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66 Example Questions

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up vote 14 down vote

added by Traci Feb 3 at 19:28

up vote 13 down vote

added by Gonza10V Feb 4 at 1:41

This one is readily and specifically answerable, and I hope that people will vote it up! – jakebeal Feb 11 at 16:22

up vote 11 down vote

added by JS3xton Jan 30 at 6:24

Would this be better with a more specific use case in mind? If there are multiple reasons for why one might want inert DNA sequences I feel like they should be different questions. Something like "I need a random, inert DNA sequence to act as a control in my [x] experiment, how can I generate it?" I like the question though – Noah Sprent Jan 30 at 18:07

Thanks for the feedback; I updated to describe insulator sequences for bacterial promoters (which was my original use case). – JS3xton Feb 4 at 21:22

up vote 11 down vote

added by Hatem Abdelrahman Jan 30 at 14:23

up vote 11 down vote

added by Roy Amhlaidh Feb 1 at 17:54

I just searched and found that apparently people are building CRISPR-based sequencing workflows now. Once you get CRISPR targeting involved, I think it edges into engineering space and ends up looking pretty SynBio. – jakebeal Feb 1 at 20:26

For those interested in learning more about Crispr-Cas9 DNA sequencing, here is the publication:Targeted nanopore sequencing with Cas9-guided adapter ligation nature.com/articles/s41587-020-0407-5 – Hatem Abdelrahman Feb 2 at 6:02

Isn't this too broad ? I feel like this kind of is a reddit type question where everyone in the community can go in a different direction. Ideally stackexchange responses have some sort of a convergence. – rkrishnasanka Feb 20 at 14:51

up vote 11 down vote

added by Ben Thuronyi Feb 8 at 16:33

Maybe rather than having the goal being overexpression (max translation), instead trying to find a specific desired translation rate. The times I see people going for max translation are the structural biologists using T7 pUC cassette where they don't really care what the RBS is and they just want to make protein go brrrr. – David Zong Feb 8 at 22:55

@DavidZong Your comment sounds like a good comment or answer on such a question! There are legitimate places where people want to overexpress, though, so I think this can be a good question. Vote it up? – jakebeal Feb 9 at 17:24

up vote 10 down vote

added by jakebeal Jan 29 at 18:03

I think discussion of general bio equipment would be better for the general bio board. This should be more focused on genetic devices, genetic engineer techniques and modeling. – Mark B Jan 29 at 21:51

I'd really like to be able to talk about calibration issues on a SynBio.SE as well, since there's not much of a protocol population on Bio.SE. – jakebeal Jan 29 at 22:24

Thanks for the comment Mark. I have begun a discussion around the scope/necessity of the SynBio.SE here: area51.meta.stackexchange.com/q/32412/211171. In my opinion, users should be allowed to ask questions here that are within the scope of SynBio, even if they're also in the scope of Bio.SE, if they're looking for SynBio-focused response. Similar to how both Ask Ubuntu.SE and Unix.SE both exist. – Noah Sprent Jan 30 at 12:44

You should allow yourselves to address your own technical questions. I'm not sure people would be permitted to answer this on Bio.SE anyway - though they certainly should be. – Mike Serfas Feb 4 at 7:23

up vote 10 down vote

added by Noah Sprent Jan 29 at 18:50

up vote 10 down vote

added by rkrishnasanka Jan 29 at 18:56

Can you elaborate on this a bit? I'm afraid I don't know about the protocols well enough --- why is isothermal PCR important, and is it cell-type specific? – jakebeal Jan 29 at 19:14

up vote 10 down vote

added by Hatem Abdelrahman Jan 29 at 19:06

I like this one! I don't know if I have a good answer, but it's a question that I think would get a lot of interesting technical answers. – jakebeal Jan 29 at 19:15

