Stack Exchange sites for science

Recently I’ve noticed the emergence of several Stack Overflow-style sites for science-related questions and answers. For those unfamiliar with Stack Overflow – it’s a question and answer ‘forum’ for computer programmers that keeps the signal-to-noise ratio very high through a carefully refined reputation system. Late last year the creators of Stack Overflow launched a hosted service called Stack Exchange, which allows anyone to start their own “Stack Overflow” based around any topic.

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http://www.flickr.com/photos/alicebartlett/ / CC BY-NC 2.0

The service is was a little pricey ($129+/month), and I suspect this is one reason why a few open source clones inspired by Stack Overflow also exist. Since then, Stack Exchange sites (or clones) have proliferated – and those working as scientists (or those interested in science) haven’t been neglected. Here are my favorites:
  • MajorGroove.org pitches itself as a ‘forum for biologists’, which it is, however most of the content currently focuses on X-ray crystallography and associated techniques. It is currently in ‘bootstrap mode’, which means that reputation requirements are a little less strict until the userbase and site activity has grown to a critical size. Is there even a need for a Stack Exchange forum for biological crystallography ? Macromolecular crystallography already has a single, central, de facto standard forum – the CCP4BB mailing list. While it may be antiquated by Web2.0 standards, CCP4BB works well for a lot of people, and there is a huge amount of useful and important information buried in it’s archives. For many crystallographers, it seems CCP4BB would only be extracted from their “cold dead hands”. Despite this, I think the Stack Overflow format will be very beneficial for people new to the field.  As a side note – I discovered MajorGroove via Graeme Winters XIA2 blog right around the time when I was considering kickstarting a “Stack Overflow for crystallography”. At the moment it seems that a small userbase of crystallographers is already established on MajorGroove and there would be no purpose for another near identical forum. Even if questions about other techniques in the biosciences start to dilute out the structural biology, one click on the ‘crystallography‘ tag or the ‘ccp4‘ tag, and you can get straight to the good stuff. (In fact this feature was deemed useful enough by Google that they decided to bless the ‘android‘ tag on Stack Overflow as the official Android Q&A forum).
  • NMRWiki Q&A (http://qa.nmrwiki.org/) is a StackExchange-clone for magnetic resonances, mostly focused on NMR, but also open to EPR/ESR and MRI users. It’s not actually running on the StackExchange platform, but uses the open source OSQA / CNPROG clone, built on top of Django. As far as I know, there is no “CCP4BB for NMR”, which makes the NMRWiki Q&A site potentially even more valuable to structural biologists than it’s crystallography centric cousin, MajorGroove. Back when I was doing my PhD using protein NMR spectroscopy as my primary technique, there were very few good resources like this online – I do less NMR these days, but you can bet that I’ll be using the NMRWiki Q&A and it’s associated wiki to refresh my memory and catch up on need methodological developments in the future.
  • BioStar (http://biostar.stackexchange.com/), a StackExchange for bioinformatics, computational genomics and systems biology questions and answers. This one is busier and better established than the above mentioned forums, probably by virtue of the fact the bioinformaticians spend more time in front of the computer than your average molecular biologist or structural biologist.
  • And, for a bit of fun: Skeptic Exchange (http://exchange.bristolskeptics.co.uk/), which covers rational questions and answers to various topics including pseudoscience, faith healing, the supernatural and alternative medicine.

Want more ? There are a bunch of science related StackExchanges listed under “Science” here: http://meta.stackexchange.com/questions/4/list-of-stackexchange-sites .. and digging back through the FriendFeed archives I see Matt Todd initiated a concise listing (which if I’d seen, I probably never would have started this post).

And now, the latest* news Stack Exchange 2.0 will be ‘free‘. It looks like they are trying to structure the new Stack Exchange ecosystem a bit like the Usenet hierarchy (comp.*, rec.* etc), with a fairly involved discussion, proposal and acceptance process for new sites – it’s unclear yet whether this approach is going to work out better than just open sourcing the whole shebang, but time will tell. My guess is that BioStar, MajorGroove and probably even an incarnation of NMRWiki Q&A will eventually become part of this formalized ecosystem.

On one hand making StackExchange sites free to run is great – it lowers the barrier to entry to allow many more sites to emerge and operate. On the other hand, as we have seen with the acquisition of FriendFeed by Facebook, not having a clear revenue stream can ultimately leave communities  (such as The Life Scientists) without any certainty in a sites future, potentially impacting growth and participation. Personally I’m much more inclined to invest time in a site if it is something like Wikipedia, where I know my contributions are very likely to live on, in some form, for decades (centuries ?) to come. Ideally the archives of these new Stack Exchange sites could become useful online resources for decades to come – but with a single company at the helm and a “Web 2.0 business model”, continued operation for even a decade seems unlikely. The one saving grace: all content on the new Stack Exchange sites will be licensed under a Creative Commons license – so if Stack Exchange itself is acquired and shut down, we will always be able to preemptively leech the archives and provide them online elsewhere. Maybe it’s strange that I’m already thinking about archiving the new Stack Exchange upon it’s demise before it’s even begun, but I think it’s important to take the long term view with our data and recorded wisdom. Unlike when in 1994 when GeoCities (R.I.P) was started, teh Internets is no longer a fad – the hard disks connected to it are fast becoming the sum of all accessible human knowledge, so we’d better make sure we can retain the good bits for a little longer than 10 years.

* – as all too common these days .. I’m a little behind the curve on this one. I meant to finish this post a month ago, but with a busy time pre-holiday, then the actual holiday, a month has gone by.

Naming in molecular biology: get comfortable with meaninglessness !

I noticed an interesting post over on BoingBoing: “Comfort with meaninglessness the key to good programmers“. It outlines some research by Dehnadi and Bornat on attributes that can predict aptitude in computer programming. They conclude that a “deep comfort with meaninglessness” is an important predictor of programming aptitude.

I think comfort with meaninglessness is an important skill in studying biology (and probably other sciences too). Many times, during the description of a system, various acronyms are thrown about as labels for entities (or ‘actors’) in that system. An important skill of the scientist is being able to follow how all the actors in the system relate to each other, without necessarily knowing anything about the specific properties of those actors. There are lots of protein and gene names which often bear very little meaning relative to the biological entity that they label, and fixating on what ‘the name’ means simply distracts from the true nature of the entity.

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That Science Blog Meme Thing Going Around

Something broke out of the picket-fence surrounding Nature Networks Blogs. I’ve never participated in a blog meme … but this one appealed to me simply because I liked the questions. I haven’t read anyone else’s answers yet, to avoid biasing my own.

1. What is your blog about?

I often ask myself this question. Being a scientist, I always feel like it should be about science, and the various biological systems I work with. I reality, it is about programming, bioinformatics, the web with the tiniest bit of structural biology thrown in. I used to blog about Linux related things occasionally, but I split that off into another blog (which gets 10 times more traffic :)).

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A “Web2.0 for Scientists Week”: signup-fest ?

So, here is my half-baked idea:

Why not have a special week where new online collaboration tools are promoted to scientists globally ?Silly logo Web2.0 for a Signupfest

Similar to the way local Linux user groups sometimes run “installfests” to install Linux for users, (just to get them over the initial interia), why not have a global “signup-fest” for the core set of online tools useful for scientific collaboration ? In each local area / University / Institute, a few Web2.0 savvy scientists could promote the event and hand-hold new users through the signup process, and help with basic usage and integration of tools. Ideally, lab groups could signup together in the same room, and make an event of it. Or in places with Wifi … a “bring your laptop” signup lunchtime event. I think you get the idea.
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