Modular Acquisition and Stimulation System for Timestamp-Driven Neuroscience Experiments

Dedicated systems are fundamental for neuroscience experimental protocols that require timing determinism and synchronous stimuli generation. We developed a data acquisition and stimuli generator system for neuroscience research, optimized for recording timestamps from up to 6 spiking neurons and entirely specified in a high-level Hardware Description Language (HDL). Despite the logic complexity penalty of synthesizing from such a language, it was possible to implement our design in a low-cost small reconfigurable device. Under a modular framework, we explored two different memory arbitration schemes for our system, evaluating both their logic element usage and resilience to input activity bursts. One of them was designed with a decoupled and latency insensitive approach, allowing for easier code reuse, while the other adopted a centralized scheme, constructed specifically for our application. The usage of a high-level HDL allowed straightforward and stepwise code modifications to transform one architecture into the other. The achieved modularity is very useful for rapidly prototyping novel electronic instrumentation systems tailored to scientific research.Comment: Preprint submitted to ARC 2015. Extended: 16 pages, 10 figures. The final publication is available at link.springer.co

EPICURE: A partitioning and co-design framework for reconfigurable computing

This paper presents a new design methodology able to bridge the gap between an abstract specification and a heterogeneous reconfigurable architecture. The EPICURE contribution is the result of a joint study on abstraction/refinement methods and a smart reconfigurable architecture within the formal Esterel design tools suite. The original points of this work are: (i) a generic HW/SW interface model, (ii) a specification methodology that handles the control, and includes efficient verification and HW/SW synthesis capabilities, (iii) a method for parallelism exploration based on abstract resources/performance estimation expressed in terms of area/delay tradeoffs, (iv) a HW/SW partitioning approach that refines the specification into explicit HW configurations and the associated SW control. The EPICURE framework shows how a cooperation of complementary methodologies and CAD tools associated with a relevant architecture can signficantly improve the designer productivity, especially in the context of reconfigurable architectures

BioScript: programming safe chemistry on laboratories-on-a-chip

This paper introduces BioScript, a domain-specific language (DSL) for programmable biochemistry which executes on emerging microfluidic platforms. The goal of this research is to provide a simple, intuitive, and type-safe DSL that is accessible to life science practitioners. The novel feature of the language is its syntax, which aims to optimize human readability; the technical contributions of the paper include the BioScript type system and relevant portions of its compiler. The type system ensures that certain types of errors, specific to biochemistry, do not occur, including the interaction of chemicals that may be unsafe. The compiler includes novel optimizations that place biochemical operations to execute concurrently on a spatial 2D array platform on the granularity of a control flow graph, as opposed to individual basic blocks. Results are obtained using both a cycle-accurate microfluidic simulator and a software interface to a real-world platform

Modeling and Mapping of Optimized Schedules for Embedded Signal Processing Systems

The demand for Digital Signal Processing (DSP) in embedded systems has been increasing rapidly due to the proliferation of multimedia- and communication-intensive devices such as pervasive tablets and smart phones. Efficient implementation of embedded DSP systems requires integration of diverse hardware and software components, as well as dynamic workload distribution across heterogeneous computational resources. The former implies increased complexity of application modeling and analysis, but also brings enhanced potential for achieving improved energy consumption, cost or performance. The latter results from the increased use of dynamic behavior in embedded DSP applications. Furthermore, parallel programming is highly relevant in many embedded DSP areas due to the development and use of Multiprocessor System-On-Chip (MPSoC) technology. The need for efficient cooperation among different devices supporting diverse parallel embedded computations motivates high-level modeling that expresses dynamic signal processing behaviors and supports efficient task scheduling and hardware mapping. Starting with dynamic modeling, this thesis develops a systematic design methodology that supports functional simulation and hardware mapping of dynamic reconfiguration based on Parameterized Synchronous Dataflow (PSDF) graphs. By building on the DIF (Dataflow Interchange Format), which is a design language and associated software package for developing and experimenting with dataflow-based design techniques for signal processing systems, we have developed a novel tool for functional simulation of PSDF specifications. This simulation tool allows designers to model applications in PSDF and simulate their functionality, including use of the dynamic parameter reconfiguration capabilities offered by PSDF. With the help of this simulation tool, our design methodology helps to map PSDF specifications into efficient implementations on field programmable gate arrays (FPGAs). Furthermore, valid schedules can be derived from the PSDF models at runtime to adapt hardware configurations based on changing data characteristics or operational requirements. Under certain conditions, efficient quasi-static schedules can be applied to reduce overhead and enhance predictability in the scheduling process. Motivated by the fact that scheduling is critical to performance and to efficient use of dynamic reconfiguration, we have focused on a methodology for schedule design, which complements the emphasis on automated schedule construction in the existing literature on dataflow-based design and implementation. In particular, we have proposed a dataflow-based schedule design framework called the dataflow schedule graph (DSG), which provides a graphical framework for schedule construction based on dataflow semantics, and can also be used as an intermediate representation target for automated schedule generation. Our approach to applying the DSG in this thesis emphasizes schedule construction as a design process rather than an outcome of the synthesis process. Our approach employs dataflow graphs for representing both application models and schedules that are derived from them. By providing a dataflow-integrated framework for unambiguously representing, analyzing, manipulating, and interchanging schedules, the DSG facilitates effective codesign of dataflow-based application models and schedules for execution of these models. As multicore processors are deployed in an increasing variety of embedded image processing systems, effective utilization of resources such as multiprocessor systemon-chip (MPSoC) devices, and effective handling of implementation concerns such as memory management and I/O become critical to developing efficient embedded implementations. However, the diversity and complexity of applications and architectures in embedded image processing systems make the mapping of applications onto MPSoCs difficult. We help to address this challenge through a structured design methodology that is built upon the DSG modeling framework. We refer to this methodology as the DEIPS methodology (DSG-based design and implementation of Embedded Image Processing Systems). The DEIPS methodology provides a unified framework for joint consideration of DSG structures and the application graphs from which they are derived, which allows designers to integrate considerations of parallelization and resource constraints together with the application modeling process. We demonstrate the DEIPS methodology through cases studies on practical embedded image processing systems

