text:
Should the first go an answer or comments?
I personally believe that community should offer the answer for the question before any other (even relevant) comment. I opening this thread, because one of the most upvoted answers is starting with statement that one should do something else instead of what the question is asking for.
The first statement is not an answer for the question... This is patronising since there is no alternative ("if anything, use FPKMs" sounds like there is something else than FPKMs to use, no?).
I would suggest to keep these comments (that are often very useful) in the END of the answers, not at the beginning. And if we decide to write them, write them with full explanation and a good alternative, not in this declarative style with a link to a blogpost. I really think that this will help keep the community healthy.
So is it just me who feel it that way?

If you are not happy with the language feel free to suggest an edit.

Why is this being closed? It's a meta discussion, so being primarily opinion based isn't a problem. It seems like a perfectly useful discussion to have, why close it?

I kind of felt that it is really just me, therefore I though that it might be good to close the thread.

I have an edit in the queue to make the "use FPKMs" a bit clearer.
I'm going to interpret your post as being, "I personally believe that the community should offer actual answers before writing opinionated commentary."
Anyway, putting the comment at the beginning there was highly appropriate. OP was essentially saying, "I'm very new and would like to do something that's almost always a bad idea because I've seen it done in a bunch of papers." Since OP is new, burying the warning at the end would likely result in OP wasting time by actually making FPKMs and then hopefully reading, "Oh, but you shouldn't do any of that, do THIS instead."

It seems that you are convinced that OP wanted to ask, "what is appropriate measure for differential expression and how to calculate it in R?", then you should suggest an edit of the question. But there might be some reasons why you might want to ask question of RPKMs - for instance reproduction of somebody else study or reviewing a strange looking R code...

I'm not convinced that OP wanted to ask anything, but past experience dictates that that's likely what was intended.

Regarding your edit, I’m tempted to reject it since it changes the meaning. The current sentence is correct (I’m using a subordinate clause starting with “which”). But I agree it could perhaps be made clearer; just not by replacing the subordinate “which” by a non-subordinate “that”.

The general position on the SE sites I am active on is that if the OP is using the wrong tool, then that should be the first thing to mention. So, if a question asks something like "How can I use ClustalW to align two gene sequences?" I think the first thing to mention is that ClustalW is obsolete and a newer tool like ClustalΩ or any of the various other modern aligners should be used instead. Or if someone asks how to use BLAST to call variants from an NGS dataset, rather than attempting to find some sort of weird hack that would make that possible, we should instead point out that there are far, far better tools for this.
So no, if I feel the OP is barking up the wrong tree, pointing that out and providing an alternative seems like the best way of starting an answer. Why waste time explaining the wrong tool instead of helping the OP choose the right one?
If it's just a question of opinion then yes, that should go at the end or not at all. But if it is a case of an XY problem or simple ignorance on the part of the OP, then pointing out the essential error in their reasoning is probably the most useful thing the answer can do.

XY seems very relevant.

Ha! That it does :)

I just think, that for XY problem, we should make an effort to find together with OP the real question and then change the question. Probably for OP it does not matter, but for others googling it does. Reformulating questions clearly and explicitly will help a lot people finding correctly linked questions and answers quickly. Maybe it is bit related to this post.

@KamilSJaron of course, if we think it's an XY problem but can't tell what the OP really wants, we should ask in the comments. However, if the objective is obvious but the method wrong, we should give the right approach. For example, if someone asks how to use blastp bit scores to find distant protein homologs, a good answer would explain that blastp is the wrong tool for this and something like PSI-BLAST or HMMER is much better.

@Kamil, I think that if a newbie is googling the wrong thing, then a question asking that wrong thing answered with a better question has value.

@wkretzsch the point of mine was, that we should not assume that what OP meant, but rather invest to clarification of question. In fact, I have more and more impression that it is not that hard here. The most of people are able to describe their problem sufficiently to be answered after few questions of someone from the community.

I personally believe that community should offer the answer for the question before any other (even relevant) comment.

I strongly believe the opposite. We should strive to be helpful. And at the risk of sounding patronising again, it’s not helpful to “help” somebody down the wrong path. Instead, we should correct them. This is the case here.
In fact, I’m usually even stricter: in this particular case there was no harm in also providing a literal answer (i.e. the code that implements FPKMs) but usually I would outright refuse to answer a misguided question, and only focus on alternatives.

The first statement is not an answer for the question... This is patronising since there is no alternative

In fact, the answer did give alternatives, and provided links with further information on the subject.
Given all this, I’d respectfully disagree with your claim that the answer was in any way patronising.

All right, seems that it is just me...
By the way, I looked at your top posts on other SE - they always answer the question and then explained it in detail.


text:
Can we have syntax highlighting?
It seems that language syntax highlighting is not working.
As I think we will have many answers involving small code fragments. Is it possible to enable this?
Few examples: 1, 2.
I used <!-- language: lang-... --> to specify the language in both cases.

Yes, and it should be auto-enabled for questions being tagged with a programming languages, like on Stack Overflow.

I thought this kind of feature would be automatically enabled by the stackexchange engine. It would be a nice addition to have it. Readability counts.

I've asked SE to activate this and they just told me they have. It should be live soon (there might be some caching issues involved).

@KonradRudolph that can be set up by mods. The tag page a mod sees also has an option to associate a tag with a language.

I mentioned this to an SE employee and they implemented it today! We now have working syntax highlighting!
Tags can have a specific language syntax associated with them. This is something that mods can set up. So, for example, if we were to ever have a perl or, more likely a bioperl tag, the mods could set it up so that it is associated with Perl syntax highlighting.
If a question isn't tagged with a tag that is associated with any specific syntax highlighting, we can still enable it using HTML comments. The syntax is as follows (using perl as an example):
<!-- language: lang-perl -->

Each code block you want to have highlighted must have a comment like the one above, an empty line, and then the code. For example, this:
<!-- language: lang-python -->

    var="foo"

Will be rendered like this:
import foo
var="bar"
otherVar = None

Each code block in a question or answer needs its own HTML comment, and you need a blank line between the comment and the first line of code, as shown above. Here's the list of currently supported languages and their identifying string (the lang prefix is not needed if a tag has the language associated with it, but it won't harm it and we're unlikely to have many such tags anyway):
none:      none   ## Useful for disabling syntax highlighting
bash:      lang-bash OR lang-bsh
c:         lang-c
clj:       lang-clj
coffee:    lang-coffee
cpp:       lang-cpp
cs:        lang-cs
csh:       lang-csh
css:       lang-css
dart:      lang-dart
erlang:    lang-erlang
go:        lang-go
hs:        lang-hs
html:      lang-html
java:      lang-java
js:        lang-js
latex:     lang-latex
lisp:      lang-lisp
lua:       lang-lua
ml:        lang-ml
pascal:    lang-pascal
perl:      lang-perl
php:       lang-php
proto:     lang-proto
py:        lang-py
r:         lang-r
rb:        lang-rb
regex:     lang-regex
rust:      lang-rust
scala:     lang-scala
sh:        lang-sh
sql:       lang-sql
vb:        lang-vb
vhdl:      lang-vhdl
xml:       lang-xml

Did this stop working? I can’t seem to get anything highlighted, see e.g. here: https://bioinformatics.stackexchange.com/a/69/29 (both tagged, and the code is explicitly marked with a language).

@KonradRudolph no, it works, it's just not very helpful for the code you posted. The snippet you had explicitly set a language for was colored but only in the words function and the 1E6 of log(1E6). The one you hadn't set explicitly wasn't colored because I hadn't associated the tag R with a language for syntax highlighting. I have now done so, so any future posts won't need the explicit <!-- language: lang-r --> anymore.

Right, I forgot how … err … minimal Stack Overflow’s syntax highlighting is. Bit bizarre, given that programming languages is their core competence.

@KonradRudolph AFAIK, they just use something developed by Google. And it does work OK for many cases. R doesn't seem to be one of them though, granted.

source: Stack Exchange

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

sort: votes


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How much this site is/ going to be on-topic to bio student lacking a proper IT and stat base?
I felt like if anyone have to learn bioinformatics in the 'proper' way, conceptually; then a base of statistics, data-modelling and computer-programing is a prerequisite. But biology students of most traditional courses; often completely  lack that  basis (such as me is one), and also, bioinformatics is taught directly on masters or equivalent grade (or maybe a little bit introduction in college or bachelor's' grade).
So, how much on topic this site is/ going to be, for such typical bio students who might ask very basic questions about bioinformatics (not expert-like one)?

I don't think that there would be any problem asking very basic questions, so long as they are asked in a way that follows the site guidelines.  StackOverflow is full of 'Hello World' questions, and there is nothing wrong with that, so long as the questions are not duplicated.  Once this site has matured, it should hopefully be able to cover even the most basic of bioinformatics questions.  It will be up to users to search for existing questions before posting, though, so as not to pollute the site with the same questions over and over.

While I totally agree with this response, I would like to add that during the private beta period we are encouraged to enrich the site with expert-level question. This probably means avoiding very basic questions until the next phase.

I wonder if this site might always be slightly "higher level" than biostars. Biostars is explicitly for helping beginners. I feel like binfo SE should not be hostile to beginners or non-experts, but would definitely aim at being less handhold-y.

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


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How do we avoid (welcome?) link-only answers?
For example, below post has 2 answers that are almost link-only-answers ^1 .
Improve a reference genome with sequencing data ^2
Maybe it is OK? Or would questions asking for a tool should simply be closed? On the other hand, bioinformatics tools/methods are not easy to find. Even if we find them, we are not sure how "good" they are.
^1: There is already a good discussion about this at main SE meta.
^2: Please read this before upvoting/downvoting: What is the "meta effect"?

