text:
2022 Moderator Election Q&A – Question Collection

The purpose of this thread was to collect questions for the questionnaire. The questionnaire is now live, and you may find it here.

Bioinformatics Stack Exchange is scheduled for an election next week, 2022-09-19. In connection with that, we will be holding a Q&A with the candidates. This will be an opportunity for members of the community to pose questions to the candidates on the topic of moderation.  Participation is completely voluntary.
Here’s how it’ll work:

Until the nomination phase, (so, until 2022-09-19 at 20:00:00Z UTC, or 4:00 pm EDT on the same day, give or take time to arrive for closure), this question will be open to collect potential questions from the users of the site. Post answers to this question containing any questions you would like to ask the candidates. Please only post one question per answer.

If your question contains a link, please use the syntax of [text](link), as that will make it easier for transcribing for the finished questionnaire.

This is a perfect opportunity to voice questions that are specific to your community and issues that you are running into currently.

We, the Community Team, will be providing a small selection of generic questions. The following two questions are guaranteed to be included:

How would you deal with a user who produced a steady stream of valuable answers, but tends to generate a large number of arguments/flags from comments?
How would you handle a situation where another mod closed/deleted/etc. a question that you feel shouldn’t have been?

The community team may also include the following three questions if the community doesn’t supply enough questions.

In your opinion, what do moderators do?
A diamond will be attached to everything you say and have said in the past, including questions, answers and comments. Everything you will do will be seen under a different light. How do you feel about that?
In what way do you feel that being a moderator will make you more effective as opposed to simply reaching 10k or 20k rep?

At the start of the nomination phase, the Community Team will select up to 8 of the top voted questions submitted by the community provided in this thread, to use in addition to the aforementioned 2 guaranteed questions. We reserve some editorial control in the selection of the questions and may opt not to select a question that is tangential or irrelevant to moderation or the election. We exclude any suggested questions that are negatively scored.

We will post the final questionnaire on the Election page. Candidates will have the option to fill out the questionnaire, and their answers will appear beneath their intro statements.
This is not the only option that users have for gathering information on candidates. As a community, you are still free to, for example, hold a live chat session with your candidates to ask further questions, or perhaps clarifications from what is provided in the Q&A.

If you have any questions or feedback about this process, feel free to post as a comment here.


text:
2022 Community Moderator Election
The 2022 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.

source: Stack Exchange

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

sort: votes


text:
2023: a year in moderation

It’s that time of the year again! As we wave goodbye to last year and welcome the new one, we have a tradition of sharing moderation stats for the preceding calendar year.
As most of you here might be 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 — folks like you. 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 in ensuring Stack Exchange sites remain a valuable source of high-quality content on the web.
So as we say goodbye to 2023 (and January 2024… ahem) and move into 2024, 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
Community User¹
Community²

All comments on a post moved to chat
5
0
0

Answer flags handled
99
20
0

Answers flagged
34
31
53

Bounties canceled
0
0
0

Comment flags handled
25
13
1

Comments deleted⁸
1,178
4
230

Comments flagged
0
0
39

Comments undeleted
30
0
0

Escalations to the Community Manager team
1
0
0

Posts bumped
0
489
0

Posts deleted⁷
89
92
115

Posts locked
1
8
0

Posts undeleted
8
0
13

Posts unlocked
0
0
0

Question flags handled⁶
226
20
0

Questions closed
37
1
0

Questions flagged⁶
207
2
36

Questions merged
2
0
0

Questions migrated
0
0
0

Questions protected
0
0
0

Questions reopened
4
0
0

Questions unprotected
0
0
0

Revisions redacted
0
0
0

Tag highlight language set
1
0
0

Tag synonyms created
0
0
0

Tag synonyms proposed
0
0
0

Tags merged
0
0
0

Tasks reviewed⁵: "Close votes" queue
63
0
10

Tasks reviewed⁵: "First answers" queue
120
0
22

Tasks reviewed⁵: "First questions" queue
367
0
16

Tasks reviewed⁵: "Late answers" queue
40
0
15

Tasks reviewed⁵: "Low quality posts" queue
26
0
0

Tasks reviewed⁵: "Reopen votes" queue
1
0
0

Tasks reviewed⁵: "Suggested edits" queue
75
7
23

Tasks reviewed⁵: "Triage" queue
0
0
0

User banned from review
0
0
0

User review-bans lifted early
0
0
0

User suspensions lifted early
1
0
0

Users contacted
1
0
0

Users deleted
0
0
0

Users destroyed⁴
7
0
0

Users suspended³
2
9
0

Footnotes
¹ This refers to the automated systems otherwise known as user #-1.
² This refers to the membership of Bioinformatics without diamonds next to their names.
³ 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.
⁴ 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.
⁵ 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.
⁶ Includes close flags (but not close or reopen votes). The community² can handle these flags by at least one person voting to close a question that has a close flag.
⁷ This ignores numerous deletions that happen automatically in response to some other action.
⁸ 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: 2022: 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 2024! ^_^

Thanks @JNat appreciated.

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


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How to write Links in Comments
What's the syntax when trying to embed links in comments?
For instance here I tried and failed.
What I tried:

[url = "www.internet.com"]words here[/url]
[url = www.internet.com]words here[/url]

like this bioinformatics stackexchange

like this: bioinformatics stackexchange
[bioinformatics stackexchange](http://bioinformatics.stackexchange.com)
You can find the relevant documentation here: https://bioinformatics.stackexchange.com/help/formatting, under "Comment formatting".

This maybe works, edit: oh. It _must _ have http at beginning.


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Should the help page "What topics can I ask about here?" be edited from the default?
Every site in the Stack Exchange network has an article entitled What topics can I ask about here?. This article helps new visitors to the site understand site norms and whether their potential question is appropriate for the community.
This article can be edited by the site's moderators by clicking the "Edit" link at the bottom of the page.
Currently, Bioinformatics' version of this page is the default generic text.
Should /help/on-topic be edited by the site's moderators to indicate what can be asked here?

As a bit of back story, we got a question on another network site which I thought could be a fit for this community; but when I went to refer the user to your help center, I found that it was the default.

Yes, it should. Thanks for the nudge.

Thanks @IanCampbell ... we certainly must do this, it's definitely needed. We'll answer when the task is complete.

Here's a start on something that could be used. Feel free to edit / improve:
Bioinformatics is the process, or art, of converting biological research outputs into something that can be better understood by other researchers. Bioinformatics can be considered as the intersection of biology, computer science, and maths or statistics. Most bioinformaticians have expertise in one or two of these areas, with more shallow knowledge in the other areas.
Bioinformatics is a very large subject area, frequently with many different solutions to the same problem. As such, it's difficult to give precise instructions on what questions are appropriate. In general, if it's about a mixture of biology and computer science or math, it's probably appropriate.
Because of the breadth of research and solutions available, the most important thing about asking questions on this site is to include plenty of context surrounding your problem to help guide answers. This makes sure that answers will be most appropriately tailored to your own problem; general questions and answers in bioinformatics are rarely helpful to anyone.

Please look around to see if your question has been asked before. It’s also OK to ask and answer your own question.

If your problem is related to an error produced from software, please include the full text of that error.

Please avoid screenshots of text. Copy & paste the text into the body of your question and use the code formatting to improve display. If you have trouble with text formatting, the community can help with that.

Please include version numbers of any software tools you use. This helps to identify any version-specific bugs or user interface changes.

If your question is not specifically on-topic for Bioinformatics Stack Exchange, it may be on topic for another Stack Exchange site. If no site currently exists that will accept your question, you may commit to or propose a new site at Area 51, the place where new Stack Exchange communities are democratically created.

could be good to remind question-writers to avoid screenshots of text, and to include versions of software/stack if asking about an issue with a particular tool.

Thanks, I've added that in.


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Notification of Mod action on SE
Stackexchange (SE) is currently subject to 'Mod action' over its policy towards ChatGPT content.
SE's initial policy is effectively to ignore ChatGPT (advanced AI) generated content if it was posted as an answer on SE. The rationale was because ChatGPT (advanced AI) detectors produced anomalous rates of false positivity with non-native English speakers from SE's internal testing. In a subsequent, more lengthy explanation the ban on ChatGPT detectors seemed more nuanced and focused around the possibility or else actual occurrence of erroneous SE account suspensions/deletions.
The underlying concern from the Mod-perspective is AI content will overrun SE content. There are other factors however.
The Mod action affects the site as follows:

Mod @terdon is on all out strike;
I perform essential Mod duties, but act in solidarity to the strike and have requested a meeting with SE HQ;
Mod @gringer is fully active.

In my case I follow due process for Mod action.
Does ChatGPT affect Bioinformatics SE?
No. I do ML development, I know it's what it's about. It would be really hard for a supervised learning algorithm (the workhorse of ChatGPT) to train against the biological context of any or all bioinformatics problems. In bioinformatics the biological context is pivotal to the solution. That layer of abstraction makes training hard, because the data scientist constructing the AI needs to understand the abstraction. At a minimum any question is spilt across 5 kingdoms. It would need a biological data scientist to help build a successful AI.
In the worst case scenario it would mean loads of Biostars content turn up here and vice-versa. That happens anyway.
ChatGPT detectors and Bioinformatics SE?
We'll never use AI detectors because it's not relevant to bioinformatics biological context (above). Every question and answer its checked. We'd spot and comment if there's a gap between the biological context and the response, when not striking of course ...

