Related papers: Izzy: a high-throughput metagenomic read simulator
Reproducibility and realistic datasets are crucial for advancing research. Unfortunately, they are often neglected as valid scientific contributions in many young disciplines, with computer science being no exception. In this article, we…
Simulations with high accuracy are an essential part of scientific research to accelerate the innovation process. They are especially useful for finding novel approaches or optimizing existing methods. Today, powerful software tools are…
A method is presented which allows for a tremendous speed-up of computer simulations of statistical systems by orders of magnitude. This speed-up is achieved by means of a new observable, while the algorithm of the simulation remains…
Recent advances in both theory and computational power have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble simulations are now widely used to compute a number of…
The current hardware landscape and application scale is driving performance engineers towards writing bespoke optimizations. Verifying such optimizations, and generating minimal failing cases, is important for robustness in the face of…
The experimental evaluation of fault-tolerance studies relies on tools that inject errors while programs are running, and then monitor the execution and the output for faulty execution. In particular, the established methodology in…
Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…
Fuzzing is utilized for testing software and systems for cybersecurity risk via the automated adaptation of inputs. It facilitates the identification of software bugs and misconfigurations that may create vulnerabilities, cause abnormal…
The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to…
Fuzzing is a popular vulnerability automated testing method utilized by professionals and broader community alike. However, despite its abilities, fuzzing is a time-consuming, computationally expensive process. This is problematic for the…
By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to…
User simulation is a valuable methodology for evaluation in Information Retrieval (IR), enabling low-cost experimentation and counterfactual analysis. However, existing simulation frameworks are primarily code-centric libraries that require…
This paper is a brief update on developments in the BioDynaMo project, a new platform for computer simulations for biological research. We will discuss the new capabilities of the simulator, important new concepts simulation methodology as…
With the steady increase in the precision of flavour physics measurements collected during LHC Run 2, the LHCb experiment requires simulated data samples of larger and larger sizes to study the detector response in detail. The simulation of…
Interactive high-performance computing is doubtlessly beneficial for many computational science and engineering applications whenever simulation results should be visually processed in real time, i.e. during the computation process.…
Hybrid systems are increasingly used in critical applications such as medical devices, infrastructure systems, and autonomous vehicles. Lince is an academic tool for specifying and simulating such systems using a C-like language with…
Reconfigurable intelligent surfaces (RISs) are considered a promising technology for boosting the coverage and for enhancing the spectral efficiency of wireless systems, as well as for taming the wireless environment. The potential benefits…
Models that can simulate how environments change in response to actions can be used by agents to plan and act efficiently. We improve on previous environment simulators from high-dimensional pixel observations by introducing recurrent…
While metagenomics has emerged as a technology of choice for analyzing bacterial populations, assembly of metagenomic data remains difficult thus stifling biological discoveries. metaSPAdes is a new assembler that addresses the challenge of…
This paper makes the case for a single-ISA heterogeneous computing platform, AISC, where each compute engine (be it a core or an accelerator) supports a different subset of the very same ISA. An ISA subset may not be functionally complete,…