scholarly journals Free and Open Source Software for Computational Chemistry Education

2021 ◽  
Author(s):  
Susi Lehtola ◽  
Antti Karttunen
Keyword(s):  
Computational Chemistry ◽  
Open Source ◽  
Open Source Software ◽  
Density Functional ◽  
Chemistry Education ◽  
Tight Binding ◽  
Industrial Applications ◽  
Bring Your Own Device ◽  
Wide Range ◽  
The Masses

Abstract Long in the making, computational chemistry for the masses [J. Chem. Educ. 1996, 73, 104] is finally here. Our brief review on various free and open source software (FOSS) quantum chemistry packages points out the existence of software offering a wide range of functionality, all the way from approximate semiempirical calculations with tight-binding density functional theory to sophisticated ab initio wave function methods such as coupled-cluster theory, both for molecular and for solid-state systems. Combined with the remarkable increase in the computing power of personal devices, which now rivals that of the fastest supercomputers in the world of the 1990s, we demonstrate that a decentralized model for teaching computational chemistry is now possible thanks to FOSS computational chemistry packages, enabling students to perform reasonable modeling on their own computing devices, in the bring your own device (BYOD) scheme. FOSS software can be made trivially simple to install and keep up to date, eliminating the need for departmental support, and also enables comprehensive teaching strategies, as various algorithms' actual implementations can be used in teaching. We exemplify what kinds of calculations are feasible with four FOSS electronic structure programs, assuming only extremely modest computational resources, to illustrate how FOSS packages enable decentralized approaches to computational chemistry education within the BYOD scheme. FOSS also has further benefits: the open access to the source code of FOSS packages democratizes the science of computational chemistry, and FOSS packages can be used without limitation also beyond education, in academic and industrial applications, for example. For these reasons, we believe FOSS will become ever more pervasive in computational chemistry.

scholarly journals Monitoring Cropping Systems: From Data Collection to Cloud Database Storage Using Open Source Software

Proceedings ◽  
2020 ◽  
Vol 30 (1) ◽  
pp. 79
Author(s):  
Ioanna Panagea ◽  
Dangol Anuja ◽  
Marc Olijslagers ◽  
Jan Diels ◽  
Guido Wyseure
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Web Application ◽  
Cropping Systems ◽  
Cropping System ◽  
Query Languages ◽  
Climatic Conditions ◽  
Raw Data ◽  
Wide Range ◽  
Study Sites

Agricultural cropping systems and experiments include complex interactions of processes and various management practices and/or treatments under a wide range of environmental and climatic conditions. The use of standardized formats to monitor and document these systems and experiments can help researchers and stakeholders to efficiently exchange data, promote interdisciplinary collaborations, and simplify modelling and analysis procedures. In the scope of the SoilCare Horizon 2020 project monitoring and assessment work package, an integrated scheme to collect, validate, store, and access cropping system information and experimental data from 16 study sites, was created. The aim of the scheme is to make the data readily available in a way that the information is useful, easy to access and download, and safe, relying only on open source software. The database design considers data and metadata required to properly and easily monitor, process, and analyse cropping systems and/or agricultural experiments. The scheme allows for the storage of data and metadata regarding the experimental set-up, associated people and institutions, information about field management operations and experimental procedures which are clearly separated for making analysis procedures faster, links between system components, and information about the environmental and climatic conditions. Raw data are entered by the users into a structured spreadsheet. The quality is checked before storing the data into the database. Providing raw data allows processing and analysing as each other user needs. A desktop import application has been created to upload the information from spreadsheet to database, which includes automated error checks of relationship tables, data types, data constraints, etc. The final component of the scheme is the database web application interface, which enables users to access and query the database across the study sites without the knowledge of query languages and to download the required data. For this system design, PostgreSQL is used for storing the data, pgAdmin 4 for database management administration, MongoDB for user management and authentication, Python for the development of the import application, Angular and Node.js/Express for the web application and spreadsheets compatible with LibreOffice Calc. The system is currently tested with data provided by the SoilCare study sites. Preliminary testing indicated that extended quality control of the spreadsheets was required from the system’s administrator to meet the standards and restrictions of the import application. Initial comments from the users indicate that the database scheme, even if it initially seems complicated, includes all the variables and details required for a complete monitoring and modelling of an agricultural cropping system.

