user52598: We have decided to see if there is sufficient critical mass to start a complementary synthetic biology SE site (by analogy, "Electronics.SE" to this site's "Physics.SE").  If interested, please follow the proposal in Area51.

Update #2: The Area51 Synthetic Biology proposal is now in its commitment phase. Most of the community coming in are from outside of StackExchange, so we particularly want to invite experienced StackExchange folks to commit and be able to help show the newly-arriving experts the ropes!

Folks from iGEM are looking to either create or join a persistent Q&A resource for synthetic biology students needing help with protocols, genetic design, etc.  Bringing a community to this site is one of the possible approaches under consideration.
I've been poking around this site the last few days, however, and most of the questions that I see here are of a much more popular science or "what's this thing in my back-yard" nature. I've also seen a rather negative response to what seemed to me a fairly straight-forward question about scale-up. Together these make me wonder whether this community would consider such questions to be de facto out of scope.
Would this site welcome an influx of technical questioners and answerers focused on the pragmatics of practicing synthetic biology?
Some potential example question titles:

"GFPmut3, EGFP, sfGFP... does it matter which GFP I use?"
"Failing to get colonies on a MoClo assembly. How to debug?"
"If I adapted a sequence found in a paper, can I share it under the OpenMTA?"
"Which assembly protocols are good to run on an OT-2?"
"What do I need to do to adapt an E. coli part for B. subtilis?"
"How can I express gRNA from a sensor using a Pol II promoter?"
"Are there any high-throughput metabolite assays for plate readers?"
"What are the most common sources of error in preparing cell-free extract?"
"Why are my OD numbers going up rather than down when I titrate my calibrant?"


Added on 1/26: committee members would appreciate comments on the scope of these questions (assuming they had evidence of work, etc.):

"I have attempted to simulate the growth of Vibrio natriegens on different media using dynamic FBA, but I'm not sure if the output I'm getting is biologically-relevant or if it's an issue with my code, can someone have a look at it for me?"
"I have attempted to model the growth of Vibrio natriegens on different media as a system of ODEs, but I'm having some difficulty understanding the mathematical notation in this paper that did something similar, can someone help me?"
"I want to model the growth of Vibrio natriegens on different media, would it be more appropriate to use a system of ODEs or dynamic FBA?"
"I want to model the growth of Vibrio natriegens on different media, and have designed a system of ODEs. Is this more quickly solved in Python or Matlab?"
"I'm want to integrate a DOE I ran to test different growth conditions in Vibrio natriegens with a system of differential algebraic equations that I have used to model my bioreactor, would Bayesian parameter estimation be applicable here?"

Would these also be appropriate here, or are they things that would have to go to Bioinformatics.SE or somewhere else?

user16866: DISCLAIMER: These are my personal (albeit informed) opinions. I would wait for additional comments, answers, and up/down voting to see what a more general community consensus might look like.

To me, the short answer is "yes, if..."
Let me explain:
 Yes 
Synthetic biology would certainly fall under the realm of acceptable topics here.

In fact, ~88 posts have already been labeled with the synthetic-biology tag as of writing this answer.

We also welcome student participation on our site. From our tour:

Biology Stack Exchange is a question and answer site for biology researchers, academics, and students

 If... 
It sounds like most of the "influx" of posts you're referring to will come from students, which might put some members on high alert due to the many low-quality posts we get globally from some students.
As I mentioned above, we do welcome students here, but we do so with the expectation that they be held to our site-wide high standards.

Again from the tour, "we're working together to build a library of detailed answers to every question about biology." Our focus is not to teach novices nor to answer homework questions. (See our homework policy and many meta discussions on the topic).

We ask that all question posters here attempt to search for an answer to their own question and explicitly indicate what research they've already done, what they learned, and what is still confusing or unknown to them. Our goal is not to simply be an answer site, but rather a site that promotes self-learning with some expert help along the way.


In summary, we do not need an influx of basic questions that can and should be answered using intro textbooks or Wikipedia. Such questions should be researched by students on their own. However, if these students still find something confusing and can explicitly describe their sincere personal efforts to understand a difficult topic, we'd be happy to help them understand. :)
Of course, such students should come to understand how our site works via the tour and help-center, and they need to follow our other guidelines for writing good-questions and types of questions to avoid asking.

I'd like to react to how I think some of the example questions you've provided would be received here:

"GFPmut3, EGFP, sfGFP... does it matter which GFP I use?"

Off-topic: asking for opinion-based answers.


"Failing to get colonies on a MoClo assembly. How to debug?"

Ok if asker provides context, what's been tried, etc.


"If I adapted a sequence found in a paper, can I share it under the OpenMTA?"

