Design and Development of Software Tools for Bio-PEPA

This paper surveys the design of software tools for the Bio-PEPA process algebra. Bio-PEPA is a high-level language for modelling biological systems such as metabolic pathways and other biochemical reaction networks. Through providing tools for this modelling language we hope to allow easier use of a range of simulators and model-checkers thereby freeing the modeller from the responsibility of developing a custom simulator for the problem of interest. Further, by providing mappings to a range of different analysis tools the Bio-PEPA language allows modellers to compare analysis results which have been computed using independent numerical analysers, which enhances the reliability and robustness of the results computed.

Statistical Inference for Partially Observed Markov Processes via the R Package pomp

Partially observed Markov process (POMP) models, also known as hidden Markov models or state space models, are ubiquitous tools for time series analysis. The R package pomp provides a very flexible framework for Monte Carlo statistical investigations using nonlinear, non-Gaussian POMP models. A range of modern statistical methods for POMP models have been implemented in this framework including sequential Monte Carlo, iterated filtering, particle Markov chain Monte Carlo, approximate Bayesian computation, maximum synthetic likelihood estimation, nonlinear forecasting, and trajectory matching. In this paper, we demonstrate the application of these methodologies using some simple toy problems. We also illustrate the specification of more complex POMP models, using a nonlinear epidemiological model with a discrete population, seasonality, and extra-demographic stochasticity. We discuss the specification of user-defined models and the development of additional methods within the programming environment provided by pomp.Comment: In press at the Journal of Statistical Software. A version of this paper is provided at the pomp package website: http://kingaa.github.io/pom

The Spermatophore in Glossina morsitans morsitans: Insights into Male Contributions to Reproduction.

Male Seminal Fluid Proteins (SFPs) transferred during copulation modulate female reproductive physiology and behavior, impacting sperm storage/use, ovulation, oviposition, and remating receptivity. These capabilities make them ideal targets for developing novel methods of insect disease vector control. Little is known about the nature of SFPs in the viviparous tsetse flies (Diptera: Glossinidae), vectors of Human and Animal African trypanosomiasis. In tsetse, male ejaculate is assembled into a capsule-like spermatophore structure visible post-copulation in the female uterus. We applied high-throughput approaches to uncover the composition of the spermatophore in Glossina morsitans morsitans. We found that both male accessory glands and testes contribute to its formation. The male accessory glands produce a small number of abundant novel proteins with yet unknown functions, in addition to enzyme inhibitors and peptidase regulators. The testes contribute sperm in addition to a diverse array of less abundant proteins associated with binding, oxidoreductase/transferase activities, cytoskeletal and lipid/carbohydrate transporter functions. Proteins encoded by female-biased genes are also found in the spermatophore. About half of the proteins display sequence conservation relative to other Diptera, and low similarity to SFPs from other studied species, possibly reflecting both their fast evolutionary pace and the divergent nature of tsetse's viviparous biology

How to Extend the Capabilities of Space Systems for Long Duration Space Exploration Systems

For sustainable Exploration Missions the need exists to assemble systems-of-systems in space, on the Moon or on other planetary surfaces. To fulfill this need new and innovative system architecture is needed that can be satisfied with the present lift capability of existing rocket technology without the added cost of developing a new heavy lift vehicle. To enable ultra-long life missions with minimum redundancy and lighter mass the need exists to develop system soft,i,are and hardware reconfigurability, which enables increasing functionality and multiple use of launched assets while at the same time overcoming any components failures. Also the need exists to develop the ability to dynamically demate and reassemble individual system elements during a mission in order to work around failed hardware or changed mission requirements. Therefore to meet the goals of Space Exploration Missions in hiteroperability and Reconfigurability, many challenges must be addressed to transform the traditional static avionics architecture into architecture with dynamic capabilities. The objective of this paper is to introduce concepts associated with reconfigurable computer systems; review the various needs and challenges associated with reconfigurable avionics space systems; provide an operational example that illustrates the needs applicable to either the Crew Exploration Vehicle or a collection of "Habot like" mobile surface elements; summarize the approaches that address key challenges to acceptance of a Flexible, Intelligent, Modular and Affordable reconfigurable avionics space system

Strategic Directions in Object-Oriented Programming

This paper has provided an overview of the field of object-oriented programming. After presenting a historical perspective and some major achievements in the field, four research directions were introduced: technologies integration, software components, distributed programming, and new paradigms. In general there is a need to continue research in traditional areas:\ud (1) as computer systems become more and more complex, there is a need to further develop the work on architecture and design; \ud (2) to support the development of complex systems, there is a need for better languages, environments, and tools; \ud (3) foundations in the form of the conceptual framework and other theories must be extended to enhance the means for modeling and formal analysis, as well as for understanding future computer systems