If there are any urgent issues flagging them by posting on meta is a good approach to getting a fast response.


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Answer in comment was deleted - what is the protocol on this site?
I seen a question whilst I was browsing (KeyError '/n' in Bio SeqUtils Package ProtParam Script) and guessed the likely issue and thus added a comment advising the user to use .rstrip('\n') to remove the newline character produced by pushing enter on a keyboard (the variable was a user input).
I have just seen my comment has been deleted, on TeX.SE we frequently post answers in comments when the fix is trivial or is fairly common knowledge that the user is not experienced enough to know. What is the protocol on this site for answers in comments or why else was my comment deleted so soon please?
I would like to contribute to this site as I am doing a PhD in de novo enzyme design so this is my kind of place.

Firstly welcome and thanks for the post. It's no problem, I'm sure the comment will be undeleted. However, the site protocol is provide answers rather than comments. Thus once your answer is in place the comment can be deleted right? Comments on this site are used to request information about the question with a view to providing a better answer. Comments are sometimes used for answers if there's lots downvoting on a site because comments avoid that. This site rarely downvotes, and frequently upvotes. therefore answers are much preferred both for you and the site per se.

Bioinformatics needs biological context and thats often missing in the question. Thats when we use comments. Which phyla is a good question because plants are different to vertebrates are different to bacteria etc .... In the case of my comment: the reason I've commented and not answered is because this a temporary answer and intend to follow with a full post later (or gringer can). @gringer is currently the most active Mod at present and I want to wait for their response. The reason gringer is the most active Mod right now is complicated. Upvoted BTW.

The official STackexchange policy for comment answers BTW is to turn them into wiki's, the idea being that this is believed to discourage comment answers in the future.

The minimum answer length is 30 characters. That should give you an idea around the minimum amount of effort we are expecting to be put into an answer. If you are answering a question, please just write it as an answer. It will make my job easier, and benefit more people in the community.
I think the amount of formatting and additional discussion around the answer you provided demonstrates the benefit of this approach. Answers improve over time, and that collective improvement is a key strength of the Stack Exchange network.
As mentioned in the Help Center section on comments, comments are for clarification, constructive criticism, and adding relevant but minor or transient information to a post.
Comments are not recommended for any of the following:

Suggesting corrections that don't fundamentally change the meaning of the post
Answering a question or providing an alternate solution to an existing answer; instead, post an actual answer (or edit to expand an existing one);
Compliments which do not add new information
Criticisms which do not add anything constructive
Secondary discussion or debating a controversial point
Discussion of community behavior or site policies

See more information here:
https://bioinformatics.stackexchange.com/help/privileges/comment
I apply these guidelines when moderating posts, and am particularly insistent on these guidelines applied to the posted question.
Answers as comments are a problem on Stack Exchange for multiple reasons, including the following:

it breaks threading
paragraph formatting is unavailable (e.g. line breaks, bullet points, scripts, tables)
it doesn't give proper credit to the person answering
there's no way for moderators to convert a comment into an answer
it breaks the "bubble to the top" approach for answers
it confuses the question promotion algorithm
it makes it hard for potential answerers to tell (from the question browser) when a question has already been answered
revision history is not available
other people can't update and improve the answer

The general policy is not to answer in comments, no matter how trivial. Comments can’t be edited, can’t be voted on, can’t be accepted, aren’t clear for future visitors to the post and are liable to be deleted at any point.
If it answers the question, just write an answer.


text:
Consensus on when markdown code formatting should be used
I've noticed that there is some missuse of markdown code formatting here. Before I go around editing it out, it would be good to come to a consensus on when it is appropriate.
In my opinion, the following is true:
Appropriate

Code blocks (obviously), e.g.
def id_func(x):
    if x.featuretype == 'gene':
        new_id = x.attributes['ID'][0]
    elif x.featuretype == 'CDS':
        new_id = '-'.join( [x.attributes['ID'][0], x.seqid, str(x.start), str(x.end)] )
    return new_id

Error messages and other formatted text output, e.g.
print("1" + '"' + str(fastaIdx) + '"' + '"' + str(mrna_id) + "'" + db.strand())
AttributeError: 'FeatureDB' object has no attribute 'strand'

Formatted data, e.g.
Seq_18  Liftoff gene    653259  653653  .       +       .       ID=QZVMAR_2781_gene_1
Seq_18  Liftoff CDS     653259  653334  .       +       .       ID=Seq_8_Seq_8_Manual.BlastoST7C_030513:00:54_1;Parent=QZVMAR_2781_gene_1
Seq_18  Liftoff CDS     653370  653458  .       +       .       ID=Seq_8_Seq_8_Manual.BlastoST7C_030513:00:54_1;Parent=QZVMAR_2781_gene_1
Seq_18  Liftoff CDS     653489  653543  .       +       .       ID=Seq_8_Seq_8_Manual.BlastoST7C_030513:00:54_1;Parent=QZVMAR_2781_gene_1
Seq_18  Liftoff CDS     653577  653653  .       +       .       ID=Seq_8_Seq_8_Manual.BlastoST7C_030513:00:54_1;Parent=QZVMAR_2781_gene_1

Referring to inline function names, e.g.

You should only use printf when....

Not appropriate

When emphasising words in a sentence
When referring to the name of a piece of software pandas or programming language python
Anything else that isn't covered by the above points

Up for discussion

When referring to filenames test.fastq

Does the comminity agree? Are there any additions or removals that people think are appropriate?

Can you please explain more about why you think it's a grey area for file names, but not appropriate for program names? They seem like similar classes of things to me.

Summary A distinction between library and function/method appears to be at the heart of this proposal. I can't see this proposal working for inline text for OO code (such as Python) because it is not practical to separate the library from a method (equivalent of a function).
Background Specifically on a spectrum from Python to pandas and then to printf. pandas is a library imported into Python. It's popular possibly because it's faster (for Python). It uses a sort of type casting, which I assume speeds its interaction with the underlying C.
Issues for inline text

For inline text what's the difference between printf (which is very C, but also Perl) and pandas, neither are standalone languages? If there is a distinction, where is the line drawn, for example what about math.h (C), numpy or for example pathlib which are all 'libraries'? If libraries are excluded (of which pandas is one) what about the methods (OOP) that they are importing? For example, would Path in pathlib library be okay (thats a method), but the pathlib library itself be excluded from the proposal?
Is there a distinction between functions and methods, i.e. between a non-OOP language and an OOP? I assume f strings or format (Python's equivalent to printf) are fine, but these are methods rather than functions. If methods were excluded it would be a bit limiting to an OOP coder.
Furthermore, OOP uses libraries and method calls in the unit of code, i.e. " library.method ". For example, the pandas library calls methods within the code not on import, so in the code below (df = pd.DataFrame()) would literally read pd.DataFrame as inline text. This is because DataFrame is the method and pd is the abbreviation for the library its from, i.e. pandas. The proposal appears to permit the method to be greyed out in inline text but the library isn't.

I assume that the proposal for pandas i.e.
import pandas as pd
df = pd.DataFrame()

Would not extend to
import pandas as pd
df = pd.DataFrame()
I hope thats right?


text:
2022: 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 2022 (and where did January go, right?) and dive head first into 2023, 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

All comments on a post moved to chat
1
0

Answer flags handled
95
58

Answers flagged
5
148

Comment flags handled
13
3

Comments deleted⁷
897
349

Comments flagged
0
16

Comments undeleted
29
0

Posts bumped
0
527

Posts deleted⁶
74
290

Posts locked
0
19

Posts undeleted
6
23

Posts unlocked
0
1

Question flags handled⁵
96
25

Questions closed
78
6

Questions flagged⁵
14
110

Questions migrated
7
0

Questions protected
0
3

Questions reopened
9
0

Tag highlight language set
1
0

Tag synonyms created
7
0

Tags merged
12
0

Tasks reviewed⁴: "Close votes" queue
52
116

Tasks reviewed⁴: "First answers" queue
48
115

Tasks reviewed⁴: "First questions" queue
104
331

Tasks reviewed⁴: "Late answers" queue
19
37

Tasks reviewed⁴: "Low quality posts" queue
12
60

Tasks reviewed⁴: "Reopen votes" queue
3
4

Tasks reviewed⁴: "Suggested edits" queue
30
69

Users destroyed³
3
0

Users suspended²
0
17

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). Community can handle these flags by at least one person voting to close a question that has a close flag.
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: 2021: 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 2023! ^_^

Thanks @JNat. Good to see you (or at least a bigger version of your icon) at the recent mods meeting.


text:
what happened to the biopython tag?
What happened to the [biopython] tag? Bioinformatics stack exchange says 0 related question to it? Is it normal? I saved a biopython tag in one of my question filters so it was working once.

