A student recently asked me for some recommendations for an article on an open science topic for a journal club. Since I haven’t jotted these down in one place before, though I might copy my reply here for my future reference, or in case anyone else is interested in my list.
There’s a variety of sub-topics one might focus on; though in my opinion there’s no good, consise overview of all of the topics in one place.
open data:
Probably my first pick for a general discussion. The perspective in Science from 2011 is probably one of my favorites, but as the title suggests is more balanced than controversial. Nice also that it focuses on Ecology in particular and touches on some of the major initiatives in our field:
- Reichman, O. J., Jones, M. B. & Schildhauer, M. P. 2011 Challenges and Opportunities of Open Data in Ecology. Science 331, 692-693. (doi:10.1126/science.1197962)
Also from the ecology perspective but with a slightly more provocative stance is:
- Hampton, S. E., Tewksbury, J. J. & Strasser, C. 2012 Ecological data in the Information Age. Front. Ecol. Environ. 10, 59-59. (doi:10.1890/1540-9295-10.2.59)
This set of interviews from Nature’s Careers column this summer might make a more interesting context for discussion (e.g. practical concerns rather than the idealistic):
- Van Noorden, R. 2013 Data-sharing: Everything on display. Nature 500, 243-245. (doi:10.1038/nj7461-243a)
open code:
In my opinion this is the upcoming big issue. Of course open source has a long history in academia, but publishers and funders have paid a lot more attention to open data and open access (Creation of repositories like Dryad; required data deposition by many leading journals; funder’s support of data synthesis initiatives, etc). Interest in the potential for open code and concerns about reliability of increasingly software-driven results seem to be growing, this article does a good job providing concrete examples:
- Ince, D. C., Hatton, L. & Graham-Cumming, J. 2012 The case for open computer programs. Nature 482, 485-488. (doi:10.1038/nature10836)
a more recent piece in Science focuses on Ecology and some of the social challenges involved:
- Joppa, L. N., McInerny, G., Harper, R., Salido, L., Takeda, K., O’Hara, K., Gavaghan, D. & Emmott, S. 2013 Troubling Trends in Scientific Software Use. Science 340, 814-815. (doi:[10.1126/science.1231535])(https://doi.org/10.1126/science.1231535))
reproducible research:
The computational side
The computational side is more straight forward; this piece in Science discusses how the Biostatistics Journal optionally checks for code reproducibility and rewards it:
- Peng, R. D. 2011 Reproducible Research in Computational Science. Science 334, 1226-1227. (doi:10.1126/science.1213847)
experimental side
On the experimental side there’s been a lot of attention too, mostly on the medical issues. This piece actually focuses on risks and challenges in experimental replication:
- Bissell, M. 2013 Reproducibility: The risks of the replication drive. Nature 503, 333-334. (doi:10.1038/503333a).
Altmetrics:
Since open science usually emphasizes valuing things not ‘traditionally’ valued (code, data, open/reproducible papers), measuring academic impact often becomes part of the discussion. This comment piece from Heather gives an excellent overview:
- Piwowar, H. A. 2013 Altmetrics: Value all research products. Nature 493, 159-159. (doi:10.1038/493159a)
open access:
Perhaps the original “open science”, not sure there is much interesting to discuss here, more of an economic issue at this point than a scientific one (in my opinion anyhow). A few other interesting things being done by publishers, e.g. as mentioned in:
- Pincock, S. 2013 Publishing: Open to possibilities. Nature 495, 539-541. (doi:10.1038/nj7442-539a)
open peer review:
Some journals have been doing this for some time; for instance this piece reflects on the experience of one of the Nature journals that has been doing it:
- Pulverer, B. 2010 Transparency showcases strength of peer review. Nature 468, 29-31. (doi:10.1038/468029a)
open citations:
A topic that doesn’t get as much attention, but with some interesting ideas, e.g.
- Shotton, D. 2013 Publishing: Open citations. Nature 502, 295-297. (doi:10.1038/502295a).