A Process-Oriented Architecture for Complex System Modelling

A fine-grained massively-parallel process-oriented model of platelets (potentially artificial) within a blood vessel is presented. This is a CSP inspired design, expressed and implemented using the occam-pi language. It is part of the TUNA pilot study on nanite assemblers at the universities of York, Surrey and Kent. The aim for this model is to engineer emergent behaviour from the platelets, such that they respond to a wound in the blood vessel wall in a way similar to that found in the human body -- i.e. the formation of clots to stem blood flow from the wound and facilitate healing. An architecture for a three dimensional model (relying strongly on the dynamic and mobile capabilities of occam-pi) is given, along with mechanisms for visualisation and interaction. The biological accuracy of the current model is very approximate. However, its process-oriented nature enables simple refinement (through the addition of processes modelling different stimulants/inhibitors of the clotting reaction, different platelet types and other participating organelles) to greater and greater realism. Even with the current system, simple experiments are possible and have scientific interest (e.g. the effect of platelet density on the success of the clotting mechanism in stemming blood flow: too high or too low and the process fails). General principles for the design of large and complex system models are drawn. The described case study runs to millions of processes engaged in ever-changing communication topologies. It is free from deadlock, livelock, race hazards and starvation em by design, employing a small set of synchronisation patterns for which we have proven safety theorems

Testing carbon farming opportunities for salinity management

An emerging prospect for farm revenue from revegetation of saline and other lands that are marginal or non-productive for agriculture is the sale of carbon credits. Australian Government schemes for carbon credits include the Carbon Farming Initiative (CFI) and the proposed Emissions Reduction Fund (ERF) Therefore, this study aimed to assess the potential for woody vegetation (trees and shrubs) established on and around salt-affected lands in the Northern Agricultural Region (NAR) to remove carbon dioxide from the atmosphere and store (sequester) the carbon in new growth. Revegetation plantings on six farms were selected for the study after the landowners expressed interest in participating in the study. Criteria for selection included: minimum of 5 ha planted on and around salt-affected land; a variety of native trees and shrub species planted; and that the plantings must be at least 10 years old. Across the six farms a total of nine sites were selected for the study. The estimates of carbon stocks in species and sites were projected forwards and backwards from the measurement ages (11 - 22 years)to age 15 years to \u27age standardise\u27 the results and facilitate comparison between species and sites. This was done using the national carbon accounting model, FullCAM

The symbiosis of concurrency and verification: teaching and case studies

Concurrency is beginning to be accepted as a core knowledge area in the undergraduate CS curriculum—no longer isolated, for example, as a support mechanism in a module on operating systems or reserved as an advanced discipline for later study. Formal verification of system properties is often considered a difficult subject area, requiring significant mathematical knowledge and generally restricted to smaller systems employing sequential logic only. This paper presents materials, methods and experiences of teaching concurrency and verification as a unified subject, as early as possible in the curriculum, so that they become fundamental elements of our software engineering tool kit—to be used together every day as a matter of course. Concurrency and verification should live in symbiosis. Verification is essential for concurrent systems as testing becomes especially inadequate in the face of complex non-deterministic (and, therefore, hard to repeat) behaviours. Concurrency should simplify the expression of most scales and forms of computer system by reflecting the concurrency of the worlds in which they operate (and, therefore, have to model); simplified expression leads to simplified reasoning and, hence, verification. Our approach lets these skills be developed without requiring students to be trained in the underlying formal mathematics. Instead, we build on the work of those who have engineered that necessary mathematics into the concurrency models we use (CSP, ?-calculus), the model checker (FDR) that lets us explore and verify those systems, and the programming languages/libraries (occam-?, Go, JCSP, ProcessJ) that let us design and build efficient executable systems within these models. This paper introduces a workflow methodology for the development and verification of concurrent systems; it also presents and reflects on two open-ended case studies, using this workflow, developed at the authors’ two universities. Concerns analysed include safety (don’t do bad things), liveness (do good things) and low probability deadlock (that testing fails to discover). The necessary technical background is given to make this paper self-contained and its work simple to reproduce and extend

The Next Generation Event Horizon Telescope Collaboration: History, Philosophy, and Culture

This white paper outlines the plans of the History Philosophy Culture Working Group of the Next Generation Event Horizon Telescope Collaboration.Comment: 23 pages, 1 figur