Aplicativos Educacionais para Smartphone e sua Integração Com o Ensino de Química

2016 ◽  
Vol 17 (5) ◽  
pp. 398
Author(s):  
Marcella Cristyanne Comar Gresczysczyn ◽  
Paulo Sérgio de Camargo Filho ◽  
Eduardo Lemes Monteiro
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Digital Technology ◽  
Chemistry Education ◽  
New Technology ◽  
Great Promise ◽  
Teaching Chemistry ◽  
Semiotic Representations ◽  
Education Improvement ◽  
Google Play

A tecnologia digital é uma grande promessa para o ensino de Química na escola, acredita-se que a implementação dessas tecnologias produz melhoria na educação. No entanto, pouco se sabe sobre a articulação coordenada dos aplicativos para smartphone propostos para este fim e as demais representações semióticas tradicionais da Ciência e efeitos sobre a aprendizagem dos alunos. É importante acrescentar que a escola ainda não conseguiu integrar todas as mudanças da sociedade com a rápida evolução das tecnologias, afastando-se dos jovens inseridos nessa evolução. Ao professor se exige um esforço para a readaptação a essa integração, o papel desse educador deverá ser ativo e responsável no enquadramento pedagógico das tecnologias, para que possa tornar-se um meio de renovação do ensino e não apenas um mero reforço de práticas tradicionais. Atualmente, na área da Educação Química, nota-se que a informatização e os aplicativos tão acessíveis a qualquer classe da população, podem proporcionar situações de aprendizagem que acabavam restritas, pelo alto custo. Nesse contexto e, com o objetivo de conhecer os aplicativos para a Educação Química e o crescimento de sua oferta para incentivar sua adoção na educação, são trazidos, nesse artigo, os resultados de uma pesquisa sobre aplicativos para Android® relacionados à área, realizada a partir da busca de aplicativos em repositórios livres tais como Free and Open Source Software - FOSS® e Google Play® disponíveis em um período de 2012 a 2016, apresentando a evolução do número de aplicativos disponíveis, os temas mais recorrentes e indicando aplicativos para a Educação Química. Palavras-chave: Ensino. Química. Aplicativos. Smartphone. Tecnologia Digital AbstractThe use of digital technology holds great promise for teaching chemistry in school, it is believed that the implementation of this new technology produces education improvement. However, little is known about the coordinated joint applications for smartphone proposed for this objective and other traditional Sciences semiotic representations and effects on the students’ learning. It is important to add that the school was still not able so far to integrate all the changes in society with the rapid technology evolution, moving away from our young people who are inserted into this evolution. To the teacher, it is required an effort to rehabilitate this integration, the educator’s role should be active and responsible in the technologies educational environment, so they can become a means of teaching renewal and not just a mere reinforcement of traditional practices. Currently, in the Chemical Education area, it is noted that the computerization and applications so accessible to any class population can provide learning situations which used to be limited due to theirhigh cost. In this context and in order to knowthe Chemistry Education applications and the growth supply to encourage their adoption in education, are coveredin this article, the results of a survey on applications for Android® related to the area, accomplished from search applications for free repositories such as Free and Open Source Software - FOSS® and Google Play® available in a period from 2012 to 2016, showing the evolution of the number of available applications, the most recurrent themes and indicating applications for Chemical Education.Keywords: Education. Chemistry. Applications. Smartphone. Digital technology.

scholarly journals Mapping the Optoelectronic Property Space of Small Aromatic Molecules

2019 ◽  
Author(s):  
Liam Wilbraham ◽  
Denisa Smajli ◽  
isabelle Heath-Apostolopoulos ◽  
Martijn Zwijnenburg
Keyword(s):  
Density Functional ◽  
Tight Binding ◽  
Structural Features ◽  
Organic Transistors ◽  
Optoelectronic Property ◽  
Aromatic Molecules ◽  
Wide Range ◽  
Property Space ◽  
Molecular Semiconductors ◽  
Broad Understanding

<p><i>We perform a high-throughput virtual screening using the xTB family of density functional tight-binding methods to map the optoelectronic property space of ~250,000 aromatic molecules and quinone derivatives that find application in organic transistors, solar-cells, thermoelectrics, batteries and photocatalysts. The large volume of data generated allows for a broad understanding of how the presence of a wide range of heteroatoms and functional groups affect the ionisation potential, electron affinity and optical gap values of these molecular semiconductors and how the structural features – on their own or in combination with one another – allow access to particular regions of the optoelectronic property space. Finally, we identify the apparent boundaries of the optoelectronic property space for these molecules: regions of property space that appear off limits for any small conjugated cyclic organic molecule.</i></p>

