text:
Please stop cross posting behavior
Please stop cross posting behavior from biostars.org, where new questions are immediately transferred to this site. If you think you need this to boost your question count over the required threshold, please think twice. What you are doing is cross posting and it will trigger the same effects as cross-posts by OP: annoying both communities and doubling the work-load. While the content license of Biostars (CC-BY-SA) technically allows you to do this, consider that this is not a sustainable way to create traffic.
-- You needed 150 questions for the public beta for example, you got 147. You want these to be genuine traffic as much as possible.
If you want to take over questions, I suggest to focus on those that are specifically complex, have no answer, or not a sufficient answer, and try to answer them here, we will then possibly put the answer on both sites to allow it to be complete and searchable.

So far, I have seen that cross-posted posted questions have been flagged. Could you provide an example? The only questions that really are migrated are from reddit.

@Kamil here is the example I am referring to: https://bioinformatics.stackexchange.com/questions/508/obtaining-uniquely-mapped-reads-from-bwa-mem-alignment

Why not? While I haven't done so, I see this as simply helping both communities. For example, I personally find biostars very hard to understand and have trouble finding the answer I want since it is too often buried in a long comment thread. I see nothing wrong with re-asking here and posting a clear answer. Conversely, I also see nothing wrong with taking a useful question from here and posting it on biostars. Could you explain your argument for this being harmful?

OK, granted, your example is particularly egregious since it is a very specific question and the text was copied verbatim(!). But would you also object to asking the same question (as opposed to blatantly copying it)?

I don't think SE encourages cross-posting generally https://meta.stackoverflow.com/questions/266053/is-it-ok-to-cross-post-a-question-between-non-stack-exchange-and-stack-exchange

@terdon, I'd just wait for while and focus on generating added value by using open questions instead of answered ones.

@Michael Ah I did not see this. I am not sure what to think about it...

@KamilSJaron I think it just looks bad...

@Michael yes, absolutely. I had posted my first comment before checking the specific question you linked to. I was thinking more along the lines of basic, general questions like "how do I convert sam to bam" or "how can I extract specific sequences from a multifasta file" and the like. Blindly copying a very specific question like this seems pointless, yes. Especially when the quoted text isn't put in a quote block.

This is an interesting shift from the last discussion about this. It's not an approach that I felt comfortable with (despite the encouragement), but think it was good to stir the hornets nest right at the start to cement the community position (or more correctly, the Stack Exchange position).

@gringer I think nobody expected you to actually repeat the entire question verbatim or to take such specific questions for which you couldn't provide clarification. I, at least, was thinking more along the lines of reasking the question as opposed to just copy/pasting it here. The difference would be that you'd make the question your own. Questions whose poster can't provide more details or guide the answerers aren't very useful. (please note that this isn't an attack on you, I know you were trying to help and the previous conversation did indeed suggest that it might be ok).

I would be for verbatim copy-paste of questions, but al least they should be older and without good answer. You can not possibly claim that it is doubling an effort if it is already "closed" question on BioStar. The problem with this particular case is, that it was very fresh question and people still actively discussing the question even it was already answered here.
-edit-
I would call it "verbatim question grave digging"!

I doubt that the question would have got the attention it did if there wasn't all this discussion about it. It was a "wall of text" question by a completely new user, with two answers already. It just so happened to be that the answers were incorrect (and already dealt with in the question). The wall of text was also useful (a classic XY problem -- looking for consistency vs Geneious mapping, rather than multiple alignments). My subsequent condensing/rewriting changed the question such that it was no longer useful to the original questioner for the specific problem.

@gringer perhaps but your (excellent) answer will be useful to future users.

FYI Am I allowed to indicate crosspost links in my questions on Stack Exchange?

How far back would you go for "verbatim question gravedigging"? Is eight days a long time? How about five weeks? or three months? Such questions are not too difficult to find, just search by creation time and pick a random page number. These are low-hanging fruit; even posts that seem to have reasonable titles have been lost in the noise.

I would try https://www.biostars.org/t/Open/?sort=votes&limit=all%20time&q= please go ahead. I will post an interesting example.

As far as I can see, there is a single occurrence of this, and the “perpetrator” even remarks:

I'm being a bit cheeky with this post, mostly to gauge whether or not the community thinks it's a good idea to do this.

Fair enough. For what it’s worth, I agree with you, Michael: I don’t think it’s a good idea to do it1.

If you think you need this to boost your question count over the required threshold, please think twice

This may have been the motivation in the past but a much more interesting question would be how we handle future cross-postings from people who want to increase the reach of their own question: condone or forbid? Different communities handle this in various ways but I’d be tempted to allow it here.

1 I feel differently for questions from Reddit, because Reddit is a discussion forum, not a Q&A site, and getting good, technical answers on Reddit can be challenging.

This is marked as the answer. Do I take its that this means we allow cross posting (i.e. users post the same question, here and shortly after having posted it elsewhere, particularly if it has a perfectly good answer there.)

@IanSudbery I honestly don’t know. I find it vaguely excessive to cross-post to BioStars and here, since these two platforms are, for all intents and purposes, competition. I still think it’s less of a problem for Reddit etc.

I recent question was posted on BioStars, where it promptly got an answer. It appears the user didn't like the answer, because the question appeared here shortly after it was answered there.

This post from Fall 2017 might be the latest word, and in July 2017 it appears we still don't have explicit consensus from the moderators.

I think copying content from other sites is fine, but only under certain specific conditions:

If a question, it should be a question you have too; it should not be something very specific to the particular person who happened to ask on the original site. If you post a question, you should be in a position to provide any clarification that might be asked of you so it should be something affecting you as well.
If you do end up copying text verbatim, it must be not only attributed (of course) but also clearly marked by placing it in a quote block:

This is a quote

We shouldn't do this just to repeat questions. It only makes sense for really general, basic things like "How can I convert bam to sam" or "How can I extract a given set of sequences from a multifasta file" and things like this.
Ideally, don't copy the original text. If you want to ask the same question, ask it again. I mean rephrase it, make it your own. Don't just copy/paste someone else's question.
When it comes to answers, things are a bit different. If a given question has already been answered well elsewhere, then it might indeed make sense to copy the answer over verbatim but only if point 2 is met: clear attribution and all quoted text in a quote box.
If you do copy an answer, it would be polite (although not essential, strictly speaking) to mark it as community wiki. This means that:

You won't get any reputation for it. Posting the work of others shouldn't be done for reputation gains.
It lowers the bar on editing and is a clear invitation to the community to edit and improve your post. That way we can really make the copied content our own.

If these criteria are met, I don't see anything wrong with copying since we will be doing it in a way that, I hope, will harm neither community and may in fact end up helping both.

I couldn't work out how to mark my questions as community wiki. The information you linked to only talks about answers being set as this.

Please note that the "community wiki" feature has been largely deprecated, and is no longer used for either of these use cases (listed in item #6).

@RobertCartaino how so? The only use the CW still has, as far as I can tell, is as a way to post something you don't want to get rep from. This is still quite common across various sites. And it does put the bar for editing sliiiiightly lower too. So why are you saying it is no longer used for these cases? I've read the "future of the CW" blog post, but that was never very clear. It does, however, quite clearly state that CW should be used for collaborative answers which is precisely what my second point here is. So what am I missing?

@RobertCartaino no longer used by whom? Do you now forbid users from  marking their answers as CW? This is really new to me, and better post announcement on MSE so that users will know of this new SE policy. Thanks.

@ShadowWizard Nobody said forbid anything. Community wiki should not be used to deprive or remove rep for an answer (as suggested here), but a user can (still) make their post community wiki. Wiki isn't particularly recommended for anything that isn't covered by other features. Collaborative answers usually means someone summarizing other answers posted below which also tends to break things like voting. If we looked it the issue close enough, we'd probably remove it.

@Robert "should not be used" said by SE employee officially is forbidding.

@RobertCartaino  "Community wiki should not be used to deprive or remove rep for an answer (as suggested here),": why? That's the only valid use I can think of for it these days and it certainly is used like that very often on many sites. And half the reason I am proposing CW here is for collaborative answers. I don't understand you reasoning against this.

@RobertCartaino also, I don't understand the distinction you'er making between using CW to "remove rep from an answer" and "a user can make their post CW". I am suggesting that a user make their post CW, not that someone forcibly does so for them. And I am not even saying the user should, only that it would be considered polite. What you are describing is news to me and to other in the TL I discussed it with and seems to contradict other meta posts by employees. Please clarify.

@RobertCartaino I would appreciate some feedback on this. Your position is at odds with that expressed by other employees, other experienced users of the network and other mods. Your statement that CW isn't used for those 2 purposes is flat out wrong since it is indeed used that way quite often. Perhaps you mean that it shouldn't be used that way, but if so, please explain why.