I think we should educate our selfs about how and what to ask here and how to answer. SE Meta is the site where questions about how does Stack Exchange sites (like this one and all the others) are asked and answered. To this regard, your link in main SE Meta clearly says:

When someone goes on Stack Overflow, the question "answer" should actually contain an answer. Not just a bunch of directions towards the answer.

So we should:

Edit to include the relevant information in the answer if it is already posted.
Avoid answering with just a link to where the answer can be find.

On the other hand we should also avoid not crediting the source of our knowledge.

Also relevant


text:
Q&A-Style Answering Own Question
Since the site is in beta, and the idea is to develop a core of high-quality questions: should we be posting what we think are good questions which we ourselves know the answers to?
For example, I could pose a hypothetical problem (or an old problem) which I have already solved, and I anticipate many others will face in the future, and present my own solution as an answer. Is this frowned upon or encouraged?

Go for it, it is encouraged.

As far as I understand, posting questions Q&A style is encouraged. That's probably why now you can even post the question and the answer at the same time through the website interface.
I was doing it myself here, and for one of two questions, there was a better answer proposed, which in my opinion is really cool.

I had a similar concern about the "high-quality-questions", so I asked about what to do with the example questions posted in the definition phase. I asked in Area 51 meta and an answer suggest posting the example questions is fine.
Posting and answering your own question is not frowned upon but  the tour page says:

Specific issues with bioinformatics
Real problems or questions that you’ve encountered

So if it a hypothetical problem it is not a good question for the site.

Posting and answering your own question is actively encouraged, not just not frowned upon. The tour guidelines (which are basically the same for all SE sites) are trying to avoid open ended hypothetical stuff. A specific problem for which you have the answer should be fine.


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Migrating bioinformatics questions from other SE sites
There are a host of Bioinformatics questions on StackOverflow, CrossValidated, and probably other SE sites as well.
Many of these questions would now be better placed here than on the site they were originally posted on. Should we actively seek out migration of good, relevant questions from other SE communities which would fit better here?

I think this should/would happen once this site is live?

Certainly new questions should be migrated when they are asked in the wrong places, but I'm not sure what the protocol is on existing questions - I think it would require an active effort to seek these out.

Yes, that would be a quite an effort, maybe mods at SE can do it automagically.

Could work. However, I imagine a number of those questions would be related to bioinformatics but still in essence code-based problems and thus better placed on StackOverflow? Not sure what others think about overlap between this site and SO in particular

There are bioinformatics questions on [biology.se], [linux.se], [so], [ubuntu.se] and almost certainly others. However, all were on topic on their sites so they cannot (and should not) be migrated. And mods can only migrate questions that are less than 60 days old anyway (speaking as a mod on other sites).

First of all, we can't migrate questions older than 60 days. Moreover, the general rule across all SE sites is that we don't migrate away things that are on topic. So assuming the questions were indeed on topic where they were asked, there is no reason to migrate them.
Instead, what we should do is when we find an interesting bioinformatics question on another site, we just ask it again here. We can either use the existing answers from the other site directly (with attribution, of course, and possibly marking as Community Wiki as well), or write our own.
But no, migration of existing questions isn't the way to go and isn't possible anyway.

The Unix & Linux SE forum gets a few bioinformatics-related questions, but they are most of the time perfectly on-topic on U&L as well.

The bioinformatics tag on SO seems nearly as active as the entire forum here, should we not be directing more of that traffic here either by migrating new questions or commenting on questions?

@Chris_Rands commenting yes, absolutely. But the general rule is that we don't migrate away things that are on topic unless the poster asks for it. Leaving a comment to let people know about this site is something else and  probably a very good idea.

Although some questions about bioinformatics might be answered in other Stack Exchange sites if they are on topic on that sites it doesn't need to be moved here unless the OP asks to move his/her question.
For example some questions are on topic both in Stack Overflow and Software Engineering, but unless the user asks the question is left where it has been asked.
See related posts in meta SE and this other post. Specially this one:

If it is a borderline question, let it live in both cultures, as the answeres will be different, programmers answering for programmers, and admins answering for admins.

If such is done; then primarily-bioinformatics questions on Biology SE could be also migrated (imported)  (later-on) to this site, so that they could be easily found together.


text:
What to do with answers inspired by BioStars?
Out of curiosity I followed the first of Pierre's BioStars links from the comments on the FASTA lengths question, and noticed that our currently accepted answer bears a strong resemblance to this answer on BioStars.
I'm not trying to start anything, or accuse anyone here, but presumably we're not here to mirror answers already available elsewhere. So I'm just wondering whether there is a policy on this sort of thing, and whether anyone knows what the license for BioStars answers is?

Just to note, let's not make it OK to post "link only" answers.

Did this change? The currently accepted answer is yours, and the Biostars answer you link is a one-sentence reference to FastQC (and no reference to FastQC is made anywhere in answers here).

It seems the answer I was referring to has been deleted

@SamStudio8 Ah, that’s a shame, because now there’s no single reference to FastQC. At any rate the BioStars answer was a single sentence so even if it were copied verbatim it would be unlikely to be (a) copyrightable or (b) ethically ownable.

The question here was specifically about nanopore reads. FastQC is not appropriate for long reads, and likely to be harmful due to the false error flags that it will throw up.

Regarding licensing for biostars posts, they're Creative Commons (version 4 if that matters). I'm personally of the opinion that biostars posts should at least be linked to so people can see where the information comes from and the original author there can get recognised. Others are, of course, free to disagree with that, but regardless I fully support your stance that there should be some sort of rough policy.

I would hesitate to use biostar as a source of information. There are low quality and sometimes completely wrong accepted answers. I would prefer to link the manual of a tool or a paper instead of biostar.

I don't think anyone is suggesting blindly believing things written on biostars (or anywhere else for that matter). When one uses any source it's one's own onus to ensure its reliability.

Sure, that sounds more than reasonable...


text:
Testing the boundaries of good questions?
In general, if you are unsure whether a question is the sort of thing we are going to want to see here, is it better to ask it on the main site and see if it gets closed, or enquire on meta first if it is in-scope?
For example:

How to correlate of two zero inflated bedgraph-like signals?
I have iCLIP read counts accross the transcriptome and I wish to know
  if the signals are correlated - that is, where one of them is high, is
  the other likely to be high.
Often when dealing with such data (e.g. iCLIP data) we know that the
  data is generally sparse - that is at most positions both signals are
  zero and this is correct, and also zero-inflated - that is many bases
  that "should" have a signal are missing that data. So just calucalting the spearmans correlation is likely to give an artifically low value.
These problems are also present if you want to correlate ChIP-seq
  signals or Mutation frequencies.
What might be a way to address this?

I asked a question similar to this on Cross-validated, but didn't get any response. I feel it might be of more interest to a bioinformatics crowd as it is a problem that seems to come up frequently in bioinformatics. But I wonder if it is too "stats-y" for here.
Anyway, my question is: Should I just post questions like this, where I am unsure, and see if people think it is good. Or should I ask for everyone on Meta to see if people think its good?
Pro's for asking first:

We don't pollute the site with low-quality, closed questions
We build a bank of reasoning why a question would be allowed or not allowed that can be reffered to in the future.

Pro's for just posting:

Might lead to a lot of boring repetative questions on meta all basically asking "Is this allowed? How about this? Not sure about this one?"
Will slow down the accumulation of questions on the site as it will take people time to answer the pre-enquiries before the question is actaully asked.

My inclination would be to just post. Perhaps (at least at the beginning), we can ask people to leave comments about why they are voting to close a question. If there's disagreement, that can go to meta to generate the bank of reasoning you mentioned. Low quality, closed questions don't feel like a pollution risk if we're also getting high quality questions.

Agreed. We're still figuring out our scope so posting often and closing often seems better.

@kevbonham Please re-post this as an answer (because that’s what it is).

@KonradRudolf done

My inclination would be to just post. Perhaps (at least at the beginning), we can ask people to leave comments about why they are voting to close a question. If there's disagreement, that can go to meta to generate the bank of reasoning you mentioned.
Low quality, closed questions don't feel like a pollution risk if we're also getting high quality questions.


text:
Can we have math layouting?
Several other communities (in particular Stats and Biology, which are closely related to Biofx.SE) have MathJax support.
This would be highly desirable here as well, since pseudocode and equations abound in bioinformatics.
Case in point, my first two answers would both benefit from it.

If it is pseudo-code or code use the code features inherit from Stack Overflow. For equations it could be, but it has an impact on the loading time of the page and SE is not eager to enable it everywhere.

@Llopis I disagree, writing equation-heavy pseudocode as code makes it harder to read. Equations are often more appropriate.

For equations I agree with you. But this require a developer from SE

@Llopis SE staff monitor local meta sites, that's why Konrad posted here. This just needs to be enabled in some setting somewhere since the infrastructure already exists for other sites in the network.

SE staff usually enables MathJax if the community shows a use for it. Two examples from one person might not be enough “shows a use”, could you find a couple more examples by different authors?

Examples that would benefit from proper Math support:

How exactly is "effective length" used in FPKM calculated?
How does the BWA-MEM algorithm assign its mapping qualities?
Normalization methods with RNA-Seq ERCC spike in?
How to correlate two zero inflated bedgraph-like signals?
Formula for k-mer coverage

Now enabled both on main and here on meta.

Awesome. Now let’s see if we can actually get people to use it …


text:
Let’s standardise some tags
Let’s standardise some tags.
For instance, there are already two competing conventions at work:

rna-seq
scrnaseq

Either both should use a dash, or none should.
I propose the slightly more readable variant: using dashes to separate ‹tech› from “seq”. That is:

rna-seq
chip-seq
scrna-seq
etc.

