Open Research across Disciplines

How the principles of open research can be applied to your discipline

Computational Modelling

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Case Studies

UKRN case study: Computational models to help understand psychological identities, and intra- and inter-group processes

University of Reading case study: an open monitoring and decision support tool which helps stakeholders in the African agricultural and financial
sectors assess the potential impact of adverse weather on agriculture

University of Reading case study: Open source modelling of the Sun’s winds

Examples of open research practices

Open Methods: Nousias, Zacharaki and Moustakas (2020) present AVATREE (https://gitlab.com/LungModelling/avatree), an open-source toolbox in C++ which is a computational modelling framework that generates Anatomically Valid Airway Tree conformations that allows simulations on broncho-constriction in obstructive pulmonary conditions (https://doi.org/10.1371/journal.pone.0230259). It also allows visualisation of spatial probability maps for airway generations projected on CT imaging data and airway tree based on local structure properties. It can be used to simulate broncho-constrictions apparent in pulmonary diseases such as asthma with the aim of improving clinical decision making.

Resources

General Resources

Open research course. https://git.fmrib.ox.ac.uk/open-science/computational-models-course
Standards and best practices. https://blogs.scientificamerican.com/the-curious-wavefunction/computational-research-in-the-era-of-open-access-standards-and-best-practices/
Introduction to computational reproducibility. https://hal.inria.fr/hal-01358082/document
Tips for reproducible computational workflows. https://scicomp.aalto.fi/scicomp/zen-of-scicomp/
The Practice of Reproducible Research, Case Studies and Lessons from the Data-Intensive Sciences. http://www.practicereproducibleresearch.org/

Open Methods

Collection of resources. https://www.comses.net/
Guidelines for modelling and simulation. https://ieeexplore.ieee.org/document/8247813

Open Data

Stodden, V., Leisch, F., and Peng, R. D., editors. (2014), Implementing Reproducible Research, Boca Raton, FL: Chapman & Hall/CRC. https://osf.io/s9tya/wiki/home/
Modeling and simulation resources (standards, databases, data policies) registered in FAIRsharing: https://fairsharing.org/search?domains=Modeling%2520and%2520simulation

Open Outputs

Preprint repository. https://arxiv.org/

This page is adapted and extended from: Farran, E. K., Silverstein, P., Ameen, A. A., Misheva, I., & Gilmore, C. (2020, December 15). Open Research: Examples of good practice, and resources across disciplines. https://doi.org/10.31219/osf.io/3r8hb