OOP and molecular biology

Steve Thompson: VADMS genetics THOMPSON at JAGUAR.CSC.WSU.EDU
Thu Aug 13 15:08:25 EST 1992

Good Afternoon bio-soft:

While at the 1992 Molecular Evolution Workshop at the Marine Biological
Laboratory in Woods Hole MA, my supervisor back home at Washington State
University asked me to query the bulletin boards regarding object oriented
programming.  My initial query and the responses posted follow below:


>Greetings Netlanders--

>My boss just asked me to post a question to the hyperspace netland:

>Would you query the nets to see how they feel about object oriented
>programming and its application to sequence analysis and molecular modelling
>in the near future?

From: schnorr at tournesol.versailles.inra.fr (Kirk Schnorr)

In my opinion, object oriented analysis programs are good to a point.  They are
good for learning to use a program in a short period of time without constantly
having to refer to the manual.  What you have to ask yourself is two questions

1) Is it worth the programming time to produce something that only makes a
program marginally easier to use? 
2) Are people qualified to ask questions about sequence analysis and molecular
modelling smart enough to use command line programming  without much

I personally prefer command line programs when possible for sequence analysis
but object oriented programs for molecular analysis.


OOP holds the best current hope for managing the next level of
complexity to be tackled.

I *highly* recommend a book called "Developing Object Oriented Software
for the macintosh".  Please note that, in spite of the title, it's NOT
specifically about Mac development, but rather, describes a strategy
for analysis, design, and implementation for object-oriented software

It's published by Addison Wesley and should be available through your
favorite geek/nerd-type bookstore :)

If you need any additional info, please let me know.

From: robison1 at husc10.harvard.edu (Keith Robison)

I just started using C++ two months ago and I love it!!  It is quite
easy to design a set of core classes useful for biology and then
have their code easily integratable into new code.  Also, many biological
concepts map onto class structures quite readily.

For example, I have one class which is a general sequence class.  This serves
as the base class for a DNA sequence class and a protein sequence class.
It is now straightforward to add new features (such as file formats) and
get them working for both DNA and protein sequences.  If I later decide
that for one class or the other (or both) a function needs DNA- or
protein-specific characteristics, I can use over-riding or virtual functions
to ensure that all the old code still works.

Keith Robison
Harvard University
Program in Biochemistry, Molecular, Cellular, and Developmental Biology
robison at ribo.harvard.edu 

From: bashford at scripps.edu (Don &)

I have written an object oriented system in C++ for doing
electrostatic calculations on proteins and other molecules.  It is
called MEAD (Macroscopic Electrostatics with Atomic Detail).  Some
calculations using it are described in Bashford & Gerwert, J. Mol.
Biol. 224 473-486 (1992).

The source code and some data files are available by anonymous ftp
from ftp.scripps.edu in the compressed tar file,
Beware of a bug in our ftp system such that "ls" does not work
but "dir" and "ls -l" do.

The current package contains data files enabling the user to reproduce
the main results of the above cited JMB paper as well as results
from an earlier lysozyme paper.  I consider this "alpha release" software
since it has been used mainly by me and my immediate collaborators.
I would be happy to have people in the wider world try it out and
let me know their bugs and critiques both from a user point of view
and an object designer/programmer point of view.

Donald Bashford
bashford at scripps.edu

Thanks to all who provided us insight into this system.  Your responses, as
always, are much appreciated.
					Sincerely, Steve Thompson

                              Steven M. Thompson
            Consultant in Molecular Genetics and Sequence Analysis
VADMS (Visualization, Analysis & Design in the Molecular Sciences) Laboratory
           Washington State University, Pullman, WA 99164-1224, USA
          AT&Tnet:  (509) 335-0533 or 335-3179  FAX:  (509) 335-0540
                  BITnet:  THOMPSON at WSUVMS1 or STEVET at WSUVM1
                   INTERnet:  THOMPSON at wsuvms1.csc.wsu.edu

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