scholarly journals ggVennDiagram: An Intuitive, Easy-to-Use, and Highly Customizable R Package to Generate Venn Diagram

2021 ◽  
Vol 12 ◽  
Author(s):  
Chun-Hui Gao ◽  
Guangchuang Yu ◽  
Peng Cai
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Source Code ◽  
R Package ◽  
Venn Diagram ◽  
Free Access ◽  
High Quality ◽  
Venn Diagrams ◽  
Label Edge ◽  
The Cost

Venn diagrams are widely used diagrams to show the set relationships in biomedical studies. In this study, we developed ggVennDiagram, an R package that could automatically generate high-quality Venn diagrams with two to seven sets. The ggVennDiagram is built based on ggplot2, and it integrates the advantages of existing packages, such as venn, RVenn, VennDiagram, and sf. Satisfactory results can be obtained with minimal configurations. Furthermore, we designed comprehensive objects to store the entire data of the Venn diagram, which allowed free access to both intersection values and Venn plot sub-elements, such as set label/edge and region label/filling. Therefore, high customization of every Venn plot sub-element can be fulfilled without increasing the cost of learning when the user is familiar with ggplot2 methods. To date, ggVennDiagram has been cited in more than 10 publications, and its source code repository has been starred by more than 140 GitHub users, suggesting a great potential in applications. The package is an open-source software released under the GPL-3 license, and it is freely available through CRAN (https://cran.r-project.org/package=ggVennDiagram).

scholarly journals Open Plot Project: an open-source toolkit for 3-D structural data analysis

Solid Earth ◽  
2011 ◽  
Vol 2 (1) ◽  
pp. 53-63 ◽  
Author(s):  
S. Tavani ◽  
P. Arbues ◽  
M. Snidero ◽  
N. Carrera ◽  
J. A. Muñoz
Keyword(s):  
Spatial Distribution ◽  
Data Analysis ◽  
Open Source ◽  
Open Source Software ◽  
Source Code ◽  
Structural Data ◽  
Geological Modelling ◽  
Analysis Tools ◽  
Transect Analysis ◽  
Selection Of

Abstract. In this work we present the Open Plot Project, an open-source software for structural data analysis, including a 3-D environment. The software includes many classical functionalities of structural data analysis tools, like stereoplot, contouring, tensorial regression, scatterplots, histograms and transect analysis. In addition, efficient filtering tools are present allowing the selection of data according to their attributes, including spatial distribution and orientation. This first alpha release represents a stand-alone toolkit for structural data analysis. The presence of a 3-D environment with digitalising tools allows the integration of structural data with information extracted from georeferenced images to produce structurally validated dip domains. This, coupled with many import/export facilities, allows easy incorporation of structural analyses in workflows for 3-D geological modelling. Accordingly, Open Plot Project also candidates as a structural add-on for 3-D geological modelling software. The software (for both Windows and Linux O.S.), the User Manual, a set of example movies (complementary to the User Manual), and the source code are provided as Supplement. We intend the publication of the source code to set the foundation for free, public software that, hopefully, the structural geologists' community will use, modify, and implement. The creation of additional public controls/tools is strongly encouraged.

Open source software as a mature library system in Armenia

Infolib ◽  
2021 ◽  
Vol 26 (2) ◽  
pp. 34-37
Author(s):  
Anna Chulyan ◽  
Keyword(s):  
Cultural Heritage ◽  
Open Source ◽  
Open Source Software ◽  
New Technologies ◽  
Digital Preservation ◽  
Free Access ◽  
Efficient Organization ◽  
Digital Repositories ◽  
High Level

The article touches upon the importance of long-term digital preservation of Armenian cultural heritage through creation of digital repositories using Open-Source Software in Armenian libraries. The research highlights the advantages of Open-Source Software in context of providing free access to digital materials, as well as its high level of functionality in order to empower libraries with new technologies for more efficient organization and dissemination of information.

