Project for the translation of SBML files into BNGL files. You can find more information about the project here.

libsbml, networkx (for state transition diagram creation), pexpect (for post atomization analysis). Check requirements.txt for specific versions of the libraries that Atomizer needs. You can also install all requirements with one command by doing

pip install -r requirements.txt

From the atomizer root directory

make; make install

./sbmlTranslator -i /path/to/sbml/file [-a] [-o output.bngl]

Optional arguments

• [-a] activates the atomizer. Otherwise only a flat translation will be provided (no molecular structure)
• [-p] activates pathway commons querying. An internet connection is required
• [-b <path/to/bionetgen>] Enables post atomization analysis.
• See [-h] for a full list of arguments

Directory Structure: |

• SBMLparser: Directory containing the main project. |

  • sbmlTranslator.py: Entry level file

  • atomizer: Contains the main implicit assumption extraction code

    • analyzeSBML.py: lexical analysis engine
    • detectOntology.py: helper file for the lexical analysis engine (levenshtein distance, convention discovery, etc.)
    • analyzeRDF.py: extracts annotation information and gets it into the atomizer data model
    • resolveSCT.py: Creates the species composition table using lexical analysis, annotation information and the stoichiometry matrix
    • moleculeCreation.py: Creates the structured molecules for use in graph-creation

  • utils: contains several utility scripts used during the atomization process

    • consoleCommands.py: Interfaces with the BioNetGen console
    • pathwaysCommons.py: Queries BioGrid and pathways commons given an RDF annotation entry
• stats: Extracts statistics of a set of atomized BioModels files