News: State Of Biostar - Future Directions (January 2013)
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gravatar for Istvan Albert
5.7 years ago by
Istvan Albert ♦♦ 77k
University Park, USA
Istvan Albert ♦♦ 77k wrote:

Hello Everyone,

A quick post on the state of Biostar and we are looking for suggestions for directions/goals that you would like to see this year.

We have just released a new version of Biostar (version 1.2.11), a release that now incorporates many of the suggestions from Help make Biostar better! Add your feedback, opinions and suggestions.. Most of these new features have been created as programming work contracted out to Luma Education, whose chief engineer has been a long time Biostar contributor.

This release also marks the presence of our first commercial sponsor Counsyl a Stanford startup founded by social entrepreneurs and philanthropists, developers of the Universal Genetic Test. Their job ad is now sponsored, meaning that it will appear on the top of the Jobs section. Their support made it possible to create this release in such a timely fashion.

For the next year we wish to expand the reach of the site and our goal is to encourage content that goes beyond installation/errors/troubleshooting. We want to promote the creation and dissemination of the hard to find expertise and knowhow that makes scientific breakthroughs possible . We are also considering the idea of making Biostar a place where bioinformatics experts and those needing the expertise could find each other. We'd be happy to hear some of your opinions on it, or any other suggestions/feedback that you may have.

As always keep up the good work! Time and again I am amazed at the value of the content that is created on this site, just reading and browsing the posts makes me a better scientist.

news biostar • 3.9k views
ADD COMMENTlink modified 5.6 years ago by João Rodrigues2.4k • written 5.7 years ago by Istvan Albert ♦♦ 77k
8
gravatar for Mary
5.7 years ago by
Mary11k
Boston MA area
Mary11k wrote:

Sweet! I like the new logo too.

I have a suggestion. This has come up in a couple of places/forum situations and people always really like the idea, but it's never been implemented as far as I know.

What some instructors tell me they need are some small project ideas that they can put students on. And there must be some bench-type folks with little problems they need solved. So what I imagine is sort of a project/dating site. But the projects would be real-life needs, not just busy work.

So I agree on the expertise matching idea--but also consider filling a smaller niche as well. I hear about this need from instructors where we do workshops, that don't have so much research infrastructure, you know? Smaller schools that need some help.

EDIT: here's the place I brought it up some time ago, and it got good votes: Project for a beginner bioinformatics student So I think there's a need for this.

ADD COMMENTlink modified 5.7 years ago by Istvan Albert ♦♦ 77k • written 5.7 years ago by Mary11k
2

The project that Nikolay Vyahhi metioned that he was working on has gone live in the meantime: rosalind.info is a Project Euler like website with lots of small bioinformatics programming problems. It doesn't have the student/expert matching component though.

ADD REPLYlink written 5.7 years ago by Jeroen Van Goey2.2k
1

Just to add my endorsement for rosalind.info - they seem to have done a great job, it's really worth checking out

ADD REPLYlink written 5.7 years ago by aidan-budd1.9k
1

Oh, yeah, that would be kinda what I had in mind. But the problem wouldn't have a specific answer, and could even have multiple solutions. It would be interesting to see how different people/groups tackle it. But the process of having to deal with someone's specs, trying to work out what they are really asking, all that stuff brings a real-life component that would matter.

ADD REPLYlink written 5.7 years ago by Mary11k
1

Interesting idea - I'll keep in mind, would be a good fit.

ADD REPLYlink written 5.7 years ago by Istvan Albert ♦♦ 77k
1

Great idea! I have too many projects on my plate, and it would be great to find beginning students who want to help tackle them!

ADD REPLYlink written 5.7 years ago by Andrew Su4.8k
7
gravatar for aidan-budd
5.7 years ago by
aidan-budd1.9k
Germany
aidan-budd1.9k wrote:

Based on my own reactions to it, I find the whole voting/reputation/badges structure an enjoyable motivation to contribute to the site - I enjoy up-voting the content I particularly like, and the feedback I receive from others for my own contributions. Indeed, I find it a wee bit funny/interesting/scary to notice how well this relatively simple construct motivates me! :)

Thus, perhaps one path to promoting increased numbers of interactions with the site from users could focus on enhancing the experience associated with voting/reputation/badges.

