Data visualisation for reproducibility BioJS Conference, 3 July 2015 Rebecca Lawrence Managing Director, F1000 Research Ltd rebecca.lawrence@f1000.com http://f1000research.com @f1000research | @rnl_s

open science publishing platform Author-led publishing: Immediate publication Transparent refereeing No editorial bias Data & software included

Reproducibility problem Begley & Ellis 2012 (Nature): 53 ‘landmark’ studies  only 6 (11%) replicated. Failure to adhere to good scientific practice: blinding, randomization, replication, sample-size calculation ‘Publish or perish’ culture  emphasis on impactful statements Lack of supporting data shared Lack of methods/technical detail Journals starting to address these issues, e.g. eLife, F1000Research

Not just sharing, but making it reusable Sharing data alone isn’t adequate Need detailed protocol/methods Need data in an understandable and reusable format For computational studies, need details of environment Replication can be time consuming and expensive Peer review of the data can be time consuming and therefore not (properly) done

Full data integration with research articles Datasets within article are citable and downloadable.

In-article data manipulation

Figures that don’t exist Simply data + code Creates opportunities to change the definition of a figure, and ultimately the journal article Colomb J and Brembs B. Sub-strains of Drosophila Canton- S differ markedly in their locomotor behavior [v1; ref status: indexed, http://f1000r.es/3is] F1000Research 2014, 3:176

Living figures FIGURE 4. In: Colomb J and Brembs B. Sub-strains of Drosophila Canton-S differ markedly in their locomotor behavior [v2; ref status: indexed, f1000r.es/57i] F1000Research 2014, 3:176

Lack of awareness of data formatting requirements challenges Lack of awareness of data formatting requirements Lack of programming expertise in many research groups Quality of the code – time and expense Reusability of code: Lack of standards Vast number of data types, output types For many publishers, complex publishing systems that are licensed in and hard to change/adapt Industry-built code often not open source Often not possible to embed visualisation tool within article page

@f1000 | @f1000research | @rnl_s Thank you! rebecca.lawrence@f1000.com @f1000 | @f1000research | @rnl_s