AntFlow builds upon Apache Ant to provide a new approach to simplifying system automation that uses pipelines of hot folders chained together to perform a given task. Using XML, it associates an automated task such as data transfer, encryption, or XML processing with a directory on the local system. Whenever a file is copied or written into the hot folder, the associated task is executed and the file is moved to the next hot folder in the pipeline for further processing.
The Biochemical ALgorithms Library (BALL) is a framework for rapid application development in molecular modeling and structural bioinformatics. BALL provides an extensive set of data structures as well as classes for molecular mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, NMR shift prediction, and visualization. Its extensibility results from an object-oriented and generic programming approach.
BALLView is an extensible viewer for bio-molecular structures. It provides all standard models and offers rich functionality for molecular modeling and simulation, including molecular mechanics methods (AMBER, CHARMM, and MMFF94 force fields), continuum electrostatics methods employing a Finite-Difference Poisson Boltzmann solver, secondary structure calculation, molecular editing and docking. Since BALLView is based on BALL (the Biochemical ALgorithms Library), it is easily extensible on the level of C++ code. In addition, it provides a Python interface with Integrated Development Environment features to allow interactive rapid prototyping.
Berkeley DB XML is a native XML database engine for use within your product. Made available as a C++ library with language bindings for Java, Perl, Python, PHP, and Tcl, it integrates directly into your application (it is not a standalone database server). It provides XQuery access into a database of document containers. XML documents are stored and indexed in their native format using Berkeley DB as the transactional database engine.
BioJava aims to provide a comprehensive set of Java components for the rapid development of applications in Bioinformatics. It contains interfaces for representing Sequences, Features, and other important bioinformatics concepts. It can also read and write sequence data in a variety of common formats and communicate with Ensembl databases and with DAS and BioCorba servers.
The BioPHP Project (formerly called GenePHP) is a non-profit, open source software project that aims to extend the PHP scripting language so that it can be used to develop bioinformatics applications. BioPHP itself is not a bioinformatics application. Rather, it is a collection of tools to help PHP developers write bioinformatics applications more rapidly than if they had to start from scratch using "vanilla" PHP.
Brook for GPUs is a compiler and runtime implementation of the Brook stream programming language for modern graphics hardware. The goals for this project are to demonstrate general purpose programing on GPUs, to provide a useful tool for developers who want to run applications on GPUs, and to research the stream language programming model, streaming applications, and system implementations.
Care2x (formerly Care 2002) is software for hospitals and health care organizations. It is designed to integrate the different information systems existing in these organizations into a single efficient system. It solves the problems inherent in a network of multiple programs that are incompatible with each other. It can integrate almost any type of services, systems, departments, clinics, processes, data, or communication that exist in a hospital. Its design can even handle non-medical services or functions like security or maintenance. All of its functions can be accessed with a Web browser, and all program modules are processed on the server side.
CGAL, the Computational Geometry Algorithms Library, is a large C++ library of geometric data structures and algorithms such as Delaunay triangulations, mesh generation, Boolean operations on polygons, and various geometry processing algorithms. CGAL is used in various areas: computer graphics, scientific visualization, computer aided design and modeling, geographic information systems, molecular biology, medical imaging, robotics and motion planning, and numerical methods.