MetaReg model file format

MetaReg models are stored in simple tab-delimited files, composed of several sections. Each section begins with a section header (starting with @) and ends with an empty line. Sample files can be found in the examples/ folder in the installation path.

File sections

Additional sections at the end of the file specify parameters passed by the application to the predictions engine.

@MODEL

This section contains a single line specifying the name of the model.

@AUTHOR

This section contains a single line specifying the authors of the model.

@SPECIES

This section contains a single line with the NCBI Taxonomy identifier of the species the model refers to.

@VARIABLE

Each line in this section contains a general description of a variable in the model. The columns in this section are:
  • Internal variable identifier
  • Variable name
  • Variable type: mRNA/activeProtein/notActiveProtein/InternalMetabolite/ExternalMetabolite/phenotype/other
  • Variable cardinality - the number of states it can attain
  • X coordinate of the variable on the model canvas
  • Y coordinate of the variable on the model canvas
  • External identifier for the variable (used for matching during data import)

@VARIABLE_ATTRIB

This section contains additional attributes of the model variables. Every line describes a single attribute of a single variable. The first column contains the internal variable identifier and the second column the name of the attribute. Supported attributes are:
  • in_logic - The internal identifier of the logic assigned to the variable. Every variable in the model has a logic and thus this attribute is compulsory.
  • n_regulators - The number of regulators for the variable - this is the number of incoming edges of the variable node in the model.
  • regulatorX (X=0,1,...) - Internal variable identifier of the Xth regulator of the variable.
  • confidence - The confidence in the variable's logic.
  • description - Free text describing the biological entity represented by the variable.
  • aliases - Aliases of the variable name (coma-separated).
  • reference - A PubMed identifier of a reference relevant to the variable.

@LOGIC

Each line in this section contains a general description of a logic in the model. Note that the number of logics can be larger than the number of variables, as variable's logic can be a superposition of several logics. The columns in this section are:
  • Internal logic identifier
  • Logic type - table/min/max/sum
  • Number of inputs into the logic
  • Logic cardinality - the number of states it can attain.
  • The name of the logic

@LOGIC_ATTRIB

This section contains additional attributes of the model logics. Every line describes a single attribute of a single logic. The first column contains the internal logic identifier and the second column the name of the attribute. Supported attributes are:
  • table - for a table variable, the value of this attribute is a space delimited list of the values of table. A table of a logic with k inputs contains 2k values.
  • inputX (X=0,1,...) - Internal logic identifier of the Xth input to the logic.

@FEEDBACK_SET

This section describes the feedback set in the model. A feedback set is a set of variables, removal of which removes all the cycles from the model and turns it into a directed acyclic graph (DAG). The feedback set is described as a list of internal variable identifiers (one per line).

@SUBNET

This section is used for executing the predictions engine. It specifies the connected component of the model on which the predictions engine is executed. The connected component is specified via an internal identifier of a variable in the component.

@CONDITIONS

This section lists the experimental data conditions loaded into the model. Every condition is listed in a separate line. The columns in this section are:
  • Internal condition identifier
  • Condition name
  • The name of the file from which the condition was obtained. This is used for visualization purposes only, and any name is valid in this column.
  • The low threshold for the values in the conditions - used for visualization purposes.
  • The high threshold for the values in the conditions - used for visualization purposes.

@CONDATTRIB

This section lists the experimental setting (variable perturbations) in every experimental conditions. Each line lists a single perturbation in a single condition. This section contains three columns:
  • Internal condition identifier
  • Internal variable identifier
  • The value of the variable in the condition

@CONDDATA

This section lists the values of the variables as measured in the different experimental conditions. Each line lists a single measurement in a single condition. This section contains three columns:
  • Internal condition identifier
  • Internal variable identifier
  • The value of the variable in the condition
For any questions, bugs and suggestions, please contact: Igor Ulitsky