Future of BioStar

[Konrad]

First of all, I’m sorry for barging in like this – I’m not an active
user of BioStar but I’ve become aware of a blog post concerning the
future of BioStar [1] by accident and I was asked by Daniel Swan to
cross-post my concerns here.

Essentially, the BioStar website is running on the Stack Exchange 1.0
platform which is due to go offline in a few months so in order to
survive BioStar has to migrate. The blog post mentioned above lists
some alternatives concerning this.

My concern is that many BioStar users are not aware of the possible
path to migrate the site to Stack Exchange 2.0. This has both
advantages and disadvantages and I don’t want to argue either case
here. I just want to make you aware of the discussion [2] and an
alternative bioinformatics proposal [3] on Area 51 (which is the Stack
Exchange 2.0 community breeding platform) and I would like to ask you
to take the time to contribute to the discussion since only *you*, the
active members of BioStar, can meaningfully decide about its future
and at the moment the activity (or even awareness of the discussion)
seems very low.

[1]: http://blog.fuzzierlogic.com/archives/509
[2]: http://discuss.area51.stackexchange.com/q/1291/319
[3]: http://area51.stackexchange.com/proposals/6729/bioinformatics

[neilfws]

No need to apologise; all contributions are welcome!

We have had some discussion regarding the future of BioStar (if you search this group, you will probably find it).  Our main concern is that we preserve the current archive of questions/answers and the user base.  If that can be done by migration "as-is" to SE2, then fine.  If not, we will find another way.  I think for our community (which you see is quite active), it's not a question of SE2 or nothing.

[Istvan Albert]

Hi Konrad,

Thanks for your post. I appreciate a well though out and detailed
argument as it helped me shape and crystallize my own arguments.
I found your blog post eye opening, but perhaps not for the reasons
you intended.

http://blog.fuzzierlogic.com/archives/509

I am greatly troubled by seeing that it is Joel Spolksy (who happens
to make use of some some arbitrary and silly numbers of posts/day etc)
who decides whether or not a Q&A site should or should not exist. This
whole committee, stages and hurdles one needs to pass etc seem little
more but a straitjacket designed to allow a third party to maintain
control, and it promotes an ideology that is counter to freedom of
expression and innovation.

You seem to forget that the problem of having to migrate today are
cause by no other entity but SE, yet you think that the solution is
to again hitch our ride to SE. I think history does repeat itself and
the same type of issues will arise with the new SE sites as well.

I optimistic that we will have a solution that both maintains the all
content of the existing BioStar yet will be fully under our own
control. As most grant proposal writers know sometimes you only get
things done due a deadline pressure (and that is approaching as in end
of April).

best,

Istvan

--
Istvan Albert
Associate Professor, Bioinformatics
Pennsylvania State University
http://www.personal.psu.edu/iua1/

[Konrad]

On Mar 22, 2:47 pm, Istvan Albert <i...@psu.edu> wrote:
> I found your blog post eye opening

Heads up: I did not author that blog posting. I just found it via
Twitter and left a comment.

In the following I will lay down some arguments why I believe that the
SE 2.0 route is *at first* the best course of action: I'll try to
convince you to at least give Stack Exchange a try.

Full disclosure: I am not in any way affiliated with Stack Exchange
nor any of its employees. My only connection to them is that I am one
of the top users on Stack Overflow and have served as temporary
moderator on the tex.stackexchange.com site during the beta phase. To
emphasise that I am *not* defensive of Stack Exchange, let me point to
a few examples [1, 2] where I have had violent disagreements with
their community management style.

> I am greatly troubled by seeing that it is Joel Spolksy (who happens
> to make use of some some arbitrary and silly numbers of posts/day etc)
> who decides whether or not a Q&A site should or should not exist.

I cannot comment on the whole process involved in deciding whether a
community site continues to exist. However, the reality is much better
than you seem to think. All evidence so far suggests that Stack
Exchange really tries their hardest to make communities work. There
have been very few examples of failed communities so far. The numbers
cited in the blog post [4] are merely an indicator of success, not a
hard reason to let a site fail, as has been made clear on the Stack
Exchange blog [5] (and there is no reason to doubt this, given the
continued existence of the GIS community [6]).

The reasons for which atheism.stackexchange.com failed will *not*
apply to any potential bioinformatics site. Low community activity was
only one (and possibly the least important) factor. More important is
the fact that the Stack Exchange format (of question-answer) is
inherently ill-suited for discussions about atheism. Until now, not a
single SE site has failed simply because it had too low activity.

