Forum: StackExchange/Area51 bioinformatics is back
17
gravatar for Pierre Lindenbaum
5 days ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum92k wrote:

i would like to bring to your attention that the old discussion of "Biostars vs StackExchange" is back.

While I don't really care about the platform, I wouldn't like that StackExchange releases a new platform without biostars.

See also : https://groups.google.com/forum/#!msg/biostar-central/bMgmtoEcQV8/NbdzVo8eRXsJ;context-place=forum/biostar-central

area51 forum biostars • 1.1k views
ADD COMMENTlink modified 2 days ago by John11k • written 5 days ago by Pierre Lindenbaum92k
12

I just don't get the impetus behind yet another site. The only answer I've seen on SE is that "biostars accepts too many low quality questions". Right, but that's also the problem with stack exchange, namely that it's a largely toxic environment for new folks.

ADD REPLYlink written 4 days ago by Devon Ryan64k
9

Low quality questions because the majority of people who come on here to learn often have no idea what they are doing and no formal training in bioinformatics. When I joined a little over a year and a half ago, my first question (on another account who's password I have forgotten) was 'how do I intersect bed files'. Literally it. Now I know enough to help other users with their own questions.

The amount that I have learned from Biostars is just crazy, and I always recommend it to people when they ask me how to get started. "Just go read Biostars posts".

I hate SE as a medium, if you ask a simple question you get downvoted to oblivion and at best you get a condescending comment about your question without even an answer. It's a horrible teaching platform.

ADD REPLYlink modified 4 days ago • written 4 days ago by Sinji2.1k
4

I completely agree with this. I started my phd as the only bioinformatics student in a molecular lab. Biostars was extremely helpful in not just in answering my questions, but also in expanding my knowledge. I learned tons from reading questions/answers that have no relevance to my phd. I don't see Biostars as just another question/answer site. I tell people routinely that I graduated from the university of biostars.

ADD REPLYlink modified 4 days ago • written 4 days ago by Damian Kao14k
4

I hate SE as a medium, if you ask a simple question you get downvoted to oblivion and at best you get a condescending comment about your question without even an answer. It's a horrible teaching platform.

I disagree with this. I have used both Biostars and SE while learning and both helped me immensely. What I like about SE is that it is truly a Q&A site: ask a straight question get a straight answer. Yes, one gets one's butt spanked here and there after some poorly formated/reasoned questions, but it also teaches something fundamental in the process: think clearly what the question is. I have quite often answered my own questions while writing a post there. It also very easy to find what I am looking for, which makes it less likely to ask duplicated questions. Actually overall I probably get more help from SE than Biostars.

Biostars has its merits, friendly community and all that, but the downside is that it can be very frustrating when one is trying to help but the information has to be dragged out of the OP clenched fits. But my major issue with Biostars is that frequently answers are deep in comments, and often answers are comments. In effect less of a Q&A site and more of a forum. It is not easy to parse threads to look for an answer. This is a solvable issue with stricter moderation: move comments to answers, or ask users to aggregate comments as an answer to clean up the clutter. Also, politely ask users to accept those answers that solved the issue. It will not make this site less friendly, but it will make it more helpful.

ADD REPLYlink written 4 days ago by A. Domingues1.2k
3

IIRC, in 2012/2013 when someone argued biostar comments are superior to SE, I said something like (couldn't find the thread): it is not because SE doesn't have the manpower to implement nested comments; it is because such comments are distracting. SE also puts a 512-character hard limit on comments, it hides some comments if there are too many, and it doesn't add comment upvotes towards the question. All these discourage you to put answers into comments. I still think biostar should follow SE. That is the best way to keep biostar as a Q&A site, not a forum.

ADD REPLYlink written 4 days ago by lh329k
3

You forget to mention that asking 'good questions' requires a more than basic background in whatever the OP is asking. This is my problem with the SE system. You are REQUIRED to know anything in order to ask anything. How does a person whose never been exposed to bioinformatics and has absolutely no idea how to computationally solve a problem, much less the keywords to search for in order to solve that problem, create a question that is clear enough to get answered on SE?

Seriously, it seems that half the time I post on there, half my post gets removed because it's 'not necessary'. SE is great for those of us who already understand the field, and the terminology, we get quick answers that are helpful, and correct. But will SE cater to those that are new to the field, and looking to START a Bioinformatics career? No. Definitely not.

