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At the outset, the goal of this program is to provide a suite of tools to aid in the back-translation of amino acid sequences in a manner that provides useful information for synthetic gene design.
This workbench tries to manage and analyze neuroscientific animal data with an emphasis on behaviorally orientated experiments. It's goal is to use the behavioral experimental data (stimulus, task, species...) as its source and perform analysis to e
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The C Protein Folding Library is a minimalistic, high-performance modular library of C functions and data structures for computing folding simulations of proteins on a wide variety of computer hardware.
DANGLE: A Bayesian inferential prediction method for protein backbone dihedral angles and secondary structure assignments, solely from sequence information, experimental chemical shifts and a database of known protein structures and their shifts.
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BARNACLE is a Python library for RNA 3D structure prediction. It can be used for probabilistic sampling of RNA structures that are compatible with a given nucleotide sequence and that are RNA like on a local length scale.
RADAR stands for Rapid Automatic Detection and Alignment of Repeats in protein sequences. RADAR identifies gapped approximate repeats and complex repeat architectures involving many different types of repeats.
Radar has moved to github (https://github.com/AndreasHeger/radar)
A colorized interactive dotplot program designed for pair-wise comparisons of RNA & DNA. The original idea was from the mind of late Prof. William J. Dreyer of Caltech. The idea is to be able to see the "tapestry" of life, which comes alive with color.
FociCounter is a simple and user-friendly program for analysis of gamma-H2AX foci. It allows to determine the number of foci in a single cell, a foci intensity as well as a cell intensity.
A web-based system for upoading, managing, sharing, and analyzing bioinformatic data. The system is primarily written in python, and runs on both linux and MacOs.
Tandem mass spectral peptide identification and validation software, similar to X!Tandem, OMSSA, MyriMatch. Suitable for single hosts through large clusters. Written in Python for simplicity, with performance-critical sections in C++.
This project implements an algorithm for segmenting protein sequences into smaller meaningful blocks. The method is based on the pure statistical approach and it uses an analogy between proteins and natural language.
This project is started out of the idea to simulate simple creatures like game of live. The goal is to build up an multi processor/host environment to simulate the building of simple live in given world environments.
Tools to perform metabolic control analyses on biochemical network models in SBML format. Allows computation of first and second order response coefficients, elasticities, first order control coefficients and first order spectral response coefficients.
Brian is a new simulator for spiking neural networks available on almost all platforms. The motivation for this project is that a simulator should not only save the time of processors, but also the time of scientists.