I'm a data scientist working at the intersection of technology and design. Reformed astrophysicist & former e-Research/data consultant.

Special e-Research Colloquium: "Data-driven, interactive scientific articles in a collaborative environment with Authorea"

This week I invited Alberto Pepe, co-founder of Authorea to give a special e-Research Colloquium at Swinburne. Alberto was in town for the   Research Bazaar Conference and gave  a keystory talk On leaving academia, without ever saying goodbye.

Most tools that scientists use for the preparation of scholarly manuscripts, such as Microsoft Word and LaTeX, function offline and do not account for the born-digital nature of research objects. Also, most authoring tools in use today are not designed for collaboration, and, as scientific collaborations grow in size, research transparency and the attribution of scholarly credit are at stake. Alberto showed us how the Authorea platform allows scientists to collaboratively write rich data-driven manuscripts on the web – articles that would natively offer readers a dynamic, interactive experience with an article’s fulltext, images, data, and code – paving the road to increased data sharing, data reuse, research reproducibility, and Open Science.

I first met Alberto last December at .Astronomy 6 in Chicago. On the first day, we had a fantastic unconference session on hacking the journal article. The room was packed and we had a really good discussion of what the ideal journal publication would look like.

Wishlist for journal publications:

  1.  A responsive design that automatically reformats double and single column views for mobile devices.  
  2. Facilitates hyperlinks within text.
  3. Facilitates interactive plots and figures
  4. Has saved ‘states’ for figures so that the author’s intent is preserved once you load the document
  5. Facilitates table data export.  Get the data, how you want the data... in a form that can be ingested by everything.
  6. Fails with grace. In 1000 years when D3 doesn’t exist, it should still look nice when we render it on the chip implanted on our optical nerves.

The second part of the session was about finding effective ways to argue these points with journals. How do we go about this? What part of the submission process is it appropriate to make suggestions? Authorea aims to implement many of these ideas as part of their product and as a proof-of-concept demonstration to the broader publishing industry.

A little bit about Alberto:

Alberto is a “recovering academic” with previous Ph.D. and Postdoc work in Astrophysics and Information Science. He holds degrees and fellowships from Harvard, UCLA, CERN, and University College London. He was born and raised in the wine-making town of Manduria, in Puglia, Southern Italy.  You can follow him on Twitter @albertopepe

Python for bioinformatics and gut microbiology.

.astronomy6 director's lunch talk (slides)