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Artificial intelligence (AI) techniques are widely applied in the life sciences. However, applying innovative AI techniques to understand and deconvolute biological complexity is hindered by the learning curve for life science scientists to…
Many kinds of Evolutionary Algorithms (EAs) have been described in the literature since the last 30 years. However, though most of them share a common structure, no existing software package allows the user to actually shift from one model…
Any cutting-edge scientific research project requires a myriad of computational tools for data generation, management, analysis and visualization. Python is a flexible and extensible scientific programming platform that offered the perfect…
Background: With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilizing sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on…
Numerical simulation of plasma discharges is often performed by models developed in-house and coupling externally and separately written codes. The MOOSE (Multiphysics Object Oriented Simulation Environment) framework provides tools for…
A graphical user interface (GUI) represents the most common option for interacting with computer systems. However, according to the literature system administrators often favor command line interfaces (CLIs). The goal of our work is to…
Study reproducibility is essential to corroborate, build on, and learn from the results of scientific research but is notoriously challenging in bioinformatics, which often involves large data sets and complex analytic workflows involving…
Most bioinformatics pipelines consist of software components that are tightly coupled to the logic of the pipeline itself. This limits reusability of the individual components in the pipeline or introduces maintenance overhead when they…
We argue for the need for a new generation of data science solutions that can democratize recent advances in data engineering and artificial intelligence for non-technical users from various disciplines, enabling them to unlock the full…
With recent advances in graphical user interfaces, more and more tasks on computers have become easier to perform. Out of the belief that creating computer programs can also be one of them, visual programming languages (VPLs) have emerged.…
When developing a (web) interface for a deductive database, functionality required by the client is provided by means of HTTP handlers that wrap the logical data access predicates. These handlers are responsible for converting between…
Recently proposed modifications of the standard particle-in-cell (PIC) method resolve long-standing limitations such as exact preservation of physically conserved quantities and unbiased ensemble down-sampling. Such advances pave the way…
Generative Programming (GP) is a computing paradigm allowing automatic creation of entire software families utilizing the configuration of elementary and reusable components. GP can be projected on different technologies, e.g.…
Effective cyber threat recognition and prevention demand comprehensible forecasting systems, as prior approaches commonly offer limited and, ultimately, unconvincing information. We introduce Simplified Plaintext Language (SPLAIN), a…
Summary: The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make modeling simpler, but largely exclude users from the process. We present an…
The Starlink Tables Infrastructure Library Tool Set (STILTS) is a powerful suite for astronomical data analysis, particularly useful when dealing with large datasets. However, like other software suites in astronomy its comprehensive syntax…
Biosciences have been revolutionized by next generation sequencing (NGS) technologies in last years, leading to new perspectives in medical, industrial and environmental applications. And although our motivation comes from biosciences, the…
MuSim is a new user-friendly program designed to interface to many different particle simulation codes, regardless of their data formats or geometry descriptions. It presents the user with a compelling graphical user interface that includes…
We describe how Python can be leveraged to streamline the curation, modelling and dissemination of drug discovery data as well as the development of innovative, freely available tools for the related scientific community. We look at various…
With more and more digital media, especially in the field of virtual reality where detailed and convincing scenes are much required, procedural scene generation is a big helping tool for artists. A problem is that defining scene…