@terdon Yes, I'm saying it should not be used that way. The variations we come up with for "you don't really 'deserve' the reputation for posting that here" is what propagates the misuse of wiki. Of course, folks are free to make their own posts wiki if they want, but suggesting it's the right thing to do in these cases is not aligned with the deprecation of that feature. Community wiki is still around because someone always cites some rare exception where it was useful eons ago, but if we looked at the issue close enough, I'm sure we could get rid of the feature entirely.

@RobertCartaino it would be great if you could post something on meta.se about this then because I've seen answers by other employees defending a different position and the general consensus in the TL when we discussed this a few days ago was also in agreement with what I'm suggesting. In any case, at least on [unix.se] and [ubuntu.se], using CW when posting an answer consisting entirely of someone else's work (the OP put an answer in a question, for example) is standard procedure and has been for a while. If the official stance is against that, the user base has not realized it.

@terdon I'm not going to do that. My role these days is to guide new sites, and I find it better to pass along thought processes through conversation as issues come up... rather than turning everything into a epic, sweeping edict.  Unfortunately, if we don't flesh out the issue to an exhaustive degree, folks tend to get worked up over outlier issues and minutia. We haven't done that yet, so that's why the feature remains.

@RobertCartaino fair enough, I thought you were issuing a (polite and restrained) "decree" which is why I asked for clarification. Still, CW does need some clarification. I guess I'll open a meta discussion when I get the chance. Anyway, thanks for the clarification.

@terdon I should probably preface these wth "this isn't our current way of thinking..." We have been really terrible at keeping the conversation going as features/issues evolve (at least compared to "the old days"), so when we virtually abandon incremental improvements and ongoing discussions until things reach near-crisis levels... we write really long (virtually unreadable IMO) meta posts about it. I hope to change that... soon.


text:
Make tags [sam] and [bam] synonyms
SAM and BAM are effectively plain-text and binary representations of the same alignment format. I'd argue these terms should be synonyms.
UPDATE: It doesn't look like we've reached a consensus, but I still think this is the best course of action. See Konrad's post below. I agree the [sam] tag should refer to the SAM specification, which includes everything that is shared between SAM and BAM, as well as issues that are SAM- or BAM-specific.

I opened a new meta question suggesting a third, master tag (sam-or-bam) as a compromise.

I'm really hesitant about this. There are a number of very BAM specific questions, mostly pertaining to how things are actually encoded (e.g., chromosome names) and how the implications of that play out in different situations (e.g., merging multiple files or replacing headers). If we do make these synonyms, then we should include CRAM in that as well.
I should also add that SAM and BAM have some different constraints. For example, SAM allows any length query (read) name, whereas BAM does not (it has a 252 character max if you want versions that are byte-aligned in memory). SAM allows arbitrary length CIGAR strings, BAM does not. These all have important different implications in downstream applications.
Edit: Note that if it's just me that opposes this then it should really be done regardless!

Interesting piece of trivia. This really should be on the main (instead of meta) site.

Give it a couple months and most of these questions will get raised organically :)

I would argue the opposite for exactly the same reason. SAM is a simple text file, BAM is not. While the two are obviously related, I really don't think a question about sam files should be tagged as bam nor a question about bam tagged as sam.
To take a very simple example, consider a question like "How can I extract all reads mapped to chr1 from a sam file" and the same one for a bam. The answer for the sam could be as simple as awk '$3=="chr1". It could be done with no specialist bioinformatics tools and just using standard *nix text processing utilities.
Granted, the same could be done for a bam file if we first pass it through samtools view, but isn't that like saying that a PDF file is the same as a text file because I can pass it through pdf2txt or similar utilities?
Finally, I would argue that these are two of the main formats used in NGS analyses and each have their place and are used by different downstream programs and in different ways. I don't see any benefit in merging these two tags and we might be losing some "resolution".
Perhaps we can revisit the question further on down the line when we've seen how the tags are being used?

I don't think that the comparison with pdf2txt holds well. bam to sam conversion is much "cleaner" than pdf to txt. That said, I have no opinion about whether sam and bam should be distinct tags or not.

I agree, regardless of the misgivings voiced in other answers; and I suggest having a tag sam (with bam being a synonym).
In addition to what Daniel said, nobody stores SAM files.
At least nobody should: there is (with the exception of Devon’s trivia) no reason to do so. So while two distinct data formats exist, they refer to the same technology. As a consequence, any question being asked about either SAM or BAM will fall in either of the following categories:

Creation or conversion between SAM and BAM (and thus deserving of both tags).

Querying a BAM file, which is solvable using tools for BAM and SAM (either by working on the BAM file directly, or by using samtools view in combination with text transformation tools).
Using the sam tag for such questions would be potentially confusing if that tag referred to a specific file format. But if the tag refers to “Sequence Alignment/Map Format Specification”, which is the official name, then that definitely covers BAM as well.

Hmm, your point about conversion makes sense, yes. Still, it feels strange to have one tag for what is really two different formats, despite their obvious link. Then again, I haven't been working with these formats for all that long, I suppose anyone who's an expert in one would be an expert in the other by default. Maybe we should just create a sam-or-bam tag and circumvent the issue?

On one hand, SAM and BAM are really not synonyms. Mixing them will make it harder to distinguish sam-specific or bam-specific questions. On the other hand, we often mix them in practice. I do the same. I am ok with one of the two solutions:

Take "sam" as the master tag and "bam" as a synonym of "sam". At present, we are taking "bam" as the master tag (see the synonym page). This should be reversed.
Keep them separate.

I object to creating a "sam-or-bam" tag.

What arguments would you give in favour of havig "sam" as the master tag rather than bam? I tend to agree because I often see the bam format as just a compressed version of sam format, the latter being what I conceptually grasp better, with its lines and fields. Some people may have question more related to compressing and indexing aspects, but my intuition is that more often questions will relate to the fields, flags, tags and so on.

@bli sam is the primary format. bam, cram, biohdf and many other binary formats are just alternative representations of sam. Naturally, "sam" should be the master.

I agree with this. I expect that anything that is specific to BAM / CRAM would be likely to be more specifically a computer programming question (and probably better placed on the issues pages of github), rather than a general bioinformatics question.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


text:
Make tags [mapping] and [read mapping] synonyms
The topic of read mapping is a sufficiently distinct subset of the more general class of sequence alignment topics to warrant a dedicated tag. However, we should collapse mapping and read-mapping as synonyms.

Mapping has distinct meaning in other subfields (e.g. family tree mapping and disease mapping). For clarity, we should not use "mapping" just for "read-mapping".

Similarly, "mapping" is used often with "QTL mapping".

Yes, having both mapping and read-mapping for the same thing doesn't make sense. However, instead of making them synonyms, I would suggest we only keep read-mapping and get rid of mapping altogether.
In general, tags whose meaning isn't clear from the tag are bad tags. In fact, mapping is a classic example of a meta tag. Briefly, meta tags are those that:

If the tag can’t work as the only tag on a question, it’s probably a
  meta-tag. Every tag you use should be able to work, more or less, as
  the only tag on a question. Meta-tags, like [beginner], [subjective],
  and [best-practices], are useless by themselves — they tell you
  nothing at all about the content of the question.
If the tag commonly means different things to different people, it’s
  probably a meta-tag. In a cruel, ironic twist, the meaning of the tag
  [subjective] itself … is actually subjective. Ditto for
  [best-practices] and [beginner]. Best practices to whom? Beginner by
  what criteria? These tags are impossible to define by anything
  remotely resembling an objective metric. In comparison, the the
  meaning of tags like [java], [c#], and [javascript] are crystal clear
  to all but the nuttiest of nutbags.

As user172818 pointed out in the comments, the term "mapping" has different meanings in different subfields. Therefore, "mapping" by itself doesn't tell us anything useful about the question; it needs to be combined with another tag (ngs, reads or whatever) in order to be informative. Therefore, it is not a useful tag and should just be removed.
The simplest way to remove tags is to just edit the questions that have them. If no questions are tagged with a given tag, the tag will be deleted from the system automatically. If, in future, we see the tag returning, we can ask for it to be blacklisted.

Since there were only 6 or so questions tagged with mapping, I went through them retagged those that were about read-mapping accordingly. However, this question:
probeset to probeset mappings between Affymetrix arrays
is about mapping between different types of affymetrix arrays. Here, I removed mapping and created a new tag affymetrix-arrays. I don't think it would be worth creating something as specific as affymetrix-array-mapping or similar.
The others were all about read-mapping and are now tagged accordingly. The mapping should now disappear and I suggest we let it fade into oblivion.

I thought I had added some info about the "mapping" tag, but I see that the "read-mapping" tag did not conserve this info. Or maybe I'm mistaken.

@bli oh damn! I'm sorry, that's my fault! The info wouldn't be conserved no, the read-mapping tag was a new tag, not a synonym so it wouldn't bring in information from elsewhere. I didn't notice you had added information to the mapping tag's wiki when I removed it. I hope it wasn't too much work.

