Forum: Shall We Go Back To Stackexchange?
gravatar for 14134125465346445
8.3 years ago by
United Kingdom
141341254653464453.5k wrote:

I can still remember the old times when an old version of SE was gathering more Q&As that what we have today. Shall we go back to stackexchange?

forum • 4.8k views
ADD COMMENTlink modified 8.3 years ago by KCC4.0k • written 8.3 years ago by 141341254653464453.5k
gravatar for Neilfws
8.3 years ago by
Sydney, Australia
Neilfws49k wrote:

When BioStar moved from Stack Exchange v1 and we were assessing the options, I was strongly in favour of migration to Stack Exchange v2. Several months later, my opinion has not altered: indeed, I feel more strongly that this would have been the better decision.

My opinion is based around 4 ideas.

  1. The best applications do one thing and do it well
  2. How effectively a site is used is strongly dependent on its design principles
  3. Websites are best implemented by professionals who have given a lot of time and thought to design
  4. Sometimes pragmatism is better than principles

First, the one thing that Stack Exchange sites do well? They provide answers to questions. However, BioStar is now trying to provide news, tutorials, videos, jobs, feed's too much and distracts from the major focus of the site.

Second: I strongly believe that site design can be used to encourage better usage and behaviour. To take some specific examples:

  • Auto-suggest for tags encourages users to reuse existing tags. This leads to better classification of questions and more effective search. The lack of this feature at BioStar has rendered tagging useless.
  • Prominent display of previous questions that are similar to the one being asked. At Stack Exchange, this is again achieved using auto-suggest. Clearly BioStar is not effective in this regard, since the same questions come up over and over again.
  • Effective preview of questions to encourage better formatting, along with prominent links to editing help. Again, BioStar is not effective in this regard since it seems almost no-one can format their code properly, leading to unreadable questions.
  • The effect of sorting/ordering on the ability to detect recent activity (addressed in Should A New Question And A Question With A New Answer Always Be Placed On The Top?).
  • Appropriate increments (and decreases) in score reward performance and encourage participation. Currently at BioStar the scoring system is obtuse, my progress feels glacial and I do not feel encouraged to answer questions. This was not the case with Stack Exchange.

And my last example: strong moderation is essential for site quality. Downvotes are a signal from the community that your question requires serious attention before it can be taken seriously. Duplicates need to be closed. Moderators need a form element where they can (or even must) explain their actions, not an optional comment.

My (subjective, anecdotal) impression is that question quality has substantially declined since moving off Stack Exchange and I'm tempted to blame some of the design decisions for this. Another factor, of course, may be an influx of new users who are ignorant of (or simply don't care about) site standards.

Third: the Stack Exchange team are professionals, with a lot of experience and ideas about what works well and what does not. I believe that people like them think about these issues so that we do not have to do so and can just get on with business. As an example, compare the top of a Stack Exchange page:


with that of BioStar:


Which provides a clearer picture of what the site does and what a user is supposed to do?

As another example, I'm sure this makes sense in the mind of a Python programmer:


but is it good design, obvious to a new user?

I think the BioStar developer team do an excellent job but the fact is: they are amateur web programmers, working on the site in their spare time. Inevitably, some important issues with major effects on site functionality go unaddressed for too long.

Fourth: to explain "pragmatism over principles." It seems to me that there were many factors favouring Stack Exchange and only one against - data licensing. Whilst I agree that this is an important issue (being very much an "open" guy), it just seems to me that it was outweighed by the other factors. In other words: was it important enough to sacrifice site functionality? I don't believe so.

Anyway - here we are and there is no going back. I do very much appreciate the hard work that has gone into developing BioStar. However, I also believe strongly that the site would be substantially improved if not by migrating to Stack Exchange than at least by applying their design and usage principles. I hope the team will think about these points and view them as constructive criticism.

