I’m Justin Clark-Casey, a research software architect at the University of Cambridge in the UK. I work on InterMine, a life sciences data integration platform and various side projects such as Buzzbang, an open-source and (as yet) extremely, extremely alpha prototype search engine for life sciences data.
I’m very interested in:
- Knowledge graphs (as used by Google, Microsoft, Wikipedia, etc.) as used in science and elsewhere.
- Open Linked Data, RDF, SPARQL, ontologies and other aspects of knowledge bases.
- Data integration in the life sciences.
- AI and machine learning, especially over knowledge graphs and linked data.
- Increased digitization of science, particularly the life sciences. This encompasses initiatives such as
- Making data FAIR (Findable, Accessible, Interoperable and Reuseable)
- Standardized workflow languages that can capture the scientific process and improve reproducibility of scientific results
- Increasing use of cloud infrastructure to accelerate and democratize scientific research.
Please don’t hesitate to hit up my Twitter or e-mail if you want to chat or collaborate on any of these topics.
I’m also active in:
ELIXIR, a distributed infrastructure for life-science information with resources across Europe. Here, I’m the ELIXIR UK node technical co-ordinator, helping the 15 member organizations of ELIXIR UK (including Imperial College and the universities of Cambridge, Oxford and Manchester) to co-ordinate their technical strategy for interoperability, data and computation across the bioinformatics infrastructure.
Bioschemas, an initiative to embed schema.org markup (as sponsored by search engines such as Google and Microsoft) in webpages and to use it to make it easier to find life sciences data in the long tail of databases.
Again, please don’t hesitate to contact me if you’d like to talk about those organizations.
Finally, in a previous life I was heavily involved with virtual-worlds, being a core developer, conference co-chair, consultant and release manager for OpenSimulator, an open-source Second Life compatible Internet-scale distributed virtual worlds implementation. This was developed by tremendous group of volunteers, along with involvement from startups, universities and large companies such as IBM and Intel. I don’t work in this area anymore but if you have questions about history or maybe just want to reminisce then please tweet me :).
- Justin Clark-Casey. Life sciences data needs to be FAIR, 2018
- Göksel Misirli, Curtis Madsen, Iñaki Sainz de Murieta, Matthieu Bultelle, Keith Flanagan, Matthew Pocock, Jennifer Hallinan, James Alastair McLaughlin, Justin Clark-Casey, Mike Lyne, Gos Micklem, Guy-Bart Stan, Richard Kitney, Anil Wipat. Constructing Synthetic Biology Workflows in the Cloud in Engineering Biology, vol. 1, no. 1, pp. 61-65, 6 2017. doi: 10.1049/enb.2017.0001
- Maxime Déraspe, Gail Binkley, Daniela Butano, Matthew Chadwick, J. Michael Cherry, Justin Clark-Casey, Sergio Contrino, Jacques Corbeil, Josh Heimbach, Kalpana Karra, Rachel Lyne, Julie Sullivan, Yo Yehudi, Gos Micklem, and Michel Dumontier. Making Linked Data SPARQL with the InterMine Biological Data Warehouse in Proceedings of the 9th International Conference Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2016), Amsterdam, The Netherlands, December 5-8, 2016.
- Justin Clark-Casey. Transferring a Virtual Environment Client Session between Independent Opensimulator Installations, 2013 5th International Conference on Games and Virtual Worlds for Serious Applications (VS-GAMES), Poole, 2013, pp. 1-3.
- Justin Clark-Casey. Scaling OpenSimulator :An Examination of Possible Architectures for an Internet-Scale Virtual Environment Network, Oxford University MSc Software Engineering Thesis 2010.
- FLOSS Weekly 72, OpenSimulator, TWiT podcast
e-mail: justincc AT justincc.org