Yes, it's normal. But it is surprising. Unused tags, tags that exist but are not actually used in any questions, are automatically removed by the system at regular intervals. So it is entirely possible that the tag did exist, as you remember, but has since been deleted because it wasn't used.
I see my fellow moderator, @M__ added it to a question recently which should mean it is now available again and won't be deleted unless it is removed from all questions again. I also added it to another I just found.
I don't know how or why this happened. I admit I don't personally pay much attention to that particular tag as I don't use biopython much, but it is surprising that we only have one question with the tag given how often we get biopython questions. So just tag any appropriate questions with it and we should be fine moving forward.

did on a couple of questions think 2 or 3 now I get the : "You have too many pending edits. Further edits cannot be submitted until prior edits have been approved."

That's OK, @pippo1980, it's better not to do too many edits at once anyway since that will just flood the front page with old questions because they were retagged.

@pippo1980 it was more like 6 or 7 edits :) But I have now approved them so you should be ready again. Just please don't add "with Biopython" to the question title if it wasn't there. Just because the OP happened to use biopython doesn't mean that is the only tool they are interested in.


text:
Biological/bioinformatic context to a question
The mods had a discussion about whether a coding question was valid without any stated relevance to bioinformatics, a typical question is "here's a bit of text how do I parse it?". The issue is that such questions could be answered on lots of different sites, not just Bioinformatics SE.
Example A current example, is how to perform a database merge/join/union operation between two dataframes. The information sought for this given question is what is the biological reason, or biological objective, for the database operation. In other words, how does this new database help further biological insight into the data set. The OP might want to augment the database to include new information for example on disease incidence outside the original study so the new db applicable to a bigger geographic area. The OP might want to correlate two specific factors of disease incidence for further analysis. In this given example, the question was simply

its not worked, here's the error log, please sort it out.

Biology The proposal is that such coding questions are cool, but the biological and/or bioinformatic background needs to be stated. What is sought is to explain the rationale or the objective behind the need to perform a given coding operation.
If we generally refer to the background information sought as 'biological/bioinformatic context'.
Rationale IMO there three good reasons for requesting the 'biological/bioinformatic context':

Miscommunication is common in many bioinformatic questions between the OP and those answering. This can result in providing a solution outside the biological objective the OP requires.
The XY problem. This is where the OP needs a solution to problem 'X' but thinks the way to answer 'X' is by solving problem 'Y', when solving the original (unstated) question is a better strategy.
The species, genus, Family, Order or even Class is not stated and a solution is provided for a completely different part of the Linnean classification system which isn't relevant. Haplotypes require a completely different set of solutions to eukaryotes, lower eukaryotes compared with higher eukaryotes, or Orders within a Class.

To expand point 1. in the database example a 'merge/join/union' operation is sought but the OP does not know the operation name and tries to describe it by creating an ad hoc technical language. If the biological reason is described the reader can then reinterpret what is sought as a technical operation and that is how many bioinformaticians think.  If the OP wants to query the database for a specific transmission factor with a join operation, but those answering think it's a union operation ... that will result in the wrong answer.
In summary, the 'biological/bioinformatic context' reduces the risk of 1., 2. and 3. by increasing the clarity of the question. That can only be a good thing.

The primary reason for adding context is that it helps to find the right solution for the problem that a person is having. I don't think that context has to be a story, but a story is usually the easiest way to find out a person's underlying problem. I agree that in general there is an issue with people not providing enough context, leading to incorrect / unhelpful answers, but don't think this question is a good example of that.
I don't have an issue with problem duplication or cross-posting (especially if it is explicitly stated / linked). If someone comes here with a problem that is a pure maths problem, or pure programming problem, that's fine by me. While they'll probably get a better answer on another site (and I would possibly guide them to do that), it's possible they feel more comfortable asking on this site, or think their problem is applicable within the very broad realm of bioinformatics.
I don't think that context has to be a story, but a story is usually the easiest way to find out a person's underlying problem.
To clarify on specific points relating to the referred-to question:

The contents of the examples they provided indicated that they were working with biological data.
It's unclear whether the question is a good example of not providing enough context, because they eventually provided input files that were sufficient to reliably demonstrate the problem. The "not enough background" point may still be applicable in this case, even if their immediate stated problem is solved. One thing to think about is whether or not this individual problem would be helpful to other viewers of the site (I would suggest it is, because it's an obscure problem with an odd cause). If so, it would be reasonable to keep it even if it doesn't provide a solution to their ultimate problem.
This was not a general database problem; they encountered a specific error using the merge function in R. This is a real function in base R; there is a help page for it.
The person asking the question was a new user. It's especially important that we (i.e. the community) put more effort into helping new users, rather than setting off quick-fire close requests and scaring them away because they get hit by the rules hammers.

Thanks, upvoted. It's agreed there's a problem. The next step is to find scenarios that are clear examples of this. No need for a 'hammer' just a reference point that can be presented as a link.


text:
PSA: Please don't post images of text
When asking or answering questions, please don't post screenshots of text. This is a very bad idea because:

You can't copy/paste the commands into answers, google searches, local files to work on a solution, or anything else.
They won't come up when searching.
The post is heavier (in terms of the amount of data) and will take longer to load. This can be a serious problem for people with slow connections.
The post is useless to people using text-based browsers or who have disabled the displaying of images.
The post is useless for people who have sight problems and are maybe accessing the site using text-to-speech software.
The image is only guaranteed to be legible on YOUR monitor.  Anyone with a different monitor (e.g. different DPI, higher resolution, viewing on a tablet etc) might be unable to read the tiny little fonts.
Image questions are often ignored.

While there are sometimes valid reasons for this (discussing colored output, or other issues where the core of the question is visual in nature), in most cases it is not useful and causes the problems listed above.
For help on formatting your posts, please see here.


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2022 Community Moderator Election Results
Bioinformatics's second moderator election has come to a close. Since there were not enough candidates for a competitive election, we simply appointed the candidates who nominated themselves as pro-tem mods, so the team would have a total of 3 moderators (more on mods stepping down below):

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!
Please also join me in thanking the following two users, who'll be stepping down from their positions as moderators:

Thank you @terdon and @M__ for stepping up!

Thank you for stepping up first!


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Anonymous public criticism of anonymous peer review
There's a current post which discusses and criticises a manuscript the OP received, which would almost certainly be part of the anonymous peer review process:
Is DEGSeq software appropriate for gene expression analysis? Are the software statistical assumptions wrong?
Essentially, this is a new post, an entirely anonymous account, publicly criticising a manuscript under anonymous peer review. This to me seems a misuse of Bioinformatics SE. Had the OP linked this to a BioRxIV manuscript that would be different, because the authors would have publicly disclosed the work.
My preference is for this post to be deleted (not closed) to prevent any sort of precedent. I think anyone could see where this is heading if left unchecked, like an "anonymous peer-review WikiLeaks".

Conclusion
I agree in this particular instance it was sufficiently vague, as the Mods said here. Its a satisfactory conclusion.
The point I'm making is it might be a precedent.
The problems I see for the future are two-fold, i.e. if this was normalised:

It potentially  breaks journal policy.

A reviewer is ideally not permitted to discuss the ms without the editors permission. Usually its with named colleague(s) within an institute and permission is granted. The name of the additional reviewer(s) are then formalised within the journal.
A reviewer is certainly not permitted to influence the other reviewers during the process of first review. This is why permission is required because only the journal knows who the other reviewers are.

It could break the UK Data Information Act  because the information is held in confidence if the authorship could be identified. It might break copyright.

If the authorship put the ms on BioRxIV then none of the above points really apply.

I have closed this question, because opinion-based answers don't work well with the StackExhange format. I'm happy to continue discussion about this issue, but don't immediately see a problem with the question as it relates to peer review:
I didn't get the impression that the person asking the question was criticising the manuscript (at least, not in a negative way). It relates to critique about a tool, rather than a paper in review. I think it is reasonable for people to have doubts about a tool or process, and ask for advice and support around that.
There is also no indication that it was anonymous peer review (although I don't understand why that's relevant, in any case).
Even if the question had been asked about specific concerns relating to a paper in review, I think it's okay to ask people for help with peer review.
I am likely to be biased in my opinion on this, at least because I recently answered a question relating to p-values used in a paper with a critique of the method (which I have now closed, in hindsight, as being opinion-based). I notice that you also commented on the same question, giving your opinion / critique about the method.
Legal issues shouldn't apply to this particular question. The question doesn't mention the paper (neither directly, nor by providing enough identifiable information), and ideas cannot be assigned copyright. A more direct question (as it pertains to legal issues) would be the p-value question, because it directly linked the paper, but there has been no discussion on that as far as I can see.

Thanks, @gringer this is okay as a compromise. Please note, there are legal issues here regarding UK Data Information and copyright as well as journal policy. Whilst I doubt this violates them, my point is it could be a precedent.

I don't see a problem with the questions to aid peer review. Contrary, I find quite refreshing to see a reviewer that bothers to dig into methods they are not very familiar with. Especially because the reviewer did not say there is anything wrong with the method, rather saying that while researching it they found a red flag and are trying to figure if the criticism is founded or not.
Why it is so worrying the question is anonymous? Perhaps I just don't see what would be the problem with it. Well, I hope that our community is strong enough to weed out unfounded criticisms if they appear among the answers. IMHO, that's why we have the "downvote" button.
This being said, I am with Gringer on the vagueness of the question. They don't explain what is the mentioned criticism and why they do/don't think it's valid.

