text:
2020: a year in moderation

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

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

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

Action
Moderators
Community¹

Users suspended²
3
5

Users destroyed³
4
0

Users deleted
3
0

Users contacted
3
0

Tasks reviewed⁴: Suggested Edit queue
18
328

Tasks reviewed⁴: Reopen Vote queue
1
38

Tasks reviewed⁴: Low Quality Posts queue
6
223

Tasks reviewed⁴: Late Answer queue
3
86

Tasks reviewed⁴: First Post queue
2
713

Tasks reviewed⁴: Close Votes queue
6
609

Questions unprotected
0
1

Questions reopened
3
0

Questions protected
0
4

Questions migrated
6
1

Questions flagged⁵
0
192

Questions closed
44
87

Question flags handled⁵
125
67

Posts unlocked
0
3

Posts undeleted
1
22

Posts locked
0
9

Posts deleted⁶
71
367

Posts bumped
0
418

Escalations to the Community Manager team
1
0

Comments flagged
0
70

Comments deleted⁷
132
535

Comment flags handled
61
9

Answers flagged
0
193

Answer flags handled
164
29

All comments on a post moved to chat
1
0

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

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

You can also check out this report on other sites

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

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


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

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

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

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

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

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

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

source: Stack Exchange

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

sort: votes


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.

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


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.


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

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

I think you would be great!

Thank you, @KamilSJaron

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

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

I thought you already were a mod!

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

Did you resign to get elected twice?! ^^

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

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

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

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

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


text:
Questions about commercial products where there are official support channels
Though inspired by this question, this tends to come up more often in relation to CLC Workbench. On occasion, people using commercial closed-source packages will post questions about using said tools or analysing their results. 99% of the time these products already have official support channels that the posters will have already payed for but either aren't using or have just hoped that we will respond faster (therefore performing the role of the company for free).
I personally am very much against answering such questions, since it has the perverse incentive of promoting companies not providing support for their products. Over on biostars we generally post something of the form, "This is a commercial product, you're already paying for support, ask the company". I would be in favor of a similar strategy here. Thoughts?
Note: The question that inspired this is not a great example, since the product in question is a wrapper around standard open-source packages. Nonetheless the site will inevitably face other examples in the future.

Personally I don't think we should restrict asking questions related to commercial products if the questions/answers could be useful to the community. However, practically speaking providing good answers may often not be possible if the products are black boxes without open-source code etc.

I think it is OK to ask such questions, users of productX might be here and have a quick answer. Or the support team of the productX might be here, too. Better to have answers here public, rather than buried in productX members only forums.

Here is the Help Center guidance about supporting your product on this site.

I would actually encourage bioinfo companies to use this SE as a Q&A platform. IMHO, this will benefit both the companies and the users, no matter whether they are using their products or not. Stackoverflow has sponsored tags and welcomes companies (to bring money :-). I don't know if SE has a similar feature.

If they actually came to the site to answer questions then I'd be all for it. Experience dictates that they won't, unfortunately.

@DevonR I would give it a try. The better tagging system here might change something. Some companies seem to be using SO often. In addition, we could encourage companies to reply here, which may help. Well, wishful thinking?

Better hopeless optimism than the opposite :)

Even though I'm a supporter of free software, I do not see a problem in answering those questions.

It is hard to define the boundaries. Proprietary software can be only a part of the pipeline (e.g. Affymetrix, Ofxord Nanopore), or can be a somewhat standard tool (e.g. PAUP, many pop.gen tools, etc).
Stackexchange doesn't have any policy against commercial software or libraries; see here.
I do not see a problem if a commercial company will answer questions write here. This will be helpful.

Having said this, it is also ok to point out to the person, that he or she can contact their support.

MinION users have official support channels and a community forum, but I'd much rather that users asked questions about MinION data analysis in a public forum. ONT has done about 3 community forum backend changes in the last 4 years, and haven't been all that interested in preserving the past history on the new forums. When the question can only be answered properly by communication with the company, I encourage the asker to contact ONT support (e.g. see this question about basecalling in the field).


