Verifiable biology

S Konur, M Gheorghe… - Journal of the Royal …, 2023 - royalsocietypublishing.org
The formalization of biological systems using computational modelling approaches as an
alternative to mathematical-based methods has recently received much interest because …

Dynamic slicing of reaction systems based on assertions and monitors

L Brodo, R Bruni, M Falaschi - International Symposium on Practical …, 2023 - Springer
Abstract Reaction Systems (RSs) are a successful computational framework inspired by
biological systems. RSs can involve a large number of reactions and entities, which makes it …

[HTML][HTML] Exploring conditional rewriting logic computations

M Alpuente, D Ballis, F Frechina, J Sapiña - Journal of Symbolic …, 2015 - Elsevier
Trace exploration is concerned with techniques that allow computation traces to be
dynamically searched for specific contents. Depending on whether the exploration is carried …

[HTML][HTML] Using conditional trace slicing for improving Maude programs

M Alpuente, D Ballis, F Frechina, D Romero - Science of Computer …, 2014 - Elsevier
Understanding the behavior of software is important for the existing software to be improved.
In this paper, we present a trace slicing technique that is suitable for analyzing complex …

Backward trace slicing for rewriting logic theories

M Alpuente, D Ballis, J Espert, D Romero - … Poland, July 31-August 5, 2011 …, 2011 - Springer
Trace slicing is a widely used technique for execution trace analysis that is effectively used
in program debugging, analysis and comprehension. In this paper, we present a backward …

Backward trace slicing for conditional rewrite theories

M Alpuente, D Ballis, F Frechina, D Romero - International Conference on …, 2012 - Springer
In this paper, we present a trace slicing technique for rewriting logic that is suitable for
analyzing complex, textually-large system computations in rewrite theories that may contain …

Inspecting rewriting logic computations (in a Parametric and Stepwise Way)

M Alpuente, D Ballis, F Frechina, J Sapiña - Specification, Algebra, and …, 2014 - Springer
Trace inspection is concerned with techniques that allow the trace content to be searched for
specific components. This paper presents a rich and highly dynamic, parameterized …

Julienne: A Trace Slicer for Conditional Rewrite Theories

M Alpuente, D Ballis, F Frechina, D Romero - FM 2012: Formal Methods …, 2012 - Springer
Trace slicing is a transformation technique that reduces the size of execution traces for the
purpose of program analysis and debugging. Based on the appropriate use of antecedents …

On Quantitative Modeling and Simulation of Biological Systems: An Open-Source Approach Using Biological Networks and Rule-Based Transformation to Hybrid …

C Brinkrolf - 2023 - pub.uni-bielefeld.de
Petri nets have been widely used for decades as a method to model parallel processes,
particularly in the field of systems biology. Over time, the basic formalism of Petri nets has …

[PDF][PDF] Parametric Exploration of Rewriting Logic Computations.

M Alpuente, D Ballis, F Frechina, J Sapiña - SCSS, 2013 - risc.jku.at
This paper presents a parameterized technique for the inspection of Rewriting Logic
computations that allows the non-deterministic execution of a given rewrite theory to be …