Forum: New features and bug fixes for Biostar to work on during Google Summer of Code
gravatar for Paolo
4.6 years ago by
Paolo110 wrote:

I am Paolo, a software engineer attending Google Summer of Code 2014 (GSoC).

GSoC is a program promoted by Google in which organizations and students work together on free and open-source coding projects for 3 months. I was selected by INCF and I'll be working on NeuroStars in the period May 19 - August 18. My mentors are Roman and Satrajit and I will work close to Istvan.

NeuroStars is a question and answer website born from the need to discuss and share knowledge about neuroscience and neuroinformatics. It originates from BioStars.

The coding period has not started yet, but so far we have a bunch of points in our minds:

  1. Deployment: improve the deployment strategy.
  2. Usability: improve the usability of the website. We should define the exact features we would like to introduce and we will be asking this community for feedback. Multi tag filtering and integration with emails could be a good example.
  3. Semantic backend: create a semantic backend such as data like questions, answers, comments, profile, etc. could be exchanged with other websites.

We will work on a fork of the Biostars codebase, but our priority is to maintain a complete compatibility between NeuroStars and Biostars such as our work could benefit both the neuroinformatics and the bioinformatics communities.

Feedback from users is very important, especially when it comes to usability: so please if you have any idea about new features or bug fixes, please share it with us. 
Some features have already been discussed here, a wrap up:

  • RSS feed to local messages.
  • Answers in Markdown.
  • "Cancel" button in "Edit comment" mode: link
  • Open search results in new tabs on right-click: link
  • Pagination with page numbers: link and link
  • Post preview: link
  • Issue with old accepted answers: link
  • Issue with images: link
  • Improve search by tag: link. Add a multi tag search option.
  • Issue with small displays: link
  • There is no clear signup button/link in the home page. In order to signup one should first click on "User Login" and then on a link in the "Quick Login" section. Maybe we should use a clearer nomenclature for the 2 processes: signup and login.
  • Dates like "4.6 years ago" are not user-friendly. Better use the following patterns:
    • just now
    • 59 sec(s) ago
    • 59 min(s) ago
    • 23 hour(s) ago
    • yesterday
    • 2 days ago
    • May 18

My blog about the GSoC experience:

bug new feature gsoc forum biostar • 4.5k views
ADD COMMENTlink modified 3.2 years ago by TriS3.5k • written 4.6 years ago by Paolo110

a comment on time formatting, for the post it is important to make an old age visible, writing "May 13, 2010" feels a little complicated because it requires that user notices the last digit of the year. I do agree however that 4.6 years is not optimal, no one really operates in fractional years and once the post is more than one year old there is little use for being overly accurate. Maybe it could be listed as "more than 4 years ago" or "almost 5 years ago"

Also "just now" could include up to 10 minutes. Then go to hours -> yesterday -> days and weeks and months. 

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by Istvan Albert ♦♦ 78k

So do you prefer to always express dates as days/weeks/months/years-ago?
I was thinking about switching to a proper date like "May 18" for the current year and "May 18, 2013" for past years. This is because dates like "5 weeks ago" or "7 months ago" make it very hard for users to know what the exact date of the post is.

ADD REPLYlink written 4.6 years ago by Paolo110

I am not sure what the right answer is, perhaps others can chime in.

Based on my own ways of using the site, my interest in a post's date is solely to judge its "freshness", how likely is that the advice is still applicable and whether there is recent activity in the thread.

It makes no difference to me f the post was on May 4th or Jun 17 of 2010 but a lot more if it was one week vs four years ago. Parsing out a date visually adds to the cognitive overhead.


ADD REPLYlink written 4.6 years ago by Istvan Albert ♦♦ 78k

Well, when it comes to tastes the usual approach is to go for "convention over configuration" (reasonable defaults), plus optional configuration. Quickly looking at similar big sites, they go on opposite directions: `reddit` does "X time ago" for all posts and `stackoverflow` goes for a hybrid approach, described below.

If we went for a compromise between readability (Istvan's) and accurate information (Paolo's approach), hybrid, like stackoverflow does, the problem lays on defining which is the amount of time required to change from the "X days/months ago" to an exact date.

