name: title class: Left, middle background-image: url(images/rawpixel/nasa-moon.jpg) background-size: cover # .whiteinline[.fancy[PhD thesis meets reproducibility]] ### .whiteinline[[1.2] Reproducibility evaluation] .whiteinline[Reproducible Research Practices (RRP'21) · April 2021] .right[.whiteinline[Carlos Granell · Sergi Trilles]] .right[.whiteinline[Universitat Jaume I]] --- name: spacecraft class: bottom, middle background-image: url(images/rawpixel/nasa-cygnus-spacecraft.jpg) background-size: cover --- template: spacecraft ## You can't guarantee success, ### but you can guarantee failure: never try. --- class: inverse, center, middle # What does research mean for a PhD thesis today? --- class: center ## Claim #1 ### All published research today has a computational component. -- ## Claim #2 ### There is a mismatch between the traditional scientific process and computation, leading to reproducibility concerns. --- class: center # What about you? -- ### Is your research dependent on computation? How much? -- ### Which computational tools do you use? Do you use them sporadically or frequently? Are general-purpose (Word, ...) or specific (SSPS,...) tools? -- ### In which phases do you use them? -- .large[data collection, data storage, data analysis, data visualisation, writing, dissemination/presentation, communication, ...] --- class: center # Data sharing in academia ### Sequel of _Tenopir and colleagues_ .large[<a name=cite-tenopir2011></a>[[Ten+11](https://doi.org/10.1371/journal.pone.0021101)]: _Data Sharing by Scientists: Practices and Perceptions_] .large[<a name=cite-tenopir2015></a>[[Ten+15](https://doi.org/10.1371/journal.pone.0134826)]: _Changes in data sharing and data reuse practices and perceptions among scientists worldwide_] .large[<a name=cite-tenopir2020></a>[[Ten+20](https://doi.org/10.1371/journal.pone.0229003)]: _Data sharing, management, use, and reuse: Practices and perceptions of scientists worldwide_] --- class: center, middle # Disciplines [[Ten+20](https://doi.org/10.1371/journal.pone.0229003)] <img src="images/tenopir2020_fig07.png" width="55%"/> --- class: center, middle # Barriers [[Ten+20](https://doi.org/10.1371/journal.pone.0229003)] <img src="images/tenopir2020_fig09.png" width="70%"/> --- class: center # What about you? -- ### Do your colleagues in your discipline share data? -- ### Do you share all or part of your data? -- ### Would you like to share data? -- ### Which are the main barriers you face to data sharing? --- class: center ## Claim #1 ### All published research today has a computational component. -- .acid[Computational reproducibility] -- ## Claim #2 ### There is a mismatch between the traditional scientific process and computation, leading to reproducibility concerns. -- .heat[Transparent research] --- class: inverse, center, middle # What does .acidinline[reproducibility] & .heatinline[transparency] mean for a PhD thesis today? --- class: center # Five selfish reasons to work reproducibly <a name=cite-markowetz2015></a>[[Mar15](https://doi.org/10.1186/s13059-015-0850-7)] -- .pull-left[ ### helps to avoid disaster ### makes it easier to write papers ### helps reviewers see it your way ### enables continuity of your work ### helps to build your reputation ] -- .pull-right[  ] --- class: center # Five selfish reasons to work reproducibly [[Mar15](https://doi.org/10.1186/s13059-015-0850-7)] .pull-left[ ### helps to avoid disaster ### makes it easier to write papers ### helps reviewers see it your way ### enables continuity of your work ### helps to build your reputation ] .pull-right[ ### .acidinline[You learn some new science] ### .heatinline[You keep your papes bug-free] ] --- class: inverse, center, middle # What's your choice? --- class: center, bottom background-image: url(images/rawpixel/clouds-nebraska.jpg) background-size: cover ## .whiteinline[Business as usual scenario and irreproducible work remains the norm] <a name=cite-hong2015></a>[[Hon+15](https://arxiv.org/abs/1504.00062)] --- class: center, middle background-image: url(images/rawpixel/beach.jpg) background-size: cover ## Or you care about .acidinline[reproducibility] and .heatinline[transparency], and you are excited to acquire new reproducible research practices and habits! --- # References <a name=bib-hong2015></a>[Hong, NPC, T Crick, et al.](#cite-hong2015) (2015). "Top tips to make your research irreproducible". In: _arXiv preprint arXiv:1504.00062_. eprint: 1504.00062. URL: [https://arxiv.org/abs/1504.00062](https://arxiv.org/abs/1504.00062). <a name=bib-markowetz2015></a>[Markowetz, F](#cite-markowetz2015) (2015). "Five selfish reasons to work reproducibly". In: _Genome Biology_ 16, p. 274. URL: [https://doi.org/10.1186/s13059-015-0850-7](https://doi.org/10.1186/s13059-015-0850-7). <a name=bib-tenopir2011></a>[Tenopir, C, S Allard, et al.](#cite-tenopir2011) (2011). "Data Sharing by Scientists: Practices and Perceptions". In: _PLoS ONE_ 6.6, p. e21101. DOI: [10.1371/journal.pone.0021101](https://doi.org/10.1371%2Fjournal.pone.0021101). URL: [https://doi.org/10.1371/journal.pone.0021101](https://doi.org/10.1371/journal.pone.0021101). <a name=bib-tenopir2015></a>[Tenopir, C, ED Dalton, et al.](#cite-tenopir2015) (2015). "Changes in data sharing and data reuse practices and perceptions among scientists worldwide". In: _PLoS ONE_ 10.8, p. e0134826. DOI: [10.1371/journal.pone.0134826](https://doi.org/10.1371%2Fjournal.pone.0134826). URL: [https://doi.org/10.1371/journal.pone.0134826](https://doi.org/10.1371/journal.pone.0134826). <a name=bib-tenopir2020></a>[Tenopir, C, NM Rice, et al.](#cite-tenopir2020) (2020). "Data sharing, management, use, and reuse: Practices and perceptions of scientists worldwide". In: _PLoS ONE_ 15.3, p. e0229003. URL: [https://doi.org/10.1371/journal.pone.0229003](https://doi.org/10.1371/journal.pone.0229003).