Compact Representation of Photosynthesis Dynamics by Rule-based Models (Full Version)

Traditional mathematical models of photosynthesis are based on mass action kinetics of light reactions. This approach requires the modeller to enumerate all the possible state combinations of the modelled chemical species. This leads to combinatorial explosion in the number of reactions although the structure of the model could be expressed more compactly. We explore the use of rule-based modelling, in particular, a simplified variant of Kappa, to compactly capture and automatically reduce existing mathematical models of photosynthesis. Finally, the reduction procedure is implemented in BioNetGen language and demonstrated on several ODE models of photosynthesis processes. This is an extended version of the paper published in proceedings of 5th International Workshop on Static Analysis and Systems Biology (SASB) 2014.Comment: SASB 2014 full pape

A process algebra for synchronous concurrent constraint programming

Concurrent constraint programming is classically based on asynchronous communication via a shared store. This paper presents new version of the ask and tell primitives which features synchronicity. Our approach is based on the idea of telling new information just in the case that a concurrently running process is asking for it. An operational and an algebraic semantics are defined. The algebraic semantics is proved to be sound and complete with respect to a compositional operational semantics which is also presented in the paper

Robustness Analysis for Value-Freezing Signal Temporal Logic

In our previous work we have introduced the logic STL*, an extension of Signal Temporal Logic (STL) that allows value freezing. In this paper, we define robustness measures for STL* by adapting the robustness measures previously introduced for Metric Temporal Logic (MTL). Furthermore, we present an algorithm for STL* robustness computation, which is implemented in the tool Parasim. Application of STL* robustness analysis is demonstrated on case studies.Comment: In Proceedings HSB 2013, arXiv:1308.572

DiVinE-CUDA - A Tool for GPU Accelerated LTL Model Checking

In this paper we present a tool that performs CUDA accelerated LTL Model Checking. The tool exploits parallel algorithm MAP adjusted to the NVIDIA CUDA architecture in order to efficiently detect the presence of accepting cycles in a directed graph. Accepting cycle detection is the core algorithmic procedure in automata-based LTL Model Checking. We demonstrate that the tool outperforms non-accelerated version of the algorithm and we discuss where the limits of the tool are and what we intend to do in the future to avoid them

Multi-agent systems as concurrent constraint processes

We present a language Scc for a specication of the direct exchange and/or the global sharing of information in multi-agent systems. Scc is based on concurrent constraint programming paradigm which we modify in such a way that agents can (i) maintain its local private store, (ii) share (read/write) the information in the global store and (iii) communicate with other agents (via multi-party or hand-shake). To justify our proposal we compare Scc to a recently proposed language for the exchange of information in multi-agent systems. Also we provide an operational semantics of Scc. The full semantic treatment is sketched only and done elsewher

Quantitative Regular Expressions for Arrhythmia Detection Algorithms

Motivated by the problem of verifying the correctness of arrhythmia-detection algorithms, we present a formalization of these algorithms in the language of Quantitative Regular Expressions. QREs are a flexible formal language for specifying complex numerical queries over data streams, with provable runtime and memory consumption guarantees. The medical-device algorithms of interest include peak detection (where a peak in a cardiac signal indicates a heartbeat) and various discriminators, each of which uses a feature of the cardiac signal to distinguish fatal from non-fatal arrhythmias. Expressing these algorithms' desired output in current temporal logics, and implementing them via monitor synthesis, is cumbersome, error-prone, computationally expensive, and sometimes infeasible. In contrast, we show that a range of peak detectors (in both the time and wavelet domains) and various discriminators at the heart of today's arrhythmia-detection devices are easily expressible in QREs. The fact that one formalism (QREs) is used to describe the desired end-to-end operation of an arrhythmia detector opens the way to formal analysis and rigorous testing of these detectors' correctness and performance. Such analysis could alleviate the regulatory burden on device developers when modifying their algorithms. The performance of the peak-detection QREs is demonstrated by running them on real patient data, on which they yield results on par with those provided by a cardiologist.Comment: CMSB 2017: 15th Conference on Computational Methods for Systems Biolog

Making Them Normal

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/68059/2/10.1177_000276427001400206.pd

Local In Vivo measures of Muscle Lipid and Oxygen Consumption Change in Response to Combined Vitamin D Repletion and Aerobic Training in Older Adults

Intramyocellular (IMCL), extramyocellular lipid (EMCL), and vitamin D deficiency are associated with muscle metabolic dysfunction. This study compared the change in [IMCL]:[EMCL] following the combined treatment of vitamin D and aerobic training (DAT) compared with vitamin D (D), aerobic training (AT), and control (CTL). Male and female subjects aged 60–80 years with a BMI ranging from 18.5–34.9 and vitamin D status of ≤ 32 ng/mL (25(OH)D) were recruited to randomized, prospective clinical trial double-blinded for supplement with a 2 × 2 factorial design. Cholecalciferol (Vitamin D3) (10,000 IU × 5 days/week) or placebo was provided for 13 weeks and treadmill aerobic training during week 13. Gastrocnemius IMCL and EMCL were measured with magnetic resonance spectroscopy (MRS) and MRI. Hybrid near-infrared diffuse correlation spectroscopy measured hemodynamics. Group differences in IMCL were observed when controlling for baseline IMCL (p = 0.049). DAT was the only group to reduce IMCL from baseline, while a mean increase was observed in all other groups combined (p = 0.008). IMCL reduction and the corresponding increase in rVO2 at study end (p = 0.011) were unique to DAT. Vitamin D, when combined with exercise, may potentiate the metabolic benefits of exercise by reducing IMCL and increasing tissue-level VO2 in healthy, older adults

Process algebra modelling styles for biomolecular processes

We investigate how biomolecular processes are modelled in process algebras, focussing on chemical reactions. We consider various modelling styles and how design decisions made in the definition of the process algebra have an impact on how a modelling style can be applied. Our goal is to highlight the often implicit choices that modellers make in choosing a formalism, and illustrate, through the use of examples, how this can affect expressability as well as the type and complexity of the analysis that can be performed