Here, one suggestion comes from me noticing that, when I notice that my reputation has taken a big jump, I'm curious about which of the posts I made were recently up-voted, and by how much.

Perhaps making information like this available to us on our profile pages would make the experience of using the site more fun, and hopefully thus increase its use? For example, for the last month/week which posts got which up-votes? Or show the distribution of the last e.g. 50 up-votes amongst our posts.

Just a thought.

ADD COMMENTlink written 5.7 years ago by aidan-budd1.9k
4
gravatar for Pierre Lindenbaum
5.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum112k wrote:

My suggestions:

some new sections:

  • Call for crowd-sourcing projects: gather a large number of people for a defined project (e.g: updating a large number of wikipedia pages, manually grabbing some informations from a large number of papers to create a database, etc... )

  • Request for comment (RFC) for bio : "I want to create a new format to describe a FASTQ record using JSON. Here is my specification v1.0 , what do you think ?"

Geotagging users.

ADD COMMENTlink written 5.7 years ago by Pierre Lindenbaum112k
3
gravatar for Woa
5.7 years ago by
Woa2.7k
United States
Woa2.7k wrote:

Embedding of mathematical expression editor tool will be a good addition IMHO

ADD COMMENTlink written 5.7 years ago by Woa2.7k

That would be indeed a nice feature. And it could be easily implemented using MathJax

ADD REPLYlink written 5.7 years ago by Botond Sipos1.6k
2

We should first asses how much math is used in posts - or perhaps not used because of the lack of this feature.

ADD REPLYlink written 5.7 years ago by Istvan Albert ♦♦ 77k

I agree. I've not yet noticed any posts which would have been improved by including maths expressions - but then that could just be that I tend not to read posts where that might be useful.

ADD REPLYlink written 5.7 years ago by aidan-budd1.9k

Most of the bioinformatics posts do not require formulas indeed. But it could be useful in the case of more "computational biology" flavoured posts concerning algorithms and statistical methods (e.g. The Effect Of The "Invgamma" Setting On Computing The Site Likelihood In Mrbayes? Having the ability to display formulas could encourage those kinds of questions and so diversify Biostar.

ADD REPLYlink written 5.7 years ago by Botond Sipos1.6k
1

Ah, so, it's like I thought - I've not seen any as (so far) I haven't read posts (that are out there) for which it would be useful.

Tricky thing to do, then, is to somehow estimate the potential benefit of including this (in terms of how it fits the goals of BioStars, number of posts for which it would be useful, and how much more useful it would make these), against the effort of including it. I guess there's no "best" way of doing this.

ADD REPLYlink written 5.7 years ago by aidan-budd1.9k

Well, the effort is just sourcing a remote JavaScript.

ADD REPLYlink written 5.7 years ago by Botond Sipos1.6k
3
gravatar for aidan-budd
5.7 years ago by
aidan-budd1.9k
Germany
aidan-budd1.9k wrote:

Maybe nice to work with/integrate/using the curated, aims-to-be-non-redundant lists of bioinformatics-related events (courses, conferences, etc.) provided by iAnn, which can be embedded in a range of different contexts/systems (e.g. Drupal), and is also available as a web service...? ISCB uses the event feed from them, for example, on their event pages.

I work on a couple of projects that use the Joomla embedding of iAnn and we're very happy with it, hence suggesting it here.

ADD COMMENTlink written 5.7 years ago by aidan-budd1.9k
3
gravatar for João Rodrigues
5.6 years ago by
João Rodrigues2.4k
Stanford University, U
João Rodrigues2.4k wrote:

A report button to message moderators/etc about a bad, duplicate, etc post. If there is such a feature, then make it a bit more visible :)

ADD COMMENTlink written 5.6 years ago by João Rodrigues2.4k

As far as I know there is no such button, but you can reach the moderators via the mailinglist: biostar-central@googlegroups.com

ADD REPLYlink written 5.6 years ago by Jeroen Van Goey2.2k

There is no such feature but now that we have private messaging it will be easier to add

ADD REPLYlink written 5.6 years ago by Istvan Albert ♦♦ 77k
2
gravatar for aidan-budd
5.7 years ago by
aidan-budd1.9k
Germany
aidan-budd1.9k wrote:

Another suggestion, following on from the answer I gave above (and indeed occurring to me as I quickly check through my wording of the above answer, to check it reads OK) i.e. along the lines of potentially enhancing the "enjoyment" of using the site via badges etc., would be:

to link badges that are associated with particular questions/answers/comments, e.g. the "popular question" or "enlightened" badges, to the respective questions/answers/comments associated with being awarded those badges. e.g. I click on my "popular question" badge, and immediately see which question(s) I have asked which meet the badge criterion.

