Free Software Tools for both Earth and Social Sciences
Software has obviously been an important component of both scientific research and engineering applications
for several decades, as well as an increasing presence in everyone's life (e.g., your mobile phone or PDA,
your car, etc). The big problems of our time have spread across disciplines, and require the collection,
management, and analysis of large amounts of data by numerous groups and individual researchers. One of
the attempts to address this issue is the use of Grid Computing to formally share both data and
computing resources, along with several software frameworks to access and analyze grid-based resources
and even run complex scientific workflows (see the Kepler Project below).
An important point to note is that these problems and related research areas go across disciplines, from
earth science to sociology, and from ecology to public policy. The links between formerly disparate fields
continue to grow and strengthen, making the understanding and use of appropriate software tools of critical
importance for everyone. Many fields have become intertwined in interesting ways, as the following two
- The National Center for Ecological Analysis and Synthesis
(NCEAS, a research group affiliated with UCSB)
brings together researchers, post-docs, and students to work on cross-cutting interdisciplinary research
that uses existing data to address major fundamental issues in ecology and allied fields, and their
application to management and policy. This work requires the development and use of new tools that not
only provide the capability to look at existing data in new ways, but also support users who come from
fields perhaps previously considered non-technical (or at least not usually known for being extremely
geeky :). The research at NCEAS has evolved into a discipline in its own right called Ecoinformatics,
and they've developed Kepler (see below) along with some related tools to help facilitate this work.
The NCEAS Ecoinformatics Program is dedicated to the
research, development and dissemination of technological tools that facilitate analysis and synthesis
in ecology and the environmental sciences.
- The Cognitive Science program at
UCSD studies areas that cut across the brain, behavior,
and computation. They have several undergraduate degree options that require significant work with both
applied math and software tools (including software development). Some of the options are actually
cutting-edge computing degrees masquerading in what may look like the Psychology Dept at first glance
(but really isn't). For example, required topics for both undergraduates and graduates include courses
in behavior, computation, and the neurobiological basis of cognition. And yes, they use Python...
But even basic problems in geography and related social sciences require the use of geospatial and
mathematical tools to work with large amounts of data with spatial attributes, as well as flexible
automated text processing. Web-enabled applications are frequently useful, and there are many other
examples below. Besides the Zope web application
framework and Python, there are many useful
software packages for users in all these fields, for everything from data ingest and transport to
analysis and visualization, whether on the web or the desktop. Another important point to note in
this case, is that these tools are not just for geeky types, science or otherwise. Python
is a prime example of a powerful tool that was designed for normal humans (as well as geeks :)
Check out some of the free books and some example Python code if you don't believe me (especially
if you're a non-programmer, you should read this).
Online Python Books and Tutorials
Scientific Modeling Frameworks
- Ptolemy II - Ptolemy II is a Java-based
component assembly framework with a graphical user interface called Vergil. The Ptolemy project studies modeling,
simulation, and design of concurrent, real-time, embedded systems. Ptolemy II's generic framework
is flexible enough to be used for many different problem domains from discrete event simulation and
modeling of communication networks, to scientific data analysis workflow tools such as Kepler
- Kepler - The Kepler project is a cross-project collaboration to
develop open source tools for Scientific Workflows (partly based on the Ptolemy II framework).
General Scientific Software
- Scientific Python - SciPy is an open source library of scientific tools
for Python. SciPy supplements the popular Numeric module, gathering a variety of high level science and
engineering modules together as a single package.
- Octave - GNU Octave is a high-level language, primarily intended for
numerical computations (compatible with Matlab).
- R - The R Project for Statistical Computing, a free software
environment for statistical computing and graphics (R is essentially the GNU implementation of the
original S language and environment). Note there are several stats textbooks written around R.
- HDF4 / HDF5 -
A general purpose library and file format for storing scientific data.
- NetCDF - NetCDF (network Common Data Form) is an
interface for array-oriented data access and a library that provides an implementation of the interface.
- UDUnits - A library for manipulating units of
GIS, Mapping, and Geospatial Data Analyis
- GRASS - GRASS GIS (Geographic Resources Analysis Support System) is an
open source, Free Software Geographical Information System (GIS) with raster, topological vector, image
processing, and graphics production functionality.
- UMN MapServer - A popular web mapping application with
support for GDAL, proj, and other tools.
- ZMapServer - a Zope interface to mapserver; currently being
re-factored into Cartographic Objects for Zope and the Python Cartographic Library.
map data in most modern web browsers, with no server-side dependencies. Use hobu's
example application to browse the state of Iowa.
- Proj.4 - Proj.4 cartographic projection software (additional grids,
eg, NAD27 available).
- GDAL (Geospatial Data Abstraction Library) - a
translator library for raster geospatial data formats.
- OGR Simple Feature Library - OGR is a C++ library for a variety of
vector file formats (also has C and Python APIs).
- OpenEV - An OpenGL/GTK/Python based graphical viewer which uses
GDAL for raster access.
- Shapelib - A library for working with ESRI shapefiles (ArcInfo
- Virtual Terrain Project - a set of software tools, including an
interactive runtime environment (VTP Enviro). The VTP libraries also use GDAL.
- gstat - a geostatistical modeling package.
Meteorological Modeling and Data Analysis Software
- LAPS - LAPS Local Analysis and Prediction System, a real-time
meteorological analysis package. You must sign up on the list and request the software.
- MM5 - Penn State/NCAR Community Mesoscale Modeling
system (needs PG Fortran compiler on Linux).
- LDM - The Unidata Local Data Manager (LDM) is a collection
of cooperating programs that select, capture, manage, and distribute meteorological data products.
- GSD - NOAA's Earth System Research Laboratory's
Global Systems Division (formerly the Forecast Systems Laboratory) develops most of the software and
modeling applications used by the National Weather Service, NCEP, and other weather agencies
Remote Sensing and Image Processing Software
- SeaDAS - Image analysis package for SeaWIFS data.
- OSSIM - Open Source Software Image Map project.
See my personal software page for info on some Gentoo ebuilds I
currently maintain, as well as some old RedHat/fedora/cAos rpm packages (and the downloads menu above).