Totally agree, but let's see how the site evolves

While at it let's create a list of tags we should avoid using/creating.

Do you think it is OK to copy paste the tag description/info from other SE sites?

@zx8754 yes, the license definitely allows that.

Agree, but unlike @Llopis, I'm ok with a little intelligent design before evolution kicks into high gear. What's the best way to do this? Edit tags that don't conform. In other SE sites, I'm way more likely to use a tag that has a big number next to it.

@kevbonham I think we can be permitted to be more authoritative about it. Case in point, I think we can agree that [tag:scrnaseq] is a terrible tag, and that we should go with my suggestion.

@KonradRudolph I agree (I might not use italicized terrible), and I just checked, it looks like I already have the authority to change that tag. I've never been in a community at this early a stage, what's the typical etiquette for modifying other people's questions?

@kevbonham shrug. I’d wait a bit more but since this got +7 votes so far and nobody so far raised an object i’d just edit the tag fairly soon. That said, I think you need 500 votes to edit on your own. Otherwise it’s put up for review but barely any user can already access the review queue.

@KonradRudolph In this case, sc-rna-seq should probably be preferred because xrna usually refers to a type of RNA, not the biological system it comes from (mRNA, tRNA, piRNA, etc. vs. single cell RNA and bulk RNA)

@MichaelSchubert Does anybody call it "sc-RNA-seq" though? I've never seen it. It's scRNA-seq.


text:
Interacting with other Q&A communities
When the proposal of Bioinformatics started there was a discussion in Biostars about the this site (and SE in general compared to Biostars). Some of the points raised are:

Unfriendly community, questions are received with down-votes
Toxic environment
Lack of support from moderators
Lack of discussion about questions
Adding more sites is diluting the user base
Cross-post with other communities
License of the code provided in Stack Exchange

How do we want the community to handle this issues?
Additionally there are also seqanswers, Bioconductor, Galaxy community and other communities (and mailing groups) around different tools and projects.

So in my opinion, the main problem with biostar is low quality of answers. I compared top biostar questions to average stackoverflow question, and the later is much better.
I think we should mainly focus on the answers quality.

The main problem with Biostars is the low quality of questions that is precisely what needs to be sorted out here.

Well, then the problem with Biostars seems to be from the quality of the site. What troubles me is that the question now on the site, many seem of low quality too. And we are just in the first day, we should correct that too

All above points are a bit exaggerated. SE is about making the internet a better place, it is not about a single user. Incentive system should be both ways, encourage good answers and good questions, upvotes/downvotes.

@zx8754 Agreed. I've only ever had positive experiences on SO and other SE sites. It might be the sorts of questions I'm looking at/asking, but the complaints always seemed strange to me. But I agree that keeping these stereotypes in mind is worthwhile, we should actively work to promote a positive atmosphere, but also good questions/answers.

On a related note - if a question is asked that has already been answered on seqanswers, support.bioconductor.org or biostars, whats the policy on pointing to that answer?

@Ian Answers must be self contained, so you can reference them with a link an write your answer

Here's my take on each of the points you raise:

Unfriendly community, questions are received with down-votes
I know many people feel this way but my experience in the SE network has been the exact opposite. Downvotes are not bad. Let me repeat that. Downvotes are not bad. They are in fact precisely what makes the SE sites so useful. We need bad posts to be downvoted, that's the only way good posts come to the top. yes, some people can take the downvotes as an insult instead of as an invitation to improve their answer. Quite simply, those people won't have a good time here so it would be better for them—and us—if they go to another site.That's not a problem, there's enough to go around.
Toxic environment
That really isn't my impression of SE and I feel that most people who feel it's toxic simply don't understand the system and consider downvotes and closed questions to be personal attacks. With the possible exception of SO which is orders of magnitude larger than any other site, most SE sites are relatively friendly as long as you put some effort into your posts. Yes, dumping your homework with no attempt to solve it and asking others to do your work for you are not well received. Well, they shouldn't be.
However, I have been quite active (>10 or 20k rep) on 4 sites of the network, I'm an elected mod on two and participate in quite a few more. I haven't felt any of them were in any way "toxic". Maybe I was lucky, granted, but I really think the "toxicity" is almost entirely born of simple misunderstandings about what the SE site are and are not.
Lack of support from moderators
I don't really know what that is supposed to mean. I see some complaints about too much moderation in the linked biostars post but none of a lack thereof. Also, most people who're not familiar with SE tend to assume that anyone who cotes to close a post or edits or does anything else that wouldn't be possible by users on traditional forums is a mod.
Lack of discussion about questions
Yes, absolutely! SE is not a forum and not the right place for disussion. But that's great! If you need a discussion, you can always go to Biostars or SeqAnswers or even our chat. This isn't a place for discussion, it's a Q&A site. That's fine: to each their own.
Adding more sites is diluting the user base
Dunno about that. I, for example, find both SeqAnswers and Biostars unpleasant, chaotic and far harder to extract useful information out of than the SE sites. Which is why I am so pleased with this proposal. So it's not so much a question of diluting the community as it is one of offering multiple venues where each of us can find their niche and the site they find most useful. There are enough bioinformaticians around by now that the community can support multiple sites, I think.
Cross-post with other communities
Why does this matter? If another community has a useful piece of information, we copy it over. That's the beauty of open licenses.
License of the code provided in Stack Exchange
Again, for me that's a feature and not a bug. Any code posted here can be used by anyone else in the community with attribution. Surely that's a good thing?

In summary, there's no reason to please everyone. This is an SE site and the SE network has clearly demonstrated that there are many, many users who enjoy their system and find it useful in their work. Other people find it too restrictive or negative or hard to deal with. That's absolutely fine. Those of us who like the SE system are free to use this site and those of us who don't are free to use the others. Nobody is forcing anyone to do anything.
So yes, we should be friendly and open and helpful to newbies. Ignorance is never a sin. On the other hand, laziness and unwillingness to put effort into your question and answer are, and I see no reason why we shouldn't have strict quality standards. Many SE sites cater to both experts and novices and the level of expertise is far less important than the effort put into a post. So as long as you don't use this site as a substitute for doing your own work, you should be welcome to ask a question of any level of expertise here. But not things that would be answered by pasting the question title into Google or Wikipedia. Some effort is required, yes.

I agree that downvotes are any important part of a good community. I'm new to the whole SE platform but maybe there's somewhere we can write a piece about how downvotes aren't bad, and how more experienced users should do their best to help while downvoting(i.e. posting the link to the duplicate or a link to the wiki article) so we don't discourage new users. Bioinformatics is a daunting field even when you have a solid background in one of the fields that are a part of it, which makes it difficult for new members to participate because the minimum knowledge is set high.

@EMiller sure, and we shouldn't be downvoting duplicates (we just close them as duplicates) nor should we download simple questions (we were all newbies once)_. Downvotes are reserved for questions that show no research effort, things like dumping your homework here for us to do for you, or ykonw txtspeak lke this crp (very poorly written but not because of the language barrier, only because of laziness). Also, downvotes on wrong answers are extremely important to separate the good from the bad.

I understand the feelings of Biostar people, at the same time competition is almost always good.
In order to address those issues I think we should do the following:

Try to be friendly to newcomers once the site is open.
Keep our answers and questions high-quality. This is really an issue for some of other websites you mentioned.
Allow some discussion.

I do not think dilution is a problem. Academia is very decentralized anyway, there are thousands of journals, a lot of software which is very similar, etc. Competition is usually good. All of the communities will have a stimulus to function better.
Also, I don't think licensing is a practical problem. This is not a software development SE.

We can't really allow discussion. The SE model doesn't really lend itself to discussion. We have the [chat] for that, but the site itself should be strictly Q&A. Not because discussion is wrong or not useful, it's just that this isn't the right place for it.

My feeling is that this site and biostars should be serving different purposes.
Biostars is, as far as I understand, explicitly about helping beginners or those without much experience to get their head around bioinformatics. I'm happy to help out their when I can to help people, but while I have posted my own questions their, I wouldn't rely on it for answers to any difficult questions I had.
I think bioinformatics SE should be a bit different: A place to go to find if other professionals have come across and solved similar problems to the one you are having. While newbies, interested amateurs and non-bioinformatics students should be welcomed, the primary target level should be higher.


text:
Where is the review button?
When I signed up for the site and look up in the part were the review button was suppose to be it wasn't there as indicated by this screen shot here.

This seems kind of weird considering the fact that I signed up for a few private beta site before and there is all ways a review button as soon as I sign in. (because of automatically getting the close privilege.)
Please note the reviews are still accessible via the link: https://bioinformatics.stackexchange.com/review
If this is just a status by design feature and not a bug sorry for the misunderstanding.

Apparently you need 350 reputation to access the review queue.


text:
What sort of questions are appropriate for Bioinformatics SE?
I have spent a lot of time on StackOverflow and am pretty familiar with the types of questions that are and are not allowed on the site.  I am a little unsure as to how well the strict question rules transfer over to this site, however.  Typically, questions that do not have concrete answers or are opinion-based are discouraged, as are requests for listing of resources.  I don't think that this level of stringency is appropriate for this site.  An example:

What is the best tool for computing gene-level expression?

This might immediately be flagged for deletion because it is both a resource request and opinion based, but keep in mind:

It can be difficult to find scientific tools, especially if the analysis or function they perform is not very common or new.
While people might have opinions on what tool is the best, there are quantifiable ways of demonstrating that some scientific tools are better or worse, which can be important to capture an upvote for future reference.
There are a lot of unknowns in science, and therefore a lot of opinions, so one could argue a lot of things as opinion-based.  Therefore, some leniency should be expected in question asking.

