Forum:Preparation for Bioinformatics.SE closing
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5.7 years ago
John 13k

If I may preface this with a little observation, i've noticed that when one bioinformatic community talks about another, the Biostars folk are consistently respectful and positive in the face of sometimes quite harsh criticism. Perhaps one needs an easy-going mindset to read/answer 10 boring questions before they come across 1 that makes them stop and think. Regardless, I hope that continues :)

So it appears that for all the reasons predicted on the other thread, the Bioinformatics SE isn't picking up the sort of steam that is perhaps desired: https://bioinformatics.meta.stackexchange.com/questions/40/is-there-a-large-enough-community-to-sustain-this-site

Now i think actually this is a bit of a shame, because any amount of effort spent making bioinformatics more of a community thing is effort well spent. A lot of the headaches in bioinformatics are dealing with decisions isolated people made, be it a weird analysis, non-intuitive tooling, data formats that don't store what other people want, etc. Less isolation is always a good thing.

But as it appears that isn't going to go through, perhaps now would be a good time for us to listen to the fair criticism that was received about Biostars and, essentially, make a prioritised list of ways Biostars could be better. Perhaps this whole SE affair will have a happy ending, if it promotes changes in the Biostars network that ultimately grows the community.

The biggest criticism i've heard of Biostars so far is the low quality questions/answers. Personally, i don't see low quality answers (which probably means i'm the one providing them...!), but i do see low-quality questions. Of course. When most people get started in the field because data.fastq was e-mailed to them by a collaborator, this is not unexpected. Perhaps the solution is to have an "advanced question" type, so one can filter on only the advanced questions (that need a certain amount of rep to ask)? I don't know. All i'm saying is, now would be a good time to think about how Biostars can fill the void that is clearly there if people want a SE so much. The end-goal would be to go to SE after the decision to close has been made, with a "we heard you and we changed - try us out now."

Otherwise... i'm worried that there will be some resentment to Biostars. I'm already starting to see it actually. The typical "our community would be much better if only yours didn't exist!" stuff. Downvote logic.

biostars Forum • 3.2k views
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I also find that there are poorly written questions on Biostars but do you think that, on other sites, people are only asking well formulated questions ? If not, how do these other sites deal with bad questions ? Maybe we're getting more low quality questions because we're more welcoming to newcomers and are willing to put some effort into understanding these questions.

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I think you've hit the nail on the head. At least on the bioinfo.SE site the "broad" questions get a lot of downvotes and then the comment section starts immediately looking like that often seen here. I've found that amusing.

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There is no low-quality content at least on the first page right now, otherwise I had closed it already ;P

Beware: there is no good metric for low or high quality of content, I know of, and reports are mostly episodical, the same might be true for the 'hostility' argument against SE. We should not get drawn into this 'alternative facts' kind of thing.

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FYI, bioinformatics.SE is going into public beta in a week.

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Correction, it's public as of a couple hours ago.

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Yeah :) In my defence, the SE guy said the minimum number of questions is 150 in the first three weeks, and it's been 3 weeks and there's 147 questions, so it's just scraping through - however i'm sure traffic will pick up now it's in public beta. The next month will be the deciding month I think. Meritocracy ftw!

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Says one more day of private beta when I checked now. So perhaps sooner than a week.

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Well, "sometime this week" according to the SE folks.

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Oh that's great! :D

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5.7 years ago

I guess that the way to avoid "new people asking bad questions" is to scare those new people away, and that is not desirable, I guess. A lot of users really depend on biostars to get their research done, without suitable support in their institute. The only thing we can ask users is to improve their question. A while ago someone suggested a post-template to make sure users think about everything they should mention (organism, technology,...). I still think that's a good idea, or have boxes open in which users have to choose the organism and technology, for more structured tags.

It might be obvious to us which information is required, but I can imagine it's not obvious when you are just getting started.

And sometimes I find it hard to find my own posts from a while ago, so yes, the search function could use an improvement.

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Seconding the 'finding my own posts' point, only yesterday I was trying to find an old answer of mine to put to a duplicate question and gave up after 5 mins of searching and scrolling because I couldn't find it.

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the way to avoid "new people asking bad questions" is to scare those new people away

This is what SE does IMO.

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Exactly. And then you artificially reduce the number of bad questions. That's cheating.

