"DEVELOPMENT OF A DECISION SUPPORT SYSTEM FOR BIOINFORMATICS.
EXTRACTION OF PROTEIN COMPLEXES FROM A PROTEIN-PROTEIN INTERACTION NETWORK: A CASE STUDY"
Decision Support Systems and Workflow Management Systems have
become essential tools for some business and scientific field. This
thesis propose a new hybrid architecture for problem solving expertise
and decision-making process, that aims to support high-quality
research in the field of bioinformatics and system biology.
The first part of the dissertation introduces the project to which belong
this thesis work, i.e. the “Bioinformatics Organized Resources -
an Intelligent System” (BORIS) project of the ICAR-CNR; the main
goal of BORIS is to provide an helpful and effective support to researchers
or experimentalist, that have no familiarity with tools and
techniques to solve computational problems in bioinformatics and system
biology.
In the second part of the thesis, the proposed hybrid architecture is
described in detail; it introduces a three-dimensional space for the
BORIS system, where the viewpoints of declarative, procedural and
process approaches are considered. Using the proposed architecture,
the system is able to help the experimentalist choosing, for a given
problem, the right tool at the right moment, to generate a navigable
Workflow at different abstraction layers, extending current workflow
management systems and to free the user from implementation details,
assisting him in the correct configuration of algorithms/services.
A case study about extraction of protein complexes from proteinprotein
interaction networks is presented, in order to show how the
system faces a problem and how it interacts with the user