The Bioinformatics Benchmark System is an attempt to build a reasonable testing framework, tests, and data, to enable end users and vendors to probe the performance of their systems. It is not trying to be the last word in informatics benchmarking, as there are simply too many codes, tests, data sets, and databases. The goal is to create a core of tests that all may download and use to probe specific elements of system performance. The end goal is to enable a pluggable set of tests, including the core tests, so that performance data may be gathered.
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.
Biogenesis simulates in a visual fashion the processes involved in the evolution of unicellular organisms in nature. It tries to be a didactic approximation to the ideas of mutation or evolution, and can be enjoyed also as an entertainment. It's intended to serve as a support to show students some basic biological facts. The idea of Biogenesis is taken from Primordial Life, but it's an independent project.
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.
OpenAlea is a modeling and simulation framework in plant ecophysiology. It is based on the Python programming language and it provides different integration tools (for tasks such as installation and compilation), a visual programming interface, and different dedicated models and libraries.
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.
COPASI is a software application for modeling and simulation of biochemical networks. The software package has a GUI that lets users define biochemical network models by entering chemical reactions and kinetic equations. A powerful simulation engine can then perform simulations of the dynamics of the networks and carry out many different computational analyses. COPASI can simulate dynamics using either an ODE approach or a stochastic chemical kinetics approach (Gillespie-type algorithms).