ASCIIMathML is a script that converts calculator-style ASCII math notation (and many LaTeX formulas) to Presentation MathML while your Web page loads. It works with HTML and XHTML files in Mozilla/Firefox/Netscape 7+ browsers, as well as in Internet Explorer 6 with MathPlayer. For example, the solutions for the equation 'ax^2+bx+c=0' are expressed in the HTML file as '(-b +- sqrt(b^2 - 4ac))/(2a)', and display as nicely formatted MathML. The script can be easily used in wikiservers and blogs, as a rudimentary MathML editor (with instant preview), and to preview math formulas as they are typed into a Web page input area.
Asymptote is a powerful descriptive 2D and 3D vector graphics language for technical drawing, inspired by MetaPost but with an improved C++-like syntax. It provides for figures the same high-quality level of typesetting that LaTeX does for scientific text. Asymptote is a programming language as opposed to just a graphics program. It can exploit the best features of script (command-driven) and graphical user interface (GUI) methods. High-level graphics commands are implemented in the language itself, allowing them to be easily tailored to specific applications.
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.
Cell Electrophysiology Simulation Environment is a framework to perform electrophysiological simulations. It can, for example, simulate cardiac myocyte electrical activity. It is useful for simulations of action potentials, individual ionic currents, and changes in ionic concentrations.
The Chemistry Development Kit (CDK) is a library of Java classes for chemo-, bioinformatics, computational chemistry, and chemometrics. It provides important algorithms like substructure search, SMILES, Gasteiger charges, QSAR descriptor calculation, 3D structure generation, 2D layout and rendering, many IO formats, atom typing, and more.
Quaternions are numbers with 4 parts: one for time and three for space. Command Line Quaternions is a set of command line functions that generate thousands of points of quaternions, which are fed into animation software. This forms the foundations of analytic animations, a logical extension of analytic geometry.
DB Visual Architect (DBVA) is a powerful tool that provides support for Object Relational Mapping (ORM) and Entity Relationship Diagrams (ERD), which assist with realizing UML designs as relational database implementations. By drawing a class diagram for the system, you can generate the required database tables and persistent source code for database manipulation. It can also be used with existing software.