This is a unix distribution I made so that I can develop from anywhere--a virtual desk if you will. Some of my friends and colleagues have found it useful, and an easily accessible place to put the operating system up is on the internet.
In Systems Biology models are created in various formats (Matlab, Java, C/C++, Python, ...). "Annotate Your Model" will help you to link your model to biological web resources by creating a CSV file containing MIRIAM annotations.
Pinkl is a library written to build flexible applications to control instruments connected to a computer using a GPIB or COM interface and take, store and plot measurements with these instruments.
This toolkit allows complete control of a microscopy setup from Labview, Matlab, Scilab, Python, .Net, VB, IgorPro, Mathematica and more. Included is a standalone program for image acquisition and scripting control of a scientific microscope.
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qips is a software package for analyzing ChIP-seq ("Chromatin ImmunoPrecipitation on sequencing") data. It finds enriched regions of arbitrary lengths and is therefore especially suited for analyzing ChIP-seq of histone marks or polymerase.
The OpenFire processor is a Xilinx MicroBlaze-compatible processor being modified for use in Cyber Physical Systems research. This material is based upon work supported by the National Science Foundation under Grant No. CPS-0932113.
ReliaFree is a Python and PyGTK based suite of tools to assist in Reliability, Availability, Maintainability, and Safety (RAMS) analyses. ReliaFree is intended to be an Open Source alternative to proprietary RAMS analyses solutions.
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This project is for particle accelerator start-to-end simulation. The project contains software infrastructure for setting up model run as service/client mode.
Model Builder is a graphical tool for designing, simulating and analyzing Mathematical models consisting of a system of ordinary differential equations(ODEs).
Shift Word Helper is a scrabble-like games helper, which includes an online dictionary client. Shift Word Helper est un bon assistant pour les jeux de mots tels que le scrabble, avec un dictionnaire en-ligne integré. English & french supported
pyComPic is a GUI (Graphical User Interface) for picprog, sdcc and gpasm written in Python. It uses pyGTK and GTK2 for the interface. It's a good choice if you want to avoid the command line. It works with all PIC programmers supported by picprog
CellPublisher is a free, open source program to improve the navigation of biological pathways. It converts CellDesigner diagrams into fully-featured maps that live inside a browser. The navigation is based on the Google maps API.
Distributed Parallel Programming for Python! This package builds on traditional Python by enabling users to write distributed, parallel programs based on MPI message passing primitives. General python objects can be messaged between processors. Ru
SynBioLib -- your toolkit for synthetic biology applications. SynBioLib aims to establish a platform on which the Synthetic Biology community can develop and share code that is common to many tasks and programs.
Data mines the voting record and other actions of Members of the UK Parliament. Extracts information from the parliament website and stores it in a database. Provides tools to analyse the information, producing statistics and tables about the MPs.
ngram is a module to compute the similarity between two strings. It is different to python's "difflib.SequenceMatcher" in that it cares more about the size of both strings. ngram is an port and extension of the perl module called "String::Trigram
Metropolis is a visualization tool for TRANSIMS traffic simulation output. It specializes in viewing the dynamic outputs of the micro-simulator, such as vehicle motion and other time-varying data.
RefineHMM refines an original hidden Markov model (HMM) to find an optimal fit
against the evolutionary group that the HMM models, and it does this using
through iterative database searches and incremental subsequent adaptation of
the seed set.