An open-source R-package and web application for high-quality probabilistic predictions in hydrology

2021 ◽  
Author(s):  
Jason Hunter ◽  
Mark Thyer ◽  
Dmitri Kavetski ◽  
David McInerney
Keyword(s):  
Open Source ◽  
Web Application ◽  
R Package ◽  
Error Model ◽  
Objective Functions ◽  
High Quality ◽  
Wide Range ◽  
Probabilistic Error

<p>Probabilistic predictions provide crucial information regarding the uncertainty of hydrological predictions, which are a key input for risk-based decision-making. However, they are often excluded from hydrological modelling applications because suitable probabilistic error models can be both challenging to construct and interpret, and the quality of results are often reliant on the objective function used to calibrate the hydrological model.</p><p>We present an open-source R-package and an online web application that achieves the following two aims. Firstly, these resources are easy-to-use and accessible, so that users need not have specialised knowledge in probabilistic modelling to apply them. Secondly, the probabilistic error model that we describe provides high-quality probabilistic predictions for a wide range of commonly-used hydrological objective functions, which it is only able to do by including a new innovation that resolves a long-standing issue relating to model assumptions that previously prevented this broad application.  </p><p>We demonstrate our methods by comparing our new probabilistic error model with an existing reference error model in an empirical case study that uses 54 perennial Australian catchments, the hydrological model GR4J, 8 common objective functions and 4 performance metrics (reliability, precision, volumetric bias and errors in the flow duration curve). The existing reference error model introduces additional flow dependencies into the residual error structure when it is used with most of the study objective functions, which in turn leads to poor-quality probabilistic predictions. In contrast, the new probabilistic error model achieves high-quality probabilistic predictions for all objective functions used in this case study.</p><p>The new probabilistic error model and the open-source software and web application aims to facilitate the adoption of probabilistic predictions in the hydrological modelling community, and to improve the quality of predictions and decisions that are made using those predictions. In particular, our methods can be used to achieve high-quality probabilistic predictions from hydrological models that are calibrated with a wide range of common objective functions.</p>

scholarly journals fullsibQTL: an R package for QTL mapping in biparental populations of outcrossing species

2020 ◽  
Author(s):  
Rodrigo Gazaffi ◽  
Rodrigo R. Amadeu ◽  
Marcelo Mollinari ◽  
João R. B. F. Rosa ◽  
Cristiane H. Taniguti ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Open Source ◽  
Qtl Analysis ◽  
Source Code ◽  
R Package ◽  
Genetic Maps ◽  
Linkage Phase ◽  
Position Effects ◽  
Genetic Features ◽  
Outcrossing Species

ABSTRACTAccurate QTL mapping in outcrossing species requires software programs which consider genetic features of these populations, such as markers with different segregation patterns and different level of information. Although the available mapping procedures to date allow inferring QTL position and effects, they are mostly not based on multilocus genetic maps. Having a QTL analysis based in such maps is crucial since they allow informative markers to propagate their information to less informative intervals of the map. We developed fullsibQTL, a novel and freely available R package to perform composite interval QTL mapping considering outcrossing populations and markers with different segregation patterns. It allows to estimate QTL position, effects, segregation patterns, and linkage phase with flanking markers. Additionally, several statistical and graphical tools are implemented, for straightforward analysis and interpretations. fullsibQTL is an R open source package with C and R source code (GPLv3). It is multiplatform and can be installed from https://github.com/augusto-garcia/fullsibQTL.

