Stack Exchange and the future of BioStar

Over the weekend I saw this tweet from Stack Overflow/Exchange founder Joel Spolsky. The content of the link he posted has served to crystallise some of my thinking of the last couple of weeks with relation to the Bioinformatics question and answer site BioStar.

The link Spolsky posted in the tweet was to a failed Stack Exchange proposal, and I found the page interesting not for the proposal, or the fact that it failed, but the clearly enumerated reasons for why it failed. Here’s a screenshot:

Atheism SE Proposal Screen Cap

To clarify the procedure here, new Stack Exchange sites are proposed by a community of users. That community was originally drawn from Stack Overflow, the extremely successful programming Q&A site, but now that there are nearly 50 active sites, the available community of proposers is much larger. Newly proposed sites have to overcome a series of hurdles before they go live, from proposal, through commitment, to a private beta, a public beta, before finally becoming a fully-fledged SE site. At the end of each of these stages, sites are assessed for the likelihood that they will become a healthy and active site. Crucially, this assessment appears to not be an individual process. It is obviously the view of the SE powers-that-be that all Q&A sites are created equal, and what works for one will work for all of them. What is worrying about this attitude is that sites that are genuinely niche and likely to have a small, but active and dedicated, community will be left by the wayside, since presumably they will be unable to generate the kind of ad-revenue that Spolsky at al are going to require to repay their investors.

BioStar is a web community reaching a crossroads. The site is running on the now-free, but inevitably unsupported Stack Exchange 1.0 platform (the process discussed above is for the SE 2.0 community). To continue to thrive, I firmly believe the site needs to move on from this platform, since it is almost certainly going to be closed down from under it within the next 12-18 months. This presents the site owners (and us, the community) with a choice.

  1. Migrate the site to SE 2.0
  2. Change to an open-source alternative Q&A platform
  3. Roll-our-own site, with the functionality we require

I will start by ruling out option 3. Bioinformatics teaches us the perils of reinventing the wheel when it is not necessary. An effort to write a custom-built platform for BioStar would be almost entirely redundant, undertaken on the free time of the community (free-time which could be better spent answering questions on BioStar), and almost certainly offer no tangible benefit over using one of the already available Q&A engines. (Think Facebook-for-Scientists…)

I used to be firmly in the camp supporting option 1. I genuinely love Stack Overflow. I have found great utility in some of the Stack Exchange family of sites. However, the attitude betrayed in both Spolsky’s tweet and the closure notice on the Atheism Stack Exchange site makes me think that BioStar would be left out in the cold if we attempted this migration. Let’s look at how BioStar measures up to these numbers:

  • Questions per day (SE 2.0 recommends – “15 questions per day on average is a healthy beta”)
    • Since 30th September 2009 BioStar has received 1,681 questions – that’s 3.13 questions per day
  • Percentage answered (SE 2.0 – “90% answered is a healthy beta”)
    • BioStar does well here. There are currently 47 questions with no upvoted answers – about 2.8%
  • User group (SE 2.0 – 150 users with 200+, 10 with 2,000+, 5 with 3,000+)
    • We have 14 users with 3,000+, 24 with 2,000+ and (by my count) 142 with 200+. But BioStar has been going for 18 months, the atheism SE site was shut down after 2 months in public beta
  • Answer ratio (SE 2.0 – “2.5 answers per question is good”)
    • I don’t have easy access to precise numbers for this, but it’s around 3 answers per question on BioStar
  • Visits per day (SE 2.0 – “1,500 visits per day is good, 500 visits per day is worrying.”)
    • I have no stats at all for this, but I’m willing to put good money on the fact that daily numbers are much closer to 500 than 1,500.

By these criteria, and judging by the Atheism Stack Exchange linked to by Spolsky, BioStar would fail to emerge from SE 2.0 beta, based on current numbers, and any effort the existing community put in to get it that far would be wasted. And I don’t think the audience of the site would be grown dramatically by it being a Stack Exchange 2.0 site. I think we have to accept that Bioinformatics is a niche subject with a relatively small potential audience, one that is not going to be especially interesting to a commercially driven exercise (such as Stack Exchange necessarily has to be).

So that leaves us with migration to an OSS alternative as the only remaining option. There are a number of platforms available, some of which offer an experience extremely close to ‘real’ Stack Exchange. I would pick one of these that allows an existing SE XML dump to be imported, and migrate the site as soon as possible, certainly within the next 6 months. There is no question that the change over will be painful, and will probably cost the site a few users, and some traffic in the first instance (the URL will have to go, for example), but I am confident in the community that has been built around the site – it will survive, and will be all the stronger for the change.

Besides, if we look at the facts in the cold, hard light of day, we really have no choice.


  1. I would be careful drawing too many parallels between a Q&A site about “Atheism” and a Q&A site about “Bioinformatics”.

    We didn’t think the atheism site was a particularly good idea from the get-go based on the topic, whereas bioinformatics has a *strong* overlap with our geeky core audience. But the community wanted such a site, so it was launched as an experiment.

    Did you look at the atheism site? There simply wasn’t much of a core topic for people to discuss. In the end, even the community members who participated on meta.atheism acknowledged that the site couldn’t survive. Furthermore, editorically, we didn’t feel Q&A on atheism was ultimately *making the internet better*, which is our goal.

    There are plenty of other topics that are doing quite well, as you can see at — and they benefit immensely from being a part of a strong topic network which actively cross-pollinates smart users.