I found the info back in my activity history:
"When dealing with associating sequencing reads to a matching position in a set of reference sequences (typically a genome)."
I'll add it to the "read-mapping" tag

@bli cool! Sorry for making you repeat your work, that's never fun :(

These few words were not a lot of work :)

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
Essential questions about our site
Looking for help I found this post about the beta sites essential questions that need to be answered. Now, that we will go to public beta soon, we could decide when to answer them:

Are questions about {subject} on or off topic?

I think we have been discussing this in meta, through several posts: Post 1, post 2, post 3 and post 4.

What should our FAQ contain?

It might be too early to propose a FAQ, but we haven't discuss it yet.

How should we tag questions about {subject}?

We have been discussing with *-seq technologies: Post

Who should the moderators be?

Recently Pro tempore moderators post

What’s the “elevator pitch” for our site?

I think these guides might be helpful, but we haven't discussed it yet.

What should our logo and site design look like?

Too early? But we could start thinking about it.

How do we promote our site?

In chat some users have been discussing efforts to promote the site in reddit, facebook and twitter.
When should start discussing about questions 2, 5 and 6?

Thanks for posting this! However, I think each of these points should be discussed in a separate post. That way, we have a specific post to link to in future about each of the issues raised here. As for the FAQ usually is a collection of questions on the main site tagged with the faq tag. Those will come as we grow. We might want to open a meta post eventually to collect them though.

@terdon Yes, I was doubting too if it was too broad, I have edited to make it less broad. By asking about the timing of the discussions

I am afraid the page you linked to is not really that relevant any more. It is in urgent need of an update. An updated version (although "unofficial") can be found here:
The Real Essential Questions of Every Beta
I would strongly suggest we all give it a read, it is useful information.
That said, let's see:

Are questions about {subject} on or off topic?
As you pointed out, this has started already and it will be an ongoing discussion and will probably last as long as the site itself. The scope of a Q&A site is constantly evolving as more edge cases appear and we will continue to refine it by posting on meta. The scope will eventually be defined by the collection of scope questions.
What should our FAQ contain?
I think that's out of date. There's not really any such thing as a speciic FAQ as far as I know. There is a meta tag faq but only moderators can use that so it's something we can revisit after we have moderators and after we have some more content on meta.
On the main site,  what we have is the "frequent" tab in the main page which you see when you click on "Questions":

That is, as far as I know, populated by the system automatically and not something we need to worry about.
That said, once we do start having enough traffic to have repeated questions and find a set of them that are asked very often, we can set up a collection of "Canonical Questions" with good answers and then use them as duplicate targets.
How should we tag questions about {subject}?
Daniel Sandage and other users have been doing a great job opening such discussions already. Again, this is going to be an ongoing process which will last as long as we do. After we've been using the site for a while, certain tagging guidelines will emerge naturally and others will be hashed out here on meta as we have ben doing these past few days.
Who should the moderators be?
Already being dealt with. The SE community managers will be selecting the pro-tem mods from among those who have been nominated. Then, if and when we graduate from a beta site to a full blown member of the SE community, we will have full democratic elections and will get to vote for our own mods.
What’s the “elevator pitch” for our site?
This one deserves its own question where we can propose different ones and vote on each. Perhaps we can do so in a few days. I think it might be a bit too early now while our scope is still being defined.
What should our logo and site design look like?
Again, I think the information on the page you linked to is dated.  In my experience, SE comes up and proposes a (usually very nice) design when we get close to graduation and that's when the community gives feedback. Of course, if anyone has any ideas they are welcome to post them as questions on meta and maybe the SE designers will take them into account but they are professionals and tend to do a pretty good job. I'd just wait until they show us what they come up with and discuss it then.
Note that no site gets any personalized graphics before full graduation so we have loads of time for this.
How do we promote our site?
This one we may as well discuss, I guess. We've already have done so in Bioinformatics Chat last week when we feared we might not make it into public beta. Once again though, I think it basically boils down to each of us sharing the news with the people we think might be interested using whatever means we find most comfortable.


text:
Serving as a "support forum" for specific tools
One of the nice features of biostars is that the site is open to people using it as a forum for supporting their own tools (i.e., as a replacement for a tool-specific email list). The tool authors that do this then follow the tag associated with their tool (e.g., IGB or trinity). So far that's already well in line with this site. However, issues will arise surrounding this as follows:

Mailing lists or other tool-specific forums are, out of necessity, a bit easier going when it comes to simplistic (you can read that as "newb" if you prefer) and duplicate questions (examples abound on the deeptools google group).
If "post on bioinformatics.SE and use/follow a tag" becomes a convenient method for tool-authors to provide support, then they'll also then want to make announcements (e.g., "version 2.0 is out with the following features ...") on the same platform. This is fine on biostars, but doesn't really fit with the SE ethos.

Some more specific background: I'm one of the developers for deepTools and spend a bit of time each week handling user support on our "google group" (i.e., a mailing list maintained and easily searchable by google). Having a mailing list is nice for the signal to noise ratio, but of course then I (or my colleagues) are the only ones providing answers to our users. In reality, >90% of questions could also be answered by other bioinformaticians with knowledge of the tool suite. Allowing people like us to migrate our support channels to this site would generate a considerable amount of extra traffic (good), but we would then need to ensure a very gentle treatment of our users (not easy) and a method to communicate releases (presumably one could use a dedicated email list for this, some tools already discriminate between an -announce and a -help email list). But of course the question is how do we, as the bioinfo.SE community, want to approach using the site for tool support when the site itself becomes the dedicated channel for said tools?

Relevant post? https://meta.stackoverflow.com/questions/251363/how-can-i-set-an-icon-on-a-tag and  https://meta.stackexchange.com/questions/48315/why-are-some-tags-colored-formatted-differently-in-meta-stackoverflow-com I doubt coloured tags would be possible

I'm a user of the snakemake workflow management tool, and snakemake has recently started using a tag in stackoverflow in order to offer support and build an FAQ: https://stackoverflow.com/questions/tagged/snakemake
They also have a google mailing list, and for me this doesn't work. Whenever I try to read something there, it takes an awful lot of time to load, and the answers are not well evidenced and readable.
I find the stackexchange format much easier to use. The only problem is when programmers having no idea what snakemake is start commenting that the question is not clear because of their lack of familiarity with the tool.

At least in my opinion snakemake could move over here, since it is the de facto workflow management system in bioinformatics :) Perhaps once the site goes public we should try to poach them from stackoverflow...

Thanks for saying that :-). However, Snakemake also has users outside of bioinformatics. Hence, I would like to keep it in a more general place. Of course, if the question is bio-related and not simply a programming question about the domain-specific language of Snakemake, it can also be posted here.

bioinformatics will have quite a lot of tool-specific questions anyway, therefore I would allow to create tags for tools that would serve as mailing lists.
We could create a special type of tag for official tool support tags if

there will be on bioinformatics.SE a member of a development team to maintain questions of that tag
maybe these questions could be automatically protected by the maintainer of the tag, but this is probably not necessary if community get used to this "official tool support tags"

I am basing my answer on assumption that having different type of tag a trivial feature request since this feature kind of exists already (moderator tag featured in meta).
The huge advantage for community of harbouring mailing lists would be the high quality answers directly from developer.
The huge advantage for developers of going for bioinformatics.SE is easy googelbility and the rest of the community answering simple questions.
Yes, I see a lot of benefits.

I also suggest to make the official tool support tag green.

I really like your colored tag idea! Hopefully something like that (A) can get implemented and (B) eventually recognized by the community so they go easy on those posters.

@DevonRyan I think (not sure though) that such tags are a corporate thing. I mean, someone has to sponsor them and, presumably, pay SE.

I have seen the corporate tags (the one of google). However that does not mean that SE will not try to create an environment that fits to needs of our community. One of Moderator pro tempore roles is "If there’s a feature request for a specific site, it’s up to that community to vet the idea in their own meta. If the idea has merit, the Moderator would bring it to the Stack Exchange team." Which sounds like a they actually want us to ask for features we want.

I agree that specific question about tools is and will be a big part of the question here. Usually other users can answer too in mailing lists of such tools but an answer from the authors/maintainers is more appreciated, because the confidence it brings, however if other people on the community answers won't solve the trust issue even if it could solve the specific problem.
Our site has guidelines (borrowed from Stack Overflow) about how to give support of tools and products. Basically it says that if a company/group wants to promote their tag the rules of Q&A still applies. At best in SO if a company pays a tag can have the logo of the product (But I couldn't find how these works). Maybe as a free substitute we could have a meta post listing the tags of tools and the users supporting them.
As a side note, there are many meta questions about companies/tools saying they can have support in SO without explaining to their users how to ask, or explaining the differences between the site and the tool. If we educate our users before posting questions here better.


text:
Accepting Nominations — Who should moderate this site?
Ideally, Moderators♦ are elected by the community, but until the community is large enough to hold a proper election, we will be appointing three provisional Moderators to fill those roles.
We need your help. Please nominate folks you would like to see become provisional moderators for this site. Your input will provide valuable insight to help us make our selections. You can read more about the process here: Moderators Pro Tempore.
The Nomination Process:

Nominate a user by posting an 'answer' below. Each nomination should be a separate answer. Use the template at the bottom of this post to complete your nomination.
Self nominations are encouraged. This is a volunteer activity, so users should not feel obligated to accept these positions. A self-nomination is simply a way to say, "I am very much interested in this, so let my record speak for itself."
Tell us about the candidates. Nominations can include links to other activities like Area 51 participation, participation in other sites, or any relevant thoughts/links that may help us make an informed decision.
Nominees! Please indicate your acceptance by editing the answer to accept/decline the nomination. And please ensure your profile email is correct so we can contact you. Optionally, you are encouraged to write a bit about yourself following your acceptance.

