The Ejs Superior Ptolemaic model illustrates Ptolemy's orbit for a superior planet. The model consists of a deferent circle, centered on a point some distance from Earth (at the eccentric point). Attached to this deferent is the center of another circle, the epicycle. The center of the epicycle... Platforms: Mac, Mac OSX

Keyword: Center, Constant, Deferent, Epicycle, Installed, Model, Models, Modify, Moves, Physics, Planet, Point, Ptolemaic, Retrograde, Simulation, Source, Speed, Superior, Variations

For this ProfDistS provides a phylogenetic framework that uses individual RNA secondary structures in reconstructing phylogenies based on sequence-structure alignments - using Profile Neighbor Joining (PNJ) with manual or iterative and automatic profile definition. Moreover, ProfDistS can deal... Platforms: Mac, Mac OSX

Keyword: Automatic, Definition, Freely, Individual, Iterative, Joining, Linux, Manual, Noncommercial, Operating, Profdists, Profile, Protein, Secondary, Sequencesavailability, Structures, Systems, Windows

The RandomWalk1D program simulates a random walk in one dimension for steps of unit length and equal time intervals. The default number of steps is N = 16 and the probability of going right or left at any step is the same (the probability p of going to the right for a single step is 0.5).... Platforms: Mac, Mac OSX

Keyword: Archive, Clicking, Compadre, Compiled, Computer, Distributed, Found, Installed, Physics, Probability, Program, Programs, Readytorun, Searching, Source, Statistical, Steps, Thermal

The Ejs Wave Packet model displays the motion of an approximate wave packet. The simulation allows an arbitrarily wave packet to be created. The default dispersion relation, with the frequency equal to the wavenumber, results in a wavepacket that does not spread. The amplitude, maximum and... Platforms: Mac, Mac OSX

Keyword: Archive, Clicking, Compiled, Created, Dispersion, Distributed, Double, Installed, Model, Modeling, Models, Modify, Motion, Packet, Physics, Relation, Simulation, Simulations, Source

The STP Sensitivity to Initial Conditions program shows 11 particles in a line with the same velocity. You can perturb the system slightly and observe how sensitive the trajectory is to a small change. The default perturbation strength is 1.00001. STP SensitivityToInitialConditions is part of a... Platforms: Mac, Mac OSX

Keyword: Additional, Archive, Aspects, Compadre, Compiled, Computer, Distributed, Doubleclicking, Found, Installed, Model, Physics, Program, Programs, Readytorun, Searching, Source, Statistical, Stp Sensitivitytoinitialconditionsjar, Thermal

The STP IdealGasNumberOfStates program numerically evaluates the number of states of an ideal gas and demonstrates finite size effects by plotting the actual number of states and the asymptotic expression. The default is two-dimensional system (d=2). STP IdealGasNumberOfStates is part of a suite... Platforms: Mac, Mac OSX

Keyword: Additional, Archive, Clicking, Compadre, Compiled, Distributed, Double, Found, Idealgasnumberofstates, Number, Numerically, Physics, Program, Programs, Readytorun, Searching, Source, States, Statistical, Thermal

The STP IsingMeanFieldSolution program uses Newton's method to calculate solutions to the mean-field approximation to the equation of state of the Ising model. The program also displays the free energy as a function of the magnetization m for given values of T and the magnetic field H. The... Platforms: Mac, Mac OSX

Keyword: Additional, Archive, Aspects, Compadre, Computer, Distributed, Fieldstp, Found, Installed, Isingmeanfieldsolution, Model, Physics, Program, Programs, Readytorun, Searching, Source, Statistical, Suite, Thermal

ProDy is a Python package designed for protein structural dynamics analysis. ProDy is developed by Ahmet Bakan and licensed under the GPLv3. New features and functions are constantly being added to ProDy. The following are the main features that are present and working fine: Protein structure... Platforms: Mac, Mac OSX

Keyword: Analysis, Calculateplot, Chainsnormal, Comparative, Comparing, Elastic, Features, Fineprotein, Functions, Matching, Models, Network, Overlaps, Parser, Powerful, Prody, Selector, Snapshots, Structure, Structures

The STP Multiplicative Process program simulates the outcome of a random multiplicative process, a product of random numbers. Examples of multiplicative processes include the distributions of incomes, rainfall, and the fragments sizes in rock crushing processes. Consider the latter for which we... Platforms: Mac, Mac OSX

Keyword: Aspects, Distributed, Fragments, Model, Multiplicative, Multiplicativeprocess, Numbers, Physics, Processes, Product, Program, Programs, Random, Readytorun, Sizes, Source, Statistical, Suite, Thermal, Timesstp

The GR Schwarzschild Particle program simulates orbits of objects around a black hole using the Schwarzschild metric. It also displays a plot of the effective potential well in which the orbiting particle resides. GR Schwarzschild Particle is part of a suite of Open Source Physics programs that... Platforms: Mac, Mac OSX

