WorldWideScience

Sample records for biological information system

  1. Marine biological data and information management system

    Digital Repository Service at National Institute of Oceanography (India)

    Sarupria, J.S.

    Indian National Oceanographic Data Centre (INODC) is engaged in developing a marine biological data and information management system (BIODIMS). This system will contain the information on zooplankton in the water column, zoobenthic biomass...

  2. Informing biological design by integration of systems and synthetic biology.

    Science.gov (United States)

    Smolke, Christina D; Silver, Pamela A

    2011-03-18

    Synthetic biology aims to make the engineering of biology faster and more predictable. In contrast, systems biology focuses on the interaction of myriad components and how these give rise to the dynamic and complex behavior of biological systems. Here, we examine the synergies between these two fields. Copyright © 2011 Elsevier Inc. All rights reserved.

  3. Biological information systems: Evolution as cognition-based information management.

    Science.gov (United States)

    Miller, William B

    2018-05-01

    An alternative biological synthesis is presented that conceptualizes evolutionary biology as an epiphenomenon of integrated self-referential information management. Since all biological information has inherent ambiguity, the systematic assessment of information is required by living organisms to maintain self-identity and homeostatic equipoise in confrontation with environmental challenges. Through their self-referential attachment to information space, cells are the cornerstone of biological action. That individualized assessment of information space permits self-referential, self-organizing niche construction. That deployment of information and its subsequent selection enacted the dominant stable unicellular informational architectures whose biological expressions are the prokaryotic, archaeal, and eukaryotic unicellular forms. Multicellularity represents the collective appraisal of equivocal environmental information through a shared information space. This concerted action can be viewed as systematized information management to improve information quality for the maintenance of preferred homeostatic boundaries among the varied participants. When reiterated in successive scales, this same collaborative exchange of information yields macroscopic organisms as obligatory multicellular holobionts. Cognition-Based Evolution (CBE) upholds that assessment of information precedes biological action, and the deployment of information through integrative self-referential niche construction and natural cellular engineering antecedes selection. Therefore, evolutionary biology can be framed as a complex reciprocating interactome that consists of the assessment, communication, deployment and management of information by self-referential organisms at multiple scales in continuous confrontation with environmental stresses. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Construction of a Linux based chemical and biological information system.

    Science.gov (United States)

    Molnár, László; Vágó, István; Fehér, András

    2003-01-01

    A chemical and biological information system with a Web-based easy-to-use interface and corresponding databases has been developed. The constructed system incorporates all chemical, numerical and textual data related to the chemical compounds, including numerical biological screen results. Users can search the database by traditional textual/numerical and/or substructure or similarity queries through the web interface. To build our chemical database management system, we utilized existing IT components such as ORACLE or Tripos SYBYL for database management and Zope application server for the web interface. We chose Linux as the main platform, however, almost every component can be used under various operating systems.

  5. Two faces of entropy and information in biological systems.

    Science.gov (United States)

    Mitrokhin, Yuriy

    2014-10-21

    The article attempts to overcome the well-known paradox of contradictions between the emerging biological organization and entropy production in biological systems. It is assumed that quality, speculative correlation between entropy and antientropy processes taking place both in the past and today in the metabolic and genetic cellular systems may be perfectly authorized for adequate description of the evolution of biological organization. So far as thermodynamic entropy itself cannot compensate for the high degree of organization which exists in the cell, we discuss the mode of conjunction of positive entropy events (mutations) in the genetic systems of the past generations and the formation of organized structures of current cells. We argue that only the information which is generated in the conditions of the information entropy production (mutations and other genome reorganization) in genetic systems of the past generations provides the physical conjunction of entropy and antientropy processes separated from each other in time generations. It is readily apparent from the requirements of the Second law of thermodynamics. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. The physics of complex systems in information and biology

    Science.gov (United States)

    Walker, Dylan

    study the interaction between popularity and quality, we introduce simple stochastic models of user behavior that approximate differing user quality and susceptibility to the common notion of popularity. We define a metric to quantify user reputation in a manner that is self-consistent, adaptable and content-blind and shows good correlation with the probability that a user behaves in an optimal fashion. We further construct a mechanism for ranking documents that take into account user reputation and provides substantial improvement in the time-critical performance of the system. The structure of complex systems have been well studied in the context of both information and biological systems. More recently, dynamics in complex systems that occur over the background of the underlying network has received a great deal of attention. In particular, the study of fluctuations in complex systems has emerged as an issue central to understanding dynamical behavior. We approach the problem of collective effects of the underlying network on dynamical fluctuations by considering the protein-protein interaction networks for the system of the living cell. We consider two types of fluctuations in the mass-action equilibrium in protein binding networks. The first type is driven by relatively slow changes in total concentrations (copy numbers) of interacting proteins. The second type, to which we refer to as spontaneous, is caused by quickly decaying thermodynamic deviations away from the mass-action equilibrium of the system. As such they are amenable to methods of equilibrium statistical mechanics used in our study. We investigate the effects of network connectivity on these fluctuations by comparing them to different scenarios in which the interacting pair is isolated form the rest of the network. Such comparison allows us to analytically derive upper and lower bounds on network fluctuations. The collective effects are shown to sometimes lead to relatively large amplification of

  7. Quantum entanglement and quantum information in biological systems (DNA)

    Science.gov (United States)

    Hubač, Ivan; Švec, Miloslav; Wilson, Stephen

    2017-12-01

    Recent studies of DNA show that the hydrogen bonds between given base pairs can be treated as diabatic systems with spin-orbit coupling. For solid state systems strong diabaticity and spin-orbit coupling the possibility of forming Majorana fermions has been discussed. We analyze the hydrogen bonds in the base pairs in DNA from this perspective. Our analysis is based on a quasiparticle supersymmetric transformation which couples electronic and vibrational motion and includes normal coordinates and the corresponding momenta. We define qubits formed by Majorana fermions in the hydrogen bonds and also discuss the entangled states in base pairs. Quantum information and quantum entropy are introduced. In addition to the well-known classical information connected with the DNA base pairs, we also consider quantum information and show that the classical and quantum information are closely connected.

  8. Systems Biology

    Indian Academy of Sciences (India)

    IAS Admin

    Systems biology seeks to study biological systems as a whole, contrary to the reductionist approach that has dominated biology. Such a view of biological systems emanating from strong foundations of molecular level understanding of the individual components in terms of their form, function and interactions is promising to ...

  9. Information theory in systems biology. Part I: Gene regulatory and metabolic networks.

    Science.gov (United States)

    Mousavian, Zaynab; Kavousi, Kaveh; Masoudi-Nejad, Ali

    2016-03-01

    "A Mathematical Theory of Communication", was published in 1948 by Claude Shannon to establish a framework that is now known as information theory. In recent decades, information theory has gained much attention in the area of systems biology. The aim of this paper is to provide a systematic review of those contributions that have applied information theory in inferring or understanding of biological systems. Based on the type of system components and the interactions between them, we classify the biological systems into 4 main classes: gene regulatory, metabolic, protein-protein interaction and signaling networks. In the first part of this review, we attempt to introduce most of the existing studies on two types of biological networks, including gene regulatory and metabolic networks, which are founded on the concepts of information theory. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Sender-receiver systems and applying information theory for quantitative synthetic biology.

    Science.gov (United States)

    Barcena Menendez, Diego; Senthivel, Vivek Raj; Isalan, Mark

    2015-02-01

    Sender-receiver (S-R) systems abound in biology, with communication systems sending information in various forms. Information theory provides a quantitative basis for analysing these processes and is being applied to study natural genetic, enzymatic and neural networks. Recent advances in synthetic biology are providing us with a wealth of artificial S-R systems, giving us quantitative control over networks with a finite number of well-characterised components. Combining the two approaches can help to predict how to maximise signalling robustness, and will allow us to make increasingly complex biological computers. Ultimately, pushing the boundaries of synthetic biology will require moving beyond engineering the flow of information and towards building more sophisticated circuits that interpret biological meaning. Copyright © 2014. Published by Elsevier Ltd.

  11. Quantum Information Biology: From Theory of Open Quantum Systems to Adaptive Dynamics

    Science.gov (United States)

    Asano, Masanari; Basieva, Irina; Khrennikov, Andrei; Ohya, Masanori; Tanaka, Yoshiharu; Yamato, Ichiro

    This chapter reviews quantum(-like) information biology (QIB). Here biology is treated widely as even covering cognition and its derivatives: psychology and decision making, sociology, and behavioral economics and finances. QIB provides an integrative description of information processing by bio-systems at all scales of life: from proteins and cells to cognition, ecological and social systems. Mathematically QIB is based on the theory of adaptive quantum systems (which covers also open quantum systems). Ideologically QIB is based on the quantum-like (QL) paradigm: complex bio-systems process information in accordance with the laws of quantum information and probability. This paradigm is supported by plenty of statistical bio-data collected at all bio-scales. QIB re ects the two fundamental principles: a) adaptivity; and, b) openness (bio-systems are fundamentally open). In addition, quantum adaptive dynamics provides the most generally possible mathematical representation of these principles.

  12. Information theory in systems biology. Part II: protein-protein interaction and signaling networks.

    Science.gov (United States)

    Mousavian, Zaynab; Díaz, José; Masoudi-Nejad, Ali

    2016-03-01

    By the development of information theory in 1948 by Claude Shannon to address the problems in the field of data storage and data communication over (noisy) communication channel, it has been successfully applied in many other research areas such as bioinformatics and systems biology. In this manuscript, we attempt to review some of the existing literatures in systems biology, which are using the information theory measures in their calculations. As we have reviewed most of the existing information-theoretic methods in gene regulatory and metabolic networks in the first part of the review, so in the second part of our study, the application of information theory in other types of biological networks including protein-protein interaction and signaling networks will be surveyed. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. Systems Biology

    Energy Technology Data Exchange (ETDEWEB)

    Wiley, H S.

    2006-06-01

    The biology revolution over the last 50 years has been driven by the ascendancy of molecular biology. This was enthusiastically embraced by most biologists because it took us into increasingly familiar territory. It took mysterious processes, such as the replication of genetic material and assigned them parts that could be readily understood by the human mind. When we think of ''molecular machines'' as being the underlying basis of life, we are using a paradigm derived from everyday experience. However, the price that we paid was a relentless drive towards reductionism and the attendant balkanization of biology. Now along comes ''systems biology'' that promises us a solution to the problem of ''knowing more and more about less and less''. Unlike molecular biology, systems biology appears to be taking us into unfamiliar intellectual territory, such as statistics, mathematics and computer modeling. Not surprisingly, systems biology has met with widespread skepticism and resistance. Why do we need systems biology anyway and how does this new area of research promise to change the face of biology in the next couple of decades?

  14. Quantum biological information theory

    CERN Document Server

    Djordjevic, Ivan B

    2016-01-01

    This book is a self-contained, tutorial-based introduction to quantum information theory and quantum biology. It serves as a single-source reference to the topic for researchers in bioengineering, communications engineering, electrical engineering, applied mathematics, biology, computer science, and physics. The book provides all the essential principles of the quantum biological information theory required to describe the quantum information transfer from DNA to proteins, the sources of genetic noise and genetic errors as well as their effects. Integrates quantum information and quantum biology concepts; Assumes only knowledge of basic concepts of vector algebra at undergraduate level; Provides a thorough introduction to basic concepts of quantum information processing, quantum information theory, and quantum biology; Includes in-depth discussion of the quantum biological channel modelling, quantum biological channel capacity calculation, quantum models of aging, quantum models of evolution, quantum models o...

  15. Structural biology at York Structural Biology Laboratory; laboratory information management systems for structural genomics

    Czech Academy of Sciences Publication Activity Database

    Dohnálek, Jan

    2005-01-01

    Roč. 12, č. 1 (2005), s. 3 ISSN 1211-5894. [Meeting of Structural Biologists /4./. 10.03.2005-12.03.2005, Nové Hrady] R&D Projects: GA MŠk(CZ) 1K05008 Keywords : structural biology * LIMS * structural genomics Subject RIV: CD - Macromolecular Chemistry

  16. Leaf LIMS: A Flexible Laboratory Information Management System with a Synthetic Biology Focus.

    Science.gov (United States)

    Craig, Thomas; Holland, Richard; D'Amore, Rosalinda; Johnson, James R; McCue, Hannah V; West, Anthony; Zulkower, Valentin; Tekotte, Hille; Cai, Yizhi; Swan, Daniel; Davey, Robert P; Hertz-Fowler, Christiane; Hall, Anthony; Caddick, Mark

    2017-12-15

    This paper presents Leaf LIMS, a flexible laboratory information management system (LIMS) designed to address the complexity of synthetic biology workflows. At the project's inception there was a lack of a LIMS designed specifically to address synthetic biology processes, with most systems focused on either next generation sequencing or biobanks and clinical sample handling. Leaf LIMS implements integrated project, item, and laboratory stock tracking, offering complete sample and construct genealogy, materials and lot tracking, and modular assay data capture. Hence, it enables highly configurable task-based workflows and supports data capture from project inception to completion. As such, in addition to it supporting synthetic biology it is ideal for many laboratory environments with multiple projects and users. The system is deployed as a web application through Docker and is provided under a permissive MIT license. It is freely available for download at https://leaflims.github.io .

  17. Frontiers in transport phenomena research and education: Energy systems, biological systems, security, information technology and nanotechnology

    Energy Technology Data Exchange (ETDEWEB)

    Bergman, T.L.; Faghri, A. [Department of Mechanical Engineering, The University of Connecticut, Storrs, CT 06269-3139 (United States); Viskanta, R. [School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907-2088 (United States)

    2008-09-15

    A US National Science Foundation-sponsored workshop entitled ''Frontiers in Transport Phenomena Research and Education: Energy Systems, Biological Systems, Security, Information Technology, and Nanotechnology'' was held in May of 2007 at the University of Connecticut. The workshop provided a venue for researchers, educators and policy-makers to identify frontier challenges and associated opportunities in heat and mass transfer. Approximately 300 invited participants from academia, business and government from the US and abroad attended. Based upon the final recommendations on the topical matter of the workshop, several trends become apparent. A strong interest in sustainable energy is evident. A continued need to understand the coupling between broad length (and time) scales persists, but the emerging need to better understand transport phenomena at the macro/mega scale has evolved. The need to develop new metrology techniques to collect and archive reliable property data persists. Societal sustainability received major attention in two of the reports. Matters involving innovation, entrepreneurship, and globalization of the engineering profession have emerged, and the responsibility to improve the technical literacy of the public-at-large is discussed. Integration of research thrusts and education activities is highlighted throughout. Specific recommendations, made by the panelists with input from the international heat transfer community and directed to the National Science Foundation, are included in several reports. (author)

  18. Integrating data from biological experiments into metabolic networks with the DBE information system.

    Science.gov (United States)

    Borisjuk, Ljudmilla; Hajirezaei, Mohammad-Reza; Klukas, Christian; Rolletschek, Hardy; Schreiber, Falk

    2005-01-01

    Modern 'omics'-technologies result in huge amounts of data about life processes. For analysis and data mining purposes this data has to be considered in the context of the underlying biological networks. This work presents an approach for integrating data from biological experiments into metabolic networks by mapping the data onto network elements and visualising the data enriched networks automatically. This methodology is implemented in DBE, an information system that supports the analysis and visualisation of experimental data in the context of metabolic networks. It consists of five parts: (1) the DBE-Database for consistent data storage, (2) the Excel-Importer application for the data import, (3) the DBE-Website as the interface for the system, (4) the DBE-Pictures application for the up- and download of binary (e. g. image) files, and (5) DBE-Gravisto, a network analysis and graph visualisation system. The usability of this approach is demonstrated in two examples.

  19. Data-intensive drug development in the information age: applications of Systems Biology/Pharmacology/Toxicology.

    Science.gov (United States)

    Kiyosawa, Naoki; Manabe, Sunao

    2016-01-01

    Pharmaceutical companies continuously face challenges to deliver new drugs with true medical value. R&D productivity of drug development projects depends on 1) the value of the drug concept and 2) data and in-depth knowledge that are used rationally to evaluate the drug concept's validity. A model-based data-intensive drug development approach is a key competitive factor used by innovative pharmaceutical companies to reduce information bias and rationally demonstrate the value of drug concepts. Owing to the accumulation of publicly available biomedical information, our understanding of the pathophysiological mechanisms of diseases has developed considerably; it is the basis for identifying the right drug target and creating a drug concept with true medical value. Our understanding of the pathophysiological mechanisms of disease animal models can also be improved; it can thus support rational extrapolation of animal experiment results to clinical settings. The Systems Biology approach, which leverages publicly available transcriptome data, is useful for these purposes. Furthermore, applying Systems Pharmacology enables dynamic simulation of drug responses, from which key research questions to be addressed in the subsequent studies can be adequately informed. Application of Systems Biology/Pharmacology to toxicology research, namely Systems Toxicology, should considerably improve the predictability of drug-induced toxicities in clinical situations that are difficult to predict from conventional preclinical toxicology studies. Systems Biology/Pharmacology/Toxicology models can be continuously improved using iterative learn-confirm processes throughout preclinical and clinical drug discovery and development processes. Successful implementation of data-intensive drug development approaches requires cultivation of an adequate R&D culture to appreciate this approach.

  20. Social insect colony as a biological regulatory system: modelling information flow in dominance networks.

    Science.gov (United States)

    Nandi, Anjan K; Sumana, Annagiri; Bhattacharya, Kunal

    2014-12-06

    Social insects provide an excellent platform to investigate flow of information in regulatory systems since their successful social organization is essentially achieved by effective information transfer through complex connectivity patterns among the colony members. Network representation of such behavioural interactions offers a powerful tool for structural as well as dynamical analysis of the underlying regulatory systems. In this paper, we focus on the dominance interaction networks in the tropical social wasp Ropalidia marginata-a species where behavioural observations indicate that such interactions are principally responsible for the transfer of information between individuals about their colony needs, resulting in a regulation of their own activities. Our research reveals that the dominance networks of R. marginata are structurally similar to a class of naturally evolved information processing networks, a fact confirmed also by the predominance of a specific substructure-the 'feed-forward loop'-a key functional component in many other information transfer networks. The dynamical analysis through Boolean modelling confirms that the networks are sufficiently stable under small fluctuations and yet capable of more efficient information transfer compared to their randomized counterparts. Our results suggest the involvement of a common structural design principle in different biological regulatory systems and a possible similarity with respect to the effect of selection on the organization levels of such systems. The findings are also consistent with the hypothesis that dominance behaviour has been shaped by natural selection to co-opt the information transfer process in such social insect species, in addition to its primal function of mediation of reproductive competition in the colony. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  1. Synthetic biology with artificially expanded genetic information systems. From personalized medicine to extraterrestrial life.

    Science.gov (United States)

    Benner, Steven A; Hutter, Daniel; Sismour, A Michael

    2003-01-01

    Over 15 years ago, the Benner group noticed that the DNA alphabet need not be limited to the four standard nucleotides known in natural DNA. Rather, twelve nucleobases forming six base pairs joined by mutually exclusive hydrogen bonding patterns are possible within the geometry of the Watson-Crick pair (Fig. 1). Synthesis and studies on these compounds have brought us to the threshold of a synthetic biology, an artificial chemical system that does basic processes needed for life (in particular, Darwinian evolution), but with unnatural chemical structures. At the same time, the artificial genetic information systems (AEGIS) that we have developed have been used in FDA-approved commercial tests for managing HIV and hepatitis C infections in individual patients, and in a tool that seeks the virus for severe acute respiratory syndrome (SARS). AEGIS also supports the next generation of robotic probes to search for genetic molecules on Mars, Europa, and elsewhere where NASA probes will travel.

  2. A framework for modeling information propagation of biological systems at critical states.

    Science.gov (United States)

    Hu, Feng; Yang, Fang

    2016-03-01

    We explore the dynamics of information propagation at the critical state of a biologically inspired system by an individual-based computer model. "Quorum response", a type of social interaction which has been recognized taxonomically in animal groups, is applied as the sole interaction rule among individuals. In the model, we assume a truncated Gaussian distribution to depict the distribution of the individuals' vigilance level. Each individual can assume either a naïve state or an alarmed one and only switches from the former state to the latter one. If an individual has turned into an alarmed state, it stays in the state during the process of information propagation. Initially, each individual is set to be at the naïve state and information is tapped into the system by perturbing an individual at the boundaries (alerting it to the alarmed state). The system evolves as individuals turn into the alarmed state, according to the quorum response rules, consecutively. We find that by fine-tuning the parameters of the mean and the standard deviation of the Gaussian distribution, the system is poised at a critical state. We present the phase diagrams to exhibit that the parameter space is divided into a super-critical and a sub-critical zone, in which the dynamics of information propagation varies largely. We then investigate the effects of the individuals' mobility on the critical state, and allow a proportion of randomly chosen individuals to exchange their positions at each time step. We find that mobility breaks down criticality of the system. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  3. Biologically inspired information theory: Adaptation through construction of external reality models by living systems.