Thank you. I think we could invite professor Michael Elowitz from Caltech to give us some insightful answer; his research is well around the physiological role of noise in gene expression.: elowitz.caltech.edu/research – Hatem Abdelrahman Jan 29 at 19:36

up vote 10 down vote

added by jakebeal Jan 29 at 19:19

up vote 10 down vote

added by rkrishnasanka Jan 29 at 19:33

This seems like quite a broad question! Would you be able to improve it by making it more specific about the kind of library and why you want to create it? Forgive me if I'm misunderstanding, I don't know that much about cello! – Noah Sprent Jan 30 at 13:01

I actually see this as a less broad question - I believe the answer would be in the form of an output file format to upload into Cello (if my older understanding of Cello is still correct). I may also be incorrect and it may be about generating a new library, at which point more context would be useful. – Traci Feb 4 at 22:00

Ah ok, that would indeed be a lot less broad, and a great question. If that is the case then I think the question could be reworded to that effect. – Noah Sprent Feb 5 at 9:09

Yup basically since Cello is a computational tool, its specific when it boils down to how make the part library (while it might be broad for different types of organisms and types of parts). I guess we will need to have flavors and tags when it boils down to "How do I use software X to do Y". – rkrishnasanka Feb 18 at 22:27

up vote 10 down vote

added by JS3xton Jan 30 at 6:09

I'd really like to know the answer to this one! I consume GenBank material all the time, but haven't actually published to it yet. All my sequence publications have been in other venues. Not knowing enough about the process, I wonder whether the second question might end up needing to get split off into a separate question in practice? – jakebeal Feb 12 at 2:24

up vote 10 down vote

added by JS3xton Jan 30 at 6:30

	Do you want to put something specific about geometric vs. arithmetic vs. median into the description, for those who don't realize this is a problem? – jakebeal Jan 30 at 13:32
	I figured that context might be more appropriate for the post itself, not the title. I also didn't want to bias the responses (I think I tried a smoothed mode once, haha). I'm happy to update the question, though, if there's consensus that those details would make it better. – JS3xton Jan 30 at 16:02
	Good question! I don't know enough about flow cytometry, but would it be specific to the experiment that you are doing? In that case would it be better for it to be "... describe my flow cytometry population?" Otherwise it seems like this might become a discussion? As I say, I don't know the area, so just a suggestion! – Noah Sprent Jan 30 at 18:11
	@NoahSprent That's a very good point. I suspect @JS3xton and I are both assuming fluorescent reporter assays, since that's what both of us have mostly done. Using tagged antibodies for sorting produces a completely different class of distributions, which should be analyzed using different statistics. There's only a few of these common cases, though, so they're all readily covered once distinguished. – jakebeal Jan 30 at 18:43

up vote 10 down vote

added by JS3xton Jan 30 at 6:34

	This one is definitely close to my heart. I suspect that the actual answer would end up being assay dependent. For example, the process for flow cytometry is a bit different than for plate reader. – jakebeal Jan 30 at 13:29
	Indeed, a nice one from @JS3xton! Actually, for plate reader, we need to relate the correction to the autofluorescence of a cell population with your same OD instead of your same Exp. Time. (autofluorescence depends on the amount of cells) – Alejandro Vignoni Jan 31 at 20:11

up vote 10 down vote

added by JS3xton Jan 30 at 6:38

One of the things I've found on other SE sites is that there's often a lot of value in compressing the more general descriptions found elsewhere (including wikipedia) into a very focused and digested answer. Wikipedia, for example, often gives many different views and options, which are thorough but difficult to sort through when trying to solve on particular problem. – jakebeal Jan 30 at 13:32

I was wondering the same thing as I posted. Some of my most frequented SE posts are direct answers to questions that are annoying to look up, though, and this question certainly qualified for me. (I think I almost always ended up wading through this page: en.wikipedia.org/wiki/Exponential_growth.) – JS3xton Jan 30 at 16:20

I definitely think simple questions, like this one, are often the most useful questions. Would like to see more like this! – Keoni Gandall Feb 1 at 14:34

