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I'm currently working as a Bioinformatics consultant/developer/researcher at Amateur musician, traveller, painter, sporadic writer and always eager to learn more about languages, plants... Too many things to do and too little time for it! Pablo is a DZone MVB and is not an employee of DZone and has posted 8 posts at DZone. You can read more from them at their website. View Full User Profile

Bio4j Go Tools

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UPDATE: This post is from March 2011 so if you are interested in this tool please check all the features and functionality that have been added from that time till now listed here:

- Bio4j GO Tools goes web (April 2011)

- GO Annotation graph visualizations with Bio4j Go Tools + Gephi Toolkit + SiGMa project (April 2011)

- Improvements in Bio4j Go Tools (Graph visualization) (June 2011)

- Cool GO annotation visualizations with Gephi + Bio4j (November 2011)

Now the original post:

As you may have seen Bio4j has already started making his way through the bioinformatics world; however there’s not as much information as there should be about the project yet.

That’s where Bio4j Go Tools comes in as the first real-world example using Bio4j as back-end.

Bio4j Go Tools is a group of Gene Ontology related services and apps. (You can find more information about this in the wiki)

The services provided so far are:
- Uniprot protein GO annotations retrieving
- GoSlim requests with custom Slim term sets.

Both services results and client-server communication are XML based following a really simple and intuitive structure.

A user-friendly AIR application has been developed allowing the user to directly use these services abstracting the logic of the different requests.

Bio4j Go Tools AIR app screenshot

Enjoy it  ;)

Published at DZone with permission of Pablo Pareja Tobes, author and DZone MVB.

(Note: Opinions expressed in this article and its replies are the opinions of their respective authors and not those of DZone, Inc.)


Armin Ehrenreich replied on Thu, 2011/12/01 - 10:40am

Why an AIR frontend ?

This GUI frontend could also be easily done in a few hours using Java. This is a Java site! 

Pablo Pareja Tobes replied on Thu, 2011/12/01 - 11:39am in response to: Armin Ehrenreich

Hi Armin,

Quoting what I say in the update of this post: "This post is actually quite old (March 2011) and got somehow published automatically" due to a misunderstanding.

Anyways, there's no AIR frontend anymore, it was replaced by a Web App (you can check it here ) combining Flex/AS3 at the client side with Java at server side, (even the AIR app was using a Java EE server with Bio4j as backend).

If you're interested in the Java server part, you can have a look at this repository which, in turn is using a good bunch of repositories all coded in Java (as well as everything related with the project Bio4j only the viewers are developed in other languages so far).
So don't worry because it does use Java quite a bit ;)



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