ADD COMMENTlink modified 8.3 years ago • written 8.3 years ago by Neilfws49k

I asked Should A New Question And A Question With A New Answer Always Be Placed On The Top? because I saw this thread. I realized that I had not provided any useful suggestions although I was concerned with some details of the new biostar. Some of my concerns, such as the ordering of questions (this is my major one), can be easily addressed if the developers are aware of them. Others, such as hint on existing tags and related questions, are harder technically, but no technical problems at this level are unsolvable as long as others have done those. We should send our feedbacks. Biostar can be improved.

ADD REPLYlink written 8.3 years ago by lh332k

I also support everything Neil said. I appreciate the effort in developing Biostar, but I can also see that the same efforts could be directed toward better objectives. The way we are doing it right now is indicative of the biggest sin in bioinformatics, which is, to spend all the energies in doing something that has already been implemented by somebody else.

ADD REPLYlink written 8.3 years ago by Giovanni M Dall'Olio27k

I know I am the minority here: I do not always think reinventing the wheel is a great sin in programming or in bioinformatics. I have reinvented a lot and learnt a lot from this process others may think as a waste of time. Sometimes we should be brave enough to restart, which may not take as much time as we thought initially. Although Neil's is a long post, only hint on related questions is technically hard. Others can be addressed in a few days at most.

ADD REPLYlink modified 8.3 years ago • written 8.3 years ago by lh332k

I agree. Reinventing the wheel is a great learning process in a lot of cases. I've always felt there is an implicit accusation of: "you must be very full of yourself if you think you can redo this process better", especially in science/programming. There needs to be a good balance between retrospection of proven methods and trust in proven methods.

ADD REPLYlink written 8.3 years ago by Damian Kao15k

edited my original answer to try to answer some of your observations

ADD REPLYlink written 8.3 years ago by Istvan Albert ♦♦ 86k
gravatar for Istvan Albert
8.3 years ago by
Istvan Albert ♦♦ 86k
University Park, USA
Istvan Albert ♦♦ 86k wrote:

This post made me look up some numbers - we have very similar number of contributions in the months before the switch as in the months after.So the assumption that the SE was somehow better is not supported by the evidence.

Biostar content cannot be moved to SE neither today nor in the future. The reason for this is that the licensing on Biostar is far more permissive than SE (before anyone wants to disagree please make sure you understand what the SE "share alike" statement actually covers).

In fact the SE licensing is the primary reason of why Biostar exists as a stand alone site.

Edit in response to Neil's post, I would rather put it here than into a new answer or comment

You are correct in that if all Biostar wanted to be is a Q&A a simpler interface would suffice. But I don't think it should stay just Q&A because I don't think the bioinformatics of the future will be as easily "condensable" to simple Q&A tidbits as a typical programming/computer science related issue.

Bioinformatics on a StackExchange platform would never turn a destination where one could also learn how to be a good bioinformatician - but I am hoping that Biostar could become that - and we are trying out different avenues to getting there. This is why we are not running a Q&A clone either - those too are too rigidly focused on just one use case.

We've switched over about seven months ago and as you point out there are flaws in the user experience - and those are all my fault. At the same time I think that we have also managed to improve on their experience: for example I would dare to say that our threaded commenting is better then theirs and I am sure there are new features that other people enjoy.

I would urge everyone to have faith - we have options and we can create any type of environment.

And perhaps threads like this should be created every six months to get to know what the community thinks of the state of BioStar and its direction. While implementing features in reasonably complex program it is not always easy to understand what the relative importance of various features are.

ADD COMMENTlink modified 8.3 years ago • written 8.3 years ago by Istvan Albert ♦♦ 86k

I appreciate all the work that has been put into Biostars. I do think it has become a 'hub' of sorts for the ever growing online bioinformatics community. Perhaps that is also part of the problem. What is Biostar supposed to be? Q&A? A bioinformatics portal? I think Neil's comments about design reflects this problem.

A Q&A needs to provide a clean interface for users to get at their information quickly. Stackexchange does that effectively. A hub/portal type of site has a whole set of different design elements. I think maybe part of the problem is the hybridization of both functionalities in one site.