FRAME-Sim: A Free-Software, Multibody-Based, Pilot in the Loop Rotorcraft Flight Simulator

2018 ◽  
Author(s):  
Andrea Zanoni ◽  
Luca Conti ◽  
Pierangelo Masarati
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Development Process ◽  
Free Software ◽  
Design Stage ◽  
Careful Planning ◽  
Modern Approach ◽  
Handling Qualities ◽  
Wide Range ◽  
Representative Model

In the context of a modern approach to the design of rotocraft, handling qualities should be the result of careful planning, rather than the output of a multitude of other choices, made primarily focusing on more immediate constraints. For a wide range of flight conditions and mission task elements, the test pilot feedback is the essential measure upon which the design choices are made. Thus, it is becoming of fundamental importance to be able to simulate a representative model of the vehicle in a pilot-in-the-loop environment as early as possible in the design stage. This work is intended to document the development process of one such system currently being realized at the facilities belonging to the Aerospace Science and Technology Department of Politecnico di Milano. Particular attention is given to the software architecture, based on the free and open-source multibody solver MBDyn. The development of a module specifically designed to exploit the environment visualization capabilities of FlightGear, also a free and open-source software, is presented.

A Longitudinal Study of Fan-In and Fan-Out Coupling in Open-Source Systems

2011 ◽  
Vol 2 (4) ◽  
pp. 1-26 ◽  
Author(s):  
Asma Mubarak ◽  
Steve Counsell ◽  
Robert M. Hierons
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Large Classes ◽  
Future Problem ◽  
Wide Range ◽  
Type Classes ◽  
Low Levels ◽  
The Relationship ◽  
Open Source Systems ◽  
Maintenance Problem

Excessive coupling between object-oriented classes is widely acknowledged as a maintenance problem that can result in a higher propensity for faults in systems and a ‘stored up’ future problem. This paper explores the relationship between ‘fan-in’ and ‘fan-out’ coupling metrics over multiple versions of open-source software. More specifically, the relationship between the two metrics is explored to determine patterns of growth in each over the course of time. The JHawk tool was used to extract the two metrics from five open-source systems. Results show a wide range of traits in the classes to explain both high and low levels of fan-in and fan-out. Evidence was also found of certain ‘key’ classes (with both high fan-in and fan-out) and ‘client’ and ‘server’-type classes with high fan-out and fan-in, respectively. This paper provides an explanation of the composition and existence of such classes as well as for disproportionate increases in each of the two metrics over time. Finally, it was found that high fan-in class values tended to be associated with small classes; classes with high fan-out on the other hand tended to be relatively large classes.

MOSQITO: an open-source and free toolbox for sound quality metrics in the industry and education

2021 ◽  
Vol 263 (5) ◽  
pp. 1164-1175
Author(s):  
Roberto San Millán-Castillo ◽  
Eduardo Latorre-Iglesias ◽  
Martin Glesser ◽  
Salomé Wanty ◽  
Daniel Jiménez-Caminero ◽  
...  
Keyword(s):  
Open Source ◽  
Programming Languages ◽  
Open Source Software ◽  
Objective Assessment ◽  
Sound Quality ◽  
Quality Metrics ◽  
Point Of View ◽  
Wide Range ◽  
Efficient Learning ◽  
High Level

Sound quality metrics provide an objective assessment of the psychoacoustics of sounds. A wide range of metrics has been already standardised while others remain as active research topics. Calculation algorithms are available in commercial equipment or Matlab scripts. However, they may not present available data on general documentation and validation procedures. Moreover, the use of these tools might be unaffordable for some students and independent researchers. In recent years, the scientific and technical community has been developing uncountable open-source software projects in several knowledge fields. The permission to use, study, modify, improve and distribute open-source software make it extremely valuable. It encourages collaboration and sharing, and thus transparency and continuous improvement of the coding. Modular Sound Quality Integrated Toolbox (MOSQITO) project relies on one of the most popular high-level and free programming languages: Python. The main objective of MOSQITO is to provide a unified and modular framework of key sound quality and psychoacoustics metrics, free and open-source, which supports reproducible testing. Moreover, open-source projects can be efficient learning tools at University degrees. This paper presents the current structure of the toolbox from a technical point of view. Besides, it discusses open-source development contributions to graduates training.

