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Stack Overflow is unhappy about its [cytoscape] tag - what would THIS community like them to do?
Hail from Stack Overflow!
Over on Meta Stack Overflow, the community has recently noticed and become grumpy about the questions in Stack Overflow's [cytoscape] tag. Many of them are purely about how to do things in the Cytoscape UI and seem to contain no programming-related problem (or else are programming-related merely in the tangential sense that they involve using Cytoscape to work with data files previously created by code the author wrote).
For better or worse, these questions are off-topic on Stack Overflow by policy, and the community there appears to me to be gearing up to close them en masse. Several of the newest questions have been closed in the last 24 hours, and as a high-rep user on Stack Overflow, I can see that more besides have accrued close votes and are likely to be closed too.
Most of these questions don't seem bad to me, at least at a glance; they're just not in-scope for Stack Overflow. The tag also has a dedicated answerer in the form of Cytoscape team member John "Scooter" Morris, and many of the questions have answers (often written by Scooter) that seem - at least upon a superficial inspection by me, a non-expert - to be useful.
Would such questions be in-scope on Bioinformatics Stack Exchange? I am not a bioinformatician, but as far as I can tell, Cytoscape is a tool originally created for, and almost exclusively used for, visualising biomolecular data by bioinformaticians. Are questions about using it therefore generally on-topic here (even if they are just software usage questions without either a programming element or a scientific element to them)? (I note that this site has three cytoscape questions already, all of which are just about installation or usage, and none are closed, but I don't want to infer too confidently from that such questions are definitely welcome here.)
It seems to me like the bioinformatics community - and thus the Bioinformatics Stack Exchange community - probably has an interest in what happens to those questions. I'd like to tentatively suggest a few things that we could ask the mods on Stack Overflow to do - if this community's approves of them. (Obviously, a lot of the points below will automatically be a bad idea if you decide these questions are generally off-topic here, too.)

Migrate all [cytoscape] questions that are off-topic on Stack Overflow and new enough to migrate from Stack Overflow to Bioinformatics, and reopen them
Ask a CM if there's a way to get an exception to the 90 day site migration limit and migrate all older off-topic questions that the Bioinformatics community thinks belong here. (I realise you won't want to be a dumping ground for Stack Overflow's garbage and will want to get to filter these; someone from this site familiar with Cytoscape could skim all the Stack Overflow [cytoscape] questions and sort them into "migrate" and "leave on Stack Overflow" bins.
Agree a stock comment to leave on closed [cytoscape] questions noting that questions about Cytoscape that are not about programming should be posted on Bioinformatics Stack Exchange or Biostars instead of on Stack Overflow, and post that comment under all the [cytoscape] questions that get closed on Stack Overflow. (That way, at least interested users who come across old questions on Stack Overflow will have a signpost pointing them to a place where their further questions will be welcome.)
(If we can't migrate them or you don't want them migrated here en masse, then...) put a historical lock on off-topic Cytoscape questions (or at least on good ones, per some way of determining "good"), instead of just closing them, so that they won't be susceptible to downvoting and auto-deletion over time.

Regardless of any of the above, it seems likely to me that someone from the Stack Overflow community will in due course reach out to Scooter and the Cytoscape team and ask them to update their documentation on where to ask for help, which currently tells them to use Stack Overflow for "questions about software installation, operation and troubleshooting". When that happens, do you want us to mention Bioinformatics Stack Exchange? Would you like those Cytoscape docs to be directing users here? (I note that Biostars is already suggested there, which makes figuring out precisely what to suggest a little more complicated.)
Finally, we could also modify the tag excerpt and tag wiki on Stack Overflow to suggest Bioinformatics Stack Exchange (and Biostars?) as an alternative place to ask about Cytoscape where non-programming questions would be on-topic - again, if you'd like us to do so.
What say you? I've proposed lots of possible actions above that I suspect would give this situation a better outcome, but most of them are things that would need this community's approval and consent before anyone from Stack Overflow does them. Are they good ideas?

Thanks @MarkAmery. It sounds to me that the problem is with Cytoscape documentation, via unauthorised commercial use of SO platform. It is ettiquette to ask via meta, like you've done. Redirecting future posts is reasonable in my opinion, but let's discuss it. I think overriding 90 day retrospect migration is unlikely, thats up to SO, because the problem in the first instance was Cytoscape documentation.
Do you have any interests to declare about Cytoscape?

"I think overriding 90 day retrospect migration is unlikely, thats up to SO" - well, in the first instance it's up to this community. There's no way anyone from the Stack Overflow mod team is even going to raise the possibility with the CMs unless you guys say you'd like it to happen.

