Forum:Biostar 2.0 released
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7.5 years ago

Biostar 2.0 is now live.

This is the result of quite a few months of work and we hope to have added valuable improvements. We may have bugs and display oddities so please bear with us while we identify and fix them.

The overarching theme is that of providing better search and navigation and improved tracking of existing content.

New features:

  1. users now can follow a post by local messages or via email (previously only users that posted in the thread were notified).
  2. search is more deeply integrated: there is instant search on the main page and within each thread similar posts are displayed in the sidebar. We found this to be a very useful way to navigate the content.
  3. the awards now also display the posts that generated them, this is also a great way to find new and interesting content.
  4. Internally the codebase has been greatly streamlined and simplified. This bodes well for the future of this and other Biostar based sites.

The concept of "user ad" has not been carried over, it is being reworked and will be implemented in a way that is useful to more people.

Fixing login problems

As long as your authentication provider reports the same email that you had on Biostars you should be able to log in directly and be connected to your old account. If you do experience problems do the following:

  1. let us know which user are you trying to log in
  2. reset your password from the login screen (forgot password link)
  3. log in with your new account
  4. connect the social account from your userpage

If your email is not accessible anymore send us an email (admin@biostars.org).

A general solution is to use Mozilla Persona instead of any other third party authenticator. One can easily set up Persona to authenticate with a very large number of providers. The important thing to remember is to have Persona authenticate via the same email that you used on Biostar

biostar Forum • 9.5k views
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7
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Thanks for all your hard work on biostars, Istvan! It's a great resource. A lot of things would be a lot harder without it.

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thanks a lot Madelaine, a lot (well all really) of my free time goes right into this site

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was the yahoo openid access removed? is that temporal or definitive? if it's a fixed decision, although I would prefer to see the yahoo login again, how can we merge new with previous accounts?

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It was removed mainly to have fewer options on the login screen. It gets confusing when there are too many options.

A general solution is to use Mozilla Persona instead of any other third party authenticator. One can easily set up Persona to authenticate with a very large number of providers. The important thing to remember is to have Persona authenticate via the same email that you used on Biostar.

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login using my YahooID through Persona worked like a charm. didn't know about this login system. thanks for the info!

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There is a problem with (some/german) Gmail accounts. For some gmail accounts Google reports user's email address as: user@googlemail.com (not gmail.com), however, most users tend to have used user@gmail.com which works nicely. Also, gmail supports the + sheme, such as user+123@gmail.com and still receive the email.

It seems like our accounts will not automatically be merged if our email-addresses recorded in biostar are not absolutely identical to the address delivered by the service provider. This might create a lot of problems, because users might not have been aware of this necessity and now cannot log into their old profiles anymore.

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well yes this is by design, we can't merge accounts otherwise. the solution (that I have neglected to mention ;-) ) is to first reset the password then connect the social login account from the user account page.

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Istvan, is it possible to add "Cancel" in "Edit comment" mode (there is only "Submit" right now)?

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hmm, missed that, I will add this later, for now just hit the back button

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Thanks for the update!

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4
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7.5 years ago

It would be great if user profiles could link out to Twitter profiles as well. I'm always looking to connect with people making useful contributions on this site, since they might be more active on social media as well.

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0
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for this and other suggestions can you open an issue for this on the tracker.

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7.5 years ago

Is anyone else able to open search results (from the new live search tool) in a new tab/window? If I right-click, they are not considered true links by the browser and therefore I am not given the option to open in a new tab. I am using the latest version of Chrome on Ubuntu 13.10.

My normal usage of Biostars (and Google for that matter) is to type my search query, then open several tabs for results that look relevant so that I can keep my original search results.

I understand that the point of the new sidebar on question pages is to provide a list of related pages so that you don't have to go back to your original search results, but there is a good chance they are not highly related to my original query.

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let me look into that, we are using a library to produce those links.

In the meantime you can use the classic search (button is right next to the live search) and when searching with that you will get real links.

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+1 for this issue

also, live search confused me at first:

  • Does it show only the first X results; are there more? (found out that answer is no, it shows all results)
  • Once I've typed my live search query, I'd like to see a page with all my search results, e.g. classic search. (can't do that) I expected that it would happen when I press enter (same as google), but instead it goes to the first hit.
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We may need to redesign the search, I am relying on a third party library

http://ivaynberg.github.io/select2/

and that imposes quite a few limitations on what is possible to do

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2
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7.5 years ago

Unfortunately, I didn't get into the correct account, but was given a new account. Also, I see that you didn't fix "the bookmark yields an upvote bug". I think you should have taken more time for the test phase

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0
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there are straightforward fixes for this, if you do not get into the correct account send email to admin@biostars.org. Then do the following:

  1. reset your password at the login screen (use the forgot password link)
  2. log into the account with your new password
  3. visit the user account page and connect your social link to the account

One can have multiple social logins to the same account.

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0
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Ok, that has worked. What about the bookmark upvote?

