Two things about Biostars

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Khader Shameer

Nov 28, 2014, 3:33:50 PM11/28/14

Dear All, 

I was having a discussion on twitter about two things related to BioStar. Posting it here to get thoughts of Istavan and others. 

1. Integrating BioStars with ISMB-Bioinformatics Wikipedia intiative 

I was chatting with Alex Bateman (Pfam / Sanger) on twitter about integrating efforts by ISMB to improve bioinformatics content on Wikipedia by leveraging expertise from BioStar community. My idea was to cross-link the Wikipedia content via BioStar in the context of a question related to a topic (for example: "transcription factor binding site prediction". Prompting those answer the question to provide edits/improve wikipedia article could help both resouces. We can also provides incentives using badges / points to the Biostar users. 

Link to discussion: 

2. Official affiliation of Biostars with ISMB and AMIA 

Following the above discussion, I thought Biostars should be the official Q&A site for both AMIA and ISMB. Officially integrating Biostars with these great organization could bring in a wide-array of questions, users and content. Biostars with its strong userbase and curated answers could also reach to a wider and newer audience. Other BioStars including Neil, Larry and Chris also supports this as a good direction to proceed. 

Link to discussion:

Thoughts, ideas, suggestions? 


Khader Shameer, Ph.D

Istvan Albert

Nov 28, 2014, 3:56:32 PM11/28/14
to, Khader Shameer
Hi Khader,

this is very timely as we are gearing up for the next release of Biostar (3.0) for Spring 2015.

This ticket describes some of the features that we envision:

Biostar already serves  number of communities like Galaxy, Bioconductor and Neurostar and I see 2015 as the year where go local to global  ;-) 

One feature that I think will make the most difference is that of content federation - unlike centralized Q&A "silos" we want Biostars instances to live in parallel and share content based on reciprocal agreements between organizations. 

For example a strictly Galaxy related question on the main Biostars could be moved by a moderator to the other organization's site with one click. In addition a search on either site may show content from the other one as well if that is relevant. It is all about opt-in by the managers of both sites - everyone retains full control over their content and shares as they see fit.

There are a number of other features that we are planning to add - for example the ability to run a workshop through an instance of Biostars (for example presentations/tutorials can be viewed and commented on)

I would love to get involved in more substantial ways with other organizations such as ISMB. For example both Galaxy and the Bioconductor project  now directly support developing new features for Biostars and for that reason we prioritize for their needs as well.

As for the Wikipedia integrations I think it is all about APIs and being able to both link back and forth in a reasonably automatic manner.



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Istvan Albert
Associate Professor, Bioinformatics
Pennsylvania State University

Khader Shameer

Nov 28, 2014, 9:55:00 PM11/28/14
to Istvan Albert,
Thank you Istavan, 

Great to hear the progress in the right direction. 

We can start with a detailed email / official letter to the Board members of ISCB to request for an official affiliation. 
A direct link from ISCB will be a great start. 

@all: Shall we start with a google-doc of letter ? 

@Pierre: Any comments on integrating WikiMedia with BioStar - any open APIs that we can use to link the contents ? Andrew Su could give us have some great suggestions here. Not sure if Andrew is on this list. 

Thanks again, 

Khader Shameer, Ph.D 

Istvan Albert

Nov 29, 2014, 8:44:38 PM11/29/14
Yes good ideas.

Contacting people directly might be better than this group as it is not that active.
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