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The Synthetic Biology Open Language is an open representational standard for encoding biological designs. As this community has been growing, it has been trying to figure out a better way than FAQs to compile ongoing Q&A expert knowledge about how to use the standard for representing designs.

As a long-standing contributor on Academia.SE, it seems to me that Biology.SE might be a good place to start building up such a Q&A compilation, adding tags, etc. We would only want to do so if this community would find it to be on topic.

Examples of questions that might be asked would be:

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

A slightly fuller example might be:

How should I represent growth media in SBOL?
Our lab is doing an experiment comparing growth in M9 media and LB. M9 is a mixture of several different chemicals, see: cshprotocols.cshlp.org/content/2010/8/pdb.rec12295.short
How do I represent that in SBOL?"

Answer:
The recommended best practice for representing mixtures (including media) in SBOL 2 is as a ModuleDefinition, with a FunctionalComponent for each ingredient and a Measure specifying the amount of each in the mixture.

I believe that Biology.SE would be a better place for this than StackOverflow because the questions are more about structuring knowledge than about programming. I believe this would be a better place than Bioinformatics because it is more stable and broader in scope.

Bottom line: would Biology.SE be receptive to an influx of SBOL practitioners asking an answering questions about this topic?

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    $\begingroup$ So far, it looks to me like the response is a mild yes. If I don't see any significant objections today, I'll pass that to the SBOL community in see if they want to start asking questions. $\endgroup$
    – jakebeal
    Commented Jul 15, 2019 at 14:31
  • $\begingroup$ I wouldn't take 2 upvotes and no answers as sufficient response to turn Biology.SE into a SBOL help desk. $\endgroup$
    – Bryan Krause Mod
    Commented Jul 15, 2019 at 15:30
  • $\begingroup$ @BryanKrause So far it's been basically crickets... is that normal for this community? I'd like to get some indication of feelings about this proposal, one way or another. $\endgroup$
    – jakebeal
    Commented Jul 15, 2019 at 15:39
  • $\begingroup$ How big would you say that the SBOL-community is, and how large of a question flood would you expect initially? $\endgroup$
    – fileunderwater
    Commented Jul 16, 2019 at 12:44
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    $\begingroup$ I'd estimate that numbers are currently in the hundreds, so not enormous. There might be more questions earlier if we tried to do an organized bootstrapping. $\endgroup$
    – jakebeal
    Commented Jul 16, 2019 at 15:54
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    $\begingroup$ Ok, good to know. As long as the first page/new question aren’t flooded with a single topic that shouldn’t be an issue. Since many users of SBOL probably have a biology background this could also lead to an influx of experts (ie possible answerers for different types of questions), which Bio-SE is in need of. $\endgroup$
    – fileunderwater
    Commented Jul 16, 2019 at 19:40
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    $\begingroup$ Personally I welcome any contribution from professionals. However, you might also consider creating an SBOL specific site. I can’t say if that’s a good idea or not, but something to be aware of. $\endgroup$
    – canadianer
    Commented Jul 18, 2019 at 17:27
  • $\begingroup$ @jakebeal Any news on this? Did you move elsewhere and/or what response did you get within the SBOL community? $\endgroup$
    – fileunderwater
    Commented Aug 12, 2019 at 13:05
  • $\begingroup$ @fileunderwater We have started adding questions on Bioinformatics.SE, where it was more clearly on topic. $\endgroup$
    – jakebeal
    Commented Aug 12, 2019 at 19:54

3 Answers 3

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Our current standards on technique-based questions are described in the help as follows (emphasis mine):

(on-topic): questions about techniques in a biological or biochemical laboratory

Questions on interdisciplinary subjects like bioinformatics are also welcome, as long as they focus on the biological part of the subject.

I'm not familiar at all with SBOL so I'm hesitant to offer too much opinion but based on the example questions you've posted I don't see any of them focused on the biological part of the subject. Probably Bioinformatics is a better place, but given they (like here) have zero questions containing the term "SBOL" it seems like you will not find any existing expert residents.

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  • $\begingroup$ Sounds like it's not a good place here, then, based on your opinion. $\endgroup$
    – jakebeal
    Commented Jul 15, 2019 at 16:28
  • $\begingroup$ @jakebeal Yes, probably not based on my opinion, but that's just my opinion. I wouldn't want to discourage your community from asking good questions here more generally, though, as long as they fit that general directive towards bioinformatics that those questions focus on the biology rather than "how to do X in (software/language/standard)": if the question is about biology and references a SBOL design that would be just fine imo. $\endgroup$
    – Bryan Krause Mod
    Commented Jul 15, 2019 at 21:52
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As long as the questions focus on practical issues encountered when working in biology and biological research, with an emphasis on the biological aspects, I think it should be fine. We are lacking “expert type” questions anyway, and (if I understand you correctly) some/many of the questions you describe should fit that description.

Even if SBOL (which I know nothing of, before googling now) is fairly domain-specific and is geared towards the modeling of biological systems, if don’t (tentatively) see a big difference between this and questions on how to represent and describe other highly conceptual models of biological systems in an accurate way, be it mathematical models of populations, cell structures or the DNA-molecule.

To make it easier for people here to decide or have an opinion; could you maybe describe the outline of one or two potential questions on SBOL that’ll you think would be useful and a fit for Bio-SE?

If I understand the issue correctly, these are a couple of current Bio-SE Qs that are conceptually similar to possible SBOL-Qs:
* How is DNA read
* DNA topology o two circular chromosomes
* Models-of-quorum-sensing-for-multi-agent-systems

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  • $\begingroup$ I gave some examples of questions in my post above. $\endgroup$
    – jakebeal
    Commented Jul 16, 2019 at 15:55
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    $\begingroup$ @jakebeal I was thinking slightly fuller Qs that give some background and biological relevance. To spark some more interest. Either way, for me personally, the addition of SBOL would be fine. $\endgroup$
    – fileunderwater
    Commented Jul 16, 2019 at 18:19
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    $\begingroup$ I think @fileunderwater and I are expressing the same opinion. This answer seems consistent with the existing guidelines in the help about what makes a question of this type on-topic. $\endgroup$
    – Bryan Krause Mod
    Commented Jul 16, 2019 at 19:02
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    $\begingroup$ @fileunderwater Example expanding my first question: "How should I represent growth media in SBOL? Our lab is doing an experiment comparing growth in M9 media and LB. M9 is a mixture of several different chemicals: cshprotocols.cshlp.org/content/2010/8/pdb.rec12295.short How do I represent that in SBOL?" Answer: "The recommended best practice for representing mixtures (including media) in SBOL 2 is as a ModuleDefinition, with a FunctionalComponent for each ingredient and a Measure specifying the amount of each in the mixture. ..." $\endgroup$
    – jakebeal
    Commented Jul 16, 2019 at 20:02
  • $\begingroup$ @jakebeal I would say; go for it. Especially if you cannot think of more suitable websites, and if you can persuade a portion of the users of SBOL. $\endgroup$
    – fileunderwater
    Commented Jul 16, 2019 at 20:09
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If you have a community that could respond to questions in your area, I would say welcome. It seems a relatively rigorously scientific area, and would dilute the unbelievable crap that is flooding the list at the moment.

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