The biology group's guidelines blandly suggest people should try to do their own research to help get better answers ... which appears to have become interpreted as a reason by some to angrily challenge anyone they think should have been able to answer their own question. Don't let that happen here. If questions are very obvious, and people ask them more than once, just find a way to merge them together. – Mike Serfas Feb 4 at 6:55

Fully agree with Mike - we don't want new researchers to come here and feel like they can't ask the "easy" questions. If they can ask "easy" questions, then it may lead to them coming back again once they have more complex questions. This should be for all skill levels within synthetic biology. – Traci Feb 4 at 22:17

show 3 more improvement suggestions

up vote 10 down vote

added by Noah Sprent Jan 30 at 13:04

A potentially very productive question, but it brings up a point: there is a lot of technical jargon in these questions, and bringing in an acronym like "DoE" for "design of experiments" seems to add to it. Should there be a guideline to tell people to explain or avoid acronyms, at least in titles, when it is feasible to do so? – Mike Serfas Feb 4 at 7:10

A good point Mike. As the site is supposed to be technical, I don't think we need to explain terms like PCR, but I agree that we should avoid jargon in general. In this case, I was actually confused about the grammar of the sentence if not using the abbreviation. Does "... for my design of experiments for optimising media conditions..." make sense? It feels like I'm missing a word. Perhaps it's enough to explain it in the full description? – Noah Sprent Feb 4 at 16:15

I was thinking "what should my design of experiments be for ..." but surely nothing enforced should get anywhere near that kind of micro-management. If people think about it that's plenty. Also, I didn't mean for this idea to extend to a phrase that isn't pretty literally the sum of its parts. To illustrate, "Polymerase chain reaction" doesn't say "thermocycling" - either you know what it is or you don't, so that is actually better left as an acronym. – Mike Serfas Feb 4 at 18:32

I suspect that jargon in titles will be fine, as long as the material gets expended in the body of the question. Titles don't want to be a whole paragraph. :-) – jakebeal Feb 5 at 11:34

up vote 10 down vote

added by jakebeal Jan 30 at 13:35

Are you referring to SBOL in general or data/visual ? – GaelC Feb 5 at 15:14

Good point, @GaelC. I've specified to SBOL 3 data model. Visual's also interesting, but separate. – jakebeal Feb 5 at 15:16

up vote 10 down vote

added by Hatem Abdelrahman Jan 30 at 14:46

up vote 10 down vote

added by Hatem Abdelrahman Jan 30 at 22:49

up vote 10 down vote

added by Cheryl Telmer Jan 31 at 18:49

up vote 10 down vote

added by Roy Amhlaidh Feb 1 at 17:47

Would this question be a better fit for Bio.SE? A more targeted question for SynBio.SE might be something like: "Should I use Q5 DNA Polymerase or Taq polymerase for the first step of my Gibson Assembly workflow?". I think it would depend upon the context given in the main body. – Noah Sprent Feb 1 at 20:57

@Noah I think that this kind of question might have an acceptable twist on the answer - while Bio.SE might answer mechanistically why Q5 is better, SynBio.SE might answer what was done to make Q5 DNA polymerase better, perhaps as a lesson for forward engineering. Ie, the Bio.SE answer might be more about the ssDNA binding domain, while the SynBio.SE answer might be more about the linker. – Keoni Gandall Feb 1 at 22:09

This is a really good point! Thanks for bringing it up. If the question were framed in that way I think it would be a great fit. – Noah Sprent Feb 1 at 23:55

up vote 10 down vote

added by Keoni Gandall Feb 1 at 22:05

This is a very good question, since it peers into a key distinction between the different techniques. People are often misled into thinking that the newest/hottest is the best for everything, without understanding the tradeoffs. We need more people to come in with votes available to vote this up! – jakebeal Feb 12 at 2:27

up vote 10 down vote

added by Keoni Gandall Feb 1 at 22:10

up vote 10 down vote

added by Keoni Gandall Feb 1 at 22:26

I really like this question, and I was actually thinking about this today! Is there a specific answer that you have in mind that's succinct? Otherwise it feels like one of those questions that will have whole review articles written about it. I suppose maybe further context in the question body might narrow the answers. – Noah Sprent Feb 2 at 21:11