Thoughts?

Another point could be that some communities might have some general form of agreement on the most appropriate tool for a specific analysis (i.e. blast for simple homology search), despite having many other alternatives.

While I agree in principle with your bullets, I think that the appropriateness of the example question you posted would depend a lot on the body of the question. If it was just that heading, it's too vague, but if the questioner lays out specific features, there might actually be an objective answer.

And there's another thing to consider - answers to questions like this will fluctuate wildly over time. We'll need to have pretty strong norms around modifying previous answers or marking old questions as out of date.

@kevbonham: this is something that occurred to me as well.  Just because an answer was the best possible solution at a given time doesn't mean it will even be close to correct 5 years from now.

@woemler right. This would be an issue on SO as well, but most of the questions I see there are referring to specific languages/versions. Are there questions like "what's the best framework for designing a website?" on SO? How do they handle that?

@kevbonham that answer simply wouldn't be accepted on SO, I don't think. On the other hand, if you said "I'm interested in creating a website with these features that runs like this..." then perhaps it would be okay.

I suggest that bioinformatics 'experts' should ask what they consider to be good questions and provide their own good answers to get this site moving in the right direction! This practice is encouraged on other sites like SO https://stackoverflow.com/help/self-answer

I also don't think that "What is the best foo" can ever be a good question. I would instead suggest something like:

Is there a comprehensive review and benchmark of the various tools for FOO? What tools had the best results?

Something like that can be answered by citing a specific review paper and the measurements there. In any case, the "best" usually depends on what you're doing. For example, while toolA might be the best for computing expression in speciesA or tissueA, toolB might fare better in another species/tissue.
So no, let's not allow "what is the best foo" questions, but instead try and make them as specific as possible while still being general enough to be worth asking.

Great answer. This would be a very good way to frame this sort of question.

Such open-ended question should be closed in my opinion. A better question for the site would be

What is better tool for computing gene-level expression A or B?

This question is still open to opinionated personal experience using the tools but can be answered with articles comparing both tools.
This way we can have a tag for gene-level-expression and group there questions comparing tool. The reader after reading the questions and articles might end up with a good knowledge of the tools available and used by the community.
As suggested in the comments:

What are the pros/cons of computing gene level expression with A or B?

This might be a better alternative

Perhaps even better: What are the pros/cons of computing gene level expression with A or B? This moves it slightly further away from opinion and towards objective fact. And is probably a better way to think about tools anyway.

But what about cases where there is an objectively better tool, C, that is not specifically part of the question?

@woemier If a better tool C exists, you can suggest so in comments either in the question or in any answer you want, and then the next question would be "pros/cons of C vs A?" and "pros/cons of C vs B?".

@Llopis agreed. I've expanded my comment into an answer below.

I have a proposal - tool questions/answers should be limited to discussions of pros/cons for a particular tool or tools. In other words, the question you posed (and bouncing off of Llopis' answer):

What are the pros/cons of computing gene level expression with A vs B?

This approach has a number of benefits:

Answers to this question can be more objective. People may still quibble about whether a particular approach is better or worse, but the upsides/downsides of any approach shouldn't generate as much disagreement
This is probably a better way to think about such questions anyway, and answers to such questions are more generalizable to different experiments/approaches. In other words, even if a questioner asks about a particular experimental setup, good answers about the pros/cons of a particular tool will likely apply to other experimental setups.
These answers are less likely to go out of date, since new software will not change the pros/cons of particular approaches, but might change what the best approach is. And even old questions about out of date software will retain value for learners (since they will contain expert thought about how to assess the value of an approach).

I'm not sure if this approach is applicable to all questions of this type, but it could certainly be applied to most. It will take more effort from questioners, since they will have to do some research to actually bring up a tool or tools, but this will probably make for better questions anyway, and there's no reason an answer couldn't bring up some new tool that wasn't asked.


text:
Adverts on Bioinfo SE
There is currently, essentially an advert on Bioinfo SE in another disguise  here. Is there any fast-track system for removing it without the standard "close vote" system?
The "close vote" system works well because there are clear grey-zones and it safe-guards equivocal judgement calls, but there has to fast-track system that circumvents this process?

The quickest way is to ping me or another moderator in the chat room. I should get a notification on my phone and be able to quickly close/delete such things.
Please note that I'll eventually notice flagged posts, but it might take a couple hours.

Thanks, @DevonRyan good to know and thanks for shutting the post down.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Importance of protecting questions
A new member has responded to a "SARS-CoV-2 synthetic origin" questions here and here with a "human origin" opinion expressed in a verbose, aggressive and non-technical manner.
I have now protected the questions.
I think the original question(s) are on-message. Phylogenetics has a long history of readdressing conspiracy that otherwise has potentially negative outcomes, e.g. threatening polio erradication in Africa e.g. here and here.
A dissenting voice is fine, but the lesson is protecting questions, meaning preventing posts from new users or low reputation users, is in fact a good idea. Perhaps delete most opinionated posts therein?

I have destroyed that user's account. We should have absolutely no tolerance for such people.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
I'm a bioinfo software developer, and I would like to use bioinformatics SE as the main platform for Q&A
I'm an author of bioinformatic software and I would like to use this stackexchange as the main platform for questions and answers (indicate this in the README). The software is recent and there is no tag yet.

Is it appropriate to redirect users to this SE?
Wouldn't that be considered an inappropriate self-advertisement
There is no tag at the moment. So I cannot subscribe. What is the best way?

Ask one of the users to ask here.
Create a single Q & A myself.
Create a tag before there are real questions.

In general it's fine to use SE as an official support forum. Snakemake currently uses stackoverflow for that purpose as well (though I'm not sure how official that is). You have quite a bit of reputation, so I think you can create a tag (if not, just ping me and mention what you'd like the tag to be). I don't think you need to worry about self-advertisement, there as no consensus that that was a problem here and I personally would find it incredibly annoying to have to mention that on an answer dealing with any software I've contributed to.

Devon, could you then please create a tag called godon? I don't seem to have the permission. If you create a stub I can update the description of the tag.

Done: https://bioinformatics.stackexchange.com/questions/tagged/godon Please suggest some content for that tag :)

Thanks a lot, Devon. I suggested a tag description some time ago, but it was not approved yet.


text:
Why does @gringer have a wiki tag?
Whilst editing the sites wiki tags I noted that @gringer was listed, alongside including formal technical nomenclature such as population genetics, allele frequencies, haplotype networks, synonymous mutations etc.... I duely filled in the @gringer wiki tag as best I understood it, but was left puzzled ... is there a greater meaning here that has escaped me?

It looks like you added it a few months ago. Perhaps by accident; you might have tried to ping them in a comment but didn't realize you were typing in the tag box.
I've suggested an edit to remove the tag, as indeed users shouldn't have their own tag (you can't be an expert in 'gringer'). One of the co-founders of Stack Exchange has his own tag on Meta Stack Exchange but that's a reasonable exception.

Ah okay ... yes I probably did


text:
Should something be done about frozen "main" chatroom?
I have noticed that the "main" chatroom for this site has been frozen. By the main chatroom I mean the room which was created when the site was created with the description "General discussion for bioinformatics.stackexchange.com".
As far as I know, the Stack Exchange chat system will still keep at least one room from freezing. (And the rooms migrated from comments and one-to-one rooms created through "start a new room with this user" do not count here.) But none of the remaining rooms has privileged position1 If you look at the rooms associated with this site, you can see that the only room which is not frozen is Bioinfomatics About The Coronavirus Pandemic.
So my questions are:

Should something be done about this? (On one hand, it is probably good for any Stack Exchange site to have a room for general discussions. On the other hand, since the room was frozen long time ago, probably it wasn't really used and nobody seems to be missing this room.)
What kind of action should be taken if the room is frozen again in the future?

1Any room can be unfrozen by moderators. Some posts where you can find more details concerning frozen rooms:

Why is the main chat room frozen?
Don't freeze a chatroom soon after a mod has unfrozen it
Main chatroom for a SE site and chatroom pruning
Main chat room for a newer site still freezes due to inactivity
A related feature request: Exclude the main chat room from automatic freezing/deletion

I've unfrozen the room, though it gets little enough traffic that I expect it will eventually get frozen again.

I think its a resource for the site, not that I've used it much, but I think I  should have used it rather than create new 'chat rooms'. I think we just need to be mindful of posting a random 'chat' into the room to keep it afloat. Its a bit like the Parsees keeping their ceremonial fire alight for the last couple of thousand years. The motto is it doesn't need a practical purpose, its just a nice idea.
One of the problems with creating a chat room for a specific dialogue is that once the conversation is done, the room is frozen and permanently archived. So next time another chat room needs to be created and presumably another ... ad infinitum and it just creates clutter. Much better to centralise this for a single chat room.


text:
UniProt survey: Tell us what protein information is important to you
Please consider filling in this survey, on behalf of UniProt:
As biological data is growing at an exponential rate, we also have to prioritise the protein information we present. In order to help us provide the data that is important to you, we would be grateful if you could fill in a short survey by Nov 4 2020: https://forms.gle/wM23hdKAvQVnbyYb9 .

