We have made major revisions to the software, incorporating the ability to compare multiple sequences to a reference sequence. Instead of a traditional alignment, the software finds islands of identical DNA, and shows the mapping of these "Anchor Points" between the compared sequences. Platforms: Mac, Mac OSX

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The Foucault Rod model displays the vibration of a circumnavigating rod. One end of the rod is firmly secured to a support. The free end of the rod has a weight attached, like the bob of a pendulum. The support of the rod is circumnavigating a central axis. The plane of swing of the Foucault rod... Platforms: Mac, Mac OSX

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The Ejs Hard Disk Gas model displays a two-dimensional gas made out of hard disks. Particles are initialized with a speed v=1 in a random direction and move with constant velocity until a collision occurs. You can modify this simulation if you have Ejs installed by right-clicking within the plot... Platforms: Mac, Mac OSX

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The Momentum Space package is a self-contained file for the teaching of the time evolution and visualization of energy eigenstates and their superpositions via momentum space in quantum mechanics. The file contains ready-to-run OSP programs and a set of curricular materials. The material focuses... Platforms: Mac, Mac OSX

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The Heating and Cooling a Sphere model computes the radial temperature distribution within a sphere as it is heated and cooled by a surrounding fluid. The sphere is broken into shells and the temperature of each shell is computed using a finite difference approximation to the radial heat equation... Platforms: Mac, Mac OSX

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The Step Barrier Scattering model shows a quantum mechanical experiment in which an incident wave (particle) traveling from the left is transmitted and reflected from a potential step at x=0. Although the analytic solution to this standard problem is well known, its visualization shows how the... Platforms: Mac, Mac OSX

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* DerApproximator is a small yet important package for getting/checking derivatives via finite-difference approximation, extracted from OpenOpt framework to be standalone Python module. It is required by FuncDesigner (for obtaining derivatives of oofuns beyond standard set without routines to... Platforms: Mac, Mac OSX

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The STP Entropy Einstein Solid program calculates the entropy of two Einstein solids that can exchange energy. The purpose of this calculation is to illustrate that the entropy is a maximum at thermal equilibrium. The default system is two Einstein solids with 50 particles each and total energy E... Platforms: Mac, Mac OSX

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A Python interface to the HepMC high-energy physics event record API This is a simple SWIG wrapper on the main classes of the HepMC event simulation representation, making it possible to create, read and manipulate HepMC events from Python code.... Platforms: Mac, Mac OSX

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The Molecular Dynamics Adiabatic Piston model shows two gas samples within a horizontal cylinder that is divided by an insulated piston that moves without friction. It is a supplemental simulation for an article by Eric Gislason "A close examination of the motion of an adiabatic piston" in the... Platforms: Mac, Mac OSX

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SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools. Background Deluged by the rate and complexity of completed genomic sequences, the need to align longer sequences becomes more urgent, and many more tools have thus been developed. In the... Platforms: Mac, Mac OSX

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The Ejs Platform on Two Rotating Cylinders model displays the model of a platform resting on two equal cylinders are rotating with opposite angular velocities. There is kinetic friction between each cylinder and the platform. The separation between the cylinders and the coefficient of kinetic... Platforms: Mac, Mac OSX

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GizmoGraph you can create points, segments (with text and/or picture), circles, ellipses, curves, plolygons and polycurves. These objects can be painted with a color. Most interesting, you can define geometrical constraints between these objects like: - drawing a parallel or a perpendicular from... Platforms: Mac, Mac OS X v10.4

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The Ejs Pendulum on an Accelerating Train model displays the model of a pendulum on an accelerating train. The problem assumes that the pendulum rod is rigid and massless and of length, L = 2, and the pendulum bob is of mass, m = 1. The initial pendulum angle and the initial velocity of the train... Platforms: Mac, Mac OSX

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This applet shows the phenomenon of the chromatic dispersion of light. Firstly it shows light dispersion through a prism. It also shows rainbows as an example of light dispersion. Platforms: Mac, Mac OSX

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OligoCounter is a Java command line program which counts overrepresented 8-14bp oligonucleotides in DNA sequences. These oligos can be useful in visualising small genomes on a global basis (see figure below), investigating repeats at certain regions, and for attributing short reads (for example... Platforms: Mac, Mac OSX

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The Partitioned Box program displays the number of particles on one half of a box as a function of time after a small hole is made in the partition dividing the box in half. The purpose of this simulation is to gain insight into the tendency of macroscopic systems to approach a well defined... Platforms: Mac, Mac OSX

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The BBL format is the main output format of the Power Graph. A BBL file describes nodes, groups of nodes (power nodes), as well as the edges between these groups of nodes (power edges). Each line contains a piece of information of the following type: * NODE {node identifier} -- Defines a single... Platforms: Mac, Mac OSX

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OntoCreator is a tool able to automatically create synthetic ontologies according to user given adjustable specifications with respect to size, distribution of certain language construct and expressivity. The current version will generate ontologies according to the ?*a*ffnet einen externen Link... Platforms: Mac, Mac OSX

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sigTOOL is a general-purpose signal processing package that runs in the MATLAB environment. It is open-source and free-of-charge. Built-in analyses are currently targeted at those working in electrophysiology and neuroscience. If you are working in these fields, sigTOOL's extensive file import... Platforms: Mac, Mac OSX

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