Having said that, I could well imagine that it would take considerable effort to change/add something as fundamental as that; but thought I'd add the idea, anyway, before I forget it, in case it is feasible to do it (and of course something the developers find interesting etc.)

ADD COMMENTlink written 5.7 years ago by aidan-budd1.9k
1

it is a bit tricky to create a two link correspondence between badges and posts - but we can make something a bit simpler but in the same spirit - allow sorting someone's contributions by various factors, votes,bookmarks, views etc. Also we'll soon be adding charts that display the accumulation of various attributes,.

ADD REPLYlink written 5.7 years ago by Istvan Albert ♦♦ 77k

I thought it'd be tricky - particularly if one badge linked to 2+ questions... thanks for the feedback, Istvan

ADD REPLYlink written 5.7 years ago by aidan-budd1.9k

Maybe an easy way of giving some of this information would be to provide the number of votes associated with each of the "contributions" that we see when we are on our profile pages and click on the "content created" tab - perhaps linked with allowing the content list to be sorted by date or number of votes

ADD REPLYlink written 5.7 years ago by aidan-budd1.9k

yes, this is very similar to what we will be adding in the near future

ADD REPLYlink written 5.7 years ago by Istvan Albert ♦♦ 77k
2
gravatar for Hranjeev
5.7 years ago by
Hranjeev1.4k
Malaysia
Hranjeev1.4k wrote:

Minor suggestion on site css - maybe a little top padding on <div class="body span9"> Looks crammy on my Chrome.

ADD COMMENTlink written 5.7 years ago by Hranjeev1.4k

it is not clear what that means, the site has been designed on Chrome and as far as I can tell looks as intended - perhaps provide a screenshot.

ADD REPLYlink written 5.7 years ago by Istvan Albert ♦♦ 77k
1

I mean it just looks better when I add .span9 {margin-top: 10px;} to the site css.

ADD REPLYlink written 5.7 years ago by Hranjeev1.4k

we added that to reduce cramminess ;-)

ADD REPLYlink written 5.6 years ago by Istvan Albert ♦♦ 77k
2
gravatar for aidan-budd
5.7 years ago by
aidan-budd1.9k
Germany
aidan-budd1.9k wrote:

I've seen this feature mentioned elsewhere, Sending Personal Messages to Users : Cool feature to implement or not [Biostar network] but I just wanted to bring it up again, as it's a feature I'd have liked to have available today i.e.: being able to send messages directly to individual BioStar members

In case the specific use-case is of interest: there was something that looked odd to me about a "Notification" in my profile (I couldn't find the text referred to in it when I visited the post), so I wanted to send a quick message to the poster to see if this was a bug, or if they'd maybe added text and then immediately deleted it or something like that. Instead I've tried (I use GoogleMail/Groups very rarely, so often get in a muddle with it) posting something about this to the appropriate GoogleGroup, I'd prefer to have been able to avoid that.

Could be that I've just failed to find out how to do this, of course!

ADD COMMENTlink modified 5.7 years ago by Istvan Albert ♦♦ 77k • written 5.7 years ago by aidan-budd1.9k
1

talking about things I've failed to find out how to do - would be great if someone could help me work out how to link to a specific post in the text. I wanted to link to Sending Personal Messages To Users : Cool Feature To Implement Or Not [Biostar Network] and so, reading the FAQ, have added "\post 43120", but looking at my text above, this hasn't been converted into a link to that post.

What should I be typing in the preview to get this working?

Thanks

Aidan

ADD REPLYlink written 5.7 years ago by aidan-budd1.9k
2

You had a comma at the end, once removed it works. I should add a fix so commas are also recognized.

ADD REPLYlink written 5.7 years ago by Istvan Albert ♦♦ 77k
1

Thanks for that, Istvan.

