Avida is an auto-adaptive genetic system designed primarily for use as a platform in Digital or Artificial Life research.
In lay terms, Avida is a digital world in which simple computer programs mutate and evolve.
Avida allows us to study questions and perform experiments in evolutionalry dynamics and theoretical biology that are intractable in real biological system.
In Avida, evolution acts on populations of self-replicating computer programs. These "digital organisms" experience natural selection through random mutations and resource competition. See the project website for more information and bug tracking.
Tierra simulated an evolutionary system by introducing computer programs that competed for computer resources, specifically processor (CPU) time and access to main memory. In this respect it is similar to core words but differs in that the programs being run in the simulation are able to modify themselves, and thereby evolve. Tierra's programs are artificial life organisms.
In Avida, every digital organism lives in its own protected region of memory, and is executed by its own virtual CPU. By default, other digital organisms cannot access this memory space, neither for reading nor for writing, and cannot execute code that is not in their own memory space. Whereas in Tierra the organisms effectively share and compete for one "brain", in Avida each one has its own brain.
A second major difference is that the virtual CPUs of different organisms can run at different speeds, such that one organism executes, for example, twice as many instructions in the same time interval as another organism. The speed at which a virtual CPU runs is determined by a number of factors, but most importantly, by the tasks that the organism performs: Tasks are logical computations that the organisms can carry out to reap extra CPU speed as bonus.Download:
Avogadro Molecular Graphics and Modelling System.
Avogadro is a molecular graphics and modelling system targetted at molecules and biomolecules. It can visualize properties like molecular orbitals or electrostatic potentials and features an intuitive molecular builder.
This project offers a flexible rendering engine and a powerful plugin architecture.
The main concept behind Avogadro is to enable a strong framework for molecular visualization and editing. Each community has their own needs and goals for an ideal tool. So Avogadro seeks to allow users to easily provide their own plugins and scripts for rendering, tools, commands... etc.
Avogadro is based on top of existing chemistry software, including Open Babel. In the future, it will offer strong scripting abilities to allow for automated demos, submission of calculations to local computational resources, and user-defined customization.
* Molecular modeller with automatic force-field based geometry optimization
* Molecular Mechanics including constraints and conformer searches
* Visualization of molecular orbitals and general isosurfaces
* Visualization of vibrations and plotting of vibrational spectra
* Support for crystallographic unit cells
* Input generation for the Gaussian, GAMESS and MOLPRO quantum chemistry
* Flexible plugin architecture and Python scripting
File formats Avogadro can read include PDB, XYZ, CML, CIF, Molden, as well as Gaussian, GAMESS and MOLPRO output.
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