About Me, work, projects and other.

High-throughput sequencing

Currently working on high-throughput sequencing at the Center for Genomics Research at Liverpool. We have multiple machines, HiSeqs, MiSeqs, MinIon and PacBio, with a dedicated team of people working on sample preparation and running the machines. Another dedicated team works on the bioinformatics and myself who does bioinformatics but spends most of the time dealing with everything between bioinformatics, the running of the machines and the compute hardware. This involves planning and implementing hardware changes, writing and configuring software and infrastructure and various scripting for the integration of machines and monitoring of machines, their processes and their status.



Besides the above biological projects, I am knowledgable on the subjects of software development, Linux (configuration, admin and customisation to the point of writing kernel modules), TCP/IP networking, electronic design, Wifi security and VoIP (mostly Asterisk and SIP). As a result, quite a few large and small projects have been documented over the years, with many undocumented and lingering in a directory. All recent projects now have an entry, and those that need it have their own page(s).

Of special interest is sshdfilter, a heuristic blocker of ssh brute force attacks.

The original (and very dated) home page lists some personal projects and personal thoughts from many years ago, when it was the fashion to have a web page.


Previous work

Previous work was in Individual Based Models, computer based simulations of bacterial evolution. The first was COSMIC, based on evolving gene interactions.That turned out to be far too computationally intensive to be practical at the time, and for many years to come. The second was COSMIC-Rules, that simplified the interactions enough to be realistically computable,  which lead to demonstrating a striking likeness to realistic situations.



Gregory, R., Darby, A.C., Irving, H., Coulibaly, M.B., Hughes, M., Koekemoer, L.L., Coetzee, M., Ranson, H., Hemingway, J., Hall, N. and Wondji, C.S., (2011). A de novo expression profiling of Anopheles funestus, malaria vector in Africa, using 454 pyrosequencing. PLoS One, e17418.

Gregory, R., Saunders, J.R., and Saunders, V.A., (2010). Rule-based simulation of temperate bacteriophage infection: restriction-modification as a limiter to infection in bacterial populations. BioSystems, 100, 166-177.

Gregory, R., Saunders, J.R., and Saunders, V.A., (2008). Rule-based modelling of conjugative plasmid transfer and incompatibility. BioSystems. 91, 201-215.

Gregory, R., Saunders, V.A., Saunders, J.R., (2007). Rule-based Computing System of Microbial Interactions and Communications : Evolution in virtual bacterial populations. BioSystems, 91, 216-230.

Gregory, R., Saunders, J.R. and Saunders V.A., (2006). The Paton Individual Based Model legacy. Biosystems, 85, 45-54.

Gregory, R., Vlachos, C., Paton, R.C., Palmer, J.W., Wu, Q.H. and Saunders, J.R., (2004). Computing Bacterial Evolvability using Individual-based Models. In Molecular Computational Models: Unconventional Approaches. Gheorghe, M. (Ed.). Idea Group, Hershey, USA.

Paton, R.C., Gregory, R., Vlachos, C., Palmer, J.W., Saunders, J.R., Wu, Q.H. (2004). Evolvable Social Agents for Bacterial Systems Modelling. IEEE Nano Biosciences. 39 p.

Gregory, R., Paton, R.C., Saunders, J.R. and Wu, Q.H., (2004). A model of bacterial adaptability based on multiple scales of interaction, in Paton, R., Bolouri, H., Holcombe, M., Parish, J. H. and Tateson, R., (Eds.) Computation in Cells and Tissues Perspectives and Tools of Thought, Series in Natural Computing, Springer: Heidelberg.

Gregory, R., Paton, R.C., Saunders, J.R. and Wu, Q.H., (2004). Parallelising a model of bacterial interaction and evolution, Biosystems, 76, pp.121-131.

Gregory, R. (2004). COSMIC: A Model of Cellular Genetic Interaction and Evolution. Ph.D thesis. The University of Liverpool. 245 p.

Vlachos, C., Gregory, R., Paton, R.C., Saunders, J.R., Wu, Q.H. (2003). Individual-Based Modelling of Bacterial Ecologies and Evolution. Comparative & Functional Genomics. Vol. 5, 1, pp. 100-104.

Gregory, R. (2002) "An Individual Based Model for Simulating Bacterial Evolution", accepted contribution to Evolvability and Individuality Workshop, University of Hertfordshire, 18-20 September 2002

Gregory, R. Paton, R.C., Wu, Q.H. & Saunders, J.R. (2001), "Computing Microbial Interactions and Communications in Real Life", paper presented to 4th International Conference on Information Processing in Cells and Tissues (IPCAT), Leuven, August.

Gregory, R. (2001) "Computing Microbial Interactions and Communications", Invited talk to Department of Microbiology, University of Wales, Cardiff, July.