Raster3D is a set of powerful tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm that is independent of any graphics hardware.
Lush is a Lisp dialect with extensions for object-oriented and array-oriented programming. It is intended as a programming environment for prototyping numerically intensive applications. Unlike alternatives like Python or SciLab, Lush is designed for easy integration of existing C/C++/Fortran codes.
PathVisio is a bioinformatics tool that lets you do everything with biological pathway diagrams. PathVisio helps you organize biological information and lets you present or publish that information easily. You can create and draw pathways, export them to many image formats, annotate them with links to online biological databases such as Ensembl, Entrez or HMDB, and add comments and literature references from pubmed. PathVisio also lets you sort through high-throughput experimental data in pathway context. This is a much more pleasant way to present data than just a large table. You can import microarray, proteomics or metabolomics data. PathVisio has a plugin interface that lets users customize it to new analysis types, new visualization methods, and new pathway formats. PathVisio is compatible with WikiPathways.
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.