3,797 research outputs found
PocketCare: Tracking the Flu with Mobile Phones using Partial Observations of Proximity and Symptoms
Mobile phones provide a powerful sensing platform that researchers may adopt
to understand proximity interactions among people and the diffusion, through
these interactions, of diseases, behaviors, and opinions. However, it remains a
challenge to track the proximity-based interactions of a whole community and
then model the social diffusion of diseases and behaviors starting from the
observations of a small fraction of the volunteer population. In this paper, we
propose a novel approach that tries to connect together these sparse
observations using a model of how individuals interact with each other and how
social interactions happen in terms of a sequence of proximity interactions. We
apply our approach to track the spreading of flu in the spatial-proximity
network of a 3000-people university campus by mobilizing 300 volunteers from
this population to monitor nearby mobile phones through Bluetooth scanning and
to daily report flu symptoms about and around them. Our aim is to predict the
likelihood for an individual to get flu based on how often her/his daily
routine intersects with those of the volunteers. Thus, we use the daily
routines of the volunteers to build a model of the volunteers as well as of the
non-volunteers. Our results show that we can predict flu infection two weeks
ahead of time with an average precision from 0.24 to 0.35 depending on the
amount of information. This precision is six to nine times higher than with a
random guess model. At the population level, we can predict infectious
population in a two-week window with an r-squared value of 0.95 (a random-guess
model obtains an r-squared value of 0.2). These results point to an innovative
approach for tracking individuals who have interacted with people showing
symptoms, allowing us to warn those in danger of infection and to inform health
researchers about the progression of contact-induced diseases
Construction and Analysis of Petri Net Model for Distributed Cyber Physical Systems
A Distributed Cyber-Physical System (DCPS) composition poses challenges in determining its emergent behaviour. These challenges occur due to (1) the appearance of causal loops of information and energy flow through cyber and physical channels and (2) inherent non-determinism in the temporally ordered flow of events within independently evolving interacting processes of Constituent Systems (CSs). Hence, there is a need to construct a model of the envisaged schematic of DCPS composition for analysis and verification of its significant properties in the conceptual design stage of the system development life cycle.
This paper presents a procedure to construct DCPS composition models in Petri net formalism using distributed abstractions. The model for each CS is obtained from elementary constructs using compositional operators. The interaction among CSs occurs through channels obtained by connecting send and receive constructs of two CSs participating in an interaction. The internal processing within a CS characterizing its primary function is abstracted in a generic passthrough construct. Representing these constructs with compositional operators results in the complete DCPS model in Petri net formalism. A toolchain with Reference net workshop (Renew) as an integrated Petri net editing and analysis platform is configured to support DCPS modelling, simulation and analysis. The Renew tool functionality has been enhanced with a plugin designed and developed by authors to facilitate the drawing of the distributed composition model.
A low-level Petri net analysis (Lola) v2.0 plugin is employed to verify the Petri net and temporal properties of the modelled DCPS scenarios. The properties of the resultant model are verified using well-established algorithms to analyze Petri nets. Further, system properties specified using temporal logic can be verified using model-checking algorithms for Petri nets. A moderately complex scenario involving interactions among six CSs illustrates the presented approach
In-silico-Systemanalyse von Biopathways
Chen M. In silico systems analysis of biopathways. Bielefeld (Germany): Bielefeld University; 2004.In the past decade with the advent of high-throughput technologies, biology has migrated from a descriptive science to a predictive one. A vast amount of information on the metabolism have been produced; a number of specific genetic/metabolic databases and computational systems have been developed, which makes it possible for biologists to perform in silico analysis of metabolism. With experimental data from laboratory, biologists wish to systematically conduct their analysis with an easy-to-use computational system. One major task is to implement molecular information systems that will allow to integrate different molecular database systems, and to design analysis tools (e.g. simulators of complex metabolic reactions). Three key problems are involved: 1) Modeling and simulation of biological processes; 2) Reconstruction of metabolic pathways, leading to predictions about the integrated function of the network; and 3) Comparison of metabolism, providing an important way to reveal the functional relationship between a set of metabolic pathways.
