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Is the Pundit Badge available?
I see the Pundit badge listed as available in the badges help section but I don't see it as an option in the "Select your next badge" section of my profile.  Also it doesn't appear that anyone has earned it so I am wondering if it is not really available to be earned.
Does anyone know the status of the Pundit badge?

It should be available, but indeed, as of current writing, no one has achieved it.

Well, it's certainly available on other sites on the network (I have it in a few), so I don't see any reason why we would be different. The "Select your next badge" simply doesn't list all available badges. The rationale for this was given by a Stack Exchange developer in this post:

It is a problem of performance.
Some of the badges are very computation/database intensive to award,
  let alone to track in (near) real-time per user.
Such badges are not trackable for this reason.

Great thanks for the clarification.

@Bioathlete Also this is a badge that you cannot do anything to get it (although posting more comments might help), so maybe it is another reason why you can set it to track in your profile


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2018: a year in moderation
It's New Year's Day in Stack Exchange land...
A distinguishing characteristic of these sites is how they are moderated:

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

While there certainly are Moderators here, a significant amount of the moderation is done by ordinary people, using the privileges
they've earned by virtue of their contributions to the site. Each of you contributes a little bit of time and effort, and together you accomplish much.
As we enter a new year, let's pause and reflect, taking a moment to appreciate the work that we do here together.
To that end, here is how the moderation done here on Bioinformatics breaks down by activity over the past 12 months:
                 Action                  Moderators Community¹
---------------------------------------- ---------- ----------
Users suspended²                                  0          5
Tasks reviewed³: Suggested Edit queue           105        403
Tasks reviewed³: Reopen Vote queue                1          8
Tasks reviewed³: Low Quality Posts queue          2         16
Tasks reviewed³: Late Answer queue                0         45
Tasks reviewed³: First Post queue                 7        412
Tasks reviewed³: Close Votes queue                5        188
Tag synonyms proposed                             0          2
Questions reopened                                4          0
Questions migrated                                3          0
Questions flagged⁴                                1         59
Questions closed                                 43         14
Question flags handled⁴                          23         37
Posts unlocked                                    1          1
Posts undeleted                                   3         16
Posts locked                                      0         12
Posts deleted⁵                                   38        199
Posts bumped                                      0        185
Comments undeleted                               11          0
Comments flagged                                  0        158
Comments deleted⁶                               310        339
Comment flags handled                           101         57
Answers flagged                                   0         55
Answer flags handled                             49          6
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 This counts every review that was submitted (not skipped) - so the 3 suggested edits reviews needed to approve an edit would count as 3, the goal being to indicate the frequency of moderation actions. This also applies to flags, etc.
⁴ Includes close flags (but not close or reopen votes).
⁵ This ignores numerous deletions that happen automatically in response to some other action.
⁶ This includes comments deleted by their own authors (which also account for some number of handled comment flags).
Wishing you all a happy new year...

source: Stack Exchange

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

sort: votes


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RStudio tag addition
I found myself asking an RStudio specific question. The question is more about how a function works within the infrastructure of the software as opposed to general use of R or of the package (Seurat). My issue is RStudio specific.
This tag could be useful for local RStudio sessions, RStudio server sessions, and RStudio cloud sessions.

I don't have anything against creating the tag, but I question whether this would be the most relevant forum for such a question. If RStudio is behaving in a very different manner then I'd think asking in their forums is a better tack. In the more likely scenario that RStudio isn't actually doing anything fundamentally different and instead this is yet another "how does Seurat do X" question then it'd be a better fit here.

I thought it'd be good to ask here because it's not just a tech support "RStudio crashes" kind of question--I think getting the answer requires looking at Seurat and the specific function and determining how its running and what could be tripping up the software in this specific environment. That said I have posted on the RStudio community forums to seek help, and haven't gotten any hits on the question.

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


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rtag suggestion
I feel like we should sort out tags related to graphics. Right now there tags
visualization, plotting, figure-explanation + tool/package specific like ggplot2.
I identify three distinct problems related to graphics:

how to visualize <my data>? -> philosophical problem
how can I reproduce figure of somebody else? -> coding/crafting problem
how to understand figure of somebody else? -> science interpretation problem

The last one has very clear tag (and I love it). But the first two are blended in visualization and plotting tags.
I suggest to remove tag plotting and add description that would correspond to following tag scheme:

how to visualize <my data>? -> visualization
how can I reproduce figure of somebody else? -> figure-reproduction
how to understand figure of somebody else? -> figure-explanation

Why do I care? I usually can not help with 1 and 3, but I really like to do 2 (especially if it's core-R graph).
Can you think of other topics related to graphics? Do you think these scheme would work? Huh?