    Science.gov (United States)

    Nakajima, Toshiyuki

    2015-12-01

    Higher animals act in the world using their external reality models to cope with the uncertain environment. Organisms that have not developed such information-processing organs may also have external reality models built in the form of their biochemical, physiological, and behavioral structures, acquired by natural selection through successful models constructed internally. Organisms subject to illusions would fail to survive in the material universe. How can organisms, or living systems in general, determine the external reality from within? This paper starts with a phenomenological model, in which the self constitutes a reality model developed through the mental processing of phenomena. Then, the it-from-bit concept is formalized using a simple mathematical model. For this formalization, my previous work on an algorithmic process is employed to constitute symbols referring to the external reality, called the inverse causality, with additional improvements to the previous work. Finally, as an extension of this model, the cognizers system model is employed to describe the self as one of many material entities in a world, each of which acts as a subject by responding to the surrounding entities. This model is used to propose a conceptual framework of information theory that can deal with both the qualitative (semantic) and quantitative aspects of the information involved in biological processes. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. Fröhlich Condensate: Emergence of Synergetic Dissipative Structures in Information Processing Biological and Condensed Matter Systems

    Directory of Open Access Journals (Sweden)

    Roberto Luzzi

    2012-10-01

    Full Text Available We consider the case of a peculiar complex behavior in open boson systems sufficiently away from equilibrium, having relevance in the functioning of information-processing biological and condensed matter systems. This is the so-called Fröhlich–Bose–Einstein condensation, a self-organizing-synergetic dissipative structure, a phenomenon apparently working in biological processes and present in several cases of systems of boson-like quasi-particles in condensed inorganic matter. Emphasis is centered on the quantum-mechanical-statistical irreversible thermodynamics of these open systems, and the informational characteristics of the phenomena.

  5. Energy and information flows in biological systems: Bioenergy transduction of V1-ATPase rotary motor and dynamics of thermodynamic entropy in information flows.

    Science.gov (United States)

    Yamato, Ichiro; Murata, Takeshi; Khrennikov, Andrei

    2017-11-01

    We classify research fields in biology with respect to flows of materials, energy, and information. We investigate energy transducing mechanisms in biology, using as a representative the typical molecular rotary motor V 1 -ATPase from a bacterium Enterococcus hirae. The structures of several intermediates of the rotary motor are described and the molecular mechanism of the motor converting chemical energy into mechanical energy is discussed. Comments and considerations on the information flows in biology, especially on the thermodynamic entropy in quantum physical and biological systems, are presented in section 3 in a biologist friendly manner. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Traceability of Biologics in The Netherlands: An Analysis of Information-Recording Systems in Clinical Practice and Spontaneous ADR Reports.

    Science.gov (United States)

    Klein, Kevin; Scholl, Joep H G; Vermeer, Niels S; Broekmans, André W; Van Puijenbroek, Eugène P; De Bruin, Marie L; Stolk, Pieter

    2016-02-01

    Pharmacovigilance requirements for biologics mandate that EU Member States shall ensure that any biologic that is the subject of a suspected adverse drug reaction (ADR) is identifiable by brand name and batch number. Recent studies showed that brand name identification is well established, whereas batch numbers are (still) poorly reported. We evaluated information-recording systems and practices in the Dutch hospital setting to identify determinants for brand name and batch number recording as well as success factors and bottlenecks for traceability. We surveyed Dutch hospital pharmacists with an online questionnaire on systems and practices in hospitals for recording brand names and batch numbers. Additionally, we performed an analysis of the traceability of recombinant biologics in spontaneous ADR reports (received between 2009 and 2014) from the Netherlands Pharmacovigilance Centre Lareb. The survey showed that brand names are not routinely recorded in the clinical practice of Dutch hospitals, whereas batch numbers are poorly recorded. Seventy-six percent of the 1523 ADR reports for recombinant biologics had a traceable brand name whereas 5% of these reports contained a batch number. The results suggest a possible relationship between the availability of brand and batch number information in clinical practice and the inclusion of this information in ADR reports for biologics. The limited traceability of brand names and batch numbers in ADR reports may be primarily caused by the shortcomings in the recording of information in clinical practice. We recommend efforts to improve information-recording systems as a first step to improve the traceability of biologics in ADR reporting.

  7. Evolution, Entropy, & Biological Information

    Science.gov (United States)

    Peterson, Jacob

    2014-01-01

    A logical question to be expected from students: "How could life develop, that is, change, evolve from simple, primitive organisms into the complex forms existing today, while at the same time there is a generally observed decline and disorganization--the second law of thermodynamics?" The explanations in biology textbooks relied upon by…

  8. The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory.

    Science.gov (United States)

    Morris, Chris; Pajon, Anne; Griffiths, Susanne L; Daniel, Ed; Savitsky, Marc; Lin, Bill; Diprose, Jonathan M; da Silva, Alan Wilter; Pilicheva, Katya; Troshin, Peter; van Niekerk, Johannes; Isaacs, Neil; Naismith, James; Nave, Colin; Blake, Richard; Wilson, Keith S; Stuart, David I; Henrick, Kim; Esnouf, Robert M

    2011-04-01

    The techniques used in protein production and structural biology have been developing rapidly, but techniques for recording the laboratory information produced have not kept pace. One approach is the development of laboratory information-management systems (LIMS), which typically use a relational database schema to model and store results from a laboratory workflow. The underlying philosophy and implementation of the Protein Information Management System (PiMS), a LIMS development specifically targeted at the flexible and unpredictable workflows of protein-production research laboratories of all scales, is described. PiMS is a web-based Java application that uses either Postgres or Oracle as the underlying relational database-management system. PiMS is available under a free licence to all academic laboratories either for local installation or for use as a managed service.

  9. Biological conversion system

    Science.gov (United States)

    Scott, C.D.

    A system for bioconversion of organic material comprises a primary bioreactor column wherein a biological active agent (zymomonas mobilis) converts the organic material (sugar) to a product (alcohol), a rejuvenator column wherein the biological activity of said biological active agent is enhanced, and means for circulating said biological active agent between said primary bioreactor column and said rejuvenator column.

  10. Static Analysis for Systems Biology

    DEFF Research Database (Denmark)

    Nielson, Flemming; Nielson, Hanne Riis; Rosa, D. Schuch da

    2004-01-01

    This paper shows how static analysis techniques can help understanding biological systems. Based on a simple example we illustrate the outcome of performing three different analyses extracting information of increasing precision. We conclude by reporting on the potential impact and exploitation o...... of these techniques in systems biology....

  11. Information Visualization for Biological Data.

    Science.gov (United States)

    Czauderna, Tobias; Schreiber, Falk

    2017-01-01

    Visualization is a powerful method to present and explore a large amount of data. It is increasingly important in the life sciences and is used for analyzing different types of biological data, such as structural information, high-throughput data, and biochemical networks. This chapter gives a brief introduction to visualization methods for bioinformatics, presents two commonly used techniques in detail, and discusses a graphical standard for biological networks and cellular processes.

  12. The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Morris, Chris [STFC Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Pajon, Anne [Wellcome Trust Genome Campus, Hinxton CB10 1SD (United Kingdom); Griffiths, Susanne L. [University of York, Heslington, York YO10 5DD (United Kingdom); Daniel, Ed [STFC Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Savitsky, Marc [University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Lin, Bill [STFC Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Diprose, Jonathan M. [University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Wilter da Silva, Alan [Wellcome Trust Genome Campus, Hinxton CB10 1SD (United Kingdom); Pilicheva, Katya [University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Troshin, Peter [STFC Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Niekerk, Johannes van [University of Dundee, Dundee DD1 5EH, Scotland (United Kingdom); Isaacs, Neil [University of Glasgow, Glasgow G12 8QQ, Scotland (United Kingdom); Naismith, James [University of St Andrews, St Andrews, Fife KY16 9ST, Scotland (United Kingdom); Nave, Colin; Blake, Richard [STFC Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Wilson, Keith S. [University of York, Heslington, York YO10 5DD (United Kingdom); Stuart, David I. [University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Henrick, Kim [Wellcome Trust Genome Campus, Hinxton CB10 1SD (United Kingdom); Esnouf, Robert M., E-mail: robert@strubi.ox.ac.uk [University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); STFC Daresbury Laboratory, Warrington WA4 4AD (United Kingdom)

    2011-04-01

    The Protein Information Management System (PiMS) is described together with a discussion of how its features make it well suited to laboratories of all sizes. The techniques used in protein production and structural biology have been developing rapidly, but techniques for recording the laboratory information produced have not kept pace. One approach is the development of laboratory information-management systems (LIMS), which typically use a relational database schema to model and store results from a laboratory workflow. The underlying philosophy and implementation of the Protein Information Management System (PiMS), a LIMS development specifically targeted at the flexible and unpredictable workflows of protein-production research laboratories of all scales, is described. PiMS is a web-based Java application that uses either Postgres or Oracle as the underlying relational database-management system. PiMS is available under a free licence to all academic laboratories either for local installation or for use as a managed service.

  13. Biological and Chemical Information Technologies

    DEFF Research Database (Denmark)

    Amos, Martyn; Dittrich, Peter; McCaskill, John

    2011-01-01

    Biological and chemical information technologies (bio/chem IT) have the potential to reshape the scientific and technological landscape. In this paper we briefly review the main challenges and opportunities in the field, before presenting several case studies based on ongoing FP7 research projects....

  14. Systems Biology of Metabolism.

    Science.gov (United States)

    Nielsen, Jens

    2017-06-20

    Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology are described, and two different types of mathematical models used for studying metabolism are discussed: kinetic models and genome-scale metabolic models. The use of different omics technologies, including transcriptomics, proteomics, metabolomics, and fluxomics, for studying metabolism is presented. Finally, the application of systems biology for analyzing global regulatory structures, engineering the metabolism of cell factories, and analyzing human diseases is discussed.

  15. Fröhlich Coherent States: Implications for Interaction in Biological Systems and Information Transfer

    Czech Academy of Sciences Publication Activity Database

    Pokorný, Jiří

    1995-01-01

    Roč. 5, č. 5 (1995), s. 831-847 ISSN 1210-0552. [Biophysical Aspects of Coherence. Praha, 11.09.1995-15.09.1995] R&D Projects: GA ČR 202/94/1055 Keywords : cellular biophysics * self-organising storage * information theory

  16. Models of neural networks temporal aspects of coding and information processing in biological systems

    CERN Document Server

    Hemmen, J; Schulten, Klaus

    1994-01-01

    Since the appearance of Vol. 1 of Models of Neural Networks in 1991, the theory of neural nets has focused on two paradigms: information coding through coherent firing of the neurons and functional feedback. Information coding through coherent neuronal firing exploits time as a cardinal degree of freedom. This capacity of a neural network rests on the fact that the neuronal action potential is a short, say 1 ms, spike, localized in space and time. Spatial as well as temporal correlations of activity may represent different states of a network. In particular, temporal correlations of activity may express that neurons process the same "object" of, for example, a visual scene by spiking at the very same time. The traditional description of a neural network through a firing rate, the famous S-shaped curve, presupposes a wide time window of, say, at least 100 ms. It thus fails to exploit the capacity to "bind" sets of coherently firing neurons for the purpose of both scene segmentation and figure-ground segregatio...

  17. Teaching systems biology.

    Science.gov (United States)

    Alves, R; Vilaprinyo, E; Sorribas, A

    2011-03-01

    Advances in systems biology are increasingly dependent upon the integration of various types of data and different methodologies to reconstruct how cells work at the systemic level. Thus, teams with a varied array of expertise and people with interdisciplinary training are needed. So far this training was thought to be more productive if aimed at the Masters or PhD level. At this level, multiple specialised and in-depth courses on the different subject matters of systems biology are taught to already well-prepared students. This approach is mostly based on the recognition that systems biology requires a wide background that is hard to find in undergraduate students. Nevertheless, and given the importance of the field, the authors argue that exposition of undergraduate students to the methods and paradigms of systems biology would be advantageous. Here they present and discuss a successful experiment in teaching systems biology to third year undergraduate biotechnology students at the University of Lleida in Spain. The authors' experience, together with that from others, argues for the adequateness of teaching systems biology at the undergraduate level. [Includes supplementary material].

  18. Text mining for systems biology.

    Science.gov (United States)

    Fluck, Juliane; Hofmann-Apitius, Martin

    2014-02-01

    Scientific communication in biomedicine is, by and large, still text based. Text mining technologies for the automated extraction of useful biomedical information from unstructured text that can be directly used for systems biology modelling have been substantially improved over the past few years. In this review, we underline the importance of named entity recognition and relationship extraction as fundamental approaches that are relevant to systems biology. Furthermore, we emphasize the role of publicly organized scientific benchmarking challenges that reflect the current status of text-mining technology and are important in moving the entire field forward. Given further interdisciplinary development of systems biology-orientated ontologies and training corpora, we expect a steadily increasing impact of text-mining technology on systems biology in the future. Copyright © 2013 Elsevier Ltd. All rights reserved.

  19. Systems Biology and Health Systems Complexity in;

    NARCIS (Netherlands)

    Donald Combs, C.; Barham, S.R.; Sloot, P.M.A.

    2016-01-01

    Systems biology addresses interactions in biological systems at different scales of biological organization, from the molecular to the cellular, organ, organism, societal, and ecosystem levels. This chapter expands on the concept of systems biology, explores its implications for individual patients

  20. Nutritional Systems Biology

    DEFF Research Database (Denmark)

    Jensen, Kasper

    and network biology has the potential to increase our understanding of how small molecules affect metabolic pathways and homeostasis, how this perturbation changes at the disease state, and to what extent individual genotypes contribute to this. A fruitful strategy in approaching and exploring the field...... biology research. The paper also shows as a proof-of-concept that a systems biology approach to diet is meaningful and demonstrates some basic principles on how to work with diet systematic. The second chapter of this thesis we developed the resource NutriChem v1.0. A foodchemical database linking...... sites of diet on the disease pathway. We propose a framework for interrogating the critical targets in colon cancer process and identifying plant-based dietary interventions as important modifiers using a systems chemical biology approach. The fifth chapter of the thesis is on discovering of novel anti...

  1. Pragmatic information in biology and physics.

    Science.gov (United States)

    Roederer, Juan G

    2016-03-13

    I will show how an objective definition of the concept of information and the consideration of recent results about information processing in the human brain help clarify some fundamental aspects of physics and biology. Rather than attempting to define information ab initio, I introduce the concept of interaction between material bodies as a primary concept. Two distinct categories can be identified: (i) interactions which can always be reduced to a superposition of physical interactions (forces) between elementary constituents; and (ii) interactions between complex bodies which cannot be expressed as a superposition of interactions between parts, and in which patterns and forms (in space and/or time) play the determining role. Pragmatic information is then defined as the link between a given pattern and the ensuing pattern-specific change. I will show that pragmatic information is a biological concept; it plays no active role in the purely physical domain-it only does so when a living organism intervenes. The consequences for physics (including foundations of quantum mechanics) and biology (including brain function) will be discussed. This will include speculations about three fundamental transitions, from the quantum to the classical domain, from natural inanimate to living systems, and from subhuman to human brain information-processing operations, introduced here in their direct connection with the concept of pragmatic information. © 2016 The Author(s).

  2. Plant Systems Biology (editorial)

    Science.gov (United States)

    In June 2003, Plant Physiology published an Arabidopsis special issue devoted to plant systems biology. The intention of Natasha Raikhel and Gloria Coruzzi, the two editors of this first-of-its-kind issue, was ‘‘to help nucleate this new effort within the plant community’’ as they considered that ‘‘...

  3. Systems biology at work

    NARCIS (Netherlands)

    Martins Dos Santos, V.A.P.; Damborsky, J.

    2010-01-01

    In his editorial overview for the 2008 Special Issue on this topic, the late Jaroslav Stark pointedly noted that systems biology is no longer a niche pursuit, but a recognized discipline in its own right “noisily” coming of age [1]. Whilst general underlying principles and basic techniques are now

  4. 7th Annual Systems Biology Symposium: Systems Biology and Engineering

    Energy Technology Data Exchange (ETDEWEB)

    Galitski, Timothy P.

    2008-04-01

    Systems biology recognizes the complex multi-scale organization of biological systems, from molecules to ecosystems. The International Symposium on Systems Biology has been hosted by the Institute for Systems Biology in Seattle, Washington, since 2002. The annual two-day event gathers the most influential researchers transforming biology into an integrative discipline investingating complex systems. Engineering and application of new technology is a central element of systems biology. Genome-scale, or very small-scale, biological questions drive the enigneering of new technologies, which enable new modes of experimentation and computational analysis, leading to new biological insights and questions. Concepts and analytical methods in engineering are now finding direct applications in biology. Therefore, the 2008 Symposium, funded in partnership with the Department of Energy, featured global leaders in "Systems Biology and Engineering."

  5. Integrative radiation systems biology

    International Nuclear Information System (INIS)

    Unger, Kristian

    2014-01-01

    Maximisation of the ratio of normal tissue preservation and tumour cell reduction is the main concept of radiotherapy alone or combined with chemo-, immuno- or biologically targeted therapy. The foremost parameter influencing this ratio is radiation sensitivity and its modulation towards a more efficient killing of tumour cells and a better preservation of normal tissue at the same time is the overall aim of modern therapy schemas. Nevertheless, this requires a deep understanding of the molecular mechanisms of radiation sensitivity in order to identify its key players as potential therapeutic targets. Moreover, the success of conventional approaches that tried to statistically associate altered radiation sensitivity with any molecular phenotype such as gene expression proofed to be somewhat limited since the number of clinically used targets is rather sparse. However, currently a paradigm shift is taking place from pure frequentistic association analysis to the rather holistic systems biology approach that seeks to mathematically model the system to be investigated and to allow the prediction of an altered phenotype as the function of one single or a signature of biomarkers. Integrative systems biology also considers the data from different molecular levels such as the genome, transcriptome or proteome in order to partially or fully comprehend the causal chain of molecular mechanisms. An example for the application of this concept currently carried out at the Clinical Cooperation Group “Personalized Radiotherapy in Head and Neck Cancer” of the Helmholtz-Zentrum München and the LMU Munich is described. This review article strives for providing a compact overview on the state of the art of systems biology, its actual challenges, potential applications, chances and limitations in radiation oncology research working towards improved personalised therapy concepts using this relatively new methodology

  6. Systems biology in animal sciences

    NARCIS (Netherlands)

    Woelders, H.; Pas, te M.F.W.; Bannink, A.; Veerkamp, R.F.; Smits, M.A.

    2011-01-01

    Systems biology is a rapidly expanding field of research and is applied in a number of biological disciplines. In animal sciences, omics approaches are increasingly used, yielding vast amounts of data, but systems biology approaches to extract understanding from these data of biological processes

  7. Applicability of Computational Systems Biology in Toxicology

    DEFF Research Database (Denmark)

    Kongsbak, Kristine Grønning; Hadrup, Niels; Audouze, Karine Marie Laure

    2014-01-01

    be used to establish hypotheses on links between the chemical and human diseases. Such information can also be applied for designing more intelligent animal/cell experiments that can test the established hypotheses. Here, we describe how and why to apply an integrative systems biology method......Systems biology as a research field has emerged within the last few decades. Systems biology, often defined as the antithesis of the reductionist approach, integrates information about individual components of a biological system. In integrative systems biology, large data sets from various sources...... and databases are used to model and predict effects of chemicals on, for instance, human health. In toxicology, computational systems biology enables identification of important pathways and molecules from large data sets; tasks that can be extremely laborious when performed by a classical literature search...

  8. Fostering synergy between cell biology and systems biology.

    Science.gov (United States)

    Eddy, James A; Funk, Cory C; Price, Nathan D

    2015-08-01

    In the shared pursuit of elucidating detailed mechanisms of cell function, systems biology presents a natural complement to ongoing efforts in cell biology. Systems biology aims to characterize biological systems through integrated and quantitative modeling of cellular information. The process of model building and analysis provides value through synthesizing and cataloging information about cells and molecules, predicting mechanisms and identifying generalizable themes, generating hypotheses and guiding experimental design, and highlighting knowledge gaps and refining understanding. In turn, incorporating domain expertise and experimental data is crucial for building towards whole cell models. An iterative cycle of interaction between cell and systems biologists advances the goals of both fields and establishes a framework for mechanistic understanding of the genome-to-phenome relationship. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

  9. Logical analysis of biological systems

    DEFF Research Database (Denmark)

    Mardare, Radu Iulian

    2005-01-01

    R. Mardare, Logical analysis of biological systems. Fundamenta Informaticae, N 64:271-285, 2005.......R. Mardare, Logical analysis of biological systems. Fundamenta Informaticae, N 64:271-285, 2005....

  10. LANGUAGE SYSTEM: INFORMATION, INFORMATIONAL CONTENT, INFORMATION TRANSFERITY

    Directory of Open Access Journals (Sweden)

    Elvira Galievna Zarifullina

    2014-10-01

    Full Text Available The article is devoted to research of language system as information system. To this point of view informational content and information transferity are properties of language as main and the most fail-safe communication instrument in human society.  In whole, informational content and information transferity are aspects of information. In that meaning the language realizes function that associated with database of information system: realization of information in formalized form, accumulation, storage and information transfer.But language itself is not an information. Information is language and speech, created with language. Language should be defined as database, because in human thought language doesn’t present as information, but as the formalized model, the system, which elements are bounded with each other and united by the algorithms. The modern forms of language existence are distributed database with multiple accesses, because language belongs to language native bearers, which use it simultaneously.

  11. The Physics behind Systems Biology

    Directory of Open Access Journals (Sweden)

    Radde Nicole E.

