software ◽  
The Other ◽  
Digital Tools ◽  
Archaeological Heritage ◽  
Common Heritage ◽  
Online Tutorials ◽  
Virtual Reconstruction ◽  
Southern Oklahoma

AbstractVirtual Reconstruction is a powerful tool broadly suited to a diverse array of archaeological heritage applications. In practice, however, reconstruction has largely focused on grand and monumental sites. Here we present two case studies–one from southern Oklahoma, the other from western Nebraska–to explore the use of this technology for more common heritage applications. The goal of this article is to advertise the dilemma we faced with communicating information on ephemeral sites and how we, as nonspecialists, solved the issue using affordable and accessible digital tools. Our workflow makes use of common tools (GIS) and open source software and online tutorials provide step by step instruction to support its replication. In presenting our experiences and the results of these efforts, we hope to spur similar applications in the use of Virtual Reconstruction to communicate information on archaeological heritage more broadly.

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