I went on and created the tag figure-reproduction (I found two questions that were candidates of this tag)

Sounds like a good structured way of tagging. However, I know from my own experience when writing a question, tagging is the last part before submitting, and usually I quickly choose tags that first pop up into my mind. So if I had a question in one of your 3 categories, I would probably tag them with plotting or visualization anyway. Maybe I would add R as well. I think not many users will do a thorough research of finding the right and perfect tag for their question. That does not mean it wouldn't be meaningful to create these tags, but I expect many 'wrongly' tagged questions as a consequence.

This is a good point. I like when the related tags would have links to each other in the excerpt.

The auto fill function for tags now, only works to extend what you are typing. So for example if you type vi, you'll get visualization, webservice, and Gviz. It would be cool to see some related tags too.

@KamilSJaron That's what excerpts are for, to guide how to use tags. About this answer, I think we can can retag the question as they come, there are few questions, so I wouldn't expect we miss some questions.

@b.nota that could be a request to the DAG team for the whole SE


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Improving the site after 1 Year!
In 10 days we will be celebrating 1 year since the launch of the site!
I think it is a good time to discuss and review how to improve the site, talk about things that are working well and things that do not need to improve. Some of them might have been brought to meta, but reviewing how are we doing with these issues will help too.
The idea is to identify issues to have in mind for the next year, and if needed start a separate question on meta for the issue.

The only thing that I mind here is that sometimes I see downvoted questions without obvious reason or comment bellow explaining what is wrong with the questions (I tried to search for one question I had in my mind, but I could not find it).
I believe that downvotes are important for answers, but not so useful for questions. We should as community take care that every user who ask "wrong question" figure out what he should ask instead and therefore I think that comments are way more appropriate.
Otherwise I think we are slowly growing and it's just matter of time. In fact Q/day are slowly increasing and of science-related betas we have second highest (we have 3.9 and machine learning had more if I remember correctly).

I think I am the one to blame on the downvotes on questions, but I usually leave a comment (I think), however I don't see many questions with a negative score. In general what I feel is the opposite, some questions receive upvotes without showing the research effort, but that's the beauty of communities with different people :D

I will try to link all the cases of downvoted not commented questions to chat from now on. I just don't find downvote to be really effective in delivering the message "you need to rephrase/improve you question", I find commenting + temporary closing way more firendly for users and the same for community (to separate good and not-sufficient questions).

Now that I downvoted and was leaving without a comment. If I find a question not useful and with lack of research, should I also leave a message?

If it would be obvious for OP how he should ask he would probably do it. So I think in any case you should leave the comment

I agree with this answer, I see too many downvoted questions. If I was a new user and get a downvote, I would leave here and go to biostars. I thought downvotes were especially meaningful for answers...

First (bigger) issue is the low number of question we have. We (barely?) made to the public beta phase with a warning regarding this issue.
There are other communities with more traction and older than bioinformatics.SE, which explains this. Still, if we want to graduate we will need to bring more people and more questions to the site.

I think we need more users, both questions and answers, after a hiatus I'm trying to be more active when I can, I think at this point it's worth us all trying to promote the site amongst colleagues as much as we can, and on social media too, perhaps someone could launch an official twitter account for the site, would that work?
I also see a lot of questions which are requests for support for specific programs, we should try reach out to the authors of such software and get them to address the questions directly on the site.  I know Ensembl do a good effort in this respect, so it would be good to see other developers active here too.  Again this is a matter of getting them involved when their software is discussed.

It the twitter account should be official it would have to come from SE. But I think a site gets one when it graduates. Good idea to try to bring here the developers of said tools, but sometimes they have their own venue too (I'm thinking in Bioconductor that has a forum for questions, and here we do get more questions too).

I personally find the Bioconductor forums and their imported email threads so annoying to read, I really wish they had chosen this platform and not the other one!


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Should we relax the requirement for disclosing affiliation on the site?
There is a general rule on the Stack Exchange network that states that if you post an answer suggesting something you are involved with (e.g. a tool you wrote or a blog post you authored or whatever), then you should explicitly state your affiliation:

The community here tends to vote down overt self-promotion and flag it as spam. Post good, relevant answers, and if some (but not all) happen to be about your product or website, that’s okay. However, you must disclose your affiliation in your answers.

