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"Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (Amber) and a package of molecular simulation programs which includes source code and demos (AmberTools).

ArcGIS Desktop is a collection of software products for building complete geographic information systems (GIS). produced by Esri. ArcGIS Desktop 9 provides an integrated GIS, combining object-oriented and traditional file-based data models with a set of tools to create and work with geographic data. The following three applications comprise the ArcGIS Desktop software suite:

CrowdLabs is a system that supports community sharing, visualization and analysis of workflows using a philosophy employed by social web sites.

CrowdLabs features the ability to interact with the workflows through a Web browser. Workflow provenance is captured allowing scientists to publish their process as well as their results. For the latter, CrowdLabs generates links to the process that can be embedded in Wiki and HTML pages, as well as LaTeX documents.

ArcGIS Explorer is a geographical information system (GIS) viewer to explore, visualize, and share GIS information. It provides a freely-distributable way to share products produced by ESRI's commercial products.

There are two versions: one for the desktop, the other on-line. The on-line version includes support for time-enabled maps.

ESRI's ArcGIS Desktop software contains ModelBuilder, which is a work flow tool that enables the creation and execution of consistent, repeatable models that are comprised of one or more processing steps. ModelBuilder can be used to ensure the integrity of a particular model or set of analytical processes through modeling, storing, and publishing complex operations and workflows. ModelBuilder workflows can be created and executed on both the desktop and over the web.

ArcMap is the map display and editing workhorse for the ESRI ArcGIS Geographical Information System (GIS) software package. It is most widely used for map creation, but also has broad capabilities for editing and analysis. The "Toolbox" available in ArcMap provides an encyclopedic array of GIS data manipulation and analysis functions for almost any application.

The Forest Sector Carbon Calculator is a tool to help users learn about how carbon stores in the forest change over time.

FRAGSTATS is a computer software program designed to work with geospatial data to help the user categorize landscape patterns and metrics, and is useful in identifying areas where land use activities have resulted in fragmentation of the landscape. The current release is version 3.3

The program is currently undergoing another major revamping, which will result in the release of version 4.0 sometime in 2011.

Fusion is a LiDAR viewing and analysis software tool developed by the Silviculture and Forest Models Team, Research Branch of the US Forest Service. Fusion also works with IFSAR and terrain data sets. LIDAR uses a laser sensor comprised of a transmitter and receiver, a geodetic-quality Global Positioning System (GPS) receiver and an Inertial Navigation System (INS) unit. The laser sensor is mounted to the underside of an aircraft.

HDFql stands for "Hierarchical Data Format query language". It is a high level language for handling HDF5 files.

HDFql provides a simpler, cleaner, and faster interface for HDF5 across C, C++, Java, Python, C# and Fortran.

HDFView is a visual tool for browsing, viewing, managing and editing HDF4 (Hierarchical Data Format) and HDF5 binary data files. HDF files are designed to contain large amounts of numerical or other data.

The tool allows you to view the hierarchical file structure, create and edit new files, groups, datasets, dataset contents, and attributes of the data.

iMacros was designed to automate the most repetitious tasks on the web. With iMacros, you can quickly fill out web forms, remember passwords, create a webmail notifier, download information from other sites, scrape the Web (get data from multiple sites), and more. You can keep the macros on your computer for your own use, or share them with others by embedding them on your homepage, blog, company Intranet or any social bookmarking service.

ImageJ is an open-source, Java-based image processing and display tool. It can read and write images in GIF, JPEG, BMP, PNG, PGM, FITS, ASCII and TIFF formats. Editing capabilities include image enhancement (e.g., smoothing, sharpening, edge detection, median filtering and thresholding), image manipulation (e.g., crop, scale, resize, rotate and flip) and even analyses (e.g., area measurement, mean brightness, standard deviation, min and max brightness and measurement of lengths and angles).

Tags: analyze, image

The IMSL Numerical Libraries provide a wide variety of mathematical and statistical algorithms written in various programming languages for easy incorporation by programmers. There are libraries for C, Fortran, Java, .NET, and Python (through wrappers). These algorithms are not only useful for desktop applications, but also can be applied to High Performance Computing (HPC) and High Throughput Computing (HTC).

