Related papers: One file to share them all: Using the COMBINE Arch…
The reproduction and replication of reported scientific results is a hot topic within the academic community. The retraction of numerous studies from a wide range of disciplines, from climate science to bioscience, has drawn the focus of…
Research collaborations are continuously emerging catalyzed by online platforms, where people can share their codes, calculations, data and results. These virtual research platforms are innovative, community oriented, flexible and secure as…
Information and data exchange is an important aspect of scientific progress. In computational materials science, a prerequisite for smooth data exchange is standardization, which means using agreed conventions for, e.g., units, zero base…
Replica Exchange (RE) simulations have emerged as an important algorithmic tool for the molecular sciences. RE simulations involve the concurrent execution of independent simulations which infrequently interact and exchange information. The…
The drive for reproducibility in the computational sciences has provoked discussion and effort across a broad range of perspectives: technological, legislative/policy, education, and publishing. Discussion on these topics is not new, but…
Energy system models have become indispensable tools for planning future energy systems by providing insights into different development trajectories. However, sustainable systems with high shares of renewable energy are characterized by…
Modern biomedical applications often involve time-series data, from high-throughput phenotyping of model organisms, through to individual disease diagnosis and treatment using biomedical data streams. Data and tools for time-series analysis…
Most particle induced X-ray emission (PIXE) data analysis codes are not focused on handling multilayered samples. We have developed an open-source library called "LibCPIXE", for PIXE data analysis. It is written in standard C and implements…
Computational biology continues to spread into new fields, becoming more accessible to researchers trained in the wet lab who are eager to take advantage of growing datasets, falling costs, and novel assays that present new opportunities…
The Open Knowledgebase of Interatomic Models (OpenKIM) project is a framework intended to facilitate access to standardized implementations of interatomic models for molecular simulations along with computational protocols to evaluate them.…
Recent advances in bioinformatics have made high-throughput microbiome data widely available, and new statistical tools are required to maximize the information gained from these data. For example, analysis of high-dimensional microbiome…
Neurophysiology research has demonstrated that it is possible and valuable to investigate sensory processing in scenarios involving continuous sensory streams, such as speech and music. Over the past 10 years or so, novel analytic…
Sharing research artifacts is known to help people to build upon existing knowledge, adopt novel contributions in practice, and increase the chances of papers receiving attention. In Model-Driven Engineering (MDE), openly providing research…
In the era of data-driven science, conducting computational experiments that involve analysing large datasets using heterogeneous computational clusters, is part of the everyday routine for many scientists. Moreover, to ensure the…
The Agent Based Model community has a rich and diverse ecosystem of libraries, platforms, and applications to help modelers develop rigorous simulations. Despite this robust and diverse ecosystem, the complexity of life from microbial…
Work in the Open Archives Initiative - Object Reuse and Exchange (OAI-ORE) focuses on an important aspect of infrastructure for eScience: the specification of the data model and a suite of implementation standards to identify and describe…
Scientific research relies on well-structured, standardized data; however, much of it is stored in formats such as free-text lab notebooks, non-standardized spreadsheets, or data repositories. This lack of structure challenges…
We introduce atomicrex, an open-source code for constructing interatomic potentials as well as more general types of atomic-scale models. Such effective models are required to simulate extended materials structures comprising many thousands…
A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine…
Biological and biomedical imaging datasets record the constitution, architecture and dynamics of living organisms across several orders of magnitude of space and time. Imaging technologies are now used throughout the life and biomedical…