Thanks @KamilSJaron I've responded above. I agree in this instance vagueness is sufficient not to be an issue. The point I'm making is the precedent.

How do you know the review is anonymous? And even if it is, how this post is breaking it? Some journals (e.g. eLife) organize meetings for reviewers so they agree on the evaluation. But most of all, why reviewers should not influence each other?! Who made those rules?
I really can't see how this can be seen as problematic. The question is not even about a method that is under peer reivew.

Its standard journal editorial policy, even for open access. I don't make the rules just follow them. I agree a minority of journals might not follow this, but its the norm. The point is the journal retains control of peer-review and it prevents anything untoward either way, i.e. one reviewer pressurising other reviewers to accept/reject outside the journals knowledge. Its very similar to the role of the Chair in a public meeting.

I don't see influencing other reviewers privately and asking a public question as the same thing. I guess I have hard times submitting to a terrible publishing norm. We have no obligations whatsoever to maintain the status quo and this community is certainly not breaking any rules by answering these questions.

Understand thanks


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Broad Institute and support for OpenWDL on Bioinformatics SE
I spotted a chat from @Geraldine_VdAuwe, almost certainly Geraldine A. Van der Auwera from the Broad Institute and one of the authors of Genomics in the Cloud by O'Reilly. Its a good book, I tracked it because I wanted to assess cross-over with 'driver mutation' stuff.
24 April 2020,

On the OpenWDL side, we've chosen this SE as the primary venue for WDL
community support as it feels like a good fit, both technically and
culturally. On the Broad side, we're going to follow suit by
encouraging people to post their Cromwell questions here.

This is good. It would be better formally announced, for example I don't read chat. It would be cool if Broad Institute could assign someone to this site to support the recommendation because there are a fair number of GATK, WDL, Cromwell questions on site. I've looked carefully at all this stuff in my case I decided custom solutions were more appropriate (don't work on human genetics).
Perhaps the Mods could write in a formal capacity to the Broad Institute? Bioinformatics SE has enough kudos: its big brother Stackoverflow is the undisputed heavy weight in online coding help.
Blurb
The announcement from Geraldine does make sense because Biostars copyrights help manuals in own its own capacity and sells them. I would assume the proceeds help support the site. However, this would be a problem for the Broad Institute and especially publishing houses such as O'Reilly because there would be legal issues about profiting from Broad Institute products that could block further publishing arrangements. Technically if official help was given on Biostars - that would fall under Biostars copyright. Bioinformatics SE must have external support and is presumably is supported from the advertising revenue of Stackoverflow, which is likely huge. There are some superb coders on Stackoverflow, a famous Perl coder (whose name I forget), is but one. For example, some Python solutions are sublime from coders who are otherwise under the IP of their employers. Bioinformatics SE is important because at present there seems just too much traffic for moderation on Stackoverflow.

Notes on O'Reilly
O'Reilly is the premier publishing house of coding books. O'Reilly famously published Larry Wall's Perl5 which was the authority on how to code in Perl, albeit it then published Damien Conway's 'Official Perl coding' (forget its title), which was a famous disaster. Who is Damien Conway - good question - he was known for 6-lines of Perl code known as 'whitening' (not very PC), but had published on object orientated Perl elsewhere.

As additional context, this message was starred by two users (now three), and was responded to in chat.

Thanks for the update. Just to point out, a number of us don't really look at chat, but that would be a good place to raise the above matter.


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Is 'low effort post' a valid close reason?
I noticed a post today with a close vote, with the reason being something along the lines of:

This is a very low effort post which could be solved with the first
google hit

I'm not doubting that's true, but is it a valid reason to close a post? Usually on SO downvotes are the way to respond to a low-effort post, not a close vote.

I would say no unless google hits bioinfo.SE, then it is a duplicate, and in that case it should be closed.

Closed votes are subject to a vote anyway on administration queue and I think (pretty certain) it is ultimately the mods decision whether to close.
The problem with 'first Google hit' as a reason is that Google's priority list is always changing. So if it is the top hit today, in a week or two it could disappear from the front page.
The other issue if we're looking up a basic e.g. coding, matter, cause you just forget, e.g. Python printing using .format, %, or f"{}" because + isn't cool then Googling stackexchange is quickest way to the solution rather than having to wade through beginners websites on how to code which can be 'not time efficient' is perhaps the politest way to say it.
To prove it ... Google

.format python printing stackoverflow

Top Google hit (for now) is here describing .format, % and f"". In fact I didn't know that `f"{}" were Python 3.6 onwards.

.format python printing

Top hit is geekforgeeks.com where there is a lot more words and less information.
... and Googling site:bioinformatics.stackexchange.com (bit of a mouthful) should be something I do more.

If a post gets five close votes from the community, then it will be closed without moderator help. Moderators can re-open closed questions if they think there is merit in that.

Thanks @gringer thats good to know


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How much mod cleaning is too much mod cleaning?
I bringing this up, because I think that is something we should discuss before it becomes too much of a problem.
There are members of community that feel there is too much moderation. The trigger for me to post this question was @ATpoint's comment about converting comments into questions:

I agree and I think @gringer should stop doing that unless a comment
get sufficient community vote as I suggested many times before.
–ATpoint

But there were other moderation problems flagged before. Namely, with deleting comments to early, but also for closing deleted questions:

Deleting comments before the question is answered
Moderators: Please do not close questions just because they are old

I do think @gringer does marvels to the cleanness of this site - stats like "fraction of answered questions" or the amounts of very clearly outdated questions a great, for big part thanks to them. So, thank you for that Gringer! But in all these "edge" cases, I am more on the side of people - I do think we should make sure people won't get too frustrated with our moderation despotism and I am afraid it might have repelled some people already.
As I belive that there is a good intention of making the webpage clean and tiny, I do think we could just, as a community, define better what are the edge cases.
Namely:

Comments to answers: What comments should be converted to answers? E.g. How many upvotes a comment must have? Or another comment saying that the previous one was a solution for them
Deleting comments: How old comments we delete to make sure we don't cut an ongoing discussion? Nothing older than 48 hours? Or something like the last comment older than 48 hours?
Closing old/outdated questions: I think this one is not much of an issue at this point, but I guess we could also agree if we do it or not. (I would leave this to the community, e.g. mod closing of questions that have >2 votes, or something like that).

I do think we all want to have a helpful community, that is useful to everyone. We just need to agree how to go about it, because our visions clearly differ.

I personally think moderation is good and works well. @Gringer's edits are useful for getting a thread moving. The one thing that could be improved as a community per se is simply encouraging a 'closed question' to be reopened if the matter is singly a question is closed too soon. Question can be closed by mistake and reversing that would help.
I personally would go further to say that IMHO moderation is a critical role of Bioinformatics SE and without it fewer questions would be answered.
There are countless examples where moderation is required, I'm going to cite a few examples:

OPs persistently supply insufficient information and the ability to answer a question is thereby restricted, there are current examples. Thus alot of the question material is in the comments.
Answers such as is 'oh thats not what I meant' happen, we've all experienced this.
Some questions are simply not adequate for Stackexchange and need removing, possibly Biology SE, who knows
'please do my homework for me' appear regularly and should rapidly wound up in my personal opinion (thats a moderation decision).

Occassionally there is a deep thereotical matter where the context doesn't matter, alot of the time its about non-disclosure.
I don't aportion blame to the OP: there is often far from adequate project supervision,  and thats often why OPs are here - that is understandable.
Summary, There has to be a point where a line is drawn and thats a key moderation role. Personally, I do feel mods do a good job and less moderation would not be cool.

The majority of the moderation I do around comments follows the following guidelines:

comments shouldn't be answers; we have answers for that.
comments shouldn't be discussions; we have chat for that. Discussions in comments are a particular problem because the voting system alters the order of comments.
comments shouldn't discuss community behavior or site policies; we have meta for that.

The important thing to keep in mind is that comments are meant to be temporary things. Comments should primarily be used to provide additional information that helps improve questions or answers. If it's important that your statement is preserved for someone reading the question or answer five years from now, it shouldn't be a comment.
I believe short answers are perfectly acceptable. Answers don't need to be perfect, and they don't need to be well-researched theses the first time they are created. They can (and should) be improved over time.
I think most of the hesitation around writing comments as answers is that people don't like giving really short answers, but they're comfortable writing short comments. I would like this culture to change, but this runs counter to statements like "this shouldn't be an answer because I don't think it's correct". Unlike other bioinformatics discussion forums, the StackExchange network allows and encourages people to downvote answers if they lack substance or are otherwise inappropriate.
It seems to me that the people who get the most upset are frequent users of other discussion forums (Biostars in particular). StackExchange allows anyone to edit and improve the questions and answers of others, which is not a very common feature.

Why do you think people get upset then? Because they don't understand the system?