Off-topic: asking for opinion-based answer AND relating to professional behavior vs actual biology.


"Which assembly protocols are good to run on an OT-2?"

Closed as being too broad, not demonstrating prior research effort, and "good" suggests the the OP would be seeking opinion-based answers (not allowed).


"What do I need to do to adapt an E. coli part for B. subtilis?"

OK if asker explicitly demonstrates prior research effort in their post (i.e., how they already tried to answer their own question). I think the broad "what do I need" design of this question would suggest lack of such research effort. A better post would question about some particular aspect of some protocol.


"How can I express gRNA from a sensor using a Pol II promoter?"

OK if asker explicitly demonstrates prior research effort in their post (i.e., how they already tried to answer their own question). My guess is that this "how" question might not demonstrate such effort, but a question honing in on some specific aspect of such a protocol might be better. (alternatively, if such a protocol is not standard, the question could be reformulated to demonstrate how they've gotten to asking this question and suggesting (ideally cited) attempts to do something similar)


"Are there any high-throughput metabolite assays for plate readers?"

Needs to explicitly demonstrate prior research effort (how they tried to answer their own question).


"What are the most common sources of error in preparing cell-free extract?"

Feels quite broad to me. Broad questions often indicate lack of prior research effort. More appropriate might be to hone in on a specific type of error and ask questions about something that is still confusing them.


"Why are my OD numbers going up rather than down when I titrate my calibrant?"

Needs to explicitly demonstrate prior research effort (how they tried to answer their own question) and to provide adequate context.



Again, these are my personal (and somewhat superficial) thoughts, so I welcome others to weigh-in further...

user948: One point I'd like to emphasize is that this is not a tutorial site or discussion forum, which many of your your example questions seem to assume. I think most of them could be edited into decent shape:

"GFPmut3, EGFP, sfGFP... does it matter which GFP I use?"
What are the differences between GFPmut3, EGFP, and sfGFP in the context of [my kind of experiment]?

"Failing to get colonies on a MoClo assembly. How to debug?"
Failing to get colonies on a MoClo assembly after 3 tries. Are there issues with my protocol [attached]?

"If I adapted a sequence found in a paper, can I share it under the OpenMTA?"
Off-topic. Maybe try Law.SE...

"Which assembly protocols are good to run on an OT-2?"
I'm trying to scale up X, starting with this protocol. Can it easily be adapted to an OT-2 robot?

"What do I need to do to adapt an E. coli part for B. subtilis?"
I'm adapting an E. coli part for B. subtilis, but X happened. Why is that, and how can I get Y instead?

"How can I express gRNA from a sensor using a Pol II promoter?"
I found this protocol for expressing gRNA from a sensor using the Pol II promoter, but it's pretty old and requires [this unavailable reagent/this undesirable condition]. What can I do to modify it?

"Are there any high-throughput metabolite assays for plate readers?"
Google and Google Scholar are your friends here.

"What are the most common sources of error in preparing cell-free extract?"
My cell-free extracts have highly variable activities and yields. Are there any tweaks I can make to my protocol [attached]?

"Why are my OD numbers going up rather than down when I titrate my calibrant?"
My ODs are increasing when I titrate my standard. This is exactly how I'm doing it, and I tried making these changes, but the results are the same. Where am I going wrong?


Starting to see a pattern here? Chatty, open-ended, truly opinion-based, and/or poorly researched questions are not on topic here, but specific questions that have the appropriate context (detailed protocols, prior research) looking for specific answers are fine. Seeking fact-based, expert opinion is okay, as that's why we (answerers) are here, but asking in such a way that answers are likely to just be personal opinions is not.
The expectation is that you put as much effort as possible into researching and answering your own question, including running the experiment multiple times, then collect all that information in a readable format and present it to us. Read the following Help Center pages over and over:

What topics can I ask about here?
What types of questions should I avoid asking?
How do I ask a good question?
Homework Questions

All users are expected to take the tour and be familiar with everything in the help center. Doing all of this ahead of time will prevent innumerable headaches down the line.
So, to answer your original question, yes we would welcome additional technical questions about synthetic biology, as long as they are in line with the site's standards and rules. I'll say it again, this is not a tutorial site or discussion forum, so please ensure your community is aware of that up front.