ADD REPLYlink written 3 days ago by Sinji2.1k
1

I think many people criticizing SE are generalizing their experiences in stack overflow (SO) to SE. SO is over crowded and diversified. It is a hell to newcomers. However, many focused SE communities are fairly friendly. If you look at the biology SE, you can see questions asked by amateurs and still get answered. You also haven't used the old biostar, I guess. It did impose stricter rules, but it was still friendly overall. As long as you put thoughts and work in your questions, even very basic ones could get sometimes epic answers.

ADD REPLYlink written 3 days ago by lh329k
1

I have very negative experiences with biology SE. Moderators seem urged to comment on every question, often commenting that they think that something is not possible (without providing support). Also I made one particularly bad experience, when a difficult question of mine within my very own domain was closed with some vague accusation that OP wouldn't understand the basics. However I felt most upset, when I opened their chat channel to comment. There I would see that the moderators had publicly used very unprofessional and derogatory langue to discuss my post (I suspect that it never crossed their mind that seemingly superficially sounding questions can address a difficult problem, or that such such questions would be asked by someone who would know the field very well - and to a level that would exceed that of other biologists like themselves that would professionally focus on other fields).

ADD REPLYlink modified 2 days ago • written 2 days ago by unksci100

Yes, and I suffered from that at the beginning, but I never had a post removed from SE. I got some slaps for poor questions and had to do some edits but otherwise fine. In the process I learned how to learn. This also means that I spend a lot of time looking for an answer before I post. Of course YMMV.

One the other hand do we want questions that show no research from the user, contain no information or are excruciatingly hard to read? Because quite a lot of these will be left without an answer.

My comment might have been read as an harsh criticism of Biostars, but I am just advocating better curation of questions and answers. Sometimes this might be as simple as telling someone that the best place to answer the question is SO or bioconductor support, and explaining how to prepare a good question. That will go a long way on improving Biostars.

Disclaimer: when I started using both SE and Biostars was a bench biologist without any knowledge of bioinformatics or programming (undergrad Turbo Pascal excluded).

ADD REPLYlink written 3 days ago by A. Domingues1.2k
1

This, exactly this. I'm already enough of an a$$ hole for the new folks to deal with, I would prefer not to inflict to stack exchange version of me on them :)

ADD REPLYlink written 4 days ago by Devon Ryan64k
2

Agreed. I'll take low quality questions any day over the toxic environment that runs rampant on Stack Exchange. As it is, I very much appreciate that BioStars isn't a part of SE.

ADD REPLYlink written 3 days ago by steve710
1

that it's a largely toxic environment for new folks

@Devon, true, for new folks, SE gives a feeling that they should leave the field immediately, new users (also new to field) feel terribly helpless, alone. This is completely opposite with Biostars, which makes it super nice. Albeit, sometime people say, you should've googled, what have you tried, previously answered..etc everyone helps solving the problem along with learning new stuff.

ADD REPLYlink written 4 days ago by venu3.5k
9

I don't see the point in diluting the user base to another community.

ADD REPLYlink written 5 days ago by WouterDeCoster16k

I agree, but whatever our opinions, a 3rd community is about to open :-)

ADD REPLYlink written 5 days ago by Pierre Lindenbaum92k
8

Can we just send everyone with a question about how to filter a fasta file based on the identifier to the new community?

ADD REPLYlink written 4 days ago by WouterDeCoster16k

@wouter, also people post already answered Biostars thread links on SE, you wrote the best example thread.

ADD REPLYlink written 4 days ago by venu3.5k

Yay, what do I win? :-P

ADD REPLYlink written 4 days ago by WouterDeCoster16k
7

Be prepared for some more cross-posts

ADD REPLYlink modified 4 days ago • written 4 days ago by venu3.5k
2

Can you remove the annoying animated GIF? It is hurting my eyes everytime I visit this thread :)

ADD REPLYlink written 4 days ago by genomax226k
1

see, on stack exchange that would have been deleted inside 30 minutes ;)

ADD REPLYlink written 4 days ago by Neilfws47k

Done! I didn't check the messages, otherwise I would've done it already :)

ADD REPLYlink written 4 days ago by venu3.5k
6

I have to say, as someone who was a SE user before a BioStars user, I do prefer it stylistically (not that that is super important). A lot of Bioinfx questions get asked on Biology.SE anyway, but often without the support of great answers.