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When was the site elevated from Beta status?
When was the big date Bioinformatics SE was no longer a beta site?
I would have thought there would have been fireworks and celebrations, or at least an announcement on this forum. Its certainly worthy of one. Congratulations.

59 sites were elevated from Betas on the 16 December. I can't tell you much more than that.
Good to have you back answering questions btw.

Its a very comprehensive answer, the link describes everything. Fairly astonished to see 'Vi and Vim' are also out of beta. I obviously underestimated both power tools.

Yeah, that one is a bit on us... moderators. We got notification by SE admins in early November about it, offering us to prepare an announcement for the community. I started writing a post for meta, but never finished it, and then I forgot about it, so really sorry about that.
Basically, we are considered a viable site. The definition of viable site is now shifting to a community strong enough to keep noise (i.e. completely unrelated, offensive or otherwise problematic questions/answers) at the site at minimum and that we do pretty well.
We won't have any time soon our own nice design of things (like small DNA badges of Biology.SE) so technically only very little changes. However, we should have a graduation election some time during 2022 or even maybe in 2023 (because so many sites were promoted at the same time).
We might have Community Promotion ads, etc in the future if they are of interest.
Finally, we won't ever have to worry that the site will be closed down (unless SE will do fine and I feel they are rather safe :-)).
So, in the end, there is only very little practical changing at the moment, but I am really excited we are a full SE community! Congratulations everyone!

Thanks @KamilSJaron its a good step forward because beta might not mean much to e.g. Pets SE, but it definitely has a meaning in coding and an exciting future.

So when do we get the visual branding goodies?

@DanielStandage they promoted plenty of sites at the same time. So I suppose it won't be too soon.


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Deleting comments before the question is answered
I received an email stating I have unread items in SE inbox. When I clicked on the link, the comments had already been deleted. I remember having a discussion with the OP in the comment section not 24h before then, and they were continuing the discussion, but all comments were gone.
Unless this is an automatic thing (which I highly doubt), this behavior makes no sense. If a mod is cleaning up comments within 24h of them being added, they should stop doing that. Given that regular users have no recourse to contest comment deletion, this is a dangerous power that should be exercised with a lot of caution, not taken as lightly as it is currently.
This is the post I'm referring to: Subsetting a Seurat object based on colnames

One of the comments was flagged as "Unkind or Unhelpful", unfortunately, I can't figure out which one it was, but looking at the four deleted comments, none of them occurs to me as unkind (although there is apparently some misunderstanding between you and the OP). As I could not spot anything pathological, I undeleted all the comments.
If the deletion of all the comments was simple cleaning, I do think that's wrong and I am fully on your side. Fresh comments within boundaries of good behaviour should not be deleted by anyone else than their authors (I guess with exception of obvious mistakes, or helping new users sort everything out).

Thank you, Kamil. I was and still am trying to understand how OP thinks their code should work, and like you say, it's not unkind. I think it's not even a misunderstanding, just a simple discussion.

To me, it did look like an honest attempt to help, so I would probably like to hear out the people that do find it "Unkind or Unhelpful".

I delete comments that look like an answer. Comments should primarily be used to help people edit the question to make it better.
Where a comment involves ongoing or extended discussion, I usually attempt to incorporate the discussion into the question, and delete the comments.
Discussions should happen in chat, not in comments, because the voting system means that discussion threads can be broken up and separated from their context.
If there's a particular point that you want to get across that helps the person solve the problem they're having, put it into an answer.

Note: this is about deleting comments in general, not about this specific situations.
As the faq says,

Comments are temporary "Post-It" notes left on a question or answer.

So, comments are meant to be deleted once they have outlived their usefulness. Comments getting deleted is normal.

Sure, I understand that, but deleting a comment while a discussion is ongoing does not fit the outliving usefulness criterion.

@RamRS that assumes the comment was useful in the first place (I don’t know whether it was or not because I cannot see the comments.)

Did you even read the post? A comment in an ongoing discussion with the OP deleted within 24h is pretty specific. I know that comments are largely ephemeral in the SE world.

@RamRS it may have been in an ongoing discussion, and it may have been specific, but it may not have been on topic for a comment. (Again, I can’t comment on this specific situation without seeing the comments, which I can’t).

I should have addressed that too - it was on topic. We were clarifying the problem at hand. Given the lack of available context, what prompted your answer here?


text:
Should we allow questions about the coronavirus?
As the flood of information, from around the world, comes in concerning the pandemic; should we create a coronavirus-bioinformatics tag and try to apply the principals of bioinformatics to it? This may help lighten the load on Biology.SE.

I have to say I've generally been against these questions since inevitably they're off-topic. I think the only regular on the site that has a relevant background to answer these is Michael G.

Whatever you think, the problem isn't nearly as bad as "Biology SE". One of the questions was "Can Coronavirus hitch a ride on a perfume particle" !!! Oh dear, good job they are not posting here, it certainly gives a whole new twist to the miasma theory :-) . Here in case you are wondering.
In contrast, I found alot of the questions on Bioinfo SE ahead of the curve and helpful.
At present two areas of bioinformatics that are relevant to COVID-19: phylogenetics and epidemiological modelling. Protein modelling is currently frustrated due to the lack of structural information for accurate modelling,
Epidemiological modelling isn't considered bioinformatics. Phylogenetics is a not a huge disapline. When accurate protein structures start kicking in, or big NGS dumps, then I think we'd have questions that would appeal to the numerous structural modellers and bioinformaticians present on the site.
My advice is just be patient and definitely try and avoid becoming "a patient" when its about COVID-19.

citation: Can a virus hitch a ride on an odour particle?

I am in physics forum. There have been questions like "can coronavirus use quantum tunneling" and "can we kill coronavirus with ultrasound". They are generally dismissed as off-topic.

It would give a whole new meaning to R0


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Bioinformatics, biostatistics and computational biology
I am wondering how others define the boundaries between bioinformatics, biostatistics, and computational biology.
In academic setting these three are treated as more or less equivalent terms or as significantly overlapping ones: genome analysis, phylogeny reconstruction, evolutionary models, modeling epidemics, calculating RNA structure, etc. All of these activities fall under any of the three titles with perhaps a slight accent on heavy data load when talking about bioinformatics or more of statistical analysis when talking about biostatistics.
However, when looking for a job in industry, the things change:

Bioinformaticians are largely expected to be able to deal with large quantities of raw data: cleaning, assembling and doing a bit of analysis;
Biostatisticians are expected to have a perfect knowledge of the experiment design and the multitude of the statistical tests;
Computational biologists are those who do not have a proper (i.e. confirmed by a diploma) bioinformatician or biostatistician training, but came to the field from elsewhere (biology, physics, etc.) Although this largely prevents them from competing for bioinformatician and biostatistician jobs, big research labs are interested in such people.

This reflects my own experience and observations, which is why I would like to know opinions of the other members of the community.

Those look good definitions and I would intuitively feel the same. One of the major hurdles I have is between epidemiological/mathematical modellers who work with disease instance data and those who work on molecular data. The latter we call bioinformatians the former mathematicians. The problem is that we could actually work together, but in practice we never do. I understand their stuff, they understand mine ... but it never really happens. It is a limitation.
Personally I would carry the definition through the ranks, so a statistician vs a biostatistician the later understands in vitro experimental data and ideally molecular data (which is harder for them). However, the actual techniques are very similiar and statisticians can adapt to molecular problems.
Personally I would see computer biologists as 'hardcore' bioinformaticians because of the speed at which they can solve problems in code.
The major problem in biology is its tribulism. Python vs Perl is one example. For intermediate level coders (like me) it makes a difference to the speed (and possibly) the robustness of a solution (like pandas is a great 'walking stick' for database solutions). However, the reality is its really about how good you are with code and there are some very strong coders on this site. Ultimately code is code.

A bit off-topic and more of a long comment, but still relevant is computational biochemist.
I and others call myself a computational biochemist and go to the bother of correcting others when called bioinformatician as I do not see myself as one in the strictest sense, but the fact I find myself answering Qs here means that the definitions are loose.
It is tribalism as @michael mentioned, but it is also separate islands. I have as much of an idea what an autozygous BAM file on an IGV plot is, as a genetics bioinformatician has about Lennard-Jones potentials. It is more cheminformatics applied to biochemistry than genetics bioinformatics applied to biochemistry. Unsurprisingly, given that biochemistry and chemistry overlap heavily —particularly in the structural and analytical subfields.
Definition
Computational biochemistry is the use of computational methods to investigate structural properties of proteins or nucleic acids. Namely studying 3D structures, generally utilising forcefield models, for example:

enzyme/theozyme engineering (not much of that in BioInfo SE as its mostly on Rosetta Forum —but I'd like to change that...)
docking
de novo structure prediction
other structural predictions (mutations, PTMs etc.)
MD simulations

For a real example, myself (gulp), I normally work on structural effect predictions —geneticists finds a mutation and wants to know more, and depending on what the effect is I will run some analyses, for example for G-protein β-subunit mutations at the interface I modelled the mutations and analysed how it affected the binding energy with the different partners. Possibly ironically given this post, I made a visualisation tool aimed at making it easier for geneticists to share and look at protein structures. During Covid I am working on docking as part of the Covid moonshot, but previously I was worked in enzyme engineering.
New tags
However, I am in half a mind to create a tag computational biochemistry and cheminformatics once I get the wiki privilege. If I do, should I retroactively edit it on past Q&As?

