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Super Smack is a benchmarking, stress testing, and load generation tool for MySQL (and PostgreSQL). Super Smack was originally written by Sasha Pachev, and then hosted and maintained by Jeremy Zawodny.

TCPBLAST measures the throughput of a TCP connection.

webbench is very simple HTTP benchmarking tool, which can benchmark both WWW and proxy servers. webbench uses fork() for simulating multiple clients and supports benchmarking by HTTP/0.9-HTTP/1.1 requests (without Keep-Alive). This benchmark is not very realistic, but can test if your HTTPD can really handle many clients at once (try to run some CGIs) without taking your machine down. I am using this program for setting maximum number of Apaches. Webbench displays results in pages/min and bytes/sec. Radim Kolar

TTCP is a benchmarking tool for determining TCP and UDP performance between 2 systems. The program was created at the US Army Ballistics Research Lab (BRL) and is in the public domain. Feel free to distribute this program but please do leave the credit notices in the source and man page intact. How to get TCP performance numbers: receiver sender host1% ttcp -r -s host2% ttcp -t -s host1 -n and -l options change the number and size of the buffers.

The Unix Benchmark Utility "ubench" is an attempt to introduce a single measure of perfomance among computer systems running various flavors of Unix operation system. The current development release tests only CPU(s) and memory. In the future releases there will be tests added for disk and TCP/IP. Ubench is taking advantage of multiple CPUs on an SMP system and the results will reflect that. o Ubench is executing rather senseless mathematical integer and floating-point calculations for 3 mins concurrently using several processes, and the result Ubench CPU benchmark. o Ubench will spawn about 2 concurrent processes for each CPU available on the system. This ensures all available raw CPU horsepower is used. o Ubench is executing rather senseless memory allocation and memory to memory copying operations for another 3 mins concurrently using several processes, and the result Ubench MEM benchmark.

Web Polygraph is a benchmarking tool for Web proxies. Polygraph distribution includes a high-performance client and server simulators. The simulators create a stream of HTTP requests that can be routed through a Web proxy. Studying proxy performance under various [stress] conditions is essential for performance tuning, evaluation of new algorithms, analysis of hardware configurations, and comparing available proxy products.

ARIADNE is a package of two programs, ariadne and prospero, that compare protein sequences and profiles using the Smith-Waterman algorithm, and assesses statistical significance using a new accurate formula, described in Mott, 2000, "Accurate Formula for P-values of gapped local sequence and profile alignments" J. Mol Biol. 300:649-659. The sequence/profile comparison algorithms used in ARIADNE are standard, and are probably not the fastest implementations available. The novel part is the method for determining statistical significance, which will give thresholds of significance that are accurate to within 5% 95% of the time. The package is written in ANSI C. You are free to incorporate the method used for assessing statistical significance into third-party code, provided you cite the above reference. The routines for assessing significance are all in gaplib.c

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).

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.

Babel is a program designed to interconvert a number of file formats currently used in molecular modeling. Babel is capable of assigning hybridization, bond order, and connectivity when these elements are not present in the input file.