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How Document became an application: new possibilities for scholarly publication

The aim of the workshop is to problematize, demystify and demonstrate new technical possibilities for authoring scientific manuscripts.

Computer assisted preparation of manuscripts for publication has for decades now functioned in two main ways: 1) manually and visually creating and arranging elements in their final form (e.g. MS Word and similar software), and 2) creating instructions for the computer to visualise and arrange the elements automatically (e.g. LaTeX).

WWW technologies have adopted the latter approach with much less emphasis on paper representation and with more pronounced interactivity. An “HTML document” over time became more akin to an “application” than to a “document” giving new possibilities for the writer and the reader.

The instruction-based approach is especially relevant for scientific publication as it has pronounced formal publication elements such as in-text references and related bibliography; visualisations, tables and other analytical outputs; in-text representations of data and code and so on. From the author’s standpoint, all of these are greatly helped by the instruction-based creation of publications. From the reader’s standpoint, the possibility of included interactive elements greatly enhances the reading experience of data-driven scientific publications.

The first part of the workshop will provide a theoretical overview of the topic and provide examples of several relevant technological solutions (R Markdown, Bookdown, Jupyter, LaTeX). Many of these solutions are currently based on extensions of Markdown, a lightweight markup language designed for easy typing and human readability. With some extensions, this language is quite powerful and flexible.

The second part of the workshop will provide a hands-on experience with how one of the most popular and advanced statistics environments, the language R, approaches this problem. R markdown is a framework that allows for programming code (e.g. R, Python and others) to be easily embedded in markdown documents. Together with supporting tools, this allows for the creation of beautiful documents containing visualisations, tables and formatted text. Elegant scientific documents as well as flashy popular presentations can be produced using the same set of tools and the same R code as a base. It is important to note that these documents embed data and code to produce the needed output rather than premade visualisations the significance of which will be discussed during the workshop.

  • Blaž RebernjakBlaž RebernjakUniversity of Zagreb

    Blaž Rebernjak was born in Zagreb in 1983, where he finished primary and secondary schools. In 2007 he obtained his MA and in 2013 his PhD… More →

  • Krešimir ZauderKrešimir ZauderUniversity of Zadar

    Krešimir Zauder was born in Zagreb, Croatia in 1980. He graduated Information science and English language and literature in 2006. In 201… More →