    2016-12-01

    Full Text Available Systems Biology is a young and rapidly evolving research field, which combines experimental techniques and mathematical modeling in order to achieve a mechanistic understanding of processes underlying the regulation and evolution of living systems. Systems Biology is often associated with an Engineering approach: The purpose is to formulate a data-rich, detailed simulation model that allows to perform numerical (‘in silico’ experiments and then draw conclusions about the biological system. While methods from Engineering may be an appropriate approach to extending the scope of biological investigations to experimentally inaccessible realms and to supporting data-rich experimental work, it may not be the best strategy in a search for design principles of biological systems and the fundamental laws underlying Biology. Physics has a long tradition of characterizing and understanding emergent collective behaviors in systems of interacting units and searching for universal laws. Therefore, it is natural that many concepts used in Systems Biology have their roots in Physics. With an emphasis on Theoretical Physics, we will here review the ‘Physics core’ of Systems Biology, show how some success stories in Systems Biology can be traced back to concepts developed in Physics, and discuss how Systems Biology can further benefit from its Theoretical Physics foundation.

  12. Information theory applications for biological sequence analysis.

    Science.gov (United States)

    Vinga, Susana

    2014-05-01

    Information theory (IT) addresses the analysis of communication systems and has been widely applied in molecular biology. In particular, alignment-free sequence analysis and comparison greatly benefited from concepts derived from IT, such as entropy and mutual information. This review covers several aspects of IT applications, ranging from genome global analysis and comparison, including block-entropy estimation and resolution-free metrics based on iterative maps, to local analysis, comprising the classification of motifs, prediction of transcription factor binding sites and sequence characterization based on linguistic complexity and entropic profiles. IT has also been applied to high-level correlations that combine DNA, RNA or protein features with sequence-independent properties, such as gene mapping and phenotype analysis, and has also provided models based on communication systems theory to describe information transmission channels at the cell level and also during evolutionary processes. While not exhaustive, this review attempts to categorize existing methods and to indicate their relation with broader transversal topics such as genomic signatures, data compression and complexity, time series analysis and phylogenetic classification, providing a resource for future developments in this promising area.

  13. Traceability of Biologics in The Netherlands : An Analysis of Information-Recording Systems in Clinical Practice and Spontaneous ADR Reports

    NARCIS (Netherlands)

    Klein, Kevin; Scholl, Joep H G; Vermeer, Niels S; Broekmans, André W; Van Puijenbroek, Eugène P; De Bruin, Marie L; Stolk, Pieter

    INTRODUCTION AND OBJECTIVE: Pharmacovigilance requirements for biologics mandate that EU Member States shall ensure that any biologic that is the subject of a suspected adverse drug reaction (ADR) is identifiable by brand name and batch number. Recent studies showed that brand name identification is

  14. Data Systems vs. Information Systems

    OpenAIRE

    Amatayakul, Margret K.

    1982-01-01

    This paper examines the current status of “hospital information systems” with respect to the distinction between data systems and information systems. It is proposed that the systems currently existing are incomplete data dystems resulting in ineffective information systems.

  15. Mammalian Synthetic Biology: Engineering Biological Systems.

    Science.gov (United States)

    Black, Joshua B; Perez-Pinera, Pablo; Gersbach, Charles A

    2017-06-21

    The programming of new functions into mammalian cells has tremendous application in research and medicine. Continued improvements in the capacity to sequence and synthesize DNA have rapidly increased our understanding of mechanisms of gene function and regulation on a genome-wide scale and have expanded the set of genetic components available for programming cell biology. The invention of new research tools, including targetable DNA-binding systems such as CRISPR/Cas9 and sensor-actuator devices that can recognize and respond to diverse chemical, mechanical, and optical inputs, has enabled precise control of complex cellular behaviors at unprecedented spatial and temporal resolution. These tools have been critical for the expansion of synthetic biology techniques from prokaryotic and lower eukaryotic hosts to mammalian systems. Recent progress in the development of genome and epigenome editing tools and in the engineering of designer cells with programmable genetic circuits is expanding approaches to prevent, diagnose, and treat disease and to establish personalized theranostic strategies for next-generation medicines. This review summarizes the development of these enabling technologies and their application to transforming mammalian synthetic biology into a distinct field in research and medicine.

  16. Electromagnetic fields in biological systems

    National Research Council Canada - National Science Library

    Lin, James C

    2012-01-01

    "Focusing on exposure, induced fields, and absorbed energy, this volume covers the interaction of electromagnetic fields and waves with biological systems, spanning static fields to terahertz waves...

  17. Mapping biological systems to network systems

    CERN Document Server

    Rathore, Heena

    2016-01-01

    The book presents the challenges inherent in the paradigm shift of network systems from static to highly dynamic distributed systems – it proposes solutions that the symbiotic nature of biological systems can provide into altering networking systems to adapt to these changes. The author discuss how biological systems – which have the inherent capabilities of evolving, self-organizing, self-repairing and flourishing with time – are inspiring researchers to take opportunities from the biology domain and map them with the problems faced in network domain. The book revolves around the central idea of bio-inspired systems -- it begins by exploring why biology and computer network research are such a natural match. This is followed by presenting a broad overview of biologically inspired research in network systems -- it is classified by the biological field that inspired each topic and by the area of networking in which that topic lies. Each case elucidates how biological concepts have been most successfully ...

  18. Information technology developments within the national biological information infrastructure

    Science.gov (United States)

    Cotter, G.; Frame, M.T.

    2000-01-01

    Looking out an office window or exploring a community park, one can easily see the tremendous challenges that biological information presents the computer science community. Biological information varies in format and content depending whether or not it is information pertaining to a particular species (i.e. Brown Tree Snake), or a specific ecosystem, which often includes multiple species, land use characteristics, and geospatially referenced information. The complexity and uniqueness of each individual species or ecosystem do not easily lend themselves to today's computer science tools and applications. To address the challenges that the biological enterprise presents the National Biological Information Infrastructure (NBII) (http://www.nbii.gov) was established in 1993. The NBII is designed to address these issues on a National scale within the United States, and through international partnerships abroad. This paper discusses current computer science efforts within the National Biological Information Infrastructure Program and future computer science research endeavors that are needed to address the ever-growing issues related to our Nation's biological concerns.

  19. Telemetry System of Biological Parameters

    Directory of Open Access Journals (Sweden)

    Jan Spisak

    2005-01-01

    Full Text Available The mobile telemetry system of biological parameters serves for reading and wireless data transfer of measured values of selected biological parameters to an outlying computer. It concerns basically long time monitoring of vital function of car pilot.The goal of this projects is to propose mobile telemetry system for reading, wireless transfer and processing of biological parameters of car pilot during physical and psychical stress. It has to be made with respect to minimal consumption, weight and maximal device mobility. This system has to eliminate signal noise, which is created by biological artifacts and disturbances during the data transfer.

  20. Excited states in biological systems

    International Nuclear Information System (INIS)

    Cilento, G.; Zinner, K.; Bechara, E.J.H.; Duran, N.; Baptista, R.C. de; Shimizu, Y.; Augusto, O.; Faljoni-Alario, A.; Vidigal, C.C.C.; Oliveira, O.M.M.F.; Haun, M.

    1979-01-01

    Some aspects of bioluminescence related to bioenergetics are discussed: 1. chemical generation of excited species, by means of two general processes: electron transference and cyclic - and linear peroxide cleavage; 2. biological systems capable of generating excited states and 3. biological functions of these states, specially the non-emissive ones (tripletes). The production and the role of non-emissive excited states in biological systems are analysed, the main purpose of the study being the search for non-emissive states. Experiences carried out in biological systems are described; results and conclusions are given. (M.A.) [pt

  1. Systems Biology and Livestock Science

    NARCIS (Netherlands)

    Pas, te M.F.W.; Woelders, H.; Bannink, A.

    2011-01-01

    Systems Biology is an interdisciplinary approach to the study of life made possible through the explosion of molecular data made available through the genome revolution and the simultaneous development of computational technologies that allow us to interpret these large data sets. Systems Biology

  2. Quantum Effects in Biological Systems

    CERN Document Server

    2016-01-01

    Since the last decade the study of quantum mechanical phenomena in biological systems has become a vibrant field of research. Initially sparked by evidence of quantum effects in energy transport that is instrumental for photosynthesis, quantum biology asks the question of how methods and models from quantum theory can help us to understand fundamental mechanisms in living organisms. This approach entails a paradigm change challenging the related disciplines: The successful framework of quantum theory is taken out of its low-temperature, microscopic regimes and applied to hot and dense macroscopic environments, thereby extending the toolbox of biology and biochemistry at the same time. The Quantum Effects in Biological Systems conference is a platform for researchers from biology, chemistry and physics to present and discuss the latest developments in the field of quantum biology. After meetings in Lisbon (2009), Harvard (2010), Ulm (2011), Berkeley (2012), Vienna (2013), Singapore (2014) and Florence (2015),...

  3. Redefining plant systems biology: from cell to ecosystem

    NARCIS (Netherlands)

    Keurentjes, J.J.B.; Angenent, G.C.; Dicke, M.; Martins Dos Santos, V.A.P.; Molenaar, J.; Van der Putten, W.H.; de Ruiter, P.C.; Struik, P.C.; Thomma, B.P.H.J.

    2011-01-01

    Molecular biologists typically restrict systems biology to cellular levels. By contrast, ecologists define biological systems as communities of interacting individuals at different trophic levels that process energy, nutrient and information flows. Modern plant breeding needs to increase

  4. Saccharomyces genome database informs human biology

    OpenAIRE

    Skrzypek, Marek S; Nash, Robert S; Wong, Edith D; MacPherson, Kevin A; Hellerstedt, Sage T; Engel, Stacia R; Karra, Kalpana; Weng, Shuai; Sheppard, Travis K; Binkley, Gail; Simison, Matt; Miyasato, Stuart R; Cherry, J Michael

    2017-01-01

    Abstract The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is an expertly curated database of literature-derived functional information for the model organism budding yeast, Saccharomyces cerevisiae. SGD constantly strives to synergize new types of experimental data and bioinformatics predictions with existing data, and to organize them into a comprehensive and up-to-date information resource. The primary mission of SGD is to facilitate research into the biology of yeast and...

  5. Electromagnetic fields in biological systems

    CERN Document Server

    Lin, James C

    2016-01-01

    As wireless technology becomes more sophisticated and accessible to more users, the interactions of electromagnetic fields with biological systems have captured the interest not only of the scientific community but also the general public. Unintended or deleterious biological effects of electromagnetic fields and radiation may indicate grounds for health and safety precautions in their use. Spanning static fields to terahertz waves, Electromagnetic Fields in Biological Systems explores the range of consequences these fields have on the human body. With contributions by an array of experts, topics discussed include: Essential interactions and field coupling phenomena, highlighting their importance in research on biological effects and in scientific, industrial, and medical applications Electric field interactions in cells, focusing on ultrashort, pulsed high-intensity fields The effect of exposure to naturally occurring and human-made static, low-frequency, and pulsed magnetic fields in biological systems Dosi...

  6. Aeronautical Information System -

    Data.gov (United States)

    Department of Transportation — The Aeronautical Information System (AIS) is a leased weather automated system that provides a means of collecting and distributing aeronautical weather information...

  7. Validation of systems biology models

    NARCIS (Netherlands)

    Hasdemir, D.

    2015-01-01

    The paradigm shift from qualitative to quantitative analysis of biological systems brought a substantial number of modeling approaches to the stage of molecular biology research. These include but certainly are not limited to nonlinear kinetic models, static network models and models obtained by the

  8. An engineering design approach to systems biology.

    Science.gov (United States)

    Janes, Kevin A; Chandran, Preethi L; Ford, Roseanne M; Lazzara, Matthew J; Papin, Jason A; Peirce, Shayn M; Saucerman, Jeffrey J; Lauffenburger, Douglas A

    2017-07-17

    Measuring and modeling the integrated behavior of biomolecular-cellular networks is central to systems biology. Over several decades, systems biology has been shaped by quantitative biologists, physicists, mathematicians, and engineers in different ways. However, the basic and applied versions of systems biology are not typically distinguished, which blurs the separate aspirations of the field and its potential for real-world impact. Here, we articulate an engineering approach to systems biology, which applies educational philosophy, engineering design, and predictive models to solve contemporary problems in an age of biomedical Big Data. A concerted effort to train systems bioengineers will provide a versatile workforce capable of tackling the diverse challenges faced by the biotechnological and pharmaceutical sectors in a modern, information-dense economy.

  9. Bioinformatics for systems biology

    National Research Council Canada - National Science Library

    Krawetz, Stephen A

    2009-01-01

    ..., requires an unprecedented level of development to collect, manage and mine the data for interesting associations. To begin to understand this information we now rely on statistical analysis to aid in our selection of the fruit from the tree. However, this often takes us on a journey into a new field for which we are not yet prepared. Samuel Joh...

  10. Parallel Information Phenomena of Biology and Astrophysics

    Science.gov (United States)

    Frieden, B. Roy; Soffer, Bernard H.

    The realms of biology and astrophysics are usually regarded as distinct, to be studied within individual frameworks. However, current searches for life in the universe, and the expectation of positive results, are guiding us toward a unification of biology and astrophysics called astrobiology. In this chapter the unifying aspect of Fisher information is shown to form two bridges of astrobiology: (i) In Section 5.1 quarter-power laws are found to both describe attributes of biology, such as metabolism rate, and attributes of the cosmos, in particular its universal constants, (ii) In Section 5.2 we find that the Lotka-Volterra growth equations of biology follow from quantum mechanics. Both these bridges follow, ultimately, from the extreme physical information EPI principle and, hence, are examples of the “cooperative” universe discussed in Chapter 1. That is, the universe cooperates with our goal of understanding it, through participatory observation. The participatory aspect of the effect (i) is the observation of biological and cosmological attributes obeying quarter-power laws. In the Lotka-Volterra quantum effect (ii) the participation is the observation of a general particle member that undergoes scattering by a complex potential. This potential causes the growth or depletion of the particle population levels to obey Lotka-Volterra equations. Effectively, the interaction potentials of a standard Hartree view of the scattering process become corresponding fitness coefficients of the L-V growth equations. The two ostensibly unrelated effects of scattering and biological growth are thereby intimately related; out of a common flow of Fisher information to the observer.

  11. Systems biology of human atherosclerosis.

    Science.gov (United States)

    Shalhoub, Joseph; Sikkel, Markus B; Davies, Kerry J; Vorkas, Panagiotis A; Want, Elizabeth J; Davies, Alun H

    2014-01-01

    Systems biology describes a holistic and integrative approach to understand physiology and pathology. The "omic" disciplines include genomics, transcriptomics, proteomics, and metabolic profiling (metabonomics and metabolomics). By adopting a stance, which is opposing (yet complimentary) to conventional research techniques, systems biology offers an overview by assessing the "net" biological effect imposed by a disease or nondisease state. There are a number of different organizational levels to be understood, from DNA to protein, metabolites, cells, organs and organisms, even beyond this to an organism's context. Systems biology relies on the existence of "nodes" and "edges." Nodes are the constituent part of the system being studied (eg, proteins in the proteome), while the edges are the way these constituents interact. In future, it will be increasingly important to collaborate, collating data from multiple studies to improve data sets, making them freely available and undertaking integrative analyses.

  12. Compositional Modeling of Biological Systems

    OpenAIRE

    Zámborszky, Judit

    2010-01-01

    Molecular interactions are wired in a fascinating way resulting in complex behavior of bio-logical systems. Theoretical modeling provides us a useful framework for understanding the dynamics and the function of such networks. The complexity of the biological systems calls for conceptual tools that manage the combinatorial explosion of the set of possible interac-tions. A suitable conceptual tool to attack complexity is compositionality, already success-fully used in the process algebra field ...

  13. Ten questions about systems biology

    DEFF Research Database (Denmark)

    Joyner, Michael J; Pedersen, Bente K

    2011-01-01

    In this paper we raise 'ten questions' broadly related to 'omics', the term systems biology, and why the new biology has failed to deliver major therapeutic advances for many common diseases, especially diabetes and cardiovascular disease. We argue that a fundamentally narrow and reductionist...... to understand how whole animals adapt to the real world. We argue that a lack of fluency in these concepts is a major stumbling block for what has been narrowly defined as 'systems biology' by some of its leading advocates. We also point out that it is a failure of regulation at multiple levels that causes many...

  14. Information Systems Security Audit

    OpenAIRE

    Gheorghe Popescu; Veronica Adriana Popescu; Cristina Raluca Popescu

    2007-01-01

    The article covers:Defining an information system; benefits obtained by introducing new information technologies; IT management;Defining prerequisites, analysis, design, implementation of IS; Information security management system; aspects regarding IS security policy; Conceptual model of a security system; Auditing information security systems and network infrastructure security.

  15. New Approaches in Cancer Biology Can Inform the Biology Curriculum.

    Science.gov (United States)

    Jones, Lynda; Gordon, Diana; Zelinski, Mary

    2018-03-01

    Students tend to be very interested in medical issues that affect them and their friends and family. Using cancer as a hook, the ART of Reproductive Medicine: Oncofertility curriculum (free, online, and NIH sponsored) has been developed to supplement the teaching of basic biological concepts and to connect biology and biomedical research. This approach allows integration of up-to-date information on cancer and cancer treatment, cell division, male and female reproductive anatomy and physiology, cryopreservation, fertility preservation, stem cells, ethics, and epigenetics into an existing biology curriculum. Many of the topics covered in the curriculum relate to other scientific disciplines, such as the latest developments in stem cell research including tissue bioengineering and gene therapy for inherited mitochondrial disease, how epigenetics occurs chemically to affect gene expression or suppression and how it can be passed down through the generations, and the variety of biomedical careers students could pursue. The labs are designed to be open-ended and inquiry-based, and extensions to the experiments are provided so that students can explore questions further. Case studies and ethical dilemmas are provided to encourage thoughtful discussion. In addition, each chapter of the curriculum includes links to scientific papers, additional resources on each topic, and NGSS alignment.

  16. Designing information systems

    CERN Document Server

    Blethyn, Stanley G

    2014-01-01

    Designing Information Systems focuses on the processes, methodologies, and approaches involved in designing information systems. The book first describes systems, management and control, and how to design information systems. Discussions focus on documents produced from the functional construction function, users, operators, analysts, programmers and others, process management and control, levels of management, open systems, design of management information systems, and business system description, partitioning, and leveling. The text then takes a look at functional specification and functiona

  17. Quantum Information Biology: From Information Interpretation of Quantum Mechanics to Applications in Molecular Biology and Cognitive Psychology

    Science.gov (United States)

    Asano, Masanari; Basieva, Irina; Khrennikov, Andrei; Ohya, Masanori; Tanaka, Yoshiharu; Yamato, Ichiro

    2015-10-01

    We discuss foundational issues of quantum information biology (QIB)—one of the most successful applications of the quantum formalism outside of physics. QIB provides a multi-scale model of information processing in bio-systems: from proteins and cells to cognitive and social systems. This theory has to be sharply distinguished from "traditional quantum biophysics". The latter is about quantum bio-physical processes, e.g., in cells or brains. QIB models the dynamics of information states of bio-systems. We argue that the information interpretation of quantum mechanics (its various forms were elaborated by Zeilinger and Brukner, Fuchs and Mermin, and D' Ariano) is the most natural interpretation of QIB. Biologically QIB is based on two principles: (a) adaptivity; (b) openness (bio-systems are fundamentally open). These principles are mathematically represented in the framework of a novel formalism— quantum adaptive dynamics which, in particular, contains the standard theory of open quantum systems.

  18. Cognition and biology: perspectives from information theory.

    Science.gov (United States)

    Wallace, Rodrick

    2014-02-01

    The intimate relation between biology and cognition can be formally examined through statistical models constrained by the asymptotic limit theorems of communication theory, augmented by methods from statistical mechanics and nonequilibrium thermodynamics. Cognition, often involving submodules that act as information sources, is ubiquitous across the living state. Less metabolic free energy is consumed by permitting crosstalk between biological information sources than by isolating them, leading to evolutionary exaptations that assemble shifting, tunable cognitive arrays at multiple scales, and levels of organization to meet dynamic patterns of threat and opportunity. Cognition is thus necessary for life, but it is not sufficient: An organism represents a highly patterned outcome of path-dependent, blind, variation, selection, interaction, and chance extinction in the context of an adequate flow of free energy and an environment fit for development. Complex, interacting cognitive processes within an organism both record and instantiate those evolutionary and developmental trajectories.

