September 2021 Meetup of the NL-RSE Community. Logo Banner

Location

The call will be conducted with the ZOOM conferencing platform. Follow Joining the Meeting instructions.

Zoom link will be sent to your email with your registration.

Registration

The registration is free.

Please register via this Eventbrite page.

Agenda

Time Responsible Type Subject
14:30 - 14:45     hello & coffee
14:45 - 15:00     Welcome and introductions
15:00 - 15:30 Adina Wagner Talk Data + Code + Software = PDF: How to write a reproducible research article
15:30 - 16:00 Giulia Guizzardi Talk Executable Research Article (ERA): Enrich a research paper with code and data
16:00 - 16:15     Break
16:15 - 16:45 Fernando Perez Talk Computing, statistics and reproducibility: pedagogical reflections
16:45 - 17:15   Discussion Panel: Reproducible research environments
17:15 - 18:00     Evaluation & Networking

Abstracts

Data + Code + Software = PDF: How to write a reproducible research article

Adina Wagner

Science is an incremental process that produces and builds up on more than just published journal articles - nevertheless, journals only rarely accept or publish formats other than text documents or PDFs. An alternative to a classic PDF is a reproducible research article, an electronic document that is automatically generated from your project’s code, data, and software, and embeds results and figures into the manuscript text as they are computed. With this, reproducible research articles combine adherence to publishers requirements with uncompromising reproducibility, increased reusability, and efficiency.

This talk will be a demonstration of one of many ways to writing an automatically reproducible research article and making it publicly available. It will walk through a traditionally published paper, and reveal the openly available reproducible research article behind it. Beyond this, it will introduce a generic framework to link and share all building blocks of a project, including code, data of any size, software, and the final manuscript.

Executable Research Article (ERA): Enrich a research paper with code and data

Giulia Guizzardi

Since 2017, eLife has been working on the concept of computationally reproducible papers. The open-source suite of tools that started life as the Reproducible Document Stack is live since August 2020 on eLife as ERA, the Executable Research Article, delivering a truly web-native format for taking published research to a new level of transparency, reproducibility and interactivity. At the moment, authors with a published eLife paper can register their interest to enrich their published work with the addition of live code blocks, programmatically-generated interactive figures, and dynamically generated in-line values, using familiar tools like R Markdown and Jupyter in combination with Stencila Hub’s intuitive asset management and format conversion interface. The resulting new ERA publication will be presented as a complement to the original published paper. Readers of ERA publications are able to inspect the code, modify it, and re-execute it directly in the browser, enabling them to better understand how a figure is generated. They are able to change a plot from one format to another, alter the data range of a specific analysis, and much more. All changes are limited to an individual’s browsing session and do not affect the published article, so anyone can experiment safely. Readers can also download the ERA publication – with all embedded code and data preserved – and use it as a basis for further study or derivative works.

Computing, statistics and reproducibility: pedagogical reflections

Fernando Perez

In this talk Fernando will discuss a course taught in the UC Berkeley statistics department, where they try to combine epistemological reflections on open and reproducible science, statistical considerations for data analysis that leads to robust and trustworthy results, and computational practices that support these ideas. They use tools from the Scientific Python and Jupyter ecosystem, and try to imbue the students with a practical appreciation of the real-world practice of open, collaborative science by working on open source projects, recently published literature and data.

The main ideas behind this approach can be implemented with other choices of tools as well, so we hope this discussion will be of interest to those who use different tools.

Call for Contributions

We are always looking for speakers and exciting topics, please contact the host Carlos Martinez if you would like to give a talk or are interested in learning about some specific topics.

Contact

If you have any questions, please contact the host Carlos Martinez