I know that to access data from the NOAA Web Server, the token must go in the header.

Accessing NOAA web service with token
For example,
curl -H "token:AbCdEfGhIjKl1234" http://www.ncdc.noaa.gov/cdo-web/api/v2/data?datasetid=GHCND&locationid=ZIP:28801&startdate=2010-05-01&enddate=2010-05-01

Where would I execute this curl command? In the windows command prompt?

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