52598: <p><strong>We have decided to see if there is sufficient critical mass to start a complementary synthetic biology SE site (by analogy, &quot;Electronics.SE&quot; to this site's &quot;Physics.SE&quot;).  If interested, please follow <a href="https://area51.stackexchange.com/proposals/125068/synthetic-biology?referrer=MWUxMzFmNGQ0YjgzNjQ2NGM1OTg0MzcwNDViYTJhYTU0MGFhMmQxOTBiOTIzNDkwMTk4YWE0ZTAwMWViNTFkYQShZvCz3DEtNOdFljc28-PvJMCbj1pphM_cMf2Ifr9z0">the proposal in Area51</a>.</strong></p>
<hr />
<p><strong>Update #2: The <a href="https://area51.stackexchange.com/proposals/125068/synthetic-biology?referrer=MWUxMzFmNGQ0YjgzNjQ2NGM1OTg0MzcwNDViYTJhYTU0MGFhMmQxOTBiOTIzNDkwMTk4YWE0ZTAwMWViNTFkYQShZvCz3DEtNOdFljc28-PvJMCbj1pphM_cMf2Ifr9z0">Area51 Synthetic Biology proposal</a> is now in its commitment phase. Most of the community coming in are from outside of StackExchange, so we particularly want to invite experienced StackExchange folks to commit and be able to help show the newly-arriving experts the ropes!</strong></p>
<hr />
<p>Folks from <a href="https://igem.org/" rel="nofollow noreferrer">iGEM</a> are looking to either create or join a persistent Q&amp;A resource for synthetic biology students needing help with protocols, genetic design, etc.  Bringing a community to this site is one of the possible approaches under consideration.</p>
<p>I've been poking around this site the last few days, however, and most of the questions that I see here are of a much more popular science or &quot;what's this thing in my back-yard&quot; nature. I've also seen a rather negative response to what seemed to me <a href="https://biology.stackexchange.com/q/97927/52598">a fairly straight-forward question about scale-up</a>. Together these make me wonder whether this community would consider such questions to be de facto out of scope.</p>
<p>Would this site welcome an influx of technical questioners and answerers focused on the pragmatics of practicing synthetic biology?</p>
<p>Some potential example question titles:</p>
<ul>
<li>&quot;GFPmut3, EGFP, sfGFP... does it matter which GFP I use?&quot;</li>
<li>&quot;Failing to get colonies on a MoClo assembly. How to debug?&quot;</li>
<li>&quot;If I adapted a sequence found in a paper, can I share it under the OpenMTA?&quot;</li>
<li>&quot;Which assembly protocols are good to run on an OT-2?&quot;</li>
<li>&quot;What do I need to do to adapt an E. coli part for B. subtilis?&quot;</li>
<li>&quot;How can I express gRNA from a sensor using a Pol II promoter?&quot;</li>
<li>&quot;Are there any high-throughput metabolite assays for plate readers?&quot;</li>
<li>&quot;What are the most common sources of error in preparing cell-free extract?&quot;</li>
<li>&quot;Why are my OD numbers going up rather than down when I titrate my calibrant?&quot;</li>
</ul>
<hr />
<p>Added on 1/26: committee members would appreciate comments on the scope of these questions (assuming they had evidence of work, etc.):</p>
<ul>
<li>&quot;I have attempted to simulate the growth of Vibrio natriegens on different media using dynamic FBA, but I'm not sure if the output I'm getting is biologically-relevant or if it's an issue with my code, can someone have a look at it for me?&quot;</li>
<li>&quot;I have attempted to model the growth of Vibrio natriegens on different media as a system of ODEs, but I'm having some difficulty understanding the mathematical notation in this paper that did something similar, can someone help me?&quot;</li>
<li>&quot;I want to model the growth of Vibrio natriegens on different media, would it be more appropriate to use a system of ODEs or dynamic FBA?&quot;</li>
<li>&quot;I want to model the growth of Vibrio natriegens on different media, and have designed a system of ODEs. Is this more quickly solved in Python or Matlab?&quot;</li>
<li>&quot;I'm want to integrate a DOE I ran to test different growth conditions in Vibrio natriegens with a system of differential algebraic equations that I have used to model my bioreactor, would Bayesian parameter estimation be applicable here?&quot;</li>
</ul>
<p>Would these also be appropriate here, or are they things that would have to go to Bioinformatics.SE or somewhere else?</p>
 16866: <p>DISCLAIMER: These are my personal (albeit informed) opinions. I would wait for additional comments, answers, and up/down voting to see what a more general community consensus might look like.</p>
<hr />
<p>To me, the short answer is &quot;<strong>yes, if...</strong>&quot;</p>
<p>Let me explain:</p>
<h3> Yes </h3>
<p><strong>Synthetic biology</strong> would certainly fall under the realm of acceptable topics here.</p>
<ul>
<li>In fact, ~88 posts have already been labeled with the <a href="https://biology.stackexchange.com/questions/tagged/synthetic-biology" class="post-tag" title="show questions tagged &#39;synthetic-biology&#39;" rel="tag">synthetic-biology</a> tag as of writing this answer.</li>
