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Proposal: Bioinformatics

It’s worth thinking in more detail about what the focus of this Q&A website should be, considering that it will overlap considerably with (at least) the following Stack Exchange websites:

The example questions we’re currently collecting are of course a way of defining the scope of the website, but they don’t necessarily serve to distinguish it from existing sites.

(There’s also the fact that competing Q&A sites exist, but I think that’s a separate question.)

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  • I just noticed that a previous proposal had virtually the same question, it even has a similar list of alternative sites: discuss.area51.stackexchange.com/q/23807/319
    – Konrad Rudolph
    Apr 18, 2017 at 11:46
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    And in my answer to that question (and in comments), I had posted a collection of real questions that, in my opinion, would have fit better in bioinformatics than in the sites they were posted to: discuss.area51.stackexchange.com/a/25856/164162
    – bli
    Apr 19, 2017 at 10:08
  • My only query as a regular Biology user is this: why is a separate bioinformatics.se needed when Biology handles almost all the bioinformatics questions reasonably well? The questions that are put on hold are mostly about coding which is the domain of Stack Overflow. This is the general policy for bioinformatics questions in Biology.
    – WYSIWYG
    May 18, 2017 at 5:59

2 Answers 2

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I think the focus of this site should be how specialists of the field deal with biological information using automation / computational tools. It should be about:

  • Specific formats used in the field, their history, their specifications, how they are to be understood, written, processed...
  • Specific programs used in the field, which one to use for what purpose, what their options are, how to use them to achieve a particular result...
  • Databases relevant to the field, how to choose them, how to query them...
  • Kinds of data used in the field, subtleties arising when processing one or the other kinds of data sharing formats or processing methods
  • It could also possibly be about mathematical / statistical models, provided they are discussed in terms of the biological data they will represent, why such model should be or shouldn't be used when dealing with such kind of data

All these themes, if discussed in another stackexchange site, will likely have difficulties attracting relevant answers, either by swamping in a larger flow of questions (I particularly think of stackoverflow here), either by the scarcity of the right kind of specialist.

I sometimes encounter bioinformatics questions in stackoverflow that are poorly understood by other kinds of programmers. They are judged to be of a bad quality, where the problem is in fact more the lack of a common background than the poor quality of the question itself.

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    I agree with all your points. Something along these lines could probably be used as a draft for the site’s “About” section.
    – Konrad Rudolph
    Apr 19, 2017 at 13:57
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I have moved my old answer to the end. It doesn't matter now as @bli's answer covers all my points and is better. Here I will give a retrospect of biostar, and explain why some of us are enthusiastic with this new proposal.

Biostar was originally a bioinformatics SE1 site created in ~2009. It attracted many good bioinformaticians who had contributed numerous high-quality answers. In 2011, the company behind SE offered to migrate biostar to SE2. The biostar community was very positive, but the maintainer wanted to implement his own Q&A backend and decided to leave SE. In the first couple of years after the transition to its own codebase, biostar was still ok, but later it gradually lags behind SE. Biostar was developed largely by one developer. As good as he is, he can't single-handedly compete with SE. As a result, biostar lacks many useful core features of SE. In addition, biostar aims to create a friendly community (which is highly appreciable), but it is too tolerant with poor questions by design. This, IMHO, alienated some top contributors who want to learn from high-quality answers given by others. Nowadays at biostar, several top users are answering most of the questions; questions outside the domain of sequencing are rarely answered.

Compared to many new SE communities, the bioinformatics community is relatively well defined and more experienced with Q&A sites. It is (at least was) also an active community, so active that SE2.0 were willing to adopt biostar without the area51 stage. I don't see overlap with SO and other SEs pose any issues. The past area51 proposals all failed solely due to the existence of biostar, not because we didn't know how to "define" a bioinformatics Q&A. Then what has been changed in this new proposal after a year? Two things: 1) more biostar users might be thinking to move; 2) the new proposal got more exposure early on. I am cautiously optimistic.

The following is the original answer:

When you ask a question on a format, a tool or an algorithm in bioinformatics, the only relevant SE site is biology. Asking the question elsewhere would receive few answers as people there don't have the background knowledge. You may ask at stackoverflow, but the site is flooded with too many programming questions. Few biologists care to join. As to biology SE, the bioinformatics tag is not very active. Questions, answers and votes are fairly infrequent. We don't have a sizable community there. If you could find a way to attract more bioinformaticians, biology SE would also work for me.

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    Interesting. Then what are the arguments behind successfully launched SEs such as "web applications", "software engineering" and "software quality assurance & testing"? Wouldn't they have more overlaps with SO and other SEs?
    – medbe
    Apr 19, 2017 at 13:51
  • @JamesJenkins can you elaborate why this kind of answer may be the sign of a likely future failure?
    – bli
    Apr 19, 2017 at 13:51
  • @JamesJenkins What makes you think/say that? This proposal has already surpassed all previous bioinformatics proposals, and has done so in record time.
    – Konrad Rudolph
    Apr 19, 2017 at 13:56
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    @JamesJenkins: you are changing the topic. The original question focuses on the overlap between a bioinformatics SE and SO/other SEs and explicitly said that discussion on "competing Q&A", i.e. biostar, is "a separate question". On the other hand, you want to know why the previous proposal failed, which actually has little to do with OP's question. The reason why the previous all failed is primarily due to the existence of biostar. The reason why a new one may succeed is because biostar is arguably on the decline and a growing number of old contributors are unhappy.
    – medbe
    Apr 19, 2017 at 15:40
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    Am I correct in interpreting this as the main impetus to move from biostars to SE is to raise the bar on questions? No offence, but the main issue with SE is that it's perceived as toxic to new comers. While how true that will be is entirely dependent on the contributors, one might expect the bias to persist. Is this what we (the bioinformatics community) really want?
    – Devon Ryan
    Apr 20, 2017 at 15:43
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    It is about balance. Excessive regulation drives new users away, which will hurt the growth of Q&A. However, excessive poor contents push top contributors away, which is equally hurting. While I agree SO is hostile, biology SE seems ok. The old biostar in SE1 was reasonably balanced, too. The new biostar is overly permissive and lacks necessary features to improve the content quality. I honestly don't know what this bioinformatics SE, if it ever enters beta, will become, but I am willing to give it a chance. If it fails again, it at least tells biostar haters that we don't need a new Q&A.
    – medbe
    Apr 20, 2017 at 16:57
  • @medbe: I'll keep my fingers crossed then :)
    – Devon Ryan
    Apr 21, 2017 at 6:46

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