I accept/decline this nomination.
Hi, I am name/location/fun fact (all optional). I live in <location>, so I am generally active on this site from <time> to <time>. Some other things you may want to know about me are…

Here is what we'll be looking for in a Moderator candidate:
We are looking for members who are deeply engaged in the community's development; members who:

Have been consistently active during the earliest weeks of this site's creation
Show an interest in their meta's community-building activities
Lead by example, showing patience and respect for their fellow community members in everything they write
Exhibit those intangible traits discussed in A Theory of Moderation

Nomination Template
To nominate a candidate, copy and paste the text below as an answer and complete your nomination writeup:

  ###Notes:
  This nominee would be a good choice because …

Could we have an update on this? It's been two weeks now.

@terdon Nomination threads generally run about 2 weeks. The selection process should be starting now-ish.

OK, I was just wondering if you'd forgotten all about us! If 2 weeks (or, for that matter, more) is normal, that's fine. Thanks for the update.

Notes:
This nominee would be a good choice because (1) Devon is a highly experienced bioinformatician; (2) he is one of the top contributors at BioStar as well as at this SE; (3) he is a long-time moderator at BioStar; (4) he is friendly to both experienced bioinformaticians and fresh newcomers, which I think is critical to build up the community here.
Edit: I accept this nomination. Note that I'm in Germany, so I'm generally active from 0900-2300 there (GMT+1). -Devon

+1 Devon Ryan is one of the most active bioinformaticians on the Internet ever. I see him everywhere online. There is no reason why Devon shouldn't be a moderator here.

I would say precisely, that because he has a lot of commitments he might not be able to invest time as moderator here. But there's people who can manage very well their time! (all the best if you become moderator)

Notes:
This nominee would be a good choice because (1) Konrad is a highly experienced bioinformatician and a top-tier programmer; (2) he is a very active SO user and familiar with general SE rules and features; (3) he has played an important role in publicly advocating this SE and pushing it to beta.

EDIT: I accept the nomination. I’m in the UK and generally online during work hours (except when travelling, which will unfortunately happen quite a bit before the end of the month). I have some experience with moderation as I used to be moderator on Skeptics.SE for a time. I like people to be nice and to get along but I also think that ensuring quality in questions and answers is important.

Worth noting Konrad has 340K rep on SO: https://stackoverflow.com/users/1968/konrad-rudolph

One small caveat to this nomination: will be travelling a lot without internet access this month.

From my interactions with Konrad on social media and other forums, I've been impressed with his breadth of experience and civil discourse. He would be a great asset to this community as a moderator!

Notes:
I suggest this user as nominee because I think his view on not closing questions too harshly shows a welcoming and constructive attitude that could make this site avoid some of the criticism that stackoverflow has attracted.
Besides, this user has been reasonably active here and in stackoverflow and has shown his interest in this site's development in making the first two nominee suggestions.
EDIT: I accept this nomination. This is Heng Li here, living in US east. I greatly appreciate the friendliness towards new users at Biostars but also value the necessity of moderation.

Thank you for nominating me. I was hesitating whether I could be a good mod, but as you gave me a vote, I will try.

omg, it's my hero. I'd love him be the mod. Please vote him.

Notes:
I have been very active on Bioinformatics SE, encouraging it through the nomination process via publicity on twitter and reddit, and participating in asking and answering questions, as well as participating in reviews throughout the private beta. I live in Wellington, New Zealand and work professionally as a bioinformatician at the Malaghan Institute of Medical Research.
I am active on SeqAnswers, reddit, the ONT community, and twitter, and spend a lot of time discussing my work with the research community. I report bugs in the FOSS bioinformatics programs that I use (mostly via github), which has led to a few research collaborations and published peer-reviewed papers (the most notable being a paper on the Trinity de-novo transcriptome assembler).
I am fairly new to StackExchange participation, but keen to learn. I've already found that participating in this community has filled in some gaps in my bioinformatics knowledge and public outreach.

Notes:
I really want this site to succeed, and I would happily serve as a pro-tem mod. I am already a moderator on two other sites of the SE network so am quite familiar with the SE system and what it means to be a mod here. I am generally active and online between around 10 AM and 1 AM EEST (GMT+2).

Notes:
I nominate myself even I have no experience with moderation on SE or BioStars, just because I would like to contribute. I would like to counterbalance my lack of experience in moderation with enthusiasm and creativity. I have hands-on experience with bioinformatics problems of evolutionary genomics (~3 years).
I live in Switzerland (GMT+1).

Notes:
Although I nominee myself it would be my first time moderating a community, I am open to suggestions about how to improve my participation in the site (independently if I became a moderator or not).
I don't answer many questions on the main site, as I am at the first stages of my career (I am ending the master of bioinformatics next month), but I'll try to improve that. I have been following WGCNA tool thorough posts in Bioconductor support forum and Biostars to answer them (The links are to my profiles there). I usually work with R and Bioconductor.
I live in Spain, so I am generally active on this site from 0900-1700 (while working) and 2100-2300 (occasionally) here (GMT+1).

Notes:
I have been trying to get exposure to this SE since the last proposal which got rejected because of lack of supporters. Since my second submission to reddit I got lot of help from gringer and Konrad in getting users to commit.
I am a bioinformatics Undergraduate so my contribution to bioinformatics SE is limited but I can help with the moderation by editing and fixing questions.
I am from Sri Lanka (GMT +5.30) so my active hours would be different and wouldn't overlap with other moderators.


text:
Why is not BIoinformatics.SE part of Biology.SE?
I found this post on Biology.SE meta and it rises a fair point. Why we have to separate in different SE site? Why bioinformatics is not a part of biology? Is there any actual advantage of being split? Is there any bioinformaic question that would not be appropriate for biology with "bioinformatics" tag?

Why not knowledge.SE? Then there only needs to be 1 SE site.

Site scope is often more determined by how the community views itself. It's not organized from the top down to minimuze overlap.
Many bioinformatics questions would actually be on-topic. Bioinformatics is also a tool for biologists, and those are generally on-topic. Questions more in the programming area are problematic, they would probably not be seen as on-topic by most of the Biology.SE community, but it's also not impossible to allow them, as long as they're not pure programming questions. But pure programming would also likely be off-topic here, and directed towards SO.
I think it would be possible to have bioinformatics as a subset of the Biology site, but there is a problem selling that to the bioinformaticians. If people look for a bioinformatics site, and don't consider a biology site, there isn't much we can do about this. Very broad sites have a serious marketing disadvantage, and it's rather difficult to overcome that for new SE sites.

Probably for the same reasons why "Ask Ubuntu" is not part of "Unix & Linux", or "Data Science" (and "Theoretical Computer Science") is not part of "Computational Science" (or "Computer Science").
The fields are simply distinct enough, and having them in different Q&A site would benefit both groups without swamping either with unrelated topics.
A question about e.g. running specific a pipeline or well known bioinformatics tool in SLURM would be (and should be) totally off-topic on "Biology", while possibly being on-topic here, as would questions about working with common bioinformatics file formats, etc. etc.
Also, your suggestion would reduce the number of tags from what's currently available on this site to just "bioinformatics", which would make it really hard for someone who's an expert in, say, Sanger sequencing (or whatever) to find and answer questions related to their field of expertise.

Just take a look at the questions tagged bioinformatics on Biology.SE:

Does DNA have the equivalent of IF-statements, WHILE loops, or function calls? How about GOTO?
What exactly are computers used for in DNA sequencing?
Is “computational biology” different from “bioinformatics”?
120-year-old gene regulation problem independently solved by a computer. How?

…
Most of these would be off-topic here. The level of expertise that these sites strive for in bioinformatics is fundamentally different. According to our preliminary site description,

Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics.

Biology.SE certainly also has a segment of professionals asking questions, but it’s also got a large segment of non-experts. Bioinformatics.SE, by contrast, explicitly strives to be a Q&A site for professionals.
Case in point: I wouldn’t think of asking a bioinformatics question on Biology.SE. Instead, I would ask it on Stack Overflow, Stats.SE, or BioStars, depending on the question.

This is really good point. If the site should be experts to experts, then biology.SE fails badly on bioinformatic topics.

sorting by votes will always show the more shallow questions with appeal to non-experts first, so I don't think this is an entirely fair comparison.

@MadScientist Fair point, but I think the level is actually representative. There are more technical questions of course; but the ratio isn’t great.