  19. Development trend of radiation biology research-systems radiation biology

    International Nuclear Information System (INIS)

    Min Rui

    2010-01-01

    Radiation biology research has past 80 years. We have known much more about fundamentals, processes and results of biology effects induced by radiation and various factors that influence biology effects wide and deep, however many old and new scientific problems occurring in the field of radiation biology research remain to be illustrated. To explore and figure these scientific problems need systemic concept, methods and multi dimension view on the base of considerations of complexity of biology system, diversity of biology response, temporal and spatial process of biological effects during occurrence, and complex feed back network of biological regulations. (authors)

  20. Systems biology: leading the revolution in ecotoxicology.

    Science.gov (United States)

    Garcia-Reyero, Natàlia; Perkins, Edward J

    2011-02-01

    The rapid development of new technologies such as transcriptomics, proteomics, and metabolomics (Omics) are changing the way ecotoxicology is practiced. The data deluge has begun with genomes of over 65 different aquatic species that are currently being sequenced, and many times that number with at least some level of transcriptome sequencing. Integrating these top-down methodologies is an essential task in the field of systems biology. Systems biology is a biology-based interdisciplinary field that focuses on complex interactions in biological systems, with the intent to model and discover emergent properties of the system. Recent studies demonstrate that Omics technologies provide valuable insight into ecotoxicity, both in laboratory exposures with model organisms and with animals exposed in the field. However, these approaches require a context of the whole animal and population to be relevant. Powerful approaches using reverse engineering to determine interacting networks of genes, proteins, or biochemical reactions are uncovering unique responses to toxicants. Modeling efforts in aquatic animals are evolving to interrelate the interacting networks of a system and the flow of information linking these elements. Just as is happening in medicine, systems biology approaches that allow the integration of many different scales of interaction and information are already driving a revolution in understanding the impacts of pollutants on aquatic systems. © 2010 SETAC.

  1. Inverse problems in systems biology

    International Nuclear Information System (INIS)

    Engl, Heinz W; Lu, James; Müller, Stefan; Flamm, Christoph; Schuster, Peter; Kügler, Philipp

    2009-01-01

    Systems biology is a new discipline built upon the premise that an understanding of how cells and organisms carry out their functions cannot be gained by looking at cellular components in isolation. Instead, consideration of the interplay between the parts of systems is indispensable for analyzing, modeling, and predicting systems' behavior. Studying biological processes under this premise, systems biology combines experimental techniques and computational methods in order to construct predictive models. Both in building and utilizing models of biological systems, inverse problems arise at several occasions, for example, (i) when experimental time series and steady state data are used to construct biochemical reaction networks, (ii) when model parameters are identified that capture underlying mechanisms or (iii) when desired qualitative behavior such as bistability or limit cycle oscillations is engineered by proper choices of parameter combinations. In this paper we review principles of the modeling process in systems biology and illustrate the ill-posedness and regularization of parameter identification problems in that context. Furthermore, we discuss the methodology of qualitative inverse problems and demonstrate how sparsity enforcing regularization allows the determination of key reaction mechanisms underlying the qualitative behavior. (topical review)

  2. Dynamics of Information Systems

    CERN Document Server

    Hirsch, Michael J; Murphey, Robert

    2010-01-01

    Our understanding of information and information dynamics has outgrown classical information theory. This book presents the research explaining the importance of information in the evolution of a distributed or networked system. It presents techniques for measuring the value or significance of information within the context of a system

  3. Nanoscale technology in biological systems

    CERN Document Server

    Greco, Ralph S; Smith, R Lane

    2004-01-01

    Reviewing recent accomplishments in the field of nanobiology Nanoscale Technology in Biological Systems introduces the application of nanoscale matrices to human biology. It focuses on the applications of nanotechnology fabrication to biomedical devices and discusses new physical methods for cell isolation and manipulation and intracellular communication at the molecular level. It also explores the application of nanobiology to cardiovascular diseases, oncology, transplantation, and a range of related disciplines. This book build a strong background in nanotechnology and nanobiology ideal for

  4. Aeronautical Information System Replacement -

    Data.gov (United States)

    Department of Transportation — Aeronautical Information System Replacement is a web-enabled, automation means for the collection and distribution of Service B messages, weather information, flight...

  5. Carbon-13 NMR spectroscopy of biological systems

    CERN Document Server

    Beckmann, Nicolau

    1995-01-01

    This book is intended to provide an in-depth understanding of 13C NMR as a tool in biological research. 13C NMR has provided unique information concerning complex biological systems, from proteins and nucleic acids to animals and humans. The subjects addressed include multidimensional heteronuclear techniques for structural studies of molecules in the liquid and solid states, the investigation of interactions in model membranes, the elucidation of metabolic pathwaysin vitro and in vivo on animals, and noninvasive metabolic studies performed on humans. The book is a unique mix of NMR methods and biological applications which makes it a convenient reference for those interested in research in this interdisciplinary area of physics, chemistry, biology, and medicine.Key Features* An interdisciplinary text with emphasis on both 13C NMR methodology and the relevant biological and biomedical issues* State-of-the-art 13C NMR techniques are described; Whenever possible, their advantages over other approaches are empha...

  6. Systems biology approach to bioremediation

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, Romy; Wu, Cindy H.; Hazen, Terry C.

    2012-06-01

    Bioremediation has historically been approached as a ‘black box’ in terms of our fundamental understanding. Thus it succeeds and fails, seldom without a complete understanding of why. Systems biology is an integrated research approach to study complex biological systems, by investigating interactions and networks at the molecular, cellular, community, and ecosystem level. The knowledge of these interactions within individual components is fundamental to understanding the dynamics of the ecosystem under investigation. Finally, understanding and modeling functional microbial community structure and stress responses in environments at all levels have tremendous implications for our fundamental understanding of hydrobiogeochemical processes and the potential for making bioremediation breakthroughs and illuminating the ‘black box’.

  7. Geographical information systems

    DEFF Research Database (Denmark)

    Möller, Bernd

    2004-01-01

    The chapter gives an introduction to Geographical Information Systems (GIS) with particular focus on their application within environmental management.......The chapter gives an introduction to Geographical Information Systems (GIS) with particular focus on their application within environmental management....

  8. 2007 Chemical Biological Information Systems

    Science.gov (United States)

    2007-01-11

    Surface roughness • Surface albedo • Bowen ratio • Canopy Height • Canopy Flow Index – Based on 1993-1994 GOES AVHRR datasets. NDIA CBIS 11 January 2007...industrial areas). • Recommended replacement: – 2004-2005 MODIS database for natural surfaces merged with the 2002 30-m LANDSAT based USGS database for...Tundra 22=Mixed Tundra 23=Bare Tundra 24= Snow or Ice 25=Partly Developed • Land Use Methodology: Surrogate for Air Quality NOx vs VOC (vary by Latitude

  9. Systems biology: the reincarnation of systems theory applied in biology?

    Science.gov (United States)

    Wolkenhauer, O

    2001-09-01

    With the availability of quantitative data on the transcriptome and proteome level, there is an increasing interest in formal mathematical models of gene expression and regulation. International conferences, research institutes and research groups concerned with systems biology have appeared in recent years and systems theory, the study of organisation and behaviour per se, is indeed a natural conceptual framework for such a task. This is, however, not the first time that systems theory has been applied in modelling cellular processes. Notably in the 1960s systems theory and biology enjoyed considerable interest among eminent scientists, mathematicians and engineers. Why did these early attempts vanish from research agendas? Here we shall review the domain of systems theory, its application to biology and the lessons that can be learned from the work of Robert Rosen. Rosen emerged from the early developments in the 1960s as a main critic but also developed a new alternative perspective to living systems, a concept that deserves a fresh look in the post-genome era of bioinformatics.

  10. Airports Geographic Information System -

    Data.gov (United States)

    Department of Transportation — The Airports Geographic Information System maintains the airport and aeronautical data required to meet the demands of the Next Generation National Airspace System....

  11. Saccharomyces genome database informs human biology.

    Science.gov (United States)

    Skrzypek, Marek S; Nash, Robert S; Wong, Edith D; MacPherson, Kevin A; Hellerstedt, Sage T; Engel, Stacia R; Karra, Kalpana; Weng, Shuai; Sheppard, Travis K; Binkley, Gail; Simison, Matt; Miyasato, Stuart R; Cherry, J Michael

    2018-01-04

    The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is an expertly curated database of literature-derived functional information for the model organism budding yeast, Saccharomyces cerevisiae. SGD constantly strives to synergize new types of experimental data and bioinformatics predictions with existing data, and to organize them into a comprehensive and up-to-date information resource. The primary mission of SGD is to facilitate research into the biology of yeast and to provide this wealth of information to advance, in many ways, research on other organisms, even those as evolutionarily distant as humans. To build such a bridge between biological kingdoms, SGD is curating data regarding yeast-human complementation, in which a human gene can successfully replace the function of a yeast gene, and/or vice versa. These data are manually curated from published literature, made available for download, and incorporated into a variety of analysis tools provided by SGD. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Integrative Systems Biology Visualization with MAYDAY

    Directory of Open Access Journals (Sweden)

    Symonsy Stephan

    2010-12-01

    Full Text Available Visualization is pivotal for gaining insight in systems biology data. As the size and complexity of datasets and supplemental information increases, an efficient, integrated framework for general and specialized views is necessary. MAYDAY is an application for analysis and visualization of general ‘omics’ data. It follows a trifold approach for data visualization, consisting of flexible data preprocessing, highly customizable data perspective plots for general purpose visualization and systems based plots. Here, we introduce two new systems biology visualization tools for MAYDAY. Efficiently implemented genomic viewers allow the display of variables associated with genomic locations. Multiple variables can be viewed using our new track-based ChromeTracks tool. A functional perspective is provided by visualizing metabolic pathways either in KEGG or BioPax format. Multiple options of displaying pathway components are available, including Systems Biology Graphical Notation (SBGN glyphs. Furthermore, pathways can be viewed together with gene expression data either as heatmaps or profiles.

  13. Lofar information system design

    NARCIS (Netherlands)

    Valentijn, E.; Belikov, A. N.

    2009-01-01

    The Lofar Information System is a solution for Lofar Long Term Archive that is capable to store and handle PBs of raw and processed data. The newly created information system is based on Astro-WISE - the information system for wide field astronomy. We review an adaptation of Astro-WISE for the new

  14. Systems biology of cellular rhythms.

    Science.gov (United States)

    Goldbeter, A; Gérard, C; Gonze, D; Leloup, J-C; Dupont, G

    2012-08-31

    Rhythms abound in biological systems, particularly at the cellular level where they originate from the feedback loops present in regulatory networks. Cellular rhythms can be investigated both by experimental and modeling approaches, and thus represent a prototypic field of research for systems biology. They have also become a major topic in synthetic biology. We review advances in the study of cellular rhythms of biochemical rather than electrical origin by considering a variety of oscillatory processes such as Ca++ oscillations, circadian rhythms, the segmentation clock, oscillations in p53 and NF-κB, synthetic oscillators, and the oscillatory dynamics of cyclin-dependent kinases driving the cell cycle. Finally we discuss the coupling between cellular rhythms and their robustness with respect to molecular noise.

  15. Systems Biology of Industrial Microorganisms

    Science.gov (United States)

    Papini, Marta; Salazar, Margarita; Nielsen, Jens

    The field of industrial biotechnology is expanding rapidly as the chemical industry is looking towards more sustainable production of chemicals that can be used as fuels or building blocks for production of solvents and materials. In connection with the development of sustainable bioprocesses, it is a major challenge to design and develop efficient cell factories that can ensure cost efficient conversion of the raw material into the chemical of interest. This is achieved through metabolic engineering, where the metabolism of the cell factory is engineered such that there is an efficient conversion of sugars, the typical raw materials in the fermentation industry, into the desired product. However, engineering of cellular metabolism is often challenging due to the complex regulation that has evolved in connection with adaptation of the different microorganisms to their ecological niches. In order to map these regulatory structures and further de-regulate them, as well as identify ingenious metabolic engineering strategies that full-fill mass balance constraints, tools from systems biology can be applied. This involves both high-throughput analysis tools like transcriptome, proteome and metabolome analysis, as well as the use of mathematical modeling to simulate the phenotypes resulting from the different metabolic engineering strategies. It is in fact expected that systems biology may substantially improve the process of cell factory development, and we therefore propose the term Industrial Systems Biology for how systems biology will enhance the development of industrial biotechnology for sustainable chemical production.

  16. Radiation interactions with biological systems.

    Science.gov (United States)

    Islam, Muhammad Torequl

    2017-05-01

    The use of radiation, especially ionizing radiation (IR), is currently attracting great attention in the field of medical sciences. However, it should be mentioned that IR has both beneficial and harmful effects in biological systems. This review aims to focus on IR-mediated physiological events in a mechanistic way. Evidence from the databases, mainly from PUBMED and SCIENCE DIRECT were considered. IR directly and/or with their lyses products (indirect) causes oxidative stresses to biological systems. These activities may be localized and systematic. Otherwise, IR-induced non-/multi-targeted effects are also evident. IR in diagnosis and cancer radiotherapy is well-known. Reactive species produced by IR are not only beneficial, but also can exert harmful effects in a biological system such as aging, genetic instability and mutagenicity, membrane lysis and cell death, alteration of enzymatic activity and metabolic events, mitochondrial dysfunction, and even cancer. Additionally, DNA adducts formation, after IR-induced DNA breakage, is a cause of blockage of DNA repair capability with an increase in cellular radiosensitivity. These may allow cellular ruin even at low IR levels. Dependent on the dose, duration of action and quality, IR plays diverse roles in biological systems.

  17. Tunable promoters in systems biology

    DEFF Research Database (Denmark)

    Mijakovic, Ivan; Petranovic, Dina; Jensen, Peter Ruhdal

    2005-01-01

    The construction of synthetic promoter libraries has represented a major breakthrough in systems biology, enabling the subtle tuning of enzyme activities. A number of tools are now available that allow the modulation of gene expression and the detection of changes in expression patterns. But, how...

  18. Information systems project management

    CERN Document Server

    Olson, David

    2014-01-01

    Information Systems Project Management addresses project management in the context of information systems. It deals with general project management principles, with focus on the special characteristics of information systems. It is based on an earlier text, but shortened to focus on essential project management elements.This updated version presents various statistics indicating endemic problems in completing information system projects on time, within budget, at designed functionality. While successful completion of an information systems project is a challenge, there are some things that ca

  19. Information theory of molecular systems

    CERN Document Server

    Nalewajski, Roman F

    2006-01-01

    As well as providing a unified outlook on physics, Information Theory (IT) has numerous applications in chemistry and biology owing to its ability to provide a measure of the entropy/information contained within probability distributions and criteria of their information ""distance"" (similarity) and independence. Information Theory of Molecular Systems applies standard IT to classical problems in the theory of electronic structure and chemical reactivity. The book starts by introducing the basic concepts of modern electronic structure/reactivity theory based upon the Density Functional Theory

  20. Statistical approach for selection of biologically informative genes.

    Science.gov (United States)

    Das, Samarendra; Rai, Anil; Mishra, D C; Rai, Shesh N

    2018-05-20

    Selection of informative genes from high dimensional gene expression data has emerged as an important research area in genomics. Many gene selection techniques have been proposed so far are either based on relevancy or redundancy measure. Further, the performance of these techniques has been adjudged through post selection classification accuracy computed through a classifier using the selected genes. This performance metric may be statistically sound but may not be biologically relevant. A statistical approach, i.e. Boot-MRMR, was proposed based on a composite measure of maximum relevance and minimum redundancy, which is both statistically sound and biologically relevant for informative gene selection. For comparative evaluation of the proposed approach, we developed two biological sufficient criteria, i.e. Gene Set Enrichment with QTL (GSEQ) and biological similarity score based on Gene Ontology (GO). Further, a systematic and rigorous evaluation of the proposed technique with 12 existing gene selection techniques was carried out using five gene expression datasets. This evaluation was based on a broad spectrum of statistically sound (e.g. subject classification) and biological relevant (based on QTL and GO) criteria under a multiple criteria decision-making framework. The performance analysis showed that the proposed technique selects informative genes which are more biologically relevant. The proposed technique is also found to be quite competitive with the existing techniques with respect to subject classification and computational time. Our results also showed that under the multiple criteria decision-making setup, the proposed technique is best for informative gene selection over the available alternatives. Based on the proposed approach, an R Package, i.e. BootMRMR has been developed and available at https://cran.r-project.org/web/packages/BootMRMR. This study will provide a practical guide to select statistical techniques for selecting informative genes

  1. International cooperative information systems

    International Nuclear Information System (INIS)

    1980-01-01

    Developing countries need mechanisms by which the information they generate themselves and development information from the rest of the world can be retrieved. The international cooperative information system is such a mechanism. Delegates to the Seminar on International Cooperative Information Systems were informed about various existing systems (INIS, AGRIS, INFOTERRA, TCDC/INRES, POPIN, DEVSIS, and INPADROC), some specialized information systems and services (CDS/ISIS and the Cassava Information Centre), and computer programs for information processing (INIS/AGRIS, CDS/ISIS, and MINISIS). The participants suggested some changes that should be made on both the national and the international levels to ensure that these systems meet the needs of developing countries more effectively. (LL)

  2. IAEA safeguards information system

    International Nuclear Information System (INIS)

    Nardi, J.

    1984-01-01

    The basic concepts, structure, and operation of the Agency Safeguards Information System is discussed with respect to its role in accomplishing the overall objectives of safeguards. The basis and purposes of the Agency's information system, the structure and flow of information within the Agency's system, the relationship of the components is the Agency system, the requirements of Member States in respect of their reporting to the Agency, and the relationship of accounting data vis-a-vis facility and inspection data are described

  3. Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

    Science.gov (United States)

    Chen, Bor-Sen; Wu, Chia-Chou

    2013-01-01

    Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. PMID:24709875

  4. Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

    Directory of Open Access Journals (Sweden)

    Bor-Sen Chen

    2013-10-01

    Full Text Available Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

  5. Systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

    Science.gov (United States)

    Chen, Bor-Sen; Wu, Chia-Chou

    2013-10-11

    Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

  6. Information system metaphors

    NARCIS (Netherlands)

    Gazendam, H.W.M.

    1999-01-01

    Metaphors are useful because they are efficient: they transfer a complex of meaning in a few words. Information systems are social constructs. Therefore, metaphors seem to be especially useful for explaining the space of possible meaning complexes or designs of information systems. Three information

  7. Mobile Student Information System

    Science.gov (United States)

    Asif, Muhammad; Krogstie, John

    2011-01-01

    Purpose: A mobile student information system (MSIS) based on mobile computing and context-aware application concepts can provide more user-centric information services to students. The purpose of this paper is to describe a system for providing relevant information to students on a mobile platform. Design/methodology/approach: The research…

  8. Micro Information Systems

    DEFF Research Database (Denmark)

    Ulslev Pedersen, Rasmus; Kühn Pedersen, Mogens

    2014-01-01

    such as medical and manufacturing. These new sensor applications have implications for information systems (IS) and, the authors visualize this new class of information systems as fractals growing from an established class of systems; namely that of information systems (IS). The identified applications...... and implications are used as an empirical basis for creating a model for these small new information systems. Such sensor systems are called embedded systems in the technical sciences, and the authors want to couple it with general IS. They call the merger of these two important research areas (IS and embedded...... systems) for micro information systems (micro-IS). It is intended as a new research field within IS research. An initial framework model is established, which seeks to capture both the possibilities and constraints of this new paradigm, while looking simultaneously at the fundamental IS and ICT aspects...

  9. Integrated inventory information system

    Digital Repository Service at National Institute of Oceanography (India)

    Sarupria, J.S.; Kunte, P.D.

    The nature of oceanographic data and the management of inventory level information are described in Integrated Inventory Information System (IIIS). It is shown how a ROSCOPO (report on observations/samples collected during oceanographic programme...

  10. Health Information Systems

    International Development Research Centre (IDRC) Digital Library (Canada)

    health information system can mean peoples' basic needs are unmet. Reducing silos and ensuring community input. Through its Governance and Equity in. Health Systems (GEHS) program, IDRC invests in research and training to help low- and middle-income countries strengthen their health information systems. The aim ...

  11. LOFAR Information System

    NARCIS (Netherlands)

    Begeman, K.; Belikov, A. N.; Boxhoorn, D. R.; Dijkstra, F.; Holties, H.; Meyer-Zhao, Z.; Renting, G. A.; Valentijn, E. A.; Vriend, W. -J.

    In this paper, we present a newly designed and implemented scientific information system for the LOFAR Long Term Archive. It is a distributed multi-tier storage and data processing system that allows a number of users to process Petabytes of data. The LOFAR Information System is designed on the base

  12. Information extraction system

    Science.gov (United States)

    Lemmond, Tracy D; Hanley, William G; Guensche, Joseph Wendell; Perry, Nathan C; Nitao, John J; Kidwell, Paul Brandon; Boakye, Kofi Agyeman; Glaser, Ron E; Prenger, Ryan James

    2014-05-13

    An information extraction system and methods of operating the system are provided. In particular, an information extraction system for performing meta-extraction of named entities of people, organizations, and locations as well as relationships and events from text documents are described herein.

  13. [Circadian rhythms and systems biology].

    Science.gov (United States)

    Goldbeter, Albert; Gérard, Claude; Leloup, Jean-Christophe

    2010-01-01

    Cellular rhythms represent a field of choice for studies in system biology. The examples of circadian rhythms and of the cell cycle show how the experimental and modeling approaches contribute to clarify the conditions in which periodic behavior spontaneously arises in regulatory networks at the cellular level. Circadian rhythms originate from intertwined positive and negative feedback loops controlling the expression of several clock genes. Models can be used to address the dynamical bases of physiological disorders related to dysfunctions of the mammalian circadian clock. The cell cycle is driven by a network of cyclin-dependent kinases (Cdks). Modeled in the form of four modules coupled through multiple regulatory interactions, the Cdk network operates in an oscillatory manner in the presence of sufficient amounts of growth factor. For circadian rhythms and the cell cycle, as for other recently observed cellular rhythms, periodic behavior represents an emergent property of biological systems related to their regulatory structure.