"Do you have any interests to declare about Cytoscape?" - no, none. I'm just a Stack Overflow user who doesn't like valuable content getting purged from the internet or its creation prevented, nor skilled and altruistic people (like Scooter seems to be) getting their work rebuffed, and would like to see if there's a way to avoid those outcomes while still satisfying the rules of SO and the network (... and while not antagonising you guys on Bioinformatics, either!).

It does seem to be blatantly off topic on SO. I think you can certainly go ahead and edit the wiki suggesting this site for biological questions and either U&L or SU for the rest. I'd wait for some more reactions here before triggering any further action (although our Meta here isn't really very active).

@terdon Yeah, I noticed the fairly inactive Meta. I was loathe to suggest this until you also brought it up, but if you want to get some eyeballs here and think it's appropriate to do so, you could always feature this question for a couple of days so it shows up in the sidebar on the main site. (Doing so routinely for questions you deem worthy of community attention might be a good policy on a site with an inactive Meta.)

Yep, I was thinking the same. It's the only way to get some eyeballs on inactive metas indeed. Done now.

@M__ By the way, something I missed before but seems worth noting - you mention "unauthorised commercial use" of SO, but Cytoscape is open source and it's not obvious to me that the Cytoscape dev team or The Cytoscape Consortium (a nonprofit) are properly understood as "commercial" orgs at all, nor that Scooter - an academic - personally receives any compensation from them. I don't think money is a pertinent part of the story here, so let's be cautious about saying anything potentially untrue about these people - we're going to want to collaborate with them on friendly terms, after all.

Thanks @MarkAmery it all looks good. Open source project focused on biological molecular data and no conflicts of interest.

An update: I've emailed Scooter. Now we wait and see what happens next!

First off, thank you for taking the time to post here and ask. That is always appreciated!
My take would be that the questions will indeed be welcome and on topic here but only as long as they are about using Cytoscape to analyze biological data. In principle, the tool itself is just a general utility to analyze network data. Yes, it is very much used in bioinformatics, but there is no reason someone can't use Cytoscape to analyze any kind of network/graph data, and we don't want questions about counting Facebook connections or whatever here.
Installing it I think would be OK. My thinking is that since it is indeed a standard workhorse for anyone analyzing biological networks, and that is a large chunk of the community, many bioinformaticians might end up needing help installing it. More importantly, even if the OP isn't working in bioinformatics, any installation issues we can resolve are likely to help someone else who is working in the field, so I would argue such questions would be helpful here.
I would therefore propose migrating questions about installation and general use, but not those that explicitly focus on data that are not from the world of bioinformatics. For such questions, those that are about using Cytoscape on non-biological data, I would suggest posting either on Unix & Linux (assuming the OS the software is used on is a *nix flavor), or Superuser if the tools is being run on Windows.
In other words, if the question is about installing the tool or using it to analyze biological data, send it to us. If the question is about using it but not to analyze biological data, send it to U&L or SU.
I don't think SE would be willing to change the 60 day limit and that would likely require dev effort and manual DB interventions so I doubt it is worth it. I would focus on the newer questions instead.

Please note that this is my personal take as a user. Don't be distracted by my diamond, if others disagree and have better proposals, they may well be right. Let's see what the community has to say.

FWIW, any CM should be able to do a mass migration IF that was desired - the tool for this was originally created to allow CMs to move questions when closing a failed site, and just takes a list of question IDs. Also... Random trivia: in years past, I used cytoscape.js for visualizing networks of users on most of these sites when investigating voting fraud, and made good use of some questions on SO when implementing that; certainly wouldn't expect a blind mass migration to be appropriate.

Thanks @Shog9, that's good to know. I had thought it was more of an actual SQL command and so would require a dev since most of the current batch of CMs aren't programmers so are, very understandably, leery of running manual commands.  I am more interested in whatever tool you have that brought this post to your attention though! I didn't even need to mention your name three times or anything :P

Was browsing MSO and saw mention of Cytoscape - still have fond memories of working with the JS lib, so followed the trail to see where it led.

@terdon Since it was me who originally raised the idea, I just want to explicitly note that I, personally, am not gonna follow up on getting questions migrated. I figure if it's gonna happen, it needs an SME to look over the questions and figure out which ones are off-topic-on-SO-but-on-topic-on-BSE & construct a list of Qs to migrate; then it ought to get run it past either the Stack Overflow mods via a mod chat or the wider community via Meta; and finally a mod needs to raise the request to a CM. As a non-mod and non-SME, I'm not up to any of that, so I wish you all well and bow out here.

