Scientific Software

Quantum GIS (QGIS) is a user friendly Open Source Geographic Information System (GIS) licensed under the GNU General Public License. QGIS is an official project of the Open Source Geospatial Foundation (OSGeo). It runs on Linux, Unix, Mac OSX, and Windows and supports numerous vector, raster, and database formats and functionalities. Quantum GIS provides a continously growing number of capabilities provided by core functions and plugins. You can visualize, manage, edit, analyse data, and compose printable maps. Get a first impression with some screenshots and a more detailed feature list.

Seismic Unix is software for processing and analyzing seismic reflection and refraction data. The Seismic Unix Project is partially supported by the Colorado School of Mines Center for Wave Phenomena Consortium Project.

Relative Permeability Explorer (RPE) is a collection of published and unpublished relative permeability curves for brine and CO2. These curves are used as parameters in multiphase flow simulations and have a significant impact on brine displacement in carbon sequestration applications. RPE is provided as a resource to researchers interested in flow of CO2 and brine through porous media.

Matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell (ala matlab or mathematica), web application servers, and six graphical user interface toolkits. Matplotlib tries to make easy things easy and hard things possible. You can generate plots, histograms, power spectra, bar charts, errorcharts, scatterplots, etc, with just a few lines of code. For a sampling, see the screenshots, thumbnail gallery, and examples directory.

SciPy (pronounced "Sigh Pie") is open-source software for mathematics, science, and engineering. It is also the name of a very popular conference on scientific programming with Python. The SciPy library depends on NumPy, which provides convenient and fast N-dimensional array manipulation. The SciPy library is built to work with NumPy arrays, and provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization. Together, they run on all popular operating systems, are quick to install, and are free of charge. NumPy and SciPy are easy to use, but powerful enough to be depended upon by some of the world's leading scientists and engineers. If you need to manipulate numbers on a computer and display or publish the results, give SciPy a try!

Plot is a scientific 2D plotting program for Mac OS X. Plot is designed for everyday plotting, it is easy to use, it create high quality plots, it allows easy and powerful manipulations and calculations of data and it is free. Plot has many data manipulation methods integrated: curve fitting, spline fit, fft smooth, least square smooth, spline interpolation, differentiation, integration, FFT, least square regression, normalizing, moving, data calculations, function generator, etc.

This application is designed to simplify the image annotation process. It allows researchers to create meta-data required by the bio-image database. It can also update, print and upload existing information. It is available for Windows and Mac OS X.

OME server is a Perl-based system for visualising, managing, and analysing microscope images and metadata. It includes a web browser interface, a threshold segmentation and tracking application (called "findSpots"), a MatLab interface, support for VisBio, LDAP, Bio-Formats and much more.

PVWATTS calculates electrical energy produced by a grid-connected photovoltaic (PV) system. Researchers at the National Renewable Energy Laboratory developed PVWATTS to permit non-experts to quickly obtain performance estimates for grid-connected PV systems within the United States and its territories. PVWatts determines the energy production and cost savings of grid-connected photovoltaic (PV) energy systems throughout the world. The PVWatts calculator was developed by the National Renewable Energy Research Lab's Electric Systems Center Resource Integration Section.

The Simple Model of the Atmospheric Radiative Transfer of Sunshine, or SMARTS, predicts clear-sky spectral irradiances. Earth's atmosphere is a continuously changing filter that modifies the sunlight that travels through it. SMARTS computes how changes in the atmosphere affect the distribution of solar power or photon energy for each wavelength of light.

Sage is a free mathematics software system licensed under the GPL. It combines the power of many existing open-source packages into a common Python-based interface.

MonoViewer - The MonoViewer allows the display of one molecule at a time. There are models of over 400 inorganic, organic and biological molecules in the MonoViewer database.
DuoViewer - The DuoViewer allows the display of two molecules side by side. There are models of over 400 inorganic, organic and biological molecules in the DuoViewer database.
MacroViewer - The MacroViewer is specialized for the display of macromolecular structures. There are models of 9 proteins, 4 nucleic acids, and 2 nucleic acid/protein complexes in MacroViewer database.
MolecularStudio - The Studio is a general use interface for all of the Molecular Library Viewer features. It allows the creation of molecular surfaces, generation of RasMol scripts, and precise movement of models.

The program PEEI calculates a discrete, numerical and approximate solution of a generic differential analytical model (i.e. a system of partial differential equations).

Excel is commonly used in the industry for business applications and is seldom seen as an engineering tool. This website shows how Excel can be used for engineering applications. It provides Excel tools to Engineers, and Engineering students, and illustrates how these can be used for Engineering analysis. It also has tips that should be of use to all Excel users.

A group of researchers at Cornell University, California Institute of Technology, and University of Wyoming are creating a digital library of algorithms and constructive mathematics that are usable for program and software construction.

R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. One of R's strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control. R is available as Free Software under the terms of the Free Software Foundation's GNU General Public License in source code form. It compiles and runs on a wide variety of UNIX platforms and similar systems (including FreeBSD and Linux), Windows and MacOS.

Surfract provides services and software for analyzing surface texture, or roughness, to support quality control, product and process design, and research. Recently featured in a paper in Nature magazine (Dental microwear texture analysis shows within species diet variability in fossil hominins), we have developed a simple user interface (Toothfrax) to allow anyone to perform the analyses described in that paper. While the interface requires a license to the Kfrax DLL's we have made trial versions of the retail dlls that will work until August 13, 2005. If you wish to participate in the 'Toothfrax' beta test please continue to the beta-test page.

The Protein Microarray Analysis Tool (ProMAT) is a data analysis application for protein microarray data. The software was developed for use with ELISA microarray experimental data by the Statistics Group and the Cell Biology and Biochemistry Group at Pacific Northwest National Laboratory. ProMAT takes microarray data (the output of microarray image analysis) where some arrays are treated with standards of known antigen concentration and some arrays are treated with samples of unknown concentration. ProMAT fits standard curves to the standards data to relate spot fluorescence to concentration. ProMAT also calculates and outputs confidence bounds on these standard curves. The tool then uses the standard curves to predict antigen concentrations for the unknown samples, along with prediction intervals.

Genetic linkage analysis is a statistical method that is used to associate functionality of genes to their location on chromosomes. The main idea is that markers which are found in vicinity on the chromosome have a tendency to stick together when passed on to offsprings. Thus, if some disease is often passed to offsprings along with specific markers, then it can be concluded that the gene(s) which are responsible for the disease are located close on the chromosome to these markers. Superlink is a computer program that performs exact genetic linkage analysis with input-output relationships similar to those in standard genetic linkage programs Linkage, Fastlink v4.1, Tlinkage, Vitesse v2.0, and Genehunter v2.1. Superlink can run larger files than previous programs.

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.