News: Biostars 3.0 is now under testing. It has groups, charms and other interesting features.
21
gravatar for Istvan Albert
4.6 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

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 pariwise aligner, reverse complement, protein translations, fetch some sequences etc. Most functionality will run at client side and not server side.

 

biostar news • 2.3k views
ADD COMMENTlink modified 4.5 years ago by Devon Ryan92k • written 4.6 years ago by Istvan Albert ♦♦ 81k
7

Markdown yessssssssssss

ADD REPLYlink written 4.6 years ago by Pierre Lindenbaum123k
1

what is Charms ? another project/ library ?

ADD REPLYlink written 4.6 years ago by Pierre Lindenbaum123k
4

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

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

ADD REPLYlink written 4.6 years ago by Istvan Albert ♦♦ 81k
2

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/

ADD REPLYlink written 4.5 years ago by Istvan Albert ♦♦ 81k
1

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

ADD REPLYlink written 4.6 years ago by Adrian Pelin2.3k

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.

ADD REPLYlink written 4.6 years ago by Istvan Albert ♦♦ 81k

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.

ADD REPLYlink written 4.5 years ago by Adamc620
5
gravatar for Adrian Pelin
4.5 years ago by
Adrian Pelin2.3k
Canada
Adrian Pelin2.3k wrote:

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.

ADD COMMENTlink written 4.5 years ago by Adrian Pelin2.3k

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.

ADD REPLYlink written 4.5 years ago by Daniel3.7k
1

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.

ADD REPLYlink written 4.5 years ago by Istvan Albert ♦♦ 81k

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.

ADD REPLYlink written 4.5 years ago by Daniel3.7k

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.

ADD REPLYlink written 4.5 years ago by Istvan Albert ♦♦ 81k
4
gravatar for Devon Ryan
4.5 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

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...

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by Devon Ryan92k
1

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. 

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by Istvan Albert ♦♦ 81k
1

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

ADD REPLYlink written 4.5 years ago by Devon Ryan92k
2
gravatar for Damian Kao
4.6 years ago by
Damian Kao15k
USA
Damian Kao15k wrote:

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.

ADD COMMENTlink written 4.6 years ago by Damian Kao15k

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

ADD REPLYlink written 4.6 years ago by Istvan Albert ♦♦ 81k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1981 users visited in the last hour