Thanks Elisabeth this is a worth while survey and this is the right place to post it. I will fill this out before the deadline.


text:
Duplicate OPs and OP deletion of response postings
There was a recent issue on Bioinfo SE here on a question about compiling gromacs for CPU or GPU (below).
It appears a question was deleted together with @MatteoFerla's response and one question remains.  Having a valid response deleted would be frustrating.
The OP denies deleting the post, but it is possible there was cross-posting within the group by different users. For example, the problem is shared within the group, one OP posts here, a second OP posts here and one OP deletes their question.
Coincidence of two independent OPs seems unlikely on technical criteria.
I propose simple protocol where the responder has the right to comment that a discarded reply has occurred and request this is avoided. The OP can issue an explanation.
Is that reasonable? We have a similar unwritten protocol for cross-posting with Biostars.
I also propose @DevonRyan cleans up the comments below @MatteoFerla's comment(s) on the OP. That ok?

Technically the response is good and the question is fine. To answer the question one would need to look up the compiling flags, which is time consuming unless your the original developer. The technical issues between CPU/GPU wouldn't be apparent to a user: GPU parallelises very large numbers of very small differential equations, which a CPU can't do and thats how GPU speeds up the calculation. The reason you need to compile two versions is related to this issue.

To clarify, I had commented on the original post —asking which card and suggesting the same as the answer that was given and on the last post along with checking the CUDA toolkit was installed correctly (the heart of the problem). I did not hope to escalate this, just make sure that everyone was clear on what is good practice. So I am happy with the deletion of my comments. Thanks and sorry everyone

Your comments on the post are fine @MatteoFerla no deletion is needed. In context its good practice to point out the history of a question particularly when you've gone to some trouble looking up the answer (which got deleted). Lets see what Devon says.

@MatteoFerla For the record you comments were quite constructive and I think you nicely pointed out the exact cause of OP's problems.

I see a related (now deleted) question by the exact same OP about trying to compile GROMACS with GPU support that is probably the one you saw. That one was lacking even more information than the more recent one, which is still lacking enough info to help OP but at least getting better.
I've cleaned up the comments on the post you noted since they're largely not relevant to the actual technical question (and were partially unhelpful. Please do note that down-voting on stackexchange is meant to be interpreted as "please work on this question more so we can help you", though I think in practice newer posters almost never actually interpret it that way (I would disable down-voting if I could, it does more harm than good).
Regarding your proposal for dealing with deleted posts we have two competing interests:

We should endeavor to restrict content to answering the question.
Context of replies is lost if one can't reference to other posts.

In general I think it's fine to reference deleted posts (possibly with a quick summary of their results). In an ideal world questions would just be rewritten entirely rather than deleted with new ones posted, but practically I think we all understand the utility of starting from a clean slate. So I would propose:

Either OP or other posters to now-deleted content should feel allowed to reference said content and comment about that (e.g., "hey, sorry about the misunderstanding in the original post, hopefully this one is clearer"). We're all humans, we need this sort of thing to not start yelling at each other.
These should be kept to a minimum, though, since it's not really answering the question at hand.
These comments may get deleted by me (or another moderator) at some later point. I personally like to keep those around for a little while, since it helps with community building.

Thanks much appreciated for the editing. 2) Sorry for my bad explaination. The idea was exactly how the comments were edited. If the OP deletes a post and thereby deletes all its replies and then makes an identifcal/very similar post (now without the previous reply), the responder has the right to point out what the OP has done and request not to do this in the comment section. The OP could offer a rationale explanation or apology in comments.

The gist is if the OP is taking the responder's goodwill for granted (which is what has happened), that is not cool and should be called out. However, just allow the OP some benefit of the doubt in case of a genuine misunderstanding. I'll clarify the post when I've a moment.

@Michael Thanks for the clarification, I've updated my reply (hopefully) accordingly.

GROMACS seems extremely niche over here, such questions can be migrated to https://mattermodeling.stackexchange.com/ with no problems at all. Even questions asking for help compiling.

@user1271772 Thanks, I didn't know about that stack, I may migrate a few questions over there in the future.


text:
Vote to undelete question ... and rationale
I triggerd a vote to undelete a question entitled

I have used TER to break the long bonds of a chain in my PDB

The question is here, deleted by the OP after it was answered by a member of the site and appropriate expert here.
I don't understand the question, but it appears to have been well answered.
It is not the first time this has happened, a new OP account deleted a question answered by the responder in very recent history (weeks), in similar circumstances and reported here.
I do feel it is important to protect valid answers and would welcome support.

I agree and have undeleted the question. If someone has provided a reasonable answer to a question then the question may NOT be deleted.

Many thanks @DevonRyan as a general principle its something I think is important.

This is a very good question, and inserting TER into PDB files is something which is often needed in the structural bioinformatics world, a world which is largely esoteric and poorly documented versus sequencing bioinformatics. It would be good to encourage structural bioinformatics questions.


text:
2020: a year in moderation

As we say goodbye to the old year and welcome the new one, we have a tradition of sharing moderation stats for the past 12 months.
As most of you here are aware, sites on the Stack Exchange network are moderated somewhat differently to other sites on the web:

We designed the Stack Exchange network engine to be mostly self-regulating, in that we amortize the overall moderation cost of the system across thousands of teeny-tiny slices of effort contributed by regular, everyday users.
-- A Theory of Moderation

That doesn't eliminate the need for having moderators altogether, but it does mean that the bulk of moderation work is carried out by regular folks. Every bit of time and effort y'all contribute to the site gives you access to more privileges you can use to help in this effort, all of which produce a cumulative effect that makes a big difference.
So as we welcome 2021, and in keeping with tradition, let us look back at what we accomplished as a community... by looking at some exciting stats. Below is a breakdown of moderation actions performed on Bioinformatics over the past 12 months:

Action
Moderators
Community¹

Users suspended²
3
5

Users destroyed³
4
0

Users deleted
3
0

Users contacted
3
0

Tasks reviewed⁴: Suggested Edit queue
18
328

Tasks reviewed⁴: Reopen Vote queue
1
38

Tasks reviewed⁴: Low Quality Posts queue
6
223

Tasks reviewed⁴: Late Answer queue
3
86

Tasks reviewed⁴: First Post queue
2
713

Tasks reviewed⁴: Close Votes queue
6
609

Questions unprotected
0
1

Questions reopened
3
0

Questions protected
0
4

Questions migrated
6
1

Questions flagged⁵
0
192

Questions closed
44
87

Question flags handled⁵
125
67

Posts unlocked
0
3

Posts undeleted
1
22

Posts locked
0
9

Posts deleted⁶
71
367

Posts bumped
0
418

Escalations to the Community Manager team
1
0

Comments flagged
0
70

Comments deleted⁷
132
535

Comment flags handled
61
9

Answers flagged
0
193

Answer flags handled
164
29

All comments on a post moved to chat
1
0

Footnotes
¹ "Community" here refers both to the membership of Bioinformatics without diamonds next to their names, and to the automated systems otherwise known as user #-1.
² The system will suspend users under three circumstances: when a user is recreated after being previously suspended, when a user is recreated after being destroyed for spam or abuse, and when a network-wide suspension is in effect on an account.
³ A "destroyed" user is deleted along with all that they had posted: questions, answers, comments. Generally used as an expedient way of getting rid of spam.
⁴ This counts every review that was submitted (not skipped) - so the 2 suggested edits reviews needed to approve an edit would count as 2, the goal being to indicate the frequency of moderation actions. This also applies to flags, etc.
⁵ Includes close flags (but not close or reopen votes).
⁶ This ignores numerous deletions that happen automatically in response to some other action.
⁷ This includes comments deleted by their own authors (which also account for some number of handled comment flags).
Further reading:

Wanna see how these numbers have changed over time? We posted a similar report here last year: 2019: a year in moderation

You can also check out this report on other sites

Or peruse detailed information on the number of questions closed and reopened across all sites

A big thank you to Shog9 for writing the queries and script to facilitate fetching and posting this data to all the sites in the network, and to Brian for the subsequent work making the whole thing more user friendly.
Wishing everyone a happy 2021!


text:
2021 Potential Moderator Election: Community Interest Check
It's time for us all to consider holding an election for a new volunteer moderators on Bioinformatics.
Three moderators were appointed when this site was created back in 2017. Since then most of them have resigned, meaning we're due for some fresh moderators. The basic job doesn't entail terribly much work, mostly going through the queue of flagged issues once or twice a day and handling them. Potential moderators could ideally also go through new posts and help handle issues there before they get flagged.
In the end, it's not a lot of work to being a moderator, and this is a relatively small SE site.
You can also take a look at Who are the site moderators, and what is their role here? and the Theory of moderation (revisited) to get a bit of a feeling as to what being a moderator actually entails.
Please leave an answer if you'd be willing to run for a moderator position, should we decide to run an election.
NOTE: This is not an official election nomination thread, just a "pulse check" to get a notion of how many people here would be willing to step up.

I'm interested in this. I run through my review queues once a day on average anyway, and I'm a moderator on biostars. If the duties are similar on this site as well, I'd do a similar job here.

I think you would be great!

Thank you, @KamilSJaron

I might also run. I haven't quite made up my mind yet, but as an ex mod, I can confirm what Devon said: the workload of moderating this site is very low and doesn't require a lot of your time.
I guess I'll decide for sure if and when we have an election, but yes, I am thinking I might run.

In case anyone cares, I decided not to run in the end because we had a fine crop of candidates, all of whom I am happy to vote for and I'd rather bring in some new blood!

I thought you already were a mod!

@RamRS I was, but then I stepped down due to various things that caused me to want to limit my connection to SE. I now feel a little better about SE and the direction they are going in, at least I've seen signs that they're honestly trying to improve on the things that bother me so I am more willing to be a mod on a second site.

