News:Biostars 3.0 is now under testing. It has groups, charms and other interesting features.

Question

[Istvan Albert]

Biostar 3.0 is now undergoing testing.

http://test.biostars.org/

The test site may be occasionally offline, broken, styling might be off etc.

Major features

Groups: sections of the site may be devoted to one particular subject. A group will be identified by a different subdomain. Posts created in a group will only be visible while visiting that group. Moderator/admins will be group specific and will be set by the group owners.

Charms: Biostar now provides a console to run bioinformatics code in. Initially we support wrappers over javascript libraries such as NTSeq by Keith Whor http://keithwhor.github.io/NtSeq/ but we plan to expand to RPC type calls to biopython and others.

Users will be able to activate other user's libraries. The goal is to provide a platform where people can write their own utility functions in the way they think it is the best then all these to be easily shared with a larger audience. Think of a "charm" like an "opinion" on how an aligner should run, what output it should provide, what it should report etc.

http://test.biostars.org/site/charms/

Note that the goal is not to turn Biostar into data analytics platform. The utility is in providing easy access to methods that otherwise would be cumbersome to run in a way that everyone can access. We need a simple pairwise aligner, reverse complement, protein translations, fetch some sequences etc. Most functionality will run at client side and not server side.

[Pierre Lindenbaum]

Markdown yessssssssssss

[Pierre Lindenbaum]

what is Charms ? another project/ library ?

[Istvan Albert]

It is like the Matrix - best if you see it for yourself:

http://test.biostars.org/site/charms/

[Istvan Albert]

A new version of charms has been made available, this should be more self descriptive with better examples that one can run

http://test.biostars.org/charms/

[Adrian Pelin]

This is really exciting! I am especially interested in the idea of Groups. I myself am interested in population genetics and comparative genomics.

[Istvan Albert]

yes me too, I will create groups for courses that I teach, events, conferences - keeps everything neatly separated yet still easy to access. Each group can be subscribed separately with messages or email.

[Adamc]

Thanks for changing the primary search back to a full results page. I've been using the classic search only on the current version, since not being able to middle-click on search result links in the primary search of the current version was somewhat maddening.

Answer 1

[Adrian Pelin]

Hello Istvan, one suggestion I have for the future of Biostars, is to manage TAGs used in posts, the way stackoverflow does it. In other words, only trusted users can create new tags, and tags are predefined. Now I can type RNA-Seq or RNASeq or RNAseq and sometimes different spellings create different tags, while if we manage them it will be more useful.

[Daniel]

If you're adding the reputation requirement for some tasks, I would recommend the stackoverflow precedent of requiring a minimum rep for old threads, i.e. if thread is over 1 year old require 50 rep to post. This would stop people new to the forum from asking questions on the bottom of old threads and the "Thanks! Me Too!" that seems to happen so frequently which pushes old things up to the front page.

[Istvan Albert]

all good ideas - I'll look into them. I will though say that limiting user interaction can be counterproductive - the content may become tighter and better defined with - but user participation may decrease and overall site utility may decline. What could work better - though would require more work and more thoughtful user interfaces is to prompt trusted users to retag, correct and rearrange content. But of course that too should be as seamless as possible.

[Daniel]

I don't think it needs to limit anyone, I just I think something that says to new users "This question is old, if you're asking a new question you should do it here" and stops them from posting on the old thread would keep things on track, and they're more likely to get a response. Also, there's nothing to stop more seasoned users who know the deal from adding new information.

[Istvan Albert]

I see, with that I agree, there is a lot of value in indicating that a thread is old and as such likely to not be the best avenue to follow up on - of course unless the question is very closely relating to the original topic. I still think it should be done with an advisory nature rather than "score based" cutoff - person A has 49 points so they cannot do it, person B has 50 points so they can - I know that it would tick me off if I fell into the former category.

By the way there is a new moderation option that allows one to move any contribution around within a thread and even to move it to a new post.

Answer 2

[Devon Ryan]

A rather useful feature that doesn't seem to be present would be to enable tagging other users in posts/comments. In essence, this would be like @someone in twitter and many other sites, which generates a message to that person so they know there's a post they might want to look at.

Edit: I realize this might be a rather late request...

[Istvan Albert]

I have been considering this and it may make it into the new release right away or shortly thereafter - the technology is there but, as it turns out, there are subtle issues at play that I never thought about before and I am not sure how to handle.

For example one obviously does not want to get another message if someone edits a post that already has @username in it. But then they very likely would want to get a message if someone edits a post an adds a new @username tag into it. So that now leads to a an unexpected complication due to the nature of the posts and that they are editable. One could check the subscriptions but those are thread (root post) based ... anyway so to put it in perspective the will is there to add this we just have to figure out what is the way to do it that does not make it overly complicated.

[Devon Ryan]

Good to know and I'm not at all surprised that this turns out to be a very complicated thing to implement correctly.

Answer 3

[Damian Kao]

I like the idea of charms. However, it might be more useful as an embedded console in posts. I can imagine a situation where someone asks how to parse a particular file and an answer might use a charm to run sample input data. Expanding charms to run python/perl/bash/javascript would be cool.

[Istvan Albert]

Interesting idea - we'd have to figure out how to save the state - it could snapshot itself into a javascript object