[Biojava-l] documentation was blast parsing and empty hits

[Schreiber, Mark]

> Good point. I have not been checking the CVS version, I was 
> working only with the latest release candidate of BioJava. My 
> assumption that nothing has been changed since 2000 is based 
> solely on the information in the Javadoc at the BioJava.org 
> site. I was under the impression that changes to the code 
> would be reflected and date in the Javadoc.

Yes, the Javadocs on the website are badly out of date (As is the
website), our bad :(
Am I beginning to sound like a broken record? Actually its not all that
bad. If you go to the download site you can get more recent docs all
nicely zipped up and ready to go :) (but that website really needs
updating)


> 
> I have no problem contributing to the BioJava effort - but I 
> am finding the learning curve to be fairly steep. Much of the 
> difficulty arises because the documentation has not been 
> consistently maintained. I find I have to go to the source 
> more often than not to find out what is really going on. When 
> I do that, I find that many of the demos and test programs 
> are out of date with the code base. On top of that, the demos 
> are really quite simple and I havent seen any source for 
> powerful apps that integrate a variety of BioJava packages.
> 

Common comment (with all of the bio.* projects). There is some more
documentation coming and we are always keen for people to ask what it is
they don't understand so we can focus on more documentation for the hard
stuff. A FAQ/ Frequently Provided Solutions site would probably be nice.
Some one might like to archive the little gems that are offered as
solutions to problems (any one looking to contribute to biojava, fame
and (possibly) fortune await).


> Is there a list of 'on going' projects associated with 
> BioJava? Is XFF being worked on anymore? What is the ssaha 
> demo? It seems to be undocumented. What is happening with 
> AGAVE? Is this even actively in use anymore? Should it be archived?
> 

Actually I was wondering about the status of some of these projects. I
guess one way to tell is to look at the last time the CVS was updated.
AGAVE is still being used in the bioinformatics world even after double
twist has gone toes up. There was some talk a while ago of using it as a
XML binding to BioJava. Some work needs to be done to make this more
seemless.

- Mark
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