However, this is mostly aimed at people selling their product. In the scientific world, tools are usually accompanied by peer reviewed articles pointing out both their flaws and their advantages. It is very common for someone to write a tool and offer it to the community for free. Therefore, it is usually easier to make an informed decision about the tool, reducing the importance of disclosing author affiliation. We also tend to be much more open about the flaws of our software (OK, not always, but often).
We want these people to post here and we want them to post about their tools. At least two of our moderators (hint: not me), for example, are authors of widely used tools. Do we really need authors of tools to explicitly state their authorship in every single post? Perhaps it would be enough to have them say so on their profiles?
My feeling is that in a professional community like this one, in a field where the vast majority of tools are free and open source anyway, it would be OK to relax this requirement. If you come here and just post links to your blog as answers, that's not cool. I also see some problems if the tool in question isn't a well known, peer reviewed one. But I feel it is very unlikely that we'll get random "script kiddies" who've written anything that could be useful in this field and even less likely that we'll get commercial spam. So if you are the author of a standard tool and many or most of your answers are about that tool, then I don't see much of a problem.
Sure, it would be great if people also mentioned that they have authored the tool, if only to lend their answer the extra authority that confers, but should we really insist on it as is done on other sites of the network? Or should we relax the requirement in the specific cases where authors of software tools post answers using those tools?
What should our rules on this be?

The fact that many of the tools presented on this site are open-source does not mean that there are not very real benefits to be derived from touting them.  This is because in an open-source world users are also testers, and because making code open-source does not mean relinquishing one's claim to authorship over that code.
As a methods developer in acadaemia, these are some benefits that I could derive from more people using my code:

Bug reports
Usability testing
Good reputation
Citations

These potential benefits, in fact, are reasons why I make my code open-source. Furthermore, the last point is, for better or for worse, the currency of acadaemia.  This currency is quite valuable to anyone looking to make a career in acadaemia and in my opinion could very much form the basis of a conflict of interest.
Sure, there may be people on this site who have already "made it" in acadaemia and therefore find the aforementioned benefits less valuable, but the same is true for monetary benefits.  That should not stop us from applying the same rules to everyone.
I don't expect long treatises on conflicts of interest, but a short sentence explaining the type of potential conflict of interest and a pointer to a poster's profile when relevant is in order.

FWIW I'm frequently in the position where I have a potential conflict of interest because part of my job is to increase usage of certain tools like GATK, so here's how I try to deal with it: (1) if someone asks "how do I do X with GATK" I just answer the question factually, no disclosure; (2) if someone asks "what tool should I use to do X", I say something like "this is how you can use GATK to do X; note that I work for the developers of GATK". I think we can ask people to make a good faith effort.

We need to keep those limits of affiliation.

This is not a social network so I don't think that a user should visit another user profile to find such information.
As in scientific papers, one discloses possible conflicts of interests in each paper, not in the user profile of the journal nor ORCID, nor ...
When providing an answer with a software one has contributed or created providing a line saying the relation with the software is not so hard or long.
A user might contribute to the site with related programs not directly his own   creations, so in those cases the line wouldn't be needed. And having to check for the profile would be cumbersome.
I hope that commercial software or people from companies might also come here to answer questions, and if they do, they should disclose their affiliation. Not requiring to state the affiliation on the answer will hurt the quality of the site on the long run.

I beg to disagree. This is a social network. Very specialized but a social network. Therefore linking you other profiles here is perfectly valid thing to do. Sometimes I also like to check who is answering this question.
However, at the same time, I think it's wise to keep requirements on users to minimum, because we are still struggling with the size of the community on this page.

@Kamil See this post. I'm not saying that you can't or shouldn't be able to track people but that the focus is not on people but on the content. If your affiliation is relevant then it is part of the value you bring to the content so it should be with the content of your answer. Also if now we lower the user requirements to minimum will raising them later work? I fear the site will disappear. Besides, we (read I) don't know if it is possible to lower the requirements of affiliation. Has any site done this?

I'll give an incredibly biased answer and say that we should just relax these rules. The tools are free as in beer and speech, so the only real interest we have in people using our tools are possible future citations. It doesn't hurt to mention on our profiles when we're the author of a particular tool, but I imagine that'd get a bit long (Pierre Lindenbaum would need a couple hundred lines for all of his stuff). There's also the complication that since this is open source software, a lot of us have contributed bits of code to other's software, but I don't think that's worth mentioning. A good rule, then, might be to just mention on your profile the major packages for which you're one of the main developers. That or maybe something like "I'm the primary developer behind BWA, minimap2, seqtk, among a number of other tools. See my github page for more details." for user172818.
At the end of the day, divulging affiliation is meant to shine light on conflicts of interest. When such conflicts don't exist (due to there being no tangible benefit to others using your stuff), such a divulgence is a "nice to have" at most and "irrelevant noise" at worst.