Does this have to do with docking? Could you give a few examples of the problems that computational biochemists deal with? How about protein and RNA structure prediction?

@Vadim I added a 'Definition' section with myself as an example —I might wear a brown paper bag now in embarrassment for the rest of the day though...

It is really interesting. My background is in condensed matter physics and I have encountered computational chemists who seems to be doing physics calculations but they are certainly neither physicists nor chemists. So it seems to me quite natural that there is an extension of this field to bio.

Oh-oh! If it's not chemistry, physics or biology. The only label left in the bag is... software engineer (minus the pay).


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"Synthetic" instead of "man-made"?
A question on Bioinformatics SE is about the possibility of coronavirus having been engineered in the lab and the question title includes the phrase "man-made", which, in my opinion, is an example of sexist language use.
Before editing the post, I wanted to double check if "synthetic" would provide the same nuance as "man-made" in the context of this question. Would there be any other word that could be used instead of "man-made"?

Either "synthetic" or "human-made" would seem to be reasonable edits in my mind and both would maintain the nuance. "Synthetic" sounds better to my native-speaker ears, for whatever that's worth.

Agreed "man-made" is not appropriate. "Synthetic" sounds cool, but "genetically engineered" is more accurate.
The question is about conspiracy theories. In my opinion its the same "logical" as the "creationists" vs. "evolutionists" (I'm a theist BTW). The problem with conspiracy theories is that its "new" every time, but its the same analysis disproves it.


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2019: 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.
And what could be more festive than a big pile of numbers?
So here is a breakdown of moderation actions performed on Bioinformatics over the past 12 months:
                 Action                  Moderators Community¹
---------------------------------------- ---------- ----------
Users suspended²                                  0          4
Users contacted                                   1          0
Tasks reviewed⁴: Suggested Edit queue            20        190
Tasks reviewed⁴: Reopen Vote queue                0         16
Tasks reviewed⁴: Low Quality Posts queue          0         45
Tasks reviewed⁴: Late Answer queue                0         56
Tasks reviewed⁴: First Post queue                 1        490
Tasks reviewed⁴: Close Votes queue                1        277
Tag synonyms proposed                             0          5
Questions reopened                                2          0
Questions migrated                                4          0
Questions flagged⁵                                1         50
Questions closed                                 41         29
Question flags handled⁵                          33         18
Posts unlocked                                    0          1
Posts undeleted                                   3         25
Posts locked                                      0          6
Posts deleted⁶                                   62        188
Posts bumped                                      0        180
Comments undeleted                                4          0
Comments flagged                                  2         87
Comments deleted⁷                               142        406
Comment flags handled                            22         67
Answers flagged                                   2         89
Answer flags handled                             72         19

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? I posted a similar report here last year: 2018: 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 you all a happy new year...


text:
Is asking about publishing in bioinformatics on topic?
I have a question about how to present bioinformatics methods for publishing in a paper. I tried asking it on Academia, but it was off topic there. Would it fit here?
More generally, would questions about the field of bioinformatics be appropriate here? Or is it just for questions about problems in bioinformatics?

Was it really off topic on academia? That seems strange, did they give a reason? Was it just opinion based?

@terdon apparently it was too much about research and not studies, which didn't suit them

I'm going to venture out on a limb and say that this is on-topic. Norms, styles, and conventions for communication and publication vary widely by discipline, so in my opinion the best place to ask questions about publishing bioinformatics methods is a bioinformatics-focused forum.
In any case, this community has been pretty inclusive of mostly-programming questions or mostly-stats questions that are couched in bioinformatics language/examples. So in general it seems natural we'd do the same for mostly-publishing questions about bioinformatics methods.


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How to encourage/create effective tagging protocol
I have seen a few questions where people want to do something like convert a file, or they ask a question about a specific programming tool. Then they don't tag the post with the programming language they are using, and or don't tag with the file formats they want to convert between.
How can we as a community moving forward encourage proper tagging? Should we make a one tag minimum, to remind people to use tags?
Possibly allow more than 5 tags. In bioinformatics it would be easy to use more than 5 tags every post. Possibly we could have 0-2 coding-language tags then have the other standard 5 tags.

Prompting to add tags and auto-suggesting tags based on text mining of the thread are some of the ideas worth considering. Not just for this SE, but for the entire Stack Exchange.

We can't change the number of allowed tags, that's part of the system. I mean, maybe we could ask Stack Exchange, but they're not very good with that sort of thing. Nor do I really think it's needed, really, 5 tags is plenty and, as you point out, many people don't even use that.
I think the best thing we can do is to simply edit the questions and add the relevant tags. The beauty of the Stack Exchange model is that it is collaborative and everyone can edit or suggest edits. So whenever you see something that can be fixed, just fix it!

I definitely agree with everything you said. I wish they had a better  mechanism like auto suggested tags option. Maybe forcing you to at least click in tag section and prompt before submitting are you sure you don't want to add in any tags. We'll just have to keep editing till all the questions and answers are fixed!


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Updating a tool-related tag to match the tool's name - markduplicate -> markduplicates
I had a question related to Picard's MarkDuplicates tool, and wanted to tag the question accordingly. There is an existing tag, called "markduplicate" but the tool's name is spelled differently.
https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.4.0/picard_sam_markduplicates_MarkDuplicates.php
Can we change this tag to the plural?  MarkDuplicates or markduplicates.

I agree the current spelling is clearly wrong and should be fixed, either by editing the tag or if that's not possible, making a new tag to replace it.


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Microbiome analysis tags needed!
We analyze the human microbiome using 16s sequencing. I couldn't find a single relevant tag for my question!
Tags Needed
General

16s
microbiome
microbial
taxonomic-assignment
16s-sequencing
dada2
otu
asv
alpha-diversity
beta-diversity
shannon
simpson
unifrac
pcoa

Software

phyloseq
dada2
qiime
qiime2
picrust
picrust2
decipher
lots lots more...
*

You can always assign tags, I know the area you are working in. OTU is commonly referred to as taxa.


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Synonymise [alignment] and [sequence-alignment]
While asking a question here, I noticed that alignment and sequence-alignment both exist. They appear to be synonymous; indeed, the alignment description reads, in its entirety:

These questions are about sequence alignment.

I understand that there's been some past debate about how to deal with alignment-related tags, but as best I can tell these two in particular are, unambiguously, exact synonyms. Synyomise them?

Sounds reasonable to me…


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Q&A section, what is it exactly?
@Terdon has requested a Q&A section on a rolling thread on an investigation about gene duplication. What is exactly meant by this and how to go about doing it?

By the way, I realize this is asking you to do a lot of work and I entirely understand if you don't want to spend even more time on this. I just can't think of any other way of keeping the really useful content you created :/

Thank you for posting this, I was about to bring it to meta myself. First, a quick summary of what happened. @Michael G answered this question but in a way that didn't give a definitive answer. Instead, Michael did what most of us are very accustomed to doing, both online and in real life: he gave the OP very useful pointers based on his extensive expertise, and asked some very relevant questions that would help him provide an answer.
The problem is that these sites, the SE network, don't do discussion well. Not only because it is against the "rules" and not only because we try to have a high signal to noise ratio, with one question and everything else being answers to that question. Another issue is that, unlike traditional online forums, the SE site mechanics don't guarantee the order of the answers. So when you have two users having a back and forth discussion, referring to "the post above" or "the post below", the post they are referring to will move depending on how the person visiting the page is sorting the answers.
So, coming back to the specific example, when I saw that this had happened I converted one of Michael's answers to a comment, I incorporated the OP's answer to his answer into the original question and deleted the rest since they had, by now, moved on to a new Q&A.
However, this new Q&A was also treated as a discussion, resulting in a bit of a mess. It now has 5 "answers", but all of them are part of a back and forth discussion between Michael and the OP. The kind of thing we're all used to doing in forums, but the sort of thing that's really not a good fit for this site. Finally, they moved on to a third Q&A, which you can find here: How to make a robust amino acid phylogeny with adequate robustness support.
As a moderator, I'm in a bit of a fix now. On either of the other two sites I moderate, I would simply close these questions as too broad or delete them outright as not following the rules of the site. However, those other sites are mature, with a lot of content and this would be a drop in the ocean. We're a much newer and sparser site, and I am very reluctant to delete outright. Not only do we need content, this is really excellent content, dammit! It's just in the wrong format. Michael spent a considerable amount of time providing very valuable help, and the OP was responsive and came back with all the detail Michael asked for. This may be a bit of a "trainwreck" (by SE standards) at the moment, but I think we could actually make a truly useful Q&A out of it.
That's why I suggested that Michael and/or the OP could maybe collect all the steps into one question. Ideally, the OP would post a new question, but this time, they would include all the detail that came out of this long discussion in the question itself. That way, Michael could distill the long conversation into one comprehensive answer to the now very comprehensive question.
I am very open to other ideas though. This was just the best way I could think of to both preserve the Q&A model and preserve what seems like a very useful exchange of knowledge that could help future readers. In their current state, the threads are unlikely to help others since it's very hard to keep track of what was said in answer to what.

