Dr Sebastian James
Department of Psychology
Research Associate
Full contact details
Department of Psychology
Cathedral Court
1 Vicar Lane
Sheffield
S1 2LT
- Profile
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I am one of the Psychology Department's computational researchers. Working in Stuart P. Wilson's group, I study the ontogeny of the brain. Ontogeny is the process by which an organism develops from inception to adulthood. It poses the question of how the complex structure that is an adult organism selforganises, instructed only by the genetic information stored in the DNA of the initial, fertilised egg cell. I try to imagine mechanisms by which this can be achieved and I write computer programs to express these ideas. In this sense, I am carrying out large, computerised thought experiments to find out how the patterning of biology can be achieved reliably (with all individuals looking the same) and how this process can be manipulated by evolutionary selection (thus, crossing over into the study of phylogeny).
The study of ontogeny in the brain is closely related to the general development of organisms. It is likely that some of the mechanisms that guide the generation of pattern and structure in the segmentation of the fly's body plan are reused to help arrange the functional organisation of the mammalian neocortex. Studying ontogeny in the context of brain development is important (and relevant within a Department of Psychology) because the way in which the brain develops is inextricably linked to the the way the brain is wired and the wiring of the brain has an important influence on the function of the brain.
This work is being carried out in collaboration with researchers in Leah Krubitzer's lab at the University of California, Davis, funded by the James S McDonnell Foundation.
I write most of my programs in the wonderfully expressive language, c++. Part of my work is developing and maintaining morphologica, a library of 'simulation support software' used by myself and other members of Stuart's lab. Morphologica can be found on github at https://github.com/ABRG-Models/morphologica.
Previously, I have worked with Sean Anderson in the Department of Automatic Control and Systems Engineering on the EU Dreams4Cars project (discovering that autonomous cars aren't going to be autonomous for a little while yet) and with Kevin Gurney, studying what it means to integrate computational models of sensory and neuromuscular control into a closed loop with a virtual world providing the sensory input (EU NoTremor project).
- Qualifications
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- MPhys (Hons), Physics, University of Manchester, 1996
- MS, Physics, Colorado State University, 1998
- PhD, Physics, The University of Cambridge, 2001
- Research interests
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Axonal and areal development of the brain, attention and learning, saccadic eye movements, numerical computation, high performance data visualization.
- Publications
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Show: Featured publications All publications
Featured publications
Journal articles
- Modelling the emergence of whisker barrels. eLife, 2020(9).
- Longitudinal vehicle dynamics : a comparison of physical and data-driven models under large-scale real-world driving conditions. IEEE Access, 8, 73714-73729. View this article in WRRO
- Limit cycle dynamics can guide the evolution of gene regulatory networks towards point attractors. Scientific Reports, 9(1). View this article in WRRO
- Building a Spiking Neural Network Model of the Basal Ganglia on SpiNNaker. IEEE Transactions on Cognitive and Developmental Systems, 10(3), 823-836. View this article in WRRO
- Integrating Brain and Biomechanical Models—A New Paradigm for Understanding Neuro-muscular Control. Frontiers in Neuroscience, 12, 1-33. View this article in WRRO
- Target-distractor synchrony affects performance in a novel motor task for studying action selection.. PLoS One, 12(5), e0176945-e0176945. View this article in WRRO
- SpineCreator: a Graphical User Interface for the Creation of Layered Neural Models.. Neuroinformatics, 15(1), 25-40. View this article in WRRO
All publications
Journal articles
- Comparing the development of cortex-wide gene expression patterns between two species in a common reference frame. Proceedings of the National Academy of Sciences, 119(41).
- Biological action at a distance: correlated pattern formation in adjacent tessellation domains without communication. PLoS Computational Biology, 18(3).
- Parallel prefix scan for the computation of axonal projection patterns in biological neural networks. Academia Letters. View this article in WRRO
- Modelling the emergence of whisker barrels. eLife, 2020(9).
- Linear system identification versus physical modeling of lateral-longitudinal vehicle dynamics. IEEE Transactions on Control Systems Technology. View this article in WRRO
- Longitudinal vehicle dynamics : a comparison of physical and data-driven models under large-scale real-world driving conditions. IEEE Access, 8, 73714-73729. View this article in WRRO
- Limit cycle dynamics can guide the evolution of gene regulatory networks towards point attractors. Scientific Reports, 9(1). View this article in WRRO
- Building a Spiking Neural Network Model of the Basal Ganglia on SpiNNaker. IEEE Transactions on Cognitive and Developmental Systems, 10(3), 823-836. View this article in WRRO
- Integrating Brain and Biomechanical Models—A New Paradigm for Understanding Neuro-muscular Control. Frontiers in Neuroscience, 12, 1-33. View this article in WRRO
- Target-distractor synchrony affects performance in a novel motor task for studying action selection.. PLoS One, 12(5), e0176945-e0176945. View this article in WRRO
- SpineCreator: a Graphical User Interface for the Creation of Layered Neural Models.. Neuroinformatics, 15(1), 25-40. View this article in WRRO
- Vortex pinning by magnetic order in ErNi2B2C. PHYSICAL REVIEW B, 63(6).
- Flux pinning, surface and geometrical barriers in YNi2B2C. Physica C: Superconductivity, 332(1-4), 173-177.
- Vortex Configurations, Matching, and Domain Structure in Large Arrays of Artificial Pinning Centers. Physical Review Letters, 88(6).
- Flux pinning mechanisms inErNi2B2C. Physical Review B, 64(9).
- Vortex pinning by magnetic order inErNi2B2C. Physical Review B, 63(6).
- Comparing cortex-wide gene expression patterns between species in a common reference frame.
Chapters
- Vortex Pinning and Dynamics in Magnetic and Non- Magnetic (RE)Ni2B2C Superconductors, Rare Earth Transition Metal Borocarbides (Nitrides): Superconducting, Magnetic and Normal State Properties (pp. 347-356). Springer Netherlands
Conference proceedings papers
- Linear System Identification of Longitudinal Vehicle Dynamics Versus Nonlinear Physical Modelling. Proceedings of 2018 UKACC 12th International Conference on Control (CONTROL) (pp 146-151), 5 September 2018 - 7 September 2018. View this article in WRRO
- Scanning Hall probe microscope images of field penetration into niobium films. Physica C: Superconductivity, Vol. 332(1-4) (pp 445-449)
Software / Code
- morphologica. Github
- Stalefish. Github Retrieved from https://snapcraft.io/stalefish
Preprints
- Target-distractor Synchrony Affects Performance in a Novel Motor Task
for Studying Action Selection, arXiv.
- Time to stop; agent-based modelling of chemoaffinity with competition, Cold Spring Harbor Laboratory.
- Modelling the emergence of whisker barrels.
- Modelling the emergence of whisker barrels. eLife, 2020(9).
- Teaching activities
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PSY6315 - The Oculomotor System