Perl Conference Handout

[Steve A. Chervitz]

Steve,

Some minor changes and a few thoughts.

> Bio::Struct
> A Perl module for reading, writing, accessing, manipulating, and analyzing
> biological macromolecular structures.
> 
> Goal: Provide a standard and convenient representation for biological
> structures, as well as core data-management and analysis features
> Status: Conceptual

You could be more specific about the class of structures and the
domain of biology:

"A Perl module for reading, writing, accessing, manipulating, and 
analyzing biological macromolecular 3D structures.

Goal: Provide a standard and convenient representation for molecular 
biological structures (nucleic acid and proteins) as well as core 
data-management and analysis features." (don't forget the period :)

>From our discussion of 2D structures in July, I think there is agreement  
that the Struct module should not deal with both 2D and 3D structures. 
Objects that represent a molecule's 2D structure would be handled by a 
different module which could be associated with either a 1D or 3D 
structure by a delegation mechanism.

Some more thoughts on the 2D vs. 3D issue: 

3D structures *contain* 2D information, so a 2D structure object should 
be derivable from a 3D structure object. If you believe Anfinsen, 1D 
sequences contain 3D (and therefore 2D) structural information. The point 
here is that there is redundancy in biological data. To be really useful, 
the Bio:: modules should account for this, keeping the violations of good 
software engineering principles to a minimum. Although tempting, we 
should not sacrifice biological robustness for the sake of good s.e.


> Bio::Object
> A rich hierarchy which attempts to encode the underlying logic of
> molecular biology within a set of standard, interoperable Perl modules.
> 
> Goal: Provide a framework to help guide the design of interoperable Perl
> classes for managing and processing molecular biological data.
> Status: Ongoing evolution; currently usable
> Special features: Extensively used as part of the SGD database
> Chief Developer: Stephen A. Chervitz sac@genome.stanford.edu

Put "Saccharomyces Genome Database" in place of "SGD database".