For the Scholarly Writing and Publishing Framework we make extensive use of these pipelines with Docker.ĭocker is – in a nutshell – a technology that lets you build virtual machines as small as possible and as powerful as necessary. Besides the advantage of working together on code, data and text, GitLab excels with the feature of building digital artifacts with configurable pipelines. GitLab is quite similar to GitHub, but open source software and free to host on a server of your choice. GitLab. Many scientists already appreciate collaboration on GitHub, a sharing platform for software, data and text. This way we can generate at the same time good-looking and machine readable versions of scientific articles from a single source. 2 Krewinkel and Winkler also intend to reduce the expense of article processing with pandoc-scholar and can convert Markdown to PDF, LaTeX, HTML, JATS XML, epub and other formats. To equip pandoc with this requirement, Albert Krewinkel and Robert Winkler wrote pandoc-scholar that we also use in our project (Krewinkel & Winkler, 2017). Pandoc-scholar. For scholarly writing the correct mention of authors and affiliation is crucial. For our framework pandoc is the first choice as it meets the requirements for scientific writing including citations, footnotes, figures and reference management. To get an impression of its concept, you can try it online. It works on the command-line and converts Markdown to LaTeX, PDF, HTML, XML, office formats and various wiki dialects. Pandoc is a converter for a large number of document types. Markdown makes single-source publishing possible as it can be converted to many different formats with Static Site Generators like Jekyll, Hugo or pandoc. Markdown can quickly be learned and can be found in many environments of the web. Markdown. In many open science and open source ecosystems the Markdown syntax for scientific writing has already become the default. Let’s have a look at these tools in detail: The article is submitted and published in an OJS instance and again can be annotated and discussed with Hypothesis. Reviewers annotate the article before submission by using Hypothesis. In short, the system can be described as: Authors write collaboratively in Markdown, a GitLab pipeline running with Docker converts the text with pandoc/pandoc-scholar to various output formats like PDF, HTML and XML. We call it a Scholarly Writing and Publishing Framework. This modular architecture is open to participation and inspiration from the community. Distinct parts can be replaced and adapted to one’s needs. Like in Unix/Linux best practices we chain our tools together to build a modular pipeline that can be extended and configured as you like. In our team we trust in the Unix philosophy that says “One job, one tool”. The Scholarly Writing and Publishing Framework The joint project of Modern Publishing is part of the program of Hamburg Open Science. We use open source tools that every scholar, library and publisher should be able to use and adapt to his and her needs. To promote Open Science and its values, Hamburg University of Technology (TUHH) and Hamburg State and University Library (SUB) are developing an Open Access framework for digital publishing. Saying this, accessibility must be mentioned as a necessary condition and another core value of open science. From the beginning of the research process, publishing is key to inform the community and society about the findings and the winding road that led to them. Open science is linked with many values such as accountability, integrity, trust, reproducibility and of course, openness. Image: Photo by John Barkiple on Unsplash
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