Scientific Computing Topics

• Software Carpentry
• The Joel Test
• Backlash on scientific computing
• Floating point numbers
  • Definition
  • What Every Computer Scientist Should Know About Floating-Point Arithmetic
  • Floating point number overview

Scientific Computing Environments

Statistical environments

S-Plus

USGS holds a license for a version of the S-Plus statistical package, and the USGS internal distribution includes USGS-developed statistical and graphics tools.

• TIBCO Spotfire S+ 8.1 for Windows with the USGS Library 4.0 Public Release
• USGS support email: GS-W Help SPLUS
• USGS support searchable archive: http://smtp.water.usgs.gov/splus_help-archive/2011/

R

R is an open-source statistical analysis system built to be functionally equivalent to S. It is gaining in popularity, and has a body of GUI's (such as RCommander) and interfaces available for it. Since R has a command-line interface, it is fairly easy to connect with other software, for example, ArcGIS. and Java Python ("Jython"). Some have described R as a "statistical scripting language."

Although the user community is very good at answering questions, the volume of questions and answers may be overwhelming.

• The R Wiki http://rwiki.sciviews.org/doku.php
• There are VERY active mailing lists http://www.r-project.org/
• Free USGS-sponsored online course: Learn R by example

Python

• The starting point for all things Python is: http://python.org

• Python, aside from being a standalone general scripting language, has become the main scripting language for the ArcGIS platform. Versions of Python 2.x and Python libraries that are included in different versions of ArcGIS are as follows:

  ArcGIS	9.3	10.0	10.1 (beta)
  Python	2.5.1	2.6.2	2.7
  NumPy	1.0.3	1.3	1.5
  matplotlib	–	–	1.0.1

• The netCDF4 module compiled for ArcGIS 10.0, 10.1 allows fairly straightforward access of netCDF and OPeNDAP data from ArcGIS Python scripts. Thanks to Rich Signell and, most of all, Christoph Gohlke (who compiled the module so it will work with Arc). Rich and Curtis Price provided this example python script.
  • The image below shows an example of a raster that has been loaded into ArcMap from a remote dataset using the netCDF4 library and the OPeNDAP access protocol.

MATLAB

MATLAB is commonly used for data and compute-intensive scientific analysis.

Known USGS MATLAB users: Rich Signell, Ashley Van Beusekom