Open Research across Disciplines

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

Biological Sciences

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Case Studies

UKRN case study: Quantitative biology and protein production in cells

University of Surrey case study: Training scientists to use genomics programs | University of Surrey

University of Glasgow case study: Research Data Management in Natural History

University of Reading case study: Building Open Lab Hardware to Tackle Antimicrobial Resistance (PDF, 175kB)

University of Manchester case study: WorkflowHub open registry for the life science community to openly share, find and reuse data processing pipelines

University of Sheffield case study: Dr Alice Pyne on DNA supercoiling and molecular recognition

Examples of open research practices

Open Data: Using and contributing to open data. Examples are reported in Table 1 of Feng et al. (2019), such as: “Species distribution records were collected from the Ocean Biogeographic Information System (OBIS; http://iobis.org, accessed February 2016), from the Global Biodiversity Information Facility (GBIF; http://gbif.org, accessed January 2016), the Reef Life Survey (RLS; http://reeflifesurvey.com, accessed February 2016) and for a few species via personal communications (Bosch et al., 2018).” (From Feng et al (2019). A checklist for maximizing reproducibility of ecological niche models. Nat Ecol Evol 3, 1382–1395. https://doi.org/10.1038/s41559-019-0972-5)

Open Data: Working alongside ‘Open Microscopy’, Glencoe Software have developed and adopted Open Microscopy Environment – Next-Generation File Formats (OME-NGFF). This is a new “Cloud-friendly data format for multi-D bioimaging data using… It has been designed from its inception to work with scalable, cloud-based data resources and for public or shared data repositories used for AI training and data publication. There are examples of using OME-NGFF for whole slide imaging (as in digital pathology), high content screening and 3D imaging of large tissue samples.”. (OME-NGFF in action;  Glencoe Software, Inc.)

Resources

General Resources

Open Methods

Open Data

Open Outputs

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