Model integration in computational biology: the role of reproducibility, credibility and utility
During the COVID-19 pandemic, mathematical modeling of disease transmission has
become a cornerstone of key state decisions. To advance the state-of-the-art host viral …
become a cornerstone of key state decisions. To advance the state-of-the-art host viral …
[PDF][PDF] Neuroscience Cloud Analysis As a Service: An open-source platform for scalable, reproducible data analysis
A key aspect of neuroscience research is the development of powerful, general-purpose
data analyses that process large datasets. Unfortunately, modern data analyses have a …
data analyses that process large datasets. Unfortunately, modern data analyses have a …
Learning from reproducing computational results: introducing three principles and the Reproduction Package
We carry out efforts to reproduce computational results for seven published articles and
identify barriers to computational reproducibility. We then derive three principles to guide the …
identify barriers to computational reproducibility. We then derive three principles to guide the …
Practical resources for enhancing the reproducibility of mechanistic modeling in systems biology
Although reproducibility is a core tenet of the scientific method, it remains challenging to
reproduce many results. Tiwari et al. recently found that they could only repeat 50% of …
reproduce many results. Tiwari et al. recently found that they could only repeat 50% of …
Reproducibility in computing research: An empirical study
In computing, research findings are often anecdotally faulted for not being reproducible.
Numerous empirical studies have analyzed the reproducibility of a variety of research. Our …
Numerous empirical studies have analyzed the reproducibility of a variety of research. Our …
CSDMS: a community platform for numerical modeling of Earth surface processes
Computational modeling occupies a unique niche in Earth and environmental sciences.
Models serve not just as scientific technology and infrastructure but also as digital containers …
Models serve not just as scientific technology and infrastructure but also as digital containers …
[PDF][PDF] Trust but verify: How to leverage policies, workflows, and infrastructure to ensure computational reproducibility in publication
This article distills findings from a qualitative study of seven reproducibility initiatives to
enumerate nine key decision points for journals seeking to address concerns about the …
enumerate nine key decision points for journals seeking to address concerns about the …
For long-term sustainable software in bioinformatics
LP Coelho - PLOS Computational Biology, 2024 - journals.plos.org
Research software has become essential in science, including in the life sciences [1, 2].
Most of this software is designed and built by research groups funded by short-term research …
Most of this software is designed and built by research groups funded by short-term research …
[PDF][PDF] Model integration in computational biology: the role of reproducibility, credibility and utility. Front
During the COVID-19 pandemic, mathematical modeling of disease transmission has
become a cornerstone of key state decisions. To advance the state-of-the-art host viral …
become a cornerstone of key state decisions. To advance the state-of-the-art host viral …
How to Sustain a Scientific Open-Source Software Ecosystem: Learning from the Astropy Project
Scientific open-source software (OSS) has greatly benefited research communities through
its transparent and collaborative nature. Given its critical role in scientific research, ensuring …
its transparent and collaborative nature. Given its critical role in scientific research, ensuring …