Mark A. O'Neill

Mark A. O'Neill is an English computational biologist with interests in artificial intelligence, systems biology, complex systems and image analysis. He is the creator and lead programmer on a number of computational projects including the Digital Automated Identification SYstem (DAISY) for automated species identification and PUPS P3, an organic computing environment for Linux.

O'Neill was educated at The King's School, Grantham, Sheffield University and University College London.

O'Neill's interests lie at the interface of biology and computing. He has worked in the areas of artificial life and biologically inspired computing. In particular, he has attempted to answer the question "can one create software agents which are capable of carrying a useful computational payload which respond to their environment with the flexibility of a living organism?"

He has also investigated how computational methods may be used to analyze biological and quasi biological systems for example: ecosystems and economies.

O'Neill is also interested in ethology, especially the emergent social ecosystems which occur as a result of social networking on the internet. His recent projects include the use of artificial intelligence techniques to look at complex socio-economic data. He has also self-published on the evolution of sex and the convergent nature of economies and ecologies.

On the computer science front, O'Neill continues to develop and contribute to a number of other open source and commercial software projects and is involved in the design of cluster/parallel computer hardware via his company, Tumbling Dice Ltd. Long-running projects include DAISY;PUPS P3 an organic computing environment for Linux; Cryopid, a Linux process freezer; the Mensor digital terrain model generation system; and RanaVision, a vision based motion detection system. He has also worked with public domain agent based social interaction models such as Sugarscape and artificial life simulators, for example physis, which is a development of Tierra.

O'Neill has been a keen naturalist since childhood. In addition to his interests in complex systems and computer science, he is a member of the Royal Entomological Society and an expert in the rearing and ecology of hawk moths. He is also currently co-ordinator of the technology special interest group (SIG) for the Royal Entomological Society.

He is also interested in the use of precision agriculture methodologies to monitor agri-ecosystems, and has been an active participant in a series of projects looking at the automatic tracking of bumblebees, and other insects using vision, and using both network analysis and remote sensing techniques to monitor ecosystem health. Latterly, he has become interested in applying these techniques in the commercial sphere to look at issues of corporate responsibility and sustainability in industries like mining and agriculture which have significant ecological footprints.

He has also been involved in both computational neuroscience and systems biology, the former association resulting in many papers while working at Oxford University. Work in the latter area led to the successful flotation in 2007 of a systems biology company, e-Therapeutics, where O'Neill was a senior scientist, assisted with the establishment of the company, and was named in a number of seminal patents.

O'Neill is a fellow of the British Computer Society, the Institute of Engineering and Technology, and the Royal Astronomical Society. He is also a chartered engineer and a chartered IT professional. He was one of the recipients of the BCS Award for Computing Technology in 1992.

• Gaston, Kevin J.; O'Neill, Mark A. (March 22, 2004). "Automated species recognition: why not?". Philosophical Transactions of the Royal Society of London. B. 359 (1444): 655–667. doi:10.1098/rstb.2003.1442. PMC 1693351. PMID 15253351. 
• O'Neill, Mark A. (2007). "DAISY: A Practical Computer-Based Tool for Semi-Automated Species Identification". In Automated Taxon Identification in Systematics, N.M.MacLeod (Ed.) CRC Press. 
• Hilgetag, Claus-C.; O'Neill, Mark A.; Young, Malcolm P. (February 9, 1996). "Indeterminacy of the Visual System" (PDF). Science. 271 (5250): 776–777. doi:10.1126/science.271.5250.776. PMID 8628990. 
• O'Neill, Mark A.; Hilgetag, Claus-C. (2001). "The Portable UNIX Programming System [PUPS]: A computational environment for the dynamical representation and analysis of complex neurobiological data". Philosophical Transactions of the Royal Society of London. B. 356 (1412): 1259–1276. doi:10.1098/rstb.2001.0912. PMC 1088514. PMID 11545702. 
• Burns, Gully A. P. C.; Hilgetag, Claus C.; O'Neill, Mark A.; Scannel, Jack; Young, Malcolm P. (2000). "Anatomical connectivity defines the organisation of cortical areas in the macaque monkey and the cat". Philosophical Transactions of the Royal Society of London. B. 355 (1393): 91–110. doi:10.1098/rstb.2000.0551. PMID 10703046. 
• Hilgetag, Claus C.; O'Neill, Mark A.; Young, Malcolm P. (2000). "Hierarchical organisation of the macaque and cat cortical sensory systems explored with a novel network processor". Philosophical Transactions of the Royal Society of London. B. 355 (1393): 71–89. doi:10.1098/rstb.2000.0550. PMID 10703045. 
• Stephan, Klaas E.; Hilgetag, Claus–C.; Burns, Gully A. P. C.; O'Neill, Marc A.; Young, Malcolm P.; Kotter1, Rolf (2000). "Computational Analysis of Functional Connectivity between Areas of Primate Cerebral Cortex". Philosophical Transactions of the Royal Society of London. B. 355 (1393): 111–216. doi:10.1098/rstb.2000.0552. 
• Watson, Anna T.; O'Neill, Mark A.; Kitching, Ian J. (2003). "A qualitative study investigating automated identification of living macrolepidoptera using the Digital Automated Identification SYstem (DAISY)". Systematics & Biodiversity. 1 (3): 287–300. doi:10.1017/S1477200003001208. 
• O'Neill, Mark A. (2010). "Implementing Smart Field Technology for Tracking and Real Time Monitoring of Invertebrates". Antenna. 34: 177–178.