Related papers: Reproducible research using biomodels
We present ReproducedPapers.org: an open online repository for teaching and structuring machine learning reproducibility. We evaluate doing a reproduction project among students and the added value of an online reproduction repository among…
Reproducibility is an important requirement in evolutionary computation, where results largely depend on computational experiments. In practice, reproducibility relies on how algorithms, experimental protocols, and artifacts are documented…
A common concern in experimental research is the auditability and reproducibility of experiments. Experiments are usually designed, provisioned, managed, and analyzed by diverse teams of specialists (e.g., researchers, technicians and…
Integrative biological simulations have a varied and controversial history in the biological sciences. From computational models of organelles, cells, and simple organisms, to physiological models of tissues, organ systems, and ecosystems,…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
Data makes science possible. Sharing data improves visibility, and makes the research process transparent. This increases trust in the work, and allows for independent reproduction of results. However, a large proportion of data from…
Security especially in the fields of IoT, industrial automation and critical infrastructure is paramount nowadays and a hot research topic. In order to ensure confidence in research results they need to be reproducible. In the past we…
With the rise of computers, simulation models have emerged beside the more traditional statistical and mathematical models as a third pillar for ecological analysis. Broadly speaking, a simulation model is an algorithm, typically…
The objective of this short report is to reconsider the subject of bioinformatics as just being a tool of experimental biological science. To do that, we introduce three examples to show how bioinformatics could be considered as an…
One of the main properties of biological systems is modularity, which manifests itself at all levels of their organization, starting with the level of molecular genetics, ending with the level of whole organisms and their communities. In a…
We advocate the use of qualitative models in the analysis of large biological systems. We show how qualitative models are linked to theoretical differential models and practical graphical models of biological networks. A new technique for…
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various…
Biological organisms adapt to changes by processing informations from different sources, most notably from their ancestors and from their environment. We review an approach to quantify these informations by analyzing mathematical models of…
In the data science courses at the University of British Columbia, we define data science as the study, development and practice of reproducible and auditable processes to obtain insight from data. While reproducibility is core to our…
When deployed in the wild, machine learning models are usually confronted with data and requirements that constantly vary, either because of changes in the generating distribution or because external constraints change the environment where…
Small to medium-scale data science experiments often rely on research software developed ad-hoc by individual scientists or small teams. Often there is no time to make the research software fast, reusable, and open access. The consequence…
Generative diffusion models showed high success in many fields with a powerful theoretical background. They convert the data distribution to noise and remove the noise back to obtain a similar distribution. Many existing reviews focused on…
Morphogenesis of complex body shapes is reproducible despite the noise inherent in the underlying morphogenetic processes. However, how these morphogenetic processes work together to achieve this reproducibility remains unclear. Here, we…
One way to investigate the precision of estimates likely to result from planned experiments and planned epidemiological studies is to simulate a large number of possible outcomes and analyse the sets of possible results. This appears to be…
As part of the investigation done by the IEEE Standards Association P2957 Working Group, called Big Data Governance and Metadata Management, the use of persistent identifiers (PIDs) is looked at for tackling the problem of reproducible…