How this should have been handled according to the SE model
With this sort of situation, the best solution is to first try and get the extra detail needed in the comments, but when that's not enough, we have the following options:

Invite the OP into a chat room (one will be created automatically if you start having a back and forth in the comments). Sort out the details there, get the extra information, and then come back and edit it into the question so the question is now in a form that can be directly answered.
Ask the OP to break the question into smaller parts. Ask the first step in one question, then everything else in follow-up questions.

Quick links for anyone trying to understand:

1st question
2nd question
3rd question

The chat room should have been first port of call, I'm not 100% how to do this but I'll figure it out. Summarizing everything into one question will be tough but maybe doable. Let me see

@MichaelG. you can create a room by visiting http://chat.stackexchange.com and clicking on the "create new room" button at the bottom of the page. However, new users won't be able to chat since you need to have at least 20 reputation (across all SE sites) to post in chat. In such cases, either ask one of the mods to explicitly grant the user access (any SE mod can do this) or start in the comments and wait until the system asks you if you want to create a room (happens after a few messages between the same 2 users). That room will always be accessible to the OP.

Thanks @terdon, but I did some time ago for "phylogenetics" and someone deleted it. Next time the OP is around we'll chat. The easiest thing for now is I will review and edit the questions to be complaint to SE format and feedback here.

Rooms with no activity are deleted after a while (several weeks or even a few months). That might be what happened.


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Medal tags, bronze, silver, gold
The medal tags for Bioinfo SE are limited, i.e. tags that lead to bronze, silver and gold badges. In particular phylogenetics is a non-medal tag but this disapline is routinely represented in questions on the site.
How can this be rectified?

The threshold on stackexchange to make a tag "medal eligible" is 100 questions. See How do "badges" work? for more on that. Consequently, the way to resolve this is for more questions with that tag to be asked (or to edit it into previous questions that should have had it).

Thanks, now I've got it

Okay, I've got it.
I've proposed a synonym between phylogenetics and phylogeny and phylip (a phylogenetics package). The phylogenetics/phylogeny synonym will help alot because manually editing these tags would be a bit messy.
On a lesser note I proposed synonym between sequence-alignments and alignments.


text:
Propose new tags for the COMBNE community
I asked a question yesterday regarding the posting of questions related to COMBINE standards and got a positive answer. However in order for a reader to filter questions related to specific COMBINE standards would it be possible create a series of new tags? I don't have enough reputation on this stack exchange to create them myself. I noticed an earlier question that requested a tag for SBOL which is itself a COMBINE standard and there was a positive response to that. A set of additional tags would include:
SBML
SBGN
CELLML
BIOPAX
NEUROML
SEDML
Further information on these standards can be found at the COMBINE web site.

Just post a question and the tags can be created. We can't create tags without questions.

ok didn't realize. Here is one question I posted a few days ago that could use the tags SBML and libSBML. link

Perfect, thanks. Daniel already tagged that with the new tags.

Excellent, thank you. I’ll post some other questions that can be tagged with the others proposed tags in the coming days

That's great! Welcome aboard!


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Proposing new tag for the Bioinformatics channel
I am a synthetic biologist working heavily on the modeling of genetic circuits and the development of software for bioinformatics. Many researchers and software developers within bioinformatics rely heavily on data standards to more easily share information between researchers and software tools. One such standard is thy Synthetic Biology Open Language (SBOL), where you can describe genetic circuits, function, experimental data, and much more.
The SBOL is a growing community withing bioinformatics and an increasing number of software tools and databases support SBOL in one way or another. However, it is a complex data model and many users might need this channel to ask/answer questions related to SBOL and probably other data models in this area of research.
I want to propose to add a tag for SBOL, so that users of this community that do use standards can tag appropriately and get answers related to this data standard.
Thank you very much!

If there are no objections within a day or so remind me to create the tag.

Just to be clear (and maybe you already know this), there is nothing stopping users from adding the sbol tag to posts now. Questions about SBOL and related topics are certainly on-topic for this site, and we'd welcome more engagement from that sub-community. Things like tags and tag descriptions are typically an indicator of (not a prerequisite for) community involvement. But I fully support Devon adding the tag and a description so that it will appear as a suggestion and an auto-complete candidate for relevant questions in the future.

I just saw another question about modeling with SBML, and I added the tags systems-biology and sbml which had not existed before. Any user with ≥150 reputation can create a new tag. https://bioinformatics.stackexchange.com/help/privileges/create-tags

Perfect thanks. Yeah I don't have the rating to add tags yet. The other widely used standard for model simulations is SED-ML

Hello, @DevonRyan. This is a friendly reminder to add the SBOL tag. Thank you!

I'll add that now. Thanks @DanielStandage for adding the others!


text:
Would this be a suitable community to post Q&As related to the COMBINE community?
I'd like to inquire about using the bioinformatics exchange to post COMBINE related questions.  COMBINE, as describe in Wikipedia is: "COMBINE, the COmputational Modeling in BIology NEtwork, is an initiative to coordinate the development of the various community standards and formats for computational models, initially in systems biology and related fields."
The COMBINE community has grown over the last 10 years, for example there were 100 attendees at the recent COMBINE workshop held in Heidelberg. COMBINE includes a number of standards, including SBML, SBGN, SBOL etc. The feeling is that it would be very useful to have a stack-overflow location where users could ask questions related to any of the COMBINE standards. Rather than try to create our own stack-exchange we wondered whether it would be ok to ask COMBINE related questions to this bioinformatics exchange? Volume would not be large so it wouldn't flood the current exchange.
To be more specific, the COMBINE standards concern modeling (SBML and CellML), pathway visualization (SBGN), relevant ontologies such as Kisao or SBO,  and biological description formats such as SBOL and BioPAX. Of all the exchanges bioinformatics appears to be the most closely related.
The kinds of questions that would most likely be posted would include how to use the standards, what software supports the standards, technical questions about the standards, and how to contribute to the standards etc.
Here are some specific questions that could be asked:

How do I specify units in an SBML model?
How do I access libsbml from Python on Linux?
Does every SBML model have to have a volume compartment?
What's the easiest way to learn SBOL, is there an introductory document I can read?
What is the symbol for a small molecule when using SBGN?
What ontology would you recommend I use to describe numerical algorithms for modeling metabolic pathways?
How can I convert SBML into a Matlab function?

I think the answer is the same as that for https://bioinformatics.meta.stackexchange.com/questions/201/would-this-be-a-good-community-for-sbol-qa


text:
Would this be a good community for SBOL Q&A?
The Synthetic Biology Open Language is an open representational standard for encoding biological designs. As this community has been growing, it has been trying to figure out a better way than FAQs to compile ongoing Q&A expert knowledge about how to use the standard for representing designs.
As a long-standing contributor on Academia.SE, it seems to me that Bioinformatics.SE might be a good place to start building up such a Q&A compilation, adding tags, etc.  We would only want to do so if this community would find it to be on topic.
Examples of questions that might be asked would be:

How should I represent growth media in SBOL?
In SBOL, how do you distinguish a circular plasmid from linear DNA?
How do I represent a sequence deletion in SBOL?
Do I need to include intermediate gene products like mRNA in order to express a gene regulatory relationship in SBOL?

I had also considered Biology.SE and asked a meta question there, but have received an opinion that focus on representation would be too data-centric and not biological enough for that community. I do believe that here would be a better place for this than StackOverflow because the questions are more about structuring knowledge than about programming.
Bottom line: would Bioinformatics.SE be receptive to an influx of SBOL practitioners asking and answering questions about this topic?

I think that sounds like a great idea. I doubt we currently have the expertise to answer such questions here, but if you bring in the experts who can answer as well as the folks needing help, then I don't see why not.
In principle, SBOL seems like it does indeed fall under the scope of computational biology and/or bioinformatics, and we can certainly handle a larger volume of questions than we have now. So yeah, assuming other people also agree, bring it on!


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When can we get out of the Public Beta?
We have been in the beta for more than 700+ days. What is the procedure and requirements to get out of the Beta stage?

There is no clear rule for this. Some sites have remained in beta for several years. For example, Board & Card Games has been in beta for 8 years and 7 months, since October 2010.
Being in beta means we don't have the same reputation thresholds for the various site privilege as graduated sites. Which is a very good thing, we aren't ready for that yet. We only have one user at >10k rep (which is what gives access to the moderator tools on graduated sites, it's 2000 for betas), no users past 20k rep (the threshold for full access, 5k on betas). Most importantly, we only have 9 users with >3000 rep, which is what is needed to be able to cast close and reopen votes, the most essential part of site maintenance.
So, if we were to graduate tomorrow, there simply wouldn't be enough users with the required rep to do site maintenance. But this isn't a problem! It doesn't mean we are at risk of losing the site, we can happily stay in beta for as long as needed.
Some relevant discussions on the main meta:

Feedback Requested: Design-Independent Graduation
Should we rename or remove the "beta" label?
Can we do something about the "graduated" label?
Graduation, site closure, and a clearer outlook on the health of SE sites

I think that the most blocking part is the low amount of questions. With such low number just 9 users are capable of maintaining the site well.

