what software do biologists need?

Ben Jones jonesbb at BELOIT.EDU
Thu Mar 18 03:41:59 EST 1993

As a biologist turned programmer I have worked in a variety of biology and
medical laboratories.  I have come across several research projects that
lack adequate software, or at least the researchers couldn't find any to do
the job.  Here's one wishful thought I heard recently.  (I can't say I
think there's a big market for this one.)

Software to recognize bird calls either live in the field (using the
built-in microphone of a Mac), or from an audio tape, especially if the
calls are mixed with other species.  It would count them, and determine
calling frequency.  It would have to be able to learn by example, so that
the researcher could start with a taped series of calls and have the
program recognize additional ones from that.  It may be possible to
determine how many different individual birds are calling either by
detecting small differences in the calls or by using a  stereo microphone
with separated heads to determine of different calls are coming from
different directions.  (I am not proposing to determine *what* directions
the calls are coming from, but only whether they are likely to be different
or not.  It seems to me it would require a three-headed microphone to
determine true direction in two dimensions.)

Lacking the above software, a software package which counts key presses or
mouse clicks, along with timing information.  It could be used manually to
count bird calls or other events.

Here's a another thought from my work in an Ophthalmology department, and
there might be a market for this:  How many biologists need to control a
computer while performing experiments in total darkness, such as during
experiments on visual processes?  Would voice-activated software for
controlling equipment be useful?  (It might be available now, in fact.)  It
would be useful even in the light if you need to keep both hands on your
equipment or if you need to keep your eyes at a microscope.

Combining elements from the two paragraphs above, software to count verbal
commands and timing information as the researcher is listening or watching
in the field.  The researcher may need to use binoculars or do birdcall
studies at night.  Naturally if he or she is only counting a single type of
event, a keypress or mouse click would be enough, but some behavioral
ecologists have a variety of behaviors they need to keep track of.

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