Related papers: ShinyCOPASI: a web-based exploratory interface for…
The development of applications for obtaining interpretable results in a simple and summarized manner in multi-state models is a research field with great potential, namely in terms of using open source tools that can be easily implemented…
The use of Shiny in research publications is investigated. From the appearance of this popular web application framework for R through to 2018, it has been utilised in many diverse research areas. While it can be shown that the complexity…
$\chi$iplot is an HTML5-based system for interactive exploration of data and machine learning models. A key aspect is interaction, not only for the interactive plots but also between plots. Even though $\chi$iplot is not restricted to any…
Statistical Shape Models of faces and various body parts are heavily used in medical image analysis, computer vision and visualization. Whilst the field is well explored with many existing tools, all of them aim at experts, which limits…
SkyPy is an open-source Python package for simulating the astrophysical sky. It comprises a library of physical and empirical models across a range of observables and a command-line script to run end-to-end simulations. The library provides…
Animal cells are both encapsulated and subdivided by lipid bilayer membranes. Beyond just acting as boundaries, these membranes' shapes influence the function of cells and their compartments. Physically, membranes are two-dimensional fluids…
There are high technological and software demands associated with conducting brain-computer interface (BCI) research. In order to accelerate the development and accessibility of BCI, it is worthwhile to focus on open-source and desired…
We present RKappa, a framework for the development and analysis of rule-based models within a mature, statistically empowered R environment. The infrastructure allows model editing, modification, parameter sampling, simulation, statistical…
Simulation is a foundational tool for the analysis and testing of cyber-physical systems (CPS), underpinning activities such as algorithm development, runtime monitoring, and system verification. As CPS grow in complexity and scale,…
This preprint presents a web app (essentially a web page-based program) with which two or more users (peers) can view and handle 3D molecular structures in a concurrent, interactive way through their web browsers. This means they can share…
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 Visual Physics Analysis (VISPA) project defines a toolbox for accessing software via the web. It is based on latest web technologies and provides a powerful extension mechanism that enables to interface a wide range of applications.…
RKappa is a framework for the development, simulation and analysis of rule-base models within the mature statistically empowered R environment. It is designed for model editing, parameter identification, simulation, sensitivity analysis and…
Despite recent advances in natural language processing, many statistical models for processing text perform extremely poorly under domain shift. Processing biomedical and clinical text is a critically important application area of natural…
Modern power systems are increasingly evolving Cyber-Physical Systems (CPS) that feature close interaction between Information and Communication Technology (ICT), physical and electrical devices, and human factors. The interactivity and…
Integrated information theory provides a mathematical framework to fully characterize the cause-effect structure of a physical system. Here, we introduce PyPhi, a Python software package that implements this framework for causal analysis…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
The chemical reaction network (CRN) is a widely used formalism to describe macroscopic behavior of chemical systems. Available tools for CRN modelling and simulation require local access, installation, and often involve local file storage,…
Background. Effectively communicating complex statistical model outputs is a major challenge in public health. This study introduces the FARSI approach (Fast, Accessible, Reliable, Secure, Informative) as a framework to enhance the…
Computational methods are driving high impact microscopy techniques such as ptychography. However, the design and implementation of new algorithms is often a laborious process, as many parts of the code are written in close-to-the-hardware…