News: Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
gravatar for Istvan Albert
8.1 years ago by
Istvan Albert ♦♦ 86k
University Park, USA
Istvan Albert ♦♦ 86k wrote:

Two recent posts made it clear that we don't have ways to directly collect feedback and suggestions regarding Biostar.

As it turns out there are quite a few suggestions that make a lot of sense and are really easy to add but were just simply forgotten among the many tasks that a site of this complexity requires.

This thread is intended to address this major oversight and it is meant to be a way for users to suggest ideas, features that they think would make the site better. If it is simple feature we will try to implement it immediately: for example just yesterday, based on a suggestion that multiple people agreed with, we increased the number of points awarded for up-votes. Similarly today we increased the number of posts per page.

For features that are more complicated we can promise to add them to the planned features. A few such features that are currently in final testing phase are the

  1. mobile interface (see sourcecode for responsive branch)
  2. intelligent tagging of questions (called the tags branch)

If you are more comfortable with sending an email direct it to

If you see bugs or want to open a more "official" issue that is easier to track please use the Biostar Issue Tracker

meta biostar news • 7.6k views
ADD COMMENTlink modified 4.1 years ago by jonasmst330 • written 8.1 years ago by Istvan Albert ♦♦ 86k

Changes as of v1.2.10 on Dec 5, 2012: the first stage of "taming the tags" - we have merged tags with different capitalization, removed tags with fewer than three posts, this has radically reduced the number of tags. Next step will be to merge tags within an edit distance of one. Also added more information on the post info line - the name of the last user that added an answer or modified the post is now also visible.

ADD REPLYlink written 8.1 years ago by Istvan Albert ♦♦ 86k

FYI bug report: If I answer a Question, it is showing as "last edit by Rm" on the Question; which I did not. (How To Choose The K Value Of Kmer In Soapdenovo?)

ADD REPLYlink written 8.1 years ago by Rm8.0k

A new version of Biostar has been released 1.2.11. We went through this thread and added a good number of requested features. Notable changes: tag completion, improved search result interface, post highlighting based on mytags settings, simplifying the main interface, made the site better suited to phone/ipad navigations and many others.

This is the first of many improvements - if your feature did not make it in this time it is still in the pipeline.

ADD REPLYlink written 8.0 years ago by Istvan Albert ♦♦ 86k

Following @Rm's idea, I would like to nominate this as the first "post of the month". It probably deserves more visibility as the number of views is still quite small compared to the number of users.

ADD REPLYlink written 8.1 years ago by Botond Sipos1.7k
gravatar for Sukhi Singh
8.1 years ago by
Sukhi Singh10k
Sukhi Singh10k wrote:

Some features that are already being talked and reported, I would include here for general opinion

1) Tagging users in posts using @

2) Sending PM to users.

3) Printable Version

4) Posting guidelines popup for new/all users.

5) While writing new post, questions with similar words/content appear.

6) Having a more sophisticated voting system for upvotes, downvotes, accepted answer, penalties.

7) More badges and their delivery.

8) A sorting filter on user's own created posts.

ADD COMMENTlink modified 8.1 years ago • written 8.1 years ago by Sukhi Singh10k

Private messaging has been added and is available as of today. See any user page. Printable format has also been added. No explicit action is necessary, the pages will get styled in a simpler way whenever printing from the browser.

ADD REPLYlink modified 8.0 years ago • written 8.0 years ago by Istvan Albert ♦♦ 86k

Did this ever get implemented? If so, it does not seem to be working. '1) Tagging users in posts using @'

ADD REPLYlink written 4.4 years ago by steve2.7k

No, I don't think so.

ADD REPLYlink written 4.4 years ago by Sukhi Singh10k
gravatar for Botond Sipos
8.1 years ago by
Botond Sipos1.7k
United Kingdom
Botond Sipos1.7k wrote:

A couple of features which I think would improve usability:

  • The SE way of highlighting posts on the front page having the users favourite tags. It makes it really easy to keep up with specific areas of interest and explore new topics at the same time (the "My Tags" page needs and extra click and it's too restricted).
  • The "old way" of prioritizing posts felt somehow more effective (as pointed out by other users).
  • The SE-style "Recent tags" and "Favourite tags" sidebar is a must-have! Especially the latter, which makes it easy to track recent posts in topics of interest.
  • Tags seem to be out of control. Tag completion, the recent tags sidebar and permission for simple users to edit tags should help with that.
ADD COMMENTlink written 8.1 years ago by Botond Sipos1.7k

Tag completion and Sidebar definitely must-haves.