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Tag [file-formats] or [data-formats] to replace [formats] tag
As of now, 5 questions have been tagged with formats and since bioinformatics in practice is 80%+ file format conversion, we can expect many more such questions!
I jest about the 80% bit...kind of...
Either way, it's important to get this tag right early on to set the appropriate tone. Just formats strikes me as a bit vague, and my first thought was to replace it with file-formats. But one could argue that this topic is relevant for converting data between different formats, even if the data is never stored in an actual file (such as in streaming processing). So perhaps data-formats is a more accurate term?
I worry that the latter, while technically more accurate, might be a bit pedantic and a turn-off for newer members of the community.
UPDATE:
Ok, I re-tagged 6 posts. Edits pending approval.

You mean it's actually 90%, right? :P

My vote goes to file-formats. While you can argue, as you did, that data-formats would be more accurate, since most of us are working on *nix systems where, famously, everything is a file, I think we can wing it with file-formats.
After all, even a pipe is actually a file, really. More to the point, as you said, the distinction is rather technical and I think we should err on the side of not confusing novices as opposed to appeasing the pedants.
In any case, formats is a classic meta tag. Formats of what? Who formats and what are they formatting? No, file-formats seems far better and instantly understandable by novice and expert alike.

I was uncertain when I started writing the question, but I had all but made up my mind by the time I finished writing it. I agree, file-formats is the way to go. I'll leave this open for a bit longer to give time for dissenting or alternative comments, then I'll clean up the tags.

@DanielStandage by the way, thanks for all these tag posts! They're a pain to write but essential if we're going to have a useful tagging system. Much appreciated!

No, I don't think we should rename "format". To me, "format" is instantly the first tag I can think of when dealing with file formats. Users will use the "format" tag from time to time anyway. In fact, if you search "format" at SO, "format" and "formatting" are by far the mostly used tags.
In addition, if you think "format" is meta-ish, "file-format" is, too, just in a little narrower scope. You still don't know whether a question tagged with file-format is about a gene annotation format, an alignment format or a variant format.


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


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Make tags [read-mapping] and [alignment] synonyms
As far as I can tell, there is no noticeable difference between the tags read-mapping and alignment. Three of the fifteen questions under these two tags use both tags, and the rest seem too similar to warrant any separation.
EDIT: Clearly I had failed to notice the quite significant difference between these terms. However, the ambiguity of the alignment tag and the way in which it is being used should be fixed. Terdon's answer below gives a good resolution of this issue.

No! When I hear "alignment" I will immediately think of protein or nucleotide multiple sequence alignments. I mean what is done by tools like t_coffee, mafft, clustal etc. That's what the word always meant when I started working in bioinformatics and I am sure I am not alone. Not everyone works in NGS analyses, you know :)
I would instead argue that precisely because the term alignment is not specific and can apply to many things, we should instead make more focused tags. So, we should have:

read-alignment : This should be a synonym of read-mapping (relevant meta post) and should be used for questions about aligning NGS reads to a genome.
sequence-alignment : this should be used for questions about sequence alignment (including protein, DNA and RNA alignments).

The alignment is a classic meta tag since there is no way of knowing what type of alignment it is describing without an additional tag to clarify. it should therefore be removed and not used at all.

I think these tags are two different things. Reads mapping refers to a process when sequencing to find the position of a read to a reference genome while alignment is comparing two (or more) sequences.
Both can be DNA, but one can align also proteins, but I haven't heard of read-mapping proteins. For instance one can align some orthologous or paralogus genes/proteins which don't need to be reads.
That said, the excerpts should make clear the distinction (if the community agrees with this) to facilitate the usage of the right tag.

That's fine until someone wants to make salmon or kallisto-specific questions, since there the distinction between mapping and alignment is clear.

I’m not even sure I’d call Salmon etc. mapping tools; rather, they’re alignment-free quantification tools. But it’s certainly true that kmer-based identification (or similar methods) is mapping, yet not necessarily alignment.


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Q&A-style answering bug where "40mins between questions" hidden by answer box
When posting a Q&A question, the warning that you can't post within 40mins of previous post is hidden by the "answer" portion of submission.  When the answer section is there (i.e. the box has been ticked) and a post is submitted, the page refreshes with seemingly no error message.  Once I unticked the "answer own question" tick box, the error message about rapid posting came up.
Ironically, I can also not post the bug report here, until 40 mins is up ;).