  14. Ten questions about systems biology

    DEFF Research Database (Denmark)

    Joyner, Michael J; Pedersen, Bente K

    2011-01-01

    In this paper we raise 'ten questions' broadly related to 'omics', the term systems biology, and why the new biology has failed to deliver major therapeutic advances for many common diseases, especially diabetes and cardiovascular disease. We argue that a fundamentally narrow and reductionist...... perspective about the contribution of genes and genetic variants to disease is a key reason 'omics' has failed to deliver the anticipated breakthroughs. We then point out the critical utility of key concepts from physiology like homeostasis, regulated systems and redundancy as major intellectual tools...... common diseases. Finally, we attempt to integrate our critique of reductionism into a broader social framework about so-called translational research in specific and the root causes of common diseases in general. Throughout we offer ideas and suggestions that might be incorporated into the current...

  15. Carbon nanomaterials in biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Pu Chun Ke [Laboratory of Single-Molecule Biophysics and Polymer Physics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29634 (United States); Qiao Rui [Department of Mechanical Engineering, Clemson University, Clemson, SC 29634 (United States)

    2007-09-19

    This paper intends to reflect, from the biophysical viewpoint, our current understanding on interfacing nanomaterials, such as carbon nanotubes and fullerenes, with biological systems. Strategies for improving the solubility, and therefore, the bioavailability of nanomaterials in aqueous solutions are summarized. In particular, the underlining mechanisms of attaching biomacromolecules (DNA, RNA, proteins) and lysophospholipids onto carbon nanotubes and gallic acids onto fullerenes are analyzed. The diffusion and the cellular delivery of RNA-coated carbon nanotubes are characterized using fluorescence microscopy. The translocation of fullerenes across cell membranes is simulated using molecular dynamics to offer new insight into the complex issue of nanotoxicity. To assess the fate of nanomaterials in the environment, the biomodification of lipid-coated carbon nanotubes by the aquatic organism Daphnia magna is discussed. The aim of this paper is to illuminate the need for adopting multidisciplinary approaches in the field study of nanomaterials in biological systems and in the environment. (topical review)

  16. Carbon nanomaterials in biological systems

    International Nuclear Information System (INIS)

    Pu Chun Ke; Qiao Rui

    2007-01-01

    This paper intends to reflect, from the biophysical viewpoint, our current understanding on interfacing nanomaterials, such as carbon nanotubes and fullerenes, with biological systems. Strategies for improving the solubility, and therefore, the bioavailability of nanomaterials in aqueous solutions are summarized. In particular, the underlining mechanisms of attaching biomacromolecules (DNA, RNA, proteins) and lysophospholipids onto carbon nanotubes and gallic acids onto fullerenes are analyzed. The diffusion and the cellular delivery of RNA-coated carbon nanotubes are characterized using fluorescence microscopy. The translocation of fullerenes across cell membranes is simulated using molecular dynamics to offer new insight into the complex issue of nanotoxicity. To assess the fate of nanomaterials in the environment, the biomodification of lipid-coated carbon nanotubes by the aquatic organism Daphnia magna is discussed. The aim of this paper is to illuminate the need for adopting multidisciplinary approaches in the field study of nanomaterials in biological systems and in the environment. (topical review)

  17. Heavy ion action on biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Kiefer, J. [Giessen Univ. (Germany). Zentrum fuer Radiologie; Brend`amour, M. [Giessen Univ. (Germany). Zentrum fuer Radiologie; Stoll, U. [Giessen Univ. (Germany). Zentrum fuer Radiologie

    1996-02-01

    Life is governed by molecular processes, particularly involving the expression and conservation of genetic information. Heavy ions deposit large amount of energy at very small scale comparable to the essential molecular structures of biological systems. This paper illustrates the special aspects of heavy ion radiobiology from a fundamental point of view. After a short summary of the structure and function of biological systems, concentrating on the cell and its constituents, the pattern of energy deposition by heavy ions is discussed. Experimental examples are the induction of molecular changes in deoxyribonucleic acid, cell killing and the formation of mutations. It is shown that a close link exists between the physical parameters and the inactivation of biological functions that is not restricted to direct particle traversals but may also be brought about by the action of far-reaching secondary electrons. (orig.).

  18. Biological Potential in Serpentinizing Systems

    Science.gov (United States)

    Hoehler, Tori M.

    2016-01-01

    Generation of the microbial substrate hydrogen during serpentinization, the aqueous alteration of ultramafic rocks, has focused interest on the potential of serpentinizing systems to support biological communities or even the origin of life. However the process also generates considerable alkalinity, a challenge to life, and both pH and hydrogen concentrations vary widely across natural systems as a result of different host rock and fluid composition and differing physical and hydrogeologic conditions. Biological potential is expected to vary in concert. We examined the impact of such variability on the bioenergetics of an example metabolism, methanogenesis, using a cell-scale reactive transport model to compare rates of metabolic energy generation as a function of physicochemical environment. Potential rates vary over more than 5 orders of magnitude, including bioenergetically non-viable conditions, across the range of naturally occurring conditions. In parallel, we assayed rates of hydrogen metabolism in wells associated with the actively serpentinizing Coast Range Ophiolite, which includes conditions more alkaline and considerably less reducing than is typical of serpentinizing systems. Hydrogen metabolism is observed at pH approaching 12 but, consistent with the model predictions, biological methanogenesis is not observed.

  19. Revitalizing executive information systems.

    Science.gov (United States)

    Crockett, F

    1992-01-01

    As the saying goes, "garbage in, garbage out"--and this is as true for executive information systems as for any other computer system. Crockett presents a methodology he has used with clients to help them develop more useful systems that produce higher quality information. The key is to develop performance measures based on critical success factors and stakeholder expectations and then to link them cross functionally to show how progress is being made on strategic goals. Feedback from the executive information system then informs strategy formulation, business plan development, and operational activities.

  20. Anion binding in biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Feiters, Martin C [Department of Organic Chemistry, Institute for Molecules and Materials, Faculty of Science, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands); Meyer-Klaucke, Wolfram [EMBL Hamburg Outstation at DESY, Notkestrasse 85, D-22607 Hamburg (Germany); Kostenko, Alexander V; Soldatov, Alexander V [Faculty of Physics, Southern Federal University, Sorge 5, Rostov-na-Donu, 344090 (Russian Federation); Leblanc, Catherine; Michel, Gurvan; Potin, Philippe [Centre National de la Recherche Scientifique and Universite Pierre et Marie Curie Paris-VI, Station Biologique de Roscoff, Place Georges Teissier, BP 74, F-29682 Roscoff cedex, Bretagne (France); Kuepper, Frithjof C [Scottish Association for Marine Science, Dunstaffnage Marine Laboratory, Oban, Argyll PA37 1QA, Scotland (United Kingdom); Hollenstein, Kaspar; Locher, Kaspar P [Institute of Molecular Biology and Biophysics, ETH Zuerich, Schafmattstrasse 20, Zuerich, 8093 (Switzerland); Bevers, Loes E; Hagedoorn, Peter-Leon; Hagen, Wilfred R, E-mail: m.feiters@science.ru.n [Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft (Netherlands)

    2009-11-15

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L{sub 3} (2p{sub 3/2}) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  1. Anion binding in biological systems

    International Nuclear Information System (INIS)

    Feiters, Martin C; Meyer-Klaucke, Wolfram; Kostenko, Alexander V; Soldatov, Alexander V; Leblanc, Catherine; Michel, Gurvan; Potin, Philippe; Kuepper, Frithjof C; Hollenstein, Kaspar; Locher, Kaspar P; Bevers, Loes E; Hagedoorn, Peter-Leon; Hagen, Wilfred R

    2009-01-01

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L 3 (2p 3/2 ) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  2. Anion binding in biological systems

    Science.gov (United States)

    Feiters, Martin C.; Meyer-Klaucke, Wolfram; Kostenko, Alexander V.; Soldatov, Alexander V.; Leblanc, Catherine; Michel, Gurvan; Potin, Philippe; Küpper, Frithjof C.; Hollenstein, Kaspar; Locher, Kaspar P.; Bevers, Loes E.; Hagedoorn, Peter-Leon; Hagen, Wilfred R.

    2009-11-01

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L3 (2p3/2) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  3. Integrated Reporting Information System -

    Data.gov (United States)

    Department of Transportation — The Integrated Reporting Information System (IRIS) is a flexible and scalable web-based system that supports post operational analysis and evaluation of the National...

  4. Nonlinear dynamics in biological systems

    CERN Document Server

    Carballido-Landeira, Jorge

    2016-01-01

    This book presents recent research results relating to applications of nonlinear dynamics, focusing specifically on four topics of wide interest: heart dynamics, DNA/RNA, cell mobility, and proteins. The book derives from the First BCAM Workshop on Nonlinear Dynamics in Biological Systems, held in June 2014 at the Basque Center of Applied Mathematics (BCAM). At this international meeting, researchers from different but complementary backgrounds, including molecular dynamics, physical chemistry, bio-informatics and biophysics, presented their most recent results and discussed the future direction of their studies using theoretical, mathematical modeling and experimental approaches. Such was the level of interest stimulated that the decision was taken to produce this publication, with the organizers of the event acting as editors. All of the contributing authors are researchers working on diverse biological problems that can be approached using nonlinear dynamics. The book will appeal especially to applied math...

  5. Creating databases for biological information: an introduction.

    Science.gov (United States)

    Stein, Lincoln

    2013-06-01

    The essence of bioinformatics is dealing with large quantities of information. Whether it be sequencing data, microarray data files, mass spectrometric data (e.g., fingerprints), the catalog of strains arising from an insertional mutagenesis project, or even large numbers of PDF files, there inevitably comes a time when the information can simply no longer be managed with files and directories. This is where databases come into play. This unit briefly reviews the characteristics of several database management systems, including flat file, indexed file, relational databases, and NoSQL databases. It compares their strengths and weaknesses and offers some general guidelines for selecting an appropriate database management system. Copyright 2013 by JohnWiley & Sons, Inc.

  6. Executive information system

    Energy Technology Data Exchange (ETDEWEB)

    Vitullo, M.; Winter, C.; Johnson, D.R.

    1984-07-01

    The Executive Information System (EIS) is a computer-based information handling system. The system has been designed and implemented for Energy Conversion and Utilization Technologies to allow program managers easy access and tracking of certain types of reporting at various levels of management interaction, to simplify the handling of program-related data, and to streamline the preparation of reporting documents and responses to requests for information from the program. The EIS is especially useful in assisting DOE program managers in the routine dissemination of reports and information. The characteristics of each component of the EIS are discussed. A user's guide to the EIS is included in this report.

  7. Medical Information Management System

    Science.gov (United States)

    Alterescu, S.; Hipkins, K. R.; Friedman, C. A.

    1979-01-01

    On-line interactive information processing system easily and rapidly handles all aspects of data management related to patient care. General purpose system is flexible enough to be applied to other data management situations found in areas such as occupational safety data, judicial information, or personnel records.

  8. Archival Information Management System.

    Science.gov (United States)

    1995-02-01

    management system named Archival Information Management System (AIMS), designed to meet the audit trail requirement for studies completed under the...are to be archived to the extent that future reproducibility and interrogation of results will exist. This report presents a prototype information

  9. Next generation information systems

    International Nuclear Information System (INIS)

    Limback, Nathan P.; Medina, Melanie A.; Silva, Michelle E.

    2010-01-01

    The Information Systems Analysis and Development (ISAD) Team of the Safeguards Systems Group at Los Alamos National Laboratory (LANL) has been developing web based information and knowledge management systems for sixteen years. Our vision is to rapidly and cost effectively provide knowledge management solutions in the form of interactive information systems that help customers organize, archive, post and retrieve nonproliferation and safeguards knowledge and information vital to their success. The team has developed several comprehensive information systems that assist users in the betterment and growth of their organizations and programs. Through our information systems, users are able to streamline operations, increase productivity, and share and access information from diverse geographic locations. The ISAD team is also producing interactive visual models. Interactive visual models provide many benefits to customers beyond the scope of traditional full-scale modeling. We have the ability to simulate a vision that a customer may propose, without the time constraints of traditional engineering modeling tools. Our interactive visual models can be used to access specialized training areas, controlled areas, and highly radioactive areas, as well as review site-specific training for complex facilities, and asset management. Like the information systems that the ISAD team develops, these models can be shared and accessed from any location with access to the internet. The purpose of this paper is to elaborate on the capabilities of information systems and interactive visual models as well as consider the possibility of combining the two capabilities to provide the next generation of infonnation systems. The collection, processing, and integration of data in new ways can contribute to the security of the nation by providing indicators and information for timely action to decrease the traditional and new nuclear threats. Modeling and simulation tied to comprehensive

  10. Tunable promoters in systems biology

    DEFF Research Database (Denmark)

    Mijakovic, Ivan; Petranovic, Dina; Jensen, Peter Ruhdal

    2005-01-01

    The construction of synthetic promoter libraries has represented a major breakthrough in systems biology, enabling the subtle tuning of enzyme activities. A number of tools are now available that allow the modulation of gene expression and the detection of changes in expression patterns. But, how...... does one choose the correct promoter and what are the appropriate methods for reading promoter strength? Furthermore, how fine should the tuning of gene expression be for some specific applications and how can the simultaneous and individual tuning of multiple genes be achieved? Some recent studies...

  11. Decision Making in Biological Systems

    DEFF Research Database (Denmark)

    Tian, Chengzhe

    -dormancy transition is primarily mediated by (p)ppGpp fluctuation. In the second topic, we discuss the transition paths between two stable steady states. We construct a simple model of coupled bistable gene circuits and demonstrate the possibility of bifurcation of transition path in biology. We then construct...... a theory to predict whether a general coupled bistable system exhibits bifurcated path or not and verify the theory through numerical simulation. We also show that a primary function of bifurcated paths is to facilitate transition by lowering the associated action. In the third topic, we discuss...

  12. Systems biology of Microbial Communities

    Energy Technology Data Exchange (ETDEWEB)

    Navid, A; Ghim, C; Fenley, A; Yoon, S; Lee, S; Almaas, E

    2008-04-11

    Microbes exist naturally in a wide range of environments, spanning the extremes of high acidity and high temperature to soil and the ocean, in communities where their interactions are significant. We present a practical discussion of three different approaches for modeling microbial communities: rate equations, individual-based modeling, and population dynamics. We illustrate the approaches with detailed examples. Each approach is best fit to different levels of system representation, and they have different needs for detailed biological input. Thus, this set of approaches is able to address the operation and function of microbial communities on a wide range of organizational levels.

  13. Design of the RFID for Storage of Biological Information

    Directory of Open Access Journals (Sweden)

    Sang-Hee Son

    2009-02-01

    Full Text Available Recent advances in RFID (radio frequency identification technology promises to create a wireless circuitry capable of interfacing with biological systems for acquisition, identification and processing of biological data based on radio frequency interaction. Thus, the RFID tag can be attached not only to consumer products and form part of the supply chain, but also to animals, plants and in particular human body. This paper describes the strategy for the design of a novel RFID tag, which stores vital biological information such as body temperature and blood pressure and heartbeat in accordance with the EPC global Class-1 standard. Biological data is obtained from a sensor technology that is based on resistance deviation-to-pulse width converter. The integrated chip consists of an analog front end, command interpreter, collision avoidance block, data storage, sensors, and interface circuitry. The system is capable of supporting heartbeats in the range of 40~200 beats per a minute and blood pressure 0~300mmHg. The proposed system employs collision free algorithm that supports access to single tag within a multiple tag environment. The approach facilitates intelligent management of patients in hospitals as part of an integrated healthcare management system.

  14. Information in the Biosphere: Biological and Digital Worlds.

    Science.gov (United States)

    Gillings, Michael R; Hilbert, Martin; Kemp, Darrell J

    2016-03-01

    Evolution has transformed life through key innovations in information storage and replication, including RNA, DNA, multicellularity, and culture and language. We argue that the carbon-based biosphere has generated a cognitive system (humans) capable of creating technology that will result in a comparable evolutionary transition. Digital information has reached a similar magnitude to information in the biosphere. It increases exponentially, exhibits high-fidelity replication, evolves through differential fitness, is expressed through artificial intelligence (AI), and has facility for virtually limitless recombination. Like previous evolutionary transitions, the potential symbiosis between biological and digital information will reach a critical point where these codes could compete via natural selection. Alternatively, this fusion could create a higher-level superorganism employing a low-conflict division of labor in performing informational tasks. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Car monitoring information systems

    Directory of Open Access Journals (Sweden)

    Alica KALAŠOVÁ

    2008-01-01

    Full Text Available The objective of this contribution is to characterize alternatives of information systems used for managing, processing and evaluation of information related to company vehicles. Especially we focus on logging, transferring and processing of on-road vehicle movement information in inland and international transportation. This segment of company information system has to monitor the car movement – actively or passively – according to demand of the company and after the processing it has to evaluate and give the complex monitoring of a situation of all the company vehicles to the controller.

  16. Health Information Systems.

    Science.gov (United States)

    Sirintrapun, S Joseph; Artz, David R

    2015-06-01

    This article provides surgical pathologists an overview of health information systems (HISs): what they are, what they do, and how such systems relate to the practice of surgical pathology. Much of this article is dedicated to the electronic medical record. Information, in how it is captured, transmitted, and conveyed, drives the effectiveness of such electronic medical record functionalities. So critical is information from pathology in integrated clinical care that surgical pathologists are becoming gatekeepers of not only tissue but also information. Better understanding of HISs can empower surgical pathologists to become stakeholders who have an impact on the future direction of quality integrated clinical care. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. Systems Biology for Organotypic Cell Cultures

    Energy Technology Data Exchange (ETDEWEB)

    Grego, Sonia [RTI International, Research Triangle Park, NC (United States); Dougherty, Edward R. [Texas A & M Univ., College Station, TX (United States); Alexander, Francis J. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Auerbach, Scott S. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Berridge, Brian R. [GlaxoSmithKline, Research Triangle Park, NC (United States); Bittner, Michael L. [Translational Genomics Research Inst., Phoenix, AZ (United States); Casey, Warren [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Cooley, Philip C. [RTI International, Research Triangle Park, NC (United States); Dash, Ajit [HemoShear Therapeutics, Charlottesville, VA (United States); Ferguson, Stephen S. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Fennell, Timothy R. [RTI International, Research Triangle Park, NC (United States); Hawkins, Brian T. [RTI International, Research Triangle Park, NC (United States); Hickey, Anthony J. [RTI International, Research Triangle Park, NC (United States); Kleensang, Andre [Johns Hopkins Univ., Baltimore, MD (United States). Center for Alternatives to Animal Testing; Liebman, Michael N. [IPQ Analytics, Kennett Square, PA (United States); Martin, Florian [Phillip Morris International, Neuchatel (Switzerland); Maull, Elizabeth A. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Paragas, Jason [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Qiao, Guilin [Defense Threat Reduction Agency, Ft. Belvoir, VA (United States); Ramaiahgari, Sreenivasa [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Sumner, Susan J. [RTI International, Research Triangle Park, NC (United States); Yoon, Miyoung [The Hamner Inst. for Health Sciences, Research Triangle Park, NC (United States); ScitoVation, Research Triangle Park, NC (United States)

    2016-08-04

    Translating in vitro biological data into actionable information related to human health holds the potential to improve disease treatment and risk assessment of chemical exposures. While genomics has identified regulatory pathways at the cellular level, translation to the organism level requires a multiscale approach accounting for intra-cellular regulation, inter-cellular interaction, and tissue/organ-level effects. Tissue-level effects can now be probed in vitro thanks to recently developed systems of three-dimensional (3D), multicellular, “organotypic” cell cultures, which mimic functional responses of living tissue. However, there remains a knowledge gap regarding interactions across different biological scales, complicating accurate prediction of health outcomes from molecular/genomic data and tissue responses. Systems biology aims at mathematical modeling of complex, non-linear biological systems. We propose to apply a systems biology approach to achieve a computational representation of tissue-level physiological responses by integrating empirical data derived from organotypic culture systems with computational models of intracellular pathways to better predict human responses. Successful implementation of this integrated approach will provide a powerful tool for faster, more accurate and cost-effective screening of potential toxicants and therapeutics. On September 11, 2015, an interdisciplinary group of scientists, engineers, and clinicians gathered for a workshop in Research Triangle Park, North Carolina, to discuss this ambitious goal. Participants represented laboratory-based and computational modeling approaches to pharmacology and toxicology, as well as the pharmaceutical industry, government, non-profits, and academia. Discussions focused on identifying critical system perturbations to model, the computational tools required, and the experimental approaches best suited to generating key data. This consensus report summarizes the discussions held.

  18. Evolution of information systems

    DEFF Research Database (Denmark)

    Kristensen, Jan

    2000-01-01

    This article offers a dynamic view of continuously changes in a specific informational system illustrated through a case study in a small network company. Central aspects of the evolutionary process will be identified and framed in relation to the informational system change. It will be argued...... that an evolutionary transformation of informational systems are preferable for small network organisations because of their need to adapt rapidly and easily to new business conditions. The IS will only be flexible if both human and technology are prepared and willing/proper configured. Changes are due to altered...

