ACFTools is a utility for manipulating X-Plane flight simulator aircraft and weapon models without using its Plane Maker. It can decode both Apple and Intel ACF/WPN formats into plain text files with a syntax similar to C, which can be edited and then re-converted into binary data. It is able to extract almost complete 3D models of aircraft (fuselage, floats, tanks, wings, stabs, propellers, engines) and write it in AC3D modeler format. Edited 3D parts can then be merged into plain text and consequently converted into binary ACF files.

ACL2 is a mathematical logic, programming language, and mechanical theorem prover based on the applicative subset of Common Lisp. It is an "industrial-strength" version of the NQTHM or Boyer/Moore theorem prover, and has been used for the formal verification of commercial microprocessors, the Java Virtual Machine, interesting algorithms, and so forth.

The aim of ADF MAGE-ML Tool is to provide a module for converting ADF files (a tab delimited file representing microarray design layout) into MAGE-ML format, and for generating an ADF from an array design described in MAGE-ML format. The module is build upon the ADF specifications and using MAGE-Stk APIs (Java). MIAME-compliance checking, a logging system, and integration of LifeScience Identifier (LSID) specifications are key components of the module. The module can be used via the command line or a graphical user interface.

AGM Build is a molecular builder and conformational editor. It can be used for interactive model preparation for molecular dynamics simulations, including association of atom types and partial charges. It features geometry editing, lattice building, building of chain molecules (e.g. proteins), chains with predetermined conformations, and charges and atom types according to selected Force Field.

AMLET is software designed to estimate multinomial and mixed logit discrete choices models, which are increasingly popular in econometry. The software supports cross- sectional and panel data, and offers various optimization methods, including the new variable sample-size approach.

APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, and biomolecular titration studies.

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.

The ATLAS (Automatically Tuned Linear Algebra Software) project is an ongoing research effort focusing on applying empirical techniques in order to provide portable performance. It provides C and Fortran77 interfaces to a portably efficient BLAS implementation, as well as a few routines from LAPACK.