Modeling and formal verification of probabilistic reconfigurable systems

In this thesis, we propose a new approach for formal modeling and verification of adaptive probabilistic systems. Dynamic reconfigurable systems are the trend of all future technological systems, such as flight control systems, vehicle electronic systems, and manufacturing systems. In order to meet user and environmental requirements, such a dynamic reconfigurable system has to actively adjust its configuration at run-time by modifying its components and connections, while changes are detected in the internal/external execution environment. On the other hand, these changes may violate the memory usage, the required energy and the concerned real-time constraints since the behavior of the system is unpredictable. It might also make the system's functions unavailable for some time and make potential harm to human life or large financial investments. Thus, updating a system with any new configuration requires that the post reconfigurable system fully satisfies the related constraints. We introduce GR-TNCES formalism for the optimal functional and temporal specification of probabilistic reconfigurable systems under resource constraints. It enables the optimal specification of a probabilistic, energetic and memory constraints of such a system. To formally verify the correctness and the safety of such a probabilistic system specification, and the non-violation of its properties, an automatic transformation from GR-TNCES models into PRISM models is introduced. Moreover, a new approach XCTL is also proposed to formally verify reconfigurable systems. It enables the formal certification of uncompleted and reconfigurable systems. A new version of the software ZIZO is also proposed to model, simulate and verify such GR-TNCES model. To prove its relevance, the latter was applied to case studies; it was used to model and simulate the behavior of an IPV4 protocol to prevent the energy and memory resources violation. It was also used to optimize energy consumption of an automotive skid conveyor.In dieser Arbeit wird ein neuer Ansatz zur formalen Modellierung und Verifikation dynamisch rekonfigurierbarer Systeme vorgestellt. Dynamische rekonfigurierbare Systeme sind in vielen aktuellen und zukünftigen Anwendungen, wie beispielsweise Flugsteuerungssystemen, Fahrzeugelektronik und Fertigungssysteme zu finden. Diese Systeme weisen ein probabilistisches, adaptives Verhalten auf. Um die Benutzer- und Umgebungsbedingungen kontinuierlich zu erfüllen, muss ein solches System seine Konfiguration zur Laufzeit aktiv anpassen, indem es seine Komponenten, Verbindungen zwischen Komponenten und seine Daten modifiziert (adaptiv), sobald Änderungen in der internen oder externen Ausführungsumgebung erkannt werden (probabilistisch). Diese Anpassungen dürfen Beschränkungen bei der Speichernutzung, der erforderlichen Energie und bestehende Echtzeitbedingungen nicht verletzen. Eine nicht geprüfte Rekonfiguration könnte dazu führen, dass die Funktionen des Systems für einige Zeit nicht verfügbar wären und potenziell menschliches Leben gefährdet würde oder großer finanzieller Schaden entstünde. Somit erfordert das Aktualisieren eines Systems mit einer neuen Konfiguration, dass das rekonfigurierte System die zugehörigen Beschränkungen vollständig einhält. Um dies zu überprüfen, wird in dieser Arbeit der GR-TNCES-Formalismus, eine Erweiterung von Petrinetzen, für die optimale funktionale und zeitliche Spezifikation probabilistischer rekonfigurierbarer Systeme unter Ressourcenbeschränkungen vorgeschlagen. Die entstehenden Modelle sollen über probabilistische model checking verifiziert werden. Dazu eignet sich die etablierte Software PRISM. Um die Verifikation zu ermöglichen wird in dieser Arbeit ein Verfahren zur Transformation von GR-TNCES-Modellen in PRISM-Modelle beschrieben. Eine neu eingeführte Logik (XCTL) erlaubt zudem die einfache Beschreibung der zu prüfenden Eigenschaften. Die genannten Schritte wurden in einer Softwareumgebung für den automatisierten Entwurf, die Simulation und die formale Verifikation (durch eine automatische Transformation nach PRISM) umgesetzt. Eine Fallstudie zeigt die Anwendung des Verfahren

