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Iozone: 'IO Zone' Benchmark Program (older 2.1 version) Iozone tests the speed of sequential I/O to actual files. Therefore, this measurement factors in the efficiency of your machine's file system, operating system, C compiler, and C runtime library. It produces a measurement which is the number of bytes per second that your system can read or write to a file. This is the 2.1 version of iozone. The new 3.x+ versions of iozone have completely changed their testing methods, thus their output is useless in comparing with older statistics.

The program thrulay is used to measure the capacity, delay, and other performance metrics of a network by sending a bulk TCP or UDP stream over it. Special features of thrulay include: * For TCP, ability to measure round-trip delay along with throughput * For UDP, ability to measure - one-way delay, with quantiles - packet loss - packet duplication - reordering * For UDP, the ability to send precisely positioned true Poisson streams (microsecond errors in sending times) * Human- and machine-readable output (ready to be fed to gnuplot)

Artemis is a DNA sequence viewer and annotation tool that allows visualisation of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. Artemis is written in Java, reads EMBL or GENBANK format sequences and feature tables, and can work on sequences of any size. ACT (Artemis Comparison Tool) is a DNA sequence comparison viewer based on Artemis. It can open two or more sequences (and their annotations/features) together with their comparisons (usually the result of running blastn or tblastx searches).

MAFFT offers a range of multiple alignment strategies, L-INS-i (accurate; recommended for <200 sequences), FFT-NS-i (standard speed and accuracy), FFT-NS-2 (fast; recommended for >2,000 sequences), etc. According to BAliBASE and other benchmark tests, L-INS-i is one of the most accurate methods currently available. MAFFT has been described: K. Katoh and H. Toh 2008 (Briefings in Bioinformatics 9:286-298) Recent developments in the MAFFT multiple sequence alignment program. K. Katoh, K. Misawa, K. Kuma and T. Miyata (Nucleic Acids Res. 30: 3059-3066, 2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.

"Primer3 is a complete rewrite of the original PRIMER program (Primer 0.5), written by Steve Lincoln, Mark Daly, and Eric Lander. See DIFFERENCES FROM EARLIER VERSIONS for a discussion of how Primer3 differs from its predecessors, Primer 0.5 and Primer v2. Primer3 picks primers for PCR reactions, considering as criteria: o oligonucleotide melting temperature, size, GC content, and primer-dimer possibilities, o PCR product size, o positional constraints within the source sequence, and o miscellaneous other constraints. All of these criteria are user-specifiable as constraints, and some are specifiable as terms in an objective function that characterizes an optimal primer pair." - from the README file

The Biopython Project is an international association of developers who are providing freely available Python tools for use in areas of computational molecular biology such as bioinformatics and genomics. Biopython is a collection of Python packages and modules created by the Biopython Project, intended to provide the basis for building bioinformatics applications in the Python language. Note that the current release is alpha quality, and not yet deemed to be stable. This port includes optional support for Biopython-CORBA, a CORBA interface built to the BioCorba standard (http://biocorba.org/).

NASTRAN-95 NASTRAN is the NASA Structural Analysis System, a finite element analysis (FEA) program completed in the early 1970's. It was the first of its kind and opened the door to computer-aided engineering. Subsections of a design can be modeled and then larger groupings of these elements can again be modeled. NASTRAN can handle elastic stability analysis, complex eigenvalues for vibration and dynamic stability analysis, dynamic response for transient and steady state loads, and random excitation, and static response to concentrated and distributed loads, thermal expansion, and enforced deformations. NOTE: There is no technical support available for this software.

The GPL Electronic Design Automation (gEDA) project has produced and continues working on a full GPL'd suite and toolkit of Electronic Design Automation tools. These tools are used for electrical circuit design, schematic capture, simulation, prototyping, and production. Currently, the gEDA project offers a mature suite of free software applications for electronics design, including schematic capture, attribute management, bill of materials (BOM) generation, netlisting into over 20 netlist formats, analog and digital simulation, and printed circuit board (PCB) layout. The gEDA/gaf suite provides schematic capture, netlisting, bill of materials generation, and many other features.

SPICE is a general-purpose circuit simulation program for nonlinear DC, nonlinear transient, and linear AC analyses. Circuits may contain resistors, capacitors, inductors, mutual inductors, independent voltage and current sources, four types of dependent sources, lossless and lossy transmission lines (two separate implementations), switches, uniform distributed RC lines, and the five most common semiconductor devices: diodes, BJTs, JFETs, MESFETs, and MOSFETs. Patch Levels I and II (including a new spec command for spectral analysis) and the level 2 JFET model are courtesy from the Macquarie University. Online documentation at:

TOCHNOG is a free finite element program with many features. TOCHNOG accepts free format input. Boundary conditions can be imposed at geometrical entities, as well as nodes and elements. Among the FE models supported are: differential equations (materials), convection-diffusion equations, Stokes and Navier-Stokes (fluids), elasticity (isotropy and transverse isotropy), plasticity (Von-Mises, Mohr-Coulomb, etc.; plastic surfaces can be arbitrarily combined). Residues in equations and error estimates for all data can be printed or plotted using gnuplot/plotmtv, CalculiX or gmsh. TOCHNOG supports a choice of description frames including Lagrangian, Eulerian and arbitrary Eulerian-Lagrangian (AEL).