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2
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That was fixed as well when reported, it will not provide a reputation increase for the user.

Now it still does increase the vote count for that post but that alone will not have a a cumulative effect on a single target. We do want to allow people to bookmark their own posts and the concern was that if the votecount would not increase in some cases then people would think the system is bugged.

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I see that an 'upvote' and a 'bookmark' gives that post an apparent 2 upvotes. Would it be logical to assume that if you're bookmarking then you would also want to upvote and group them as one, rather than allowing a user two points of power and unfairly weighting that answer?

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Well people tend to use the site in various ways it is not that straightforward to generalize. What you say makes sense but may not be the way people end up using the site.

I think that a bookmark should be worth more than an upvote at least when it comes to expressing the value of the post, so in a way getting two points for both upvoting and bookmarking is perhaps not ideal but not so bad either.

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7.5 years ago
Woa ★ 2.9k

Hi,

Can such a section like "Journal/Article watch" be added? Where people can cite and discuss about some journal papers?

Thanks

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we can add features like that, but we need a way to gauge how many would make use it - alas just asking is often insufficient because when posed with a question most say yes but then they don't actually use it. If you find support for the idea we can do it.

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7.5 years ago

ailsjflsjfslkfj

Another minor glitch: The CKedit widget seemingly disables the spell-checking of the browser (chrome), but I think I had it working in CKeditor in another application.

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1
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spell checking should now work

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it does now on firefox. thanks Istvan.

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It affects firefox's spellcheck similarly. I'd hate to see how many typos I've made as of late!

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I'll look into this, spell check should definitely work, probably I missed a settings

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7.5 years ago
Prakki Rama ★ 2.5k

The following are not the issues, but would ease the users like me while using the Biostars forum.

  1. While going through the unanswered questions, if I have to reach 15th page, I need to click 15 times, which seems painful while helping to answer the users. A better option I would feel, is having 1 2 3 4......10 (like google), where I can directly go to 10th page in one click.
  2. Secondly, when answering the questions, If I try to login, I am redirected to Home page of Biostar. I am again in need to search the question and answer it. It would be a nice option, If I am redirected to the same page, when I was trying to login.

These are just my suggestions. I know maintaining a site like this not an easy task. But, I would like to be a part of building a better forum for my fellow Bioinformaticians.

Thank you very much.

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2
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ok, since this was brought up repeatedly we will add accessing pages by numbers,

The login should have redirected correctly, there is a hidden parameter that should remember the location where an authenticated action was requested, it could be that it does not work for some reason, we'll take a look at that as well.

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Thank you Istvan. One more to add, while typing the text and formatting code, the option in previous biostar version of previewing the text was very helpful, before posting. I hope having this feature will also benefit Biostar forum users.

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7.4 years ago
Danielk ▴ 620

I am not able to upvote questions or answers on mobile. I can however upvote comments. Is that intended?

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it is on the todo list, the voting widgets for the main posts are not yet ported over to phone, the regular widgets seemed to take up too much space

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I'm having a similar issue on my desktop. The website will have the mobile format if my browser's window size is too small.

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that is how it is supposed to work though (shows a different format if the viewport is too small) - now we may resize a little too early. I will look into to switching only when the window is very small.

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I don't have any problem with the format change other than losing the ability to upvote questions and answers while in mobile mode.

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7.5 years ago

And another one:

Seems like accepted answers from the previous version are not displayed. I didn't find a single accepted answer!

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should work but I have to investigate, most likely it is a stylesheet issue, the class is not applied properly due to a recent change.

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Could you please look at this job-post:

Scientific Technical Writer -- Help us write papers about GATK!

it looks like it has an accepted answer in the list view (yellow answer count), but it hasn't.

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7.5 years ago

And another one:

Pagination is clumsy.

Pagination allows only one step forward or backwards in the question list, how often do I have to click to for example get to the first BioStar question of all time?

https://www.biostars.org/?page=638&sort=update&limit=all%20time&q=

works, but then it must be easy to display a "last" and "first" button.

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It is easy to display that information, the question is whether it is a good idea to have that displayed all the time. It is well documented that people do not like to paginate at all, pages 2 and 3 get tiny fraction of visits for any website. It just adds to the text and options on the page.

So the rationale was that having that information may not be that useful.After all if someone wants to go there all they need to be is a resourceful and they can get there, like you demonstrated as well.

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That's a good point, don't like pagination either. Could we then increase the number of items on the front page, or make it even user defined? I'd rather scroll down 100 questions than press 'next'.

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We can raise that limit, probably not 100 though since that would lead to these gigantic pages that would put a strain on generating and pushing them out. I will test out some values.

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I've raised the number of items per page from 25 to 40, we'll monitor how this works out

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7.5 years ago
Radwen ▴ 20

I used to login via gmail but I am surprised to have another account (probably old)

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I would keep the old account, it is a better reflection on a user's activity.