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@wouter: more than cheating, it is not encouraging beginners. How can the field/community grow with such strong restrictions? How can the knowledge is passed to next generation?

P.S: I was once blocked from SE, I gave my best to compose the question with my the then programming knowledge.

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Obviously, yes, it doesn't only improve your stats but also cracks down on those users who need the support the most.

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Depends what SE site. StackOverflow has this tendency, but I find that this is not the case in biology SE, where users usually comment on how to improve a question rather than downvote.

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Yes I am in agreement with such kind post templates and structured tags. And to be honest when someone hits it those tags they will definitely see similar question popping up. Is it possible to do that? like how we also see in SO where while typing a question if its similar there are pop-ops or SEO brings forth such similar string matches. I do not know how complex will it be but this can be a feature for not only redundant but also low-quality stuff. For redundant as I mention in a comment that posts can be merged and notifications will be reached to the users.

I also will voice out something which I mentioned earlier. Whenever a newbie is joining they should receive an email of how to use the community and how to improve their quality of questioning, what kind of hit and search they can do and how they should use all the features of the site. This makes them go through the manual once and we might be able to tackle redundant queries and low-quality queries.

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Can't you use google to search previous posts on biostars?

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Yeah, but if you're...prolific in posting... then even that works poorly.

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5.7 years ago

To be fair to the bioinfo.SE site, I don't know how it can reasonably be expected to succeed when it stays in a private beta. The bar for submitting questions and interacting is then higher than reasonable. Anyway, I wouldn't write the site off just yet, though I agree that it's probably not going to last.

Anyway, my biggest takes are as follows:

1. Some technical infrastructure development would be quite nice. The delineation between the question and meta section on SE keeps things a bit cleaner. Likewise, the chat thing could be useful, though honestly with twitter already heavily in use I'm not sure how necessary it really is (perhaps for the direct communication between moderators, since the last thing I want is yet ANOTHER way for people to directly send me their questions (in fact, someone is doing just that right now on the bioinfo.SE site!)).
2. Perhaps an ability to filter questions by submitter's reputation would be nice. That'd remove complaints about "question quality". I find such complaints largely absurd since the field is mostly comprised by people with no formal training...but whatever.

Update: 3. I like that I don't have to reload pages on bioinfo.SE, it'd be nice to have that here too.

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My take on filtering questions is that it would turn Biostars into a site "for experts by experts".

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Perhaps pre-screening would be a better option. If we (say mods) could get a whack at new questions before they make it to main page (for say 15 mins from time of posting) they could be flagged for additional clarification, repeat questions, answers previously found on biostars etc).

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This is a good idea. How about a new section at the top like "Screening", and if you have 0 rep your posts can only be tagged as 'screening' type (rather than question, forum, etc). The main landing page doesn't display posts of the screening type. If a user asks a question that cannot be answered (due to not enough info), it never leaves screening. However, any user can visit Screening and answer a question if they wish. That would cut probably more than 50% of the low-quality-questions from the main page, and I think it could be set up pretty easily as it's just a minor tweak to the main-page's SQL query to exclude the screening type.

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This would then be a nicer version of what's on SE, where questions from new people are flagged for review but otherwise immediately posted.

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I agree to Devon and he is pretty on point. I would just say something which I noticed that the experienced users and experts should refrain from. I have seen a lot of low-quality questions being answered by our experts and experienced users as well. I know it is difficult to resist but I guess we have a lot let it go as well. Maybe a newbie can answer them, gives them a chance to articulately answer some problems with reasoning. In turn, experts should refrain from such answers so that they are unattended and then we do not attend to such low-quality queries. If a newbie can answer it, well and good else they can be moderated or retired.

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I understand your motive, but I'm not sure if I agree with refraining from answering bad/easy(?) questions. I would only do so for repetitive offenders.

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I would say it can be left unattended for some time and see if a newbie can answer it else someone else can who is an expert depending on the fact it's not low quality or redundant. I suppose by that time moderator will be able to see the content and take a decision of merging it to the similar query made and user gets a notification.

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One reason Biostars is popular is due to near instant gratification (if that is the right word to use) that users get. Many new users (while they should have searched biostars before) post a question (true for most questions asking for script/one-liners/R type questions) and generally have those answered under 15 mins. Presumably this allows them to go forward with whatever they are trying to accomplish.