Review of Open Source Software (OSS)

2012 ◽  
pp. 26-40
Author(s):  
Bhasker Mukerji ◽  
Ramaraj Palanisamy
Keyword(s):  
Developing Countries ◽  
Public Sector ◽  
Open Source ◽  
Open Source Software ◽  
Low Cost ◽  
Source Code ◽  
Developed Countries ◽  
Economic Resources ◽  
Large Pool ◽  
Public Sector Organizations

The popularity of Open Source Software (OSS) in developing countries is quiet evident from its widespread adoption across government departments and public sector organizations. The use of OSS saves economic resources of cash starved countries, provides an opportunity to promote e-government, and to utilize their resources in other sectors. Many developing countries have a large pool of skilled developers who can modify the source code of the OSS at a very low cost. Many governments in developing and developed countries have switched to OSS which probably encourages others to follow the trend. It was not possible to follow the adoption trend in all the developing countries but the usage of OSS in countries like India, Brazil, and Venezuela provides us an insight. The successful adoption of OSS requires thorough analysis of its advantages as well as the issues associated with it. This chapter will provide an overview of OSS, characteristics of OSS developers, and their motivation to volunteer by contributing in OSS projects, followed by the advantages and issues associated with OSS.

Key Concepts and Definitions of Open Source Communities

2010 ◽  
pp. 753-760
Author(s):  
Ruben van Wendel de Joode ◽  
Sebastian Spaeth
Keyword(s):  
Software Development ◽  
Open Source ◽  
Open Source Software ◽  
Online Communities ◽  
Source Code ◽  
Professional Organizations ◽  
Large Numbers ◽  
Key Concepts ◽  
Open Source Communities ◽  
Do So

Most open source software is developed in online communities. These communities are typically referred to as “open source software communities” or “OSS communities.” In OSS communities, the source code, which is the human-readable part of software, is treated as something that is open and that should be downloadable and modifiable to anyone who wishes to do so. The availability of the source code has enabled a practice of decentralized software development in which large numbers of people contribute time and effort. Communities like Linux and Apache, for instance, have been able to connect thousands of individual programmers and professional organizations (although most project communities remain relatively small). These people and organizations are not confined to certain geographical places; on the contrary, they come from literally all continents and they interact and collaborate virtually.

Open Source Web Portals

2012 ◽  
Vol 4 (4) ◽  
pp. 16-32
Author(s):  
Vanessa P. Braganholo ◽  
Bernardo Miranda ◽  
Marta Mattoso
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Source Code ◽  
Web Portals ◽  
Web Portal ◽  
Easy Task ◽  
User Community

Open source software is required to be widely available to the user community. To help developers fulfill this requirement, Web portals provide a way to make open source projects public so that the user community has access to their source code, can contribute to their development, and can interact with the developer team. However, choosing a Web portal is not an easy task. There are several options available, each of them offering a set of tools and features to its users. The goal of this article is to analyze a set of existing Web portals (SourceForge.net, Apache, Tigris, ObjectWeb, and Savannah) in the hopes that this will help users to choose a hosting site for their projects.

Open Source in Government

2011 ◽  
pp. 1287-1290 ◽  
Author(s):  
D. Berry
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
General Public ◽  
Source Code ◽  
Computer Software ◽  
Free Software ◽  
Software Projects ◽  
Software Companies ◽  
Develop Software ◽  
Software Distribution

