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The Research Informatics Small Research Facility sits within the Centre for Medicines Discovery (CMD) and provides data management, research computing and computational chemistry expertise. With over 16 years of experience providing solutions and expertise within the Structural Genomics Consortium (SGC), we support CMD research within Oxford as well as within research organisations around the world including large-scale multi-national consortia in early-stage drug discovery pipelines. We are able to provide customised support for your informatics and data management needs with rapid, and often bespoke, solutions and support.

How we can help You

  • End to end data management for protein production, small molecule identification, structural and chemical biology, using the Laboratory Information Management Systems (LIMS), Scarab
  • Research computing expertise and solutions, particularly in the structural biology space
  • Target informatics, supporting early decision-making processes
  • Web application development, providing bespoke solutions for data capture, analysis and dissemination
  • Computational chemistry software and expertise, supporting small molecule design and optimisation in chemical biology campaigns
  • IT infrastructure expertise for the design and implementation of scalable and efficient platforms to support data management and informatics needs

Contact Information

Please contact us via risrf@cmd.ox.ac.uk to discuss your needs.

Notable Achievements

  • ELISALIMSELISALIMSDesign, build and stand-up of a bespoke LIMS platform (‘ELISALIMS’) to support the University’s high-throughput ELISA serology platform for SARS-CoV-2 pandemic testing [1]. We completed the work for ELISALIMS within 6 weeks from initial design and continue to support and develop the platform
  • Provision of comprehensive end-to-end data management platform and support to the COMBAT SARS-CoV-2 broad phenotyping consortium. This included implementing policies, identifier systems, sample tracking solutions and dataset tracking

 

 

  • Scarab web platformScarab web platformRapid implementation of data management solutions to support the multi-national EU/IMI EUbOPEN project. Capture, deposition and dissemination of broad data types from a highly federated structural and chemical biology programme in the UK, EU, USA and Canada [2,3]
  • Development of custom visualisation solutions [4-6] to support data dissemination for human proteome-scale business intelligence.  ChromoHub and UbiHub’s web interfaces are powered by our technology

 

 

  • Michelanglo platformMichelanglo platformDefined and drove a new way of presenting structural biology data to non-structural biologists. The iSee platform [7-10] pioneered the interactive visualisation of protein structures contextualised by mini papers. This has been further developed into a contemporary platform, Michelanglo [11]
  • Design, build and support of the CMD’s IT and research computing platforms, ensuring that IT ‘just works’ and enables the science of the CMD and the SRF’s customers

 

 

These are a small handful of successes in recent years and reflect the diversity in expertise and capabilities at many different scales and breadths of data that we offer.

References

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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