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OSODOS: Open Science, Open Data, Open Source

About this project

This repository contains reading/teaching materials that touch on the following topics:

  • Open Access scholarly publishing
  • Open Source software development
  • Open Data integration and sharing

These materials are intended to be freely disseminated as an e-book and/or a website, which can be accessed at:

Directory layout

  • data - contains any structured data files that are needed for publishing the materials. This includes machine readable bibliographic data, and possibly other types of data, such as tables or lists.
  • docs - contains i) the prose itself, in markdown format ii) any embedded images, iii) the prose as generated HTML.
  • node_modules - contains Node.js dependencies. As this is 3rd party code that we haven't touched this should probably be removed.
  • src - contains any scripts needed for publishing the materials. This includes scripts for processing the bibliography.
  • book.json - a configuration file in JSON format for the gitbook generator.
  • _config.json - a configuration file for the gh-pages website. This is possibly an orphaned file to be deleted (as we use the gitbook as a website).

How to build/publish

  1. Check to see if the Mendeley library has newer records than the markdown bibliography. If yes, export the Mendeley library to BibTeX (using the Mendeley Desktop program) and commit it to the repository, overwriting the current bibtex export.
  2. Run the conversion script, i.e.: python src/ data/references.bib > docs/REFERENCES/
  3. Run the gitbook builder, i.e. gitbook build . docs/gitbook
  4. Commit and push, e.g. git commit -m 're-generated' --all && git push. It takes a minute for the updated site to be 'live'.

Disclaimers, terms and conditions

This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.