DNA sequencers output a large set of very long biological data strings that we should persist in databases rather than basic text file systems. Many different data models and database management systems (DBMS) may deal with both storage and efficiency issues regarding genomic datasets. Specifically, there is a need for handling strings with variable sizes while keeping their biological meaning. Relational database management systems (RDBMS) provide several data types that could be further explored for the genomics context. Besides, they enforce integrity, consistency, and enable good abstractions for more conventional data. We propose the relational text data type to represent and manipulate biological sequences and their derivatives. We present a logical schema for representing the core biological information, which may be inferred from a given biological conceptual data schema and the corresponding function manipulations. We implement and evaluate these stored functions into an actual RDBMS for both efficacy and efficiency. We show that it is possible to enforce basic and complex requirements for the genomic domain. We claim that the well-established relational text data type in RDBMS may appropriately handle the representation and persistency of biological sequences. We base our approach on the idea of domain-specific abstract data types that can store data with semantically defined functions while hiding those details from non-technical end-users.

Propositional Dynamic Logic (PDL) is a multi-modal logic used for specifying and reasoning on sequential programs. Petri Net is a widely used formalism to specify and to analyse concurrent programs with a very nice graphical representation. In this work, we propose a PDL to reasoning about Petri Nets. First we define a compositional encoding of Petri Nets from basic nets as terms. Second, we use these terms as PDL programs and provide a compositional semantics to PDL Formulas. Finally, we present an axiomatization and prove completeness w.r.t. our semantics. The advantage of our approach is that we can do reasoning about Petri Nets using our dynamic logic and we do not need to to translate it to other formalisms. Moreover our approach is compositional allowing for construction of complex nets using basic ones.

We upgrade [3] to a complete proof of the conjecture NP = PSPACE that is known as one of the fundamental open problems in the mathematical theory of computational complexity; this proof is based on [2]. Since minimal propositional logic is known to be PSPACE complete, while PSPACE to include NP, it suffices to show that every valid purely implicational formula ρ has a proof whose weight (= total number of symbols) and time complexity of the provability involved are both polynomial in the weight of ρ. As is [3], we use proof theoretic approach. Recall that in [3] we considered any valid ρ in question that had (by the definition of validity) a “short” tree-like proof π in the Hudelmaier-style cutfree sequent calculus for minimal logic. The “shortness” means that the height of π and the total weight of different formulas occurring in it are both polynomial in the weight of ρ. However, the size (= total number of nodes), and hence also the weight, of π could be exponential in that of ρ. To overcome this trouble we embedded π into Prawitz’s proof system of natural deductions containing single formulas, instead of sequents. As in π, the height and the total weight of different formulas of the resulting tree-like natural deduction ∂1 were polynomial, although the size of ∂1 still could be exponential, in the weight of ρ. In our next, crucial move, ∂1 was deterministically compressed into a “small”, although multipremise, dag-like deduction ∂ whose horizontal levels contained only mutually different formulas, which made the whole weight polynomial in that of ρ. However, ∂ required a more complicated verification of the underlying provability of ρ. In this paper we present a nondeterministic compression of ∂ into a desired standard dag-like deduction ∂0 that deterministically proves ρ in time and space polynomial in the weight of ρ.2 Together with [3] this completes the proof of NP = PSPACE.Natural deductions are essential for our proof. Tree-to-dag horizontal compression of π merging equal sequents, instead of formulas, is (possible but) not sufficient, since the total number of different sequents in π might be exponential in the weight of ρ – even assuming that all formulas occurring in sequents are subformulas of ρ. On the other hand, we need Hudelmaier’s cutfree sequent calculus in order to control both the height and total weight of different formulas of the initial tree-like proof π, since standard Prawitz’s normalization although providing natural deductions with the subformula property does not preserve polynomial heights. It is not clear yet if we can omit references to π even in the proof of the weaker result NP = coNP.