03 September 2007

Open Science Means Open Source

The need for open access and open data in science seems obvious enough - even enough some persist in denying it. But as science becomes increasingly digital, with ever-greater dependence on computers and software, there is another aspect, as Nature Methods has recognised (but some months back - I've only just caught this):

The minimum level of disclosure that Nature Methods requires depends on how central the software is to the paper. If a software program is the focus of the report, we expect the programming code to be made available. Without the code, the software—and thus the paper—would become a black box of little use to the scientific community. In many papers, however, the software is only an ancillary part of the method, and the focus is on the methodological approach or an insight gained from it.

In these cases, releasing the code may not be a requirement for publication, but such custom-developed software will often be as important for the replication of the procedure as plasmids or mutant cell lines. We therefore insist that software or algorithms be made available to readers in a usable form. The guiding principle is that enough information must be provided so that users can reproduce the procedure and use the method in their own research at reasonable cost—both monetary and in terms of labor.

However, the editorial rightly points out that releasing the code as open source has huge advantages:

Some authors who favor the highest degree of transparency and sharing for their software elect to develop their programs in an open-source environment. By doing so, the authors not only provide accessibility and transparency, they also allow the community to build upon their own developments and make continuous improvements to the tool. Open-source software has become extremely popular in various fields. In microscopy, for example, image analysis software tends to be modular, and users benefit from the flexibility of being able to replace some modules with others in an open-source framework. Despite the tremendous added value of open source, other authors prefer to release a compiled version of their program, so as to protect commercial interests tied to sophisticated custom-designed software. This option is not optimal because it turns the program into a black box, but it may be acceptable if the operations performed by the software are sufficiently clear.

Although it is probably appropriate that Nature Methods, given its focus, should be the first to articulate this issue, it is important to appreciate that its logic applies to all scientific publishing where computers are involved. Without open source, there can be no open science - the only kind that is worthy of the name. (Belatedly via Flags and Lollipops.)


Peter Suber said...

Glyn: Good catch. Can you include a link to the editorial, even if it leads to a pay-per-view screen for most of us? Or at least a date? I couldn't find the editorial in the current, September issue.


glyn moody said...

Stupid me: now fixed. In fact the credit isn't mine, but another blogger, whose original I couldn't find, but I have now (also inserted). I see it was back in March, but it popped up in the RSS feed today for reasons that escape me.

Ah well, better late than never....