I don't think "easy" questions should be disallowed on this site. They're not so great for the beta phase, but are a great way to encourage new bioinformatics recruits to visit this site.

@gringer As long as they don't flood the site and make it unattractive for experts.


text:
Are stories useful for bioinformatics questions?
I've just had a look at the fastest FASTA/FASTQ question, and felt that it was a bit lacking in substance. It was an answerable, specific question, and all the answers seem to concentrate on a single them (i.e. the fastest program execution time), so in that sense it was a reasonable question to be asked.
However, the question felt a bit too divorced from my own world for it to seem like a real bioinformatics question. What I felt was missing was a bit of an explanation around why the question was being asked. Sometimes it makes sense to be able to code up something quickly, but other times the solution needs to be as accurate as possible.
Do we want to encourage more storytelling in the questions that are asked? I understand that there are many people who just want someone to get to the point, but am curious to know if a bit more context in the questions would help both new people visiting the site and people answering the questions.

Yep, I think we should encourage stories with questions. It helps to identify XY questions and in bioinformatics everything is context dependent. Next time, I will try to write the story with the question right away...

A bit of background is always useful to give context. I recommend normally to write at least a few sentences or paragraph unless you know exactly what you are doing.
Also, this accumulates more alternative terms related to the problem, which makes the question easier to find, in case one does not know the exact technical terms.
In this case it was ok, I guess.
However, bioinformatics questions especially from newcomers are prone to a priori choice of tools, ill defined problems, and the XY- problem. The risk is that what you are semantically describing is not a good solution to the biological problem.


text:
Please refrain from closing proper but imperfect questions so quickly
I have been thinking about this for a while. This recently on-hold question really touches my nerve. The question is put on hold due to being too "broad". I will use it as an example to explain my concerns.
First, "broad" (as well as "off-topic" etc) is subjective. In this particular case, I think the question is on the border line at best. I certainly would not vote to close it, even though I am actually quite picky. To most new NGS users, they would think this is a fine question, too.
Second, even if "broad", this question is interesting and useful. It has attracted 4 upvotes in 13 hours, which is relatively fast in this new SE. The answer tells me something new and equally interesting. It has got 5 upvotes, too.
Third, broad questions may inspire epic answers. For this question, someone familiar with QC might take the chance to give a succinct but comprehensive review of existing QC tools and measurements, something you occasionally see at SO or other SE sites. This would be invaluable to everyone. You can't get such an answer from a specific question on a particular technical problem with a QC tool.
Fourth, at this particular time we are struggling to pass the private beta phase, I speculate that closed questions are not counted. @RobertCartaino said we had less than 75 questions a couple of days ago. However, as @gringer pointed out, we had 77 questions almost at the same time. In addition, on the question page, we have 102 questions right now, but on the Area51 page, we only have (15+1)*4.9=78.4 questions. Why the difference?
Finally, even if not just for private beta, we need both experts AND new users to keep this site alive. To me, the questions here are a little too "narrow". They focus too much on specific technical issues. Questions slightly deviating from this focus quickly got downvoted or closed. Note that we are competing with BioStar. Although criticized for all the problems, its broadness and friendliness to newcomers are undeniable. If we keep closing border-line questions so aggressively, we would push new users to biostar and finally kill this SE, again.
So, please refrain from closing proper but imperfect questions so quickly.
EDIT: here is a list of questions that are currently closed or put on hold.

Influential papers. I wouldn't vote to close it, but I can understand why others want.
Bioinformatics vs biostatistics vs computational biology. Hmm... same comment as above.
Stable download URL. A little general, but I think it touches a real problem. I have voted to reopen it.
QC for NGS. This is the question I was mentioning at the beginning. It is a proper question.
Smalt. This is a good bioinformatics question and should not get closed.
Public multi-omics dataset. This is a good and relevant question. Many newcomers will have the same question. The answer has got 6 upvotes.
Constructing gene network. I am not familiar with the topic enough to tell.
NGS metadata schema. OP was essentially asking what relationships are common to general schemas. This is a proper question and should not be closed. Even if there were no general solutions, this would not make the question itself non-specific.
Scripting parallel processing. Closed due to off-topic. I don't think it is bad enough to merit a closure. @DevonRyan's answer is informative. Note that OP is a highly experienced SO user. He/she did not show up after this question.
On bootstrapping. Closed due to off-topic. OP has really put a lot of efforts into the question. The answers are good, too. I don't think it is that off-topic, either. We use bootstrapping often. Again, we pushed a potential new user away.
Genome vs transcriptome. Closed due to off-topic. New bioinformatics students with a CS background are likely to have the same question. I don't see we should close it. Again, OP was asking only one question and then gone.
Difference between common formats. Closed due to too general. I don't see the point: a basic question may look general to experts, but it is often a good one to many people. The answers are very helpful.

Related to this, I'm amused that a question regarding which shell is most popular (completely off-topic, but potentially useful for new folks to know) got a bunch of answers while some of those listed above were shut down very quickly.

I have recommended re-opening a few of the off-topic questions, because it seems like the people that closed them have a very specific idea of bioinformatics that doesn't match the broad definition.

My understanding of the stackexchange culture is that questions attracting lots of off-target or subjective answers are discouraged. When the scope of the question is unclear (as I believe to be the case for the nerve-touching question), then the question should be changed to encourage answers that target a particular area. It is possible for questions to be edited and reopened if they can be improved.

QC for NGS specificaly asks for "What are other popular means for such QC?" Is that a "proper question" for the site? The first question ("What are good means for performing QC or NGS reads?") might be OK if good is measurable or comparable IMO.

I cannot edit your question but the list of questions that are currently closed can be found at https://bioinformatics.stackexchange.com/search?q=closed%3Ayes

@gringer it's not about having a specific idea of what bioinformatics means but about having a specific idea about what a good question for this site is. Many fascinating questions are simply off topic or too broad to be addressed here. That doesn't mean the questions are bad, it only means that an SE site isn't the right place for them.

This is an excellent point. The goal of a private beta is to seed the site with some questions, answers, and members. Everyone here is interested in having this site succeed. Let's not ruin those chances. StackExchange wants to see activity. If you really hate the question, downvote it, so at least everyone else has a chance to see it. Don't close it unless it's clearly not relevant. Once the site is approved and there is a healthy community, we can be more selective. Treat this baby gently for now.
Keep in mind, one of the top SO questions is: "How to exit the Vim editor?". This could have been closed because it's off-topic (not programming).

On the contrary, during the early beta, it's especially important to keep questions high-quality. Overly broad questions help nobody. They always turn out to be crap when you look back a few months afterwards, and they're poor advertising for the site (nobody needs yet another collection of influential papers).

I wouldn't consider many of those examples overly broad. I agree about influential papers, but genome vs transcriptome is definitely relevant. Some people just feel that it's too basic. SO (the gold standard) has plenty of easy questions.

My only caution is to urge you not to trade in good moderation practices for the sake of holding onto more questions. That will reflect poorly on a site more so than having a few less questions — but otherwise a good balance to consider.

Only my 4th point touches this particular beta issue. All the others are general advice which IMO would help to build a friendly and sustainable community. I was a long-time moderator at biostar. I have some experiences with moderating and some hope for what this community should look like. Thanks for the caution anyway.

Please don't confuse "well defined scope" with "unfriendly". We do not compete with BioStars, they allow discussion and have a far more lenient scope. The success of the SE model is precisely that we only deal with specific questions that have an actual correct answer. Closing things that don't fit the SE model is essential to developing a healthy site.
If you want such broad questions as "What is the best foo for bar?" then you should absolutely go ask them on SeqAnswers or BioStars where they would be welcome. We are not in direct competition with those sites; we aim to build an SE-style site here, so no chit-chat, strict scope and exclusively questions and answers.
So no lists ("what is your favorite foo?"), no polls ("Who else thinks that bar is better than foo?") etc. While I agree that we might want to be a little bit more lenient during the beta phase, we can't do so at the expense of quality. And the notion that closing questions is somehow "
unfriendly" is one we should root out from the very beginning. It isn't unfriendly, just like downvotes aren't mean. These are the only tools we have to keep the site focused, on topic and with a high signal to noise ratio.
Now, of course broad and off-topic are subjective. But that's what this very meta is for: here is where we will hash out the details of our scope. And that's also why it takes 5 people to close a post: it's subjective, so we need consensus. Not closing is not the answer.
In addition, please note that "closing" isn't actually closing. It is putting a question "on hold". As soon as the question poster (the OP) or anyone else edits a recently closed question, that question is put into the "reopen" queue where users can vote to reopen it. If three do, the question is reopened and no harm done.
So, putting questions on hold is a very useful way of telling the OP to please fix the issues with their question to make it fit the site better. It is absolutely not a one way street, and can be reversed relatively easily. Especially in a small community like this one.

That said, here's my personal take on the examples you listed:

Influential Papers: this is the very definition of a question that is a bad fit for SE. it is asking for a long list, there is no "right" answer, it will be awful to try and maintain it. This sort of open-ended list request is explicitly off topic on any site of the SE network.

