lazar (Lazy-Structure-Activity Relationships) is a tool for the prediction of toxic activities of chemical structures. lazar derives predictions from databases with experimental toxicity data. It searches in these databases for compounds with similar structures and calculates the prediction from their measured activities.
ClusterControl is a Web interface to simplify distributing and monitoring (bioinformatics) applications on Linux cluster systems. It is based on a modular concept that enables integration of command line oriented programs into the application framework of ClusterControl. The system enables integration of different applications accessed through one interface and executed on a distributed cluster system. It uses Apache, PHP, and OpenPBS or Sun Grid Engine.
CellProfiler is a system for analyzing cell images. It is designed for biologists without training in computer vision or programming to make quantitative measurements of cells in thousands of images automatically. It is implemented using Matlab, but compiled standalone versions are available.
Virtual Token Descriptor for eXtensible Markup Language (VTD-XML) refers to a collection of efficient XML processing technologies centered around a non-extractive XML parsing technique called Virtual Token Descriptor (VTD). Depending on the perspective, VTD-XML can be viewed as either an XML parser, a native XML indexer or a file format that uses binary data to enhance the text XML, an incremental XML content modifier, an XML slicer/splitter/assembler, or an XML editor/eraser.
Xholon is a flexible tool for multi-paradigm (UML 2, ABM, SBML, NN, GP, PSys, CA, etc.) modeling, simulation, design, execution, and transformation. It is based on generic Java and XML building blocks, and optionally packaged as an Eclipse plugin for UML/SysML/FSM simulation. The Xholon project explores the idea of software as systems of linked nodes, organized hierarchically. The Xholon toolkit supports this back-to-basics approach, and demonstrates practical benefits through examples from numerous domains.
ImageJ is an image processing program inspired by NIH Image for the Macintosh. It can display, edit, analyze, process, save, and print 8-bit, 16-bit, and 32-bit images. There are modules for biology, astronomy, nuclear medicine, physics, and more. If you can take a picture of something, whether with a microscope, a telescope, an oscilloscope, an xray machine, or a scanner, then this program will let you enhance, manipulate, and measure the results.
SENTENSA Knowledge Miner is a platform independent tool for searching any text. SENTENSA uses robust methods of indexing and searching text, leveraging experience from more than 20 years of information retrieval. SENTENSA products offer advanced text retrieval solutions for large databases that will make your searches for key information fast and effective. You can index on one platform and query on another.
The Sample Inventory Program (SIP) is a laboratory inventory management system (LIMS) for Zope. Many integration tests exist for various aspects of the SIP application, ranging from command line importing of samples and project configuration to CSV Web-based importing of sample modifications.
Blossoc is a linkage disequilibrium association mapping tool that attempts to build (perfect) genealogies for each site in the input, score these according to non-random clustering of affected individuals, and judge high-scoring areas as likely candidates for containing disease affecting variation. Building the local genealogy trees is based on a number of heuristics that are not guaranteed to build true trees, but have the advantage over more sophisticated methods of being extremely fast. Blossoc can therefore handle much larger data sets than more sophisticated tools, but at the cost of sacrificing some accuracy.