Bacterial Acquisition in Juveniles of Several Broadcast Spawning Coral Species

Coral animals harbor diverse microorganisms in their tissues, including archaea, bacteria, viruses, and zooxanthellae. The extent to which coral-bacterial associations are specific and the mechanisms for their maintenance across generations in the environment are unknown. The high diversity of bacteria in adult coral colonies has made it challenging to identify species-specific patterns. Localization of bacteria in gametes and larvae of corals presents an opportunity for determining when bacterial-coral associations are initiated and whether they are dynamic throughout early development. This study focuses on the early onset of bacterial associations in the mass spawning corals Montastraea annularis, M. franksi, M. faveolata, Acropora palmata, A. cervicornis, Diploria strigosa, and A. humilis. The presence of bacteria and timing of bacterial colonization was evaluated in gametes, swimming planulae, and newly settled polyps by fluorescence in situ hybridization (FISH) using general eubacterial probes and laser-scanning confocal microscopy. The coral species investigated in this study do not appear to transmit bacteria via their gametes, and bacteria are not detectable in or on the corals until after settlement and metamorphosis. This study suggests that mass-spawning corals do not acquire, or are not colonized by, detectable numbers of bacteria until after larval settlement and development of the juvenile polyp. This timing lays the groundwork for developing and testing new hypotheses regarding general regulatory mechanisms that control bacterial colonization and infection of corals, and how interactions among bacteria and juvenile polyps influence the structure of bacterial assemblages in corals

Induction of Larval Metamorphosis of the Coral Acropora millepora by Tetrabromopyrrole Isolated from a Pseudoalteromonas Bacterium

The induction of larval attachment and metamorphosis of benthic marine invertebrates is widely considered to rely on habitat specific cues. While microbial biofilms on marine hard substrates have received considerable attention as specific signals for a wide and phylogenetically diverse array of marine invertebrates, the presumed chemical settlement signals produced by the bacteria have to date not been characterized. Here we isolated and fully characterized the first chemical signal from bacteria that induced larval metamorphosis of acroporid coral larvae (Acropora millepora). The metamorphic cue was identified as tetrabromopyrrole (TBP) in four bacterial Pseudoalteromonas strains among a culture library of 225 isolates obtained from the crustose coralline algae Neogoniolithon fosliei and Hydrolithon onkodes. Coral planulae transformed into fully developed polyps within 6 h, but only a small proportion of these polyps attached to the substratum. The biofilm cell density of the four bacterial strains had no influence on the ratio of attached vs. non-attached polyps. Larval bioassays with ethanolic extracts of the bacterial isolates, as well as synthetic TBP resulted in consistent responses of coral planulae to various doses of TBP. The lowest bacterial density of one of the Pseudoalteromonas strains which induced metamorphosis was 7,000 cells mm−2 in laboratory assays, which is on the order of 0.1 –1% of the total numbers of bacteria typically found on such surfaces. These results, in which an actual cue from bacteria has been characterized for the first time, contribute significantly towards understanding the complex process of acroporid coral larval settlement mediated through epibiotic microbial biofilms on crustose coralline algae