JHOVE2 is open source software for characterization of digital objects. Characterization captures the information about a digital object that describes that object's significant technical properties. For example, for a digital image file, JHOVE2 can identify the precise file format, as well as the salient technical properties of the file, such as resolution, bit-depth, and color-space. Capturing this information supports digital preservation analysis and decision making.

JMP is a desktop software package designed by SAS for dynamic data visualization and statistical data exploration. JMP includes an interactive graph builder that supports a wide variety of two- and three-dimensional graph types, and statisical reports are displayed along with plots for assessment and interpretation. Data can be loaded into JMP from common desktop file formats (e.g.

Mathematica is a computational platform used by scientists, engineers and mathematicians. Mathematica has support for equation solving, numerical analysis, as well as graphing and visualization. Mathematica has import and export filters for tabular data, images, video, sound, CAD, GIS documents and biomedical formats. There is support for data mining tools such as cluster analysis, sequence alignment and pattern matching as well as text mining support.

MATLAB is an interactive data analysis and visualization environment that can be used to perform computationally-intense operations on large data sets efficiently. MATLAB also provides a high level programming language that supports rapid development of work-flow scripts and Graphical User Interface applications to automate repetitive tasks.

MetaMorph is an industry standard image analysis suite and capture platform.

The MetaMorph software suite supports a wide array of microscopes, cameras, and precision stages used in bioresearch. The software provides acquisition, processing, and analysis features that allow researchers to build custom imaging systems for solving experimental problems in cellular imaging.

Tags: analyze, image

MrBayes is a program for doing Bayesian phylogenetic analysis including phylogenetic reconstruction. Bayesian inference of phylogeny is based on the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem.

National Instruments LabVIEW is a sophisticated application for the creation and management of engineering and scientific measurement, test, data collection and control systems. LabVIEW includes a graphical user interface that allows external hardware devices such as mechanical or electronic sensors to be configured and operated using "point-and-click" methods. Networks of sensors and processing devices can be joined together using flowchart-like "wire" connectors.

NodeXL is a free, open-source template for Excel 2007 and 2010 that lets you enter a network edge list, click a button, and see the network graph, all in the Excel window.

Ocean Data View (ODV) is desktop software for analysis and visualization of oceanographic, atmospheric and other geo-referenced profile or time-series data.

Basic features:

GNU Octave is a high-level language, primarily intended for numerical computations. It provides a command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with MATLAB. It may also be used as a batch-oriented language.

OpenBUGS is software for running Markov Chain Monte Carlo (MCMC) simulations following Bayesian statistical theory. It is one of two software packages created for Bayesian Inference Using Gibbs Sampling, or BUGS. OpenBUGS is so named because it runs on multiple operating systems; the WinBUGS software can be used with Windows operating systems (see WinBUGS tool in the DataONEpedia for details).

Oriana is a tool for calculating statistics for circular or radial data (angles or directions measured in degrees, time of day, day of week, month of year, etc.). It can be used for orientation data (direction taken from a point), for describing and comparing species temporal distributions and ranges, and other types of data that are not directly handled in most statistics packages.

Panoply is a cross-platform application which plots geo-gridded arrays from netCDF, HDF and GRIB datasets. It supports the following operations:

Project Trident is a scientific workflow workbench that allows users to author workflows visually by using a catalog of existing activities and complete workflows. The workflow workbench provides a tiered library that hides the complexity of different workflow activities and services for ease of use. Trident supports: analysis and visualization worksflows; composing, running, cataloging experiments as workflows, as well as capturing of provenance information.

SAS Enterprise Miner streamlines the data mining process to create predictive and descriptive models based on analysis of large amounts of data. Data can be accessed from local files or from remote database connections. SAS data mining software uses a point-and-click interactive interface to create workflows and analysis diagrams, and then execute them. SAS Miner can transform and manipulate data using filters and statistical analyses to extract desired data from large datasets.

