Method for finding metabolic properties based on the general growth law. Liver examples. A General framework for biological modeling

We propose a method for finding metabolic parameters of cells, organs and whole organisms, which is based on the earlier discovered general growth law. Based on the obtained results and analysis of available biological models, we propose a general framework for modeling biological phenomena and discuss how it can be used in Virtual Liver Network project. The foundational idea of the study is that growth of cells, organs, systems and whole organisms, besides biomolecular machinery, is influenced by biophysical mechanisms acting at different scale levels. In particular, the general growth law uniquely defines distribution of nutritional resources between maintenance needs and biomass synthesis at each phase of growth and at each scale level. We exemplify the approach considering metabolic properties of growing human and dog livers and liver transplants. A procedure for verification of obtained results has been introduced too. We found that two examined dogs have high metabolic rates consuming about 0.62 and 1 gram of nutrients per cubic centimeter of liver per day, and verified this using the proposed verification procedure. We also evaluated consumption rate of nutrients in human livers, determining it to be about 0.088 gram of nutrients per cubic centimeter of liver per day for males, and about 0.098 for females. This noticeable difference can be explained by evolutionary development, which required females to have greater liver processing capacity to support pregnancy. We also found how much nutrients go to biomass synthesis and maintenance at each phase of liver and liver transplant growth. Obtained results demonstrate that the proposed approach can be used for finding metabolic characteristics of cells, organs, and whole organisms, which can further serve as important inputs for many applications in biology (protein expression), biotechnology (synthesis of substances), and medicine.Comment: 20 pages, 6 figures, 4 table

DRIVER Technology Watch Report

This report is part of the Discovery Workpackage (WP4) and is the third report out of four deliverables. The objective of this report is to give an overview of the latest technical developments in the world of digital repositories, digital libraries and beyond, in order to serve as theoretical and practical input for the technical DRIVER developments, especially those focused on enhanced publications. This report consists of two main parts, one part focuses on interoperability standards for enhanced publications, the other part consists of three subchapters, which give a landscape picture of current and surfacing technologies and communities crucial to DRIVER. These three subchapters contain the GRID, CRIS and LTP communities and technologies. Every chapter contains a theoretical explanation, followed by case studies and the outcomes and opportunities for DRIVER in this field

Scalable processing of aggregate functions for data streams in resource-constrained environments

