Gene Regulatory Interaction Formulator For Inquiring Networks
Gene Regulatory Interaction Formulator For Inquiring Networks (griffin) is a java library for inference and analysis of Boolean Network models.
Using a simple file interface, griffin takes as inputs biologically meaningful constraints and turns them into a symbolic representation. Using a SAT engine, griffin explores the Boolean Network search space, finding all satisfying assignments that are compatible with the specified constraints.
Current biological constraints include:
- Postive and negative known gene regulations
- Postive and negative hypothetical regulations
- Exact set of steady states
- Extended set of steady states
- Wildtype and mutant steady states
- Input-output individual transitions
- Known cyclic attractors
- Trap subspaces
- Arbitrary state-space trajectories
- A posteriory refinement of models