SPYDER is a free software environment for visualization, numerical calculation, and data analysis. It provides a graphical development environment for the Python programming language and leverages many scientific and engineering packages including Matplotlib, NumPy and others. It is available on Windows, Mac OS X, and GNU/Linux.

Simulink is an add-on package for MATLAB that supports simulation and model-based design using a graphical block-programming scheme. An interactive graphical editor is provided for building models and simulations based on an extensive library of customizable program blocks and custom code. A Model Explorer application supports inspection and editing of models, signals, parameters and generated code.

SpatiaLite is an extension to the SQLite database that enables it to support spatial data.

SpatiaLite is conformant to OpenGIS specifications. It has the following features:

Spotfire is a data analysis and visualization tool. It allows users to perform ad-hoc analysis and build custom analytic applications. It supports data imports from spreadsheets and relational databases, as well as real-time and event-driven data. Besides visualization, Spotfire also incorporates statistics functions.

Spotfire Miner is software for data mining of large datasets. It is sold commerically by TIBCO.

Users can connect to remote or local datasets, apply statistical and methodological filters, clean and transform the data, and finally apply a model to produce the desired mined data. Statistical models include clustering, regression analysis, and principal components analysis. Models based on historical data can then be used to predict future results based on newly mined data.

SPSS is a desktop statistical software package that is centered around modeling and statistics. SPSS can access data from many different proprietary and open source data sets and has decent graphing and very good statistical modeling capabilities. One weakness (Up to version 17), is the presentation quality of graphs. Other packages do a much better job at data presentation.

IBM SPSS Amos is a tool used for structural equation modeling. It features drag-and-drop drawing tools and produces graphics of final models for presentation.

Amos uses standard methods – including regression, factor analysis, correlation and analysis of variance. It can be used to create models to test hypotheses and confirm relationships amongst variables.

STATISTICA is a proprietary analytical software package developed by StatSoft that includes data visualization, data analysis, data management, and data mining tools. It is a primarily graphical user interface (GUI) application.

Tableau supports the analysis of tabular data from spreadsheets and relational databases. The tool provides a visual interface that allows users to import data and interactively explore the data through visualizations. These visualizations are created through a graphical user interface that allows users to build queries by dragging and dropping attribute names from tables and spreadsheets.

Tika java class library available through the Apache group. It supports media type detection based on file type signatures, metadata extraction and text parsing and extraction.

Supported Document Formats:

TMI-Orion is a manufacturer of data sensors and data loggers. They have custom software called QLEVER to configure, test, record data and perform basic statistics on the data streams resulting from the sensors. The software can manage the sensors (in some cases remotely), and evaluate sensor battery life and technical performance.

Triana is an open source problem solving environment that combines an intuitive visual interface with powerful data analysis tools. It can be used for a range of tasks, such as signal, text and image processing, and Triana includes a large library of pre-written analysis tools and the ability for users to integrate their own tools. Recently a custom writer was attached to the Triana GUI allowing Triana to generate Pegasus/Condor input files for the GriPhyN project.

Tags: analyze, GUI, workflow

UCINET is a comprehensive package for the analysis of social network data as well as other 1-mode and 2-mode data. Social network analysis methods include centrality measures, subgroup identification, role analysis, elementary graph theory, and permutation-based statistical analysis. In addition, the package has strong matrix analysis routines, such as matrix algebra and multivariate statistics.

Integrated with UCINET is the NetDraw program for drawing diagrams of social networks.

WEKA is a data mining tool. It is a collection of standard machine learning algorithms organized and presented to the user as a workbench. The algorithms can be applied directly to a dataset from the workbench or called from Java code. New classifiers, filters etc can be added through the GUI.

WEKA is written in Java and runs on platforms that support Java. It is available under the GNU Public License (GPL).

WinBUGS is software for running Markov Chain Monte Carlo (MCMC) simulations following Bayesian statistical theory. It is one of two software packages created for Bayesian Inference Using Gibbs Sampling, or BUGS. WinBUGS is so named because it runs on windows operating systems; the OpenBUGS software can be used on other operating systems (see OpenBUGS entry).

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