The fact remains that Stack Exchange does not close communities "just
because". This will not happen to a rebooted BioStar.

> This
> whole committee, stages and hurdles one needs to pass etc seem little
> more but a straitjacket designed to allow a third party to maintain
> control, and it promotes an ideology that is counter to freedom of
> expression and innovation.

I can say with certainty that this is false. Until now, Stack Exchange
has shown the greatest respect and restraint in their demeanour
towards communities. There have been very few clashes and most were
based on bad communication and swiftly resolved (with apologies from
Stack Exchange [7]). There is no reason to suspect that Stack Exchange
is trying to straitjacket communities or to impose ideologies that run
afoul of freedom of expression and innovation.

> You seem to forget that the problem of having to migrate today are
> cause by no other entity but SE, yet you think that the solution is
> to again hitch our ride to SE.

Their original business model failed, it's as simple as that (and I
won't even try to defend that). But I can turn your argument on its
head: without SE, there would be no BioStar so you think parting ways
is the solution? Neither argument makes any particular sense.

> I think history does repeat itself and
> the same type of issues will arise with the new SE sites as well.

The same kind of problems can potentially arise with *any* hosted
platform though. Self-hosting is of course an alternative but it's
more time-consuming and costs money.

I still urge you to consider the advantages of staying with Stack
Exchange and upgrading to the 2.0 platform:

* Better software. Let's face it, no other q'n'a software will even
come close to the functionality today provided by Stack Exchange since
they've got a team of full-time employed top-notch programmers working
on it. This also includes reliability, efficiency and stability.
* Excellent marketing. I am going ahead and say that an independent
site will *never* get the same traction that a Stack Exchange 2.0 site
will -- not by a long shot.
* Chat. I'm not a great fan of chats myself but I have to say, the
Stack Exchange chats are nifty because they just *work*.
* Free support and hardware trouble-shooting, free backups and data
security. Basically, free everything.
* Professional design.

And yes, there *are* points that speak against Stack Exchange
adoption:

* You give up control to some extent; the site will still controlled
largely by the community but the official owner will be Stack
Exchange. Revenues through advertisement go to them (but I wouldn't
over-estimate this).
* As mentioned above, some conflicts *may* arise. But these have all
been between individuals, never (to my knowledge) between the
community and Stack Exchange.

[1]: http://meta.programmers.stackexchange.com/questions/1293/1294#1294,
see comments
[2]: http://meta.english.stackexchange.com/questions/557/558#558, see
comments
[4]: http://area51.stackexchange.com/proposals/2732
[5]: http://blog.stackoverflow.com/2010/12/no-artificial-intelligence-in-area-51/
[6]: http://blog.stackoverflow.com/2010/10/when-will-my-site-graduate/
[7]: http://blog.stackoverflow.com/2010/10/domain-names-the-wrong-question/

[Giovanni Marco Dall'Olio]

One question: will the move to the SE 2.0 engine be for free? Or will we have to pay a subscription after the move?
If the switch to the 2.0 is for free, I would vote for giving it a try. We will still be able to plan a switch to other solutions afterwards, but in the meantime we will have access to the newer features. We will also be able to test these new features and eventually give useful feedback to SE, which would be a way to pay for all the services we have used for free.
To me, the fact that they are pushing people to move to the 2.0 seems understandable: they just don't want anyone to stick with older implementations of the software that they won't support, and in some way, it is like when your operating system asks you to update all the software installed when there are any available.

In any case, compared to other companies (Microsoft?) the people that programmed the SE have done a very good job in making everything available for free.
We have been able to use the SE beta for free until now; the SE sites are open and don't require paid subscriptions, and all the discussions are released with a creative commons license.
Even if tomorrow they change their minds and start requiring a subscription, we will always be able to move to other solutions and retain all the discussions open. If they want to create a business about all the efforts they have done, I think it is fair, but in any case they will always leave us the option to switch to an alternative. It reminds me of what happens for wordpress and other similar open source projects.

About the post on the Atheism SE site, it probably has created only confusion and we should forget about it. It seems to me that the numbers have been used just as an excuse to close a website who could have been potentially troubling and not particularly useful. The case for biostar is different: while there are a lot of websites about atheism and religions in Internet, there are very few forums on bioinformatics; moreover, discussions on biostar are about technical problems and not ideologies; and finally, biostar has already been proved to contribute to the scientific community, having been acknowledged in some papers and having helped completing many others.