Keyword: Archive, Clicking, Compadre, Compiled, Distributed, Double, Found, General, Installed, Particle, Physics, Program, Programs, Readytorun, Relativity, Schwarzschild, Schwarzschild Particlejar, Searching, Source, Visualizations

This script inactivates only the columns in a spreadsheet from which the script is run whose column labels are in another spreadsheet specified by the user. Any inactive columns in the other spreadsheet are not used in inactivating columns in the current spreadsheet. Non-unique columns in the... Platforms: Mac, Mac OSX

Keyword: Column, Columns, Current, Inactivates, Inactivating, Inactive, Labels, Nonunique, Script, Spreadsheet, Supported

Script for manipulating tree (*.t, *.trprobs, *.con) and parameter (*.p) files from MrBayes (v.3). The script exctracts trees and (by default) the taxon translation table and the trailing ``end;'' from a MrBayes tree file. A number of options are available: Any contiguous interval of trees can... Platforms: Mac, Mac OSX

Keyword: Altnexus, Extracted, Format, Labels, Lengths, Mrbayes, Numbers, Present, Printed, Printedbranch, Printinga, Random, Removed, Sequence, Setting, Thinned, Trees

The Falling Cup with Ball model shows a mass attached to the inside of a cup with a light spring. The cup is held upside down with the mass hanging out of the cup, then released from rest. What happens when the cup is released? 1. The mass will extend the spring, like a parachute, due to air... Platforms: Mac, Mac OSX

Keyword: Archive, Click, Compiled, Created, Distributed, Double, Ejs Mech Newton Fallingcupwithballjar, Falling, Installed, Model, Modeling, Original, Position Fthe, Program, Pulled, Readytorun, Simulations, Spring, Upside

This script inactivates only the rows in a spreadsheet from which the script is run whose row labels are in another spreadsheet specified by the user. Any inactive rows in the other spreadsheet are not used in inactivating rows in the current spreadsheet. Non-unique rows in the current... Platforms: Mac, Mac OSX

Keyword: Current, Inactivates, Inactivating, Inactive, Labels, Nonunique, Script, Spreadsheet, Supported

GeoMeTree is a python program to compute the geodesic path between two phylogenetic trees. Further details on the algorithm and the use of the program can be found in the manual (pdf). Platforms: Mac, Mac OSX

Keyword: Algorithm, Compute, Details, Found, Geodesic, Geometree, Manual, Phylogenetic, Program, Python, Treesfurther

The STP IdealBoseGasIntegral program numerically determines the value of the chemical potential of an ideal Bose gas for a given temperature and density. STP IdealBoseGasIntegral is part of a suite of Open Source Physics programs that model aspects of Statistical and Thermal Physics (STP). The... Platforms: Mac, Mac OSX

Keyword: Additional, Archive, Clicking, Compadre, Compiled, Computer, Double, Found, Idealbosegasintegral, Installed, Model, Physics, Program, Programs, Readytorun, Searching, Source, Statistical, Stp Idealbosegasintegraljar, Thermal

SEMPHY is a tool for data-intensive phylogenetic reconstruction. SEMPHY infers phylogenies by Maximum Likelihood, the most established criterion for finding the correct phylogenetic tree. SEMPHY searches for both the most likely topology of the evolutionary tree, and the optimal lengths of its... Platforms: Mac, Mac OSX

Keyword: Account, Accuracy, Amongsite, Belowthe, Description, Estimation, Improve, Joining, Likelihood, Maximum, Methods, Neighbor, Phylogenetic, Publications, Section, Semphy, Taking, Version

The EJS Slipping and Rolling Wheel Model shows the motion of a wheel rolling on a floor subject to friction. The simulation allows the user to change the initial translational and rotational velocities of the wheel, v and ?Ya*, the mass, radius, and mass distribution, R, m, and C of the wheel. By... Platforms: Mac, Mac OSX

Keyword: Archive, Clicking, Compiled, Distributed, Double, Installed, Model, Modeling, Modelquot, Modify, Quotopen, Readytorun, Rolling, Simulation, Simulations, Slipping, Wheel

This script takes genotypes from two different arrays and creates a consensus spreadsheet, and two optional spreadsheets. In order to run this script two spreadsheets of mapped genotype data are required. The spreadsheets may also contain non-marker mapped columns as they will be skipped when... Platforms: Mac, Mac OSX

Keyword: Alleles, Applied, Assigned, Coded, Field, Genotypes, Ids, Manner, Mapped, Marker, Names, Nucleotide, Script, Spreadsheet, Spreadsheets, Strand

The STP EinsteinSolids program displays the energy distribution of an Einstein solid in thermal contact with another Einstein solid. The purpose of this program is to explore the distribution of energy between two systems in thermal contact. The default state is two Einstein solids, system A and... Platforms: Mac, Mac OSX

Keyword: Additional, Aspects, Clicking, Contact, Distributed, Distribution, Einstein, Einsteinsolids, Energy, Model, Physics, Program, Programs, Readytorun, Solid, Source, Statistical, System, Thermal