On cost-effective reuse of components in the design of complex reconfigurable systems

Design strategies that benefit from the reuse of system components can reduce costs while maintaining or increasing dependability—we use the term dependability to tie together reliability and availability. D3H2 (aDaptive Dependable Design for systems with Homogeneous and Heterogeneous redundancies) is a methodology that supports the design of complex systems with a focus on reconfiguration and component reuse. D3H2 systematizes the identification of heterogeneous redundancies and optimizes the design of fault detection and reconfiguration mechanisms, by enabling the analysis of design alternatives with respect to dependability and cost. In this paper, we extend D3H2 for application to repairable systems. The method is extended with analysis capabilities allowing dependability assessment of complex reconfigurable systems. Analysed scenarios include time-dependencies between failure events and the corresponding reconfiguration actions. We demonstrate how D3H2 can support decisions about fault detection and reconfiguration that seek to improve dependability while reducing costs via application to a realistic railway case study

Towards a new methodology for design, modelling, and verification of reconfigurable distributed control systems based on a new extension to the IEC 61499 standard

In order to meet user requirements and system environment changes, reconfigurable control systems must dynamically adapt their structure and behaviour without disrupting system operation. IEC 61499 standard provides limited support for the design and verification of such systems. In fact, handling different reconfiguration scenarios at runtime is difficult since function blocks in IEC 61499 cannot be changed at run-time. Hence, this thesis promotes an IEC 61499 extension called reconfigurable function block (RFB) that increases design readability and smoothly switches to the most appropriate behaviour when a reconfiguration event occurs. To ensure system feasibility after reconfiguration, in addition to the qualitative verification, quantitative verification based on probabilistic model checking is addressed in a new RFBA approach. The latter aims to transform the designed RFB model automatically into a generalised reconfigurable timed net condition/event system model (GRTNCES) using a newly developed environment called RFBTool. The GR-TNCES fits well with RFB and preserves its semantic. Using the probabilistic model checker PRISM, the generated GR-TNCES model is checked using defined properties specified in computation tree logic. As a result, an evaluation of system performance and an estimation of reconfiguration risks are obtained. The RFBA methodology is applied on a distributed power system case study.Dynamische Anforderungen und Umgebungen erfordern rekonfigurierbare Anlagen und Steuerungssysteme. Rekonfiguration ermöglicht es einem System, seine Struktur und sein Verhalten an interne oder externe Änderungen anzupassen. Die Norm IEC 61499 wurde entwickelt, um (verteilte) Steuerungssysteme auf Basis von Funktionsbausteinen zu entwickeln. Sie bietet jedoch wenig Unterstützung für Entwurf und Verifikation. Die Tatsache, dass eine Rekonfiguration das System-Ausführungsmodell verändert, erschwert die Entwicklung in IEC 61499 zusätzlich. Daher schlägt diese Dissertation rekonfigurierbare Funktionsbausteine (RFBs) als Erweiterung der Norm vor. Ein RFB verarbeitet über einen Master-Slave-Automaten Rekonfigurationsereignisse und löst das entsprechende Verhalten aus. Diese Hierarchie trennt das Rekonfigurationsmodell vom Steuerungsmodell und vereinfacht so den Entwurf. Die Funktionalität des Entwurfs muss verifiziert werden, damit die Ausführbarkeit des Systems nach einer Rekonfiguration gewährleistet ist. Hierzu wird das entworfene RFB-Modell automatisch in ein generalised reconfigurable timed net condition/event system übersetzt. Dieses wird mit dem Model-Checker PRISM auf qualitative und quantitative Eigenschaften überprüft. Somit wird eine Bewertung der Systemperformanz und eine Einschätzung der Rekonfigurationsrisiken erreicht. Die RFB-Methodik wurde in einem Softwarewerkzeug umgesetzt und in einer Fallstudie auf ein dezentrales Stromnetz angewendet