TitleBodyTechnical Expertise RequiredCostAdditional Information
Apache Velocity

Velocity is a Java-based template engine. Its template language references objects defined in Java code. When Velocity is used for web development, Web designers can work in parallel with Java programmers to develop web sites.

Velocity has broader uses, such as generation of SQL, PostScript and XML from templates. It can be used either as a standalone utility for generating source code and reports, or as an integrated component of other systems.

iMacros for Firefox

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.

Web professionals can use iMacros for functional, performance, and regression testing of web applications. The built-in STOPWATCH command captures precise web page response times. iMacros also includes support for many AJAX elements.

iMacros can be combined with other extensions such as Greasemonkey, Web Developer, Firebug, Stylish, Download Statusbar, NoScript, PDF Download, Foxmarks, Fasterfox, All-in-One Sidebar, Megaupload, Foxyproxy, Flashblock and Adblock.

Basic programming skillsFree



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. The programming feature supports functional, procedural, and object oriented styles of programming.

Basic programming skillsCost-basis

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OAIster is a freely accessible search engine for open access web resources, available from OCLC. OAIster uses the Open Access Initiative Protocol for Metadata Harvesting (OAI-PMH) to harvest records from websites. OAIster contains over 25 million records from all disciplines and subjects contributed by over 1,000 libraries, archives, and repositories. The records harvested by OAIster use Dublin Core (unqualified) metadata format. Repository managers running OAI-compliant repositories can contribute records for open access web resources. OAIster records can be searched separately at the website, and are incorporated into OCLC Worldcat.

No programmingFree

SAS is an integrated system of software that enables everything from data access across multiple sources to complex manipulations of data files to performance of sophisticated statistical analyses and data visualizations. Three of SAS' most popular software products that are commonly used by ecologists are Base SAS, SAS/STAT, and SAS/GRAPH. SAS is available for Windows and UNIX platforms. GUIs make SAS accessible to novice users and the command-line interface facilitates development of programs for complex data processing.

Basic programming skillsCost-basis
  • Khattree, Ravindra and Dayanand N. Naik. 2000. Multivariate Data Reduction and Discrimination with SAS Software. Cary, NC: SAS Institute Inc. 978-1-58025-357-4
  • Littell, Ramon C., George A. Mi lliken, Walter W. Stroup, Russell D. Wolfinger, and Oliver Schabenberger. 2006.SAS for Mixed Models, Second Edition. Cary, NC: SAS Institute Inc. ISBN: 978-1-59047-500-3
  • SAS Essentials: A Guide to Mastering SAS for Research. 2010. Elliott, Alan C. and Wayne A. Woodward. San Francisco: John Wiley and Sons, Inc. ISBN: 978-0470461297
  • Delwiche, Lora D. and Susan J. Slaughter. 2008. The Little SAS Book: A Primer (Fourth Edition). Cary, NC: Sas Institute Inc. ISBN: 978-1-59994-725-9
  • Burlew, Michele. 2009. Combining and Modifying SAS Data Sets: Examples, Second Edition. Cary, NC: SAS Institute Inc. ISBN: 978-1-59047-920-9
SAS Enterprise Miner

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.

Spotfire Miner

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.

Basic programming skillsCost-basis
The Predictive Ecosystem Analyzer (PEcAn)

The Predictive Ecosystem Analyzer (PEcAn) is an integrated ecological bioinformatics toolbox and data assimilation system that synthesizes information contained in ecological models, data, and expert knowledge. This is done using modern statistical methods and state-of-the art ecosystem models. PEcAn has a web interface that enables users to run ecosystem models, as well as a suite of R packages that can be used for model-data fusion and more sophisticated analysis.

Basic programming skillsFree

PEcAn can be used to run ecosystem models through a web-based user interface, while advanced analyses can be performed using its suite of R packages. New models can be linked to PEcAn through the creation of model-specific wrapper functions that convert translate to and from the standard formats used by PEcAn. Although PEcAn is currently coupled to three diverse ecosystem models, it can be coupled to a broad class of simulation models. Integrating a new model requires writing a wrapper in R to convert inputs and outputs to and from the standards used by PEcAn, and registering the model and computer in the database.
PEcAn source repository is hosted at GitHub: (http://github.com/PecanProject/pecan). See the Wiki (http:// github.com/PecanProject/pecan ) for more information.
LeBauer, D.S., D. Wang, K. Richter, C. Davidson, & M.C. Dietze. (2013). Facilitating feedbacks between field measurements and ecosystem models. Ecological Monographs. doi:10.1890/12-0137.1
Wang, D, D.S. LeBauer, and M.C. Dietze (2013) Predicting yields of short-rotation hybrid poplar (Populus spp.) for the contiguous US through model-data synthesis. Ecological Applications doi:10.1890/12-0854.1
Dietze, M.C., D.S LeBauer, R. Kooper (2013) On improving the communication between models and data. Plant, Cell, & Environment doi:10.1111/pce.12043


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).

No programmingFree