The octave-forge package is the result of The GNU Octave Repositry project,
which is intended to be a central location for custom scripts, functions and
extensions for GNU Octave. contains the source for all the functions plus
build and install scripts.
This is benchmark.
The package contains code used to benchmark speed of Octave.
Iorate is a general purpose storage I/O benchmarking tool.
Iorate was created in 1997 by Vince Westin of EMC while working with Cliff
Burrell of FedEx to fill a need to perform a set of storage I/O benchmarks.
Though Iorate was developed by EMC staff with EMC resources there are no
EMC-specific pieces to the testing, it just tests storage.
Railsbench is a small collection of ruby scripts which make measuring
raw performance of rails apps a snap. All tests are run from the
command prompt, making performance regression testing easy.
Sipp is a performance test tool / traffic generator for the SIP protocol.
It comes with a few basic SipStone user-agents scenarios (UAC & UAS), i
establishing and releasing multiple calls with the INVITE and BYE methods.
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.
BCFtools is a set of utilities that manipulate variant calls in the
Variant Call Format (VCF) and its binary counterpart BCF. All
commands work transparently with both VCFs and BCFs, both
uncompressed and BGZF-compressed.
The bedtools utilities are a suite of tools for performing a wide range of
genomics analysis tasks. The most widely-used of these tools enable genome
arithmetic, i.e., set theory on the genome. For example, with bedtools one
can intersect, merge, count, complement, and shuffle genomic intervals from
multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF.
Although each individual utility is designed to do a relatively simple task,
e.g., intersect two interval files, more sophisticated analyses can be
conducted by stringing together multiple bedtools operations on the command
line or in shell scripts.
The BioCocoa framework provides developers with the opportunity to add
support for reading and writing BEAST, Clustal, EMBL, Fasta, GCG-MSF, GDE,
Hennig86, NCBI, NEXUS, NONA, PDB, Phylip, PIR, Plain/Raw, Swiss-Prot and
TNT files by writing only three lines of code.
The framework is written in Cocoa (Objective-C).
LICENSE: LGPL2 or later
The BioJava Project is an open-source project dedicated to providing Java
tools for processing biological data. This will include objects for
manipulating sequences, file parsers, CORBA interoperability, access to
ACeDB, dynamic programming, and simple statistical routines.
The BioJava library is useful for automating those daily and mundane
bioinformatics tasks. As the library matures, the BioJava libraries will
provide a foundation upon which both free software and commercial packages
can be developed.
ClustalW2 is a general purpose multiple sequence alignment program for
DNA or proteins. It produces biologically meaningful multiple sequence
alignments of divergent sequences. It calculates the best match for the
selected sequences, and lines them up so that the identities,
similarities and differences can be seen. Evolutionary relationships
can be seen via viewing Cladograms or Phylograms.