A new tool for the performance analysis of massively parallel computer systems

We present a new tool, GPA, that can generate key performance measures for very large systems. Based on solving systems of ordinary differential equations (ODEs), this method of performance analysis is far more scalable than stochastic simulation. The GPA tool is the first to produce higher moment analysis from differential equation approximation, which is essential, in many cases, to obtain an accurate performance prediction. We identify so-called switch points as the source of error in the ODE approximation. We investigate the switch point behaviour in several large models and observe that as the scale of the model is increased, in general the ODE performance prediction improves in accuracy. In the case of the variance measure, we are able to justify theoretically that in the limit of model scale, the ODE approximation can be expected to tend to the actual variance of the model

Web Services: A Process Algebra Approach

It is now well-admitted that formal methods are helpful for many issues raised in the Web service area. In this paper we present a framework for the design and verification of WSs using process algebras and their tools. We define a two-way mapping between abstract specifications written using these calculi and executable Web services written in BPEL4WS. Several choices are available: design and correct errors in BPEL4WS, using process algebra verification tools, or design and correct in process algebra and automatically obtaining the corresponding BPEL4WS code. The approaches can be combined. Process algebra are not useful only for temporal logic verification: we remark the use of simulation/bisimulation both for verification and for the hierarchical refinement design method. It is worth noting that our approach allows the use of any process algebra depending on the needs of the user at different levels (expressiveness, existence of reasoning tools, user expertise)

Assessing the association between pre-course metrics of student preparation and student performance in introductory statistics: Results from early data on simulation-based inference vs. nonsimulation based inference

The recent simulation-based inference (SBI) movement in algebra-based introductory statistics courses (Stat 101) has provided preliminary evidence of improved student conceptual understanding and retention. However, little is known about whether these positive effects are preferentially distributed across types of students entering the course. We consider how two metrics of Stat 101 student preparation (pre-course performance on concept inventory and math ACT score) may or may not be associated with end of course student performance on conceptual inventories. Students across all preparation levels tended to show improvement in Stat 101, but more improvement was observed across all student preparation levels in early versions of a SBI course. Furthermore, students' gains tended to be similar regardless of whether students entered the course with more preparation or less. Recent data on a sample of students using a current version of an SBI course showed similar results, though direct comparison with non-SBI students was not possible. Overall, our analysis provides additional evidence that SBI curricula are effective at improving students' conceptual understanding of statistical ideas post-course regardless student preparation. Further work is needed to better understand nuances of student improvement based on other student demographics, prior coursework, as well as instructor and institutional variables.Comment: 16 page

Hybrid performance modelling of opportunistic networks

We demonstrate the modelling of opportunistic networks using the process algebra stochastic HYPE. Network traffic is modelled as continuous flows, contact between nodes in the network is modelled stochastically, and instantaneous decisions are modelled as discrete events. Our model describes a network of stationary video sensors with a mobile ferry which collects data from the sensors and delivers it to the base station. We consider different mobility models and different buffer sizes for the ferries. This case study illustrates the flexibility and expressive power of stochastic HYPE. We also discuss the software that enables us to describe stochastic HYPE models and simulate them.Comment: In Proceedings QAPL 2012, arXiv:1207.055

Quantifying the implicit process flow abstraction in SBGN-PD diagrams with Bio-PEPA

For a long time biologists have used visual representations of biochemical networks to gain a quick overview of important structural properties. Recently SBGN, the Systems Biology Graphical Notation, has been developed to standardise the way in which such graphical maps are drawn in order to facilitate the exchange of information. Its qualitative Process Diagrams (SBGN-PD) are based on an implicit Process Flow Abstraction (PFA) that can also be used to construct quantitative representations, which can be used for automated analyses of the system. Here we explicitly describe the PFA that underpins SBGN-PD and define attributes for SBGN-PD glyphs that make it possible to capture the quantitative details of a biochemical reaction network. We implemented SBGNtext2BioPEPA, a tool that demonstrates how such quantitative details can be used to automatically generate working Bio-PEPA code from a textual representation of SBGN-PD that we developed. Bio-PEPA is a process algebra that was designed for implementing quantitative models of concurrent biochemical reaction systems. We use this approach to compute the expected delay between input and output using deterministic and stochastic simulations of the MAPK signal transduction cascade. The scheme developed here is general and can be easily adapted to other output formalisms

Computational Modeling for the Activation Cycle of G-proteins by G-protein-coupled Receptors

In this paper, we survey five different computational modeling methods. For comparison, we use the activation cycle of G-proteins that regulate cellular signaling events downstream of G-protein-coupled receptors (GPCRs) as a driving example. Starting from an existing Ordinary Differential Equations (ODEs) model, we implement the G-protein cycle in the stochastic Pi-calculus using SPiM, as Petri-nets using Cell Illustrator, in the Kappa Language using Cellucidate, and in Bio-PEPA using the Bio-PEPA eclipse plug in. We also provide a high-level notation to abstract away from communication primitives that may be unfamiliar to the average biologist, and we show how to translate high-level programs into stochastic Pi-calculus processes and chemical reactions.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005