Related papers: ShinyCOPASI: a web-based exploratory interface for…
The linked micromaps approach was originally developed as an improvement to choropleth maps for displaying statistical summaries connected with spatial areal units, such as countries, states, and counties. Two R packages to create linked…
We introduce the Piquasso quantum programming framework, a full-stack open-source software platform for the simulation and programming of photonic quantum computers. Piquasso can be programmed via a high-level Python programming interface…
Astronomy and cosmology have embraced the internet. We routinely and successfully use the internet as a repository for sharing code, publications and information, and as a computational resource. However the interactive nature of the web,…
Liquid Chromatography Mass Spectrometry (LC-MS) is an indispensable analytical technique in proteomics, metabolomics, and other life sciences. While OpenMS provides advanced open-source software for MS data analysis, its complexity can be…
In recent years, tremendous effort has been spent to modernizing communication infrastructure in Cyber-Physical Systems (CPS) such as Industrial Control Systems (ICS) and related Supervisory Control and Data Acquisition (SCADA) systems.…
Summary: heatmaply is an R package for easily creating interactive cluster heatmaps that can be shared online as a stand-alone HTML file. Interactivity includes a tooltip display of values when hovering over cells, as well as the ability to…
An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers a highly interactive visualization and…
Motivation: Omics data, such as transcriptomics or phosphoproteomics, are broadly used to get a snap-shot of the molecular status of cells. In particular, changes in omics can be used to estimate the activity of pathways, transcription…
We have built an open-source software system for the modeling of biomolecular reaction networks, SloppyCell, which is written in Python and makes substantial use of third-party libraries for numerics, visualization, and parallel…
The SunPy Project is a community of scientists and software developers creating an ecosystem of Python packages for solar physics. The project includes the sunpy core package as well as a set of affiliated packages. The sunpy core package…
Determining molecular abundances in astrophysical environments is crucial for interpreting observational data and constraining physical conditions in these regions. Chemical modelling tools are essential for simulating the complex processes…
A recent study showed that more than 70% of researchers fail to reproduce their peers's experiments and more than half fail to reproduce their own experiments. Obviously, from a perspective of scientific quality this is a more than…
Motivated by the need to emulate workload execution characteristics on high-performance and distributed heterogeneous resources, we introduce Synapse. Synapse is used as a proxy application (or "representative application") for real…
Advances in computational chemistry have produced high-dimensional datasets on atmospherically relevant molecules. To aid exploration of such datasets, particularly for the study of atmospheric aerosol formation, we introduce PhiPlot: a…
In many scenarios, such as emergency response or ad hoc collaboration, it is critical to reduce the overhead in integrating data. Ideally, one could perform the entire process interactively under one unified interface: defining extractors…
We present an overview of Sherpa, an open source Python project, and discuss its development history, broad design concepts and capabilities. Sherpa contains powerful tools for combining parametric models into complex expressions that can…
Network data mining has become an important area of study due to the large number of problems it can be applied to. This paper presents NOESIS, an open source framework for network data mining that provides a large collection of network…
The ability to quantify stochastic fluctuations present in biochemical and other systems is becoming increasing important. Analytical descriptions of these fluctuations are attractive, as stochastic simulations are computationally…
astroquery is a collection of tools for requesting data from databases hosted on remote servers with interfaces exposed on the internet, including those with web pages but without formal application program interfaces (APIs). These tools…
We introduce Synapse motivated by the needs to estimate and emulate workload execution characteristics on high-performance and distributed heterogeneous resources. Synapse has a platform independent application profiler, and the ability to…