An Integrated System to Manage Crosscutting Concerns in Source Code

Evolution of software systems accounts for the largest part of their lifecycle and costs. Software engineers therefore, more often than developing new systems, work on complex, existing ones that they have to understand in order to modify them. Understanding such systems requires insight into the various concerns the systems implement, many of...

Renovation of idiomatic crosscutting concerns in embedded systems

Crosscutting concerns are phenomena that are present in almost any (embedded) software system. They arise if the implementation of a concern "a requirement or design decision" does not fit neatly into the modular decomposition of a software system. A crosscutting concern cannot be confined to a single modular unit and therefore becomes scattered...

Evaluating Dynamic Analysis Techniques for Program Comprehension

Program comprehension is an essential part of software development and software maintenance, as software must be sufficiently understood before it can be properly modified. One of the common approaches in getting to understand a program is the study of its execution, also known as dynamic analysis. While many such approaches have been proposed...

Understanding Ajax applications by connecting client and server-side execution traces

Ajax-enabled Web applications are a new breed of highly interactive, highly dynamic Web applications. Although Ajax allows developers to create rich Web applications, Ajax applications can be difficult to comprehend and thus to maintain. For this reason, we have created FireDetective, a tool that uses dynamic analysis at both the client (browser...

Test Suite Comprehension for Modular and Dynamic Systems

The two main topics of this dissertation are plug-in-based systems and test suite comprehension. In particular, challenges during testing plug-in-based systems are revealed, and reverse engineering based techniques to support developers during test suite comprehension are presented.

Genome duplication and mutations in ACE2 cause multicellular, fast-sedimenting phenotypes in evolved Saccharomyces cerevisiae

Laboratory evolution of the yeast Saccharomyces cerevisiae in bioreactor batch cultures yielded variants that grow as multicellular, fast-sedimenting clusters. Knowledge of the molecular basis of this phenomenon may contribute to the understanding of natural evolution of multicellularity and to manipulating cell sedimentation in laboratory and...

Reverse engineering of free form shell structures: From point cloud to finite element model

Many free form shell structures that have been designed and build in previous decades are fascinating structures. We can learn from these structures by analysing them and studying their structural behaviour. However, in some cases the geometry of these structures is not available; most notably the shapes of shell structures designed and build by...

Elimination of sucrose transport and hydrolysis in Saccharomyces cerevisiae: a platform strain for engineering sucrose metabolism

Many relevant options to improve efficacy and kinetics of sucrose metabolism in Saccharomyces cerevisiae and, thereby, the economics of sucrose-based processes remain to be investigated. An essential first step is to identify all native sucrose-hydrolysing enzymes and sucrose transporters in this yeast, including those that can be activated...

Reverse Engineering of existing reinforced concrete slab bridges

Most bridges in the Dutch infrastructure are built before 1985 and have experienced increasing traffic intensities and loads. On the other hand, the structural (design) codes have changed over the years. A frequently faced problem in practice is that the original design calculations and technical drawings of a large percentage of the existing...

Structural analysis of Heinz Isler’s bubble shell

This paper presents a detailed structural analysis of a bubble shell engineered by Heinz Isler. Through 3D scanning the geometry of this shell structure has become available to the authors. Structural analysis has not been possible before since the geometry of the shell was not available. The bubble shell was Isler’s most built type of shell. In...

Evolutionary engineering reveals amino acid substitutions in Ato2 and Ato3 that allow improved growth of Saccharomyces cerevisiae on lactic acid

In Saccharomyces cerevisiae, the complete set of proteins involved in transport of lactic acid across the cell membrane has not been determined. In this study, we aimed to identify transport proteins not previously described to be involved in lactic acid transport via a combination of directed evolution, whole-genome resequencing and reverse...

Inside the Matrix: CTI Frameworks as Partial Abstractions of Complex Threats

The Cyber Threat Intelligence (CTI) field has evolved rapidly and most of its reporting is now fairly stan-dardized. Where the Cyber Kill Chain was its sole reference framework 5 years ago, today ATT&CK is the de facto standard for reporting adversary tactics, techniques and procedures (TTPs). CTI frameworks are effectively abstraction...

Guided Malware Sample Analysis Based on Graph Neural Networks

Malicious binaries have caused data and monetary loss to people, and these binaries keep evolving rapidly nowadays. With tons of new unknown attack binaries, one essential daily task for security analysts and researchers is to analyze and effectively identify malicious parts and report the critical behaviors within the binaries. While manual...

Extending Source Code Pre-Trained Language Models to Summarise Decompiled Binaries

Binary reverse engineering is used to understand and analyse programs for which the source code is unavailable. Decompilers can help, transforming opaque binaries into a more readable source code-like representation. Still, reverse engineering is difficult and costly, involving considering effort in labelling code with helpful summaries....