I've been learning How Unix Works over the past month, and thought
that I'd share some of the highlights in relation to biology
computing. Many of you are already enscounced in Unix and this
may be Old Stuff. If so, you may have comments on useful points
that I've missed or have garbled.
One of the current interests in computational molecular biology is
making the rapidly growing databases more accessible to
scientists. One option is friendly software running on central or
departmental computers, which seems easier than keeping personal
computers supplied with up-to-date multi-megabyte data. X-Windows
is the Unix (and VMS) sibling of a Macintosh or MS-Windows graphic
user interface. The main attribute of X-Window software in my
mind is that it is networkable -- software and data reside on a
central computer where they can be better updated and shared among
groups of researchers.
I'd like to hear your comments on whether X-Windows software for
molecular biology will grow in importance over the coming decade
over personal computer software. Also, are you currently using X-
Window software? Do you expect to in the next year or so?
Object oriented programming languages, such as C++, provide a more
rapid way of developing and updating complex software that manages
a graphic user interface.
InterViews is a good C++ based, X-Windows toolkit for Unix that
provides an extensible program foundation, in much the same way as
MacApp does for the Macintosh. The importance of an object
oriented programming language with a good application skeleton,
such as C++/InterViews or C++/MacApp, is that the general program
and user interface handlers are already there. A programmer need
only install functions specific to the task and customize it as
needed, saving much labor.
Installing Unix system, gcc and g++ compilers, X-Windows and
InterViews software on an A/UX Macintosh took me about a week.
Learning enough C++ and InterViews to build a simple Drosophila
database browser took me another week. My strong impression is
that the C++ / InterViews combination is a rapid and powerful way
to build networkable programs, and is well suited to programmers
developing biological applications.
While InterViews is currently only available for X-Windows on
Unix, it is designed so that other window systems may be
incorporated in the future. This would let programmers develop
one program to run on many window platforms, including Mac and MS-
Windows.
Software Cited:
-- InterViews, a C++, X Windows toolkit. Anonymous ftp to
interviews.stanford.edu.
-- GNU C and C++ (gcc and g++) compilers. See Usenet newsgroups
gnu.g++.* and gnu.gcc.*
-- X Windows. See Usenet newsgroup comp.windows.x
--
Don Gilbert gilbert at bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405
