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        "author": "Ryan Suderman",
        "author_email": "ryants@lanl.gov",
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        "description": "TRuML: A translator for rule-based modeling\n===========================================\n\nSummary\n-------\nTRuML is a Python application designed to translate models written in either Kappa or the BioNetGen language (BNGL)\ninto the other language.  Currently TRuML is only compatible with Python 2 and work is being done to adapt TRuML for\nuse with Python 3.  Documentation can be found on `Read the Docs <https://truml.readthedocs.io>`_\n\nUsage\n-----\nTRuML is invoked on the command line using the command ``truml``.  All options can be seen with the ``-h`` or ``--help``\nflags::\n\n    truml -h\n\nConversion of a model written in BNGL to the Kappa language is done using the command::\n\n    truml -b model.bngl\n\nThe corresponding Kappa model will then exist in the same directory as the source BNGL file.  The reverse translation\nis done in an equivalent manner::\n\n    truml -k model.ka\n\nVarying levels of verbosity can be achieved.  TRuML uses Python's logging library to track the translation process,\nand it's default logging level is WARNING.  The ``-v`` (``--verbose``) and ``-d`` (``--debug``) flags will set the\nlogging level to INFO and DEBUG, respectively.  The logging output can be redirected to a file with the ``-l`` (``--log_file``)\nflag and a corresponding file name.\n\nNote that TRuML only translates the model structure.  It does not consider any simulation or simulation perturbation\ndirectives from either language.\n\nCaveats\n-------\nThe two languages are not interchangeable (there are models in both languages that cannot be exactly translated to the\nother).  In many cases, TRuML will raise issues explicitly.  However the languages are both still under development and\nunidentified incompatibilities could cause the translation process to crash.  Some cases that cannot be exactly translated\ninclude:\n\nBNGL to Kappa\n*************\n - Patterns containing molecules in complex but without explicit binding::\n\n    A().B()\n\nKappa to BNGL\n*************\n - Models containing infinities (``[inf]``)\n\nFinally, the BioNetGen language is interpreted slightly differently for different simulation engines.  The NFsim engine\ndoes not consider molecularity constraints on the right hand side of the rule.  As this is similar to Kappa's purely\nlocal pattern representation (which cannot consider right hand side molecularity), TRuML assumes this convention.\n\n\n",
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        "name": "TRuML",
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        "summary": "Translation between BNGL models and Kappa models",
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