On the other hand, I think the 'attitude' on SE is a lot more hostile some times. There is a bit of an air of condescension that I don't see on BioStars.

Just makes me think of this:

enter image description here

ADD REPLYlink written 4 days ago by jrj.healey1.2k
6

The existence of things like Forum, Discussion, and Job posts on biostars are great and would be sad to see go. Is there anything comparable on stackexchange? The stackexchange networks are notoriously hostile to things that don't have a ridiculously narrow Q&A format

ADD REPLYlink written 4 days ago by cmdcolin460

This is a good point - Tutorials and the Job Board, in particular are really nice.

ADD REPLYlink written 4 days ago by Chris Miller18k
1

Bar for commitments appears to be pretty low so I assume that is going to be reached. People who regularly contribute here could decide to stay away from other platform. Are you planning to?

ADD REPLYlink written 5 days ago by genomax226k
1

I'm certainly not planning to start sinking time into another platform.

ADD REPLYlink written 2 days ago by Lars Juhl Jensen10k

Are you planning to?

why not ? but again, I would like to avoid the creation of a 3rd community.

ADD REPLYlink written 5 days ago by Pierre Lindenbaum92k

avoid the creation of a 3rd community

How can that be achieved?

ADD REPLYlink written 5 days ago by genomax226k
1

in the "old time", both communities could be merged:

https://groups.google.com/forum/#!msg/biostar-central/bMgmtoEcQV8/NbdzVo8eRXsJ;context-place=forum/biostar-central

but it remains Istvan 's choice :-)

ADD REPLYlink written 5 days ago by Pierre Lindenbaum92k
4

I have grown to deeply dislike the monoculture and centralization of modern "social networks" where facebooks, twitters and stackexchanges dominate every aspect of our lives.

The greatest differentiating factor of Biostars relative to all of the alternatives is that it is different, independent and is not integrated with the massive information tracking industry. People posting here are not tracked, their actions are not mined then resold etc.

ADD REPLYlink written 2 days ago by Istvan Albert ♦♦ 70k

Tagging: Istvan Albert

ADD REPLYlink written 5 days ago by genomax226k
1

Only 'pro' I could see to a Bioinfx.SE coming around would be if it actually replaced BioStars (not that I want that to happen ;) ). That would at least have the benefit of Istvan and co not having to run the site themselves and deal with the development. But maybe they enjoy it - I don't know :P. If BioStars merged with a new SE meaning the user base remained, that could work (all the mods etc would be transferrable and if the large, supportive, community here could dilute the tw*ts on SE sufficiently, Bioinfo.SE could be the only nice place to be on the whole domain haha

ADD REPLYlink written 4 days ago by jrj.healey1.2k
11
gravatar for Chris Miller
4 days ago by
Chris Miller18k
Washington University in St. Louis, MO
Chris Miller18k wrote:

I can see why lousy search, difficult UI, etc are frustrating to some folks. BioStars has the community and knowledgebase, but there doesn't seem to be a clear plan to improve the site, and reach feature parity with SE. Istvan, would you care to weigh in on those topics?

More than anything, I just want to avoid fragmentation of the community.

ADD COMMENTlink written 4 days ago by Chris Miller18k
1

I am no developer so I am not sure how much effort is involved but @Istvan in principle has agreed to several wishlist items (replacing the default search engine on main page, being one of the top) over the last year or so. I think he has been busy with his regular life (and the handbook).

Like some of us who contributed on the handbook perhaps developers amongst us will step forward to help improve Biostars on the whole.

Something good is bound to come out of SE development.

ADD REPLYlink modified 4 days ago • written 4 days ago by genomax226k
1

It's fair, and I don't expect Istvan to single-handedly shoulder the load. It would be great to have a development roadmap that's transparent to the community, as well as recruitment of contributors (paid or volunteer), if the platform is going to continue to grow. Right now, things seem to have stagnated: https://github.com/ialbert/biostar-central

ADD REPLYlink written 4 days ago by Chris Miller18k
1

I agree with the search being suboptimal - on the other hand, we always have Google and as a matter of fact that is how the majority of users come in from.