I'm not sure it's true that conflicts of interest arise only from tangible benefits. A developer might advocate for their tool out of ego even if they don't get any direct benefit out of it. That's a form of bias, and as the reader I would want to know that relationship exists between the commenter and the thing they're recommending.

I don't think it's so important to disclose affiliations to a tool if the question is specifically about that tool, but if I were asking for general advice about how best to solve a problem, I'd prefer to know if the solution someone recommends is something that they wrote. Citations = promotions = $$ so I think there is a conflict of interest. In any case, it's certainly not unbiased advice. I also think it's useful to have rules in place in case people do start running amok with self promotion. I would prefer to see tweaks to how rules are enforced rather getting rid of them altogether.

Oh, yes, the question here is first of all only to open a discussion and second is suggesting we might want to relax the rules, not get rid of them altogether.

You get promoted for citations? I want to work where you are :)

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Is it appropriate to ask for method papers on specific topics?
Is it appropriate to ask questions here that fall into the literature survey realm?
Some of the bioinformatics citation trails are a rats nest and it can be difficult to find appropriate methods papers for implementing software (e.g., sequence alignment methods, sequence similarity methods).
Furthermore, limited library access can make it difficult to perform a full literature survey on a topic, and sometimes it would be helpful to have a second/third/n set of eyes to ensure the completeness/authority of the articles/resources I've dug up so far.
These types of questions might range from finding the original method paper for a specific algorithm (e.g. Average Nucleotide Identity), to putting together a complete literature survey on a very specific topic (e.g., Four Russians Speedup for Dynamic Programming) - answers to the latter might be a community wiki, or even identifying an existing literature survey.
For instance:

"What are the original articles that describe Algorithm X?"
"Are there any methods papers that describe how to implement Algorithm X?"
"Which articles describe refinements to Algorithm X?"

In some cases, it would be helpful to be able to track the progress of a topic (e.g., following improvements on Dynamic Programming for pairwise sequence alignment). I imagine answers to these types of questions might be curated lists of citations with light commentary.
These types of questions could potentially be tagged with a literature-survey tag in addition to the topic tag.
Note: I am not suggesting that actual documents (e.g., PDF) be shared, only citation information and commentary.
Alternatively, is there a more appropriate way to ask these types of questions here?

With sci-hub, there's no such thing as "limited library access" any more :)

@DevonRyan I'm not offering an opinion on Sci-Hub, just linking this here for reference: Is it illegal for someone in the USA to access Sci-Hub?

@DevonRyan Now that I'm revisiting this question, I'd like to assert that Sci-Hub does not address the problem of finding relevant literature. For the record, I am surprised that a moderator on a site that adheres to international copyright laws would promote copyright violation.

You shouldn’t be that surprised, probably the majority of us who have published papers find closed access absurd and use sci-hub. That’s pretty much the norm these days ( especially in bioinformatics).

I think this would be a very good idea, whilst implementing things formally with code is one thing, as is why can't I get X to do Y or work style questions, as an academic pursuit and for quite a number of us bioinformaticians in academia we often need to reference existing publications.  As the OP suggest finding the correct, best publication, and or original work can be hard.
Correctly referencing work is very important for two reasons:

So there is a formal record of how and algorithm works and that we refer to existing or original works in our publications / documentation rather than re inventing the explanation, i.e. not reimplementing the documentation.
It gives the authors of the original implementation credit via a citation, which in todays metric driven academic world is essential. Too many publications in the generic molecular biology domain miss out or exclude references for bioinformatics algorithms / program and anything we can do to increase awareness of these publications is a good thing.

I don't think the idea of posting in academia is a good one at all, I was unaware of it's existence, and frankly I'll never bother to read questions there, the coding as well as academic / publishing side of bioinformatics are equally important, and as an ecosystem they both need each other, consequently this SE instance should support both as first class problems.

Thank you - I was feeling like I was alone on this proposal (the main reason that I have not participated on this forum). Your points above reinforce my thoughts on this topic.