Open source software (OSS) is computer software that has its underlying source code made available under a licence. This can allow developers and users to adapt and improve it (Raymond, 2001). Computer software can be broadly split into two development models: • Proprietary, or closed software, owned by a company or individual. Copies of the binary are made public; the source code is not usually made public. • Open-source software (OSS), where the source code is released with the binary. Users and developers can be licenced to use and modify the code, and to distribute any improvements they make. Both OSS and proprietary approaches allow companies to make a profit. Companies developing proprietary software make money by developing software and then selling licences to use the software. For example, Microsoft receives a payment for every copy of Windows sold with a personal computer. OSS companies make their money by providing services, such as advising clients on the GPL licence. The licencee can either charge a fee for this service or work free of charge. In practice, software companies often develop both types of software. OSS is developed by an ongoing, iterative process where people share the ideas expressed in the source code. The aim is that a large community of developers and users can contribute to the development of the code, check it for errors and bugs, and make the improved version available to others. Project management software is used to allow developers to keep track of the various versions. There are two main types of open-source licences (although there are many variants and subtypes developed by other companies): • Berkeley Software Distribution (BSD) Licence: This permits a licencee to “close” a version (by withholding the most recent modifications to the source code) and sell it as a proprietary product; • GNU General Public Licence (GNU, GPL, or GPL): Under this licence, licencees may not “close” versions. The licencee may modify, copy, and redistribute any derivative version, under the same GPL licence. The licencee can either charge a fee for this service or work free of charge. Free software first evolved during the 1970s but in the 1990s forked into two movements, namely free software and open source (Berry, 2004). Richard Stallman, an American software developer who believes that sharing source code and ideas is fundamental to freedom of speech, developed a free version of the widely used Unix operating system. The resulting GNU program was released under a specially created General Public Licence (GNU, GPL). This was designed to ensure that the source code would remain openly available to all. It was not intended to prevent commercial usage or distribution (Stallman, 2002). This approach was christened free software. In this context, free meant that anyone could modify the software. However, the term “free” was often misunderstood to mean no cost. Hence, during the 1990s, Eric Raymond and others proposed that open-source software was coined as a less contentious and more business-friendly term. This has become widely accepted within the software and business communities; however there are still arguments about the most appropriate term to use (Moody, 2002). The OSMs are usually organised into a network of individuals who work collaboratively on the Internet, developing major software projects that sometimes rival commercial software but are always committed to the production of quality alternatives to those produced by commercial companies (Raymond, 2001; Williams, 2002). Groups and individuals develop software to meet their own and others’ needs in a highly decentralised way, likened to a Bazaar (Raymond, 2001). These groups often make substantive value claims to support their projects and foster an ethic of community, collaboration, deliberation, and intellectual freedom. In addition, it is argued by Lessig (1999) that the FLOSS community can offer an inspiration in their commitment to transparency in their products and their ability to open up governmental regulation and control through free/libre and open source code.

Free Access to Law and Open Source Software

2011 ◽  
pp. 373-381
Author(s):  
Daniel Poulin ◽  
Andrew Mowbray
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Free Access ◽  
Scholarly Writing ◽  
Legal Information ◽  
Judicial Decisions ◽  
International Projects ◽  
Primary Materials ◽  
Preparatory Work ◽  
Common Vision

Law consists of legislation, judicial decisions, and interpretative material. Public legal information means legal information produced by public bodies that have a duty to produce law and make it public. Such information includes the law itself (so-called primary materials) as well as various secondary (interpretative) public sources such as reports on preparatory work and law reform and resulting from boards of inquiry and available scholarly writing. The free access to law movement is a set of international projects that share a common vision to promote and facilitate open access to public legal information. The objectives of this chapter are to outline the free access to law movement, to set out the philosophies and principles behind this, and to discuss the role that open source software has played both in terms of its use and development.

scholarly journals Open Source Paradigm: A Synopsis of The Cathedral and the Bazaar for Health and Social Care

2016 ◽  
Vol 23 (2) ◽  
pp. 488
Author(s):  
Tim Benson
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Social Care ◽  
Source Code ◽  
Comprehensive Description ◽  
The Third ◽  
It Impacts ◽  
Health And Social Care ◽  
Software Engineers ◽  
Closed Source

Background: Open source software (OSS) is becoming more fashionable in health and social care, although the ideas are not new. However progress has been slower than many had expected.Objective: The purpose is to summarise the Free/Libre Open Source Software (FLOSS) paradigm in terms of what it is, how it impacts users and software engineers and how it can work as a business model in health and social care sectors.Method: Much of this paper is a synopsis of Eric Raymond’s seminal book The Cathedral and the Bazaar, which was the first comprehensive description of the open source ecosystem, set out in three long essays. Direct quotes from the book are used liberally, without reference to specific passages. The first part contrasts open and closed source approaches to software development and support. The second part describes the culture and practices of the open source movement. The third part considers business models.Conclusion: A key benefit of open source is that users can access and collaborate on improving the software if they wish. Closed source code may be regarded as a strategic business risk that that may be unacceptable if there is an open source alternative. The sharing culture of the open source movement fits well with that of health and social care.

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