ADD REPLYlink written 8.3 years ago by Damian Kao15k

That's funny, I was under the impression that when the 'decision' was taken to not migrate to SE v2 that the possibility was always open for this to be reconsidered in the future. I'm pretty surprised to discover this is apparently not the case (though I note that this tool: suggests there is no legal issue here - though I'm sure there will be some significant technical issues, due to the divergence of the platforms)

ADD REPLYlink modified 8.3 years ago • written 8.3 years ago by Simon Cockell7.3k

What I meant it is not possible under the current (as well as the original, old Biostar) licensing terms. Someone would have to take the responsibility of re-licensing the content and then sign a legal agreement with SE and by that give them full ownership of all content. Only this act would allow them to impose their custom "share alike" clause. In essence this makes the re-licensor responsible for all the legal implications.

ADD REPLYlink modified 8.3 years ago • written 8.3 years ago by Istvan Albert ♦♦ 86k

I wonder if people have the impression that Ubuntu and "Ask Ubuntu" has already found interesting ways to solve the multiple-site problem, by flowing information between its Q&A-style content and its forum-style ( content, as well as keeping its multiple tutorial-style, wiki-style ( and even long-lived guides ( in line and well indexed. Q&A-style content with a short shelf life drops down the heap of the list quickly, more long-lived tutorial-like Q&A responses are commonly reused, some of them are flown into tutorials and wikis... If they have been doing all this for years, instead of wanting to re-define their Q&A Ask Ubuntu SE site as something different than originally designed for, could it be that this is the best solution that pleases everybody?

ADD REPLYlink modified 8.3 years ago • written 8.3 years ago by Biostar User360

I agree with you that for a specific application, we can do better than SE. There is always room for improvement, even for the best Q&A site. On programming, I do not trust professionals that much. However, I also have to agree with Neilfs that SE right now provides better user experiences. In my view, we should be able to mimic the basic functionality of SE in the first place. We may tune its behavior when we confidently feel the change is really a step forward.

ADD REPLYlink written 8.3 years ago by lh332k

@Istvan: The point about licensing went over my head. I read the legalese, but I still have no idea what the issue is. Can you or perhaps someone else mention a scenario related to licensing where I can do one thing under stack exchange and not under Biostars. For the moment, my usage of code from Stack Overflow and Biostars is identical. I have never contemplated any differences. (Not saying there aren't any.)

ADD REPLYlink modified 8.3 years ago • written 8.3 years ago by KCC4.0k

Here is the share alike clause:

ADD REPLYlink written 8.3 years ago by Istvan Albert ♦♦ 86k

So if anyone publishes a paper with code pasted from SE, we are supposed to cite SE, author, and link to the post?

ADD REPLYlink written 8.3 years ago by Damian Kao15k

I will use this thread to give my suggestions. I think we can see more topics in the first page on SE. I prefer more questions, too. 15 topics per page seem too few to me.

ADD REPLYlink written 8.3 years ago by lh332k
gravatar for Prohan
8.3 years ago by
United States
Prohan350 wrote:

Yes - not sure what the real motivation was to move away.

ADD COMMENTlink written 8.3 years ago by Prohan350
gravatar for Ido Tamir
8.3 years ago by
Ido Tamir5.1k
Ido Tamir5.1k wrote:

Plus SE:

  • The software is better there
  • They are also starting this career thing, which could help people get jobs or find interesting candidates.
  • voting morale is better there
  • the name would have to change and biostars is not so good

Minus SE:

  • Software is good enough (and can be improved, because its open source I read)
  • Its under community control, so sections e.g forums, jobs, journal club etc.. can be - and were - added. SE does not have these options.
  • I am missing the stats for your claim that there are less visitors here

edit: I forgot my own summary judgment: No I don't think a change is necessary

ADD COMMENTlink modified 8.3 years ago • written 8.3 years ago by Ido Tamir5.1k

Some comments in defense of biostars:

  • biostars has a career thing, too:
  • voting morale depends on the community, not the platform. If this community would move back to SE the voting morale would not change much.