ADD REPLYlink written 8.1 years ago by 141341254653464453.5k

Most of the above have now been added - there will be a feature where a tag can be edited in some form - we have greatly reduced (merged) the number of tags but should still be fewer for them to be really useful.

ADD REPLYlink written 8.0 years ago by Istvan Albert ♦♦ 86k
gravatar for Alex Paciorkowski
8.1 years ago by
Rochester, NY USA
Alex Paciorkowski3.4k wrote:

I overall think the site is doing pretty well. Although this is just a casual observation, there appears to be a diverse user base with several people who know a lot checking in pretty frequently. A good range of programming languages are covered -- and it seems like at least once a week there's a good question that elicits a variety of answers with code in C, Python, Perl, R, awk, etc...

I think we can do better encouraging new visitors to improve their questions, and do a little bit of work on their own first. I'm just not really a fan of snarkiness, and I wonder if some of the recent posting Istvan mentions stems from responses some new users may have gotten that makes them feel shut down too quickly. But this is a hard one to solve -- I agree that making the "posting guidelines" pop up might be helpful -- but I still wonder if people will read them. I think actually people do read them, but if you are a real beginner it's still hard to know how to formulate a good question, guidelines or not. PerlMonks has a chatterbox feature, that I wonder might be implemented here -- you can see who's logged in, and float a newbie "trial balloon" question in the chatterbox first and see if you get any bites. Sometimes this allows the user to better formulate their question/issues before committing a formal post.

Also, I feel like the badge system worked a lot better on the old version of Biostar. That was fun. It's kind of a healthy way to encourage competitiveness. Anyone else miss the old badge system?

Oh, yeah, and tags used to work better too. What happened?

ADD COMMENTlink modified 8.1 years ago • written 8.1 years ago by Alex Paciorkowski3.4k

re: snarkiness - I read a couple of comments recently that I found reasonably snarky, and found myself actually wanting to downvote them for this reason (my feeling being that, on average, snarkiness reduces the utility of a comment/post), but as far as I can see, I can't downvote a comment. I could have completely missed that this is possible, of course, or it may be deliberate.

However, it's my suggestion for a feature: ability to downvote comments

ADD REPLYlink written 8.0 years ago by aidan-budd1.9k
gravatar for Ben
8.1 years ago by
Edinburgh, UK
Ben2.0k wrote:

I think the biggest problem is the ratio of interesting and challenging Qs to the daily "I've got some sequencing data and need to do bioinformatics on it" type. Obviously this is a tough thing to change, if we impose some (e.g.) rep limit for asking a question, it's an extra barrier to attracting new users. Having said that, are there any stats on user retention? What proportion of registered users only ask or are involved in a single question? Is that one poorly-phrased question worth having?

And to take the converse, the highly experienced researchers who do most the of the answering here probably only rarely find themselves with a question they can't answer with google... But this leads onto what I think is a strength of Biostar: That reasonably open-ended discussions are permitted as well as the traditional strict Q & A. It's really interesting to hear the PIs and post-docs give their opinions on best practices, techniques, software packages etc. probably moreso than just people correcting R scripts and handing out perl one-liners.

On a different topic, I am not really fussed about "badges" - they're especially difficult to obtain here due to the relatively low traffic and the highest of them are only really awarded to the broad discussiony "what's the best programming language?" type questions. I'd be happy for them to be removed to be honest, I think reputation points are enough to encourage positive interaction, but assuming many would oppose that, I'd at least not want them to be expanded.

ADD COMMENTlink written 8.1 years ago by Ben2.0k

I just wanted to comment on the badges part of your post. I personally like the idea of them. They are something to reward the obsessive compulsive among us and make nice milestones for different types of activities. At some point they become less interesting but for the beginner they can be a fun way to encourage participation. However, I agree with you that the way they are set up currently doesn't work well for this forum. I suspect this is mostly just carry-over from stack exchange. I think if they were "tuned" for this ecosystem they could work much better.

ADD REPLYlink written 8.1 years ago by Obi Griffith19k

Fair points and it seems several people agree with you; maybe I'm just bitter about not being awarded them.

ADD REPLYlink written 8.1 years ago by Ben2.0k

i too like the badges - I'm interested in ways to motivate/stimulate interaction within communities/networks such as BioStar (looking for lessons to apply to other networks I'm involved in), and so part of the reason I'm using BioStar quite a lot at the moment, is to get a feeling for what I find motivating about engagement. And I found, to my surprise, that the badges were, for me at least, a fun motivator. So I guess it's one of those things that works for some people, and not for others.

