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.

scholarly journals Vascular flow simulations using SimVascular and OpenFOAM

2021 ◽  
Author(s):  
Swetha Yogeswaran ◽  
Fei Liu
Keyword(s):  
Fluid Dynamics ◽  
Blood Flow ◽  
Open Source ◽  
Open Source Software ◽  
Flow Analysis ◽  
Coarctation Of The Aorta ◽  
Patient Specific ◽  
Specific Information ◽  
Imaging Data ◽  
Set Up

AbstractApplications of computational fluid dynamics (CFD) techniques to aid in the diagnosis and treatment of cardiovascular disease have entered the research domain in recent years, due to their ability to provide valuable patient-specific information without risks associated with highly invasive procedures. SimVascular [1] [2] is an open-source software which allows streamlined processing and CFD blood flow analysis of medical imaging data. OpenFOAM [3] is a proven open-source software which allows for versatile modeling of various fluid dynamics phenomena. In this study, both SimVascular and OpenFOAM simulations are set up with identical computational mesh, similar numerical schemes, boundary conditions, and material properties, to model blood flow in the coronary artery of a 10 year old patient with Coarctation of the Aorta (CoA) who underwent end-to-side anastomosis. Difference in the flow fields such as flow rate, pressure, vorticity, and wall shear stress between SimVascular and OpenFOAM are analyzed. Similar results are obtained in both simulations up to a certain model time, before the results become drastically different. Both the similarities and differences are documented and discussed.

scholarly journals Protecting the Informational Commons using a Blockchain-based Technology: The case of Free/Libre Open Source Software and Public Biobanks (Preprint)

2019 ◽  
Author(s):  
Nikolaos Evangelatos ◽  
Sudhakara Upadya ◽  
Julien Venne ◽  
Kapaettu Satyamoorthy ◽  
Helmut Brand ◽  
...  
Keyword(s):  
Political Economy ◽  
Open Source ◽  
Open Source Software ◽  
Physical Reality ◽  
Free Riding ◽  
Digital Networks ◽  
Economic Activities ◽  
Common Resources ◽  
Digital Era ◽  
Set Up

BACKGROUND Digitalization leads to a re-institutionalization of research and economic activities, where informational common resources play an ever-increasing role in economic growth. Especially in the case of the biological sciences and the bioeconomy, informational commons arrangements, such as public biobanks and free/libre open source software (FLOSS), are of paramount importance. However, it has been argued that such arrangements are vulnerable to violations such as the free-riding problem that renders them unsustainable. Consequently, it has been argued, the enclosure of the informational common resources is the only means to effectively exploit them. OBJECTIVE Given the social and economic importance of the informational commons, the new digital environment requires a regulation of their social embedment that will guarantee their protection from both violations and enclosures, i.e., a new political economy is needed. In this context, the need for a core common infrastructure, stretching from the physical to the logical and content layer of the information environment, has been highlighted. METHODS Focusing on the interaction between two biological commons, namely public biobanks and the free/libre open source software, we have set up an ecosystem using a blockchain-based technology. The proposed ecosystem consists of four components: the FLOSS (library), the applications that use FLOSS, the biobanks that have the data requested from the applications and the source validators. The latter act as the computing nodes of the blockchain: they keep track of the different versions of the FLOSS maintained by the various applications, and provide the validation check on whether the version of the FLOSS used by an application is registered with the ecosystem. Prior to gain access to the data, the application needs to get the version identifier key of the library it is using. RESULTS The proposed regulatory mechanism protects the informational commons from the free-riding problem and guarantees their sustainability without hampering their operational framework. Our model demonstrates the interdependence and protection of the informational commons not as an abstracted theoretical exercise, but rather as a physical reality on the ontological matrix. CONCLUSIONS Blockchain-based technologies can be used in cases where informational commons interact with each other over digital networks, protecting them from the free-riding problem and securing their sustainability. In this sense, it has far-reaching implications as it could serve as a generic law in the new political economy of the digital era.

scholarly journals Enabling External Inquiries to an Existing Patient Registry by Using the Open Source Registry System for Rare Diseases: Demonstration of the System Using the European Society for Immunodeficiencies Registry (Preprint)

2019 ◽  
Author(s):  
Raphael Scheible ◽  
Dennis Kadioglu ◽  
Stephan Ehl ◽  
Marco Blum ◽  
Martin Boeker ◽  
...  
Keyword(s):  
Open Source ◽  
Rare Diseases ◽  
Open Source Software ◽  
European Society ◽  
Patient Registries ◽  
Patient Organizations ◽  
Registry System ◽  
Decentralized Search ◽  
Custom Software ◽  
Set Up