  19. Systems biology and biomarker discovery

    Energy Technology Data Exchange (ETDEWEB)

    Rodland, Karin D.

    2010-12-01

    Medical practitioners have always relied on surrogate markers of inaccessible biological processes to make their diagnosis, whether it was the pallor of shock, the flush of inflammation, or the jaundice of liver failure. Obviously, the current implementation of biomarkers for disease is far more sophisticated, relying on highly reproducible, quantitative measurements of molecules that are often mechanistically associated with the disease in question, as in glycated hemoglobin for the diagnosis of diabetes [1] or the presence of cardiac troponins in the blood for confirmation of myocardial infarcts [2]. In cancer, where the initial symptoms are often subtle and the consequences of delayed diagnosis often drastic for disease management, the impetus to discover readily accessible, reliable, and accurate biomarkers for early detection is compelling. Yet despite years of intense activity, the stable of clinically validated, cost-effective biomarkers for early detection of cancer is pathetically small and still dominated by a handful of markers (CA-125, CEA, PSA) first discovered decades ago. It is time, one could argue, for a fresh approach to the discovery and validation of disease biomarkers, one that takes full advantage of the revolution in genomic technologies and in the development of computational tools for the analysis of large complex datasets. This issue of Disease Markers is dedicated to one such new approach, loosely termed the 'Systems Biology of Biomarkers'. What sets the Systems Biology approach apart from other, more traditional approaches, is both the types of data used, and the tools used for data analysis - and both reflect the revolution in high throughput analytical methods and high throughput computing that has characterized the start of the twenty first century.

  20. Radical production in biological systems

    International Nuclear Information System (INIS)

    Johnson, J.R.; Akabani, G.

    1994-10-01

    This paper describes our effort to develop a metric for radiation exposure that is more fundamental than adsorbed dose and upon which a metric for exposure to chemicals could be based. This metric is based on the production of radicals by the two agents. Radicals produced by radiation in biological systems commonly assumed to be the same as those produced in water despite the presence of a variety of complex molecules. This may explain why the extensive efforts to describe the relationship between energy deposition (track structure) and molecular damage to DNA, based on the spectrum of radicals produced, have not been successful in explaining simple biological effects such as cell killing. Current models assume that DNA and its basic elements are immersed in water-like media and only model the production and diffusion of water-based radicals and their interaction with DNA structures; these models lack the cross sections associated with each macro-component of DNA and only treat water-based radicals. It has been found that such models are not realistic because DNA is not immersed in pure water. A computer code capable of simulating electron tracks, low-energy electrons, energy deposition in small molecules, and radical production and diffusion in water like media has been developed. This code is still in at a primitive stage and development is continuing. It is being used to study radical production by radiation, and radical diffusion and interactions in simple molecular systems following their production. We are extending the code to radical production by chemicals to complement our PBPK modeling efforts. It therefore has been developed primarily for use with radionuclides that are in biological materials, and not for radiation fields

  1. Air System Information Management

    Science.gov (United States)

    Filman, Robert E.

    2004-01-01

    I flew to Washington last week, a trip rich in distributed information management. Buying tickets, at the gate, in flight, landing and at the baggage claim, myriad messages about my reservation, the weather, our flight plans, gates, bags and so forth flew among a variety of travel agency, airline and Federal Aviation Administration (FAA) computers and personnel. By and large, each kind of information ran on a particular application, often specialized to own data formats and communications network. I went to Washington to attend an FAA meeting on System-Wide Information Management (SWIM) for the National Airspace System (NAS) (http://www.nasarchitecture.faa.gov/Tutorials/NAS101.cfm). NAS (and its information infrastructure, SWIM) is an attempt to bring greater regularity, efficiency and uniformity to the collection of stovepipe applications now used to manage air traffic. Current systems hold information about flight plans, flight trajectories, weather, air turbulence, current and forecast weather, radar summaries, hazardous condition warnings, airport and airspace capacity constraints, temporary flight restrictions, and so forth. Information moving among these stovepipe systems is usually mediated by people (for example, air traffic controllers) or single-purpose applications. People, whose intelligence is critical for difficult tasks and unusual circumstances, are not as efficient as computers for tasks that can be automated. Better information sharing can lead to higher system capacity, more efficient utilization and safer operations. Better information sharing through greater automation is possible though not necessarily easy.

  2. Systems biology of fungal infection

    Directory of Open Access Journals (Sweden)

    Fabian eHorn

    2012-04-01

    Full Text Available Elucidation of pathogenicity mechanisms of the most important human pathogenic fungi, Aspergillus fumigatus and Candida albicans, has gained great interest in the light of the steadily increasing number of cases of invasive fungal infections.A key feature of these infections is the interaction of the different fungal morphotypes with epithelial and immune effector cells in the human host. Because of the high level of complexity, it is necessary to describe and understand invasive fungal infection by taking a systems biological approach, i.e., by a comprehensive quantitative analysis of the non-linear and selective interactions of a large number of functionally diverse, and frequently multifunctional, sets of elements, e.g., genes, proteins, metabolites, which produce coherent and emergent behaviours in time and space. The recent advances in systems biology will now make it possible to uncover the structure and dynamics of molecular and cellular cause-effect relationships within these pathogenic interactions.We review current efforts to integrate omics and image-based data of host-pathogen interactions into network and spatio-temporal models. The modelling will help to elucidate pathogenicity mechanisms and to identify diagnostic biomarkers and potential drug targets for therapy and could thus pave the way for novel intervention strategies based on novel antifungal drugs and cell therapy.

  3. Dynamical systems in population biology

    CERN Document Server

    Zhao, Xiao-Qiang

    2017-01-01

    This research monograph provides an introduction to the theory of nonautonomous semiflows with applications to population dynamics. It develops dynamical system approaches to various evolutionary equations such as difference, ordinary, functional, and partial differential equations, and pays more attention to periodic and almost periodic phenomena. The presentation includes persistence theory, monotone dynamics, periodic and almost periodic semiflows, basic reproduction ratios, traveling waves, and global analysis of prototypical population models in ecology and epidemiology. Research mathematicians working with nonlinear dynamics, particularly those interested in applications to biology, will find this book useful. It may also be used as a textbook or as supplementary reading for a graduate special topics course on the theory and applications of dynamical systems. Dr. Xiao-Qiang Zhao is a University Research Professor at Memorial University of Newfoundland, Canada. His main research interests involve applied...

  4. Cognitive biology dealing with information from bacteria to minds

    CERN Document Server

    Auletta, Gennaro

    2011-01-01

    Providing a new conceptual scaffold for further research in biology and cognition, this text introduces the new field of cognitive biology, treating developing organisms as information processors which use cognition to control and modify their environments.

  5. Molecular eyes: proteins that transform light into biological information

    NARCIS (Netherlands)

    Kennis, J.T.M.; Mathes, T.

    2013-01-01

    Most biological photoreceptors are protein/cofactor complexes that induce a physiological reaction upon absorption of a photon. Therefore, these proteins represent signal converters that translate light into biological information. Researchers use this property to stimulate and study various

  6. Set membership experimental design for biological systems

    Directory of Open Access Journals (Sweden)

    Marvel Skylar W

    2012-03-01

    Full Text Available Abstract Background Experimental design approaches for biological systems are needed to help conserve the limited resources that are allocated for performing experiments. The assumptions used when assigning probability density functions to characterize uncertainty in biological systems are unwarranted when only a small number of measurements can be obtained. In these situations, the uncertainty in biological systems is more appropriately characterized in a bounded-error context. Additionally, effort must be made to improve the connection between modelers and experimentalists by relating design metrics to biologically relevant information. Bounded-error experimental design approaches that can assess the impact of additional measurements on model uncertainty are needed to identify the most appropriate balance between the collection of data and the availability of resources. Results In this work we develop a bounded-error experimental design framework for nonlinear continuous-time systems when few data measurements are available. This approach leverages many of the recent advances in bounded-error parameter and state estimation methods that use interval analysis to generate parameter sets and state bounds consistent with uncertain data measurements. We devise a novel approach using set-based uncertainty propagation to estimate measurement ranges at candidate time points. We then use these estimated measurements at the candidate time points to evaluate which candidate measurements furthest reduce model uncertainty. A method for quickly combining multiple candidate time points is presented and allows for determining the effect of adding multiple measurements. Biologically relevant metrics are developed and used to predict when new data measurements should be acquired, which system components should be measured and how many additional measurements should be obtained. Conclusions The practicability of our approach is illustrated with a case study. This

  7. Control and Information Systems

    OpenAIRE

    Jiri Zahradnik; Karol Rastocny; Juraj Spalek

    2003-01-01

    The article deals with main tends of scientific research activities of Department of Control and Information Systems at the Faculty of Electrical Engineering of University of Zilina and its perspectives in this area.

  8. Matter Tracking Information System -

    Data.gov (United States)

    Department of Transportation — The Matter Tracking Information System (MTIS) principle function is to streamline and integrate the workload and work activity generated or addressed by our 300 plus...

  9. Control and Information Systems

    Directory of Open Access Journals (Sweden)

    Jiri Zahradnik

    2003-01-01

    Full Text Available The article deals with main tends of scientific research activities of Department of Control and Information Systems at the Faculty of Electrical Engineering of University of Zilina and its perspectives in this area.

  10. Audit Information Management System

    Data.gov (United States)

    US Agency for International Development — USAID/OIG has initiated its new Audit Information Management System (AIMS) to track OIG's audit recommendations and USAID's management decisions. OIG's in-house...

  11. Enforcement Information System

    Data.gov (United States)

    Department of Transportation — EIS is an automated management information system that tracks the FAA’s enforcement actions on a nationwide basis. EIS is the FAA’s primary database for tracking...

  12. Industrialized Information Systems Development

    DEFF Research Database (Denmark)

    Havn, Erling; Bansler, Jørgen P.

    1996-01-01

    The production of application software is rapidly being industrialized. Computer manufacturers and software houses produce a rapidly growing number of generic software applications and systems, and more and more user companies choose to build their computer-based information systems with such gen......The production of application software is rapidly being industrialized. Computer manufacturers and software houses produce a rapidly growing number of generic software applications and systems, and more and more user companies choose to build their computer-based information systems...

  13. Adaptable data management for systems biology investigations

    Directory of Open Access Journals (Sweden)

    Burdick David

    2009-03-01

    Full Text Available Abstract Background Within research each experiment is different, the focus changes and the data is generated from a continually evolving barrage of technologies. There is a continual introduction of new techniques whose usage ranges from in-house protocols through to high-throughput instrumentation. To support these requirements data management systems are needed that can be rapidly built and readily adapted for new usage. Results The adaptable data management system discussed is designed to support the seamless mining and analysis of biological experiment data that is commonly used in systems biology (e.g. ChIP-chip, gene expression, proteomics, imaging, flow cytometry. We use different content graphs to represent different views upon the data. These views are designed for different roles: equipment specific views are used to gather instrumentation information; data processing oriented views are provided to enable the rapid development of analysis applications; and research project specific views are used to organize information for individual research experiments. This management system allows for both the rapid introduction of new types of information and the evolution of the knowledge it represents. Conclusion Data management is an important aspect of any research enterprise. It is the foundation on which most applications are built, and must be easily extended to serve new functionality for new scientific areas. We have found that adopting a three-tier architecture for data management, built around distributed standardized content repositories, allows us to rapidly develop new applications to support a diverse user community.

  14. Adaptable data management for systems biology investigations

    Science.gov (United States)

    Boyle, John; Rovira, Hector; Cavnor, Chris; Burdick, David; Killcoyne, Sarah; Shmulevich, Ilya

    2009-01-01

    Background Within research each experiment is different, the focus changes and the data is generated from a continually evolving barrage of technologies. There is a continual introduction of new techniques whose usage ranges from in-house protocols through to high-throughput instrumentation. To support these requirements data management systems are needed that can be rapidly built and readily adapted for new usage. Results The adaptable data management system discussed is designed to support the seamless mining and analysis of biological experiment data that is commonly used in systems biology (e.g. ChIP-chip, gene expression, proteomics, imaging, flow cytometry). We use different content graphs to represent different views upon the data. These views are designed for different roles: equipment specific views are used to gather instrumentation information; data processing oriented views are provided to enable the rapid development of analysis applications; and research project specific views are used to organize information for individual research experiments. This management system allows for both the rapid introduction of new types of information and the evolution of the knowledge it represents. Conclusion Data management is an important aspect of any research enterprise. It is the foundation on which most applications are built, and must be easily extended to serve new functionality for new scientific areas. We have found that adopting a three-tier architecture for data management, built around distributed standardized content repositories, allows us to rapidly develop new applications to support a diverse user community. PMID:19265554

  15. DISEASE MANAGEMENT INFORMATION SYSTEM

    OpenAIRE

    Bens Pardamean; Anindito; Anjela Djoeang; Nana Tobing

    2013-01-01

    The study designed an information system model for Disease Management (DisMan) that met the specifications and needs of a consumer electronics manufacturer. The diseases monitored by this study were diabetes, hypertension and tuberculosis. Data were collected through interviews with the companyâs human resources department and occupational health provider. As for the model, literature and online research were conducted to collect health standards and information system standards on existing D...

  16. Measuring cell identity in noisy biological systems

    Science.gov (United States)

    Birnbaum, Kenneth D.; Kussell, Edo

    2011-01-01

    Global gene expression measurements are increasingly obtained as a function of cell type, spatial position within a tissue and other biologically meaningful coordinates. Such data should enable quantitative analysis of the cell-type specificity of gene expression, but such analyses can often be confounded by the presence of noise. We introduce a specificity measure Spec that quantifies the information in a gene's complete expression profile regarding any given cell type, and an uncertainty measure dSpec, which measures the effect of noise on specificity. Using global gene expression data from the mouse brain, plant root and human white blood cells, we show that Spec identifies genes with variable expression levels that are nonetheless highly specific of particular cell types. When samples from different individuals are used, dSpec measures genes’ transcriptional plasticity in each cell type. Our approach is broadly applicable to mapped gene expression measurements in stem cell biology, developmental biology, cancer biology and biomarker identification. As an example of such applications, we show that Spec identifies a new class of biomarkers, which exhibit variable expression without compromising specificity. The approach provides a unifying theoretical framework for quantifying specificity in the presence of noise, which is widely applicable across diverse biological systems. PMID:21803789

  17. Quantum information and the problem of mechanisms of biological evolution.

    Science.gov (United States)

    Melkikh, Alexey V

    2014-01-01

    One of the most important conditions for replication in early evolution is the de facto elimination of the conformational degrees of freedom of the replicators, the mechanisms of which remain unclear. In addition, realistic evolutionary timescales can be established based only on partially directed evolution, further complicating this issue. A division of the various evolutionary theories into two classes has been proposed based on the presence or absence of a priori information about the evolving system. A priori information plays a key role in solving problems in evolution. Here, a model of partially directed evolution, based on the learning automata theory, which includes a priori information about the fitness space, is proposed. A potential repository of such prior information is the states of biologically important molecules. Thus, the need for extended evolutionary synthesis is discussed. Experiments to test the hypothesis of partially directed evolution are proposed. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  18. Advanced fire information system

    CSIR Research Space (South Africa)

    Frost, PE

    2007-01-01

    Full Text Available The South African Advanced Fire Information System (AFIS) is the first near real-time satellite-based fire monitoring system in Africa. It was originally developed for, and funded by, the electrical power utility Eskom, to reduce the impact of wild...

  19. Editorial overview : Systems biology for biotechnology

    NARCIS (Netherlands)

    Heinemann, Matthias; Pilpel, Yitzhak

    About 15 years ago, systems biology was introduced as a novel approach to biological research. On the one side, its introduction was a result of the recognition that through solely the reductionist approach, we would ulti- mately not be able to understand how biological systems function as a whole.

  20. Information system INIS

    International Nuclear Information System (INIS)

    Kyncl, J.

    1979-01-01

    INIS is the abbreviation for the International Nuclear Information System operated by IAEA in cooperation with its member countries. The function of the INIS system whose aim is to provide the member countries with information on nuclear literature is based on the decentralized input data preparation, centralized checking and on the creation of a unified data base and on the decentralized output materials processing. Czechoslovakia is represented in INIS by the Nuclear Information Centre which has been taking active part in the building and development of INIS since its very beginning. It provides for the use of output INIS materials by users in Czechoslovakia, this by means of a computerized network. The Czechoslovak Nuclear Information Centre has since 1978 been using a teleprocessing terminal connected to the IAEA central processor by means of a telephone line, which allows direct access to the INIS data base. (Ha)

  1. Management Information System

    Science.gov (United States)

    1984-01-01

    New Automated Management Information Center (AMIC) employs innovative microcomputer techniques to create color charts, viewgraphs, or other data displays in a fraction of the time formerly required. Developed under Kennedy Space Center's contract by Boeing Services International Inc., Seattle, WA, AMIC can produce an entirely new informational chart in 30 minutes, or an updated chart in only five minutes. AMIC also has considerable potential as a management system for business firms.

  2. Magnetic Actuation of Biological Systems

    Science.gov (United States)

    Lauback, Stephanie D.

    Central to the advancement of many biomedical and nanotechnology capabilities is the capacity to precisely control the motion of micro and nanostructures. These applications range from single molecule experiments to cell isolation and separation, to drug delivery and nanomachine manipulation. This dissertation focuses on actuation of biological micro- and nano-entities through the use of weak external magnetic fields, superparamagnetic beads, and ferromagnetic thin films. The magnetic platform presents an excellent method for actuation of biological systems due to its ability to directly control the motion of an array of micro and nanostructures in real-time with calibrated picoNewton forces. The energy landscape of two ferromagnetic thin film patterns (disks and zigzag wires) is experimentally explored and compared to corresponding theoretical models to quantify the applied forces and trajectories of superparamagnetic beads due to the magnetic traps. A magnetic method to directly actuate DNA nanomachines in real-time with nanometer resolution and sub-second response times using micromagnetic control was implemented through the use of stiff DNA micro-levers which bridged the large length scale mismatch between the micro-actuator and the nanomachine. Compared to current alternative methods which are limited in the actuation speeds and the number of reconfiguration states of DNA constructs, this magnetic approach enables fast actuation (˜ milliseconds) and reconfigurable conformations achieved through a continuous range of finely tuned steps. The system was initially tested through actuation of the stiff arm tethered to the surface, and two prototype DNA nanomachines (rotor and hinge) were successfully actuated using the stiff mechanical lever. These results open new possibilities in the development of functional robotic systems at the molecular scale. In exploiting the use of DNA stiff levers, a new technique was also developed to investigate the emergence of the

  3. COMMUNICATIONS AND INFORMATION SYSTEMS

    Directory of Open Access Journals (Sweden)

    Dănuţ ŢIGĂNUŞ

    2011-01-01

    Full Text Available This essay assesses the communications and information systems (CIS in support of the civilian and military structures deployed in the European Union led crises management operations and missions. The article emphasizes the specific structure and function of CIS taking in consideration the particularities of EU led missions. The integration of the EU institutional networks and systems with the national systems provided by the EU member states is considered a key element. The analysis-part of this paper starts with the specific EU command and control system for crises management missions based on two autonomous solutions and one relying on NATO capabilities. Further, it continues with the challenges of the classifi ed information exchange at the operational theatre level. The most important contribution of this article is based on the long term vision implementation measures for the CIS structure, roles, functions and services provided and the information management infrastructure. CIS deployment mechanisms are described with references to the practical situation of the CIS deployed in support of crises management operations and missions. Two important defi nitions are provided regarding the CIS for crisis management and their roles in the specific EU operational environment. The system view of the operational CIS is depicted and analysed also, with a focus on the integration aspects of the infrastructure as the information transport layer for the information exchange flow. The last part of the article focuses on the CIS functions for the deployed systems which are detailed alongside with the C2 and Information Exchange Requirements in the EU operational environment. The variety of the theoretical approaches to determine the CIS infrastructure for EU-led civilian and military missions triggers the conclusion that the planning and implementation process is extremely complex especially in the context of the new security environment and requires

  4. Biological diversity in the patent system.

    Directory of Open Access Journals (Sweden)

    Paul Oldham

    Full Text Available Biological diversity in the patent system is an enduring focus of controversy but empirical analysis of the presence of biodiversity in the patent system has been limited. To address this problem we text mined 11 million patent documents for 6 million Latin species names from the Global Names Index (GNI established by the Global Biodiversity Information Facility (GBIF and Encyclopedia of Life (EOL. We identified 76,274 full Latin species names from 23,882 genera in 767,955 patent documents. 25,595 species appeared in the claims section of 136,880 patent documents. This reveals that human innovative activity involving biodiversity in the patent system focuses on approximately 4% of taxonomically described species and between 0.8-1% of predicted global species. In this article we identify the major features of the patent landscape for biological diversity by focusing on key areas including pharmaceuticals, neglected diseases, traditional medicines, genetic engineering, foods, biocides, marine genetic resources and Antarctica. We conclude that the narrow focus of human innovative activity and ownership of genetic resources is unlikely to be in the long term interest of humanity. We argue that a broader spectrum of biodiversity needs to be opened up to research and development based on the principles of equitable benefit-sharing, respect for the objectives of the Convention on Biological Diversity, human rights and ethics. Finally, we argue that alternative models of innovation, such as open source and commons models, are required to open up biodiversity for research that addresses actual and neglected areas of human need. The research aims to inform the implementation of the 2010 Nagoya Protocol on Access to Genetic Resources and the Equitable Sharing of Benefits Arising from their Utilization and international debates directed to the governance of genetic resources. Our research also aims to inform debates under the Intergovernmental Committee on

  5. Biological Diversity in the Patent System

    Science.gov (United States)

    Oldham, Paul; Hall, Stephen; Forero, Oscar

    2013-01-01

    Biological diversity in the patent system is an enduring focus of controversy but empirical analysis of the presence of biodiversity in the patent system has been limited. To address this problem we text mined 11 million patent documents for 6 million Latin species names from the Global Names Index (GNI) established by the Global Biodiversity Information Facility (GBIF) and Encyclopedia of Life (EOL). We identified 76,274 full Latin species names from 23,882 genera in 767,955 patent documents. 25,595 species appeared in the claims section of 136,880 patent documents. This reveals that human innovative activity involving biodiversity in the patent system focuses on approximately 4% of taxonomically described species and between 0.8–1% of predicted global species. In this article we identify the major features of the patent landscape for biological diversity by focusing on key areas including pharmaceuticals, neglected diseases, traditional medicines, genetic engineering, foods, biocides, marine genetic resources and Antarctica. We conclude that the narrow focus of human innovative activity and ownership of genetic resources is unlikely to be in the long term interest of humanity. We argue that a broader spectrum of biodiversity needs to be opened up to research and development based on the principles of equitable benefit-sharing, respect for the objectives of the Convention on Biological Diversity, human rights and ethics. Finally, we argue that alternative models of innovation, such as open source and commons models, are required to open up biodiversity for research that addresses actual and neglected areas of human need. The research aims to inform the implementation of the 2010 Nagoya Protocol on Access to Genetic Resources and the Equitable Sharing of Benefits Arising from their Utilization and international debates directed to the governance of genetic resources. Our research also aims to inform debates under the Intergovernmental Committee on Intellectual

  6. Using geographic information systems

    International Nuclear Information System (INIS)

    Winsor, R.W.

