TODO

General:
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1.  Implement try: blocks more fully
2.  Make use of Log::Log4perl and Sys::SigAction to make this more robust
3.  Make the installation self-explanatory
4.  perldoc autodie
6.  perldoc Moose
7.  perldoc DBIx::Class
8.  DBIC::Schema::Loader
9.  Catalyst

Importing:
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1.  Swissprot, EMBL support are untested
2.  Better generic fasta support
3.  Import my Blast->Import function into prf_daemon

BLAST:
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1.  Make a pretty graphical BLAST output like NCBI's
2.  I have a tonne of BLAST data showing potentially extended ORFs
    This needs to find a real home and a way to efficiently examine it.

Folding algorithms:
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1.  Maybe pknotsRG
2.  The new java algorithm from the Korean lab
3.  ilm?

PBS:
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1.  PBS support is pretty awesome right now, I think this is done.

Randomization:
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1.  Make it so users can pick and choose the randomization algorithms
2.  Make it possible to regenerate randomization data

Http interface:
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1.  Make further use of the javascript, AJAX, and jquery
2.  Failover to other database nodes works great, but document it.
3.  General cleanups, and get someone with some aesthetic sense to look at it.

Command Line interface:
-----------------------
1. Document Document Document that shit.

Database Access:
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1.  Recently split genome into genome and gene_info, this means there needs to be a 
    careful audit of the code to make sure selects are going to the correct places
2.  I am making a lot of redundant select statements when joins would be smarter
    Start fixing that.

Graphing:
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1.  SVG::TT::Graph is so pretty, move some to that.
2.  Document it!

Configuration system:
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1.  Cut out redundant options
2.  Document how awesome that configuration system is!