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Should we allow questions where the title is not a question?
I think there are too many entries where the title is not a question.
Related discussions:
How do I write a good title?
Should question titles be phrased as questions? (A straw poll)

There's no reason to require that titles be questions. That's just going to make them longer than always needed.

OK. I was under the impression that titles had to be questions, but apparently that's not the case.

I very much prefer titles to be a fully formed question, yes. However, requiring it goes a little too far, I think. I also disagree to some extent with the related discussion “How do I write a good question title?”, which exemplifies my grievance: I believe that, contrary to what answers there claim, starting a title with “How do I …” is not only OK but actually desirable: it focuses the subsequent discussion. “fooing the bar” invites so much more discussion than “How do I foo the bar?” in my experience.
For context, I’m often editing unclear question titles on Stack Overflow, and 90% of the time1 the title becomes much clearer when phrased as a question.

1 Admittedly I just made that number up. But it feels right.

I take your point, but where this is a problem, it's more that the "question" isn't a question or doesn't make clear what the exact question is. The title is just a symptom.
Looking at it another way, there are many suitable titles that aren't strictly questions (e.g. "Limitations of single molecule sequencing", "Searching for gene expression data by cell line", "Visualisation of long read RNA-Seq splicing"). Insisting on a strict form is wasted effort.

Thanks, yes I agree.


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

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

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

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

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

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

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


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[alignment], [sequence-alignment], [read-alignment] and [msa] tags
Let's decide here on the status for different tags related to alignment.
There are two groups of questions.

One is related to pairwise and multiple sequence alignments and algorithms. This field is definitely old and it was one of the keystones in the bioinformatics development. You get question like alignment tools supporting codons, RNA alignments editing or full genome alignments.
Another one is related to read alignment/mapping. We mostly get mapping software related questions like obtaining uniquely mapped reads, BWA-MEM scoring or  building genome index.

Of course read alignment is a series sequence alignment steps. In practice, however, most of the current [alignment] questions are specific only to read mapping software, and has nothing to do with sequence alignment methods.
I think we need to think about tags pragmatically, it is a way for people to follow what they are interested in, and clearly these two areas are of interest for different people. In that line, it is worth noting that meta-tags are considered useless and should be avoided.

If the tag can’t work as the only tag on a question, it’s probably a meta-tag
If the tag commonly means different things to different people, it’s probably a meta-tag

These are the results from our quite diverse lab, where some people are working with RNA-seq data. Clearly just [alignment] is ambiguous.
In the current form [alignment] is a meta-tag.
Meta-tagging is explicitly discouraged.
I see two ways of dealing with this.
Two separate tags
For the read alignment I propose using [read-alignment] tag. It's unambiguous.  Using [alignment] wouldn't be fair because a) sequence alignment preceded read alignment b) some people (including me) still think about sequence alignment by default c) if you search google scholar for "alignment", four out of five top results will be related to sequence alignment.
For the sequence alignment I propose [sequence-alignment]. I wouldn't use [alignment] for the same reason as above (it's ambiguous). [msa] is a poor choice, since msa is considered to be an extension of pair-wise alignment.
Use [alignment] only for the sequence alignment
In this case we have to remove the [alignment] tag from all the read-mapping questions, where the alignment itself is not a problem. Maybe replacing it with [read-mapping] in some cases.
What are your suggestions?
P.S. It goes without saying, that a question related to both read alignment and sequence alignment could be tagged with the both tags. E.g. "Is it practical to use Smith–Waterman algorithm inside XYZ-mapper".

Please don't downvote this question if you disagree with the proposal. The question is basically asking what to do. If you feel that keeping a single tag and keeping it named alignment is the right option, then downvote my answer, not the question.