Did you resign to get elected twice?! ^^

@KamilSJaron well, I need to get my validation from somewhere, right? :P More seriously, I was very, very disappointed in Stack Overflow Inc. and how they behaved and didn't feel up to moderating more than one site. It somehow felt like too much of an endorsement of the company. I kept my first mod post since that was in the first community I really got deeply involved with, but resigned my other two. I now feel much better towards the company, they've taken some important steps for me, so I felt OK with coming back to mod here again.

Damn, I completely forgot about that affair (and I did not know that's why you stepped down). What were the nicer things SE did after that? Anyway, I just filled my self-nomination, so it's on!

You did? Great! We need good candidates! As for what they did better, there's a new person at the helm and since she joined, there has been a marked change in how the company interacts with the community. Both publicly in Meta and with the various moderators across the network. Enough so to make me much more enthusiastic about participating again.

That sounds great, then I am looking forward to see your candidacy :-)

I think you probably won't be seeing my candidacy. I am more than happy with all three of the candidates who have stepped forward so far, so I think I'll leave you all to it! We have three fine candidates already.


text:
Announcing a Pro Tempore election
Summary: Bioinformatics Stack Exchange will begin the nomination stage for a special election on April 12 to bring in two more moderators.
For full details of the process, see the announcement on Meta Stack Exchange. The timeline:

Starting on April 12, users can nominate themselves. Users can also ask questions on meta for potential moderators to answer. (Use the discussion and election tags.)

On April 19, if there are three or more candidates, we'll run an election. If not, I'll simply appoint the candidates. (There's a small chance we'll need to remove a nomination, but I doubt that will come up.)

If there is an election, I'll announce the results on meta on April 27.

(Note for current moderators: there's no need to nominate yourself even though you'll likely get an email saying you should. The system assumes the first election is a graduation election, which would mean moderators would need to be re-elected. This isn't that sort of election.)
If you have any questions about the process, please stick them in an answer here.


text:
2021 Community Moderator Election
The 2021 Community Moderator Election is now underway!
Community moderator elections have three phases:

Nomination phase
Primary phase
Election phase

Most elections take between two and three weeks, but this depends on how many candidates there are.
Please visit the official election page at
https://bioinformatics.stackexchange.com/election
for more detail, and to participate!
If you have general questions about the election process, or questions for moderator candidates, feel free to ask them here on meta -- just make sure your questions are tagged election.


text:
2021 Community Moderator Election Results
Bioinformatics Stack Exchange's first moderator election has come to a close, the votes have been tallied, and the two new moderators are:

They'll be joining the existing crew shortly — please thank them for volunteering, and share your assistance and advice with them as they learn the ropes!
For details on how the voting played out, you can download the election results here, or view a summary report online.

Yay! Congratulations to you both!

JNat, it appears that the first hyperlink is not working!

Looks like someone fixed it in the meantime, @user1271772

Thank you for your trust folks <3

Thank you. Those results are quite the motivator for me!

Congratulations @gringer and @Kamil! It was a privilege being a candidate alongside you guys and I know you'll be great mods. I look forward to working more with you!

Significantly belated congrats and a good response from @RamRS


text:
Adding additional question guidance
I've noticed that the best Bioinformatics SE questions are where people ask about a specific problem they're having with their own data (or programs they're using). How would people feel about putting additional guidance in the "Ask Question" page, e.g. by adding guidance / tips to a right-hand sidebar?
Something like:
Hi, welcome to Bioinformatics StackExchange. Our community works best at answering specific questions about bioinformatics problems. Here are some tips to help get the best answers:

Be specific about your problem; preferably ask a single question
Add context - why are you trying to do this?
Add detail; the more the better, as long as it's relevant

If there are input files, show the first few lines
If there are output files, show the first few lines
If there's an error, show the entire error message
If you're asking about issues with a program, version numbers can help

Share your problem-solving research:

what did you try to overcome your problem?
why it did not work for you?

Thanks for asking. We hope you have a great time here!
Update: here is an example of a general question that lacks context and is not tied to a specific problem. Is it appropriate to ask these types of questions? Is it useful to the community to ask and/or answer questions like this?

I like the idea! A clear "Welcome to bioinformatics.SE" page/panel could really improve the quality of newcomers' questions.
I never had too much problems with a bit more general questions or hypothetical scenarios, the only one that gets to me is when people make no effort. So I would add to the list (ask for the research in a nice way)

Share your problem-solving research:

what did you try to overcome your problem?
why it did not work for you?

We could also add a few link to good questions.
-- edit --
re generality: I belive there is a balance. "What is the current/recommended way to *build graph reference genome?" is within my boundaries, "How far we are from having a tricoder?" is not.
I guess I mean to say, is that majority of decisions in bioinformatics require a subjective opinion. Who has a capacity to go through all the new methods and do the benchmarking?! In reality, we use things that are good enough and we know that work and that's why I don't mind if answers require some opinions.
*replace by anything that has more than one soltuion.

If we're going to allow general questions, then this page also needs to be changed.

I like the idea of adding links to examples, and the "share your research" bit.

I tried to elaborate a bit more about the generality, not sure if I managed. That's perhaps the problem - it's hard to phrase how general questions are ok, so perhaps we can leave it as it is and just be forgiving?

I think that with context relating to a specific issue both questions are okay (e.g. I'm doing a study that requires remote observation of blood biochemistry, and something like a tricorder would be really useful...). However, general questions without context lead to XY problems; it's much harder to find answers to satisfy the person asking the question,

If you have a burning question that doesn't fit well within the StackExchange system (e.g. general discussion, advice, hypothetical situations, or opinions), we recommend posting on the bioinformatics subreddit.

Does bioinf.SE have a major problem with such questions? I'm not sure that there's any need for explicit text discouraging any particular kind of question. (Certainly it's good to encourage relevant details, evidence of research, etc, as the rest of your draft guidance does. But IMHO discouraging anything could remain unstated.)
In particular, I think official bioinf.SE pages (like the Ask a Question sidebar) should not be in the business of directing people to reddit. It might be appropriate to have a wiki page or similar listing all the other known bioinformatics Q&A-style resources; but we should not be recommending any one of them in particular.

It's a StackExchange thing (e.g. see this page); the format doesn't work well with questions where it's hard to evaluate useful and not useful answers. Such questions invite more comments than answers.

I know what the reasoning is. I'm suggesting it's not very applicable to bioinf.SE, because (1) we don't have such a volume of questions that discouraging anything is particularly necessary; (2) the level of expertise here is such that the answers to such questions would likely be interesting nonetheless. Anyway, my point is not that such questions should be explicitly allowed — instead, that judging “fit within the StackExchange system” is a measure on a subjective scale, and we gain nothing from writing instructions trying to disallow such a nebulous category of questions.

Okay, fair enough; I've got rid of the general question paragraph. We will need to get that page changed, though.


text:
About posting queries in stack bioinformatics
If I have posted a question in Biostars and have not obtained answers, can I use the same query for finding answers in Stack bioinformatics?

Go right ahead. Just make sure you've waited long enough (say 3-4 days excluding weekends) and link the biostars post in your post here. Similarly, edit your biostars post and add the link to the new StackExchange post there.

I may add that you should critically ask yourself why the question did not receive answers. Was it simply a very specific question and people with the required expertise were not around, or did it lack details, formatting or clarity. If the latter please consider adding all this before submitting a new question.

As Ram mentioned in his comment, there's nothing strictly forbidding this. It is, however, best to give it a few days before reposting here and please do link to the post on biostars. The goal with all of this is to not duplicate effort across sites (so users finding the question here can easily check if it was already answered elsewhere). Community effort is finite and we'd like to ensure that it's spent efficiently.

This is a long comment and not an answer

@ATpoint points out that there is a reason why Qs go unanswered and I could not agree more. The 81% answer-rate is below the 90% stated in Area51. I looked at my followed tags (comp-biochem) to categorise them and there seems to rarely be a lack of technical know-how.

comment suggestion or link to answer (here, here, here, here, here)
file not found or badly formatted (here, here)
impossible task (here, here, here)
repost (here)
user was doing SARS-CoV-2 drug repurposing (here)
user has already best solution (here)
beyond my expertise (here —java, here —R)

Okay, this may be biased as advanced questions get asked in the ccp4 bulletin-board (ccp4bb), and in certain tools have their own discussion forum, such as Rosetta commons.


text:
Moderators: Please do not close questions just because they are old
I just had an old question of mine closed by a moderator with the following comment:

I’m voting to close this question because it was asked a long time ago, and it is likely that an answer is no longer useful to the person who asked the question, or to the general bioinformatics community. Please feel free to edit the question and update it if you feel it's important to get an answer. – 7 hours ago

I then checked the mod's profile and saw that they've actually closed a total of nine questions with the same comment! I'm sure the mod means well, but this is a problem. First, a question's age is irrelevant, questions can be answered at any time and on SE sites we answer for the broader community not for the OP alone. So even if the OP has abandoned the question, that is no reason to assume that nobody else would benefit from an answer. So why would you want to forcibly bar a question from ever being answered?
Perhaps more importantly, there is no rule that says old questions should be closed, so I don't understand by what authority someone would presume to make this choice. Moderators have the ability to single-handedly close questions, but that should only be used for things that are blatantly off topic. Otherwise, it feels like the moderator is just imposing their own preferences and getting to choose what questions stay and what questions are closed. Again, I am sure the mod meant well, but this feels like crossing a very important line.
So, please reopen all of the questions you've closed just for being old. That is not how these sites work, you didn't come to meta to see if this is what the commnunity wants and, in my own opinion, closing such questions actively harms the site for no benefit whatsoever. The most important thing though is that closing such questions is imposing one person's choice on the rest of the community with no discussion or consultation. Please don't do this.