From Social Simulation to Integrative System Design

As the recent financial crisis showed, today there is a strong need to gain "ecological perspective" of all relevant interactions in socio-economic-techno-environmental systems. For this, we suggested to set-up a network of Centers for integrative systems design, which shall be able to run all potentially relevant scenarios, identify causality chains, explore feedback and cascading effects for a number of model variants, and determine the reliability of their implications (given the validity of the underlying models). They will be able to detect possible negative side effect of policy decisions, before they occur. The Centers belonging to this network of Integrative Systems Design Centers would be focused on a particular field, but they would be part of an attempt to eventually cover all relevant areas of society and economy and integrate them within a "Living Earth Simulator". The results of all research activities of such Centers would be turned into informative input for political Decision Arenas. For example, Crisis Observatories (for financial instabilities, shortages of resources, environmental change, conflict, spreading of diseases, etc.) would be connected with such Decision Arenas for the purpose of visualization, in order to make complex interdependencies understandable to scientists, decision-makers, and the general public.Comment: 34 pages, Visioneer White Paper, see http://www.visioneer.ethz.c

System-on-chip Computing and Interconnection Architectures for Telecommunications and Signal Processing

This dissertation proposes novel architectures and design techniques targeting SoC building blocks for telecommunications and signal processing applications. Hardware implementation of Low-Density Parity-Check decoders is approached at both the algorithmic and the architecture level. Low-Density Parity-Check codes are a promising coding scheme for future communication standards due to their outstanding error correction performance. This work proposes a methodology for analyzing effects of finite precision arithmetic on error correction performance and hardware complexity. The methodology is throughout employed for co-designing the decoder. First, a low-complexity check node based on the P-output decoding principle is designed and characterized on a CMOS standard-cells library. Results demonstrate implementation loss below 0.2 dB down to BER of 10^{-8} and a saving in complexity up to 59% with respect to other works in recent literature. High-throughput and low-latency issues are addressed with modified single-phase decoding schedules. A new "memory-aware" schedule is proposed requiring down to 20% of memory with respect to the traditional two-phase flooding decoding. Additionally, throughput is doubled and logic complexity reduced of 12%. These advantages are traded-off with error correction performance, thus making the solution attractive only for long codes, as those adopted in the DVB-S2 standard. The "layered decoding" principle is extended to those codes not specifically conceived for this technique. Proposed architectures exhibit complexity savings in the order of 40% for both area and power consumption figures, while implementation loss is smaller than 0.05 dB. Most modern communication standards employ Orthogonal Frequency Division Multiplexing as part of their physical layer. The core of OFDM is the Fast Fourier Transform and its inverse in charge of symbols (de)modulation. Requirements on throughput and energy efficiency call for FFT hardware implementation, while ubiquity of FFT suggests the design of parametric, re-configurable and re-usable IP hardware macrocells. In this context, this thesis describes an FFT/IFFT core compiler particularly suited for implementation of OFDM communication systems. The tool employs an accuracy-driven configuration engine which automatically profiles the internal arithmetic and generates a core with minimum operands bit-width and thus minimum circuit complexity. The engine performs a closed-loop optimization over three different internal arithmetic models (fixed-point, block floating-point and convergent block floating-point) using the numerical accuracy budget given by the user as a reference point. The flexibility and re-usability of the proposed macrocell are illustrated through several case studies which encompass all current state-of-the-art OFDM communications standards (WLAN, WMAN, xDSL, DVB-T/H, DAB and UWB). Implementations results are presented for two deep sub-micron standard-cells libraries (65 and 90 nm) and commercially available FPGA devices. Compared with other FFT core compilers, the proposed environment produces macrocells with lower circuit complexity and same system level performance (throughput, transform size and numerical accuracy). The final part of this dissertation focuses on the Network-on-Chip design paradigm whose goal is building scalable communication infrastructures connecting hundreds of core. A low-complexity link architecture for mesochronous on-chip communication is discussed. The link enables skew constraint looseness in the clock tree synthesis, frequency speed-up, power consumption reduction and faster back-end turnarounds. The proposed architecture reaches a maximum clock frequency of 1 GHz on 65 nm low-leakage CMOS standard-cells library. In a complex test case with a full-blown NoC infrastructure, the link overhead is only 3% of chip area and 0.5% of leakage power consumption. Finally, a new methodology, named metacoding, is proposed. Metacoding generates correct-by-construction technology independent RTL codebases for NoC building blocks. The RTL coding phase is abstracted and modeled with an Object Oriented framework, integrated within a commercial tool for IP packaging (Synopsys CoreTools suite). Compared with traditional coding styles based on pre-processor directives, metacoding produces 65% smaller codebases and reduces the configurations to verify up to three orders of magnitude