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 …
alternative to mathematical-based methods has recently received much interest because …
Dynamic slicing of reaction systems based on assertions and monitors
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 …
biological systems. RSs can involve a large number of reactions and entities, which makes it …
[HTML][HTML] Exploring conditional rewriting logic computations
Trace exploration is concerned with techniques that allow computation traces to be
dynamically searched for specific contents. Depending on whether the exploration is carried …
dynamically searched for specific contents. Depending on whether the exploration is carried …
[HTML][HTML] Using conditional trace slicing for improving Maude programs
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 …
In this paper, we present a trace slicing technique that is suitable for analyzing complex …
Backward trace slicing for rewriting logic theories
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 …
in program debugging, analysis and comprehension. In this paper, we present a backward …
Backward trace slicing for conditional rewrite theories
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 …
analyzing complex, textually-large system computations in rewrite theories that may contain …
Inspecting rewriting logic computations (in a Parametric and Stepwise Way)
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 …
specific components. This paper presents a rich and highly dynamic, parameterized …
Julienne: A Trace Slicer for Conditional Rewrite Theories
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 …
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 …
particularly in the field of systems biology. Over time, the basic formalism of Petri nets has …
[PDF][PDF] Parametric Exploration of Rewriting Logic Computations.
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 …
computations that allows the non-deterministic execution of a given rewrite theory to be …