    So, I’d say support the proposal:

    My wife is a scientist, and I’m happy to put my support behind that proposal

  2. I’m going to agree with Jeff. I was one of the most active users on atheism.SE, and I’m not at all active on BioStar.

    But despite this, I’ve made it clear *from the beginning* that I was expecting atheism.SE to fail: this simply isn’t a q’n’a friendly topic. Furthermore, there already *are* established atheism web communities which didn’t adopt the new platform at all.

    As for BioStar, there are of course several reasons for its slow going. I think one of the reasons is failure of marketing. I’m a bioinformatician and although I *had* heard of the site before (putting me ahead of 99.999% of bioinformaticians) I just had no incentive to ever go there. *That said*, I actually think that a bioinformatics knowledge base isn’t only useful, it’s *essential* and I think with the right marketing it would be a success.

    One of the good things about the Stack Exchange 2.0 approach is the free marketing that new sites inevitably get (Jeff mentioned cross-pollination: that’s it).

    I don’t actually know how much the user bases overlap but there *are* bioinformaticians who are quite active on Stack Overflow, and certainly also on other sites such as Cross Validated. Getting a few of these active people to commit to a bioinformatics proposal should not be a problem.

    My suggestion is: give it a shot, and if the SE 2.0 approach fails there is still time to settle on an alternative platform.

    FWIW, the skeptics Stack Exchange was in a similar dilemma and although it’s too early to judge I’d say that they are doing quite fine at the moment. The question volume is certainly lower than on other sites but I’m not expecting as momentous a failure as for atheism.SE because the skeptics.SE approached the problem from a different angle – the q’n’a angle.

  3. It is encouraging that each SE site is considered on its individual merits. Jeff, I think you should be aware of how it looks when a site is closed down with such a stark list of statistics. It makes people (well, me at least) think ‘oh look, they closed it down cos the numbers didn’t add up’ – which is discouraging.

    I think the problem with the Bioinformatics SE proposal as it stands is that it is positioned, intentionally or otherwise, as a *competitor* to BioStar. A site that would steal mindshare and undermine the hard work put in by the core community at BioStar, many of whom would not be motivated to repeat the effort they have put in here to make the new site a success.

    This “suck it and see” approach to a SE 2.0 site would be just fine, if it were a continuation of what we have managed to achieve with BioStar, rather than a complete recapitulation from scratch, that disenfranchises the existing community contributors, moderators and administrators.

  4. I agree Simon. I would only accept the Bioinformatics SE proposal if we could save all the work that has been achieved for Biostar to this new engine.

  5. “I think the problem with the Bioinformatics SE proposal as it stands is that it is positioned, intentionally or otherwise, as a *competitor* to BioStar.”

    I believe this is simply a misunderstanding on your part. There is no competition simply because BioStar currently has no SE 2.0 equivalent, there is no BioStar proposal. And the problem with starting one now would be that it would have to split resources with the (already quite mature) bioinformatics proposal, unnecessarily diminishing its force. In fact, if BioStar created an own SE 2.0 proposal on Area 51, these two proposals *should* be merged to have any success at all.

    That said, it may make sense from a branding perspective to merge the bioinformatics proposal *into* the (yet to be created) BioStar proposal rather than the other way round. Not sure if this is possible.

  6. “Jeff, I think you should be aware of how it looks when a site is closed down with such a stark list of statistics. It makes people (well, me at least) think ‘oh look, they closed it down cos the numbers didn’t add up’ – which is discouraging.”

    Atheism.SE wasn’t closed because it had poor stats; the site failed because it failed to produce interesting content. It wasn’t “the numbers didn’t add up” but rather “no self-respecting atheist would read this site.”

    I tried really hard to make Atheism.SE work – I was the second highest ranked user – and I am happy it’s gone. It wasn’t a good site.

    A bioinformatics SE site is unlikely to suffer of the same problems.

  7. In addition to the other responses, I would also keep in mind that the beta phase is not a 90-day do-or-die situation. 90 days is simply the absolute minimum threshold. If a site is “making the internet better”, then we are happy to let it stay in beta as long as it needs to grow into a healthy site. We are not asking you to put effort into a site only to rip it away because it didn’t grow fast enough even if the site is good. Looking at the beta phase and graduation has come up a couple times:

    As you can see, we have a number of sites in beta past 90 days that are continuing to grow for their graduation:

    The Atheism site had poor stats, but as Borror0 mentioned, the poor stats were a result of the lack of interesting content on the site. It wasn’t a site that was making the internet better – even supporters of the site saw that it wasn’t working. This is the same with the other 2 sites that have been closed.

    Bioinformatics is a vastly different type of topic than Atheism. There are only so many questions you can ask about Atheism. I don’t see that being true with bioinformatics.

    Don’t underestimate the value of being a part of the network and cross-pollination. All sites (including betas) are listed on and when a site graduates, it gets listed in the footer of the other launched sites. We’ve noticed that even unrelated sites get a boost from that.

    Basically, if a site is working, we’re happy to let it stay in beta as long as it needs to continue to grow and become a healthy site. Shutting down a site is an exception, done when it is obvious the site just isn’t working, and this has been because of topic/scope more than anything else. We aren’t asking people to put in effort to a site only to rip it away because it is a bit smaller than a number we’ve set. If a site has quality content, every thing else will follow.

  8. My point about the atheism site in particular, which I think still stands, is that nowhere on the page I link to is there any rationale for the closure other than the list of stats. This gives the impression to the average visitor, who may know nothing about the site or its history, that it was closed due to disappointing numbers. And that impression led to the analysis I present here. If it requires multiple people to comment on individual blog posts to “correct” that impression, then maybe you’re doing it wrong.

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