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PyCogent is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for: controlling third-party applications; devising workflows; querying databases; conducting novel probabilistic analyses of biological sequence evolution; and generating publication quality graphics. It is distinguished by many unique built-in capabilities (such as true codon alignment) and the frequent addition of entirely new methods for the analysis of genomic data.

ADMesh is a program for processing triangulated solid meshes. Currently, ADMesh only reads the STL file format that is used for rapid prototyping applications, although it can write STL, VRML, OFF, and DXF files. Features * Read and write binary and ASCII STL files * Check STL files for flaws (i.e. unconnected facets, bad normals) * Repair facets by connecting nearby facets that are within a given tolerance * Fill holes in the mesh by adding facets. * Repair normal directions (i.e. facets should be CCW) * Repair normal values (i.e. should be perpendicular to facet with length=1) * Remove degenerate facets (i.e. facets with 2 or more vertices equal) * Translate in x, y, and z directions * Rotate about the x, y, and z axes * Mirror about the xy, yz, and xz planes * Scale the part by a factor * Merge 2 STL files into one * Write an OFF file * Write a VRML file * Write a DXF file * Calculate the volume of a part

atlc is a program designed for finding the properties (characteristic impedance, inductance per meter, capacitance per meter, velocity factor, electric field distribution) of any transmission line with 2 or 3 conductors (i.e. a normal line or coupler). It uses the finite difference method to determine these properties, and can handle any cross section. The program atlc needs to know shape of the transmission line's cross section. This cross section is stored in a data file, which happens to be a Windows bitmap file. The bitmap file is read by atlc, following which the program performs the analysis. Look in /usr/local/share/examples/atlc for some examples.

Cascade is a program for analyzing the noise and distortion performance of a cascade of elements in an electronic system. A typical application of cascade is the analysis of a receiver. A text description of the receiver block diagram consisting of things like amplifiers, mixers, and filters is entered into cascade. Each element is characterized by its gain and optionally noise figure, and third order intercept point. The program then analyzes the system and produces a report detailing the performance at each stage. A summary is produced which shows the relative contributions to the total system performance of each block. This allows easy identification of what limits system performance.

ChipVault is a VHDL and Verilog Chip Design Organization tool which improves design efficiency by: - Providing the ability to Navigate and Edit files Hierarchically. - Automatically generating Schematic Component Port views of VHDL and Verilog RTL files. - Automating RTL instantiation and template generation. - Providing Revision Control (designed for HW, not SW development). - Supporting External Tool Hooks (bottom-up vcoms,etc). - Providing an Issue Tracking Log with sorting. - Providing Netlist sorting and hierarchy viewing. - Supporting web-sharing of RTL files (both encrypted and clear). - Fast and Nimble.

GTKWave is a fully featured GTK+ based wave viewer for Unix and Win32 which reads LXT, LXT2, VZT, and GHW files as well as standard Verilog VCD/EVCD files and allows their viewing.

MeshDev is a mesh comparison software. It accepts two meshes as input and computes the geometrical deviation between the two meshes. It return numerical values and can optionaly generate visual results (with a pseudo-colored mesh corresponding to the measured deviation) in OpenInventor format.

MeshLab is an open source, portable, and extensible system for the processing and editing of unstructured 3D triangular meshes. The system is aimed to help the processing of the typical not-so-small unstructured models arising in 3D scanning, providing a set of tools for editing, cleaning, healing, inspecting, rendering and converting this kind of meshes.

pdnMesh: A finite element program ================================= Copyright (C) 2001-2005 Sarod Yatawatta pdnMesh is a program that can solve 2D potential problems (Poisson Equation) and eigenvalue problems (Helmholtz Equation) using the Finite Element Method. Common applications occur in electromagnetics, heat flow and fluid dynamics. It can solve problems using both Nodal Based Formulation and Edge Based (Vector) Formulation. The features of the program are as follows. * Automatic mesh generation according to given boundaries. * Adaptive and Interactive mesh refinement. * Problem solution using Cholesky Decomposition or Conjugate Gradient Method with sparse storage. * Eigenvalue solution using LAPACK. * (Optionally) Eigenvalue solution using QR iteration with shifts. * Generating plots of contours, mesh and gradient on screen. * Generating Encapsulated Postscript plots of contours and mesh. * Generating a data file of the mesh to be used by other solvers. * Can import DXF files generated by CAD programs. * GUI is available with glut and GTK/GTKGLExt. Needs OpenGL.

Ngspice is the name of a project and of a program in the project. Spice is the famous circuit simulator developed by the CAD Group of the University of California at Berkeley (UCB). The NG prefix has a lot of meanings: Next Generation, New Good, etc. Choose or invent the one you prefer. The ngspice project aims to improve the capabilities of the Spice3 circuit simulator. The heart of the project is the ngspice program, a circuit simulator derived from spice3f5.