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This workshop is aimed at bringing together and creating synergies between researchers working on software agents, on the one hand, and bioinformatics and computational biology, on the other hand, to discuss relevant issues and approaches aimed at assessing and promoting the adoption of innovative technologies in such fields.
Bioinformatics and computational biology are emerging disciplines that use information technology to organize, analyze, and distribute biological information in order to answer complex biological questions. As for bioinformatics, it typically refers to activities that involve researching, developing, or applying computational tools and techniques aimed at dealing with biological data –including those to acquire, store, organize, archive, analyse, or visualize them. As for Computational Biology, it refers to the development and use of analytical data and theoretical methods, mathematical modelling and simulation techniques aimed at studying biological, behavioural, and social systems. The amount of available information is constantly increasing, and it is difficult to exploit available data from all sources. Many of the available data are interrelated, but it is currently difficult to identify, select, clean, or use all relevant data, as different tools use different data formats with different semantics. There is a need to devise methods aimed at learning and discovering knowledge by “intelligently” combining these distributed data and information sources. In particular, after experiments are run, interpreting results requires gathering together potentially related data. Also, the context in which an experiment is run, such as the hypothesis to be tested or the legal constraints of the institution, may inform which resources are appropriately combined, again requiring “intelligence”. Moreover, some classical problems could be better tackled by resorting to a suitable computational paradigm using various interaction protocols, e.g., cooperation or competition.
Furthermore, recent progresses in the application of bioinformatics and computational biology to biomedicine has made it essential to devise technological platforms able to ensure appropriate support to research activities performed in the area of life sciences. The increasing amount, complexity, and heterogeneity of biological data, together with the increasing production of the corresponding scientific literature, raised novel challenges. To support the most relevant tasks, a new generation of infrastructures, systems, and data mining algorithms still needs to be developed –able to perform, in particular, human genome analysis, protein interactions analysis, and molecular dynamics simulations.
In principle, the workshop will mainly focus on the benefits of adopting agent technology in: (i) storing, accessing, and distributing relevant biological data, (ii) implementing the automation of information-gathering and information-inference processes in biological settings, (iii) simulating and modelling biological systems.
Many applications, strictly or loosely related with bioinformatics and computational biology, would benefit from agent technology. To give the reader a flavour of the relevant classes of applications, let us recall:
- repetitive and time consuming activities (e.g., mapping disease genes, analyzing microarray data),
- knowledge management, such as integration of different knowledge sources,
- modelling of complex, dynamic systems,
- classical data analysis problems (e.g., gene identification, 3D / 2D protein structure prediction),
- state-of-the-art techniques that may be improved by adopting agent technology (e.g., micro-arrays).