[Biojava-l] BioJava 3 Proposals

Richard Holland holland at ebi.ac.uk
Thu Nov 8 13:53:09 UTC 2007

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Dear BioJava users,

The BioJava developers are considering options for the future
development of the BioJava toolkit. We consider that it needs
improvement in a few major areas to make it easier to use and
understand, and also faster and more scalable.

The options are to either rewrite large parts of the existing code,
working within the existing interfaces and paradigms, or to develop a
new set of BioJava packages from the ground up in order to take
advantage of lessons learned from the design patterns of the existing code.

The BioJava developers have spent the last couple of months discussing
ideas and proposals related to these options on a Wiki page, and would
now like to open this discussion to all users of BioJava and the
bioinformatics community in general. We would like to invite anyone who
has any ideas or suggestions to contribute these to the Wiki page,
and/or to comment on the ideas and suggestions that have already been
posted there.

Here is a link to the Wiki page, and also a link to the associated Talk
page where much of the discussion has taken place so far:


It is our intention to leave the discussion open until mid-January
2008 when we will summarise it and use it as the basis of a plan of
action. We will then distribute the summary and the action plan via the
BioJava website.

We look forward to hearing your comments and ideas. Please do remember
to make them directly to the Wiki page so that they are preserved in
context, making it easier for us to summarise them later!

(on behalf of all BioJava developers)

PS. Just to reassure you, this is NOT a plan to drop the existing
codebase. It will continue to exist, but the outcome of these
discussions will determine whether we will continue to develop and
support it or start afresh with a clean slate and a new codebase.
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