Community Organizations: Changing the Culture in Which Research Software Is Developed and Sustained

Software is the key crosscutting technology that enables advances in mathematics, computer science, and domain-specific science and engineering to achieve robust simulations and analysis for science, engineering, and other research fields. However, software itself has not traditionally received focused attention from research communities; rather, software has evolved organically and inconsistently, with its development largely as by-products of other initiatives. Moreover, challenges in scientific software are expanding due to disruptive changes in computer hardware, increasing scale and complexity of data, and demands for more complex simulations involving multiphysics, multiscale modeling and outer-loop analysis. In recent years, community members have established a range of grass-roots organizations and projects to address these growing technical and social challenges in software productivity, quality, reproducibility, and sustainability. This article provides an overview of such groups and discusses opportunities to leverage their synergistic activities while nurturing work toward emerging software ecosystems

Journal of Open Source Software (JOSS) : design and first-year review

This article describes the motivation, design, and progress of the Journal of Open Source Software (JOSS). JOSS is a free and open-access journal that publishes articles describing research software. It has the dual goals of improving the quality of the software submitted and providing a mechanism for research software developers to receive credit. While designed to work within the current merit system of science, JOSS addresses the dearth of rewards for key contributions to science made in the form of software. JOSS publishes articles that encapsulate scholarship contained in the software itself, and its rigorous peer review targets the software components: functionality, documentation, tests, continuous integration, and the license. A JOSS article contains an abstract describing the purpose and functionality of the software, references, and a link to the software archive. The article is the entry point of a JOSS submission, which encompasses the full set of software artifacts. Submission and review proceed in the open, on GitHub. Editors, reviewers, and authors work collaboratively and openly. Unlike other journals, JOSS does not reject articles requiring major revision; while not yet accepted, articles remain visible and under review until the authors make adequate changes (or withdraw, if unable to meet requirements). Once an article is accepted, JOSS gives it a digital object identifier (DOI), deposits its metadata in Crossref, and the article can begin collecting citations on indexers like Google Scholar and other services. Authors retain copyright of their JOSS article, releasing it under a Creative Commons Attribution 4.0 International License. In its first year, starting in May 2016, JOSS published 111 articles, with more than 40 additional articles under review. JOSS is a sponsored project of the nonprofit organization NumFOCUS and is an affiliate of the Open Source Initiative (OSI)

Journal of Open Source Software (JOSS): design and first-year review.

This article describes the motivation, design, and progress of the Journal of Open Source Software (JOSS). JOSS is a free and open-access journal that publishes articles describing research software. It has the dual goals of improving the quality of the software submitted and providing a mechanism for research software developers to receive credit. While designed to work within the current merit system of science, JOSS addresses the dearth of rewards for key contributions to science made in the form of software. JOSS publishes articles that encapsulate scholarship contained in the software itself, and its rigorous peer review targets the software components: functionality, documentation, tests, continuous integration, and the license. A JOSS article contains an abstract describing the purpose and functionality of the software, references, and a link to the software archive. The article is the entry point of a JOSS submission, which encompasses the full set of software artifacts. Submission and review proceed in the open, on GitHub. Editors, reviewers, and authors work collaboratively and openly. Unlike other journals, JOSS does not reject articles requiring major revision; while not yet accepted, articles remain visible and under review until the authors make adequate changes (or withdraw, if unable to meet requirements). Once an article is accepted, JOSS gives it a digital object identifier (DOI), deposits its metadata in Crossref, and the article can begin collecting citations on indexers like Google Scholar and other services. Authors retain copyright of their JOSS article, releasing it under a Creative Commons Attribution 4.0 International License. In its first year, starting in May 2016, JOSS published 111 articles, with more than 40 additional articles under review. JOSS is a sponsored project of the nonprofit organization NumFOCUS and is an affiliate of the Open Source Initiative (OSI)

Software Carpentry: Programming with GAP

A half-day introduction to programming in the computational algebra system GAP (http://www.gap-system.org/), developed and maintained by Alexander Konovalov. The template for the Software Carpentry lesson is developed and maintained by the Software Carpentry team

Common Workflow Language User Guide

Huge thanks to @tobyhodges for bulk converting from the existing user guide to Carpentry style

The Journal of Open Source Software

<div>Poster presented at SIAM CSE17 PP108 Minisymposterium: Software Productivity and Sustainability for CSE and Data Science<br></div><div><br></div><div><b>Abstract:</b></div>This poster describes the motivation and progress of the Journal of Open Source Software (JOSS), a free, open-access journal designed to publish brief papers about research software. The primary purpose of JOSS is to enable developers of research software to receive citation credit equivalent to typical archival publications. JOSS papers are deliberately extremely short, and are required to include a short abstract describing the purpose and functionality of the software, authors and their affiliations, and key references, as well as link to an archived version of the software (e.g., DOI obtained from Zenodo). Upon acceptance, papers receive a CrossRef DOI. Rather than a review of a lengthy software paper (including, e.g., methodology, validation, sample results), JOSS submissions undergo rigorous peer review of both the abstract and software itself, including documentation, tests, continuous integration, and licensing. The JOSS review process is modeled on the established approach of the rOpenSci collaboration. The entire submission and review process occurs openly on GitHub; papers not yet accepted remain visible and under review until the authors make appropriate changes for acceptance---unlike other journals, papers requiring major revision are not rejected. Since its public release in May 2016, JOSS has published 26 accepted papers as of September 2016, with an additional 20 submitted and under review

Introducing JOSS: The Journal of Open Source Software

Talk presented at the 2017 Python in Science Conference (SciPy), on 13 July 2017 in Austin, TX.<div><br></div><div><b>Abstract</b></div><div>This talk describes the motivation and progress of the Journal of Open Source Software (JOSS), a free, open-access journal designed to publish brief articles about research software. The primary purpose of JOSS is to enable developers of research software to receive citation credit equivalent to typical archival publications. Rather than a review of a lengthy software paper (including, e.g., methodology, validation, sample results), JOSS submissions undergo rigorous peer review of both the abstract and software itself, including documentation, tests, continuous integration, and licensing. The JOSS review process is modeled on the established approach of the rOpenSci collaboration. The entire submission and review process occurs openly on GitHub; articles not yet accepted remain visible and under review until the authors make appropriate changes for acceptance—unlike other journals, articles requiring major revision are not rejected. JOSS published 111 articles in its first year (May 2016–2016), with >50 articles under review.<br></div

alex-konovalov/gap-lesson: aachen2018

GAP Software Carpentry Lesso

swcarpentry/instructor-training: Software Carpentry: Instructor Training

A two-day introduction to modern evidence-based teaching practices, built and maintained by the Carpentry community

Data Carpentry Shell Genomics Lesson

Initial release of Data Carpentry Shell Genomics Lesson