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7.5 years ago
martenson ▴ 380

It would be nice if old shortcuts were properly redirected. E.g. https://www.biostars.org/show/tag/galaxy/ would redirect to https://www.biostars.org/t/galaxy/

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good observation, it has been done now.

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7.5 years ago
Daniel ★ 3.8k

What's the deal with images? Old pages are showing blanks i.e. Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems

and when I try to upload a screenshot of that page, it seems url only (no local hosting) and also, I can't get it to accept my url: https://drive.google.com/file/d/0B1HqS9WXTqfmc0o4YjQ1VWJWbHc

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looks different for me: images overflow the right panel (latest Chrome)

https://www.dropbox.com/s/e78cwhy9qe08slx/Screenshot%202014-04-14%2012.19.55.png

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there are two problems there allright, I think it may be both that the site loads up images from both http and https sources, the second is that the image is not resized properly. We'll investitage.

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0
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Some posts still seems to have problem in showing Images like this. Is it that the link is broken or problem with loading the image?

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0
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The url for the image is no longer valid, so that's not a biostar problem. I'd update the question, but I'm not 100% sure that it's figure S3 that's being mentioned (it probably is, but perhaps I'm mistaken).

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Ok. Thank you.

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7.5 years ago
Neilfws 49k

Most of my messages now seem to begin with "0 minutes ago: Congratulations!" This makes it difficult to see the "real" messages, such as new question comments.

I assume this will settle down once the new system has processed all my old content?

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I raised the limit of the awards that are given out (when it is a backlog), one or more rounds should fix it.

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7.5 years ago
liqingyan ▴ 20

I found no way to add a new post.I login in through google account.

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There is a link called New Post on your top bar.

It should probably be made more visible though. I'll look into that.

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There is only 3 links on the top bar. Latest, Home, You.

I login by my google account, is that the cause?

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oops, my bad, it seems you are viewing on a small screen (phone or small tablet) and for those we have a different interface where, as it turns out, we did not actually have a New Post link ... it is now fixed, It is now under the 'You' tab.

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Entering edit mode
7.5 years ago

Here's another minor issue, especially when compared to SO:

Tags can't be searched, they just appear ordered by frequency, but as they are spread out on several pages it is very hard to find a certain tag.

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7.5 years ago

A new issue that I'm running into now is that I can't seem to up vote answers or posts when using an iPad. I can up vote comments, but there's simply no button for that for answers and posts (or am I blind?). This seems to be the only feature missing from the interface (so moderating and such seems to work fine).

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what type of ipad do you have and how do you hold it? ;-)

there are really different interfaces to biostar: 1. desktop, 2. large ipad held in landscape mode, 3. smaller than a full size ipad held in landscape mode (ipad in portrait mode, ipad mini, all phones)

this third, the smallest does not have a voting box by design, it seemed to take too much space on a phone

now the way this triggers is by browser size (you can test it by resizing the browser as well). Perhaps this should only hide the voting box when the screen is really tiny on the phone, I'll look into it.

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Must be smaller than full size. Either way, holding it in portrait solves things...can't believe I didn't think about that!

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7.4 years ago

Are the Ads going to be implemented in Biostar 2.0 as well? Or it i a feature that is going to be deleted?

In my opinion, they were a nice way to advertise works related to bioinformatics. In one month of exposition, I got about 300 visits to a database advertised, which is a very good result for me.

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Not sure what to do there. It was used by so few people (for running ads) that for most heavy users it was boring to have the same thing using up space on the top.

I am thinking a bulletin board section where one can post announcements.

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I had the feeling that just before switching to Biostar 2.0 the Ads were being used more actively. I remember that were usually about 6-8 Ads active at the same time, which seems to be a fair number (more Ads would be too much).

I don't know if the Ads were annoying for all the people, and how much. For me, they were not annoying, except maybe in the mobile version, where they occupied a lot of space. In any case, I remember discovering some useful tools and resources thanks to the Ads - for example, I still remember learning about BEDOPS from one of the first Ads.

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7.0 years ago
Prakki Rama ★ 2.5k

Would it be nice to put drop down option something like "Tip" or "Suggestion" while creating a new post. For example, while running different tools, users may find a particular parameter to be used or not to be used which might lead to an error or something drastic, or may be some specific type of input required to properly run the tool. Allowing an user to post that "Tip" which he figured spending quite a bit of time under that software page, will let others also directly go that page and take that precaution before running that tool on their data.

For example, I was trying to run a software called Censor. Everything regarding the input seemed to be correct. But it took quite a bit of time to actually cross through the error. Finally, I figured that input header should not have any pipe symbols to run the software. By putting this kind of information as a "Tip" on the specific software page (or post) with its version number, the user who is intending to run in future will take this as a caution before running it. In this way, a collection of all the "do's and do not's" for all the software in longterm will prove to be very valuable resource. I would like to hear your opinions on this.

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0
Entering edit mode

thanks for the feedback, we'll be working on new features in early 2015 (typically major features are rolled out at the beginning of the year when I have more time to code)

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