I am folding my previous answer, EDIT and comments into this new answer.

sequence-alignment includes read alignment. This is both conceptually and practically correct. The most widely used read alignment format is SAM, which is an acronym of "Sequence Alignment/Map" format. i.e. SAM is a sequence alignment format. This naming was unanimously approved by the 1000g committee consisting of many top experts in the field. Having worked with various sequence alignments for many years, I simply can't accept we exclude read alignment from sequence alignment.
The biggest problem with sequence-alignment is that it means different things to different people. Those in phylogenetics may think it means traditional alignment exclusively. Those who have only worked with NGS data naturally think of read alignment. In fact, this tag includes both fields. Forcing this tag to only mean traditional alignment is a wrong thing we should stop populating. It will also lead to confusion to NGS people.
A meta tag is an excessively broad or excessively ambiguous tag. Telling excessive broadness and ambiguity is sometimes subjective. An obvious meta tag (e.g. "best practice") can be put on almost all questions without narrowing the questions down to a specific field. Currently, we have two less obvious meta tags text and reference due to excessive ambiguity. text does not represent a field in bioinformatics. It could mean text mining or text processing, two distinct fields. Similarly reference could mean reference genome (I have retagged all questions taking this meaning) or literature, again two distinct topics. Importantly, a tag is not necessarily meta if it can be divided to more specific subfields. Actually, a true meta tag often can't be subdivided because it lacks a clear scope.
To me, alignment is not meta because it clearly defines a subfield in bioinformatics. If we think "alignment" is meta, "read-alignment" would be meta, too, because it includes both DNA read alignment and RNA read alignment. I can't just follow read-alignment if I am only interested in RNA-seq. In addition, alignment is frequently a safe fallback tag when the asker is not familiar with the different types of alignment. I predict it would keep popping up with time even if we retagged all current questions.
I don't think there is a right terminology for "alignments that are not read alignment" because each other type of alignment belongs to its own field and often uses distinct algorithms (at least partly). I think at the current stage, the best we can do is to create a tag for a smaller category of "traditional alignment". I propose to use "msa" (with "multiple-sequence-alignment" being a synonym) for MSA, "rna-structure-alignment" for RNA structure-aware alignment and "full-genome-alignment" for genome-vs-genome or assembly-vs-genome alignment.

Conceptually bioinformatics is biology, and why do we need a separate SE? :)
From the practical point of view, I suggest you check the questions. They are conceptually very different and most of current [alignment] question have nothing to do with the sequence alignment itself.
Also, I explain why msa is not a good choice of tag. Otherwise we should have another one for pairwise alignment, which sounds too specific.

In any case, [alignment] in a current form is a meta-tag. We should do something about it; and introducing msa doesn't solve the problem.

Yes, but not to everyone and tags should be understandable in the same way by everyone irrespective of their subfield. So since alignment can and does mean different things to different people, it isn't a good tag. You are an expert in the field, so of course you understand that read alignment and sequence alignment are essentially the same thing. Others, however, can be confused by this. Plus, the word is so ambiguous that I'm willing to bet we'll end up having people tagging questions about left-aligning variants or even printf output with alignment.

@user172818 I agree completely that [alignment] is a correct term. But it doesn't make it a useful tag (e.g. I would probably subscribe to [sequence-alignment], but not to [read-alignment]). I know that you have a proficient experience in both, but it doesn't mean everyone does; you can subscribe to both. And again, when read-alignment problem is really boils down to sequence alignment, one can use both tags. Tags are not about ontology, it's about filtering the content. Could you have a look at the blog post on meta-tags?

@user172818 There are two separate issues here: i) whether we should have separate tags for "traditional" sequence alignment and short read alignment and ii) what should those tags be. My main issue here and, I think, Iakov's, is that we need separate tags for the two. What that tag should be is debatable but I feel very strongly that we need to have different tags for these two types of alignment. Now, using sequence-alignment and read-alignment seems the most natural and obvious to me. That doesn't in any way suggest that read alignment is not a form of sequence alignment!

[cont] Of course reads are sequences and aligning them is a form of "sequence alignment". But that's not what most people would think of when they hear the term "sequence alignment", I think. Most of us would think of Clustal & co and not BWA & co. But we could have another wording if you like. As long as we have two separate tags for it.

As for alignment by itself, that is a meta tag. The definition is not subjective at all: it is a tag that, by itself, does not define what the question is about and needs a second tag for clarification. "Alignment" is ambiguous. It can refer to aligning NGS reads, whole genomes, proteins, genes, RNA, structural alignments, left-aligning variants. . . And it has meanings outside jargon, in everyday language as well. This is not a good tag.

