ICTs




METADONEA graphical environment for your modeling language 

Information system engineering 





APPLICATIONS
Quantum Mechanics and Dynamics
 Abinit  compute charge density and electronic structure of molecules with Density Functional Theory
 ADF  quantum chemistry software package based on Density Functional Theory (DFT)
 Ampac  fullyfeatured semiempirical quantum mechanical program
 ATAT  Alloy Theoretic Automated Toolkit, a collection of alloy theory tools
 Atomistix ToolKit  software tool for firstprinciples electronicstructure and transport calculations
 CPMD (Car–Parrinello Molecular Dynamics)  plane wave and pseudopotential implementation of Density Functional Theory
 Dalton  molecular electronic structure program
 DFTB+  fast and efficient standalone implementation of the Density Functional based Tight Binding (DFTB) method
 FPLO  fullpotential localorbital minimumbasis code to solve the KohnSham equations on a regular lattice
 GAMESS  program for ab initio molecular quantum chemistry
 Gaussian  electronic structure program
 MOLPRO  complete system of ab initio programs for molecular electronic structure calculations
 MOPAC  semiempirical quantum chemistry program based on Dewar and Thiel's NDDO approximation
 NWchem  electronicstructure code that is suitable to perform complex calculations on molecular structure
 ORCA  ab initio, DFT and semiempirical SCFMO package
 PLH  ab initio polymer program
 Siesta  electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids
 Turbomole  ab initio electronic structure program
 TRex  automatized Romberg procedure for finite field differentiation for a geometrical progression of fields
 VASP (Vienna Abinitio Simulation Package)  package for performing abinitio quantummechanical molecular dynamics using pseudopotentials and a plane wave basis set
 VTST  a VASP package variant for finding saddle points and evaluating transition state theory (TST) rate constants
 WIEN2k  augmented plane wave plus local orbitals program for calculating crystal properties
Photonics and Material Simulations
 Meep  FDTD simulation software package to model electromagnetic systems
 MPB  computes definitefrequency eigenstates of Maxwell's equations in periodic dielectric structures for arbitrary wavevectors
Molecular Mechanics and Dynamics
 Accelrys Discovery Studio  modeling and simulation software for protein modeling and computational chemistry
 Accelrys Materials Studio  software environment for molecular modeling
 Adaptive Poisson Boltzmann Solver (APBS)  software package for the numerical solution of the PoissonBoltzmann equation
 GOLD Suite  program for calculating the docking modes of small molecules into protein binding sites
 Gromacs  versatile package to perform molecular dynamics
 LAMMPS  large scale classical molecular dynamics code
 MDynaMix  general purpose molecular dynamics code for simulations of mixtures of rigid or flexible molecules
 NAMD  molecular dynamics code designed for simulation of large biomolecular systems
 PyRosetta  interactive Pythonbased interface to Rosetta
 Rosetta  protein sequence analysis suites
 Sybyl  molecular modeling and computational informatics platform
 Tinker  complete and general package for molecular mechanics and dynamics, with some special features for biopolymers
Crystallography
 Adxv  program to display XRay diffraction images
 CCP4  collection of disparate programs covering most of the computations required for macromolecular crystallography
 CNS  program that provide a flexible multilevel hierachical approach for the most commonly used algorithms in macromolecular structure determination
 CSD  the Cambridge Structural Database
 Coot  program for model building, model completion and validation
 Mosflm/iMosflm  program for integrating single crystal diffraction data from area detectors
 Naccess  program that calculates the accessible area of a molecule from a PDB
 SIR  program for the solution and refinement of crystal structures using single crystal data
 Phenix  automated macromolecular crystallography software suite
 XDS  software for processing singlecrystal monochromatic diffraction data recorded by the rotation method
Numerical Analysis
 MATLAB  numerical computing environment
 Octave  highlevel programming language, primarily intended for numerical computations
Physics and Astrophysics
 DDSCAT  program for calculating scattering and absorption of light by irregular particles
 eDDA  program for electrondriven discretedipole approximation
Agentbased Modeling
 RePast  family of advanced agentbased modeling and simulation platforms
Bioscience
 13CFLUX  toolkit for Metabolic Flux Analysis
 MicrobeTracker Suite  software package designed to detect and outline microbial cells in microscopy images and to analyze fluorescence signal inside them
Phylogenetics
 Bayesian Evolutionary Analysis Sampling Trees (BEAST)  program for Bayesian MCMC analysis of molecular sequences
 Genetic Algorithm for Rapid Likelihood Inference (GARLI)  program that performs phylogenetic inference using the maximumlikelihood criterion
 MrBayes  program for the Bayesian estimation of phylogeny
Statistics and Data Analysis
 The R Project for Statistical Computing  environment for statistical computing and graphics
 Regression Analysis of Time Series (RATS)  statistical package for time series analysis and econometrics
 STATA  generalpurpose statistical software package
Economy and Finance
 Dynare  software platform to solve, simulate and estimate macroeconomic models