ADD REPLYlink written 8.0 years ago by aidan-budd1.9k

Admins have access to the data which could be used to generate useful stats and reports about usage. I'll try to make some time for looking into this.

ADD REPLYlink written 8.1 years ago by Neilfws49k

I am very close to adding an query API (probably this weekend) that depending on the URL and its parameters returns a JSON string with information. Very similar to this this will make it a lot easier to answer various questions of the ones people want to pose.

ADD REPLYlink written 8.1 years ago by Istvan Albert ♦♦ 86k

This sounds like a "restful" way to make it ;-)

ADD REPLYlink written 8.1 years ago by Manu Prestat4.0k
gravatar for Martin A Hansen
8.1 years ago by
Martin A Hansen3.0k
Martin A Hansen3.0k wrote:

1) Search results were presented nicer in the old version at Stack Exchange.

ADD COMMENTlink written 8.1 years ago by Martin A Hansen3.0k

This has been completely reworked

(I am now going over this thread adding comments to mark what has been completed)

ADD REPLYlink written 8.0 years ago by Istvan Albert ♦♦ 86k
gravatar for SES
8.1 years ago by
Vancouver, BC
SES8.4k wrote:

Having more functionality on the user pages would be nice.

  • For example, the ability to search through our old questions/comments by keyword would come in handy.
  • Also, I think bringing back the old layout of the user pages, like the graphs of activity/reputation, would be fun and might make it easier to understand how reputation is awarded.

I agree with others about the tag system. It seems like the tags are not being used accurately or effectively. Perhaps tags could be suggested based on the content of the question or the title. This may be difficult to implement, but I can't think of an alternative other than for the admins to retag every post, which is not a good use of their time.

I'm also unclear how the badge system is working these days. Is it the same, and are the badges the same as SE? Maybe that list of badges could be modified/expanded because some are likely unobtainable, and its unclear what some mean, like "Beta Tester."

ADD COMMENTlink written 8.1 years ago by SES8.4k

Re: tags - there were several answers/questions/posts by others that I thought might benefit from adding some additional tags. Looking through the documents/FAQ for the site, it seemed that retagging of this kind might be appreciated, but it wasn't clear to me how to do it, or if that's only e.g. moderators have the ability to do that.

Thus, something in the FAQs about retagging might be useful

ADD REPLYlink written 8.0 years ago by aidan-budd1.9k
gravatar for Josh Herr
8.1 years ago by
Josh Herr5.7k
University of Nebraska
Josh Herr5.7k wrote:

I'm in agreement with Sukhdeep (+1) although I think we all could place different priorities to some of the potential features that have been discussed. While having posts in a printable format is not a pressing issue for me, this might be important to others.

One area that others have seemed to stress is the issue of posting guidelines. I think we spend a lot of time reading questions that are hard to discern what is actually being asked, and, ultimately, have been answered previously. I know some have resisted the idea to expand the forum to include other areas (jobs, blog posts, etc.), but I think the idea of having tutorials (and/or primers and/or lists of key publications in an area) is important and could quell "question repeating".

Perhaps a new user should go through a quick tutorial of how to use the forum and how to introduce questions? I like the idea of similar questions and topics appearing when someone enters a tag for a new post -- in any event, I think there is a lot of great resources already at the site that is getting lost in repeated questions.

ADD COMMENTlink written 8.1 years ago by Josh Herr5.7k
gravatar for Damian Kao
8.1 years ago by
Damian Kao15k
Damian Kao15k wrote:

I have some comments on design. Here is a mockup of what I think the navigation system should be:

Couple of points

  • If we want this site to function as both a Q&A and community portal, we should make that clear and separate the two types of entries into 'Questions' and 'Posts'
  • It's a subtle difference, but I think we should place 'ask a question' and 'post a message' in the sub tabs instead of a general 'post a message' in the main tabs. Putting them in the sub tabs will better distinguish the two functions and hopefully lead to less people asking questions in the forum or planet sections.
  • Mouse over effects on the main tabs will change the sub tabs. When mouse is off the main tabs, it will revert back to current tab.
ADD COMMENTlink written 8.1 years ago by Damian Kao15k

that superscript idea is great - I fretted a lot about it, pushed out the change to adopt it

for you and everyone else, thanks for the contributions everything is read and will be addressed one way or another, some sooner tagging, searching especially others in due time

ADD REPLYlink written 8.1 years ago by Istvan Albert ♦♦ 86k

Great , Thanks for being quick and reactive.