@user172818 then let's use different names! All I am really arguing in favor of is to not have a single tag describing "traditional" sequence alignment and NGS-style aligning of reads to a genome. If your objection is only to using the tag sequence-alignment only for the former, then let's use another name for it. How about multiple-sequence-alignment and read-alignment? I would argue against genome-alignment since that could be for aligning genomes, and against msa since that's not very descriptive.

I don't see an easy distinction between sequence-alignment and read-alignment. It could perhaps be argued that if someone is mapping and aligning lots of reads to a genomic reference, then that's read-mapping, and if alignment is not being done at the same time (e.g. Kallisto, Salmon), then that's quasi-mapping or pseudo-alignment.

I agree with this. To me the word alignment will always mean aligning sequences to each other and not aligning reads to a genome. Yes, the two are not really different under the hood, but that's not the point. Tags serve two main uses:

They make it easier to search for topics;
They help experts find questions they are interested in (through marking a tag as a favorite).

Although the underlying methods involved in both multiple sequence alignments and read mapping are not fundamentally different, the tools used for each are. Also, the people interested in each and knowledgeable about each are not always the same. I, for example, am far more familiar with sequence alignment than with aligning reads.
So, given that we have two sets of not necessarily overlapping experts and two different subjects, having two tags makes sense. The tags should serve to clearly mark what a question is about. Tagging something with alignment is not really informative since we don't know what kind of alignment we are referring to. In general, I am in favor of making tags be as descriptive and unambiguous as possible.
I would therefore be in favor of using sequence-alignment for multiple sequence alignments using tools like t_coffee of MAFFT and read-alignment for tools like bwa or bowtie that align reads to a reference. We should then remove the alignment tag since it isn't enough to explain what a question is about by itself.


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


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How do we feel about questions that are essentially about text parsing?
A lot of the daily tasks of a bioinformatician can be boiled down to simple text parsing. Yes, we will be dealing with text files containing some form of biological data, but the answer might not really require any biological knowledge at all. For example, this question was posted on Unix & Linux today:

I have 2 files. File1 is:
chr19 4124051 4124250 1
chrX  154458151   154458200   2
chr22 37019451    37019600    3
chr15 74995401    74995550    4
chr12 128823901   128824100   5

and File2 is:
chr19 4124051 4124250 1   CUP
chr15 74995401    74995550    4   CUP
chr12 128823901   128824100   5   CUP
chr12 122752651   122752950   8   CUP
chr13 113297001   113297350   9   CUP

and I would like to have a File3 like this:
chr19 4124051 4124250 1 CUP
chrX  154458151   154458200   2
chr22 37019451    37019600    3
chr15 74995401    74995550    4 CUP
chr12 128823901   128824100   5 CUP

I'd like to merge the two files according to column 4 of File1, and
  adding values of column 5 from File2 to the last column of File1
  whenever there is a match.

This is obviously someone working in bioinformatics but the question itself is not really about bioinformatics. Nevertheless, it is relatively typical of the type of thing a bioinformatician does every day.
So, should we allow such questions even if they could be answered by anyone with knowledge of regular expressions and basic text parsing tools? If the question is one that a bioinformatician could encounter, should we consider it on topic even if it can be expressed as a general text parsing issue?

I think as soon as we mention the tool we want to use, it should be off-topic and worth migrating? Otherwise we will just be duplicating content over SE network?

@zx8754 first, the OP often doesn't know the tool. More importantly, the issue with text parsing Qs is that they are very often specific to the particular data being parsed. So duplicates aren't that clear. Also, I know I spend a lot of my time doing this sort of thing and very often help colleagues with it. Text parsing is very relevant to bioinformatics. Finally, there are sometimes considerations that a layperson won't be aware of (I can think of FASTA parsing questions, for example, where the OP didn't explain that the sequence can span multiple lines). Those are better served here.

Yes, agreed, if OP doesn't mention the tool, then it will be OK, as it will collect all solutions using different tools. But once the tool is specified, then regardless of bio knowledge anyone with particular tool proficiency would be able to answer the question, hence duplication over SE network and needs migrating (and most likely dupe hammered). Besides, I think most of SE traffic is coming form Google searches, so why would it matter which SE the Q is posted.

