Promoting Open Source Science

Open source science certainly seems to be catching on lately: there have been as many articles on the subject in the last few months as in the prevous few years. Here's a good one, an interview with Walter Jessen. This is his definition of what open source science means:

Open Source Science is a collaborative and transparent approach to science. To me, it means four things:

1. Open Source: the use of open and freely accessible software tools for scientific research and collaboration.
2. Open Notebook: transparency in experimental design and data management.
3. Open Data: public accessibility of scientific data, which allows for distribution, reuse and derived works.
4. Open Access: public access to scholarly literature.

It's well-worth reading, not least for its useful links to related sites.

Follow me @glynmoody on Twitter or identi.ca.

Open Source Dendrochronology

How could I resist this story? Aside from the great headline, it's about old-style closed-source science being challenge by open science, with open data - the only kind, if you think about it:

Dendrochronology is the study of tree-rings to determine when and where a tree has grown. Everybody knows that trees produce one ring every year. But the rings also vary in width according to each year's local weather conditions. If you've got enough rings in a wood sample, then their widths form a unique "bar code". Collect enough samples of various ages from buildings and bog wood, and you can join the bar codes up to a reference curve covering thousands of years.

Dendrochronology has a serious organisational problem that impedes its development as a scientific discipline and tends to compromise its results. This is the problem of proprietary data. When a person or organisation has made a reference curve, then in many cases they will not publish it. They will keep it as an in-house trade secret and offer their paid services as dendrochronologists. This means that dendrochronology becomes a black box into which customers stick samples, and out of which dates come, but only the owner of the black box can evaluate the process going on inside. This is of course a deeply unscientific state of things. And regardless of the scientific issue, I am one of those who feel that if dendro reference curves are produced with public funding, then they should be published on-line as a public resource.

But there is a resistance movement: amateur dendrochronologists such as my buddies Torbjörn Axelsson and Åke Larsson. They practice open source data transparency on the net, which means that arguably amateur dendrochronology is at this time more scientific than the professional variety.

I think it's also interesting because the story shows that, even in specialised areas like dendrochronology, openness makes a big difference to how the science is conducted - and how reliable its results are. (Via @BoraZ.)

Follow me @glynmoody on Twitter or identi.ca.

Peer-Reviewed Open Journal of Science Online

One of the most eloquent proponents of the idea of open science is Cameron Neylon. Here's an interesting post about bringing peer review to online material:

many of the seminal works for the Open Science community are not peer reviewed papers. Bill Hooker’s three parter [1, 2, 3] at Three Quarks Daily comes to mind, as does Jean-Claude’s presentation on Nature Precedings on Open Notebook Science, Michael Nielsen’s essay The Future of Science, and Shirley Wu’s Envisioning the scientific community as One Big Lab (along with many others). It seems to me that these ought to have the status of peer reviewed papers which raises the question. We are a community of peers, we can referee, we can adopt some sort of standard of signficance and decide to apply that selectively to specific works online. So why can’t we make them peer reviewed?

The Real Reason to Celebrate GNU's Birthday

As you may have noticed, there's a bit of a virtual shindig going on in celebration of GNU's 25th birthday (including Stephen Fry's wonderfully British salute, which really, er, takes the cake....). Most of these encomiums have dutifully noted how all the free and open source software we take for granted today – GNU/Linux, Firefox, OpenOffice.org and the rest – would simply not exist had Richard Stallman not drawn his line in the digital sand. But I think all of these paeans rather miss the point....

On Open Enterprise blog.

A Question of Open Chemistry

I've written about open science and open notebook science before, but here's an excellent round-up of open chemistry:

The next generation of professional chemists are far more likely to be in tune with web-based chemistry, treating blogs and social networking sites as professional tools in the same manner as email. For Open Chemistry advocates, the inevitable passage of time may be enough to usher in their revolution.

(Via Open Access News.)

They Gave Me of the Fruit...

...and I did eat:

But now an international scientific counterculture is emerging. Often referred to as “open science,” this growing movement proposes that we err on the side of collaboration and sharing. That’s especially true when it comes to creating and using the basic scientific tools needed both for downstream innovation and for solving broader human problems.

Open science proposes changing the culture without destroying the creative tension between the two ends of the science-for-innovation rope. And it predicts that the payoff – to human knowledge and to the economies of knowledge-intensive countries like Canada – will be much greater than any loss, by leveraging knowledge to everyone’s benefit.

"Sharing the fruits of science", it's called. Nothing new, but interesting for the outsider's viewpoint. (Via Open Access News.)

This is GOOD SCIENCE!

"Open notebook science" is a great term devised by Jean-Claude Bradley - great, because it makes explicit exactly where you can find, read and hack the source code that underlies open science. One of the best observers of that world, Bill Hooker, has an interesting comment on a fellow researcher's adoption of the open notebook approach:

It's also, to be honest, just plain fun to snoop around in someone else's lab notes! I was amused to note that Jeremiah talks to and about himself in his notebook, the same way I do -- "if I weren't so stupid I'd...", "next time load the control first, doofus", etc. I wonder if everyone does that?

Now, where have I heard this sort of thing before?

This is GOOD CODE!

Yeah, yeah, it's ugly, but I cannot find how to do this correctly, and this seems to work...Most of this was trial and error...Urghh

The programming comments of a very young Linus Torvalds as he hacked version 0.01 of a little program called Linux during the summer of 2001. Coincidence? I don't think so....