Related papers: Documenting Bioinformatics Software Via Reverse En…
Software has long been established as an essential aspect of the scientific process in mathematics and other disciplines. However, reliably referencing software in scientific publications is still challenging for various reasons. A crucial…
Benchmarking, which involves collecting reference datasets and demonstrating method performances, is a requirement for the development of new computational tools, but also becomes a domain of its own to achieve neutral comparisons of…
Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative"…
We introduce SciWING, an open-source software toolkit which provides access to pre-trained models for scientific document processing tasks, inclusive of citation string parsing and logical structure recovery. SciWING enables researchers to…
Since underlying hardware components form the basis of trust in virtually any computing system, security failures in hardware pose a devastating threat to our daily lives. Hardware reverse engineering is commonly employed by security…
Context: Backsourcing is the process of insourcing previously outsourced activities. When companies experience environmental or strategic changes, or challenges with outsourcing, backsourcing can be a viable alternative. While outsourcing…
Replication of scientific experiments is critical to the advance of science. Unfortunately, the discipline of Computer Science has never treated replication seriously, even though computers are very good at doing the same thing over and…
In this work, we investigate the problem of revealing the functionality of a black-box agent. Notably, we are interested in the interpretable and formal description of the behavior of such an agent. Ideally, this description would take the…
Since the advent of next-generation sequencing in the early 2000s, the volume of bioinformatics software tools and databases has exploded and continues to grow rapidly. Documenting this evolution on a global and time-dependent scale is a…
This article attempts to describe specific mental techniques that are related to resolving very complex tasks in software engineering. This subject may be familiar to some software specialists to different extents; however, there is…
Software engineering is extremely information-intensive. Every day developers work with source code, version repositories, issue trackers, documentation, web-based and other information resources. However, three key aspects of information…
Computational research and data analytics increasingly relies on complex ecosystems of open source software (OSS) "libraries" -- curated collections of reusable code that programmers import to perform a specific task. Software documentation…
In this paper, we present our experience based on a reengineering project. The software project is to re-engineer the original system of a company to answer the new requirements and changed business functions. Reengineering is a process…
Good software documentation encourages good software engineering, but the meaning of "good" documentation is vaguely defined in the software engineering literature. To clarify this ambiguity, we draw on work from the data and information…
Due to the growing complexity of software systems, there has been a dramatic increase and industry demand for tools and techniques on software refactoring in the last ten years, defined traditionally as a set of program transformations…
Integrating research evidence into practice is one of the main goals of Evidence-Based Software Engineering (EBSE). Secondary studies, one of the main EBSE products, are intended to summarize the best research evidence and make them easily…
While mastered by some, good scientific writing practices within Empirical Software Engineering (ESE) research appear to be seldom discussed and documented. Despite this, these practices are implicit or even explicit evaluation criteria of…
How many times have you tried to re-implement a past CAV tool paper, and failed? Reliably reproducing published scientific discoveries has been acknowledged as a barrier to scientific progress for some time but there remains only a small…
Hardware Reverse Engineering (HRE) is a technique for analyzing integrated circuits. Experts employ HRE for security-critical tasks, like detecting Trojans or intellectual property violations, relying not only on their experience and…
Open science describes the movement of making any research artefact available to the public and includes, but is not limited to, open access, open data, and open source. While open science is becoming generally accepted as a norm in other…