@zx8754 actually, we never migrate away a question if it is on topic on the site where it was posted. If we decide these are also on topic here, they should not be migrated. The only case for migration would be if we decide they're explicitly off topic here.

I would say we should allow these, yes. I opened a similar discussion about questions pertaining to biology and the consensus there seems to be clearly in favor of allowing them.
I feel this site only makes sense if our scope is essentially "Any question that a bioinformatician might face in the process of doing their job". We should aim to be a one-stop site for all questions that could be affecting someone trying to do bioinformatics. And since so much of bioinformatics is essentially parsing text files, it makes sense to me to allow them here.
I have seen such questions all over the place in the Stack Exchange network over the years. They are posted on Stack Overflow, Unix & Linux, Ask Ubuntu, and probably other sites too. I think all of those should come here and find a home.
Naturally, this would only apply if the text parsing in question is somehow connected to bioinformatics and not something like extracting text from a movie subtitle file or whatever.

Agreed with the explicit caveat that the text being processed should have at least a vague relevance to bioinformatics/biology. We don't want questions related to using grep to find something specific in /etc :)

@DevonRyan yes, of course. I added a note to that effect.

I agree, plus, I think often it takes a someone with a clear understanding of the file format to provide a good answer. For example, this SO question made no reference to bioinformatics until I added some tags and it was only then that it got a good answer (from Konrad). Other answers clearly didn't understand that FASTA permits multiple sequence lines https://stackoverflow.com/questions/44264127/filtering-a-weird-text-file-in-python Sometimes it's even worse and the OP actually describes the file format wrongly, so it takes a bioinformatician to know this and provide the correct answer

@Chris_Rands yes, precisely. I have often had to clarify such things to people answering bioinformatics-related parsing questions on [linux.se] too.

On one hand, posting this kind of question in Unix & Linux SE or stackoverflow may cause general and/or very efficient solutions to show up, due to the presence in those communities of people quite capable with general text handling skills.
On the other hand, such people might not be aware of bioinformatics tools specifically designed to efficiently solve the problem. If such tools exist, contributors to bioinformatics SE are more likely to know about them, and the answer may be of interest to a higher proportion of the readers here than in stackoverflow or Unix & Linux SE.
It is of course up to the poster to decide whether to post here or in another site, and I think we should probably accept such questions if we think that my "On the other hand" point is relevant, that is, on the basis that someone may come up with an answer based on the use of a tool specifically used in the bioinformatics field.

Of course it is up to the poster! That's not debatable. The question is whether we will consider such topics on topic here or not. Any form of text parsing question is already on topic on sites like [so], [linux.se], [ubuntu.se] and even [apple.se], [su] and [elementaryos.se]. We're not going to move them if they're on topic where they were asked. But should we accept them if they are asked here?

I would say that we should generally accept them on the basis that they can be of interest to other bioinformaticians, and especially on the basis that someone may provide an answer based on specific tools for bioinformatics.

Yes, me too. Could you edit your answer to clarify that that is your position then please?

I tried to edit my post accordingly.

I think we should accept these questions, if they relate to biological data, for two reasons:

The answer might reasonably be of interest to other bioinformaticians (This is mentioned in other answers).
An acceptable solution might reasonably use a framework commonly used in bioinformatics, but not by anyone else. A hypothetical example: One could imagine that an acceptable answer converts the files to BED format and then merges them using bedtools.
On other SE sites I would consider using bedtools for anything as too specific/off-topic.


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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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Are questions about installing bioinformatics tools on topic?
Should we allow questions asking for help installing specific tools? Some of the tools that are commonly used in bionformatics are non-trivial to install. They can require other packages, environment variables etc.
On the one hand, the programs are indeed specific to bioinformatics, on the other hand, the issues faced when installing them could be applicable to pretty much any program distributed in similar ways.
So, what do we do? Is "I am trying to install GATK and get this error" a valid topic for us? Should we send them to existing tech support sites of the SE network, or do we keep them here?

Just a reminder that some tools don't have support sites, and the support (if any) is contacting with the authors of the tools

@Llopis I was referring to other sites on the Stack Exchange network where software installation issues are on topic. Places like [su], [unix.se], [apple.se], [ubuntu.se] etc. I edited to clarify.

