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The other benchmark modules provide excellent timing for specific parts of your code. This module aims to allow you to easily time the progression of your code. The stopwatch analogy is that at some point you get a new stopwatch and start timing. Then you note certain events using lap. Finally you stop the watch and then print out a summary. The summary shows all the events in order, what time they occurred at, how long since the last lap and the percentage of the total time. Hopefully this will give you a good idea of where your code is spending most of its time. The times are all wallclock times in fractional seconds. That's it.

The computer program avida is an auto-adaptive genetic system designed primarily for use as a platform in Digital or Artificial Life research. The avida system is based on concepts similar to those employed by the tierra program developed by Tom Ray. It is a population of self-reproducing strings with a Turing-complete genetic basis subjected to Poisson-random mutations. The population adapts to the combination of an intrinsic fitness landscape (self-reproduction) and an externally imposed (extrinsic) fitness function provided by the researcher. By studying this system, one can examine evolutionary adaptation, general traits of living systems (such as self-organization), and other issues pertaining to theoretical or evolutionary biology and dynamic systems.

Crux is a software toolkit for molecular phylogenetic inference. It is structured as a set of Python modules, which makes it possible to quickly develop Python scripts that perform unique, non-canned analyses. Features include: * Tree log-likelihoods can be computed under a variety of models, including all specializations of GTR+I+G and mixture models. Tree likelihoods can be computed in parallel via pthreads. * Bayesian Markov chain Monte Carlo (MCMC) methods (with Metropolis coupling) can sample among non-nested models using reversible model jumps. * Crux is capable of simulating character data under any model its likelihood engine is capable of. * The neighbor joining (NJ) and relaxed neighbor joining (RNJ) implementations are among the fastest in existence. * Pairwise distances between sequences can be computed based on percent identity, or using methods that correct for multiple hits (Jukes-Cantor, Kimura, and logDet).

The European Molecular Biology Open Software Suite (EMBOSS) is a comprehensive set (about 100) of open source tools for genetic sequence analysis. EMBOSS is produced by the European Molecular Biology Network (EMBnet - http://www.embnet.org/). All EMBOSS tools are all built around the same set of core libraries - AJAX and NUCLEUS - and therefore share a unified user interface, have similar "look and feel", and implement a uniform sequence addressing methodology. The various components of EMBOSS are distributed under the GPL, except the core libraries which are under the LGPL. EMBASSY packages are third party applications which have been integrated with the EMBOSS suite, but which are not included in the base EMBOSS distribution for licensing or other reasons. The EMBASSY packages live in the biology/embassy port.

GPL Cver is a full 1995 P1364 Verilog standard HDL simulator. It also implements some of the 2001 P1364 standard features including all three PLI interfaces (tf_, acc_ and vpi_) as defined in the 2001 Language Reference Manual (LRM). Verilog is the name for both a language for describing electronic hardware called a hardware description language (HDL) and the name of the program that simulates HDL circuit descriptions to verify that described circuits will function correctly when the are constructed. Verilog is used only for describing digital logic circuits. Other HDLs such as Spice are used for describing analog circuits. There is an IEEE standard named P1364 that standardizes the Verilog HDL and the behavior of Verilog simulators. Verilog is officially defined in the IEEE P1364 Language Reference Manual (LRM) that can be purchased from IEEE. There are many good books for learning that teach the Verilog HDL and/or that teach digital circuit design using Verilog.

OpenSCAD is a software for creating 3D CAD objects. Unlike most free software for creating 3D models, it does not focus on the artistic aspects of 3D modelling but instead on the CAD aspects. Thus it is more suitable for creating 3D models of machine parts but perhaps not when creating computer-animated movies. OpenSCAD is not an interactive modeller. Instead it is something like a 3D-compiler that reads in a script file that describes the object and renders the 3D model from this script file. This gives designers full control over the modelling process and enables them to easily change any step in the modelling process or make designes that are defined by configurable parameters.

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.

SMS::Send is intended to provide a driver-based single API for sending SMS and MMS messages. The intent is to provide a single API against which to write the code to send an SMS message. At the same time, the intent is to remove the limits of some of the previous attempts at this sort of API, like "must be free internet-based SMS services". SMS::Send drivers are installed separately, and might use the web, email or physical SMS hardware. It could be a free or paid. The details shouldn't matter. You should not have to care how it is actually sent, only that it has been sent (although some drivers may not be able to provide certainty).

Seyon is a complete full-featured telecommunications package for the X Window System. Its features include: - Dialing directory that supports an unlimited number of entries. - Terminal emulation window using any terminal emulation program that supports X. This defaults to xterm. - Script language to automate tedious tasks such as logging into remote hosts. - Unlimited number of slots for external file transfer protocols. - Support for zmodem auto-download. - Translation modes. Seyon can perform useful translations on the user's input. - Interactive setting of program parameters. - On-line help. - Modem speeds up to 115200 bps. - Software (XON/XOFF) and hardware (RTS/CTS) flow control. - Session capture to a file. - Temporary running of a local shell in the terminal emulation window. Seyon is intended to be both simple and extensively configurable. Almost every aspect of Seyon can be configured via the resources to suit the user's taste.

viewfax displays one or more fax files in an X11 window. The input files may be either raw, single-page faxes received by a fax modem with a program such as mgetty, or tiff files such as those used by hylafax. The first (or only) page of "PC-Research"-style (DigiFAX) files produced by the ghostscript dfaxhigh or dfaxlow drivers can also be displayed. Input files using any common fax encoding such as group 3 (1 and 2 dimensional) and group 4 can be displayed. The fax images are rendered at full resolution and then successively scaled down by a linear factor of 2 prior to display, until they fit on the screen. The display can be controlled interactively using mouse and keyboard commands.