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![TiFoSi simulation example]
Use ***comments*** to raise questions or give support to other users (bubble icon at the top-right corner). Keep your comments organized! General comments must be kept in the main webpage, comments about *Visualization Tools* must be kept in that webpage, and so forth. Comments not satisfying this or irrelevant to the TiFoSi community will be automatically eliminated.
The design and implementation of TiFoSi adhere to the following guidelines:
- **Fast and efficient.** The complexity of the simulations of tissues make interpreted languages highly inefficient in terms of execution speed. Thus, the code must be based in a high-end compiled language (in the case of TiFoSi C++).
- **User friendly.** Previous efficient software solutions for simulating epithelial dynamics following a vertex model approach rely on the knowledge of a high-end computer language (i.e., C++). In order to circumvent this major disadvantage TiFoSi relies on XML configuration files with a syntax and modularity aim at clearly defining in silico experiments. A Python parser then interprets the configuration file and modifies the C++ source code. The learning curve to create configuration files is fast and we provide an extensive manual that explains all the possibilities of the code with examples.
- **Open.** TiFoSi uses free open source languages (GNU g++ and Python 3) and the code is available under a GNU license. TiFoSi has been extensively tested in Linux OS (Ubuntu) but will run in any platform where GNU g++, make, and Python 3 are installed.
- **Data oriented.** Tissue simulations presents endless possibilities
in terms of the conceivable experiments. Thus, focusing on the development of a graphical frontend, both from the point of view of the input (configuration file) and the output, would make the code extremely complex, would pose problems in terms of its platform portability, and would make the code less flexible for implementing some functionalities. For these reasons TiFoSi input and output is data oriented. On the one hand, as mentioned above, input is based on an XML configuration file. On the other hand, TiFoSi produces a comprehensive collection of output files and logs (ANSI text) that report on all the possible relevant information of the tissue simulation including cells geometrical properties, energy, acting forces, protein expression levels, cell lineage tracking information, and properties of division events and tissue topology changes.
- **Community Sustained.** We aim at developing a community of TiFoSi users and developers. Thus, the TiFoSi website has been conceived as a repository of configuration files, visualization tools, and further modifications of the code, and as a forum to discuss issues and questions among users and developers.