I vote yes, since I totally agree that some of these are a real nightmare to install (I'm not laying blame, I'm also responsible for this). As always, as certain amount of, "Here's what I've tried" should be expected. At least if we answer these here they'll be picked up by search engines, the same can't always be said for other random forums.

I would say yes, too.


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Should pure statistics questions be on topic?
This question was prompted by differential gene expression complex design no replicates.
While that question isn't very clear, it seems to be essentially asking for help on applying statistical methods to get a result. It isn't asking for help on a bioinformatics method, but for help on choosing the right statistical approach to analyze the results of a wet-lab experiment (RNAseq). If this were asking for bioinformatics methods for analyzing RNAseq data, that would be fine, of course, but if the OP is requesting for help on choosing the right statistical approach, do we consider that on topic?
Note that if the answer requires you to understand the underlying biology, then of course it should be on topic. I am thinking of situations where the details of the dataset are irrelevant and the question is one of pure stats which could be aplicable to any field.

I generally agree with @Ian Sudbery, but I would phrase this as I would prefer that the site's purview be "anything an expert bioinformatician might reasonably know that has at least a tangential relationship to bioinformatics". This would include statistics, biology, and some more general CS related questions provided they have some clear relationship to bioinformatics.
I should note that this makes it exactly the same as biostars, the scope of which some people don't like.

My feeling about the distinction about here and biostars is that biostars is explicitly aimed at beginners, where as I feel it would be useful if this could be a place where experts found it useful to ask questions as well as answering them. Questions where the answers wouldn't be completely obvious to anyone who had been in bioinformatics for a while, but required properly specialised knowledge about a sub-area, weather that was the stats of an unusual datatype, how to implement a particular algorithm efficiently, or a genome annotation feature particular to a specific species/assembly.

I think the scope of biostar is good. It is the other things that concern me more.

I'm not sure how explicitly biostars is aimed at beginners, but it's certainly become that way.

@IanSudbery ideally, we should be able to do both. I mean both help experts and help novices. I don't see the two as mutually exclusive.

DevonRyan: I'm sure I'd seen that somewhere, can't find it now though. @terdon absolutely, I'm just commenting on the idea that also supporting experts could be something that distinguishes us from biostars (even if biostars not supporting experts is by accident rather than design).

I think stats if very much on-topic. If we want the site to be useful for experts to ask questions and get informed answers from other experts, rather than a site where newbies are just instructed on how to install a piece of software, or where to find the limma manual, how to convert one file format or one gene id format to another (and other sites already fill this niche, then I think many of these will effectively be stats questions.
There is already an SE site dedicated to statistics, but in my experience questions that are about the stastics of bioinformatics rarely get helpful answers there. Partly I believe that this is because by the time you've explained the requisite bio background to understand the question, people have switched off. Here we get better engagement.
For example, I asked effectively the same question on here and on cross-validated.. After nearly 2 years the cross-validated answer has no useful responses, while the one here got answers very quickly.
Of course this is probably related to how you view bioinformatics, which I basically regard as a branch of applied statistics these days.

I am thinking about situations where the bio part of the question is irrelevant. if you need to understand the underlying biology to be able to answer the question, then it belongs here. No argument there. If, however, the biology is irrelevant and the question is one of pure stats, then I think it belongs elsewhere. I'll try and edit my question to make that distinction clearer. That said, I personally view bioinformatics as theoretical biology and absolutely not as statistics. Of course, that's because my background is in biology.

Take a look at my questions linked - its basically pure stats (how do a characterise the relationship between two spatially resolve count variable with high amounts of missing data). But unless you can explain why you are trying to do that, you don't get any answer other than "why on earth would anyone want to do that".
What is theoretical biology other than mechanistic modelling (which I grant isn't stats) and statistical modelling.

I'd say your question is on topic, yes. But that's because it is about a particular type of data whose characteristics you need to know in order to deal with it. In other words, a typical example of a case where you need to understand the underlying biology in order to provide an answer. Note that the answer you got is basically "use these standard bioinformatics tools" and not "use this stats method". (I won't answer the "what is bioinformatics" question here since it would derail the discussion; happy to chat about it though!)

