PATIKAPro.ppt

PATIKAPro Complexity of Molecular Networks Pathway A set of related chemical reactions Signal follows a pathway Active pathway determines cell’s response PATIKA provides… Integrated environment for modeling pathways A well defined ontology, A collaborative open knowledge base Powerful querying and analysis options, Dynamic visualization ONTOLOGY States Transitions Molecules have states Every state can be associated with one or more transitions. A state is either Substrate Product Effector (activator/inhibitor) Complexes A group of states: molecular complex. Bind relations between members. Abstractions Nested groupings of states and transitions: Categorized according to biological meaning: Regular abstractions Homology Abstractions Incomplete Abstractions Example: Regular Abstractions A certain subgraph of the “big picture” which defines a certain biological concept Usually referred in the scientific community such as: Apoptotic Pathway Glucose Cycle Can arbitrarily intersect and be nested Regular abstractions Homology and Incomplete Homology Abstraction Evolutionary relation Incomplete Abstraction Represent incomplete information content Cell Model In a cell, molecules are confined in compartments, the sub-cellular well defined locations. MODEL DESIGN Object Oriented Design Model Interfaces Concrete Implementations DB level with persistence functionality S level, with observable logic and no drawing information V level with full visualization and observer logic Design Patterns: Design Patterns: Other Patterns State for editor states like select/zoom/create etc. Command for do/undo support Flyweight for bioentity keywords Strategy for various querying operations Observer for multiple views Visitor for graph-search algorithms Cross cutting problems 3 Types: Inherent in the biological domain Inherent in the software domain Raises due to integration of 3rd party software Cross cutting concerns: Multiple Views Every subject must Provide a subject m