.. MeCoSim documentation master file, created by sphinx-quickstart on Fri Sep 14 11:00:53 2012. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. MeCoSim documentation *********************************** .. centered:: MeCoSim |version| released |today| 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: .. figure:: MeCoSim.jpg :align: right :height: 260 px :width: 360 px .. raw:: html :file: indexPreamble.html * **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: .. figure:: images/videos.png :align: right :height: 200 px :width: 460 px .. toctree:: :maxdepth: 3 getting_started/videos .. getting_started/manual * :download:`Foundational paper`, to illustrate the initial goal and philosophy of MeCoSim. * :download:`User manual`, showing the basic features and operation in MeCoSim. * :download:`MeCoSim Quick MeCoSim Apps Development Guide`, contribution from Luis Felipe Macías providing a quick guide to develop new MeCoSim-based applications by means of customization. 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. .. toctree:: :maxdepth: 2 case_studies/case_studies 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 ==================================== * :download:`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 ----------- .. container:: boldlink .. figure:: images/p-lingua-logo.gif :align: center :width: 60 px * `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 `_. ----------------------------------------------- .. container:: boldlink .. figure:: images/pmcgpu-logo.png :align: center :width: 60 px * `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. ----------------------------------------------- .. container:: boldlink .. figure:: images/rgnc-logo.jpg :align: center :width: 70 px * `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.