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The set of tools for biopolymer sequence analysis together
with GUI to work with biopolymer sequence databases.
The tools include pairwise and multiple alignment, philogenetic tree construction and other.
A C++ development library designed to make common operations on DNA and protein sequences easy. libGenome provides functionality to read, write, and manipulate sequence and annotation data in several file formats.
X_batch is a plugin for SPM2, which allows the user to create, store, exchange and execute custom batch scripts and record information into a Protege-based ontology.
Phight - a phylogeny tree building program
Currently, it supports Likelihood method and distance method. This program will includes diagnostic function as a special feature.
The Portable Cray Bioinformatics Library is a C implementation of the proprietary Cray Bioinformatics Library. It is designed to run on a wide variety of platforms in either 32- or 64-bit mode on either big or little endian architectures.
GEOSS: Gene Expression Open Source System (used to be called Genex Va)
GEOSS is a secure, multiuser, gene expression database and analysis package. GEOSS is distinguished by a well developed web based user interface, and analysis/reporting.
What is it:<br>
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A simulation of a very simplified aunts nest. <br>
It is a restricted area (square) fullfill with aunts and rice.<br>
Rice is first randomly positionned in the area and aunts will sort it in a
unique batch. <br>
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GATA is a graphic alignment tool for comparative sequence analysis. It makes use of BLAST to graphically align two DNA sequences, creating box- line- box representations of window scored local alignments. GATA also displays extensive GFF gene annotation.
The Synaptic Simulator is a program which simulates models of single neuronal synapses and compartments, complex constructs of such models. Furthermore the program is able to regain parameters by fitting simulated results with experimental data.
This is a generalized rack widget written using the Gnome Canvas, which is specifically targeted for scientific operations (including Chemistry/Biology). The main purpose of the widget would to visualize standardized containers such as microtiter plates.
Sight provides a friendly interface to create and connect agents for bioinformatics. The workflow supports multiple responses to a single request, structure transforms, filters and request history access.Can talk with ordinary http servers (get and post)
HomGL is a web-based tool for comparing gene lists obtained e.g. by
microarray studies. Unigene, Locus Link & Homology databases are used
to compare gene lists with different accession numbers and between different
organisms.
A Java software for 3D visualization of graphs/networks. It implements many graph layout algorithms (such as force-directed methods), graph generators (such as scale-free networks) and graph modifiers. Most functions can be accessed through its GUI.
open SPEAR stands for open Simulator of Physical Environment for Agents Research. It is a C++ library designed to build efficient simulation of multi-agents and robotics simulation. The main audience for this project is the robotician/artificial life com
BioEra is DSP visual designer that can be used to create interfaces between human being and a machine with using bio signals like EEG, QEEG, HEG, EMG, ECG, GSR, EOG, visual/sound entrainment and others.
Set of Java packages to apply Genetic Algorithms to any kind of problem. Various genetic operators are implemented and an example shows of how the system could be applied to digital circuit evolution.
Cluster Networks are a new style of neural simulation / neural network modeling, that models networks of neural populations ("clusters") that transform and transmit information using precisely-timed, graded bursts ("pulses" or "volleys") of firing.
(OBSOLETE) trace_utils is a program for processing sequencing trace data. The main goal of this program is to provide a completely free software in detecting SNPs like what polyphred has done, but with even higher accuracy and more flexibility.
Amplicon is a Python script for designing PCR primer sets. Amplicon is written in Python 2.3 and Tkinter 8.4. The current script was created for Windows and an executable is available. Future versions of the script should be able to run on Linux and Mac
IslandEv distributes a Genetic Algorithm (like <a href="/projects/jaga">JaGa</a>) across a network (see <a href="/projects/distrit">DistrIT</a>) using an island based coevolutionary model in which neighbouring islands swap migrating individuals every