    1997-01-01

    A true Geographic Information System (GIS) is a computer mapping system with spatial analysis ability and cartographic accuracy that will offer many different projections. GIS has evolved to become an everyday tool for a wide range of users including oil companies, worldwide. Other systems are designed to allow oil and gas companies to keep their upstream data in the same format. Among these are the Public Petroleum Data Model developed by Gulf Canada, Digitech and Applied Terravision Systems of Calgary, the system developed and marketed by the Petrotechnical Open Software Corporation in the United States, and the Mercury projects by IBM. These have been developed in an effort to define an industry standard. The advantages and disadvantages of open and closed systems were discussed. Factors to consider when choosing a GIS system such as overall performance, area of use and query complexity, were reviewed. 3 figs

  7. Human factors information system

    International Nuclear Information System (INIS)

    Goodman, P.C.; DiPalo, C.A.

    1991-01-01

    Nuclear power plant safety is dependent upon human performance related to plant operations. To provide improvements in human performance, data collection and assessment play key roles. This paper reports on the Human factors Information System (HFIS) which is designed to meet the needs of the human factors specialists of the United States Nuclear Regulatory Commission. These specialists identify personnel errors and provide guidance designed to prevent such errors. HFIS is a simple and modular system designed for use on a personal computer. It is designed to contain four separate modules that provide information indicative of program or function effectiveness as well as safety-related human performance based on programmatic and performance data. These modules include the Human Factors Status module; the Regulatory Programs module; the Licensee Event Report module; and the Operator Requalification Performance module. Information form these modules can either be used separately or can be combined due to the integrated nature of the system. HFIS has the capability, therefore, to provide insights into those areas of human factors that can reduce the probability of events caused by personnel error at nuclear power plants and promote the health and safety of the public. This information system concept can be applied to other industries as well as the nuclear industry

  8. Enterprise Information Systems Outsourcing

    DEFF Research Database (Denmark)

    Pries-Heje, Jan; Svejvig, Per

    2009-01-01

      Outsourcing is now a feasible mean for Enterprise Information Systems (EIS) cost savings, but do however increase the complexity substantially when many organizations are involved. We set out to study EIS outsourcing with many interorganizational partners in a large Scandinavian high...

  9. Introducing systems biology for nursing science.

    Science.gov (United States)

    Founds, Sandra A

    2009-07-01

    Systems biology expands on general systems theory as the "omics'' era rapidly progresses. Although systems biology has been institutionalized as an interdisciplinary framework in the biosciences, it is not yet apparent in nursing. This article introduces systems biology for nursing science by presenting an overview of the theory. This framework for the study of organisms from molecular to environmental levels includes iterations of computational modeling, experimentation, and theory building. Synthesis of complex biological processes as whole systems rather than isolated parts is emphasized. Pros and cons of systems biology are discussed, and relevance of systems biology to nursing is described. Nursing research involving molecular, physiological, or biobehavioral questions may be guided by and contribute to the developing science of systems biology. Nurse scientists can proactively incorporate systems biology into their investigations as a framework for advancing the interdisciplinary science of human health care. Systems biology has the potential to advance the research and practice goals of the National Institute for Nursing Research in the National Institutes of Health Roadmap initiative.

  10. Physical methods for investigating structural colours in biological systems

    NARCIS (Netherlands)

    Vukusic, P.; Stavenga, D. G.

    2009-01-01

    Many biological systems are known to use structural colour effects to generate aspects of their appearance and visibility. The study of these phenomena has informed an eclectic group of fields ranging, for example, from evolutionary processes in behavioural biology to micro-optical devices in

  11. GPSR: A Resource for Genomics Proteomics and Systems Biology

    Indian Academy of Sciences (India)

    Simple Calculation Programs for Biology Other Methods · PowerPoint Presentation · Slide 6 · Slide 7 · Prediction of B-Cell Epitopes · Slide 9 · Slide 10. Slide 12 · Slide 13 · Limitations of existing web services · GPSR: A Resource for Genomics Proteomics and Systems Biology · Important Information in Manual for Develpers.

  12. Computing handbook information systems and information technology

    CERN Document Server

    Topi, Heikki

    2014-01-01

    Disciplinary Foundations and Global ImpactEvolving Discipline of Information Systems Heikki TopiDiscipline of Information Technology Barry M. Lunt and Han ReichgeltInformation Systems as a Practical Discipline Juhani IivariInformation Technology Han Reichgelt, Joseph J. Ekstrom, Art Gowan, and Barry M. LuntSociotechnical Approaches to the Study of Information Systems Steve Sawyer and Mohammad Hossein JarrahiIT and Global Development Erkki SutinenUsing ICT for Development, Societal Transformation, and Beyond Sherif KamelTechnical Foundations of Data and Database ManagementData Models Avi Silber

  13. Advances in metabolome information retrieval: turning chemistry into biology. Part II: biological information recovery.

    Science.gov (United States)

    Tebani, Abdellah; Afonso, Carlos; Bekri, Soumeya

    2017-08-25

    This work reports the second part of a review intending to give the state of the art of major metabolic phenotyping strategies. It particularly deals with inherent advantages and limits regarding data analysis issues and biological information retrieval tools along with translational challenges. This Part starts with introducing the main data preprocessing strategies of the different metabolomics data. Then, it describes the main data analysis techniques including univariate and multivariate aspects. It also addresses the challenges related to metabolite annotation and characterization. Finally, functional analysis including pathway and network strategies are discussed. The last section of this review is devoted to practical considerations and current challenges and pathways to bring metabolomics into clinical environments.

  14. Nuclear criticality information system

    International Nuclear Information System (INIS)

    Koponen, B.L.; Hampel, V.E.

    1981-01-01

    The nuclear criticality safety program at LLNL began in the 1950's with a critical measurements program which produced benchmark data until the late 1960's. This same time period saw the rapid development of computer technology useful for both computer modeling of fissile systems and for computer-aided management and display of the computational benchmark data. Database management grew in importance as the amount of information increased and as experimental programs were terminated. Within the criticality safety program at LLNL we began at that time to develop a computer library of benchmark data for validation of computer codes and cross sections. As part of this effort, we prepared a computer-based bibliography of criticality measurements on relatively simple systems. However, it is only now that some of these computer-based resources can be made available to the nuclear criticality safety community at large. This technology transfer is being accomplished by the DOE Technology Information System (TIS), a dedicated, advanced information system. The NCIS database is described

  15. Complex biological and bio-inspired systems

    Energy Technology Data Exchange (ETDEWEB)

    Ecke, Robert E [Los Alamos National Laboratory

    2009-01-01

    The understanding and characterization ofthe fundamental processes of the function of biological systems underpins many of the important challenges facing American society, from the pathology of infectious disease and the efficacy ofvaccines, to the development of materials that mimic biological functionality and deliver exceptional and novel structural and dynamic properties. These problems are fundamentally complex, involving many interacting components and poorly understood bio-chemical kinetics. We use the basic science of statistical physics, kinetic theory, cellular bio-chemistry, soft-matter physics, and information science to develop cell level models and explore the use ofbiomimetic materials. This project seeks to determine how cell level processes, such as response to mechanical stresses, chemical constituents and related gradients, and other cell signaling mechanisms, integrate and combine to create a functioning organism. The research focuses on the basic physical processes that take place at different levels ofthe biological organism: the basic role of molecular and chemical interactions are investigated, the dynamics of the DNA-molecule and its phylogenetic role are examined and the regulatory networks of complex biochemical processes are modeled. These efforts may lead to early warning algorithms ofpathogen outbreaks, new bio-sensors to detect hazards from pathomic viruses to chemical contaminants. Other potential applications include the development of efficient bio-fuel alternative-energy processes and the exploration ofnovel materials for energy usages. Finally, we use the notion of 'coarse-graining,' which is a method for averaging over less important degrees of freedom to develop computational models to predict cell function and systems-level response to disease, chemical stress, or biological pathomic agents. This project supports Energy Security, Threat Reduction, and the missions of the DOE Office of Science through its efforts to

  16. Philosophy of Systems and Synthetic Biology

    DEFF Research Database (Denmark)

    Green, Sara

    2017-01-01

    This entry aims to clarify how systems and synthetic biology contribute to and extend discussions within philosophy of science. Unlike fields such as developmental biology or molecular biology, systems and synthetic biology are not easily demarcated by a focus on a specific subject area or level...... computational approaches, about the relation between living and artificial systems, and about the implications of interdisciplinary research for science and society. The entry can be openly accessed at the webpage of the Stanford Encyclopaedia of Philosophy: https://plato.stanford.edu/entries/systems-synthetic-biology/...... of organization. Rather, they are characterized by the development and application of mathematical, computational, and synthetic modeling strategies in response to complex problems and challenges within the life sciences. Proponents of systems and synthetic biology often stress the necessity of a perspective...

  17. Information sciences experiment system

    Science.gov (United States)

    Katzberg, Stephen J.; Murray, Nicholas D.; Benz, Harry F.; Bowker, David E.; Hendricks, Herbert D.

    1990-01-01

    The rapid expansion of remote sensing capability over the last two decades will take another major leap forward with the advent of the Earth Observing System (Eos). An approach is presented that will permit experiments and demonstrations in onboard information extraction. The approach is a non-intrusive, eavesdropping mode in which a small amount of spacecraft real estate is allocated to an onboard computation resource. How such an approach allows the evaluation of advanced technology in the space environment, advanced techniques in information extraction for both Earth science and information science studies, direct to user data products, and real-time response to events, all without affecting other on-board instrumentation is discussed.

  18. Information Systems Efficiency Model

    Directory of Open Access Journals (Sweden)

    Milos Koch

    2017-07-01

    Full Text Available This contribution discusses the basic concept of creating a new model for the efficiency and effectiveness assessment of company information systems. The present trends in this field are taken into account, and the attributes are retained of measuring the optimal solutions for a company’s ICT (the implementation, functionality, service, innovations, safety, relationships, costs, etc.. The proposal of a new model of assessment comes from our experience with formerly implemented and employed methods, methods which we have modified in time and adapted to companies’ needs but also to the necessaries of our research that has been done through the ZEFIS portal. The most noteworthy of them is the HOS method that we have discussed in a number of forums. Its main feature is the fact that it respects the complexity of an information system in correlation with the balanced state of its individual parts.

  19. Anesthesia information management systems

    Directory of Open Access Journals (Sweden)

    Feri Štivan

    2014-08-01

    Full Text Available Introduction: The use of anesthesia information management systems (AIMS is on the increase. This is particularly true for academic anesthesia departments. The main reasons for slow adoption of these systems in the past are financial barriers associated with implementation of these systems and their not so traditionally obvious potential to improve patient care. In addition, a major obstacle to acceptance of this technology is the concern of users over the impact of the electronic anesthesia record on malpractice exposure.Conclusions: The experience reported by departments using AIMS indicates that these systems are useful for managing malpractice risk. AIMS can enhance the efficiency and effectiveness of preoperative, intraoperative, and post-operative anesthesia care. However, AIMS are able to increase the quality of care and improve operating room efficiency only with careful planning, installation, and customization. Strengths, weaknesses, opportunities and threats (SWOT analysis performed for AIMS could help departments in making better decisions when implementing AIMS.

  20. Appropriation of Information Systems

    DEFF Research Database (Denmark)

    Kjærgaard, Annemette Leonhardt; Jensen, Tina Blegind

    2008-01-01

    This paper explores the use of cognitive mapping for eliciting users' sensemaking during information system (IS) appropriation. Despite the potential usefulness of sensemaking, few studies in IS research use it as a theoretical lens to address IS appropriation. A possible reason for this may...... be that sensemaking does not easily lend itself to be used in practice. We introduce cognitive mapping as a way to elicit users' sensemaking and illustrate its value by reporting on findings from an empirical study of the introduction of an Electronic Patient Record (EPR) system. The contribution of the paper...

  1. Engineering Review Information System

    Science.gov (United States)

    Grems, III, Edward G. (Inventor); Henze, James E. (Inventor); Bixby, Jonathan A. (Inventor); Roberts, Mark (Inventor); Mann, Thomas (Inventor)

    2015-01-01

    A disciplinal engineering review computer information system and method by defining a database of disciplinal engineering review process entities for an enterprise engineering program, opening a computer supported engineering item based upon the defined disciplinal engineering review process entities, managing a review of the opened engineering item according to the defined disciplinal engineering review process entities, and closing the opened engineering item according to the opened engineering item review.

  2. Identification of "pathologs" (disease-related genes from the RIKEN mouse cDNA dataset using human curation plus FACTS, a new biological information extraction system

    Directory of Open Access Journals (Sweden)

    Socha Luis A

    2004-04-01

    Full Text Available Abstract Background A major goal in the post-genomic era is to identify and characterise disease susceptibility genes and to apply this knowledge to disease prevention and treatment. Rodents and humans have remarkably similar genomes and share closely related biochemical, physiological and pathological pathways. In this work we utilised the latest information on the mouse transcriptome as revealed by the RIKEN FANTOM2 project to identify novel human disease-related candidate genes. We define a new term "patholog" to mean a homolog of a human disease-related gene encoding a product (transcript, anti-sense or protein potentially relevant to disease. Rather than just focus on Mendelian inheritance, we applied the analysis to all potential pathologs regardless of their inheritance pattern. Results Bioinformatic analysis and human curation of 60,770 RIKEN full-length mouse cDNA clones produced 2,578 sequences that showed similarity (70–85% identity to known human-disease genes. Using a newly developed biological information extraction and annotation tool (FACTS in parallel with human expert analysis of 17,051 MEDLINE scientific abstracts we identified 182 novel potential pathologs. Of these, 36 were identified by computational tools only, 49 by human expert analysis only and 97 by both methods. These pathologs were related to neoplastic (53%, hereditary (24%, immunological (5%, cardio-vascular (4%, or other (14%, disorders. Conclusions Large scale genome projects continue to produce a vast amount of data with potential application to the study of human disease. For this potential to be realised we need intelligent strategies for data categorisation and the ability to link sequence data with relevant literature. This paper demonstrates the power of combining human expert annotation with FACTS, a newly developed bioinformatics tool, to identify novel pathologs from within large-scale mouse transcript datasets.

  3. The Geographical Information System

    Directory of Open Access Journals (Sweden)

    Jürgen Schweikart

    2008-12-01

    Full Text Available The Geographical Information System, normally called GIS, is a tool for representing spatial relationships and real processes with the help of a model. A GIS is a system of hardware, software and staff for collecting, managing, analysing and representing geospatial information. For example, we can study the evolution of an infectious disease in a certain territory, perform market analysis, or locate the best ways to choose a new industrial site. In substance, it is data manipulation software for that allows us to have, both the graphic component, that is a territorial representation of the reality that you want to represent, and the data components in the form of a database or more commonly, calculation sheets. Geographical data are divided in spatial data and attribute data: Spatial data are recorded as points, lines and polygons (vectorial structure. In other words, the survey systems have been projected to acquire information in accordance to elementary cells corresponding to a territorial grid (raster structure. It also includes remote sensing data.

  4. Introduction to Network Analysis in Systems Biology

    OpenAIRE

    Ma’ayan, Avi

    2011-01-01

    This Teaching Resource provides lecture notes, slides, and a problem set for a set of three lectures from a course entitled “Systems Biology: Biomedical Modeling.” The materials are from three separate lectures introducing applications of graph theory and network analysis in systems biology. The first lecture describes different types of intracellular networks, methods for constructing biological networks, and different types of graphs used to represent regulatory intracellular networks. The ...

  5. PathSys: integrating molecular interaction graphs for systems biology

    Directory of Open Access Journals (Sweden)

    Raval Alpan

    2006-02-01

    Full Text Available Abstract Background The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately. Results Here we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast (S. cerevisiae and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping. Conclusion Results from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at http://brak.sdsc.edu/pub/BiologicalNetworks.

  6. Biological Systems Thinking for Control Engineering Design

    Directory of Open Access Journals (Sweden)

    D. J. Murray-Smith

    2004-01-01

    Full Text Available Artificial neural networks and genetic algorithms are often quoted in discussions about the contribution of biological systems thinking to engineering design. This paper reviews work on the neuromuscular system, a field in which biological systems thinking could make specific contributions to the development and design of automatic control systems for mechatronics and robotics applications. The paper suggests some specific areas in which a better understanding of this biological control system could be expected to contribute to control engineering design methods in the future. Particular emphasis is given to the nonlinear nature of elements within the neuromuscular system and to processes of neural signal processing, sensing and system adaptivity. Aspects of the biological system that are of particular significance for engineering control systems include sensor fusion, sensor redundancy and parallelism, together with advanced forms of signal processing for adaptive and learning control. 

  7. Nuclear information access system

    International Nuclear Information System (INIS)

    Ham, C. H.; Yang, M. H.; Yoon, S. W.

    1998-01-01

    The energy supply in the countries, which have abundant energy resources, may not be affected by accepting the assertion of anti-nuclear and environment groups. Anti-nuclear movements in the countries which have little energy resources may cause serious problem in securing energy supply. Especially, it is distinct in Korea because she heavily depends on nuclear energy in electricity supply(nuclear share in total electricity supply is about 40%).The cause of social trouble surrounding nuclear energy is being involved with various circumstances. However, it is very important that we are not aware of the importance of information access and prepared for such a situation from the early stage of nuclear energy's development. In those matter, this paper analyzes the contents of nuclear information access system in France and Japan which have dynamic nuclear development program and presents the direction of the nuclear access regime through comparing Korean status and referring to progresses of the regime

  8. Systems biology in critical-care nursing.

    Science.gov (United States)

    Schallom, Lynn; Thimmesch, Amanda R; Pierce, Janet D

    2011-01-01

    Systems biology applies advances in technology and new fields of study including genomics, transcriptomics, proteomics, and metabolomics to the development of new treatments and approaches of care for the critically ill and injured patient. An understanding of systems biology enhances a nurse's ability to implement evidence-based practice and to educate patients and families on novel testing and therapies. Systems biology is an integrated and holistic view of humans in relationship with the environment. Biomarkers are used to measure the presence and severity of disease and are rapidly expanding in systems biology endeavors. A systems biology approach using predictive, preventive, and participatory involvement is being utilized in a plethora of conditions of critical illness and injury including sepsis, cancer, pulmonary disease, and traumatic injuries.

  9. Plant systems biology: insights, advances and challenges.

    Science.gov (United States)

    Sheth, Bhavisha P; Thaker, Vrinda S

    2014-07-01

    Plants dwelling at the base of biological food chain are of fundamental significance in providing solutions to some of the most daunting ecological and environmental problems faced by our planet. The reductionist views of molecular biology provide only a partial understanding to the phenotypic knowledge of plants. Systems biology offers a comprehensive view of plant systems, by employing a holistic approach integrating the molecular data at various hierarchical levels. In this review, we discuss the basics of systems biology including the various 'omics' approaches and their integration, the modeling aspects and the tools needed for the plant systems research. A particular emphasis is given to the recent analytical advances, updated published examples of plant systems biology studies and the future trends.

