MeCoSim documentation

Overview

MeCoSim (Membrane Computing Simulator) is a software that offers the users a General Purpose Application to model, design, simulate, analyze and verify different types of models based on P systems. Some of the main features of MeCoSim are the following:

• Simulation of models of P systems under different initial conditions. It enables the load of P-Lingua based models, parsing, edition, debugging, and different simulation types.
• Visualization capabilities for analyzing P systems: alphabet, membrane structure, multisets and graphs viewers.
• Highly customizable platform for defining inputs, outputs, parameters and graphs for each model of a family of P systems.
• Repositories system for the visual management of available online resources, including plugins, custom applications, models and scenarios.
• Export option for releasing end-user applications for solving practical problems, abstracting P system functionalities.
• Plugins architecture, permitting the extension of the functionality with Java jars or external non-Java programs. MeCoSim is written in Java.
• Auto-update capability, using the latest release of the program whenever it runs.

Download

MeCoSim is available at this site, by means of an Install button to download, install and run the program. It is based on Java technology, multi-platform and was tested in 12 platforms, including Windows XP/Vista/7/8PR, Mac OS X 10.7.4 Lion, Solaris 11.11, and Linux (Ubuntu 10.10, 12.04, 14.04, Biolinux, Oracle linux, Red Hat).

Its download and installation is based on IzPack and Getdown technologies, providing multi-platform and auto-update capabilities. Once installed, do not care more anymore about new versions. When MeCoSim runs, availability of new releases is checked, installing modified packages if any.

Getting started

The best resources to start using MeCoSim are included in this user guide, including a number of useful videos for ilustrating the main features and functionalities:

• User guide
  • Curso matvida (Spanish)
  • Quick start
    • Installation and first use
    • Custom apps
    • Models
    • Scenarios
  • Working with models and simulations
    • Debug
    • Simulation
    • Repositories management
    • Plugins
    • Help - About
  • Playlist
    • User guide videos playlist

• Foundational paper, to illustrate the initial goal and philosophy of MeCoSim.
• User manual, showing the basic features and operation in MeCoSim.
• MeCoSim Apps Quick Development Guide, contribution from Luis Felipe Macías providing a quick guide to develop new MeCoSim-based applications by means of customization.

• Curso matvida (Spanish)

Case studies

MeCoSim development started in 2010, and a number of case studies have been analyzed since then, covering many variants of P systems, different areas of interest and application domains. This section tries to collect a non-exhaustive but as complete as possible of those case studies, grouped by areas. The examples contain, at least, some snippets of code, along with the minimal needed files to run some scenario in MeCoSim. The number of scenarios and the level of detail may vary among the different case studies, possibly including detailed descriptions, references to related publications, charts and videos.

• Case studies
  • Cell like P systems
  • Tissue like P systems
  • Spiking neural P systems
  • Population Dynamics P systems
  • Simple Kernel P systems
  • Others

If you have developed some case study and you have information please let us know (lvalencia@us.es) and we will be happy to include your work in our repository.

Publications

• Foundational paper, to illustrate the initial goal and philosophy of MeCoSim.

Acknowledge the authors...

If you are interested in using MeCoSim software and your results are going to be published, consider citing the publication: MeCoSim: A general purpose software tool for simulating biological phenomena by means of P Systems (view at publisher). For a detailed description of the cite and options to export to bibtex format please go to this URL.

Useful links

Inside RGNC

• P-Lingua Web site.

  It allocates the main information about P-Lingua project, P-Lingua language, pLinguaCore framework and related information, led by Ignacio Pérez-Hurtado. It includes the link to a web analyzer based on P-Lingua: P-Lingua Web Analyzer.

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• PMCGPU, Parallel Simulators for Membrane Computing on the GPU.

  Software project leaded by Miguel Ángel Martínez del Amor, with the aim of bringing together all the researchers working on the development of parallel simulators for P systems, specially those using the GPU, including some simulators based on CUDA.

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• Research Group on Natural Computing.

  Research Group that leads the development of MeCoSim and P-Lingua, with a great activity in the field of Membrane computing. In this page we can find a large number of publications about P systems, simulation and software tools.

External projects

Other interesting software projects working with P systems are the following:

• Infobiotics Workbench.

  Computational framework for modelling, simulating, analyzing and visualize the results of stochastic P systems, in the field of computational systems and synthetic biology.

• Meta Plab.

  Virtual laboratory to assisting modellers of Metabolic P systems both to understand the internal mechanisms of biological systems and to forecast, in silico, their response to external stimuli, environmental condition alterations or structural changes.