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then we should not think or complain about redundant questions or even low-quality queries. Most of these type of queries are as a matter of fact not that mind boggling or tricky. They are pretty straight-forward and also if a better search is made users can find similar problems and solve it. But they rely on us and we help them. We also amount to risk of setting score of redundancy or low-quality queries. I actually do not like to term them low-quality since they seem to low for experts but for a newbie, it should not be. These queries can be reframed in a better way to get a structure. But am mentioning it as low-quality since I see a lot of users mentioning about them. For me as of now the most important will be to tackle the redundant posts and that will really help both users and also the site.

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5.7 years ago

My main gripe with Biostars is the absence of a decent search engine. But then the site has survived many years without one so it doesn't seem like a critical feature.

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I think the difficulty searching adds to the repeated low quality questions.

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Search plus inability to look at previous messages. Current biostars code seems to cut those off arbitrarily (e.g. if I want to look at my past messages via the message button at top) and only shows the last days worth or so.

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I agree to the point of having a better search engine on the Biostars and that might lead to a lot of improvement tbh. We can take cues from bioinfo.SE to make this site much more presentable and remove some glitches that we have whcih are rightly being pointed out by the users who are here for a long time. About low quality questions, I always agree there are but we do not chide or rebuke but take them along to make them understand and get a grasp. We are not commercial entity like theirs. Obviously we can always monitor and filter low quality questions and merge them or put certain tags that can actually help the users.

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Yes it survived many years....and that would be my main point. The site is dated. However. I do also understand that time is limited and nobody ... has time to do it.

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5.7 years ago
me ▴ 750

Low quality questions is not a problem that can be solved. Stackexchange sites have this as much and also worse than biostars. While I am not a super active biostars user. I do monitor it. The nice thing about biostars is that it does not tie the community to one commercial party. While there are benefits to doing so, our community with seqanswers and biostars show that this is not required. I feel that too often people jump on the "for free" forgetting about what happens if it stops being free.

Because the stack exchange site does not offer to take all biostars content and absorb it, it will by default spit the community. If it does bioinformatics.se become public/active, I think I will write a bot that replicates all their questions here. And if answered here put a post there about it. I hope that such an action will guide new community members to this community and avoid splitting it.

The semantic web community has been burned by SE changing their mind and I wouldn't want to have this happen to this community either.

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5.7 years ago
Daniel ★ 3.9k

I think that could be solved quite easily with (1 ) a more restricted set of tags for questions to stop fragmenting, and (2) allowing them to be community-suggested so that new users don't have to be blamed for misattributing a question (this works quite well for games on steam) i.e.

Based on community votes this question has been tagged: Beginner, RNAseq, samtools

Secondly, having a 'drop tag' filter option on the main page for users so you can view the full submissions but exclude specific tags i.e. beginner, or a language you can't help with, or job postings etc. would be good. Currently the option is there to go to specific tags, but the inverse would be more helpful in my opinion.

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tags improvement is definitely a good suggestion but it will work well with improved search engine. I reckon what about merging questions and answers of a more similar kind or basic kinds that have a similar answer into one have put the comments and answers into one thread. This is usually seen in Quora. I do not if we can do it in BIostars. It is just a suggestion

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5.7 years ago
Rohit ★ 1.5k

I personally find it easier to grab questions with google using "question+biostar" than a key-word search on biostars itself. Can there be a feature extension that says google near the search box instead of restricting it to the keyword search in the site alone? Hopefully I am not pointing out something that is too much of a hassle, since the site-developers have always put in their own time without pay - something much more than you can ask for.

Additionally, I remember biostars having a downvote feature in the beginning which was later removed (or did I mix up). The problem with this is that it deters newbies as Wouter pointed out. There can be a feature which requires approval of a moderator for new questions, but this takes up personal time of the moderators, which might not be apt. So a lmgtfy before posting new ones would be nice.

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This is such a common request i'm sure it is not unreasonable. It might be difficult to solve though, as full-text-search of a database is usually very slow unless one uses an index designed for it like Apache Lucene or similar. I don't know the backend of Biostars well enough to know if this is easy or hard to do, but I do know the admins are aware of it. I'm hoping that the admins appreciate that if there was ever a good time to add this feature it would be now - but i also appreciate it's probably easier said than done.