I found that the "Similar Posts" column in the right column is the best way to find relevant content.

One of the mistakes we initially made is that we rewrote Biostars too frequently (on a yearly basis almost). This took a lot of effort - for example, there is a fully rewritten but never released (and already obsolete) version of Biostars.

The current delay is by design - we want to let the ideas age a little bit more, to allow us to figure out what is it what we really need rather than what we think should have.

ADD REPLYlink written 2 days ago by Istvan Albert ♦♦ 70k

If the SE-like search function could be implemented on Biostars that would be great. So often google fails to turn up an answer/SE thread that is right, yet when I come to post a question, the suggested similar questions are more often than not, what I was looking for all along.

ADD REPLYlink written 4 days ago by jrj.healey1.2k

Well, I guess that's a feature we definitely can improve on, and probably isn't impossible. A problem which is harder to solve is that new people often don't even know which terms to search for.

ADD REPLYlink written 4 days ago by WouterDeCoster16k

Like you and I have asked people many times - if posters can formulate a succinct title for their question, some of those words are likely going to be appropriate search terms.

ADD REPLYlink modified 4 days ago • written 4 days ago by genomax226k

Yeah I think the latter is very much the 'nature of the beast'. That will never really go away - and probably shouldn't, because that means there are constantly new people (myself included) coming in to the field. Bioinformatics is an interesting discipline because its something that very few people ever have any formal training in, but people will find themselves needing to do increasingly.

ADD REPLYlink written 4 days ago by jrj.healey1.2k
6
gravatar for Alex Reynolds
3 days ago by
Alex Reynolds18k
Seattle, WA USA
Alex Reynolds18k wrote:

One thing I like about BioStars is that the cool kids can't gang up and vote down people they don't like. Unlike official SE sites, say, with all the cool kids who get to vote down people whose views they don't like. Which really sucks. I'm glad we don't have that bullshit here. (I mean, we have a cool-kid problem, unfortunately, but at least the damage the cool kids do is limited to them just opening their big mouths.)

ADD COMMENTlink modified 3 days ago • written 3 days ago by Alex Reynolds18k

:D

ADD REPLYlink written 2 days ago by John11k
5
gravatar for Damian Kao
3 days ago by
Damian Kao14k
UK
Damian Kao14k wrote:

I think the main problem people have with BioStar boils down to an identity crisis. Is BioStar a Q and A site or a forum?

A Q and A type site requires the question to be technical and precise. If someone asks how to convert a format to another format, that can be easily answered.

But if someone asks what is the best method of assembling this genome given X, Y and Z, then there really are no clear answers that can be given. Cases like that requires more of a discussion which then becomes a long chain of comments.

An argument can be made that these types of more abstract and less technical questions do not belong on BioStar. However, I've personally benefitted hugely from the forum-type discussions that occurs within these questions. I think there are a lot of people out there that do not have the computational support or community in their local area to discuss these topics. And BioStars has become the bioinformatics community for them.

On the other hand, I can also see how these long messy comment chains ruins the organization of the site with redundant questions and vague answers.

Maybe the solution is to actually implement a real forum interface along side the Q and A interface. However, I can see that as being a lot of work to put on Istvan. Another solution is to just migrate to SE for Q/A and use SeqAnswers for forum type discussions.

ADD COMMENTlink written 3 days ago by Damian Kao14k
4

Yes, the most useful questions on SE tend to be off-topic and under threat by the rigid Asperger people who run those sites.

ADD REPLYlink written 3 days ago by Jeremy Leipzig16k
3

You are used to the forum-like biostar – you want to discuss a lot in comments. In a proper Q&A format, if you think you know better on this genome assembly problem, provide another answer. Explain clearly why it is better than other alternatives and let users play the judge. When someone reach the question via a google search, they read a few answers and make a choice based on the votes and the arguments you present in answer. They can also unfold comments if they have enough background to make their own judgement. I agree forum-like discussions are needed sometimes (e.g. this thread), but a lot of comments in biostar are unnecessary and distractive.

ADD REPLYlink written 3 days ago by lh329k

Perhaps there is a happy medium? Maybe certain stellar threads could be archived in to an FAQ style separate region of the domain, and rather than rehashing the same straighforward questions, people can be directed there. Though I suppose this is sort of what the Handbook is.

