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.
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.
Algraeph is a tool for manual alignment of linguistic graphs, such as phrase structure trees or dependency structures, where each node corresponds to a subsequence of the analyzed input sentence. It allows you to express the similarity between two graphs by aligning their nodes and attaching relation labels to these alignments. Graphs are read from one or more graphbanks (or treebanks) in the GraphML or Alpino formats. Alignment relations are user-defined and are stored in a simple XML format, which can be used for further processing. The resulting parallel graph corpus is a useful data set for many tasks in computational linguistics and natural language processing.
Allegro Common Lisp is a full ANSI Common Lisp (1994) implementation. It contains many extensions, including 32- and 64-bit native compilation, efficient built-in memory management, foreign functions (for interfacing with other languages), multiprocessing, UNICODE and locale support, XML/HTML parsers, a Web client and server, GTK+ interface (1.2 and 2.0), Java interface, OLE interface (Windows only), profiler, regular expressions, an XML RPC implementation, native Lisp RPC, sockets, DLL and shared library support, and more.
Alliance CAD System is a set of EDA tools and portable cell libraries for VLSI design. It covers a wide range of the standard design flow (from VHDL up to layout). It includes a VHDL simulator, RTL synthesis tools, place and route tools, netlist extractor, DRC, and a layout editor.
AnimalTracker can be used to track the position of animals and their behavior in the context of an observation. Users can draw a map of the area and position the animals on it. The application can then calculate the distance between the animals and the distribution of them on the map across a specified time period. All data can be exported as tables to be used in spreadsheet applications or statistics programs.