Software Map

xpress-analyzer is a suite of programs for
analyzing functional genomics data. Programs
are included for analysis of variance, multiple
test correction for significance tests, a non-
linear least square fitting algorithm (four
parameters), general linear models,
Kolmogorov-Smirnov distance, nearest
neighbor algorithm, principal component
analysis, and Student's t-test. It is intended
to be used as a faster alternative to R on
large data sets.

SENTENSA Knowledge Miner is a platform independent
tool for searching any text. SENTENSA uses robust
methods of indexing and searching text, leveraging
experience from more than 20 years of information
retrieval. SENTENSA products offer advanced text
retrieval solutions for large databases that will
make your searches for key information fast and
effective. You can index on one platform and query
on another.

GENtle is bioinformatics software for everyday
molecular biology tasks. It features DNA and amino
acid sequence display and editing, database
management, plasmid maps, restriction and
ligation, alignments, sequencer data import,
calculators, gel image display, primer design,
virtual PCR, online database access, graph/spectra
display, PHYLIP interface, and more.

Wunderbar is a program which is able to identify mislabeled samples in genotype data when a few extra independent genotypes are available ("genetic barcoding"). Wunderbar calculates the likelihood that genotype mismatches have occurred by chance. It is capable of reliable and sensitive detection of sample mismatches and swaps even in the presence of numerous genotyping errors and in the presence of linkage disequibrilium between the individual genotypes. It only requires a few SNPs to work well.

CanvasXpress is a JavaScript library based on the HTML5 canvas tag that provides a generic and simple way to display genomics data. It supports bar graphs, line graphs, bar-line combination graphs, box plots, dot plots, area graphs, stacked graphs, percentage-stacked graphs, correlation plots, Venn diagrams, heat maps, Newick trees, 2D-scatter plots, 2D-scatter bubble plots, 3D-scatter plots, pie charts, networks (or pathways), and a genome browser. It also supports a few data transformations like log and exponential transformation, z-score, percentile transformation, and ratio. It also supports grouping of samples, zooming, events, and more.

open SPEAR stands for open Simulator of Physical
Environment for Agents Research. It is a C++
library designed to build an efficient
multi-agents and robotics simulation. The main
audience for this project is the
robotics/artificial life community.

The QDist package implements the O(n log^2 n) time
method for computing the quartet distance between
unrooted evolutionary trees.

MCS PGA 64 Filter Amp Controller is a small
program that uses Qt 3.x to control the
MultiChannelSystems Programmable Gain Amp
(http://www.multichannelsystems.com), 64 channel
version. This filteramp is a custom piece of
equipment typically used in neuronal electronics.
This program uses the serial port to set the gains
on this programmable amplifier. It is a clone of
the Windows version of this program that MCS
normally supplies with its filter amp. It is 100%
compatible UI-wise with the Windows version.

The Sample Inventory Program (SIP) is a laboratory
inventory management system (LIMS) for Zope. Many
integration tests exist for various aspects of the
SIP application, ranging from command line
importing of samples and project configuration to
CSV Web-based importing of sample modifications.

aisconvert is a toolkit for processing genetic data in RAW (23andme) format. It currently supports, through the command line, Half-IBD (Identity by descent) aka HIRs between two or any number of files (in distances and cM), RAW2PED conversion, regions of homozygosity, and merging of two snip files.

Teem is a software framework for conducting
artificial evolution experiments. It particular,
it provides lots of facilities for evolutionary
robotics. It can be combined with a variety of
libraries and programs to form a powerful platform
for anything from evolution of simple Braitenberg
behaviour to complex steady state evolutionary
experiments involving groups of robots.

NetworkX is a Python package for the creation,
manipulation, and study of the structure,
dynamics, and functions of complex networks. The
potential audience includes mathematicians,
physicists, biologists, computer scientists, and
social scientists.

PhosphoFind locates and quantifies phosphorylated
peptides and proteins from a set of four MALDI
mass spectra run in linear positive, linear
negative, reflectron positive, and reflectron
negative modes.

MuGeN is a package for interactively exploring
multiple annotated genomes simultaneously,
possibly mixed with computational analysis
results. Map information can be loaded from
various sources, and resulting images can be
exported in different formats. Both an interactive
GUI based environment and a batch mode program are
provided.