Biojava Versus Biojavax

Question

[Andrea_Bio]

Hi

I'm new to BioJava so please forgive my ignorance.

I believe BioJavaX is an extension to BioJava and that it is part of the latest release of BioJava 1.7.1 (I can certainly see a BioJavaX directory with code files in my download anyhow).

Are these tutorial here http://www.biojava.org/wiki/BioJava:CookBook http://www.biojava.org/wiki/BioJava:Tutorial

applicable to BioJavaX? I have read that some things are done differently in BioJavaX but I can't find any specific tutorial for it. I need to learn biojava and I don't want to waste my time learning biojava if i should be learning biojavaX if you see what i mean

Many thanks in advance

Answer 1

[biobot 0.0.77.a.1099]

The main tutorials apply to the org.biojava.* classes, not org.biojavax.*. The wiki history shows that most of the tutorial pages were originally uploaded in 2006, which predates biojavax.

The code is currently in flux while BioJava 3 is being developed. There is a new BioJava 3 cookbook in development too.

[biobot 0.0.77.a.1099]

I can't give a fair answer to that question; I used to be a core developer for BioJava, but in the end found its domain model too difficult to work with. Try the biojava-dev mailing list, you are sure to get some good advice there.

[Andrea_Bio]

I believe BioJava3 will be significantly different. At this point in time is it worth learning BioJava or waiting for Biojava3? I read that biojava3 is in the beta stage but I don't know when it will be ready. My only concern is that I might get easily confused between the 2 if I learn them both in a short time frame.