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A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.
A Java library and set of tools to quickly and easily manipulate graphs (set of nodes and edges) and dynamic graphs. The principal trait of this library is its ability to manage (create, edit, layout, display) continuously evolving graphs.
The development of this project now takes place on Github. Visit the official Graphstream website at http://graphstream-project.org
Cyberinfrastructure Shell (CIShell) is an open source, community-driven framework/application for the integration and utilization of datasets, algorithms, tools, and computing resources. Algorithms can be integrated using most programming languages.
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The SPASE Toolkit contains a set of command-line applications which can be used to generate, validate, referentially check, use and organize resource descriptions written in SPASE XML.
primeHandle is a set of data management tools in support of the PrIMe Initiative (http://primekinetics.org). primeHandle includes graphical user interfaces for searching through data collections, editing and submitting data to the PrIMe Data Depository.
SPASE Model is a collection of tools for working with the structured data model information. Tools can convert the relational version of the data model into various expressions, including XSD, XMI and PDF documentation.
Sanchay is a collection of tools and APIs for language researchers. It has some implementations of NLP algorithms, some flexible APIs, several user friendly annotation interfaces and Sanchay Query Language for language resources.
Nevada is a tool for interactive visualization of dynamic networks. Unlike other dynamic network visualization tools it's focussing on visualizations preserving the user's mental-map. Import of Pajek files is supported.
Software tools for building interactive information visualization applications. Prefuse supports a rich set of features for data modeling, visualization, animation, and interaction for both Java (prefuse) and Flash (prefuse flare).
The Databionics ESOM Tools offer many data mining tasks using Emergent Self-Organizing Maps. Visualization, clustering, and classification of high-dimensional data using databionics principles can be performed interactively or automatically.
Tools for finite automata simulation, minimization and grammar utilities (left recursion removal, context free grammar simplification and transformation to Chomsky Normal Form).
Open2Dprot is an open-source proteomics project for the development of bioinformatic tools for n-dimensional protein expression data analysis of quantified protein expression across multiple samples from research experiments.
MASQOT-GUI is an open-source, platform-independent application for two-channel microarray spot quality control. Included is a set of tools for gridding, segmentation, quantification, multivariate spot quality assessment and data visualization.
Software Development Toolkit and Libraries to support the adoption of MIMOSA and Open O&M Initiatives. The libraries and toolkits will focus on basic implementation of DAO, XML, and Web Service tools.
Thea, Tools for High-throughput Experiment Analysis, is an integrated information processing system dedicated to the annotation of data issued from classification systems with biological information coming from a knowledge base.
GeNetDB, contraction of Genetic Network Database, is a bioinformatic platform destined to the study of genetic regulatory networks. It contains in one place the data and the way to study them, providing the user an access to all tools needed for his work
JMAT : Java MATrix tools package.
Provides an easy-to-use class of matrix with MATLAB-like functions and syntax. JMAT also includes plots and histograms in 2D or 3D, an expression parser, and some statistic simulation tools.
jATLAS is a Java implementation of ATLAS [Architecture and Tools for Linguistic Analysis Systems]. For more information, see http://jatlas.sourceforge.net.
The MathForge Application Environment provides users a broad range of Java-based math tools (calculation, visualization, presentation and communication via MathML) and allows developers to leverage existing code while extending MathForge.
JAMATO : JAva MAtrix TOols package
Provides an easy-to-use class of matrix with MATLAB-like functions.
Jamato also includes Data Plots in 2D or 3D, Histograms in 2D or 3D, an expression parser, and some basic statistic simulation tools.