Cytoscape looks like a well-developed open source tool, and we have had similar requests from a couple of developers in the past. I'm happy for questions to be migrated over, even if they don't explicitly mention a bioinformatics project, as long as they relate to a specific problem.
This question is an example of a generally-applicable Cytoscape question that isn't explicitly about bioinformatics (which I'd be happy to be migrated here):
https://stackoverflow.com/questions/48177816/how-to-change-nodes-color-individually-in-cytoscape/48326939#48326939
It is applicable to a general Cytoscape problem, and answers would help people who use Cytoscape for its intended purpose.
Updating the documentation for Cytoscape would also be a good idea.
FWIW, I don't as a general rule modify answers or posts to remove chatty text (despite this being against the official Stack Exchange policy). If the answers are otherwise good quality, I don't mind gratitude or other similar embellishments.

Agreed, if the question is broad enough that it could well be applied to a bioinformatics issue, we should welcome it. I would still close questions that are explicitly not about a biological question, say if the OP is trying to plot connections between movies and actors or whatever, but if they don't make it explicit, and the question can be asked when working in bioinformatics, bring it on.

Okay so in summary from the Mod side of things, the answer is 'yes' to all questions. It's a well-developed open-source project focused on bioinformatics with the OP having no conflict of interest. The singular request is to update the documentation for this site.
Lets wait to see what other members might want to say. Whether we've anyone knowledgeable about Cytoscape is a different question.

I expect we have many people knowledgeable about cytoscape. It is a standard workhorse for network analysis, so anyone who's worked on PPI networks or gene regulatory networks is very likely to have a good working knowledge of cytoscape. I've used it a lot myself, and I doubt I'm alone.

Okay thanks @terdon, I just do this de novo via graph theory.

Hi all -- Cytoscape trouble-maker here.  Sounds good to us!  We've updated our documentation to point to bioinformatics.stackexchange.com and I will now include that in my weekly triage.  It would be really helpful if we could migrate as many of the Stack Overflow [cytoscape] but not [cytoscape.js] tagged posts over to here to provide some context.  By the way, any questions about network biology, even if they don't explicitly involve Cytoscape are welcome.


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Would questions on whole cell modeling get answers at this site?
I am self-learning about whole cell modeling, specifically An introduction to whole-cell modeling and Fundamentals of Systems Biology: From Synthetic Circuits to Whole-cell Models. While my background is decades of programming, for cellular biology it is only skimming through a few books. While I can ask the authors and research groups questions directly I would prefer to only ask them specific questions and get answers to more general topic questions related to whole cell modeling elsewhere; e.g. if I ask about BioNetGen that would general, but asking how to tie BioNetGen in with other software and methodologies specific to the groups would be to specific for here.
So are there people at this site who can answer questions about whole cell modeling in general?

Could you give a more specific example? It sounds like it would likely be on topic but since it isn't my field, I can't be sure from your description. But as a general rule, asking about using bioinformatics tools and/or frameworks is on topic, yes.

@terdon I don't have any specific questions now, but if I do I will ask in the regular site. I did have one specific question but figured it out, e.g. Can someone compare and contrast BNGL (BioNetGen Language) with SBML (System Biology Markup Lanague)?

@GuyCoder that would be a nice question to have, remember that you can self answer your questions too. (And I would like to know the answer to that question without digging the formatting descriptions ;)

I guess it will depend on the question. I  would expect it to be on topic, in principle, so give it a go!

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rtag suggestion
I feel like we should sort out tags related to graphics. Right now there tags
visualization, plotting, figure-explanation + tool/package specific like ggplot2.
I identify three distinct problems related to graphics:

how to visualize <my data>? -> philosophical problem
how can I reproduce figure of somebody else? -> coding/crafting problem
how to understand figure of somebody else? -> science interpretation problem

The last one has very clear tag (and I love it). But the first two are blended in visualization and plotting tags.
I suggest to remove tag plotting and add description that would correspond to following tag scheme:

how to visualize <my data>? -> visualization
how can I reproduce figure of somebody else? -> figure-reproduction
how to understand figure of somebody else? -> figure-explanation

Why do I care? I usually can not help with 1 and 3, but I really like to do 2 (especially if it's core-R graph).
Can you think of other topics related to graphics? Do you think these scheme would work? Huh?

I went on and created the tag figure-reproduction (I found two questions that were candidates of this tag)

Sounds like a good structured way of tagging. However, I know from my own experience when writing a question, tagging is the last part before submitting, and usually I quickly choose tags that first pop up into my mind. So if I had a question in one of your 3 categories, I would probably tag them with plotting or visualization anyway. Maybe I would add R as well. I think not many users will do a thorough research of finding the right and perfect tag for their question. That does not mean it wouldn't be meaningful to create these tags, but I expect many 'wrongly' tagged questions as a consequence.

This is a good point. I like when the related tags would have links to each other in the excerpt.

The auto fill function for tags now, only works to extend what you are typing. So for example if you type vi, you'll get visualization, webservice, and Gviz. It would be cool to see some related tags too.

@KamilSJaron That's what excerpts are for, to guide how to use tags. About this answer, I think we can can retag the question as they come, there are few questions, so I wouldn't expect we miss some questions.

