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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 simple project which attempts to emulate real life in the launching of a trebuchet. Requires a python compiler, and the python modules for math, gtk, pygame, random, and numpy. Please note: this is an early version and is in alpha.
A HTML scraper that uses machine learning frameworks to extract labelled fields from raw HTML. The project also involves the development of a tool to display the semi structured data generated by the scraper component.
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Spyse is a software framework for building multi-agent systems. It allows Python developers to build distributed intelligent systems of multiple cooperative agents based on FIPA, OWL, SOA and many others. Spyse is designed for ease-of-use and fun.
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.
AudioSavant is a music visualization software that is aimed to allow students to get a better understanding of music. It is based in the OLPC's TamTam application, with a set of modifications from the information visualization world.
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ConDEnSE (Confidential Data Enabled Statistical Exploration) will be a web-based environment for statistical analysis of confidential data from various database sources, based on Plone and R, and using the Jackknife method of confidentiality protection.
The aim of project is creating program environment for solving some integral equations, arising at solving mathematical problems of the diffraction theory.
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.
MATmute is a MATLAB code mutation system targeted at developers of scientific software. The package includes a mutator, a MATLAB function to call the mutator and run the mutants, and some examples to demonstrate how to use the system.
Use SASSIE to generate and manipulate large numbers of molecular structures and then calculate the SAXS, SANS, and neutron reflectivity profiles from atomistic structures. Use for intrinsically disordered proteins. We need alpha-testers and developers.
Use of USB to Serial and USB to Parallel BUS CONVERTERS available from ElectronicBRICKS at http://electronicbricks.blogspot.com/search/label/usb-Brick.
The project holds the files for the Explorer Post 6201 Programming in Python project. The project for 2006 is an information organizer (final name TBD).
The scikits.timeseries python module provides classes and functions for manipulating, reporting, and plotting time series of various frequencies. The focus is on convenient data access while leveraging the existing functionality in numpy.
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.
This program is a User Interface to run command-line applications in any python-enabled system.
Batch execution is available for files in a folder or in subfolders.
pyOBD-II (a.k.a. "pyobd2") is a Python library for communicating with OBD-II vehicles. Its goal is to make writing programs for vehicle diagnostics and monitoring vehicle data as easy as possible. Relies on pySerial to communicate with ELM scanners.