--
Giovanni Dall'Olio, phd student
Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain)

My blog on bioinformatics: http://bioinfoblog.it

[Konrad]

> One question: will the move to the SE 2.0 engine be for free? Or will we
> have to pay a subscription after the move?

There will be no fee, Stack Exchange 2.0 communities are completely
free. Basically, nobody “owns” the community any more (at the moment
BioStar has an owner) so there’s nobody in the position to pay any
fees. All the content will be owned by the community and the site will
be operated by Stack Exchange (and the elected (!) moderators).

I’m not exactly sure about the technicalities of moving an existing
Stack Exchange 1.0 site over to 2.0 though – this is something best
answered by somebody from Stack Exchange (I’m emailing their community
coordinator with a request for comment).

Regards,
Konrad

[Konrad]

I forgot to mention, a lot of questions about the general process are
already answered at http://area51.stackexchange.com/faq though this
site lacks some specific infos concerning migration of existing sites.

[David Quigley]

I have not seen any software platform that works as well as Stack
Exchange for Q&A. The basic paradigm of community rating of questions
and answers combined with decentralized moderation is much, much
better than free-form bulletin boards. Although the points system is
at one level irrelevant to the purpose of the site, it provides a
subtle or not-so-subtle motivation to provide high-quality questions
and answers. I would hate to see biostar move completely off of a
system with these characteristics. These ecosystems are very fragile,
and I think starting over from scratch would be fatal to a very useful
tool.

I took a look at the SE clone at osqa.net. I'm surprised that SE
apparently tolerates a wholesale cloning of their entire site, both
look and feel and methodology, open source or not. I have to wonder if
that will always be the case. If you could pick up the site and move
it to that platform without changing much of anything, then that might
be a viable option. Still, I think the best outcome would be the one
with the least change: staying within the same software system.

Cheers,
David

[Andra Waagmeester]

I came here via area51.stackexchange.com. Personally I don't like the reasoning where biostar is "demanded" to change towards SE2.0. I have expressed my concern there (according to the -1's I have stepped on some toes, my apologies it was not my intention to offend). As I understand now biostar is doomed anyhow. Is this correct?

I am small biostar user, extremely happy with its existence. But I have some concerns if moving to SE2 is a good thing. Let me give an example. 

Due to my experiences with biostar, I played a bit with other SE platforms. Being a parent of twins, I engaged with the same enthusiasm in Parenting.se as with biostar. I lost confidence after two weeks. Parenting in my opinion is to subjective to be suitable for the SE platform. But my biggest concern with SE2 is that others can actually change your question. At first I don't see any problem there, except for the fact that if someone changes the question, he/she should become the main author of the question. Otherwise you are putting words in someone's mouth. But after giving it some thought, I consider this policy dangerous.  Let me give an example.

I asked this question http://parenting.stackexchange.com/questions/28/at-what-age-should-siblings-stop-sharing-their-bedroom. Quite quickly the  question was changed into "at what age same-sex siblings, etc". This was not my question and it indeed changed the direction of the answers given. I was able to go back to the initial question, but but the effect was already there. I find it strange that people can change questions. For me this is a principle concern. People (me included) do ask bad questions (although some say that bad question don't exist ;) ), but in biostar this is dealt with by commenting or proposing to delete question. I do believe this should be the way to go. 

Anyhow, it is just my opinion. It would be a pity if biostar would cease to exist, but it is not the end of the world. 

[Chris Miller]

FWIW, wuestions can be edited by moderators on Biostar as well, though
we tend to use a light hand and only edit where meanings are unclear.

I'm not sure what you mean by "Biostar is doomed". There is some
discussion as to whether hosting it on SE2.0 or a custom-built site is
the best approach, but I can assure you that there is a strong
community devoted to keeping BioStar around.

-Chris

[Istvan Albert]

On Wed, Jun 22, 2011 at 12:40 PM, Andra Waagmeester
<andra.wa...@gmail.com> wrote:

> I find it strange that people can change
> questions. For me this is a principle concern.

One of the main reasons for exploring alternatives to the SE platform
is to be able to alter
the way the site works. Features of the like you mention do not seem
particularly well suited for
the type of use cases that we have.

I have been out of the country for a few weeks and the development of
the new platform stalled a bit.
It is very close, most of the functionality is there.

Fear not however, nothing is doomed, no plug is being pulled.