Regarding the first research task (Algorithms for Sequence Analysis), the results varied from elementary problems or underlying data structures that are in the basis of many bioinformatics tools, such as such finding median strings, characterizing the language of sequence motifs, proposing new methods for the problem of order preserving pattern matching, or obtaining better characterization of link-cut trees and splay trees to more complex tasks, such as discovering signaling pathways by analyzing protein interaction graphs, developing better genome assembly algorithms, or even achieving a better understanding of how the brain works by studying the human brain connectome.
For the second research task (Compression and indexing techniques for repetitive data), the results obtained demonstrated that compact data structures can be applied to exploit repetitiveness in three important application scenarios where such repetitiveness arises: (1) Bioinformatics, (2) spatio-temporal data, and (3) trajectory data. The results involved collaboration between the expertises of the different groups involved in the project, which greatly facilitated such collaborations.
Finally, results of the third research task (Data structures and algorithms for networks analysis) included new compact trip representation over networks, efficient representations of multidimensional data over hierarchical domains, succinct data structures for self-indexing ternary relations, which can be applied to RDF datasets representing information from biological fields, and compressed representations of dynamic binary relations, in particular of graphs and networks that change over time, which can be exploited to dynamic graphs and networks from any field.
We have developed several prototypes that integrate the research results of the consortium. In particular, these prototypes focused on three different use cases: an assembly tool, a trajectory management tool and a network visualization tool. In the first two cases, new easy-to-use and open-source web tools have been developed and made available to the public. The third prototype, a network visualization and management tool, turned finally into the integration of research results into a previously-existing tool. This software is also publicly available as a downloadable tool or as a free online service.