</ul>
<p>We also welcome student participation on our site. From our <a href="https://biology.stackexchange.com/tour">tour</a>:</p>
<blockquote>
<p>Biology Stack Exchange is a question and answer site for biology researchers, academics, and <strong>students</strong></p>
</blockquote>
<h3> If... </h3>
<p>It sounds like most of the &quot;influx&quot; of posts you're referring to will come from students, which might put some members on high alert due to the many low-quality posts we get globally from some students.</p>
<p>As I mentioned above, we <em>do</em> welcome students here, but we do so with the expectation that they be held to our site-wide <a href="https://biology.stackexchange.com/help/how-to-ask"><em>high standards</em></a>.</p>
<ul>
<li><p>Again from the tour, &quot;we're working together to build a <em><strong>library of detailed answers</strong></em> to every question about biology.&quot; Our focus is not to teach novices nor to answer homework questions. (<strong>See our <a href="https://biology.stackexchange.com/help/homework">homework policy</a></strong> and many <a href="https://biology.meta.stackexchange.com/search?q=homework">meta</a> discussions on the topic).</p>
</li>
<li><p>We ask that all question posters here attempt to search for an answer to their own question and explicitly indicate what research they've already done, what they learned, and what is still confusing or unknown to them. Our goal is not to simply be an answer site, but rather a site that promotes self-learning with some expert help along the way.</p>
</li>
</ul>
<p>In summary, we do not need an influx of basic questions that can and <em>should</em> be answered using intro textbooks or Wikipedia. Such questions should be researched by students on their own. <em>However</em>, if these students still find something confusing and can explicitly describe their sincere personal efforts to understand a difficult topic, we'd be happy to help them understand. :)</p>
<p>Of course, such students should come to understand how our site works via the <a href="https://biology.stackexchange.com/tour">tour</a> and <a href="https://biology.stackexchange.com/help">help-center</a>, and they need to follow our other guidelines for writing <a href="https://biology.stackexchange.com/help/how-to-ask">good-questions</a> and <a href="https://biology.stackexchange.com/help/dont-ask">types of questions to avoid asking</a>.</p>
<hr />
<p>I'd like to react to how I think some of the example questions you've provided would be received here:</p>
<ul>
<li><p>&quot;GFPmut3, EGFP, sfGFP... does it matter which GFP I use?&quot;</p>
<ul>
<li><strong>Off-topic: asking for opinion-based answers.</strong></li>
</ul>
</li>
<li><p>&quot;Failing to get colonies on a MoClo assembly. How to debug?&quot;</p>
<ul>
<li><strong>Ok if asker provides context, what's been tried, etc.</strong></li>
</ul>
</li>
<li><p>&quot;If I adapted a sequence found in a paper, can I share it under the OpenMTA?&quot;</p>
<ul>
<li><strong>Off-topic: asking for opinion-based answer AND relating to professional behavior vs actual biology.</strong></li>
</ul>
</li>
<li><p>&quot;Which assembly protocols are good to run on an OT-2?&quot;</p>
<ul>
<li><strong>Closed as being too broad, not demonstrating prior research effort, and &quot;good&quot; suggests the the OP would be seeking opinion-based answers (not allowed).</strong></li>
</ul>
</li>
<li><p>&quot;What do I need to do to adapt an E. coli part for B. subtilis?&quot;</p>
<ul>
<li><strong>OK if asker explicitly demonstrates prior research effort in their post (i.e., how they already tried to answer their own question). I think the broad &quot;what do I need&quot; design of this question would suggest lack of such research effort. A better post would question about some particular aspect of some protocol.</strong></li>
</ul>
</li>
<li><p>&quot;How can I express gRNA from a sensor using a Pol II promoter?&quot;</p>
<ul>
<li><strong>OK if asker explicitly demonstrates prior research effort in their post (i.e., how they already tried to answer their own question). My guess is that this &quot;<em>how</em>&quot; question might not demonstrate such effort, but a question honing in on some specific aspect of such a protocol might be better. (alternatively, if such a protocol is not standard, the question could be reformulated to demonstrate how they've gotten to asking this question and suggesting (ideally cited) attempts to do something similar)</strong></li>
</ul>
</li>
<li><p>&quot;Are there any high-throughput metabolite assays for plate readers?&quot;</p>
<ul>
<li><strong>Needs to explicitly demonstrate prior research effort (how they tried to answer their own question).</strong></li>
</ul>
</li>