@b.nota that could be a request to the DAG team for the whole SE

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Are (brain) imaging signal processing questions on topic?
So as an example, here 's a brain imaging signal processing question on CogSci. Although this question is well-prepared and on topic there, it will very likely never receive an answer.
This type of question also appears sometimes at Bio.SE.
Now I'd like to migrate the linked question, and perhaps others too if applicable.
Are signal processing questions on imaging on topic and welcomed here?

tldr: At present, such questions are probably less likely to get answered here than where they are.
I would have thought you'd have more cog. neuro. folks on CogSci than we would here (I'm one of the few neuroscientists here). While I think one could argue that biological image and signal processing questions fall under the purview of bioinformatics, in practice I don't foresee anyone on the site currently being familiar enough with the topics to offer any real help. Most of the time bioinfo is an umbrella term for NGS, microarray, proteomics and (sometimes) structure. So while I don't personally think such posts are strictly off-topic, I also don't think it's worth migrating them. I hope for this to change in the future as the site's user-base increases.
Update: See also this meta question from earlier. Maybe if we make this site a hub for such questions we can encourage those communities to join. I would certainly welcome that.

Thanks I'll leave them where they are then. Cheers.

Bioinformatics is just as much things like comparative genomics, phylogenetics etc. I'm always surprised when I encounter people who think of it as being essentially the four things you mentioned.

Yeah, I'm all for encouraging the broader field to participate. We NGS folks just overwhelm everyone else with our shear numbers.

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Are electrophysiology questions on topic?
As a mod on Bio and CogSci I am faced with quite some posts that are overlapping in all three fields. In the field of Bioinformatics I see a lot of questions (relatively spoken, as the absolute number of hardcore bioinformatics questions is, well, relatively low on both sites so to speak :-) going unanswered, simply because we lack the expertise.
Now it's about electrophysiology related questions, as a recent example see How to analyse EEG files recorded from BVA?. So this specific question is on the analysis of EEG data, but I think we should gather ERP, ECoG, single-fiber recordings and what not in this realm too and try to address the global picture here.
Now I'm not talking about hardcore signal processing questions (different stack), but there are quite often questions like:

Program w gives output x, but I need output y for use in program z (data/file conversion issues);
I use program w that outputs x, but output parameter y is missing from x, where is it (OP screwed up settings and misses some output parameter)?
Or in case of the linked question, I use program w (EEGLab) and output x doesn't make sense (OP doesn't know what they are doing).

Are these sort of questions on topic and welcomed here?

My personal definition of bioinformatics has always been "any application of computers to answer biological questions". By that definition, what you're asking which essentially boils down to analyzing biological data in silico would indeed be on topic.
However, we are a very new site and our scope isn't yet as clear as it could be. Many of the young whippersnappers current crop of bioinformaticians seem to think that bioinformatics is only NGS analysis. We certainly have an over representation of NGS folks in our user base, anyway. This might mean that we will indeed become a resource primarily for NGS questions. I hope we won't since I think it would be a shame to limit our scope that way, but scope is something that grows out of community consensus so we'll just have to wait and see.
So, I would say that yes, they are on topic or, at least, they could be. This is my own personal opinion as a user, however, I am not expressing the view of the community or of the moderation team. But I would say bring them over and we'll see how they do. I fear most of them will probably not get useful answers but only because we don't have many users who're experts in that field. Still worth a try though.

That's awesome terdon. The thing is that this type of question won't be answered over at CogSci; we lack the expertise in that arena. I could migrate that type of question to Bio, but I doubt it will be received warmly over there. I know it would be better off here for sure. I promise the numbers are not so big so we won't be blemishing your nice and shiny %answered site stat ;-) Btw - congratz with your mod-ship here!!

@AliceD you're welcome and right back at'cha :). I want to stress though that this is just my own opinion and not What The Mods Say® or anything. So the community might well decide that they're off topic. Still, we won't know unless we try. In any case, format conversion questions are often simple text parsing issues and those are explicitly on topic. So those, at least, should do fine here.

I understand it may be not everyone's pov. That's why I was a little hesitant to accept the answer up until the point I saw that shiny diamond >__<

whippersnappers?? haha  O.O


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2022 Community Moderator Election Results
Bioinformatics's second moderator election has come to a close. Since there were not enough candidates for a competitive election, we simply appointed the candidates who nominated themselves as pro-tem mods, so the team would have a total of 3 moderators (more on mods stepping down below):

They'll be joining the existing crew shortly — please thank them for volunteering, and share your assistance and advice with them as they learn the ropes!
Please also join me in thanking the following two users, who'll be stepping down from their positions as moderators:

Thank you @terdon and @M__ for stepping up!

Thank you for stepping up first!

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