Open Chemistry, JupyterLab, REST, and Quantum Chemistry

Hanwell, Marcus D.; Harris, Chris; Genova, Alessandro; Haghighatlari, Mojtaba; Khatib, Muammar El; Avery, Patrick; Hachmann, Johannes; Jong, Wibe A. de

doi:10.22541/au.158687268.81852407

Cited by 7 publications

(9 citation statements)

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“…48 As of 2022, Kitware has more than 200 employees and their FOSS projects span many fields of science and technology, including quantum chemistry. 49 Due to the relatively small market for specialized scientific software, the availability of public research funding has always played a key role in the development of computational chemistry software. Related to future development of FOSS in science, the European Commission has outlined Open Science as their policy priority and the standard method of working under its research and innovation funding programs.…”

Section: Maintenance and User Supportmentioning

confidence: 99%

Free and open source software for computational chemistry education

Lehtola

Karttunen

2022

WIREs Comput Mol Sci

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After decades of waiting, computational chemistry for the masses is finally here. Our brief review on free and open source software (FOSS) 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, covering both molecular and 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 in the 1990s, we demonstrate that a decentralized model for teaching computational chemistry is now possible thanks to FOSS 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 driving its adoption: 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.

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Section: Maintenance and User Supportmentioning

confidence: 99%

Free and open source software for computational chemistry education

Lehtola

Karttunen

2022

WIREs Comput Mol Sci

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Section: Maintenance and User Supportmentioning

confidence: 99%

Free and Open Source Software for Computational Chemistry Education

Lehtola

Karttunen

2022

Preprint

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Long in the making, computational chemistry for the masses [J. Chem. Educ. 1996, 73, 104] is finally here. Our brief review on free and open source software (FOSS) 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, covering both molecular and 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 in the 1990s, we demonstrate that a decentralized model for teaching computational chemistry is now possible thanks to FOSS 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 driving its adoption: 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.

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“…All applications provide support for executing the analysis. REANA projects are executed via the CLI in a remote REANA cloud, and this also applies to ReproZip, which in addition to a remote cloud also provides a In use in use [40] in use [2] in use [41] in use [42] in use [43] --in use [44] in ReproServer for executing code online. Gigantum's local client allows users to run code in the browser.…”

Section: Reprozipmentioning

confidence: 99%

Publishing computational research - a review of infrastructures for reproducible and transparent scholarly communication

Konkol

Nüst

Goulier

2020

Res Integr Peer Rev

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Background: The trend toward open science increases the pressure on authors to provide access to the source code and data they used to compute the results reported in their scientific papers. Since sharing materials reproducibly is challenging, several projects have developed solutions to support the release of executable analyses alongside articles. Methods: We reviewed 11 applications that can assist researchers in adhering to reproducibility principles. The applications were found through a literature search and interactions with the reproducible research community. An application was included in our analysis if it (i) was actively maintained at the time the data for this paper was collected, (ii) supports the publication of executable code and data, (iii) is connected to the scholarly publication process. By investigating the software documentation and published articles, we compared the applications across 19 criteria, such as deployment options and features that support authors in creating and readers in studying executable papers. Results: From the 11 applications, eight allow publishers to self-host the system for free, whereas three provide paid services. Authors can submit an executable analysis using Jupyter Notebooks or R Markdown documents (10 applications support these formats). All approaches provide features to assist readers in studying the materials, e.g., one-click reproducible results or tools for manipulating the analysis parameters. Six applications allow for modifying materials after publication. Conclusions: The applications support authors to publish reproducible research predominantly with literate programming. Concerning readers, most applications provide user interfaces to inspect and manipulate the computational analysis. The next step is to investigate the gaps identified in this review, such as the costs publishers have to expect when hosting an application, the consideration of sensitive data, and impacts on the review process.

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Open Chemistry, JupyterLab, REST, and Quantum Chemistry

Cited by 7 publications

References 0 publications

Free and open source software for computational chemistry education

Free and open source software for computational chemistry education

Free and Open Source Software for Computational Chemistry Education

Publishing computational research - a review of infrastructures for reproducible and transparent scholarly communication

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