<li><p>&quot;What are the most common sources of error in preparing cell-free extract?&quot;</p>
<ul>
<li><strong>Feels quite broad to me. Broad questions often indicate lack of prior research effort. More appropriate might be to hone in on a <em>specific</em> type of error and ask questions about something that is still confusing them.</strong></li>
</ul>
</li>
<li><p>&quot;Why are my OD numbers going up rather than down when I titrate my calibrant?&quot;</p>
<ul>
<li><strong>Needs to explicitly demonstrate prior research effort (how they tried to answer their own question) and to provide adequate context.</strong></li>
</ul>
</li>
</ul>
<p>Again, these are my personal (and somewhat superficial) thoughts, so I welcome others to weigh-in further...</p>
 948: <p>One point I'd like to emphasize is that <em><strong>this is not a tutorial site or discussion forum</strong></em>, which many of your your example questions seem to assume. I think most of them could be edited into decent shape:</p>
<ul>
<li><p><strong>&quot;GFPmut3, EGFP, sfGFP... does it matter which GFP I use?&quot;</strong></p>
<p><em>What are the differences between GFPmut3, EGFP, and sfGFP in the context of [my kind of experiment]?</em></p>
</li>
<li><p><strong>&quot;Failing to get colonies on a MoClo assembly. How to debug?&quot;</strong></p>
<p><em>Failing to get colonies on a MoClo assembly after 3 tries. Are there issues with my protocol [attached]?</em></p>
</li>
<li><p><strong>&quot;If I adapted a sequence found in a paper, can I share it under the OpenMTA?&quot;</strong></p>
<p>Off-topic. Maybe try Law.SE...</p>
</li>
<li><p><strong>&quot;Which assembly protocols are good to run on an OT-2?&quot;</strong></p>
<p><em>I'm trying to scale up X, starting with this protocol. Can it easily be adapted to an OT-2 robot?</em></p>
</li>
<li><p><strong>&quot;What do I need to do to adapt an E. coli part for B. subtilis?&quot;</strong></p>
<p><em>I'm adapting an E. coli part for B. subtilis, but X happened. Why is that, and how can I get Y instead?</em></p>
</li>
<li><p><strong>&quot;How can I express gRNA from a sensor using a Pol II promoter?&quot;</strong></p>
<p><em>I found this protocol for expressing gRNA from a sensor using the Pol II promoter, but it's pretty old and requires [this unavailable reagent/this undesirable condition]. What can I do to modify it?</em></p>
</li>
<li><p><strong>&quot;Are there any high-throughput metabolite assays for plate readers?&quot;</strong></p>
<p>Google and Google Scholar are your friends here.</p>
</li>
<li><p><strong>&quot;What are the most common sources of error in preparing cell-free extract?&quot;</strong></p>
<p><em>My cell-free extracts have highly variable activities and yields. Are there any tweaks I can make to my protocol [attached]?</em></p>
</li>
<li><p><strong>&quot;Why are my OD numbers going up rather than down when I titrate my calibrant?&quot;</strong></p>
<p><em>My ODs are increasing when I titrate my standard. This is exactly how I'm doing it, and I tried making these changes, but the results are the same. Where am I going wrong?</em></p>
</li>
</ul>
<p>Starting to see a pattern here? Chatty, open-ended, truly opinion-based, and/or poorly researched questions are not on topic here, but <em>specific</em> questions that have the appropriate context (detailed protocols, prior research) looking for <em>specific</em> answers are fine. Seeking fact-based, expert opinion is okay, as that's why we (answerers) are here, but asking in such a way that answers are likely to just be personal opinions is not.</p>
<p>The expectation is that you put as much effort as possible into researching and answering your own question, including running the experiment multiple times, then collect all that information in a readable format and present it to us. Read the following Help Center pages over and over:</p>
<ul>
<li><a href="https://biology.stackexchange.com/help/on-topic">What topics can I ask about here?</a></li>
<li><a href="https://biology.stackexchange.com/help/dont-ask">What types of questions should I avoid asking?</a></li>
<li><a href="https://biology.stackexchange.com/help/how-to-ask">How do I ask a good question?</a></li>
<li><a href="https://biology.stackexchange.com/help/homework">Homework Questions</a></li>
</ul>
<p>All users are expected to take the <a href="https://biology.stackexchange.com/tour">tour</a> and be familiar with everything in the help center. Doing all of this ahead of time will prevent innumerable headaches down the line.</p>
<p>So, to answer your original question, yes we would welcome additional technical questions about synthetic biology, <em>as long as they are in line with the site's standards and rules</em>. I'll say it again, this is not a tutorial site or discussion forum, so please ensure your community is aware of that up front.</p>