BACKGROUND The German Network on Primary Immunodeficiency Diseases (PID-NET) utilizes the European Society for Immunodeficiencies (ESID) registry as a platform for collecting data. In the context of PID-NET data, we show how registries based on custom software can be made interoperable for better collaborative access to precollected data. The Open Source Registry System for Rare Diseases (<i>Open-Source-Registersystem für Seltene Erkrankungen</i> [OSSE], in German) provides patient organizations, physicians, scientists, and other parties with open source software for the creation of patient registries. In addition, the necessary interoperability between different registries based on the OSSE, as well as existing registries, is supported, which allows those registries to be confederated at both the national and international levels. OBJECTIVE Data from the PID-NET registry should be made available in an interoperable manner without losing data sovereignty by extending the existing custom software of the registry using the OSSE registry framework. METHODS This paper describes the following: (1) the installation and configuration of the OSSE bridgehead, (2) an approach using a free toolchain to set up the required interfaces to connect a registry with the OSSE bridgehead, and (3) the decentralized search, which allows the formulation of inquiries that are sent to a selected set of registries of interest. RESULTS PID-NET uses the established and highly customized ESID registry software. By setting up a so-called OSSE bridgehead, PID-NET data are made interoperable according to a federated approach, and centrally formulated inquiries for data can be received. As the first registry to use the OSSE bridgehead, the authors introduce an approach using a free toolchain to efficiently implement and maintain the required interfaces. Finally, to test and demonstrate the system, two inquiries are realized using the graphical query builder. By establishing and interconnecting an OSSE bridgehead with the underlying ESID registry, confederated queries for data can be received and, if desired, the inquirer can be contacted to further discuss any requirements for cooperation. CONCLUSIONS The OSSE offers an infrastructure that provides the possibility of more collaborative and transparent research. The decentralized search functionality includes registries into one search application while still maintaining data sovereignty. The OSSE bridgehead enables any registry software to be integrated into the OSSE network. The proposed toolchain to set up the required interfaces consists of freely available software components that are well documented. The use of the decentralized search is uncomplicated to use and offers a well-structured, yet still improvable, graphical user interface to formulate queries.

scholarly journals Online Survey on Open Journal Systems in Germany and the Network OJS-de.net

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Alexandra Büttner ◽  
Sabine Gehrlein ◽  
Stefanie Clormann
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Online Survey ◽  
Digital Systems ◽  
Collaborative Project ◽  
German Research ◽  
German Speaking ◽  
Survey Results ◽  
The University ◽  
Open Journal Systems

At the beginning of 2015 an online survey on the open source software Open Journal Systems (OJS) was launched in Germany to determine how the software is used at German research institutions and what scholars require when working with OJS. The survey was launched by the collaborative project OJS-de.net, a network initiative to support the use of the software in the German publishing landscape. It is a joint effort of the Center for Digital Systems (CeDiS) at the Freie Universität Berlin, Heidelberg University Library, and the Kommunikations-, Informations-, Medienzentrum (KIM) at the University of Konstanz. The following article presents an overview of the survey results and shows how these are implemented by OJS-de.net to improve the software adaption for German speaking researchers.Au début de l’année 2015, un sondage en ligne sur le logiciel open source Open Journal System (OJS) a été lancé en Allemagne, afin de savoir comment il est utilisé et mis en œuvre dans les institutions de recherche allemandes, et de déterminer les attentes qu’ont les chercheurs en l’utilisant et ce qui peut au contraire leur manquer. L’enquête a été lancée par le projet collaboratif « OJS-de.net », une nouvelle initiative collective allemande visant à encourager l’utilisation du logiciel OJS dans le paysage éditorial allemand. C’est un effort conjoint du Center for Digital Systems (CeDiS) de la Freie Universität Berlin, de la bibliothèque universitaire de Heidelberg, et du Kommunikations-, Informations-, Medienzentrum (KIM) de l’université de Constance. L’article qui suit présente un aperçu des résultats de l’enquête, et montre comment ils sont exploités par « OJS-de.net » pour améliorer l’adaptation du logiciel aux chercheurs germanophones.

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.

Vascular flow simulations using SimVascular and OpenFOAM (Preprint)

2021 ◽  
Author(s):  
Swetha Yogeswaran ◽  
Fei Liu
Keyword(s):  
Fluid Dynamics ◽  
Blood Flow ◽  
Open Source ◽  
Open Source Software ◽  
Flow Analysis ◽  
Coarctation Of The Aorta ◽  
Patient Specific ◽  
Specific Information ◽  
Imaging Data ◽  
Set Up

UNSTRUCTURED Applications of computational fluid dynamics (CFD) techniques to aid in the diagnosis and treatment of cardiovascular disease have entered the research domain in recent years, due to their ability to provide valuable patient-specific information without risks associated with highly invasive procedures. SimVascular is an open-source software which allows streamlined processing and CFD blood flow analysis of medical imaging data. OpenFOAM is a proven open-source software which allows for versatile modeling of various fluid dynamics phenomena. In this study, both SimVascular and OpenFOAM simulations are set up with identical computational mesh, similar numerical schemes, boundary conditions, and material properties, to model blood flow in the coronary artery of a 10 year old patient with Coarctation of the Aorta (CoA) who underwent end-to-side anastomosis. Difference in the flow fields such as flow rate, pressure, vorticity, and wall shear stress between SimVascular and OpenFOAM are analyzed. Similar results are obtained in both simulations up to a certain model time, before the results become drastically different. Both the similarities and differences are documented and discussed.