For sure, I like the forum-esque nature of Biostars compared to SE, but it would be a shame to lose the Q/A which also more often than not works nicely.

ADD REPLYlink written 3 days ago by jrj.healey1.2k
5
gravatar for Charles Plessy
3 days ago by
Charles Plessy1.6k
Japan
Charles Plessy1.6k wrote:

Biostars's engine is is Free software while StackExchange's engine is proprietary. Given the importance of opening source code in bioinformatics and science in general, I hope that the community will appreciate and continue to post on Biostars, that gives the example to follow.

ADD COMMENTlink written 3 days ago by Charles Plessy1.6k
4

Not sure the open source argument works. If someone takes an open source project and fixes a bug or forks the code to make an improved tool, the world is slightly better and everyone is happier. If someone makes a new Biostars, it's a big mess (see this post).

Biostars is not a software. It's a community. If anything, the software is probably the weakest part of Biostars (as highlighted by many comments in this post) and the biggest draw of StackExchange.

ADD REPLYlink modified 2 days ago • written 2 days ago by igor3.9k
3
gravatar for Lluís R.
4 days ago by
Lluís R.380
Spain, Barcelona
Lluís R.380 wrote:

When Bioconductor opened its own support.bioconductor forking Biostars I don't recall any post about diluting the user base.

That said, the reason of Biostars being separated from StackExchange was the license. And StackExchange has made efforts to provide guidance about the license of the code in their site. Which I resume as: if you copy textually from anywhere, copy also the link to the place otherwise do as you like. If pieces of your software end up having mixed license, so it is. But you can overpass the requirements and SE will not persecute you.

However in the same answer from Ivstar show that the goal of Biostars is to be "a destination where one could also learn how to be a good bioinformatician". So to this regards a Q&A site in Stack Exhange will not overlap with Biostars. Biostars is for learning to be a good bioinformatician. Bioinformatics.SE would be for learning how to do bioinformatics.

I usually go to Biostars, suppport.bioconductor and Stack Exchange sites, as long as I learn how to do what I want/need I will keep going wherever I find the answer.


I like much more the possibility to downvotes of StackExchange. The point of StackExchange is not to rule all the Q&A sites, but to provide a quality content of questions and answers. (Like The Biostar Handbook aims to provide "the most accurate and relevant information" in bioinformatics). My opinion is pretty much in the same lines as this old answer after moving out from SE1.
Here I can post a question related, without any effort and if people is willing I get free answers, which I am not sure it is on the lines of learning to be a good bioinformatician if I don't put effort solving my problems before asking... Surely the expectation in StackExchange (and support.bioconductor to some extent) is to show effort before posting the question but that makes better bioinformaticians and better professionals.

ADD COMMENTlink written 4 days ago by Lluís R.380
3

Seems to be an assumption by some that mechanisms to help people improve their questions equates with being hostile and condescending, and upsets or drives away users. In my experience, the more common result is that people do indeed edit and improve their questions.

ADD REPLYlink written 2 days ago by Neilfws47k
2

It is much more different, bioconductor support is mainly to help with the questions related to bioconductor packages and R programming in bioinformatics, while Biostars is a general bioinformatics plateform. A new SE site similar to biostars will not bring any thing new.

ADD REPLYlink written 3 days ago by Sirus730

Bioconductor converted its long-running mailing list to a biostars site and then closed the list. The same goes for the Galaxy biostar site.

I personally view the possibility for down votes as a strong negative. It's better to ignore crap questions than to give the submitter the perceived feedback of "your question is crap, go away."

ADD REPLYlink modified 4 days ago • written 4 days ago by Devon Ryan64k
3

Downvotes on SE also reduce the reputation points of the voter, so they can't exactly be handed out like candy.

ADD REPLYlink written 4 days ago by A. Domingues1.2k

That's a good point at least.

ADD REPLYlink written 4 days ago by Devon Ryan64k
2

I am a long time supporter of downvote and played an important role in bringing back post closing (though biostar still lacks the vote-to-close feature). Many early biostar users also favored downvote. When used properly, these harsh mechanisms help to maintain the quality of a Q&A site. The old biostar had downvote. It worked well. I did remember a few discussions about how and when to cast downvote and to close posts, but these were all minor. Generally, it is easy to find a few isolated cases where downvote hurts hard, but when you sum up the tiny benefit of downvote in most other cases, it is huge.