ADD REPLYlink modified 8.1 years ago • written 8.1 years ago by Sukhi Singh10k
gravatar for Manu Prestat
8.1 years ago by
Manu Prestat4.0k
Lyon, France
Manu Prestat4.0k wrote:

The 'New Post" link is too hard to find. It should be the easiest/fastest thing to see when the home page shows up. I would see it like a button, same kind as the notification or the "show all" boxes...

ADD COMMENTlink modified 8.1 years ago • written 8.1 years ago by Manu Prestat4.0k

We moved it to the side - I think that should help

ADD REPLYlink written 8.0 years ago by Istvan Albert ♦♦ 86k
gravatar for Rm
8.1 years ago by
Danville, PA
Rm8.0k wrote:

Few points to add

  • Display of related/linked questions links.

  • I agree "New Post" is hard to find

  • Top/Active Tags of the Day.

  • Sending PM to users: would be a bad idea since it might initiate spam.

  • Can we have a separate section like "Topic of the Week/Month" to encourage users to ask or write about that topic in little more detail.

ADD COMMENTlink written 8.1 years ago by Rm8.0k

Topic/Post of the week sounds good. May be one should have certain reputation(points) to send PM, this will discourage spam.

ADD REPLYlink modified 8.1 years ago • written 8.1 years ago by Sukhi Singh10k
gravatar for JC
8.1 years ago by
JC12k wrote:

A captcha system when you submit a new question for new or low-score users to avoid spam bots.

ADD COMMENTlink modified 8.1 years ago • written 8.1 years ago by JC12k
gravatar for lh3
8.1 years ago by
United States
lh332k wrote:

For a question shown in the home page, the time stamp should be the last modified time, not the creation time. The user name should correspond to the user who made the last modification to the question or answer, not the author of the original question. This is the SE behavior and I like that way because I want to know when and who made the last change without clicking the question.

In SE, changing tags also changes the time stamp. I would prefer not to do that. In the old biostars, someone has changed the tags of hundreds of questions. While I really appreciated that, pushing all the old questions to the first page made me lose the track of recent questions.

Also in SE, if I modify my own question/answer in one (or five; cannot remember) minute, a revision will not be created. This is also the behavior of many forums. It is preferred.

ADD COMMENTlink modified 8.1 years ago • written 8.1 years ago by lh332k
gravatar for jnfass
8.1 years ago by
jnfass30 wrote:

I'm hoping someone else can point out my stupidity, but when I look at a search result that's an "answer", I don't see a way to get back to the original question. Perhaps this isn't the general feedback this post was looking for, but unless I'm totally missing something (very possible), it's an issue that needs improvement.

ADD COMMENTlink written 8.1 years ago by jnfass30

sorry about that, turns out that this is a bug that we'll fix - normally it would load up the entire thread but a later change coupled to the way the search works introduced a problem

ADD REPLYlink written 8.1 years ago by Istvan Albert ♦♦ 86k
gravatar for Andrew Su
8.0 years ago by
Andrew Su4.9k
San Diego, CA
Andrew Su4.9k wrote:

Allow up-voting (and down-voting) from the "index" pages (e.g., Getting people to vote more is a good thing, so the easier it is the better...

ADD COMMENTlink written 8.0 years ago by Andrew Su4.9k

Would it be best to attach these comments to the new thread Istvan started up a few (now 7) days ago? State of Biostar - future directions (January 2013) , so that new ideas get placed in the most recent list of suggestions etc.?

ADD REPLYlink written 8.0 years ago by aidan-budd1.9k
gravatar for jonasmst
4.1 years ago by
jonasmst330 wrote:

Reviving an old thread, feel free to move it somewhere more appropriate.