Most of the answers did suggest using existing tools, but I didn't find those answers useful, there were generally answering a different (but related) question.The two most useful answers were the second half of CloudyGloudy's answer and Sasha Favorov which pointed to a preprint dealing with the same problem (which is a very stats heavy paper).

Well, my main point is that any answer you receive would require a relatively deep understanding of the kind of data you have and therefore your question isn't purely about statistics. Have a look at the one I cite in my  question. That looks like it can be answered by any statistician. There's no need to know about RNAseq, it's essentially an issue of comparing data points.

I left an answer for the question you referenced just before I saw your post here. I'm not sure its true that any statistician could answer it. You'd need to know, for example, that RNA-seq data is negatively binomially distributed, that log TPM can in some cases be estimated by a normal, that the model is likely to need to be fit to many thousands of genes...

Fair enough. That might not be the best example then. But do you feel that questions that can be answered by any statistician without needing to udnerstand the details of the experimental method used should be on topic?

Sure, if someone came on and asked "How do I carry out a t-test?" or "how do I use R to fit a normal linear model" then that absolutely wouldn't be on-topic.

Yes, those are the types of question I am thinking of. I tried to make that clearer with my edit: "Note that if the answer requires you to understand the underlying biology, then of course it should be on topic. I am thinking of situations where the details of the dataset are irrelevant and the question is one of pure stats which could be aplicable to any field."

Okay, sure. I'm interested though why your response to this question is different to your answer to "How do we feel about questions that are essentially about text parsing?"

Ha! Um. shuffles feet. Probably because I hate stats and enjoy text parsing. Which is an absolutely crappy excuse. But you make a very good point, it doesn't make sense to treat the two differently.

I just revisited this. I think the community is clearly in favor of stats questions, and your last comment showed up my own obvious hypocricy given how I feel about text parsing. I guess my initial position was based more on my ignorance and visceral fear of stats (I'm a biologist at heart) than on any real scientific reason. So I accepted Devon's answer since it was the most upvoted.

Just to chip in, I'm strongly in favour of stats questions being fine given a biological context because they'll be a bioinformatics solution somewhere.
Modern bioinformatics appears to have become removed from its "statistically pure" origins but it moves cycles. At present many think (perhaps correctly at present) the volume of genomics data renders "the statistical model" irrelevant, but things change. When "the statistical model" is king, the reality is the method was shoe-horned from another area of stats/maths. The "shoe-horning" process is quite important, because your trying to place a generic solution into a biological context and the translation isn't always neat.
Example 1
For example, we just had a question asking whether "clustering analysis" can replace molecular phylogeny ... the answer is no and this question was asked about 40 years ago. However, a general statistician wouldn't be aware of the biological rational as to why, nor aware of the huge row broke out in evolution about "the correct method to build a phylogeny" and took a decade to resolve.
Example 2
A good example of "statistical methodological cycles" is machine learning (ML), which is currently fashionable, but has been on the go since the '50s. Purists describe "AI winters" (sounds like Game of Thrones, but before GoT). This is where funders pull out because the original PIs overstated their case. Without AI winters its application to bioinformatics would be much more mainstream (possibly). The reality is that many major genomics packages Sauret (whatever its called), don't implement "full-blooded" ML solution, so there's lots of ground for change.
Example 3
Finally an older but brilliant example (brilliant man) of the importance of empirical statistics specifically applied to bioinformatics was Ron Fisher's F-statistics (e.g. Fst). Fisher was a statistical purist who founded large chunks of modern statistical theory, but also applied that expertise to biological questions (just don't ask about his political views). F-statistics are used in vast numbers of bioinformatics packages and population genomics including R and I've no doubt they'll be a BioPython solution somewhere.
My advice "resist popularism" :-)

I would say that questions that are asking for help on statistics and nothing else should not be on topic. While statistics are an integral tool of a bioinformatician, they are not really part of bioinformatics. They're an integral tool of any quantitative science.
There is already an SE site dedicated to statistics, and I feel such questions would be better served there.
Note that I am not advocating that any mention of stats would make the question off topic, only that if the question is just asking for statistics help, it doesn't belong here.


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

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

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

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

Bug reports
Usability testing
Good reputation
Citations

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

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

We need to keep those limits of affiliation.

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

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

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

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

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

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

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

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