StringMol Artificial Life Simulator Service
The StringMol Artificial Life simulator has been added as a YouShare service.
StringMol is an ALife simulator which uses a simple model of the individual molecular agent. In StringMol, there is no virtual CPU and all operations are carried out on the sequence of the individual, rather than storing values in a stack. Despite the simplicity of the implementation, StringMol is capable of generating surprisingly innovative programs. StringMol is written in the C++ programming language, and we compiled version 0.2.1 for our CentOS5 Linux servers, and wrapped it as a service. Two input files must be specified, plus a numerical selection of the type of simulation that is to be executed (bi-molecular interaction, simulation of a single container of molecules, or simulation of a population of containers of molecules). The number of output files that are created depends on the number of replicate trials specified in the configuration of the simulation. These files are collected into a single zipped file in .tgz format that forms the output of the service.
More information on StringMol can be found at:
Specification of the stringmol chemical programming language version 0.2. Technical Report YCS-2010-458, Univ. of York. Hickinbotham, S., Clark, E., Stepney, S., Clarke, T., Nellis, A., Pay, M., and Young, P. (2012b).
Diversity from a monoculture: Effects of mutation-on-copy in a string-based artificial chemistry. In ALife XII, Odense, Denmark, August 2010. MIT Press. Hickinbotham, S., Clark, E., Stepney, S., Clarke, T., Nellis, A., Pay, M., and Young, P. (2010).
Another new service for the artificial life (ALife) community is the Avida service. This service is based on the Avida scientific software package, that allows a user to experiment with populations of actively evolving computer programs.
The input to the service is a zipped or tgzed archive file, consisting of avida configuration files in the root folder of the archive. These configuration files must contain the file avida.cfg.
The output of the service is an archive file consisting of the avida output folder, in tgz format. A log file is also produced.
To find the service on the YouShare portal, search for avida in the service search box. Some examples for execution are available from the run examples panel.
The service uses version Avida 2.12.4. More information on Avida can be found at http://avida.devosoft.org/
The Tierra artificial life (ALife) simulator has been added to YouShare as a service.
Tierra is a computer simulation developed by ecologist Thomas S. Ray in the early 1990s in which computer programs compete for central processing unit (CPU) time and access to main memory. In this context, the computer programs in Tierra are considered to be evolvable and can mutate, self-replicate and recombine.
The service is based upon Tierra version 6_02, with the patch from Matthias Rav (http://tierra.lolwh.at/) and is implemented on CentOS5 Linux.
The service takes a zipped (.zip, .tgz, .tar.gz) folder as its input. This input folder should contain:
- a "soup" config file, specifying a subfolder where the remaining input files can be found
- a subfolder containing;
- an opcode file (e.g. "opcode.map" from the tierra installation)
- genome files for all genomes listed at the end of the “soup” file
The output from the service is a tgz’ed folder containing the “standard” tierra outputs.
The service does some checking that the input folder contains valid data. If not, the service will fail, giving the reason in the resulting log file.
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