Then horrendous config variables such as "POST_TIMESTAMP_READABLE" would popup in `` with a hardcoded default of, for instance, 6 months to achieve the hybrid effect:

just now, 10 min ago, 4 months ago... up to 6 months ago. Then it changes to 22 May 2014.

To me, it really does sound like we are over{engineering || thinking} a tiny feature, so personally I would leave it as it is, we have more interesting stuff to tackle, IMHO.

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by Roman Valls Guimerà510

Ok, let's drop the date thing for now. Btw for future reference this library might be interesting:

ADD REPLYlink written 4.6 years ago by Paolo110

Hi, when users comment on the unanswered questions, it does not seem to be coming up in the latest posts. Although it comes in Recent Replies, I think the option of showing up the commented post (without answers) at the top of the posts would benefit the users, if there are any improved answers from other biostars. What is your opinion on this?

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by Prakki Rama2.2k

Pushing a post to the top when it receives a comment may have unintended consequences:

1. badly written posts usually get comments asking the user to fix the question, these posts would not deserve to be pushed to the top

2. at any give time there is a lot of activity on the site on older, more established posts. These then would push new questions off the main page quite quickly and thus moving them out of sight. 


ADD REPLYlink written 4.6 years ago by Istvan Albert ♦♦ 78k

Would it be possible to not have edits by Biostar push posts to the top? I'm not sure it makes sense to have a post re-frontpaged when it gets retagged (or whatever).

ADD REPLYlink written 4.6 years ago by Devon Ryan86k

Yes, the bothers me as well a bit, it is a holdover from the SE era where editing a post was thought to correlate with people reworking the post and adding relevant information to it. This does occasionally happen but it is more often that we just reformat or correct  a typo in the post.

A good solution may be to ignore post placement change for recent (within a week) edits but keep the behavior when the edit alters an older post. I will add this latter.

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by Istvan Albert ♦♦ 78k

This is an older post of course, and GSoC is over with but isn't the exact opposite of what we want? The way this is phrased seems to suggest when Biostars edits some 5 year old post it would pop back up on the front page. Personally this is the behaviour I find irritating when browsing the front page :)

ADD REPLYlink written 3.2 years ago by Dan Gaston7.1k

True. Your points are reasonable.

ADD REPLYlink written 4.5 years ago by Prakki Rama2.2k
gravatar for Giovanni M Dall'Olio
4.6 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

Another good feature would be to improve the formatting of source code in the posts. For example, there are manny js libraries for adding color-highlighting for different programming languages (e.g. I am not sure if this is already implemented, but I can not find it in the new version of Biostar.


ADD COMMENTlink written 4.6 years ago by Giovanni M Dall'Olio26k

Source code should go in a scrollable box.

This way it won't take the whole screen when someone post too many lines.

Also it will help readability and keeping the code together (at present each line of code shows like a different paragraph, with blank space between each line).


ADD REPLYlink written 4.4 years ago by Hugues250

we tried other javascript syntax highlighters in the past but those ended up misformatting XML so radically that we had to remove it. The other alternative was to process the post server side via a syntax highlighter like Pygments (GitHub does this) but since posts are a mixture of text and code we need to parse the post as HTML split it into these pieces, highlight the parts that are appropriate then concatenate back together. It ends up being some complexity to it.

I would love to have a javascript highlighter that just works so I am going to evaluate highlight.js right away

ADD REPLYlink written 4.6 years ago by Istvan Albert ♦♦ 78k
gravatar for Daniel
4.6 years ago by
Cardiff University
Daniel3.7k wrote:

Re: feature suggestion, I think protecting old popular questions is a good way to keep the front page fresh and not keep dredging up old questions unnecessarily, for example in this stackoverflow question which has the following tag:


protected by tchrist Aug 1 '12 at 23:50

This question is protected to prevent "thanks!", "me too!", or spam answers by new users. To answer it, you must have earned at least 10 reputation on this site.


For an example of where this would help, check out the newest comments on How To Remove The Same Sequences In The Fasta Files?

ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by Daniel3.7k

In case anyone goes to How To Remove The Same Sequences In The Fasta Files? and doesn't see the "thanks!" in question, I've deleted it. This would indeed be a nice feature to have!

ADD REPLYlink written 4.6 years ago by Devon Ryan86k

 I always feel uneasy when we have discourage positive sentiments.

Someone expressing their thanks is a positive action, it feels good for both the sender and receiver. It is just that is not helpful for all other people that may be involved in the discussion. If everyone thanked everyone else  the site would have a lot less utility.

But maybe the solution is to be smarter about it. For example if we notice that a comment/answer is really just a thank you then send it via email to the target but don't actually post it. Instead inform the user that the thanks have been sent to the target but won't be posted as it does not add to the discussion.

ADD REPLYlink written 4.6 years ago by Istvan Albert ♦♦ 78k

But people can still always do comments on answers, thanking people. This was more about discouraging users from posting "Thanks!" as answers to a question just because they're new to the site and don't realise that it's not the correct way.


Alternatively, there could always be a "Thanks User for this question" button like below, but I'm not sure what it would achieve different to counting your upvotes (example:

ADD REPLYlink written 4.6 years ago by Daniel3.7k

I see,

we do have a moderation feature that moves an answer into a comment to the top level post. usually this is not the right action as the comment may need to go to a specific post. But perhaps we can add that as the improvement.

ADD REPLYlink written 4.6 years ago by Istvan Albert ♦♦ 78k
gravatar for Giovanni M Dall'Olio
4.6 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

Some random ideas:

- a mobile application. Not sure if this would be really useful, though

- allow to customize the categories shown at the top of the page (Latest, Open, RNA-Seq, Chip-Seq, SNP, Assembly), putting one's favorite tags

- allow to configure how to get notifications by email for favorite posts and private messages

- integration with some third party paper commenting system - such as pubmed, citeulike, or one of the new.

ADD COMMENTlink written 4.6 years ago by Giovanni M Dall'Olio26k

I'd also like to be able to customise the categories. Also, it would be nice for the numbers to disappear once you've seen the posts, even if you saw them in a different category. Eg, If I click on Latest, then I should have seen everything that's new, so all numbers should disappear from all other categories.

ADD REPLYlink written 4.6 years ago by Emily_Ensembl16k

Thanks Giovanni for the suggestions! As a GSoC mentor for this project, here's my opinion on those.

  1. I would downvote the mobile application idea:
  2. +1
  3. Already done in BioStars2, needs some rethinking UI-wise, since it only appears in the first post and it's a bit "hidden" besides the first "ADD COMMENT" button.
  4. We thought ORCID would be a good start, works for you?
ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by Roman Valls Guimerà510

1: agreed :-)
3: ok, I missed that
4: yes, it can be a good starting point, specially if other services start referring to ORCID ids.

Another improvement may be to add more information to the profile page. For example, many people have both an academic web page, and a personal bioinformatics-related blog, and it would be good to have an extra space to specify both.

ADD REPLYlink written 4.6 years ago by Giovanni M Dall'Olio26k
gravatar for Mary
4.6 years ago by
Boston MA area
Mary11k wrote:

This is a teeny thing, but I could have used it recently. Can I have embedded tweets? I think the bioinformatics community is really effective on twitter, and sometimes discussions stem from good tweets about issues or papers. I needed to show one recently that was my source of a question and it just linked, not embedded.

ADD COMMENTlink written 4.6 years ago by Mary11k

The Twitter embedding feature is now live thanks to Paolo !

pasting a twitter url like the one above should produce 

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by Istvan Albert ♦♦ 78k

Grazie! I think the bioinformatics community is good at twitter and a lot of useful tweets fly.

ADD REPLYlink written 4.3 years ago by Mary11k

Great idea, I'll try to add it this week:

ADD REPLYlink written 4.6 years ago by Istvan Albert ♦♦ 78k

I might help out with this feature, but I want to make sure we all agree on the main use case scenario.
- John is a Biostar user; he also has a Twitter account;
- John reads an interesting public tweet (his own tweet or by someone else) and he wants to embeed it in a Biostar post;
- John creates a new Biostar post, clicks on the "Embeed a tweet" button and pastes the url of the tweet;
- Biostar automatically fetches the tweet and embeds its text in the Biostar post.

