====================== MaSyMoS documentation! ====================== Welcome to the MaSyMoS-Documentation! "**Ma**\ nagement **Sy**\ stem for **Mo**\ dels and **S**\ imulations" is a Neo4J based database for SBML and CellML Models as well as simulation descriptions in SED-ML format. In addition, MaSyMoS contains bio-ontologies that are most frequently used for the annotation of models, i.e., GO, ChEBI, SBO, KiSAO. All data is represented as a Graph and can be queried using Cypher. A description of the underlying database is available from our latest publication in [Oxford DATABASE](http://www.ncbi.nlm.nih.gov/pubmed/25754863). .. WARNING:: OLD VERSION OF Log4j used - this software is vulnarable to the Log4Shell-Bug - `Issue exists here `__. - do not run MaSyMoS on the public internet Source Code, Feedback and Contribution ###################################### - 🔬 Find the `MaSyMoS project on GitHub `__. - 📝 Read open issues or `create new ones for feature requests and bugs `__. - 🔧 Contribute to the project after reading the :ref:`contrib_main`. Modules ======= - `MaSeMiWa - MaSyMoS SEEK middleware `__ Table of Content ################ .. toctree:: :maxdepth: 2 :name: maintoc :includehidden: .. toctree:: :caption: Overview and Installation :maxdepth: 2 main_overview main_setup docs_docker .. toctree:: :caption: How to use MaSyMoS :maxdepth: 2 use_cli use_morre use_troubleshooting .. toctree:: :caption: Contribution and Development :maxdepth: 2 contrib_main contrib_start contrib_rtfd License ####### .. literalinclude:: ../../LICENSE :language: text .. Indices and tables .. ################## .. .. * :ref:`genindex` .. * :ref:`modindex` .. * :ref:`search`