+1 It seems unusual and without precedent on other stacks to close a question with net +3 score and no answer. These are usually the kind of questions which should be left open and encouraged to answer, as they represent difficult to answer but useful and well written questions.

@user438383 yes, exactly. All 9 of the questions closed in this way had a net positive score ranging from 3 all the way to 8.

I agree. We should not assume that all old and non-answered questions are not interesting or unnecessary.
However, I also do see that bioinformatics is a fast evolving discipline and some of the unanswered questions are very quickly outdated. I do think it would be handy to have "question is outdated" closing reason. In this example, the OP must have talked about millions of Canu versions ago, it might be still a valid question, but I would not be surprised if Canu would have a completely different job distrbution mechanism. So, I would say in those cases, it would be handy to at least add a version of software people are asing about (but that would be probs the best specified very early on when talking about bugs).
Anyway, my whole point is - there is a fine line between old and outdated and we should try our best to never cross it.

The main issue is that this sort of thing should be left to the community. Moderators shouldn't close questions just because they're old. In fact, mods should try to avoid closing questions unless they are blatantly off topic since they close with a single vote and therefore don't have any oversight. So if the community wants to close them, fine. But the mods should not.

Next, I would like to see some arguments for what harm such questions do. What benefit is there in deleting them? In your example, maybe it was a bug that has been fixed but maybe it is still a problem today. Unless we know it is no longer relevant, what do we gain by closing the question? Upvoted closed questions won't be deleted, they'll just stay there but cannot be answered. Why not leave them alone and maybe they even get an answer some day? I just don't see the point in closing them even if we did have some rule that would support it.

Bioinformatics Stack Exchange has an existing canned site-specific close reason:

Questions describing a problem that can't be reproduced and seemingly went away on its own (or went away when a typo was fixed) are off-topic as they are unlikely to help future readers.

I used this as a base, and added additional clarification to make it more obvious that it's fine to reopen a question if it seems useful (especially if the question can be improved / updated).
https://bioinformatics.stackexchange.com/help/reopen-questions
These questions were not closed just because they were old; they were closed because they had no answers, and there had been no question activity for a long time. In most cases, there were additional close reasons; I just thought that the above was the most appropriate. If you notice that your question is not getting answered, try here for some inspiration:
https://bioinformatics.stackexchange.com/help/no-one-answers
StackExchange encourages users to keep questions and answers current, in particular by bumping old posts that have no accepted answers. This means that old questions, even if inactive, will still get exposure in the new queue from time to time. Where this exposure doesn't encourage activity, it's an indication to me that the question is not sufficiently relevant to this community. I'm not interested in reopening these unanswered questions (which, to clarify, haven't been touched in years) unless they are modified to update and/or improve the question (or voted on to reopen by multiple users).
My bigger concern is in new questions that are rapidly closed, especially when they are created by new users to the site (e.g. here. I don't like this practise; it leads to anxiety in new users - what's the point of posting if my question won't be good enough for the rapid closers?
Update: After discussion, I have decided to no longer use this canned close reason, as its interpretation is ambiguous. Where questions remain that I closed with this reason (i.e. have not been edited or had a few votes for reopening), I have altered my close reason to one of the non-site-specific reasons and added additional clarification.

Thanks for replying. That close reason is for problems that cannot be reproduced (which doesn't apply here) or which went away on their own (again, not applicable). It's for things that only the OP experiences and nobody can reproduce on their machines, suggesting the issue is too specific, or for things that were just simple typos and so unlikely to help future visitors. It isn't in any way about "old" questions.

As you point out, the SE system actually bumps old questions, precisely because they could still be useful! If the community doesn't feel they are relevant, then the community can vote to close them. However, having a mod do so on their own is just that mod imposing their personal take on whether the question is useful. All of the questions you closed were upvoted, meaning that the community found them useful. Just because nobody has been able to answer them doesn't mean that anyone should decide they should never get answered and mod-hammer them closed. Please don't do this.

Finally, the last thing we want to do is encourage users to go and make meaningless edits to old questions and unnecessarily bumping them. That's actually generally frowned upon: that's what the community bot is for. We should edit to make our posts as good as we can, but we are not encouraged to just edit to bump them. So yes, I could offer a bounty, but the rest of the suggestions in "help/no-one-answers" aren't relevant to this situation.

Please reopen these questions. If you really feel so strongly that they should be closed, then take it to meta and try to formulate a rule for this, but please don't do it single-handedly as you have done. Again, I'm sure you feel this is good for the site, but it comes across as though you feel you can ignore the rules and close anything you don't like. I have no doubt that this isn't what you want, but it really comes across that way so again please reopen the questions you closed just because they're old.

I'm sorry gringer, but this really isn't up to you. You can't just say you're not interested in reopening, you are going against well established precedent across all of the SE network and stepping beyond your remit as a mod. This is really, really not cool. I also passed this by some of the other network mods in the Teacher's Lounge, this isn't a mod's job.


text:
Would someone be able to migrate my question?
I don't have the requisite 250 rep required to migrate a question to https://biology.stackexchange.com/.
Would a mod be able to do that?

IMO this is more suited to https://medicalsciences.stackexchange.com/

@user438383 good idea. I added it there: https://medicalsciences.stackexchange.com/q/27603/20431


text:
2021: a year in moderation

As we say goodbye to the old year and welcome the new one, we have a tradition of sharing moderation stats for the preceding calendar year.
As most of you here are aware, sites on the Stack Exchange network are moderated somewhat differently to other sites on the web:

We designed the Stack Exchange network engine to be mostly self-regulating, in that we amortize the overall moderation cost of the system across thousands of teeny-tiny slices of effort contributed by regular, everyday users.
-- A Theory of Moderation

That doesn't eliminate the need for having moderators altogether, but it does mean that the bulk of moderation work is carried out by regular folks. Every bit of time and effort y'all contribute to the site gives you access to more privileges you can use to help in this effort, all of which produce a cumulative effect that makes a big difference.
So as we say goodbye to 2021, let us look back at what we accomplished as a community... by looking at some exciting stats. Below is a breakdown of moderation actions performed on Bioinformatics over the past 12 months:

Action
Moderators
Community¹

Users suspended²
0
4

Users destroyed³
1
0

Users deleted
1
0

Users contacted
1
0

Tasks reviewed⁴: Suggested Edit queue
38
176

Tasks reviewed⁴: Reopen Vote queue
4
40

Tasks reviewed⁴: Low Quality Posts queue
6
51

Tasks reviewed⁴: Late Answer queue
5
57

Tasks reviewed⁴: First questions queue
21
118

Tasks reviewed⁴: First Post queue
39
316

Tasks reviewed⁴: First answers queue
0
52

Tasks reviewed⁴: Close Votes queue
29
283

Revisions redacted
1
0

Questions reopened
22
0

Questions migrated
1
0

Questions merged
1
0

Questions flagged⁵
1
79

Questions closed
105
44

Question flags handled⁵
53
26

Posts undeleted
11
21

Posts locked
1
5

Posts deleted⁶
91
380

Posts bumped
0
527

Escalations to the Community Manager team
2
0

Comments undeleted
32
0

Comments flagged
1
39

Comments deleted⁷
1,239
215

Comment flags handled
34
6

Answers flagged
0
116

Answer flags handled
98
18

Footnotes
¹ "Community" here refers both to the membership of Bioinformatics without diamonds next to their names, and to the automated systems otherwise known as user #-1.
² The system will suspend users under three circumstances: when a user is recreated after being previously suspended, when a user is recreated after being destroyed for spam or abuse, and when a network-wide suspension is in effect on an account.
³ A "destroyed" user is deleted along with all that they had posted: questions, answers, comments. Generally used as an expedient way of getting rid of spam.
⁴ This counts every review that was submitted (not skipped) - so the 2 suggested edits reviews needed to approve an edit would count as 2, the goal being to indicate the frequency of moderation actions. This also applies to flags, etc.
⁵ Includes close flags (but not close or reopen votes).
⁶ This ignores numerous deletions that happen automatically in response to some other action.
⁷ This includes comments deleted by their own authors (which also account for some number of handled comment flags).
Further reading:

Wanna see how these numbers have changed over time? We posted a similar report here last year: 2020: a year in moderation

You can also check out this report on other sites

Or peruse detailed information on the number of questions closed and reopened across all sites

Wishing everyone a happy 2022! ^_^


text:
Can questions in pharmacometrics fit in the Bioinformatics stackexchange?
Pharmacometrics is an interdiciplinary field which in short tries to answer questions about drugs and drug development (specifically pharmacokinetics nd pharmacodynamics given trial data) using statistical models and various software tools (R, Python, Perl and a growing set of domain specific libraries and tools like NONMEM, PsN, Pharmpy, monolix, pumas and others).
I have tried to find a place on Stack Exchange to use for questions in pharmacometrics and the bioinformatics is so far the best fit I can find. Do you think it would be appropriate to add tags for pharmacometrics here?

Yes, it can fit here. Bioinformatics is a very broad area, which I would describe as using an interpreted data source to improve the quality of biological research.
Feel free to encourage other people in your area to visit this site and either ask or answer questions.

In my opinion it is bioinformatics.which is simply under represented here. So, I feel, whilst it is of course polite to ask it is difficult to consider it in any other technical disapline.
I'm well aware of the field because it was one of the early runners in deep learning, which is one way to process the data in question (but far from an orthodox approach). So its same stuff vectorization of C- based compounds and the like, parameterisation, training, testing, retraining. Same old. It stems from the well trodden loop of try a compound, have a guess at tweaking the structure, retesting the new structure, non-target drug effects, tweak it again and say 'hey maybe some bioinformatics will make better guesses'.
In addition, protein structural modelling is part of the field and there is a long standing presence here from @MatteoF and @Greener(sp?) et al
"Pharmacodynamics given trial data" will be focused around its own set of statistical methods, which most of us will probably not hold expertise in, nor the packages that implement these statistical methods, but that's bioinformatics per se.