This dissertation addresses these problems of in silico systems analysis of biopathways. We developed a software system to integrate the access to different databases, and exploited the Petri net methodology to model and simulate metabolic networks in cells. It develops a computer modeling and simulation technique based on Petri net methodology; investigates metabolic networks at a system level; proposes a markup language for biological data interchange among diverse biological simulators and Petri net tools; establishes a web-based information retrieval system for metabolic pathway prediction; presents an algorithm for metabolic pathway alignment; recommends a nomenclature of cellular signal transduction; and attempts to standardize the representation of biological pathways.
Hybrid Petri net methodology is exploited to model metabolic networks. Kinetic modeling strategy and Petri net modeling algorithm are applied to perform the processes of elements functioning and model analysis. The proposed methodology can be used for all other metabolic networks or the virtual cell metabolism. Moreover, perspectives of Petri net modeling and simulation of metabolic networks are outlined.
A proposal for the Biology Petri Net Markup Language (BioPNML) is presented. The concepts and terminology of the interchange format, as well as its syntax (which is based on XML) are introduced. BioPNML is designed to provide a starting point for the development of a standard interchange format for Bioinformatics and Petri nets. The language makes it possible to exchange biology Petri net diagrams between all supported hardware platforms and versions. It is also designed to associate Petri net models and other known metabolic simulators.
A web-based metabolic information retrieval system, PathAligner, is developed in order to predict metabolic pathways from rudimentary elements of pathways. It extracts metabolic information from biological databases via the Internet, and builds metabolic pathways with data sources of genes, sequences, enzymes, metabolites, etc. The system also provides a navigation platform to investigate metabolic related information, and transforms the output data into XML files for further modeling and simulation of the reconstructed pathway.
An alignment algorithm to compare the similarity between metabolic pathways is presented. A new definition of the metabolic pathway is proposed. The pathway defined as a linear event sequence is practical for our alignment algorithm. The algorithm is based on strip scoring the similarity of 4-hierarchical EC numbers involved in the pathways. The algorithm described has been implemented and is in current use in the context of the PathAligner system.
Furthermore, new methods for the classification and nomenclature of cellular signal transductions are recommended. For each type of characterized signal transduction, a unique ST number is provided. The Signal Transduction Classification Database (STCDB), based on the proposed classification and nomenclature, has been established. By merging the ST numbers with EC numbers, alignments of biopathways are possible.
Finally, a detailed model of urea cycle that includes gene regulatory networks, metabolic pathways and signal transduction is demonstrated by using our approaches. A system biological interpretation of the observed behavior of the urea cycle and its related transcriptomics information is proposed to provide new insights for metabolic engineering and medical care
Generation of architectures for distributed intelligence systems
Cover title. "Invited paper to appear in the Proceedings of the 1989 IEEE International Conference on Control and Applications (ICCON '89), Jerusalem, Israel, April 1989."Includes bibliographical references.Supported by the Office of Naval Research. N00014-84-K-0519Alexander H. Levis
Modeling of the Glycolysis Pathway in Plasmodium falciparum using Petri Nets
Malaria is one of the deadly diseases, which affects a large number of the world’s population. The Plasmodium falciparum parasite during erythrocyte stages produces its energy mainly through anaerobic glycolysis, with pyruvate being converted into lactate. The glycolysis metabolism in P. falci-parum is one of the important metabolic pathways of the parasite because the parasite is entirely dependent on it for energy. Also, several glycolytic enzymes have been proposed as drug targets. Petri nets (PNs) have been recognized as one of the important models for representing biological pathways. In this work, we built a qualitative PN model for the glycolysis pathway in P. falciparum and analyzed the model for its structural and quantitative properties using PN theory. From PlasmoCyc files, a total of 11 reactions were extracted; 6 of these were reversible and 5 were irreversible. These reactions were catalyzed by a total number of 13 enzymes. We extracted some of the essential reactions in the pathway using PN model, which are the possible drug targets without which the pathway cannot function. This model also helps to improve the understanding of the biological processes within this pathway
A Calculus for Molecular Interaction Maps
Molecular Interaction Maps are a graphical formalism used by biologists to describe complex interactions between molecules. We provide a formal description of MIMs using process algebras and determine its computational power
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