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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:

  1. 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).
  2. 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?

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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.

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    $\begingroup$ 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... $\endgroup$
    – Devon Ryan
    Commented Jun 6, 2017 at 7:42
  • $\begingroup$ 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. $\endgroup$
    – Johannes Köster
    Commented Jun 6, 2017 at 21:49
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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.

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  • $\begingroup$ I also suggest to make the official tool support tag green. $\endgroup$
    – Kamil S Jaron
    Commented Jun 5, 2017 at 21:14
  • $\begingroup$ 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. $\endgroup$
    – Devon Ryan
    Commented Jun 5, 2017 at 21:16
  • $\begingroup$ @DevonRyan I think (not sure though) that such tags are a corporate thing. I mean, someone has to sponsor them and, presumably, pay SE. $\endgroup$
    – terdon Mod
    Commented Jun 7, 2017 at 19:43
  • $\begingroup$ 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. $\endgroup$
    – Kamil S Jaron
    Commented Jun 7, 2017 at 21:16
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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.

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