The number questions are low I agree (I think it has increased from 2.2. to 2.3 since I've been here), although I'll be citing BioinfoSE in Acknowledgements ... so little by little.

The amount of questions are low due to BioStars.org and Biology SE. The former is looking more and more dated, but the community is more active. So the growth will be slow... About Biology SE are we supposed migrate questions from there to here and if so how?? (example: 1, 2)

Just to note, the number of questions per day is steadily rising, or perhaps more accurately has recently jumped. When I first joined the site, not so long ago (less than 6 months), it was 2.2/2.4 questions per day and has currently jumped to 2.8 questions per day. As long as that trajectory continues, then this is a stable beta, which in the fullness of time would be expected to be a full site. I don't think there is any reason to hurry.

As of today it is 3.3 questions per day ... its a non-linear function, my favourite

Woooaaa wait here today September 26, 2019
The number of vists is 1,517 (!!) ... so the site now has two scores of "Excellent".
The number of questions is 3.1 per day ... so whilst ever it on the trajectory towards a full launch its is here to stay.


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It's a bad idea to delete answers that include criticism towards the question
I recently answered a question which was promptly deleted by a mod, I realized now. I know I am new in this site, but I have been a long time user of SE sites and I think this decision is flawed. Here's why:

First off I think my criticism is on point. Those of you who have been a SE user for a long while must have seen your fair share of such questions. They don't age well. This has been discussed over and over again..
Secondly, the answer actually addresses the shortcomings and potential pitfalls, with relevant examples.
Last but not least, I did finish off with actual advice which answers the question.

By deleting an answer like this, you are essentially making it unaccessible for new users as well as the OP. It's not like I could have fit all that content into a comment...
I think this is a case of overzealous moderation. If it was SO where you get thousands of questions, and many useless answers, I'd get it. But for a site in Beta, I think it's a bad idea.

First of all, thank you for coming here and posting in such a civil and calm way. That is very much appreciated and isn't always easy when you feel you've been slighted.
Here's what I was thinking when I deleted your answer. First, most of your answer was a critique on the question. While I don't disagree with any of the points you raised, critiquing the question isn't a valid answer. Also, even absolutely valid criticisms, as yours were, are likely to be taken the wrong way so I felt your post might lead to more drama than the question was worth.
Only the 5th paragraph of your post was actually directly answering the question and that was:

I would echo on the previous answer and suggest that you get a good laptop (enough cores and ram, good battery life, light to carry etc) and try to see if your institute has access to some computational resource. There are many national clusters that provide access to large number of nodes and/or nodes with up to 512GB (or more) RAM, redundant and practically unlimited storage. Possibly nodes with GPUs etc..

You are recommending a "good" laptop with "enough" cores and RAM. Presumably, if the OP knew what constituted a good laptop and enough cores and RAM, they wouldn't have needed to ask the question in the first place :)
So your answer looked to me like an attack on the OP. A mild, civil and justified attack, mind you, but still not something that belongs in an answer. And I didn't see that it was providing a specific answer which is why I didn't just edit the commentary out of it.

Here's a screenshot of the deleted answer for those who can't see it.

Sure, that's the only way to have a fair discussion :) But regarding the statement "Presumably, if the OP knew what constituted a good laptop and enough cores and RAM, they wouldn't have needed to ask the question in the first place" honestly if you dont know what constitutes a good laptop you have no business doing bioinformatics :)  In any case, I meant no attack but rather to give description of why the question is a difficult one to answer, and likely not relevant in the long run. I see your points, and respectfully disagree, but that's ok as long as I am concerned

Smiley or not, the comment "honestly if you dont know what constitutes a good laptop you have no business doing bioinformatics :)' is a form of gatekeeping that is generally not helpful.

Your answer contained no concrete hardware specs.
Questions like that usually get closed due to being "opinion based", which is fair enough. Though I'll note that there needs to be a place for those questions and if a site like this ever wants to dominate bioinfo Q&A then it will need to address such things every year or two.

There actually is a site for this: [hardwarerecs.se].

Sure, but you'd figure the people in a given community would generally give better recommendations.

Ah right, I thought you were suggesting that there should be a place that isn't this one. I guess we could do hardware recommendations if the question were specific enough. Something like "I will be analyzing whole exome runs of human, and will need to store N samples' data, what do I need?". If it is specific enough to have a definitive answer, I don't see why we can't field it here.

I don't think "doesn't age well" is grounds for question deletion, especially in a Bioinformatics setting. That criticism applies to a lot of the answers that I've given.
When I've noticed that an answer is popular and includes out-of-date information I update it. This is allowed, and seems to be expected. Things change over time, opinions change, and different solutions bubble up as people discover better ways to do stuff.

Having read the responder I support the site admin for deleting the post as part of its long term direction.
The thing about the Bioinformatics site is that it is very notably less aggressive than the much larger "Stackoverflow" site. This is fundamentally why I quit getting involved there, not for want of expertise. There are some legends in the coding world that routinely post on Stackoverflow: David Cross is almost as famous as Damian Conway in Perl and routinely contributes. In fairness some posters on that site are persuasively encouraging "Modern Perl" against the tide of Python/Javascript (Cross is one), but there are routine posters who are just plain rude.
There is no problem with "aggression" if you are right, but if what you are saying is possibly opinionated or else not exactly the whole truth is a bit off-putting. I've given an example below.
From a technical point of view, I like the responder here pointing out GPU. There is no doubt this is a correct answer in specific context, but there was no underlying explanation about what GPU was about. GPU is very cool and a GPU cluster very, very trendy in Tensorflow calculations, but the OP needed to be informed of the calculations where GPU is required, and what the whole GPU rather than CPU thing is about. I thought GPU was for gamers until I got involved in Tensorflow.

Example
A good example of "aggression" concealing a informatics truth is the question

"Can I hide my Perl code from prying eyes"

The answer is a resounding "yes" there are quite a few ways to do this and if layered would really lock it down, but the Perlish response is "no its open source" and everyone applauds. Now this answer isn't true, but no-one wants to describe the ways to do this because the responder saying "no its open source" will attempt to unpick the proposed solution and this defeats the entire object of concealing code.


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Proposal: remove [filtering] tag, replace with [quality-control] when appropriate
As of 2019-01-28, there are 16 posts tagged with [filtering]. This is an ambiguous and, at least in some cases, unhelpful term. Some of these posts are about quality control, some are about ranking, some are about data sampling, and some are about eliminating redundancy.
I propose we eliminate the [filtering] tag. The [quality-control] tag can replace it as appropriate, while in many other cases it can probably just be removed.

I'd suggest the following changes

Replace [filtering] with [quality-control]:

Output from vcftools missingness
Delete all 4 lines of a fastq read from a fastq file using read ID
Error filtering SNPs with Plink
Single-cell RNA sequencing (scRNA-seq): filtering cells by transcript counts, how to choose cutoffs?
Filter out outliers of the scRNA-seq (heterogenous cells)
Filtering step for read counts data

Remove [filtering] tag; these are about reducing sequence redundancy, which (as common as it is) probably doesn't warrant its own tag

How do I find identical sequences in a FASTA file?
How can longest isoforms (per gene) be extracted from a FASTA file?
How can I extract the longest N isoforms per gene from a fasta file?

I'm not sure about the remaining posts. Some might be improved by dropping the [filtering] tag, or by replacing it with a different tag, or maybe it's the best term to use and we should simply clarify usage on the tag wiki.

How to safely and efficiently convert subset of bam to fastq?
Filter BAM file for read pairs where one or both of the reads starts with a given sequence pattern
How to filter Ensembl cDNA and ncRNA FASTA files by primary assembly?
Select top 100 genes ranked by variance in read counts
Why does a very strong BLAST hit get lost when I change num_alignments, num_descriptions or max_target_seqs parameter?
Filtering out all seqs with mutations of list2 from list1
Any fast options to query large VCF bed intervals?

I agree that filtering isn't a very good tag, but I don't think quality-control covers it either. For instance, removing specific reads from a fastq file doesn't seem to come under quality control (although the specific question you cite was indeed a quality issue). Maye we need a parsing tag?

Well, it depends on why one is removing reads. If you want to reduce the size of the data, it's sampling. If you want to get rid of contaminant reads, it's quality control. If you want to more closely examine reads with particular nucleotide composition, that's...filtering? There are a lot of operations we can do on read data (or any data)--sorting/ranking, sampling, deduplicating, etc.--and not all of them need a tag.

I guess? Maybe we should just stick to the relevant format tags (fastq, sam, vcf, gff etc) and leave it at that?

What was the outcome of this discussion? I have pretty strong opinions on this topic but don't want to make a fuss if it's already been decided and dealt with.

@Geraldine_VdAuwera Please do share your opinions in an answer. I'm less sure of my initial assessment, and I certainly don't think the mods/high-rep users ever converged on a consensus.