Scientific Data Analysis Software

"Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos. The current version of the code is Amber version 9, which is distributed by UCSF.

The Arctic Science and Technology Information System (ASTIS) database contains over 59,000 records describing publications and research projects about northern Canada. ASTIS is maintained by the Arctic Institute of North America at the University of Calgary, and is part of the Canadian Polar Information Network.

These tools are used to create data images for the Atmospheric Visualization Collection at www.nsdl.arm.gov. Through this collaborative workspace our goal is to make these codes easier to modify for use on other datasets as well as more useful for education and research with the Atmospheric Radiation Measurement dataset. Various NSDL Communication tools are available to allow contributions to this project. Your participation in making our goal possible would be greatly appreciated. We are also using the NSDL Communication Portal's Wiki tool for developing lesson plans. Educators are encouraged to use this "lesson plan sandbox" to collaborate on development of lesson plans that use our atmospheric data.

Audio Abacus is a project of the Psychology Department's Sonification Lab at the Georgia Institute of Technology, overseen by Bruce Walker, PhD. Sonifications and auditory graphs are very good at providing information about trends and patterns. However, extracting the exact (or nearly exact) value of the data at a given point is a different task, and requires a different auditory interface. One approach is to have each note of a scale represent a data value. Several approaches have been taken in this vein. Our Audio Abacus takes a new twist on this method, and has been implemented as a simple software package that allows the listener to estimate the actual values of the data, in addition to the overal trends of the data set.

Bootstrap Simulation and Two-Dimensional Monte Carlo Simulation: Dealing with Variability and Uncertainty, Mixture Distributions, Measurement Error, and Censored Data. AuvTool is a software tool for statistical analysis of variability and uncertainty associated with fitting parametric probability distributions to data sets. It was developed for the Office of Research and Development(ORD) of U.S. Environmental Protection Agency, Research Triangle, NC.

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.

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.

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 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.

ChucK is a new audio programming language for real-time synthesis, composition, and performance, which runs on MacOS X, Windows, and Linux. ChucK presents a new time-based concurrent programming model, which supports a more precise and fundamental level of expressiveness, as well as multiple, simultaneous, dynamic control rates, a precise and straightforward concurrent programming model, and the ability to add, remove, and modify code, on-the-fly, while the program is running, without stopping or restarting. It offers composers, researchers, and performers a powerful and flexible programming tool for building and experimenting with complex audio synthesis programs, and real-time interactive control.

CiteULike is a free service to help academics to share, store, and organise the academic papers they are reading. When you see a paper on the web that interests you, you can click one button and have it added to your personal library. CiteULike automatically extracts the citation details, so there's no need to type them in yourself. It all works from within your web browser. There's no need to install any special software.

Computational Infrastructure for Geodynamics (CIG) is a membership-governed organization that supports and promotes Earth science by developing and maintaining software for computational geophysics and related fields. On behalf of its Member Institutions, CIG is now working under a Cooperative Agreement with the National Science Foundation to develop, support, and disseminate open source software for the greater geodynamics community. CIG consists of: (a) a coordinated effort to develop reusable, well-documented and open-source geodynamics software; (b) the basic building blocks an infrastructure layer of software by which state-of-the-art modeling codes can be quickly assembled; (c) extension of existing software frameworks to interlink multiple codes and data through a superstructure layer; (d) strategic partnerships with the larger world of computational science and geoinformatics; and (e) specialized training and workshops for both the geodynamics and larger Earth science communities.

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® Project is to develop, implement, deploy, and evaluate mechanisms and policies that support High Throughput Computing (HTC) on large collections of distributively owned computing resources. Guided by both the technological and sociological challenges of such a computing environment, the Condor Team has been building software tools that enable scientists and engineers to increase their computing throughput.

Dapple is a global data explorer designed to provide an open and optimal environment for visualizing, presenting and sharing massive quantities of geoscientific data on desktop computers. Dapple lets you browse, discover and display graphically rich data from global and corporate spatial servers � Geosoft DAP servers, NASA servers, USGS servers, and the many, many WMS servers currently available. The Dapple project is an open-source activity sponsored by Geosoft and derived from the NASA World Wind open source project. Dapple represents our effort to make this powerful technology accessible and useful to professional earth scientists. Dapple can only be installed under Windows XP.

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.