ADD REPLYlink written 5.7 years ago by aidan-budd1.9k
2
gravatar for aidan-budd
5.7 years ago by
aidan-budd1.9k
Germany
aidan-budd1.9k wrote:

How about providing a representation of the activity within BioStar as a network e.g. produced from Cytoscape?

Members could be nodes, edges could be interactions between members (e.g. contribution to the discussion/answers within the same question)?

Doesn't add any obvious (to me) functionality; rather, I was thinking in terms of outreach, capturing attention for the project - might be a cute image (or even interactive network thingy) to have on a front page, or when making a flyer, or so. Might offer nice/interesting (maybe even useful?) ways of charting/representing changes in the dynamics of the site?

I wouldn't expect this to have any priority - surely there are more useful things to be worked on - but maybe there are Cytoscape fanatics out there who might enjoy doing such a thing (I can barely load a network to the thing, so I'm not aforementioned fanatic... :) )

Just throwing the idea out there, though, before it disappears again almost instantly from my lousy memory.

ADD COMMENTlink written 5.7 years ago by aidan-budd1.9k
2
gravatar for aidan-budd
5.7 years ago by
aidan-budd1.9k
Germany
aidan-budd1.9k wrote:

Another suggestion, this time concerning the presentation of results after a search.

I just spent maybe 5 minutes trying to locate this question; I knew it was out there, I knew it had BioStar in the title, I knew it was initiated by Istvan, but still it was tricky to find it, I assume because there are other questions in them.

I think this would have been easier for me to do if: - one could query questions to match words only in the title, and by user (perhaps also user who asked the question)? - one could change the sort order of results to make it by date (of question being asked, of last modification (answer, comment, edit)

Not sure how useful this would be for others, but several times now I've hoped/wished for this, so maybe it'd be fairly useful, at least in certain situations.

(Sorry if the above functionality is already there and I just missed it, I looked a bit around to see if it was there and couldn't see it)

ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by aidan-budd1.9k
2
gravatar for aidan-budd
5.7 years ago by
aidan-budd1.9k
Germany
aidan-budd1.9k wrote:

Another comment/suggestion - I was looking just now for an article that I think was posted in the Forum section.

It wasn't clear to me how to search just in this section, maybe that's an option that could be presented as a tab for restricting our view (i.e. in addition to the "Show All","My Tags","News" etc. tabs)?

ADD COMMENTlink written 5.7 years ago by aidan-budd1.9k
0
gravatar for zx8754
5.7 years ago by
zx87545.0k
London
zx87545.0k wrote:

Another suggestion, adding complexity levels to questions. Once the question is posted, Admins and/or Users with high reputation (5K+, 10K+?) can assign complexity level to the question: Easy, Moderate, Hard, or score of 1-10. Based on assigned levels the answerers get higher/lower points :)

ADD COMMENTlink written 5.7 years ago by zx87545.0k
2

Although the idea of adding complexity levels is interesting, I kind of disagree with the philosophy of the solution (adding power/work to specifically designated users). I would find it more elegant to have some kind of systematic rule (say the questions that have had a short and accepted answer within a short time after posting could be labelled easy, and questions having had large contributions during a large period of time would be labelled hard). Just my two cents.

ADD REPLYlink written 5.7 years ago by Leonor Palmeira3.6k

BioStar has opened my eyes to stack-exchange-style forums. Looking around a bit, there is a fair amount of discussion about what makes for a good/most effective system; I guess (as others have already commented elsewhere) it depends a lot on the desired outcome/effect of the system.

Naively, I thought that even though each of us can only vote on one question/comment/answer once, the hope/idea is that the good/very valuable content will "just" receive more votes, and hence get its reward. But I've much less experience of this kind of site than others, and it seems like things aren't as simple as that.

Could it be useful for "us" to dig around amongst posts that we think are very valuable, but which are harder to find than we would hope/expect by (what we find to be) obvious ways of looking for them, and use these to test different ideas on?

ADD REPLYlink written 5.7 years ago by aidan-budd1.9k

I do agree that would be nice to be able to reward really valuable content.

ADD REPLYlink written 5.7 years ago by Istvan Albert ♦♦ 77k
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