Fragmentation/the front page is bloated:

  • General: My impression is that Biostars is currently trying to solve too many problems in the same place.
  • Too many colors in the count-box, and it's not intuitive what they represent. I think I've understood them from linking colors to question titles (light green = answered question, but not accepted; dark green + gold text = answered question, and accepted; dark green, white text: tool?; red = unanswered question; dark blue = tutorial?; orange = job?; purple = news?), and I find it confusing. Speaking of colors, the dark red text color on the tags could be changed to something more easy on the eyes.
    • Suggestion: Keep it minimal for the questions, like on Stack Overflow: Unanswered: No highlight, answered: Light highlight, answered+accepted: Strong highlight. Also, a personal preference: Lighter/more modern colors. Also personal preference: No background (currently grey) on the votes. A light border like on SO is prettier.
  • Separate questions into implementation/programming and methodological questions, where the former is about specific problems with programming language and tools (e.g. resolve Bowtie error, how to sort a list in python) and the latter is about how to approach a scientific question (e.g. how to do DE gene expression, how many replicates do I need).
    • Suggestion: Different "subs" within Biostars: E.g.,
  • Separate questions from posts about jobs, news, tutorials and tools. Coming from Stack Overflow, I'm used to having the main feed/front page containing questions only, and I think including jobs etc in the main feed makes it bloated. Related, it doens't make sense to have answers on job-listings and news posts. Comments are great, however.
    • Suggestion: Again, different "subs":,,,
  • Header is crowded/too big and confusing.
    • Suggestion: Again, something like SO: A narrow actionbar at the top with the logo (with a dropdown for different subs). A small inbox-icon with notification-badges when something's changed. Maybe a single button for notifications for messages/comments/answers and votes. A help button, a search bar, and a profile button with reputation. Also, "My posts", "My tags", "Following" and "Bookmarks" could be moved to the user page, no need to have it in the header.
  • Right sidebar is rarely relevant (to me), and only contributes to bloat the front page (what are 'recent locations' anyway?).
  • The globe on the bottom, while fancy, only adds noise to the page in my opinion.

Questions and answers:

  • Questions are poorly formulated/ambiguous/confusing, resulting in long comment threads to figure out what is actually asked. I've seen suggestions about guidelines, and I think we could benefit for being more aggressive. There are a lot of "Question about X" titles, and "How to do Y" questions. For programming questions, there could be a prompt about providing a minimal, complete, and verifiable example including what they've tried, what they're expecting to happen and what is happening/not working. Also, guidelines on how to phrase titles.
    • Suggestion: Ability to downvote questions. Maybe with a minimum reputation requirement. Also, downvoters should be prompted to explain what's wrong with the questions. Downvoted questions should remain for users to experience what poorly asked questions look like.
  • Users answer their own question instead of commenting. From my experience, users are confused about the difference between answers and comments. Sometimes it's also the other way around, answers get posted in the comments, when they're perfectly acceptable answers.
    • Suggestion: Warn users when attempting to answer their own question, instruct them to comment instead.
  • Users rarely accept answers. Answering questions often end with a "Thanks, it works!" comment, without the answer being accepted.
    • Suggestion: Prompt users to accept answers (e.g. as a notification upon login) when there's been a while since somebody answered their question (e.g. a day or two). Maybe also give a small rep boost for accepting answers (SO gives +2).

Meta section:

  • I had a hard time finding a meta page when searching for a place to post suggestions to the site. I'd love to see a meta sub (e.g. A related question directed me to the forums, which seems like a mix of meta discussions and ...regular questions? The first post on the forums right now is "Check Kmer Count Results", which sounds like it belongs on the questions page (in my utopia, on, and not in the forums.
    • Suggestion: Move/refactor forum into a distinct meta-page, for instance Move/downvote questions not beloning in the forum.
ADD COMMENTlink written 4.1 years ago by jonasmst330

Also (probably most relevant for meta-posts): Up the character-limit a bit.

ADD REPLYlink written 4.1 years ago by jonasmst330

You'll get used to the colours if you spend some more time here. I don't believe in fragmenting the forum, I don't expect that to change things. I find the right part very useful to track where there is activity (from a moderator point of view).

I see you mention that you come from StackOverflow. A lot of us here don't like the stack overflow culture, so trying to fragment biostars in subs and implement downvoting will give you a lot of resistance. Downvoting has been discussed often and a lot, I don't think that discussion should be started again and again. A recent discussion is this one Why can't we downvote on this forum?

Suggestion: Warn users when attempting to answer their own question, instruct them to comment instead.

Suggestion: Prompt users to accept answers (e.g. as a notification upon login)

Those are useful suggestions I would say. Perhaps Istvan Albert can comment...

ADD REPLYlink written 4.1 years ago by WouterDeCoster45k

Alright, I see your point about the downvotes. Maybe it's not the best approach to improve question/title phrasing. As someone who only browse this site for Q&A, separating those from everything else would be a welcome uncluttering of the feed.

ADD REPLYlink written 4.1 years ago by jonasmst330
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