In my opinion the site would benefit more of specific troubles finding or replicating an implementation of a paper than looking for the original reference of something. We already have a tag figure-explanation to explain when some bioinformatic paper/figure is not clear to the reader.
You can always (if it is on topic, etc...) post in academia where they have a specific tag literature-search when someone ask for a paper or a reference. They also have a bioinformatics tag, so you can tag your question with both, and you probably will get the same answers as you would get here or better ones (At the end this site is still in beta).

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


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Divide tags by technology and target application?
Reviewing an edit I realized we have some duplicated tags or at least somehow redundant.
We have scrnaseq, rna-seq and single-cell.
Some numbers:

scrnaseq: 25 questions
scrnaseq & rna-seq: 9
rna-seq & single-cell: 7
scrnaseq & rna-seq & single-cell: 1 (If we approve the linked edit that would be 2)

Should we remove remove scrnaseq in favor of rna-seq and single-cell?
Or should we retag those 7 questions with both tags in favor of scrnaseq ?
Related discussion: Let’s standardise some tags
As stated in the comments of the related discussion I think that the usage of these tags should differentiate between technology and target of the technology. Here rna-seq describes a technology and single-cell describes the target of a technology so it would be possible to have other technology targeting the same single cell such as metabolomics or methylation assays, or...

I would actually be in favor of removing single-cell. As you pointed out, by itself, single-cell isn't telling us much. It isn't enough to define a subject, it only tells us what a question is about when combined with another tag. This seems to me to fit the definition of a meta tag, a tag that can't stand alone and only qualifies other tags.
As a general rule, each tag should be able to stand alone. If it only makes sense when combined with another tag, then it isn't helpful.
So, I would suggest we completely remove the single-cell and instead use scrnaseq. I would also suggest creating single-cell-rnaseq
 and making scrnseq a synonym of it. I think it is best to have explicit tags where possible.  Having this synonym would mean that when someone tags with scrnaseq, the question would be tagged with single-cell-rnaseq instead, but you could still search for scrnaseq and find the relevant questions.
Then, if and when we start getting questions about other single-cell targeting technologies, we can create tags for them.

I would argue that single-cell as pointed by Devon is used for questions about peculiarities and problems associated with that kind of analysis. See for example this question that used "scATAC-seq".

@Llopis are there any issues that are specific to single cell experiments as opposed to this type of single cell experiments? Can someone be an expert in "single cell" in general? If the answer is no (I think it is no, but I don't really know much about this), then the tag isn't helpful. Think of tags as a way of directing experts to the questions they are interested in, as well as a general way of categorizing. If there really are problems shared by all single-cell approaches, then maybe the tag is useful, but if not, let's replace it with more specific ones.

I don't know much about single cell experiments just what I learned here. But I see that they have a common problems, like the large sparsity, (batch effects ?), and mechanical problems that affect the analysis.

@Llopis OK, if there really are similar enough that someone could be an expert in "single-cells", then the tag might make sense.

Maybe we can wait a little to know what problems do people have before judging. I'm sure we'll get more question in those kind of analysis

Why not change single-cell to single-cell-sequencing then? I suspect that other sc-seq methods are going to present a lot of the same issues that scrnaseq do

I would propose adding scrnaseq to the 7 rna-seq & single-cell posts. scRNA-seq is a popular enough method in its own right with peculiarities that it warrants its own tag, in my opinion.


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Would questions on whole cell modeling get answers at this site?
I am self-learning about whole cell modeling, specifically An introduction to whole-cell modeling and Fundamentals of Systems Biology: From Synthetic Circuits to Whole-cell Models. While my background is decades of programming, for cellular biology it is only skimming through a few books. While I can ask the authors and research groups questions directly I would prefer to only ask them specific questions and get answers to more general topic questions related to whole cell modeling elsewhere; e.g. if I ask about BioNetGen that would general, but asking how to tie BioNetGen in with other software and methodologies specific to the groups would be to specific for here.
So are there people at this site who can answer questions about whole cell modeling in general?

Could you give a more specific example? It sounds like it would likely be on topic but since it isn't my field, I can't be sure from your description. But as a general rule, asking about using bioinformatics tools and/or frameworks is on topic, yes.

@terdon I don't have any specific questions now, but if I do I will ask in the regular site. I did have one specific question but figured it out, e.g. Can someone compare and contrast BNGL (BioNetGen Language) with SBML (System Biology Markup Lanague)?

@GuyCoder that would be a nice question to have, remember that you can self answer your questions too. (And I would like to know the answer to that question without digging the formatting descriptions ;)

I guess it will depend on the question. I  would expect it to be on topic, in principle, so give it a go!