1,721,109 research outputs found
Computational approaches to understanding nutrient metabolism and metabolic disorders
No full textComputational methods are becoming more and more essential to elucidate biological systems. Many different approaches exist with pros and cons. This paper reviews the most useful technologies focusing on nutrient metabolism and metabolic disorders. Space limitation prevents from exploring the examples in details, but pointers to the relevant papers are reported
Comparison of syntactic error handling in LR parsers
No full textError recovery techniques for LR parsers presented in the literature are described and classified. The techniques considered range from the non‐correcting ones to interactive and incremental ones. Also, some of the techniques presented are compared and evaluated. An example showing the advantages and the disadvantages of each class of strategies is given and is used as a guideline for classifying syntax errors according to the recovery strategies which are more adequate to correct them
Efficient formulation of the rejection-based algorithm for biochemical reactions with delays
No full textThe rejection-based stochastic simulation algorithm (RSSA) is an exact simulation for realising temporal behaviour of biochemical reactions. It reduces the number of propensity updates during the simulation by using propensity bounds of reactions to select the next reaction firing. We present in this paper a new efficient formulation of RSSA and extend it for incorporating biochemical reactions with time delays. Our new algorithm explicitly keeps track of the putative firing times of reactions and uses these to select the next reaction firing. By using such a representation, it can efficiently handle biochemical reactions with delays and achieve computational efficiency over existing approaches for exact simulation
On the decidability and complexity of the structural congruence for beta-binders
No full textAbstractBeta-binders is a recent process calculus developed for modelling and simulating biological systems. As usual for process calculi, the semantic definition heavily relies on a structural congruence. The treatment of the structural congruence is essential for implementation. We present a subset of the calculus for which the structural congruence is decidable and a subset for which it is also efficiently solvable. The obtained results are a first step towards implementations
A stochastic semantics for BioAmbients
No full textWe consider BioAmbients, a calculus for specifying biological entities and for simulating and analysing their behaviour. We extend BioAmbients to take quantitative information into account by defining a stochastic semantics, based on a simulation stochastic algorithm, to determine the actual rate of transitions
A causal semantics for CCS via rewriting logic
No full textWe consider two operational semantics for CCS defined in the literature: the first exploits proved transition systems (PTS) and the second rewriting logic (RL). We show that the interleaving interpretation of both semantics agree, in that they define the same transitions and exhibit the same non-deterministic structure. In addition, we study causality in CCS computations. We recall its treatment via PTS, exhibiting the notion of causality presented in the literature, and we show how to recast it in the RL semantics via suitable axioms. Also in this case, the two semantics agree
- …