The two caveats I would hold are:

If the question was cost-effectiveness of a given drug therapy, that isn't a biological processes so would be outside Bioinformatics SE. If for example, its focused around comparative efficacy .. that is biological.
Finally, I also definitely get the impression this ain't singly medical statistics, this is computational biochemistry, possibly within a trial population. In medical stats the biology of compound X is almost irrelevant and that would be more appropriate for Cross-validation Stackexchange than Bioinformatics SE in my opinion.

Yes! I'm sure we'd be happy to take it.
However, do consider that stats.stackexchange may be a better place to get feedback on questions that are mainly statistical in nature. Of course, I am sure that that bioinformatics.stackexchange would have useful answers to such questions as well. But perhaps sometimes you may find your questions redirected to stats.stackexchange.


text:
Review queue: first question and first answer silver awards
I have a distinct hunch that the 'silver badge award' statistics for first question and first answer sections of the review queue have been 'zeroed', possibily following the upgrade from Bioinformatics SE beta. I dunno, because I don't consign my review stats to memory.
For example, some of the long term senior members here have statistics of '1 review' in both queues and can't possibly represent their contribution over such an extended period.
Has anyone else a comparable hunch?

Alright, I got a better response from the moderator's forum.
There used to be a different queue category - First posts, that got split into two "First questions" and "First answers". And there has been a Proposal for awarding credit towards First Questions/Answers badges based on First Posts activity. There is also a ? mark that gives you the info about number of tasks that got carried over

So the total numbers are just after the split, while the badge numbers are carrying over credit from reviewing the original "First Post" queue. The only part I am still unsure by, is why it's contributing to my gold badge only, but I suppose that's because I got a silver badge for these review tasks already (which would suggest that reviewing tasks are actually different than upvotes - the clock does not restart with an awarded badge. I might edit this post once I have ~200 more first questions reviewed).

Thank you @KamilSJaron that all makes sense. SE have done a good job, just not told anyone about it. I agree the previous silver must have been awarded (I haven't checked mine but presume so) and then zeroed the silver count. The tally carries onto gold. I should have twigged, there were 6 review queues and there are now 7 queues.

First of all - thanks for all the reivewing work do do!
And yeah, there is something a bit strange about that. At least the number "reviews all-time" is for sure off.
As on the following screenshot - it says there were 202 reviews of first question in all-time. Which is obviously a bs, both you and myself have more than that (we both have the silver badge for 250 review tasks). But then I am quite puzzled how can I have 27/250 progress on "Reviewer" badge as I have it already.

One thing I have noticed before with upvoting badges is that once you get the silver badge, it restarts the count for the gold badge, so to get the gold badge you need 910 vote counts, not 600. I think the same is with reviewing, so to whatever your badge progress is, you got to add 251.
You got the Reviewer badge for this category on Mar 23 2020, assuming a constant rate of queue processing you should have a few hundred review tasks done by now :-).
Would you like me to ask on the moderator forum?

Hi @KamilSJaron that would be cool, thanks. The official total number of reviews of all time for first answer is '49' ...


text:
Request to delete answer on WDL question
Could the mods kindly look at the 'answer' to:
Pulling Multiple Files via rsync with WDL
Its been there 17 hours. The username is also an issue. I've no links to WDL, but the post is intentional slander.

WDL is workflow description language, started by Broad Institute

I've deleted it now. Thanks for flagging it.

Thank you for your swift response @DevonRyan


text:
Citing BioSE as algorithm support
I am seeking permission to cite https://bioinformatics.stackexchange.com as  support for a new algorithm to identify specific mutations across large sequence databases. There isn't an equivalent calculation. The code is OOP/AOP Python with extensive parallelisation and optimisation.
In the first instance the algorithm is released via Docker in < 2 months and more widely through mainstream distribution channels thereafter.

Here's the historic response. I would assume this agreement  remains active.
I'm a bioinfo software developer, and I would like to use bioinformatics SE as the main platform for Q&A

Yes, this is fine. Thanks for asking.

Huge thanks @gringer much appreciated

I am happy with this - it sounds like a relevant piece of software and the more relevant high-quality questions that we have the expertise to answer the better!

Thanks for your support and approval @user438383 democracy is good.


text:
I am resigning as a moderator
it's been an honour to help the bioinfo.SE to be a clean, constructive and kind space for sharing our expertise in bioinformatics. However, I recently quit my job and taking some time off and I don't think I would be able to continue to be moderator for quite long period of time, hence the resignation.
I am not leaving bioinformatics, I will be around at some point. I just need my time off and I think it's a good time to leave the mod role for more eager members of our community :-).
Thank you all for your contributions, it's been a great to witness the community coming together and be part of it.
--- edit ---
Thank you for the support! But I feel I should clarify. I am fine, I resigned because I have another job lined up for this autumn. I really just wanted to get a proper break before I get back to the working life.

Good luck and keep your chin up.  We all go through the same feelings now and then.

I'm very sorry to hear about this @KamilSJaron and thank you for all the time and dedication you have put into the community.
Bioinformatics and the broader world of computation is on a strong upward trajectory and its fantastic (and not surprising) you've a new post lined up.
I am glad you are sticking around Bioinfo. SE. If you're back to the millstone in the autumn, reassess then perhaps?

Ah, sorry. Now I realized how misleading was what I wrote. I am really alright, I just want the break. Thank you for the support though!

Thanks @KamilSJaron I've updated my response. Thanks for informing us.


text:
2022 Potential Moderator Election: Community Interest Check
UPDATE: The election has now been scheduled. Thanks for all who expressed interest in nominating.

The last bioinfo mod elections happened 465 days ago and with the recent power vacuum created by my resignation, we all kind of feel it's the time to consider to have another mod elections. However, for the elections to have any point, we would need at least a handful of ambitious candidates, so here comes the million-dollar question.
Can you see yourself carrying the diamond badge? If you would be happy to self-nomitate yourself, please post an answer to this question!
The next steps will depend how many responses we will get, so don't be shy :-).

Thanks for helping out with keeping the site up and running.
Self-nominating as a current moderator, for completeness.

Sorry to see you go again @KamilSJaron.
I'm definitely more than happy to be a candidate for an election.


text:
Announcing a “Graduation” election for 2022
Summary: Bioinformatics Stack Exchange will begin the nomination stage for an election on September 19th, 2022, as your “graduation” election!
The timeline:

On September 12, 2022, I'll post a question collection post on Meta, so that the community can post questions they'd like to see the candidates answer.

Starting on September 19, 2022, users can nominate themselves. The top questions collected on the previous week will be compiled into a questionnaire on the election page, so that potential moderators can answer them.

The existing moderator team will need to run in the election if they wish to keep their positions.

On September 26, 2022, if there are 4 or more candidates, we'll run an election. If not, I'll extend the nomination period for a week. If, at the end of that extension period there are still less than 4 candidates, I'll simply appoint the candidates who've nominated (and aren't already pro-tem mods) and we'll default to considering this a "pro-tem election" just to try to bring the total number of moderators on the site up to 3, to account for some of the current mods who are stepping down from their position (for full details of the process, see the announcement on Meta Stack Exchange). (There's a small chance we'll need to remove a nomination.)

If there is an election, I'll announce the results on meta on October 4, 2022 (or October 11, 2022, if we need to extend the nomination period).

If you have any questions about the process, please stick them in an answer here.


text:
Message from a shy user
How can I make sure I'm not distracting researchers from their work, with a bunch of questions.
I feel I could ask a lot, primarily because I have studied very little.
I don't think I could ask a lot, if I had studied a lot.
I don't really think my questions will not permit the descriptive aspects of the science to progress.
I, also, think, my questions, might lead to progress.
Am I invited to ask, on this site?
Thanks.

That's actually a great question. I think the is a balance, and whether to post or not is something you will have to decide about. Here are some considerations before posting...
You should not ask questions that are already answered on this (or other) stack exchange site. This necessarily requires you do some sort of research. I think (at least) you should try to google the question phrased in a bunch of different ways. It's fairly possible that the answer does exist online, but you just don't know what to search for, but that is fine, but it should be clear that you (or the poster) made an effort to find the answer your/themselves.
There is also the factor of "how much useful is this going to be for others". Those that are of general interest are always very welcomed questions. You can see that some of the old questions are really heavily used resource, while some other are so specific are seen only few times. So, more general question you will have, the better. Sometimes it is good to think if you can phrase your question in a more general way.
Finally, consider how frequently you post yourself and how keen are people to help you out (I think there is a bit of common sense). If it feels all alright, it probably is. SE folks are not the subtlest in explaining to people what's sub-optimal about their questions.
So to sum up, you can ask as many relevant questions as you want, even if they are basic, if you don't annoy the heck out of the community (and you will be able to tell). Stuff to make people like your questions:

Be concrete, give details, but cohesive and preferentially reproducible (with toy data and small snippets of code).
Show initiative and do your own research, that will both help others to understand the true source of your problem, but also make you more relatable.
Disclaim everything that should be disclaimed - is it homework? Are you a developer of the method you are discussing? etc.
Be polite and kind, but don't write "Thanks" or apologize for basic questions, that is all fine. Gratitude should be expressed through upvotes or accepting the right answer (that makes the answer more useful for the next person facing the same problem).

So don't worry THAT much, just ask :-)