ADD REPLYlink modified 4 days ago • written 4 days ago by lh329k
1

The down votes never say "go away" to the user but to the question. But it might discourage a bit posting. That's why I think Facebook dislike wasn't introduced until much recently.

ADD REPLYlink written 4 days ago by Lluís R.380
1

It will definitely discourage posting. I have a lab member who tried to do some of his own analysis, asked a question on SE, got like 3 comments and never posted again. Just gave me the data to analyse.

ADD REPLYlink modified 3 days ago • written 3 days ago by Sinji2.1k

It may not be intended to mean that, but regardless that's the perception.

ADD REPLYlink written 4 days ago by Devon Ryan64k
1
gravatar for WouterDeCoster
3 days ago by
Belgium
WouterDeCoster16k wrote:

So one of the "issues" it seems with biostars is that not always the (best) answer is posted as an answer, but rather hidden in comments. That's something we can easily improve on. Whenever a thread gets answered, we can either move the comment to an answer and toggle accepted status (mods) or ask users to summarise and repost their solution as an answer, and have that post be the accepted answer.

ADD COMMENTlink written 3 days ago by WouterDeCoster16k

That may not always be easy. One of the things that has been on my wish list (expressed before) is the ability for mods to mark (deeply embedded) comments as supplemental question(s)/answer(s). If a comment can't be moved (or deleted since that makes all children of that comment invisible) it can still be given some prominence or crosslinked in the original post automatically.

ask users to summarise and repost their solution as an answer, and have that post be the accepted answer

We know that is pretty unlikely. A high % of users do not bother to "accept" the answers (let us say unknowingly). Only way that may happen is if mods were to do it (after a waiting period of a day or so) as we come across these threads that seem to have acceptable answers.

ADD REPLYlink modified 3 days ago • written 3 days ago by genomax226k

If it's clear that this solution helped OP I don't see a problem with mods 'toggling accepted status' for answers. Waiting a few days is fair, but not necessary.

After all, the aim of this is that someone with a similar issue easily finds the solution in the thread and doesn't have to go in those deeply embedded comments...

ADD REPLYlink written 3 days ago by WouterDeCoster16k

I was not referring to toggling accept switch but rather the suggestion that

to summarise and repost their solution as an answer

if it was deeply embeded in a chat with credit being given to the person answering the question.

ADD REPLYlink modified 3 days ago • written 3 days ago by genomax226k

Oh right. Yes, that would indeed depend on the user. We can try :-)

ADD REPLYlink written 3 days ago by WouterDeCoster16k
1

Perhaps something that might help a few more threads get marked as answered would be for an OP to get a message in their inbox after a week (?) of post inactivity prompting them to revisit and accept an answer if possible? If it only makes 5% of people actually do so, that's probably still a large number of threads.

ADD REPLYlink written 3 days ago by jrj.healey1.2k

That sounds worth trying, also no real disadvantages to this.

ADD REPLYlink modified 3 days ago • written 3 days ago by WouterDeCoster16k
1
gravatar for John
2 days ago by
John11k
Germany
John11k wrote:

SKUB

There are 101 ways one could make a stronger, healthier bioinformatics community, but honestly whether you have nested comments or downvotes on the forum UI....... i just don't see it as a big deal. How many of us went into Bioinformatics because we're real particular about our user interfaces? :P

Let's talk about making a chatroom/wiki people actually want to use, or a community data repo, or a podcast that wont send you to sleep, etc etc.

In fact this thread really highlights the most severely lacking tool in our community's tool box - the ability to brainstorm and throw ideas around without making an official post or something. IRC does that, but there's only ever ~5 people online at a time.

Bottom line, I don't think S.E. is going to offer anything Biostars doesn't, at least not in a meaningful way, but i also don't feel its going to fragment the community. So... "meh"

ADD COMMENTlink written 2 days ago by John11k
2

How many of us went into Bioinformatics because we're real particular about our user interfaces?

Bioinformatics as a community should probably be more concerned about user interfaces. Definitely lots of room for improvement there.

ADD REPLYlink written 2 days ago by igor3.9k
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