Note: only public tweets can be fetched with this strategy (not an issue since almost all tweets are public).
Question: do we want to embed also replies to that tweet?
Question: imagine we embed a tweet and its replies in a Biostar post; Biostar users then reply to that post; the effect is that we moved the conversation from Twitter to Biostar which is maybe good for the people following the conversation in Biostar but not for those following the conversation in Twitter.

ADD REPLYlink written 4.4 years ago by Paolo110

Public tweets, yes. For my purposes, the way it works in Wordpress would be sufficient. Here's a recent blog post I did that shows what I had in mind, as it appears when it loads right: . The whole post is here, but for some reason they are flaky for me today in firefox, working fine in chrome: . All I do is paste the link I get from the timestamp of a tweet, and I get what you see. Replies can get lengthy, so I would say no--but anyone could go look at the conversation from clicking the timestamp if they were interested. My use of this would be like in that blog post--making people aware of a conversation or tool or paper or something. Whether the conversation continued in one, or the other place, doesn't matter to me. As much as I like twitter and a lot of bioinformatics folks are on it, not everyone is.

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by Mary11k

A twitter-related request that came up here: please add tweet link to posts. It would be great if there was a tweet button to make it easier to share posts with the twittersphere. For those of us to lazy to copy a link and text for a tweet.

ADD REPLYlink written 4.5 years ago by Obi Griffith17k
gravatar for Giovanni M Dall'Olio
4.6 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

An improvement may be to add more information in the "New Post" page. Some people get confused when opening a new post, and they are not sure on which category to use. For example, this post was originally opened as "Tool", while it was a Question. Maybe you could add a dynamic field in the New Post page, containing an explanation of the type of post currently selected, with some examples.

I also have a question. Where are the Moderator Tools in the new Biostar? In the previous version there it was a section for checking the list of recently closed questions, the list of users potentially spamming, and so on. I confess that I never used the moderator tools very much, so they would not be a priority for me.

ADD COMMENTlink written 4.6 years ago by Giovanni M Dall'Olio26k

The moderator log has not been added back, did not really seem to have gotten that much use, it generates a log message on server side

 we'll mark that as a needed feature

ADD REPLYlink written 4.6 years ago by Istvan Albert ♦♦ 78k
gravatar for Hugues
4.4 years ago by
Oslo, Norway
Hugues250 wrote:

For many questions, no answer is marked as accepted. Consequently it is hard to judge whether a question still needs to be addressed. In fact I may not even read a question that already has an answer.

Arguably, it may be due to the new or inexperienced users who may not be familiar with Stack Exchange; they just need to be kindly reminded, in a comment.

Suggestion: Feature the "opened" questions on the front page. Hide the "accepted" questions under another tab.

ADD COMMENTlink written 4.4 years ago by Hugues250
gravatar for Daniel
4.5 years ago by
Cardiff University
Daniel3.7k wrote:

Another usability suggestion; Highlighting the 'new' comments/answers when you're returning to a page.

When you receive a notification that someone has commented on a post you have also commented on, if you want to click through to see the context there is no quick way to see where that comment sits, resulting in scrolling up and down to find the most recent comment/answer.

Coloured highlighting of new comments for example? 

ADD COMMENTlink written 4.5 years ago by Daniel3.7k

Doesn't it usually jump to the position of the new post? It just did that when I clicked on the link to your answer.

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by Emily_Ensembl16k
gravatar for TriS
3.2 years ago by
United States, Buffalo
TriS3.5k wrote:

Even if a bit late I'll chip in with a very simple thought: how about making the links from answers go to a new page/tab? since lots of post use links to reference (part of) the answers, I see it as more organized to keep the original Biostar page open. 

I guess at the end it goes down to preferences, but I do believe this can be useful and pretty trivial to implement compared to other major improvements.

ADD COMMENTlink written 3.2 years ago by TriS3.5k
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