Crop Updates 2005 - Farming Systems

This session covers forty four papers from different authors: PLENARY 1. 2005 Outlook, David Stephens and Nicola Telcik, Department of Agriculture FERTILITY AND NUTRITION 2. The effect of higher nitrogen fertiliser prices on rotation and fertiliser strategies in cropping systems, Ross Kingwell, Department of Agriculture and University of Western Australia 3. Stubble management: The short and long term implications for crop nutrition and soil fertility, Wayne Pluske, Nutrient Management Systems and Bill Bowden, Department of Agriculture 4. Stubble management: The pros and cons of different methods, Bill Bowden, Department of Agriculture, Western Australia and Mike Collins, WANTFA 5. Effect of stubble burning and seasonality on microbial processes and nutrient recycling, Frances Hoyle, The University of Western Australia 6. Soil biology and crop production in Western Australian farming systems, D.V. Murphy, N. Milton, M. Osman, F.C. Hoyle, L.K Abbott, W.R. Cookson and S. Darmawanto, The University of Western Australia 7. Urea is as effective as CAN when no rain for 10 days, Bill Crabtree, Crabtree Agricultural Consulting 8. Fertiliser (N,P,S,K) and lime requirements for wheat production in the Merredin district, Geoff Anderson, Department of Agriculture and Darren Kidson, Summit Fertilizers 9. Trace element applications: Up-front verses foliar? Bill Bowden and Ross Brennan, Department of Agriculture 10. Fertcare®, Environmental Product Stewardship and Advisor Standards for thee Fertiliser Industry, Nick Drew, Fertilizer Industry Federation of Australia (FIFA) SOIL AND LAND MANAGEMENT 11. Species response to row spacing, density and nutrition, Bill Bowden, Craig Scanlan, Lisa Sherriff, Bob French and Reg Lunt, Department of Agriculture 12. Investigation into the influence of row orientation in lupin crops, Jeff Russell, Department of Agriculture and Angie Roe, Farm Focus Consultants 13. Deriving variable rate management zones for crops, Ian Maling, Silverfox Solutions and Matthew Adams, DLI 14. In a world of Precision Agriculture, weigh trailers are not passé, Jeff Russell, Department of Agriculture 15. Cover crop management to combat ryegrass resistance and improve yields, Jeff Russell, Department of Agriculture and Angie Roe, Farm Focus Consultants 16. ARGT home page, the place to find information on annual ryegrass toxicity on the web, Dr George Yan, BART Pty Ltd 17. Shallow leading tine (SLT) ripper significantly reduces draft force, improves soil tilth and allows even distribution of subsoil ameliorants, Mohammad Hamza, Glen Riethmuller and Wal Anderson, Department of Agriculture PASTURE ANS SUMMER CROP SYSTEMS 18. New annual pasture legumes for Mediteranean farming systems, Angelo Loi, Phil Nichols, Clinton Revell and David Ferris, Department of Agriculture 19. How sustainable are phase rotations with Lucerne? Phil Ward, CSIRO Plant Industry 20. Management practicalities of summer cropping, Andrea Hills and Sally-Anne Penny, Department of Agriculture 21. Rainfall zone determines the effect of summer crops on winter yields, Andrea Hills, Sally-Anne Penny and David Hall, Department of Agriculture 22. Summer crops and water use, Andrea Hills, Sally-Anne Penny and David Hall, Department of Agriculture, and Michael Robertson and Don Gaydon, CSIRO Brisbane 23. Risk analysis of sorgum cropping, Andrea Hills and Sally-Anne Penny, Department of Agriculture, and Dr Michael Robertson and Don Gaydon, CSIRO Brisbane FARMER DECISION SUPPORT AND ADOPTION 24. Variety release and End Point Royalties – a new system? Tress Walmsley, Department of Agriculture 25. Farming system analaysis using the STEP Tool, Caroline Peek and Megan Abrahams, Department of Agriculture 26. The Leakage Calculator: A simple tool for groundwater recharge assessment, Paul Raper, Department of Agriculture 27. The cost of Salinity Calculator – your tool to assessing the profitability of salinity management options, Richard O’Donnell and Trevor Lacey, Department of Agriculture 28. Climate decision support tools, Meredith Fairbanks and David Tennant, Department of Agriculture 29. Horses for courses – using the best tools to manage climate risk, Cameron Weeks, Mingenew-Irwin Group/Planfarm and Richard Quinlan, Planfarm Agronomy 30. Use of seasonal outlook for making N decisions in Merredin, Meredith Fairbanks and Alexandra Edward, Department of Agriculture 31. Forecasts and profits, Benefits or bulldust? Chris Carter and Doug Hamilton, Department of Agriculture 32. A tool to estimate fixed and variable header and tractor depreciation costs, Peter Tozer, Department of Agriculture 33. Partners in grain: ‘Putting new faces in new places’, Renaye Horne, Department of Agriculture 34. Results from the Grower group Alliance, Tracey Gianatti, Grower Group Alliance 35. Local Farmer Group Network – farming systems research opportunities through local groups, Paul Carmody, Local Farmer Group Network GREENHOUSE GAS AND CLIMATE CHANGE 36. Changing rainfall patterns in the grainbelt, Ian Foster, Department of Agriculture 37. Vulnerability of broadscale agriculture to the impacts of climate change, Michele John, CSIRO (formerly Department of Agriculture) and Ross George, Department of Agriculture 38. Impacts of climate change on wheat yield at Merredin, Imma Farré and Ian Foster, Department of Agriculture 39. Climate change, land use suitability and water security, Ian Kininmonth, Dennis van Gool and Neil Coles, Department of Agriculture 40. Nitrous oxide emissions from cropping systems, Bill Porter, Department of Agriculture, Louise Barton, University of Western Australia 41. The potential of greenhouse sinks to underwrite improved land management in Western Australia, Richard Harper and Peter Ritson, CRC for Greenhouse Accounting and Forest Products Commission, Tony Beck, Tony Beck Consulting Services, Chris Mitchell and Michael Hill, CRC for Greenhouse Accounting 42. Removing uncertainty from greenhouse emissions, Fiona Barker-Reid, Will Gates, Ken Wilson and Rob Baigent, Department of Primary Industries - Victoria and CRC for Greenhouse Accounting (CRCGA), and Ian Galbally, Mick Meyer and Ian Weeks, CSIRO Atmospheric Research and CRCGA 43. Greenhouse in Agriculture Program (GIA), Traci Griffin, CRC for Greenhouse Accounting 44. Grains Greenhouse Accounting framework, D. Rodriguez, M. Probust, M. Meyers, D. Chen, A. Bennett, W. Strong, R. Nussey, I. Galbally and M. Howden CONTACT DETAILS FOR PRINCIPAL AUTHOR

The Next Generation Event Horizon Telescope Collaboration: History, Philosophy, and Culture

This white paper outlines the plans of the History Philosophy Culture Working Group of the Next Generation Event Horizon Telescope Collaboration