Related papers: ShinyCOPASI: a web-based exploratory interface for…
RidePy enables fast computer simulations of on-demand mobility modes such as ridehailing or ridepooling. It strongly focuses on modeling the mobility service itself, rather than its customers or the environment. Through a combination of…
Modular programming is a development paradigm that emphasizes self-contained, flexible, and independent pieces of functionality. This practice allows new features to be seamlessly added when desired, and unwanted features to be removed,…
We introduce RuleVis, a web-based application for defining and editing "correct-by-construction" executable rules that model biochemical functionality, which can be used to simulate the behavior of protein-protein interaction networks and…
It is necessary to improve the concepts of the present web based graphical user interface for the development of more flexible and intelligent interface to provide ease and increase the level of comfort at user end like most of the desktop…
While many students now interact with web apps across a variety of smart devices, the vast majority of our Nifty Assignments still present traditional user interfaces such as console input/output and desktop GUI. In this tutorial session,…
COnstraint-Based Reconstruction and Analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental data and quantitative prediction of physicochemically and biochemically feasible phenotypic states. The…
Shape complementarity of molecular surfaces at the interfaces is a well-known characteristic of protein-protein binding regions, and it is critical in influencing the stability of the complex. Measuring such complementarity is at the basis…
Building and maintaining knowledge about specific interface technologies is a challenge. Current solutions include standard file-based document repositories, wikis, and other online tools. However, these solutions are often only available…
Microbial networks, representing microbes as nodes and their interactions as edges, are crucial for understanding community dynamics in various environments. Analyzing microbiome networks is crucial for identifying keystone taxa that play…
Cormas is an agent-based simulation platform developed in the late 90s by the Green research at CIRAD unit to support the management of natural resources and understand the interactions between natural and social dynamics. This platform is…
PolyMAPS is an open-source library that helps researchers to initialize LAMMPS molecular dynamics simulations. It introduces an integrated workflow by combining preparation, launching, visualization, and analysis into a single Jupyter…
Flaky tests obstruct software development, and studying and proposing mitigations against them has therefore become an important focus of software engineering research. To conduct sound investigations on test flakiness, it is crucial to…
Major advancements in fields as diverse as biology and quantum computing have relied on a multitude of microscopic techniques. All optical, electron and scanning probe microscopy advanced with new detector technologies and integration of…
Research software plays a crucial role in advancing scientific knowledge, but ensuring its sustainability, maintainability, and long-term viability is an ongoing challenge. To address these concerns, the Sustainable Research Software…
We present the ALPS (Algorithms and Libraries for Physics Simulations) project, an international open source software project to develop libraries and application programs for the simulation of strongly correlated quantum lattice models…
PoPPy is a Point Process toolbox based on PyTorch, which achieves flexible designing and efficient learning of point process models. It can be used for interpretable sequential data modeling and analysis, e.g., Granger causality analysis of…
In this paper, we present a novel research software, called PEGASE, suitable for the design, validation and deployment of advanced control strategies for complex multi-domain energy systems. PEGASE especially features a highly efficient…
Motivation: The rapid growth of biological data has intensified the need for transparent, reproducible, and well-documented computational workflows. The ability to clearly connect the steps of a workflow in the code with their description…
Species distribution models (SDMs) are one of the most common statistical methods to assess species occupancy and geographic distribution patterns. With the increasing complexity of ecological data, many methodological approaches have been…
We present Conedy, a performant scientific tool to numerically investigate dynamics on complex networks. Conedy allows to create networks and provides automatic code generation and compilation to ensure performant treatment of arbitrary…