Bioinformatics vs biostatistics vs computational biology: the distinction between these terms (or rather between the first and last, the middle is quite different) is very much a question of personal opinion. There aren't really very strict definitions and everyone sort of uses them as they like. There are no sources we can cite to support our "definition". I don't see how this could be anything other than "my opinion vs yours".

Stable download URL: This isn't "a little general", it is incredibly broad. Even if such stable URLs existed, what would an answer be? Should it have a list of the stable URLs for all NCBI databases, EnsEMbl, UniProt, Gene Ontology, STRING, TGI, UCSC . . . Database N? There are dozens if not hundreds of such databases around. If the question were edited to make it about one specifically, that would be fine but as it is, it is basically looking for a discussion of the (very real) problem of changing URLs. That would be a great topic for the Bioinformatics Chat, but it isn't a good question for the main site.

QC for NGS.: I am afraid I strongly disagree with you on this one. That is a very, very broad question. If it were asking for the differences between specific QC tools, that would be answerable. But "what else is there" isn't really answerable. How can there be one good answer? The problem can already be seen in the existing answers. There are currently three answers, each of which is suggesting another tool. The answers are all variations of "I like this one".
Ideally, questions on SE should have one correct answer. How can the OP accept one of the ones they've received? How is one more correct than any others? This would be a great question for a site designed to allow discussion. This isn't such a site though, this is strictly Q&A.

SMALT: The question has been edited so that it no longer asks why SMALT is "so popular" for bacterial data and is simply asking for what features make it different or particularly well suited to bacterial genomes. That's great! This is indeed answerable with a single, correct answer. The original was asking why it was "the most popular" and that isn't really answerable without opinion.

Public multi-omics dataset.: I voted to close this one as too broad asking the OP to provide more information. The question was indeed edited and made more specific and it was reopened. Yay!

Constructing gene network.: this is the clearest case of the lot. The OP wanted to construct a network of 100000 different proteins and their interactions. This is obviously impossible since there is no species with so many proteins (or anywhere near so many). A discussion in the comments clarified that the OP is working on something that has nothing to do with biology and just mistakenly thought that biology could give a good dataset for what they want to do. So the question isn't even about bioinformatics, really.

NGS metadata schema: This one I would agree is fine and wouldn't have closed it either.

Scripting parallel processing.: agreed. I think we should allow such general computing questions when they are the sort of thing that a bioinformatician can encounter in their daily work.

Bootstrapping: I can understand this closure. The term isn't from bioinformatics nor specific to it. It comes from statistics and is in fact a common expression in English (although obviously in a different context). Still, it is something that is relevant to bioinformatics so personally I would consider it on topic.

Genome vs transcriptome : In this case, one could argue that the question shows a lack of research (although it is hard for us "experts" to gauge how hard it would be for a layman to find this). Lack of research, however, is a good reason to downvote, not to close. The question itself seems perfectly on topic.

Difference between common formats: this one seems like it should be on topic, agreed. I don't think it's a particularly useful question seeing as the three formats are used for very different things but, again, that might be because I am too used to them. No reason to close, anyway.

+1 for pointing out that this entire endeavour is not about "SE vs Biostars".

Yes, I agree that this site shouldn't be about competing with Biostars - its should be here to serve a different audience.

The question about SMALT never made a claim that it is the most popular aligner for bacterial data and wasn't changed at all. The only edit was an update of the title (so popular => better for) and splitting into paragraphs. See the edit history: https://bioinformatics.stackexchange.com/posts/308/revisions

@Karel the edit changed from "why is it so popular" which is purely opinion based (because people like it) to "why is it better than other mappers" which is a claim that can be refuted or proven. That's a pretty importan difference. but you're right, it never made that claim; I thought it had, my bad.

We should not close a question just because it can be reworded in a better way. What is more important is the intention.

@user172818 absolutely. If we can understand the intent behind the question, we should edit and fix it, not close. I didn't mean to suggest otherwise; did I do so? On the other hand, it is important to understand that closing isn't final. That's why it's called "putting on hold" first and only becomes "closed" if the question isn't edited. If it is edited, it is automatically put into the reopen queue and we can vote to reopen it.

“We do not compete with BioStars” — Yes, we do. Very directly. BioStars may be less focused than we are, but that doesn’t not make it a competitor, it just makes it less focused (and is one of the reasons I don’t like it). In fact, this platform will be a failure unless it manages to pull the vast majority of the Q&A traffic from BioStars over. If that isn’t competition, I don’t know what is.

@KonradRudolph yes, OK, there is some competition but I see BioStars as a better place to ask things that require more discussion whereas here will be more focused and strictly Q&A. So while some questions would indeed fit both site, many others wouldn't because they are posted more as discussion topics than as specific questions with one (or few) correct® answers. I see room for both sites to exist in parallel.


text:
Computational biology but not gene sequences?
I see that this site is focused on sequencing and genomics. I'm wondering if other fields that combine computations and biology are on-topic. Such as:

molecular dynamics simulations,
analyzing 3d macromolecular structures (from PDB),
proteomics.

These communities, from what I see, use primarily mailing lists to ask questions. More than a year ago there was a proteomics.SE proposal (that didn't make it like most of the proposals). I remember because at the same time I was proposing crystallography.SE. I tried hard to convince crystallographers, in particular developers of computational methods in macromolecular crystallography, to join it. Of course we were far from making it and it was just a waste of time. I read the Robert's post about chances that bioinformatics.SE will not get out of the private beta. Maybe widening the scope (to bioinformatics in the broad meaning of this word) would help?

I think that's just what we've gotten so far and shouldn't be taken as an indication of the site's scope.

I believe that that molecular dynamics and protemics are as well bioinformatics as well. it is only that we (sequencing people) dominate by numbers, therefore sequencing questions will be always predominant on any bioinformics site.
It would be awesome if there would be a community of bioinformatians doing protemics. There are even more obscure fields that could come here, like theoretical population genetics, which is largely based on explicit simulations...
I think any biologically motivated computational question / problem is appropriate.
--- edit ---
and it would be really great to get all the people here in less than a week together with at least 50 questions!

I reached to a proteomics guy who brought it up on their mailing list (although they are not so enthusiastic about SE after their proposal failed). Someone could try reaching to other bioinformatics communities.

Any sub-field of bioinformatics should be on topic here. NGS happens to be the most popular subject among the few people who have participated so far, but that doesn't mean the site is dedicated to NGS analyses. In fact, I hope it won't be, since that would be a shame.
Personally, my main expertise is in comparative genomics and PPI networks, for example, and I've only been working with NGS for less than two years. So I am looking forward to posts about other aspects of bioinformatics.
I would consider proteomics to be absolutely on topic. Crystallography, maybe less so unless the question is about the computational aspect of it. Basically, any application of computers to answer a biological question should be on topic here as far as I'm concerned. But the site is most certainly not limited to NGS analyses, that would be a shame.


text:
Is there a large enough community to sustain this site?
Update:
This site has passed the final evaluation! Barring any technical delays, Bioinformatics SE should go public sometime this week.
Great work everyone!

(original post)
Spread the word. In less than a week, this site will undergo a private beta evaluation. I had to postpone the pro tem nomination thread — typically posted today — because there simply isn't a large enough community signed on to support this site.
We need to increase your numbers. Typically we need about 150 questions in three weeks of private beta to be considered viable. That number is not arbitrary — it's the minimum bar of activity we've needed for a site to remain viable in the 180+ sites we've launch. And that's a bare minimum.
You have less than half that.
Fair warning: Simply having the same people ask more questions is not sustainable and not a solution for giving the appearance of organic growth. You need more users.
What can you do to help?
We've got a week, so nobody is writing this site off. I just wanted to give you this heads up in case there's a group of users waiting in the wings for this site to go public. Spread the word — We need more users NOW. This is the final stage we use to determine if there is enough interest to sustain a healthy site.
Pass the word. We. need. more. users. now.
Good luck!

Did the other 180 sites have a big community in other sites?

77 in not smaller than half of 150, but I got the point...

I tried to spread the word by posting comments pointing to this site under bioinformatics questions in other stackexchange sites that hadn't got a satisfactory answer, but I realize that this site is still private. How can I efficiently attract users if I need to send individual invitations?

Something I've only recently noticed: I can invite people to participate in this private beta by filling in the "invite fellow experts" form at the right hand side of the main page.

Konrad raises a good point. Most of the target audience for this site won't be on SE. Signing up for a private beta is not as simple as all that if you're not an active SE user so that might be a significant hurdle to overcome. Would it be possible to make it a public beta first and then see if it ever graduates as opposed to killing the site while still private? I expect to be very active here, but would need more questions closer to my particular area of expertise and that would take a broader audience.

Since it doesn't seem like anyone wants me to add it into the "question" itself, here's a  link to the current question count (112 at the time of posting this comment).

"You have less than half that." --> Where do you see the question count? Do you look at the same number as in the link given by gringer? (honest question, just to make sure we are looking at the same count)

Are we going to close the site in a week?