scholarly journals A New Attempt to Establish the International Radiocarbon Soils Database (IRSDB)

Radiocarbon ◽  
2010 ◽  
Vol 52 (3) ◽  
pp. 1405-1410 ◽  
Author(s):  
Peter Becker-Heidmann ◽  
Pascal Heidmann
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Data Input ◽  
Web Interface ◽  
Joint Effort ◽  
Close Collaboration ◽  
Recent Developments ◽  
Version Control System ◽  
Community Portal ◽  
Set Up

Twenty years after the first International Radiocarbon Database Workshop, and 13 yr after the setup of a preliminary structure for a worldwide database on 14C dates of soils, sound reasons and excuses for not establishing a real and globally accessible database have diminished. Climate change itself is widely accepted as reality now, and the strong demand of the modeling community for reliable data of the carbon pool—especially in soils—has been maintained. With the steadily increasing capacity of 14C dating facilities, these data can be and are produced. Nevertheless, they still cannot be accessed easily and equally enough. Now, decreased costs of hardware and recent developments of the internet enable the IRSDB to be implemented, in a joint effort. As a seed, a test server has been set up, with open-source software, housing the database in alpha-stage, a web interface, and a community portal. Thus, the development of the design as well as the data input of the database is done in close collaboration of the users of the database, the laboratories, soil scientists, archaeologists, modelers, other scientists, and interested laypersons. In order to guarantee the longtime independence of the availability and usability of the database from vendors or changing standards, only widely used open-source software and open standards are used. Therefore, the development of plug-ins for data input from laboratory databases or output to different required formats as well as interfaces to GIS and other software is possible. A version control system takes care of the integrity of the data.

scholarly journals Enabling External Inquiries to an Existing Patient Registry by Using the Open Source Registry System for Rare Diseases: Demonstration of the System Using the European Society for Immunodeficiencies Registry

10.2196/17420 ◽  
2020 ◽  
Vol 8 (10) ◽  
pp. e17420
Author(s):  
Raphael Scheible ◽  
Dennis Kadioglu ◽  
Stephan Ehl ◽  
Marco Blum ◽  
Martin Boeker ◽  
...  
Keyword(s):  
Open Source ◽  
Rare Diseases ◽  
Open Source Software ◽  
European Society ◽  
Patient Registries ◽  
Patient Organizations ◽  
Registry System ◽  
Decentralized Search ◽  
Custom Software ◽  
Set Up

Background The German Network on Primary Immunodeficiency Diseases (PID-NET) utilizes the European Society for Immunodeficiencies (ESID) registry as a platform for collecting data. In the context of PID-NET data, we show how registries based on custom software can be made interoperable for better collaborative access to precollected data. The Open Source Registry System for Rare Diseases (Open-Source-Registersystem für Seltene Erkrankungen [OSSE], in German) provides patient organizations, physicians, scientists, and other parties with open source software for the creation of patient registries. In addition, the necessary interoperability between different registries based on the OSSE, as well as existing registries, is supported, which allows those registries to be confederated at both the national and international levels. Objective Data from the PID-NET registry should be made available in an interoperable manner without losing data sovereignty by extending the existing custom software of the registry using the OSSE registry framework. Methods This paper describes the following: (1) the installation and configuration of the OSSE bridgehead, (2) an approach using a free toolchain to set up the required interfaces to connect a registry with the OSSE bridgehead, and (3) the decentralized search, which allows the formulation of inquiries that are sent to a selected set of registries of interest. Results PID-NET uses the established and highly customized ESID registry software. By setting up a so-called OSSE bridgehead, PID-NET data are made interoperable according to a federated approach, and centrally formulated inquiries for data can be received. As the first registry to use the OSSE bridgehead, the authors introduce an approach using a free toolchain to efficiently implement and maintain the required interfaces. Finally, to test and demonstrate the system, two inquiries are realized using the graphical query builder. By establishing and interconnecting an OSSE bridgehead with the underlying ESID registry, confederated queries for data can be received and, if desired, the inquirer can be contacted to further discuss any requirements for cooperation. Conclusions The OSSE offers an infrastructure that provides the possibility of more collaborative and transparent research. The decentralized search functionality includes registries into one search application while still maintaining data sovereignty. The OSSE bridgehead enables any registry software to be integrated into the OSSE network. The proposed toolchain to set up the required interfaces consists of freely available software components that are well documented. The use of the decentralized search is uncomplicated to use and offers a well-structured, yet still improvable, graphical user interface to formulate queries.

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