I don't have a particular answer yet, but I'd like to know potential techniques. It is something I have to figure out soon though, for some folks I'm working with. I'd normally put further context in the body – Keoni Gandall Feb 3 at 18:09

up vote 10 down vote

added by Keoni Gandall Feb 2 at 20:18

Not sure why this is downvoted, as I think this is a legitimate question. Maybe it needs more specifics on the strains being used: i.e., B. subtilis 168, E. coli Nissile 1917, etc? – Traci Feb 5 at 12:39

I agree! I think the questioner could add more information about their problem in the body, and the answers could choose to be more direct about their problem or more general about the question. – Noah Sprent Feb 5 at 14:51

Yea I guess being more specific is important, but I've had this question come up in the general case with local iGEM teams before, so though it would be useful to have an answer. – Keoni Gandall Feb 6 at 15:20

As a person who had to do synthetic biology in B. subtilis during my PhD, I think this is a worthy question. Answers from traditional biologists are usually something like "what are you talking about? just use this strong RBS that we always use". Getting insights from synbio people working with less-common organisms can be incredibly helpful. – castillohair Feb 9 at 17:34

up vote 10 down vote

added by Gonza10V Feb 4 at 1:45

This is a good question, I guess one improvement would be to be to specify what assembly method we are talking about because there might be different software for different types of specification methods. – rkrishnasanka Feb 20 at 15:04

up vote 10 down vote

added by Traci Feb 4 at 22:11

up vote 10 down vote

added by Andy Hu Feb 5 at 20:45

This is a really good "soft" question, I think. There's more than one perspective on this, which is OK and would likely just result in more than one answer. It's a well-formed question, however, about two interacting but separate concepts, and so would not be fully open-ended. – jakebeal Feb 11 at 16:24

up vote 10 down vote

added by dvb Feb 8 at 13:03

that's a good one, there are such examples, and would be nice to extend on that – MolbOrg Feb 13 at 22:31

up vote 10 down vote

added by David Zong Feb 8 at 23:03

I really like this one! It's very simple, and would have an answer that focuses more on regulation than technology. It's also a really good, fundamental question about working in the area. – jakebeal Feb 8 at 23:12

up vote 10 down vote

added by Ayush Pandey Feb 12 at 11:02

Very, very good question, with a very clear answer that can be given. Nicely formulated! – jakebeal Feb 12 at 11:30

up vote 10 down vote

added by ygorl Feb 12 at 15:47

This is an interesting one... I suspect that in an actual site, a lot would depend on the details of what sort of reliability was needed and why (e.g., mining for new parts vs. understanding off-target effects). But I can definitely see a viable question in here! – jakebeal Feb 12 at 16:01

up vote 10 down vote

added by rchurt Feb 13 at 23:16

I like this question a lot: this is a very clear comparison between two directly competing technologies, which can lead to answers that lay out a good comparison framework. – jakebeal Feb 16 at 15:07

up vote 10 down vote

added by Bryan Bartley Feb 16 at 12:46

Really good, on point question here – jakebeal Feb 16 at 15:04

up vote 10 down vote

added by Brad0440 Feb 19 at 14:18

This is a very good and on-point question with clear answers grounded in recent scientific papers. – jakebeal Feb 19 at 14:21

up vote 9 down vote

added by Noah Sprent Jan 29 at 17:05

up vote 9 down vote

added by jakebeal Jan 29 at 17:17

up vote 9 down vote

added by Noah Sprent Jan 29 at 17:26

I think this would definitely need more detail in the main question about why the asker wanted to model the growth rate. This might have an impact on which technique they choose. – Noah Sprent Jan 30 at 12:16