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The Open Source Toolkit – meet our new Channel Editors for Software

The Open Source Toolkit welcomes Nikoleta E. Glynatsi and Yo Yehudi as Channel Editors for Software.

The Open Source Toolkit gathers articles, projects and resources describing hardware and software that can be applied in research, education and/or healthcare settings. Until now, the emphasis has been on hardware, so we are delighted to welcome Nikoleta E. Glynatsi and Yo Yehudi as new Channel Editors with expertise in software to help us expand the scope of the Channel. With their leadership, we aim to be a catalyst in demonstrating how Open Source software can revolutionize and democratize computer science by making it freely accessible and reproducible, enabling faster dissemination and progress.

A note from the new channel editors

Greetings everyone, we are the new editors of the Open Source Toolkit and we will be focusing on the software side of things. There are several criteria that apply in our channel updates, with an aim to highlight examples of high-quality open source research software that follows commonly accepted good practice.

For example, is the software described in the published manuscript accessible and installable? Accessibility refers to whether there is need for a license in order to run the software (e.g. are there prohibitive costs associated with running the software? Free or low-cost alternatives are more accessible), and whether the software is accessible via hosting services (such as GitHub, Gitlab etc). Furthermore, whether the software is installable refers to whether there is enough documentation that one of us can successfully install and run it in some way. Installation notes, tutorials, even a readme file can always make a difference to the software. We aim to showcase research software  that can be easily used and re-used by the scientific community.

There are several other criteria that can have a positive reflection on the project. Is there a community supporting the project? A project with a strong community is less likely to be dropped in the near the future. The correctness of the software and thus the results stated in the published manuscript are of high importance. These can be reassured by the use of automated tests. Tests also allow for easier contributions to the project and reproducibility of the work. Other practices that make a research reproducible? Release tags. We will also keep an eye out for them.

Take a look at the new Channel Editors’ first Software-themed update here!

About us

Yo Yehudi

I’m a software engineer at InterMine, an open source biological data warehouse based at the Department of Genetics in the University of Cambridge. I spend a lot of my time writing open source code (you can check my GitHub profile), as well as focussing on the community-oriented aspects of open source.

While working on InterMine, I noticed that it’s not at all uncommon for scientific software to have papers published about it with nary a source code link to be seen. This is rather concerning when you consider that if the code is wrong, the science is also going to be wrong! In response, I founded Code Is Science in 2017 to try to fix this, and will soon be launching a manifesto stating that scientific code needs to be open source, peer reviewed, and cited. I’m a Software Sustainability Institute Fellow, a board member of the Open Bioinformatics Foundation, and an enthusiastic Mozilla volunteer, working as a mentor and cohort host in the Mozilla Open Leaders program.

Nikoleta E. Glynatsi

I am currently a second year PhD student in the School of Mathematics at Cardiff University and a Fellow of the Sustainable Software Institute. My research focuses on game theory and the study of cooperative behaviour, more specifically in the pioneering field of the Iterated Prisoner’s Dilemma. My work includes using machine learning approaches to train complex behaviour.

I am a research software developer and a contributor to several open source projects, including the Axelrod Library and Arcas. I am also an active member of the UK Python community, which includes being a co-organiser of the UK Django Girls workshops. You can find me on twitter @NikoletaGlyn and on GitHub Nikoleta-v3.

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