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.
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.
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.
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.
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.
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.
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.
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.
octopus is a program aimed at the ab initio virtual experimentation on a hopefully ever increasing range of systems types. Electrons are describe quantum-mechanically within the Density-Functional Theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the Pseudopotential approximation.
abi2xml is a command line utility to convert an ABI trace file to an XML file. ABI trace files contain DNA sequence data and are produced by ABI PRISM TM 377 DNA sequencers. This bioinformatics utility is written in C++ with the Qt library and is available for Windows, Mac OS, and Linux.