Scientific Software

NLTK is a leading platform for building Python programs to work with human language data. It provides easy-to-use interfaces to over 50 corpora and lexical resources such as WordNet, along with a suite of text processing libraries for classification, tokenization, stemming, tagging, parsing, and semantic reasoning, wrappers for industrial-strength NLP libraries, and an active discussion forum.

Spark is a library of code that can be used to process data in parallel on a cluster. The basic idea of Spark is parallelism, meaning Spark breaks the data into pieces, sends the pieces to differnt computers for processing, then sends the results back and process the combination to get the final result. More specifically, the basic computing paradigm is: distribute a large data set on multiple nodes, map functions row by row, group data by a key, and then perform aggregate operations. Sparkling Water, the happy marriage between open source technologies Apache Spark and H2O. It combines the advanced machine-learning algorithms from H2O with the execution power of Spark.

FDS is a computational fluid dynamics (CFD) model of fire-driven fluid flow. The software solves numerically a form of the Navier-Stokes equations appropriate for low-speed, thermally-driven flow with an emphasis on smoke and heat transport from fires. Smokeview is a visualization program that is used to display the results of an FDS simulation. FDS and Smokeview version 4 have been officially released (8/24/2004). A setup program for Windows containing FDS, Smokeview, documentation and example files is available for download. Updated FDS (September 1, 2004) and Smokeview (September 7, 2004) executables are also available for download. The FDS and Smokeview software in particular are provided as a public service by the National Institute of Standards and Technology (NIST).

Melts is a software package for modeling crystallization of magmatic systems. MELTS is written in ANSI C with an X11/Motif Graphical User Interface. Executable versions are available for a wide variety of "UNIX"-level workstations.

TensorFlow™ is an open source software library for numerical computation using data flow graphs. Nodes in the graph represent mathematical operations, while the graph edges represent the multidimensional data arrays (tensors) communicated between them. The flexible architecture allows you to deploy computation to one or more CPUs or GPUs in a desktop, server, or mobile device with a single API. TensorFlow was originally developed by researchers and engineers working on the Google Brain Team within Google's Machine Intelligence research organization for the purposes of conducting machine learning and deep neural networks research, but the system is general enough to be applicable in a wide variety of other domains as well.

The freeware version of ACD/ChemSketch provides chemical drawing capabilities, surpassing other popular commercial products. The freeware contains tools for tautomer prediction, 2D structure cleaning, and 3D optimization and viewing, capabilities which are not even included in some of the commercial packages from other software producers. Also included is an IUPAC systematic naming capability for molecules with fewer than 50 atoms and 3 rings. The capabilities of ACD/ChemSketch can be further extended and customized by programming tools using an included Basic-type language, ACD/ChemBasic. The Freeware software is presently limited to version 5.0. Commercial ACD/ChemSketch is available as version 8.0.

uDig is an open source (LGPL) desktop application framework, built with Eclipse Rich Client (RCP) technology. The goal of uDig is to provide a complete Java solution for desktop GIS data access, editing, and viewing.

The Rapid Earthquake Viewer (REV) gives you access to data from seismograph stations around the world. REV monitors the earth and posts information about recent earthquakes so you can see where they happened and view the seismograms from global seismograph stations for every notable earthquake. REV even lets you check up on seismograph stations in your area, so if you think you felt the ground shake, check REV.

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

BOINC is an open-source software platform for computing using volunteered resources. Scientists use BOINC to create a volunteer computing project, giving you the computing power of thousands of CPUs. Universities use BOINC to create a Virtual Campus Supercomputing Center. Companies use BOINC for desktop Grid computing.

Condor is a specialized workload management system for compute-intensive jobs. Like other full-featured batch systems, Condor provides a job queueing mechanism, scheduling policy, priority scheme, resource monitoring, and resource management. Users submit their serial or parallel jobs to Condor, Condor places them into a queue, chooses when and where to run the jobs based upon a policy, carefully monitors their progress, and ultimately informs the user upon completion. Condor can be used to manage a cluster of dedicated compute nodes (such as a "Beowulf" cluster). In addition, unique mechanisms enable Condor to effectively harness wasted CPU power from otherwise idle desktop workstations.

The goal of the Condor

Since 2002 the OGSA-DAI Project has been working to develop an effective solution to the challenge of Internet-scale data integration. Our product - OGSA-DAI

Tools from Microsoft Research and our research partners to support computational science and its use in other research disciplines.

Program for Climate Model Diagnosis and Intercomparison (PCMDI) develops and maintains several software packages specifically tailored to the climate community. Software contained in this portal includes CDAT (Climate Data Analysis Tools) and the Climate Model Output Rewriter (CMOR).

The Seismic Handler software package is a powerful seismic waveform analysis tool. There is an interactive part (Motif version) for observatory purposes (e.g. daily routine analysis) and a command line version for scientific research.

ORFEUS (Observatories and Research Facilities for European Seismology) hosts a page containing links to seismological software (freeware). A wide range of tools are available (statistics, modelling, earthquake location, data processing, ray tracing) in a number of different platforms (MATLAB, Sun, UNIX, Fortran).

Cornell University Professor Rick Allmendinger has created several structural geology programs and made them available for download via anonymous FTP. The programs cover stereographic projections, fault kinematic analysis, fault/fold forward modeling, strain rate calculations, and more.

FoX is an XML library written in Fortran 95. It allows software developers to read, write and modify XML documents from Fortran applications without the complications of dealing with multi-language development. FoX can be freely redistributed as part of open source and commercial software packages.

FoX is largely the result of work by Toby White during the eMinerals project. Toby is now platform lead at Timetric and FoX is currently maintained by Andrew Walker (Bristol Earth Sciences). The code was developed from earlier work by Alberto Garcia and Jon Wakelin. Much of the FoX_wkml module was written by Gen-Tao Chiang (Cambridge Earth Sciences).

PostGIS has been developed by Refractions Research as a project in open source spatial database technology. PostGIS is released under the GNU General Public License. PostGIS adds support for geographic objects to the PostgreSQL object-relational database. In effect, PostGIS "spatially enables" the PostgreSQL server, allowing it to be used as a backend spatial database for geographic information systems (GIS), much like ESRI's SDE or Oracle's Spatial extension.

Commonly referred to as GRASS, this is free Geographic Information System (GIS) software used for geospatial data management and analysis, image processing, graphics/maps production, spatial modeling, and visualization. GRASS is currently used in academic and commercial settings around the world, as well as by many governmental agencies and environmental consulting companies. GRASS is an official project of the Open Source Geospatial Foundation.