P.S.: If anyone with some Django-skills and ideas wants to improve the site, here is the code:

ADD REPLYlink written 8.3 years ago by Philipp Bayer6.9k
gravatar for KCC
8.3 years ago by
Cambridge, MA
KCC4.0k wrote:

Perhaps nobody else feels this way, but as dumb as it sounds, the fact that the Stack Exchange 'points' system has values that are about ten times larger seems more encouraging to me and perhaps helps their 'voting morale'.

ADD COMMENTlink written 8.3 years ago by KCC4.0k

I agree (see under "second" in my post). When scores creep up by 1 or 2 points after writing a major contribution, it does not encourage people to do more.

ADD REPLYlink written 8.3 years ago by Neilfws49k

I never thought it that way and I wanted to make the system more ... you know ... scientific ... where one knows exactly how many votes they got. But maybe it is not the right way - I don't really feel strongly either way

Making the score display as being 10 times larger is a very easy "fix", I just implemented that in three minutes - if you guys want to go that way just say so, and I am pushing it out.

ADD REPLYlink written 8.3 years ago by Istvan Albert ♦♦ 86k

I also prefer the SE scoring system: upvote=10, downvote=-10, accepted=15, upcomment=?... My view is that for details we should stick to SE as long as we do not have a strong opinion against it.

ADD REPLYlink modified 8.3 years ago • written 8.3 years ago by lh332k

the new scoring method is now enabled - for now everything is a multiple of 10, the accepted answer scoring change will have to take a little more work

ADD REPLYlink written 8.3 years ago by Istvan Albert ♦♦ 86k

Wow! +10 for responsiveness.

ADD REPLYlink written 8.3 years ago by KCC4.0k

Also since we are discussing this - downvoting is currently disabled at the infrastructure level, alas there is a pattern of use that makes it very discouraging for a new user to recover from a bad reputation

What happens is that a badly formulated question (often by a non-native speaker) is readily downvoted but then downvotes don't seem to be removed even if the question is fixed. Then, upvotes are rarely given to newbie questions - this all leads to a new person having a negative rep for a long time (usually forever).

When the new code-base was being developed we had a discussions about downvotes and I opposed them but still added this feature because of the consensus, see below. In practice it still did not seem to work.

ADD REPLYlink modified 8.3 years ago • written 8.3 years ago by Istvan Albert ♦♦ 86k

In SE, downvoting a post requires a penalty of 1 point for the person downvoting. So, people don't over abuse downvoting, because it reduce their scores.

The penaly of -1 did not make sense in the previous system used in Biostar, because the penalty was too big. Nobody would have paid a penalty of 100% to make a downvote, so we had to remove the whole functionality. Now that we are back to the +10 system, we could also reintroduce the penalty of -1 for downvoting.

I think that the system implemented in SE makes sense and brings people into making more constructive criticisms. People need to have a very good reason for downvoting a question, and are forced to think whether the downvoting is correct. I don't see a good reason to remove this system from biostar.

ADD REPLYlink modified 8.3 years ago • written 8.3 years ago by Giovanni M Dall'Olio27k

Is the argument here that fine-tuning and constantly updating the scoring system according to the evolving behavior of users will make the site better? Is this the case in SE, which has been adapting its system from the experience of running sites ranging from 1.5M users (stackoverflow) to sites with 500 users? If not, clearly SE is doing something wrong...

ADD REPLYlink written 8.3 years ago by Biostar User360

I was surprised by the increase in points, after reading this thread, makes sense. Great job. btw, I also consider that BioStar must continue as it is now, separated from SE.

ADD REPLYlink written 8.3 years ago by JC12k

just a small correction: on SE, downvotes are -2 for the author of the post, and -1 for the person downvoting.

ADD REPLYlink written 8.3 years ago by Giovanni M Dall'Olio27k

My view is really different than everyone else, I don't like such big numbers, ofcourse there can be different scores for upvote, downvote & accepted but scaling them 10 times is scary, after being on the site for long time!!

ADD REPLYlink written 8.3 years ago by Sukhi Singh10k

The point scaling on Biostar has always been a little jarring for me since I spend a lot of time on other stack exchanges.

ADD REPLYlink written 8.3 years ago by KCC4.0k
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