Robert presumably doesn't want to update the question as the situation changes.

You need more users.

Then make the site public.
It’s as simple as that.
Unlike other Beta SE sites, there are already large, competing Bioinformatics Q&A sites on the internet1, so unlike for other sites people won’t go out of their way to subscribe to a private site here. There’s simply not enough demand.
Now, I’ll be the first to say that the competing Q&A sites are very unsatisfactory for various reasons. But they exist, and they represent large parts of the professional bioinformatics community. A private Bioinf.SE isn’t an attractive competition. In order to become attractive it has to offer more than the competition, not less. This means: open the site, and implement crucial, missing usability features.
Robert, you’ve been in this business a while, you know how communities work. So I’m honestly surprised that this comes as a shock to anybody at Stack Exchange.
It’s worth noting that Stack Exchange should have a vested commercial interest in successful communities. And while I appreciate the extent to which commercial interests have taken a backseat to community building at Stack Exchange, maybe it’s worth considering the pros of giving some support to a Bioinformatics.SE community.

1 I count at least four: Biostars, Bioconductor Support, /r/bioinformatics (etc), and SEQanswers.

Strongly agree. Given the apparent number of bioinfo.SE area 51 proposals it would be a shame for this site to get closed before giving it a proper (i.e., public and more than 2 weeks) chance at succeeding.

Yes, basically this. First, a lot of old good questions have been asked at biostar. They are rarely asked again here. Second, between a 8-year-old platform open to public and a two-week-old site in private beta, it is no-brainer for most casual users to choose the former option. No matter how good some think this SE is, it won't take over biostar in months at least, not to speak two weeks in private beta.

I don't totally get the concept of 'private beta', so it is by invitation only? Why not just make it public?

We are not going to launch a proposed site still in a "proving phase" on an unsuspecting public. Signing on for a controlled private beta is how we develop this site and this community in preparation for opening day... not to have the opening day first. Besides, simply going public has never caused the spontaneous bump in traffic like you might expect.

@Robert Is there any experience moving people from one community to others? It is hard to get people register in a private beta if they've never been in SE

Wouldn't they just need to sign in with google/facebook/etc. credentials?

@Michael I am not sure how the private beta work, but let's say that bioinformatics is not actively displayed. Only if you search for "site:bioinformatics.stackexchange.com" which then display the log in which says: "To log in, you must have commited to the Area 51 site proposal and received the invitation email."

@RobertCartaino “Besides, simply going public has never caused the spontaneous bump in traffic like you might expect.” Of course not. Community growth takes time. But for bioinformatics this community already exists, it’s just elsewhere. Sure, bioinformatics is not entirely unique in this regard. I still think that the growth of a bioinformatics.SE site would be much steeper than for other communities. In particular since many in this community used to be on SE before they migrated away with Biostars.

Note: It's not exactly by invitation only. All people from outside can still register when you send them the Visit link. I've commented on that reddit post, so hopefully more people will join.

@RobertCartaino Looking at Area 51 now http://area51.stackexchange.com/proposals/109245/bioinformatics it seems like the site is still not getting enough traffic/users, despite the public release?

@Chris_Rands I don't know what you mean by "not getting enough." To get a custom design...? No — See Graduation, site closure, and a clearer outlook on the health of SE sites

@RobertCartaino Ah thank you for the link, I was merely basing this on the red "Needs Work" flags on Area 51, but I was not clear on the process actually

I don't think we're getting a good representation of questioners among the people who are able to participate in the private beta. Bioinformatics is too broad for a small private beta to work well.
You're asking for more users among the people who have already committed to participate in the site, which is only a bit over 200. 100 of those users have a high profile in other sites (at least, but pretty close to 100), which means that current users are more likely to be answerers than questioners.
It feels fake for me to ask questions that I already know the answer to, and yet the questions that are most often asked on bioinformatics forums (and most useful to bioinformaticians) are the ones that are frequently established knowledge in a different area. For the questions that I do have, it's unlikely that a large number of other committed bioinformaticians have the precise specialisation required to provide useful answers.
I could perhaps take some questions from BioStars, SeqAnswers, and the nanopore community forums, but that does not feel like the ethically-correct thing to do. I wouldn't be asking questions that I want to know the answer to, and a fairly good answer is likely to already be available on the other sites (after spending ages wading through the crud).

I think its perfectly legitimate to ask here questions that are already asked and answered elsewhere (provided the original version is linked): this enriches this site and gives these "FAQ" more visibility, makes them easier to find. I see stack exchange partly as a repository for FAQ, partly as a site to get expert answers on more particular issues. Both are useful. I particularly benefit from the "FAQ repository" aspect of stackoverflow regarding programming issues.

It is absolutely legitimate to ask and answer your own question only to share knowledge! It is in fact actively encouraged on the Stack Exchange sites. Please do so!

Okay, this is a culture I'm really not familiar with. I'll see what I can do about changing the way I approach this site.

Two very good points to highlight: "more likely to be answerers than questioners" and "does not feel like the ethically-correct thing to do".

done; I've highlighted those points in my answer

I don't see anything ethically wrong with reproducing content with attribution. Why not? And I certainly see nothing wrong with reproducing a question and just asking the same thing here. Why would it be ethically wrong?

It's stealing traffic from a different site, generates reputation with minimal effort, and can end up being attributed to the copier rather than the original source. An extreme example of that would be GallowBoob on reddit. There are people on SeqAnswers (and probably also BioStars) who emphasise cross-posts, and appear to be pointing them out as bad things (e.g. see https://www.quora.com/Do-people-not-like-it-if-I-cross-post-posts-on-seqanswers-and-biostars-org). I'd rather not alienate Biostar users before we're even out of beta, if I can help it.

Or after we're out of it! Absolutely. But why would reproducing content with attribution be a bad thing? But OK, say that can be misconstrued, why would it be wrong to ask the same question? You don't need to copy anything, just ask a question and get answers here.

A person would be gaining fake reputation; reputation that is acquired because they just happened to pick a good, popular question before anyone else on the StackExchange site.

Attribution can be ignored, and a verbose, well-researched question transferred across to StackExchange would make it more likely that people wouldn't click on (or notice) the attributed link. Search engines would be more likely to attribute the question (or answers) to the most frequented site, regardless of the origin of the question. This is a problem in research papers (e.g. see http://www.gringene.org/portfolio.html#MAOA), and I have trouble believing that StackExchange would be immune to this.

@gringer The important thing is that the best answers are easy to find and recognised as good answers. The primary goal of Q&A sites are to provide answers. Answers available in more sites means better accessibility of answers. Who gets reputation or what site gets traffic are secondary issues, in my opinion.

@gringer "the person would be gaining fake reputation; " -> you can make the question  community wiki.

I think this is a little bit the wrong question, it should be "Is there a large enough community to support two almost identical sites." The core of the problem is that there is a community already on biostars and in principle all the users you want are already here: https://www.biostars.org/user/list/?sort=reputation&limit=all%20time&q=
Some have predicted that this beta might not work, simply because there is already this established site, and I mostly agree with them. Bioinformatics is a scientific field with a growing but limited audience compared to other topics like programming. In my opinion, it is unlikely that there exists a large potential scientific community that is so far put off by the technical limitations and other shortcomings that surely BioStars.org has, and that is also able and willing to invest time into QA. In other words, the people who are available are most likely already engaged, and for most of the other scientist the tiny differences are marginal compared to large scientific problems of interest.
To make people transition to the SE brand, you needed to offer them some added value. Indeed the SE technology is superior, but that is not good enough. Certainly BioStars has a superior user base from interested beginner to PhD students to senior researchers and professors, with enthusiasm and experience in Q&A. That knowledge base will certainly attract more questions because there is a much better chance to get a competent answer. Just to add some figures, on biostars, there were >300 posts this week, and >60 today, from a total of 35,000 users.
What is more, as it turns out, one cannot take over the reputation from the other site, thus I have decided that I am not available for doing much on bioinformatics.SE, because why start out as a rookie here again?

How do you use your reputation in Biostars?

I am a moderator, I like to delete spam, suspend users, close and delete posts, edit posts, move posts ;) also it looks good on my CV.

But being moderator is independent of the reputation AFAIK. Here you can vote to close, and delete from almost the beginning, editing from the beginning, and you don't need to move post unless you become elected. And being a moderator here it will look as good

Hm, then it just looks good...

Indeed I would sometimes prefer the vote-to-close over being the sole responsible. I remember though when I was trying to comment in another SE site, I even could not do that. Also, there are other things here I don't like, like the stupid "You can only edit a comment for 5minutes" thing.

Well you can always add a new one. Yes you can't post comments in other people question unless you have 50 reputation. But it is easily obtained if your questions or answers are good. check it out here

Biostars does have an existing user base, yes. Personally, I find it extremely hard to use and despite really enjoying Q&A (I am very active on the various sites here), I never really got into biostars. And while I have on occasion found useful answers there—even a few excellent ones—overall, I've always been very disappointed with the noise and lack of quality of Biostars when compared to successful SE sites. Point is, different strokes for different folks.

