Research Informatics

As an integral member of the CMD, our group provides comprehensive data management across all stages of the institute’s research and supports CMD Pillars. Our bespoke, highly customised Scarab laboratory information management system (LIMS) streamlines data capture through CMD’s drug discovery research pipeline, from protein production and purification to structural and chemical biology. We are dedicated to the development of advanced databases, sophisticated software solutions, and intuitive web applications that meet evolving research. We continuously enhance our IT infrastructure to ensure robust, scalable and reliable solutions to meet growing research demands.

A part of the Research Informatics group operates also as a Small Research Facility (RI SRF) extending its comprehensive services beyond the CMD. By leveraging our expertise in informatics, we deliver tailored solutions that enhance research efficiency and productivity. For more information about our services, please visit our Platform website.

example projects and tools

• Implementation of data management solutions to support the multi-national EU/IMI EUbOPEN Consortium. End-to-end capture, deposition and dissemination of broad data types from a highly federated structural and chemical biology programme in the UK, EU, USA and Canada [1,2] More information: EUbOPEN
• Design a robust and bespoke data management solution that support protein production, structural biology processes and capture lead optimisation data from the AI-driven Structure-enabled Antiviral Platform (ASAP) AViDD Center, funded by National Institute of Allergy and Infectious Diseases (NIH-NIAID) in order to facilitate seamless integration and data sharing publicly with the broader scientific community. More information:  ASAP Discovery Consortium, Antiviral Drug Discovery (AViDD) Centers for Pathogens of Pandemic Concern
• TargetDB is a powerful tool designed to streamline the process of querying multiple publicly available databases in order to provide an integrated view of all information related to potential drug targets. TargetDB is continuously developed in collaboration with the Alzheimer’s Research UK Oxford Drug Discovery Institute. [3]
• Web application development to support Professional Services’ workflows within the Nuffield Department of Medicine, University of Oxford
• Clinical data management using tailored solutions to assist data analysis in Cartography project, including harmonisation and visualisation of diverse clinical metadata. More information: Oxford-Janssen Cartography Collaboration
• REDCap data management for multiple clinical trials and studies.
• Data management to support the drug discovery pipeline at the Alzheimer's Research UK Oxford Drug Discovery Institute.

Notable achievements

• Design, build and stand-up of a bespoke LIMS platform (‘ELISALIMS’) to support the UK Government/ONS’s COVID-19 Surveillance programme involving high-throughput ELISA serology platform for SARS-CoV-2 pandemic testing [4]. We completed the work for ELISALIMS within 6 weeks from initial design and provided end-to-end data management from sample acquisition through analysis, QC and delivery on a daily basis to ONS & IQVIA.
• Provision of data unified sample management and data warehouse platform to support to the COMBAT multi-omic blood atlas consortium [5]. This enabled over a hundred researchers from 20 different university departments to work on the same data at the same time in the same place.
• Development of custom visualisation solutions [6-8] to support structural biology data dissemination at the human proteome-scale.  ChromoHub and UbiHub’s web interfaces are powered by our technology.Defined and drove a new way of presenting structural biology data to non-structural biologists. The iSee platform [9-12] pioneered the interactive visualisation of protein structures contextualised by mini papers and was adopted by a number of journals. This has been further developed into a contemporary platform, Michelanglo [13] and VENUS [14].

references

1. Damerell, D., Strain-Damerell, C., Garsot, S., Joyce, S., Barrett, P., & Marsden, B. (2018). SATurn: A modular bioinformatics framework for the design of robust maintainable web-based and standalone applications. Bioinformatics, 35(2), 349-351. doi:10.1093/bioinformatics/bty549
2. Liu, L., Damerell, D., Koukouflis, L., Tong, Y., Marsden, B., & Schapira, M. (2019). UbiHub: a data hub for the explorers of ubiquitination pathways. Bioinformatics, 35(16), 2882-2884. doi:10.1093/bioinformatics/bty1067
3. Stephane De Cesco, John B. Davis, Paul E. Brennan (2020). TargetDB: A target information aggregation tool and tractability predictor. PLoS ONE 15(9): e0232644. doi:10.1371/journal. pone.0232644
4. Lumley, S. F., O'Donnell, D., Stoesser, N. E., Matthews, P. C., Howarth, A., Hatch, S. B., . . . Walker, A. S. (2020). Antibody Status and Incidence of SARS-CoV-2 Infection in Health Care Workers.. The New England journal of medicine. doi:10.1056/nejmoa2034545
5. Covid-19 Multi-omics Blood ATlas (COMBAT) Consortium (2022), A blood atlas of COVID-19 defines hallmarks of disease severity and specificity. Cell 185, 916–938. doi:10.1016/j.cell.2022.01.012
6. Liu, L., Zhen, X. T., Denton, E., Marsden, B. D., & Schapira, M. (2012). ChromoHub: a data hub for navigators of chromatin-mediated signalling.. Bioinformatics, 28(16), 2205-2206. doi:10.1093/bioinformatics/bts340
7. Deane, C., Marsden, B. D., Wall, I. D., Green, D. V. S., & Bradley, A. R. (2017). WONKA and OOMMPPAA – analysis of protein-ligand interaction data to direct Structure Based Drug Design. Acta Crystallographica Section D: Biological Crystallography, D73, 279-285. doi:10.1107/S2059798316009529
8. Wang, M., Mok, M. W., Harper, H., Lee, W. H., Min, J., Knapp, S., . . . Schapira, M. (2010). Structural genomics of histone tail recognition.. Bioinformatics, 26(20), 2629-2630. doi:10.1093/bioinformatics/btq491
9. Marsden, B. D., Abagyan, R., & Lee, W. H. (2011). Visualisation and efficient communication in structure-based lead discovery. Unknown Journal, 176-189. doi:10.2174/978160805142711101010176
10. Lee, W. H., Yue, W. W., Raush, E., Totrov, M., Abagyan, R., Oppermann, U., & Marsden, B. D. (2011). Interactive JIMD articles using the iSee concept: Turning a new page on structural biology data. Journal of Inherited Metabolic Disease, 34(3), 565-567. doi:10.1007/s10545-011-9334-4
11. Lee, W. H., Atienza-Herrero, J., Abagyan, R., & Marsden, B. D. (2009). SGC--structural biology and human health: a new approach to publishing structural biology results.. PLoS One, 4(10), e7675. doi:10.1371/journal.pone.0007675
12. Raush, E., Totrov, M., Marsden, B. D., & Abagyan, R. (2009). A new method for publishing three-dimensional content. PLoS ONE, 4(10). doi:10.1371/journal.pone.0007394
13. Ferla, M. P., Pagnamenta, A. T., Damerell, D., Taylor, J. C., & Marsden, B. D. (2020). MICHELANGLo: sculpting protein views on web pages without coding. Bioinformatics, 36(10), 3268-3270. doi:10.1093/bioinformatics/btaa104
14. Matteo P. Ferla, Alistair T. Pagnamenta, Leonidas Koukouflis, Jenny C. Taylor and Brian D. Marsden (2022). Venus: Elucidating the Impact of Amino Acid Variants on Protein Function Beyond Structure Destabilisation. Journal of Molecular Biology, 434, 167567. doi: 10.1016/j.jmb.2022.167567