Open Source Software Development Challenges

2021 ◽  
pp. 33-62
Author(s):  
Abdulkadir Seker ◽  
Banu Diri ◽  
Halil Arslan ◽  
Mehmet Fatih Amasyalı
Keyword(s):  
Literature Review ◽  
Software Development ◽  
Open Source ◽  
Systematic Literature Review ◽  
Open Source Software ◽  
Digital Libraries ◽  
Common Code ◽  
Wide Range ◽  
Data Source ◽  
Source Study

GitHub is the most common code hosting and repository service for open-source software (OSS) projects. Thanks to the great variety of features, researchers benefit from GitHub to solve a wide range of OSS development challenges. In this context, the authors thought that was important to conduct a literature review on studies that used GitHub data. To reach these studies, they conducted this literature review based on a GitHub dataset source study instead of a keyword-based search in digital libraries. Since GHTorrent is the most widely known GitHub dataset according to the literature, they considered the studies that cite this dataset for the systematic literature review. In this study, they reviewed the selected 172 studies according to some criteria that used the dataset as a data source. They classified them within the scope of OSS development challenges thanks to the information they extract from the metadata of studies. They put forward some issues about the dataset and they offered the focused and attention-grabbing fields and open challenges that we encourage the researchers to study on them.

Molybdenum nitrides from structures to industrial applications

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Zainab N. Jaf ◽  
Hussein A. Miran ◽  
Zhong-Tao Jiang ◽  
Mohammednoor Altarawneh
Keyword(s):  
Density Functional ◽  
Petroleum Industry ◽  
Industrial Applications ◽  
Molybdenum Nitride ◽  
Adsorbed Hydrogen ◽  
Hydrogen Atoms ◽  
Activation Barriers ◽  
Platform Chemicals ◽  
Wide Range ◽  
Review Reports

Abstract Owing to their remarkable characteristics, refractory molybdenum nitride (MoN x )-based compounds have been deployed in a wide range of strategic industrial applications. This review reports the electronic and structural properties that render MoN x materials as potent catalytic surfaces for numerous chemical reactions and surveys the syntheses, procedures, and catalytic applications in pertinent industries such as the petroleum industry. In particular, hydrogenation, hydrodesulfurization, and hydrodeoxygenation are essential processes in the refinement of oil segments and their conversions into commodity fuels and platform chemicals. N-vacant sites over a catalyst’s surface are a significant driver of diverse chemical phenomena. Studies on various reaction routes have emphasized that the transfer of adsorbed hydrogen atoms from the N-vacant sites reduces the activation barriers for bond breaking at key structural linkages. Density functional theory has recently provided an atomic-level understanding of Mo–N systems as active ingredients in hydrotreating processes. These Mo–N systems are potentially extendible to the hydrogenation of more complex molecules, most notably, oxygenated aromatic compounds.

scholarly journals The Role of Free/Libre and Open Source Software in Learning Health Systems

2017 ◽  
Vol 26 (01) ◽  
pp. 53-58
Author(s):  
C. Paton ◽  
T. Karopka
Keyword(s):  
Open Source ◽  
Health Systems ◽  
Open Source Software ◽  
Grey Literature ◽  
Critical Role ◽  
Patient Data ◽  
It Infrastructure ◽  
Management Tools ◽  
Wide Range

Summary Objective: To give an overview of the role of Free/Libre and Open Source Software (FLOSS) in the context of secondary use of patient data to enable Learning Health Systems (LHSs). Methods: We conducted an environmental scan of the academic and grey literature utilising the MedFLOSS database of open source systems in healthcare to inform a discussion of the role of open source in developing LHSs that reuse patient data for research and quality improvement. Results: A wide range of FLOSS is identified that contributes to the information technology (IT) infrastructure of LHSs including operating systems, databases, frameworks, interoperability software, and mobile and web apps. The recent literature around the development and use of key clinical data management tools is also reviewed. Conclusions: FLOSS already plays a critical role in modern health IT infrastructure for the collection, storage, and analysis of patient data. The nature of FLOSS systems to be collaborative, modular, and modifiable may make open source approaches appropriate for building the digital infrastructure for a LHS.

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