The fast evolution of data analytics platforms has resulted in an increasing demand for real-time data stream processing. From Internet of Things applications to the monitoring of telemetry generated in large datacenters, a common demand for currently emerging scenarios is the need to process vast amounts of data with low latencies, generally performing the analysis process as close to the data source as possible. Devices and sensors generate streams of data across a diversity of locations and protocols. That data usually reaches a central platform that is used to store and process the streams. Processing can be done in real time, with transformations and enrichment happening on-the-fly, but it can also happen after data is stored and organized in repositories. In the former case, stream processing technologies are required to operate on the data; in the latter batch analytics and queries are of common use. Stream processing platforms are required to be malleable and absorb spikes generated by fluctuations of data generation rates. Data is usually produced as time series that have to be aggregated using multiple operators, being sliding windows one of the most common abstractions used to process data in real-time. To satisfy the above-mentioned demands, efficient stream processing techniques that aggregate data with minimal computational cost need to be developed. However, data analytics might require to aggregate extensive windows of data. Approximate computing has been a central paradigm for decades in data analytics in order to improve the performance and reduce the needed resources, such as memory, computation time, bandwidth or energy. In exchange for these improvements, the aggregated results suffer from a level of inaccuracy that in some cases can be predicted and constrained. This doctoral thesis aims to demonstrate that it is possible to have constant-time and memory efficient aggregation functions with approximate computing mechanisms for constrained environments. In order to achieve this goal, the work has been structured in three research challenges. First we introduce a runtime to dynamically construct data stream processing topologies based on user-supplied code. These dynamic topologies are built on-the-fly using a data subscription model de¿ned by the applications that consume data. The subscription-based programing model enables multiple users to deploy their own data-processing services. On top of this runtime, we present the Amortized Monoid Tree Aggregator general sliding window aggregation framework, which seamlessly combines the following features: amortized O(1) time complexity and a worst-case of O(log n) between insertions; it provides both a window aggregation mechanism and a window slide policy that are user programmable; the enforcement of the window sliding policy exhibits amortized O(1) computational cost for single evictions and supports bulk evictions with cost O(log n); and it requires a local memory space of O(log n). The framework can compute aggregations over multiple data dimensions, and has been designed to support decoupling computation and data storage through the use of distributed Key-Value Stores to keep window elements and partial aggregations. Specially motivated by edge computing scenarios, we contribute Approximate and Amortized Monoid Tree Aggregator (A2MTA). It is, to our knowledge, the first general purpose sliding window programable framework that combines constant-time aggregations with error bounded approximate computing techniques. A2MTA uses statistical analysis of the stream data in order to perform inaccurate aggregations, providing a critical reduction of needed resources for massive stream data aggregation, and an improvement of performance.La ràpida evolució de les plataformes d'anàlisi de dades ha resultat en un increment de la demanda de processament de fluxos continus de dades en temps real. Des de la internet de les coses fins al monitoratge de telemetria generada en grans servidors, una demanda recurrent per escenaris emergents es la necessitat de processar grans quantitats de dades amb latències molt baixes, generalment fent el processat de les dades tant a prop dels origines com sigui possible. Les dades son generades com a fluxos continus per dispositius que utilitzen una varietat de localitzacions i protocols. Aquests processat de les dades s pot fer en temps real amb les transformacions efectuant-se al vol, i en aquest cas la utilització de plataformes de processat d'streams és necessària. Les plataformes de processat d'streams cal que absorbeixin pics de freqüència de dades. Les dades es generen com a series temporals que s'agreguen fent servir multiples operadors, on les finestres són l'abstracció més habitual. Per a satisfer les baixes latències i maleabilitat requerides, els operadors necesiten tenir un cost computacional mínim, inclús amb extenses finestres de dades per a agregar. La computació aproximada ha sigut durant decades un paradigma rellevant per l'anàlisi de dades on cal millorar el rendiment de diferents algorismes i reduir-ne el temps de computació, la memòria requerida, l'ample de banda o el consum energètic. A canvi d'aquestes millores, els resultats poden patir d'una falta d'exactitud que pot ser estimada i controlada. Aquesta tesi doctoral vol demostrar que es posible tenir funcions d'agregació pel processat d'streams que tinc un cost de temps constant, sigui eficient en termes de memoria i faci ús de computació aproximada. Per aconseguir aquests objectius, aquesta tesi està dividida en tres reptes. Primer presentem un entorn per a la construcció dinàmica de topologies de computació d'streams de dades utilitzant codi d'usuari. Aquestes topologies es construeixen fent servir un model de subscripció a streams, en el que les aplicación consumidores de dades amplien les topologies mentre s'estan executant. Aquest entorn permet multiples entitats ampliant una mateixa topologia. A sobre d'aquest entorn, presentem un framework de propòsit general per a l'agregació de finestres de dades anomenat AMTA (Amortized Monoid Tree Aggregator). Aquest framework combina: temps amortitzat constant per a totes les operacions, amb un cas pitjor logarítmic; programable tant en termes d'agregació com en termes d'expulsió d'elements de la finestra. L'expulsió massiva d'elements de la finestra es considera una operació atòmica, amb un cost amortitzat constant; i requereix espai en memoria local per a O(log n) elements de la finestra. Aquest framework pot computar agregacions sobre multiples dimensions de dades, i ha estat dissenyat per desacoplar la computació de les dades del seu desat, podent tenir els continguts de la finestra distribuits en diferents màquines. Motivats per la computació en l'edge (edge computing), hem contribuit A2MTA (Approximate and Amortized Monoid Tree Aggregator). Des de el nostre coneixement, es el primer framework de propòsit general per a la computació de finestres que combina un cost constant per a totes les seves operacions amb tècniques de computació aproximada amb control de l'error. A2MTA fa us d'anàlisis estadístics per a poder fer agregacions amb error limitat, reduint críticament els recursos necessaris per a la computació de grans quantitats de dades

From service-oriented architecture to service-oriented enterprise

Service-Oriented Architecture (SOA) was originally motivated by enterprise demands for better business-technology alignment and higher flexibility and reuse. SOA evolved from an initial set of ideas and principles to Web services (WS) standards now widely accepted by industry. The next phase of SOA development is concerned with a scalable, reliable and secure infrastructure based on these standards, and guidelines, methods and techniques for developing and maintaining service delivery in dynamic enterprise settings. In this paper we discuss the principles and main elements of SOA. We then present an overview of WS standards. And finally we come back to the original motivation for SOA, and how these can be realized

Challenges for the comprehensive management of cloud services in a PaaS framework

The 4CaaSt project aims at developing a PaaS framework that enables flexible definition, marketing, deployment and management of Cloud-based services and applications. The major innovations proposed by 4CaaSt are the blueprint and its lifecycle management, a one stop shop for Cloud services and a PaaS level resource management featuring elasticity. 4CaaSt also provides a portfolio of ready to use Cloud native services and Cloud-aware immigrant technologies

Engineering environment-mediated coordination via nature-inspired laws

SAPERE is a general multiagent framework to support the development of self-organizing pervasive computing services. One of the key aspects of the SAPERE approach is to have all interactions between agents take place in an indirect way, via a shared spatial environment. In such environment, a set of nature-inspired coordination laws have been defined to rule the coordination activities of the application agents and promote the provisioning of adaptive and self-organizing services

Autopoiesis in Virtual Organizations

Virtual organizations continuously gain popularity because of the benefits created by them. Generally, they are defined as temporal adhocracies, project oriented, knowledge-based network organizations. The goal of this paper is to present the hypothesis that knowledge system developed by virtual organization is an autopoietic system. The term “autopoiesis†was introduced by Maturana for self-productive systems. In this paper, Wikipedia is described as an example of an autopoietic system. The first part of the paper covers discussion on virtual organizations. Next, autopoiesis’ interpretations are delivered and the value of autopoiesis for governance of virtual organizations is presented. The last parts of the work comprise short presentation of Wikipedia, its principles and conclusions of Wikipedia as an autopoietic system.autopoiesis , autopoietic system, Wikipedia.