[cont] There are way, way more bioinformaticians out there than are active on Biostars and there, as in SE, the site is supported by essentially a small, core set of users who enjoy answering questions and are knowledgeable enough to do so. It's that kind of relatively small group of committed users that we need here; there's no reason to bring in everyone from Biostars. We just need a similar group of experts. And judging by the amount of bioinformatics questions I've seen on other SE sites already, not eveyone is on Biostars or SeqAnswers either.

Honestly, I don't see the level of noise as very distracting, also we are doing our best to keep it low, I am a mod myself. There are many excellent folks there, and they are - imho - the best experts in the field, that at the same time have enough time and motivation, to do QA besides writing papers and grant applications. I don't believe that there is a large cryptic pool of labile researchers that have both expertise and intention, and that could be recruited in addition. But please go ahead and try.

@Michael I'm not the only one who put biostars on his CV I guess :P It's always crazy when interviewing places (or now people interviewing with me) to constantly bump into people who "know" me from biostars.

@Michael I'm sure you do do your best to keep it low. But that's just it, to someone used to the SE model, the noise is still very high. The answer I want is as often found lost in some obscure comment as in an actual answer. And of course there are some extremely knowledgeable people on biostars! The "best" experts in the field might be pushing it, but experts yes, absolutely. I dunno, as I said, I never enjoyed Biostars but got addicted to SE very fast. It just comes down to what a person prefers. You can't even downvote on Biostars!

Just to clarify, I meant there's an intersection:" (best experts in the field) AND (time and motivation)"

With respect to down-votes, this will also put off some people, and many people on biostars explicitly wanted to remove this, as they value a more friendly community, possibly because bioinformatics is by and large an academic community. People who favor learning by positive and negative feed-back, like me, might appreciate down-votes. However it is not clear that having down-votes would attract more people than it repels. As I said earlier, I appreciate the superior feature set of SE, but it is not very relevant for the depth of scientific discourse.

People interested in the conversation on biostars regarding this post should see here

@Michael that's fine, which is why we need both communities. The idea that downvotes are "unfriendly" is a misunderstanding. Instead, they are very useful and the only way we have of pushing wrong information to the bottom and letting the correct answer float to the top. So those who consider having their errors pointed out "unfriendly" should indeed stick with biostars. Those who feel otherwise can come here. And this, unlike biostars, is not a site for scientific discourse. That's the point. This is strictly a Q&A site. No discussion, no chit-chat.

@terdon I've not heard people object to downvoting answers, but rather questions.

Well, either way. Personally, I find poorly written (as in no effort; obviously, people making mistakes because English isn't their native langauge is not an issue) questions are a huge waste of everyone's time. So a downvote is useful there too. Albeit less so.

I don't understand why there should be a high activity for the site to be useful. I get that no activity at all can be a problem, but so far, this site has been useful to me: I asked questions and got relevant answers in a reasonable time. That's what stack exchange is all about, isn't it?
I see that 90% of questions have answers so far, and that there are more than 2 answers per question in average. More relevant would be the rate of questions having an accepted answer, though.
Small communities have merits. I think that if the activity is too intense, it gets sometimes difficult to have one's question answered, because questions get easily swamped in the flow of questions. So far, with a few questions per day, I'm able to read all question titles: I won't miss a question I could answer or that could be interesting for me.
I guess the need for moderators is dependent on the site's activity: if the activity is low, the site does not need many moderators.

I imagine there is a certain overhead to managing every site. It's not economically feasible to manage many sites that have negligible traffic. You also need many active users to set a relatively high bar to becoming a moderator. If there are few users, it's easy to become a moderator and that potentially leads to problems.


text:
Is it okay to ask questions regarding being a bioinformatician?
I was wondering if the Bioinformatics SE is a good place to post questions relating to the process of research in bioinformatics.

Example:

What is the proper way to format a PK/PD model for a published report?

Question:

Is it okay to ask questions relating to being a bioinformatician, rather than just the subject matter itself?

I am not sure if other Stack Exchange sites would be better suited for this type of subject matter, such as the Academia Stack Exchange.

I think that presenting/visualising data is very significant part of bioinformatcs and it should be questioned (and answered). So the example of yours I find completely fine.
However, I would try to cut questions like "What languages should bioinformatian learn?", "How to apply for a grant in bioinformatics?" or "Where to publish good bioinformatics research?", just because it is not really constructive.
As conclusion, I think it would be very hard to define a border.

I agree to this point. Visualization is an integral part and community should help each other to get these problems sorted. Getting to know about grants and publication information, should not be the prerogative of the community. Rather these should be something that their employing institutions should take care of.

I guess "grants and publication information" can be asked on academia stack exchange.

"How to apply for a grant in " would likely get shot down on other SE sites as well. It's not a very specific question.


text:
Standard language for comments asking for an improved question?
One of the first things I needed to learn when coming to SO for the first time was how to ask a good question. I suspect I'm not alone in this. I was fortunate to have responses to my first (poorly asked) questions that:

Explained why asking the question well was important
Explained the steps I could take to improve my question

And they did so in an insistent but friendly way. This positive reinforcement (combined with the requirement that I do more work) allowed me to learn how to ask better questions without getting discouraged. I often think that the bad reputation that SO has among many people is that their first experience(s) asking questions were treated rudely or just downvoted with no explanation.
So I'm wondering if we should have some standard language people can use for some common question faux pas. I was prompted to ask by Iakov Davydov's response to this question, which I think is a good start. Friendly but clear on what additional steps should be taken.
So the actual question: should we have a bank of standard responses? This might increase the chances that (a) people will comment to explain to people how questions can be improved and that (b) those responses will be welcoming to new users while training them to ask better questions.

Where / in what form would a bank of standard responses be stored?

Relevant userscript: AutoReviewComments, which automatically stores 'canned comments' that you can customise. I find it immensely useful on Stack Overflow to provide quick guidance and save some time.

@bli right here, probably, as an answer to this very question. Other sites on the SE network have similar posts. Here's one from [ubuntu.se]: https://meta.askubuntu.com/q/1323/85695

I think this is a very good idea but maybe we should not expect an answer so soon. Let's see what kind of questions we get and figure out what type of information is most often missing.

Link to your question post is broken.


text:
Should we allow questions about biology?
How do we feel about questions about biological principles that can be confusing to a bioinformatician with no background in biology? While purely biological questions should, I think, be off topic and migrated to Biology, what about questions from bioinformaticians trying to interpret their results?
For example, if someone were to ask about what these weird 0/1 things they see in a VCF file, should we explain what haplotypes and zygosity are? If someone asks about how a PPI network is generated, should we explain ChIP or Y2H methods here?
Basically, how strict is our definition of bioinformatics? This is a subfield of biology, after all.

Isn't bioinformatics a subfield of informatics? The question about what is bioinformatics is a though one. BTW +1

@Llopis heh, I admit I may be biased since I come from a background of biology and not computers. I always thought of it as a field of biology and not of informatics. I guess it depends on what you do though. On the other hand, all universities I am familiar with that offer bioinformatics, consider it part of biology and the courses are run by the biology departments. Not that that means much, of course :)

The way the word bioinformatics is used these days pretty much suggests any part of biology that involves the use of computers to process data. Once upon a time bioinformatics dealt with the best ways to organised, store, and cross-reference biological data. It was fair to call it subfield of informatics. But most bioinformatician these days wouldn't know the first thing about databases, and as commonly used, itis a subfield of biology.

@IanSudbery when/where was this? My first contact with the term was in 2001 or so as an undergraduate and then it already meant "any application of computers to answer biological questions". I know some people used "computational biology" for that, and "bioinformatics" for developing tools etc, but I only came across that term more than 10 years later while doing my post doc.

I think we should indeed explain biological concepts as long as those are clearly relevant to the work of a bioinformatician. So, a general question about transcription should be off topic, but a question about the biological interpretation of computational data (blast output, for example) should be allowed.
A simple example would be a question about interpreting a sequence alignment. While it may look like bioinformatics, it is very hard to interpret such alignments usefully without some basic knowledge about the biological concepts of sequence evolution, the chemical properties of amino acids, protein domains, exons, introns etc. So a good answer would have to include at least some "pure" biology.
I think it will be very hard to set out specific guidelines for this so early in the site's life, but perhaps this is something to bear in mind going forward. I expect that in the following weeks we will start getting such borderline questions and I hope we can get to a consensus about them using real examples.
In the meantime, I propose that as a rule of thumb, we should allow any questions that arise from bioinformatic analyses. If it turns out those are too permissive and too "wet", we can reassess.

I think that biology questions should be accepted (those relevant to a bioinformatician, as @terdon mentioned).
Bioinformatics is a combination of biology, computer science, and statistics. People with specialisation in one of those areas have a "ground knowledge" and would tend to treat questions as simple that people coming from other areas would find difficult. I don't think it's a good idea to expect that visitors to this site will have expert knowledge in all three areas.