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

  • Life sciences dataset. https://www.nature.com/sdata/
  • UK Biobank. https://www.ukbiobank.ac.uk/
  • GenBank: an annotated collection of publicly available genetic sequences, maintained by the National Centre for Biotechnology Information (NCBI). https://www.ncbi.nlm.nih.gov/genbank/
  • Biology resources (standards, databases, data policies) registered in FAIRsharing: https://fairsharing.org/browse/subject?term=Biology
  • The FAIR Cookbook is a collection of birds-eye view recipes on the FAIR components, the infrastructure needed, and a set of applied examples in the Life Sciences, offering a deep dive in technical aspects of FAIR data management. This is a ‘live resource’, because recipes are added and improved, collaboratively and iteratively, in an open manner. The objective of the FAIR Cookbook is to develop and disseminate guidance and processes needed to make and keep data FAIR in the Life Sciences. https://faircookbook.elixir-europe.org

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