  10. Justifying an information system.

    Science.gov (United States)

    Neal, T

    1993-03-01

    A four-step model for the hospital pharmacist to use in justifying a computerized information system is described. In the first step, costs are identified and analyzed. Both the costs and the advantages of the existing system are evaluated. A request for information and a request for proposal are prepared and sent to vendors, who return estimates of hardware, software, and support costs. Costs can then be merged and analyzed as one-time costs, recurring annual costs, and total costs annualized over five years. In step 2, benefits are identified and analyzed. Tangible economic benefits are those that directly reduce or avoid costs or directly enhance revenues and can be measured in dollars. Intangible economic benefits are realized through a reduction in overhead and reallocation of labor and are less easily measured in dollars. Noneconomic benefits, some involving quality-of-care issues, can also be used in the justification. Step 3 consists of a formal risk assessment in which the project is broken into categories for which specific questions are answered by assigning a risk factor. In step 4, both costs and benefits are subjected to a financial analysis, the object of which is to maximize the return on investment to the institution from the capital being requested. Calculations include return on investment based on the net present value of money, internal rate of return, payback period, and profitability index. A well-designed justification for an information system not only identifies the costs, risks, and benefits but also presents a plan of action for realizing the benefits.

  11. The use of information theory in evolutionary biology.

    Science.gov (United States)

    Adami, Christoph

    2012-05-01

    Information is a key concept in evolutionary biology. Information stored in a biological organism's genome is used to generate the organism and to maintain and control it. Information is also that which evolves. When a population adapts to a local environment, information about this environment is fixed in a representative genome. However, when an environment changes, information can be lost. At the same time, information is processed by animal brains to survive in complex environments, and the capacity for information processing also evolves. Here, I review applications of information theory to the evolution of proteins and to the evolution of information processing in simulated agents that adapt to perform a complex task. © 2012 New York Academy of Sciences.

  12. Planning for information systems

    CERN Document Server

    King, William R

    2015-01-01

    Edited by one of the best-known and most widely respected figures in the field, ""Planning for Information Systems"" is a comprehensive, single source overview of the myriad ideas and processes that are identified with IS planning. While many chapters deal with high level strategic planning, the book gives equal attention to on-the-ground planning issues.Part I, 'Key Concepts of IS Planning', focuses on how IS planning has evolved over the years; business-IS strategic alignment; and the role of dynamic organizational capabilities in leveraging IS competencies. Part II, 'The Organizational IS P

  13. Feedback dynamics and cell function: Why systems biology is called Systems Biology.

    Science.gov (United States)

    Wolkenhauer, Olaf; Mesarovic, Mihajlo

    2005-05-01

    A new paradigm, like Systems Biology, should challenge the way research has been conducted previously. This Opinion article aims to present Systems Biology, not as the application of engineering principles to biology but as a merger of systems- and control theory with molecular- and cell biology. In our view, the central dogma of Systems Biology is that it is system dynamics that gives rise to the functioning and function of cells. The concepts of feedback regulation and control of pathways and the coordination of cell function are emphasized as an important area of Systems Biology research. The hurdles and risks for this area are discussed from the perspective of dynamic pathway modelling. Most of all, the aim of this article is to promote mathematical modelling and simulation as a part of molecular- and cell biology. Systems Biology is a success if it is widely accepted that there is nothing more practical than a good theory.

  14. Dimensionality reduction of bistable biological systems.

    Science.gov (United States)

    Zakharova, A; Nikoloski, Z; Koseska, A

    2013-03-01

    Time hierarchies, arising as a result of interactions between system's components, represent a ubiquitous property of dynamical biological systems. In addition, biological systems have been attributed switch-like properties modulating the response to various stimuli across different organisms and environmental conditions. Therefore, establishing the interplay between these features of system dynamics renders itself a challenging question of practical interest in biology. Existing methods are suitable for systems with one stable steady state employed as a well-defined reference. In such systems, the characterization of the time hierarchies has already been used for determining the components that contribute to the dynamics of biological systems. However, the application of these methods to bistable nonlinear systems is impeded due to their inherent dependence on the reference state, which in this case is no longer unique. Here, we extend the applicability of the reference-state analysis by proposing, analyzing, and applying a novel method, which allows investigation of the time hierarchies in systems exhibiting bistability. The proposed method is in turn used in identifying the components, other than reactions, which determine the systemic dynamical properties. We demonstrate that in biological systems of varying levels of complexity and spanning different biological levels, the method can be effectively employed for model simplification while ensuring preservation of qualitative dynamical properties (i.e., bistability). Finally, by establishing a connection between techniques from nonlinear dynamics and multivariate statistics, the proposed approach provides the basis for extending reference-based analysis to bistable systems.

  15. Redefining plant systems biology: from cell to ecosystem.

    Science.gov (United States)

    Keurentjes, Joost J B; Angenent, Gerco C; Dicke, Marcel; Dos Santos, Vítor A P Martins; Molenaar, Jaap; van der Putten, Wim H; de Ruiter, Peter C; Struik, Paul C; Thomma, Bart P H J

    2011-04-01

    Molecular biologists typically restrict systems biology to cellular levels. By contrast, ecologists define biological systems as communities of interacting individuals at different trophic levels that process energy, nutrient and information flows. Modern plant breeding needs to increase agricultural productivity while decreasing the ecological footprint. This requires a holistic systems biology approach that couples different aggregation levels while considering the variables that affect these biological systems from cell to community. The challenge is to generate accurate experimental data that can be used together with modelling concepts and techniques that allow experimentally verifying in silico predictions. The coupling of aggregation levels in plant sciences, termed Integral Quantification of Biological Organization (IQ(BiO)), might enhance our abilities to generate new desired plant phenotypes. Copyright © 2010 Elsevier Ltd. All rights reserved.

  16. Stochastic transport processes in discrete biological systems

    CERN Document Server

    Frehland, Eckart

    1982-01-01

    These notes are in part based on a course for advanced students in the applications of stochastic processes held in 1978 at the University of Konstanz. These notes contain the results of re­ cent studies on the stochastic description of ion transport through biological membranes. In particular, they serve as an introduction to an unified theory of fluctuations in complex biological transport systems. We emphasize that the subject of this volume is not to introduce the mathematics of stochastic processes but to present a field of theoretical biophysics in which stochastic methods are important. In the last years the study of membrane noise has become an important method in biophysics. Valuable information on the ion transport mechanisms in membranes can be obtained from noise analysis. A number of different processes such as the opening and closing of ion channels have been shown to be sources of the measured current or voltage fluctuations. Bio­ logical 'transport systems can be complex. For example, the tr...

  17. Genomes, Phylogeny, and Evolutionary Systems Biology

    Energy Technology Data Exchange (ETDEWEB)

    Medina, Monica

    2005-03-25

    With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics and computer science are now known as systems biology. Here I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.

  18. Graphics processing units in bioinformatics, computational biology and systems biology.

    Science.gov (United States)

    Nobile, Marco S; Cazzaniga, Paolo; Tangherloni, Andrea; Besozzi, Daniela

    2017-09-01

    Several studies in Bioinformatics, Computational Biology and Systems Biology rely on the definition of physico-chemical or mathematical models of biological systems at different scales and levels of complexity, ranging from the interaction of atoms in single molecules up to genome-wide interaction networks. Traditional computational methods and software tools developed in these research fields share a common trait: they can be computationally demanding on Central Processing Units (CPUs), therefore limiting their applicability in many circumstances. To overcome this issue, general-purpose Graphics Processing Units (GPUs) are gaining an increasing attention by the scientific community, as they can considerably reduce the running time required by standard CPU-based software, and allow more intensive investigations of biological systems. In this review, we present a collection of GPU tools recently developed to perform computational analyses in life science disciplines, emphasizing the advantages and the drawbacks in the use of these parallel architectures. The complete list of GPU-powered tools here reviewed is available at http://bit.ly/gputools. © The Author 2016. Published by Oxford University Press.

  19. Advanced information processing system

    Science.gov (United States)

    Lala, J. H.

    1984-01-01

    Design and performance details of the advanced information processing system (AIPS) for fault and damage tolerant data processing on aircraft and spacecraft are presented. AIPS comprises several computers distributed throughout the vehicle and linked by a damage tolerant data bus. Most I/O functions are available to all the computers, which run in a TDMA mode. Each computer performs separate specific tasks in normal operation and assumes other tasks in degraded modes. Redundant software assures that all fault monitoring, logging and reporting are automated, together with control functions. Redundant duplex links and damage-spread limitation provide the fault tolerance. Details of an advanced design of a laboratory-scale proof-of-concept system are described, including functional operations.

  20. The AMMA information system

    Science.gov (United States)

    Fleury, Laurence; Brissebrat, Guillaume; Boichard, Jean-Luc; Cloché, Sophie; Mière, Arnaud; Moulaye, Oumarou; Ramage, Karim; Favot, Florence; Boulanger, Damien

    2015-04-01

    In the framework of the African Monsoon Multidisciplinary Analyses (AMMA) programme, several tools have been developed in order to boost the data and information exchange between researchers from different disciplines. The AMMA information system includes (i) a user-friendly data management and dissemination system, (ii) quasi real-time display websites and (iii) a scientific paper exchange collaborative tool. The AMMA information system is enriched by past and ongoing projects (IMPETUS, FENNEC, ESCAPE, QweCI, ACASIS, DACCIWA...) addressing meteorology, atmospheric chemistry, extreme events, health, adaptation of human societies... It is becoming a reference information system on environmental issues in West Africa. (i) The projects include airborne, ground-based and ocean measurements, social science surveys, satellite data use, modelling studies and value-added product development. Therefore, the AMMA data portal enables to access a great amount and a large variety of data: - 250 local observation datasets, that cover many geophysical components (atmosphere, ocean, soil, vegetation) and human activities (agronomy, health). They have been collected by operational networks since 1850, long term monitoring research networks (CATCH, IDAF, PIRATA...) and intensive scientific campaigns; - 1350 outputs of a socio-economics questionnaire; - 60 operational satellite products and several research products; - 10 output sets of meteorological and ocean operational models and 15 of research simulations. Data documentation complies with metadata international standards, and data are delivered into standard formats. The data request interface takes full advantage of the database relational structure and enables users to elaborate multicriteria requests (period, area, property, property value…). The AMMA data portal counts about 900 registered users, and 50 data requests every month. The AMMA databases and data portal have been developed and are operated jointly by SEDOO and

  1. Geographic Information Systems.

    Science.gov (United States)

    Wieczorek, William F; Delmerico, Alan M

    2009-01-01

    This chapter presents an overview of the development, capabilities, and utilization of geographic information systems (GIS). There are nearly an unlimited number of applications that are relevant to GIS because virtually all human interactions, natural and man-made features, resources, and populations have a geographic component. Everything happens somewhere and the location often has a role that affects what occurs. This role is often called spatial dependence or spatial autocorrelation, which exists when a phenomenon is not randomly geographically distributed. GIS has a number of key capabilities that are needed to conduct a spatial analysis to assess this spatial dependence. This chapter presents these capabilities (e.g., georeferencing, adjacency/distance measures, overlays) and provides a case study to illustrate how GIS can be used for both research and planning. Although GIS has developed into a relatively mature application for basic functions, development is needed to more seamlessly integrate spatial statistics and models.The issue of location, especially the geography of human activities, interactions between humanity and nature, and the distribution and location of natural resources and features, is one of the most basic elements of scientific inquiry. Conceptualizations and physical maps of geographic space have existed since the beginning of time because all human activity takes place in a geographic context. Representing objects in space, basically where things are located, is a critical aspect of the natural, social, and applied sciences. Throughout history there have been many methods of characterizing geographic space, especially maps created by artists, mariners, and others eventually leading to the development of the field of cartography. It is no surprise that the digital age has launched a major effort to utilize geographic data, but not just as maps. A geographic information system (GIS) facilitates the collection, analysis, and reporting of

  2. Decarboxylation mechanisms in biological system.

    Science.gov (United States)

    Li, Tingfeng; Huo, Lu; Pulley, Christopher; Liu, Aimin

    2012-08-01

    This review examines the mechanisms propelling cofactor-independent, organic cofactor-dependent and metal-dependent decarboxylase chemistry. Decarboxylation, the removal of carbon dioxide from organic acids, is a fundamentally important reaction in biology. Numerous decarboxylase enzymes serve as key components of aerobic and anaerobic carbohydrate metabolism and amino acid conversion. In the past decade, our knowledge of the mechanisms enabling these crucial decarboxylase reactions has continued to expand and inspire. This review focuses on the organic cofactors biotin, flavin, NAD, pyridoxal 5'-phosphate, pyruvoyl, and thiamin pyrophosphate as catalytic centers. Significant attention is also placed on the metal-dependent decarboxylase mechanisms. Copyright © 2012 Elsevier Inc. All rights reserved.

  3. Tunable promoters in synthetic and systems biology

    DEFF Research Database (Denmark)

    Dehli, Tore; Solem, Christian; Jensen, Peter Ruhdal

    2012-01-01

    in synthetic biology. A number of tools exist to manipulate the steps in between gene sequence and functional protein in living cells, but out of these the most straight-forward approach is to alter the gene expression level by manipulating the promoter sequence. Some of the promoter tuning tools available......Synthetic and systems biologists need standardized, modular and orthogonal tools yielding predictable functions in vivo. In systems biology such tools are needed to quantitatively analyze the behavior of biological systems while the efficient engineering of artificial gene networks is central...

  4. Metabolic systems biology: a brief primer.

    Science.gov (United States)

    Edwards, Lindsay M

    2017-05-01

    In the early to mid-20th century, reductionism as a concept in biology was challenged by key thinkers, including Ludwig von Bertalanffy. He proposed that living organisms were specific examples of complex systems and, as such, they should display characteristics including hierarchical organisation and emergent behaviour. Yet the true study of complete biological systems (for example, metabolism) was not possible until technological advances that occurred 60 years later. Technology now exists that permits the measurement of complete levels of the biological hierarchy, for example the genome and transcriptome. The complexity and scale of these data require computational models for their interpretation. The combination of these - systems thinking, high-dimensional data and computation - defines systems biology, typically accompanied by some notion of iterative model refinement. Only sequencing-based technologies, however, offer full coverage. Other 'omics' platforms trade coverage for sensitivity, although the densely connected nature of biological networks suggests that full coverage may not be necessary. Systems biology models are often characterised as either 'bottom-up' (mechanistic) or 'top-down' (statistical). This distinction can mislead, as all models rely on data and all are, to some degree, 'middle-out'. Systems biology has matured as a discipline, and its methods are commonplace in many laboratories. However, many challenges remain, especially those related to large-scale data integration. © 2016 The Authors. The Journal of Physiology © 2016 The Physiological Society.

  5. Pesticide Product Information System (PPIS)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Pesticide Product Information System contains information concerning all pesticide products registered in the United States. It includes registrant name and...

  6. Labor Agreement Information System (LAIRS)

    Data.gov (United States)

    Office of Personnel Management — The Labor Agreement Information Retrieval System (LAIRS) is a database containing historical information on labor-management relations in the Federal Government. It...

  7. From Information System to Information and Knowledge System

    OpenAIRE

    Grundstein, Michel; Arduin, Pierre-Emmanuel; Rosenthal-Sabroux, Camille

    2014-01-01

    International audience; In this paper we notice that all definitions of information system never make a clear distinction between the notion of information and the notion of knowledge. We propose to clarify differences between data, information and knowledge by suggesting a model of an Enterprise’s Information and Knowledge System (EIKS) supported by a Digital Information System. Then, based on our knowledge management research, we propose to transpose the Enterprise’s Knowledge Management Sy...

  8. New approaches in mathematical biology: Information theory and molecular machines

    International Nuclear Information System (INIS)

    Schneider, T.

    1995-01-01

    My research uses classical information theory to study genetic systems. Information theory was founded by Claude Shannon in the 1940's and has had an enormous impact on communications engineering and computer sciences. Shannon found a way to measure information. This measure can be used to precisely characterize the sequence conservation at nucleic-acid binding sites. The resulting methods, by completely replacing the use of ''consensus sequences'', provide better models for molecular biologists. An excess of conservation led us to do experimental work on bacteriophage T7 promoters and the F plasmid IncD repeats. The wonderful fidelity of telephone communications and compact disk (CD) music can be traced directly to Shannon's channel capacity theorem. When rederived for molecular biology, this theorem explains the surprising precision of many molecular events. Through connections with the Second Law of Thermodyanmics and Maxwell's Demon, this approach also has implications for the development of technology at the molecular level. Discussions of these topics are held on the internet news group bionet.info-theo. (author). (Abstract only)

  9. Biological risk factors in informal recyclers of Medellin city, 2005

    Directory of Open Access Journals (Sweden)

    Viviana L. Ballesteros

    2008-06-01

    Full Text Available The informal recyclers constitute a vulnerable population to problems of health by their constant exhibition to biological, chemical, physical and social risks, without protection. Objective: this work identify the biological risk facts to which the informal recyclers of the Bazaar of the Bridges of Medellin city. Methods: it was performed a Cross-sectional study. The sample was no probabilistic with 88 recyclers and the analysis unit was the informal recycler. It was applied a survey, a guide of observation of the activity of the recycler and were studied variables of person, place, time, type of biological risk facts, frequency of exhibition, felt morbidity and measures of protection. The analysis was statistical descriptive. Results: it was identified biological risk facts related to the contact with material in decomposition (96.6%, contaminated material (96.6%, animals (62.5% and arthropoda (79.5%. The se The se--curity measures to protect them from biological risk facts are used in less than 52% of recyclers; in addition, only 13.6% of the population were vaccinated, which increases the probability of becoming ill in this population. Conclusions: that the informal recyclers are exposed to different biological risk facts with little prevention, causing that population be vulnerable for the acquisition of infectious diseases.

  10. Teaching information literacy skills to sophomore-level biology majors.

    Science.gov (United States)

    Thompson, Leigh; Blankinship, Lisa Ann

    2015-05-01

    Many undergraduate students lack a sound understanding of information literacy. The skills that comprise information literacy are particularly important when combined with scientific writing for biology majors as they are the foundation skills necessary to complete upper-division biology course assignments, better train students for research projects, and prepare students for graduate and professional education. To help undergraduate biology students develop and practice information literacy and scientific writing skills, a series of three one-hour hands-on library sessions, discussions, and homework assignments were developed for Biological Literature, a one-credit, one-hour-per-week, required sophomore-level course. The embedded course librarian developed a learning exercise that reviewed how to conduct database and web searches, the difference between primary and secondary sources, source credibility, and how to access articles through the university's databases. Students used the skills gained in the library training sessions for later writing assignments including a formal lab report and annotated bibliography. By focusing on improving information literacy skills as well as providing practice in scientific writing, Biological Literature students are better able to meet the rigors of upper-division biology courses and communicate research findings in a more professional manner.

  11. Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli

    DEFF Research Database (Denmark)

    Chang, Roger L.; Andrews, Kathleen; Kim, Donghyuk

    2013-01-01

    Improve the System A "systems biology" approach may clarify, for example, how particular proteins determine sensitivity of bacteria to extremes of temperature. Chang et al. (p. 1220) integrated information on protein structure with a model of metabolism, thus associating the protein structure of ...

  12. EURASIP journal on bioinformatics & systems biology

    National Research Council Canada - National Science Library

    2006-01-01

    "The overall aim of "EURASIP Journal on Bioinformatics and Systems Biology" is to publish research results related to signal processing and bioinformatics theories and techniques relevant to a wide...

  13. Graduate Curriculum for Biological Information Specialists: A Key to Integration of Scale in Biology

    Directory of Open Access Journals (Sweden)

    Carole L. Palmer

    2007-12-01

    Full Text Available Scientific data problems do not stand in isolation. They are part of a larger set of challenges associated with the escalation of scientific information and changes in scholarly communication in the digital environment. Biologists in particular are generating enormous sets of data at a high rate, and new discoveries in the biological sciences will increasingly depend on the integration of data across multiple scales. This work will require new kinds of information expertise in key areas. To build this professional capacity we have developed two complementary educational programs: a Biological Information Specialist (BIS masters degree and a concentration in Data Curation (DC. We believe that BISs will be central in the development of cyberinfrastructure and information services needed to facilitate interdisciplinary and multi-scale science. Here we present three sample cases from our current research projects to illustrate areas in which we expect information specialists to make important contributions to biological research practice.

  14. A framework for evolutionary systems biology.

    Science.gov (United States)

    Loewe, Laurence

    2009-02-24

    Many difficult problems in evolutionary genomics are related to mutations that have weak effects on fitness, as the consequences of mutations with large effects are often simple to predict. Current systems biology has accumulated much data on mutations with large effects and can predict the properties of knockout mutants in some systems. However experimental methods are too insensitive to observe small effects. Here I propose a novel framework that brings together evolutionary theory and current systems biology approaches in order to quantify small effects of mutations and their epistatic interactions in silico. Central to this approach is the definition of fitness correlates that can be computed in some current systems biology models employing the rigorous algorithms that are at the core of much work in computational systems biology. The framework exploits synergies between the realism of such models and the need to understand real systems in evolutionary theory. This framework can address many longstanding topics in evolutionary biology by defining various 'levels' of the adaptive landscape. Addressed topics include the distribution of mutational effects on fitness, as well as the nature of advantageous mutations, epistasis and robustness. Combining corresponding parameter estimates with population genetics models raises the possibility of testing evolutionary hypotheses at a new level of realism. EvoSysBio is expected to lead to a more detailed understanding of the fundamental principles of life by combining knowledge about well-known biological systems from several disciplines. This will benefit both evolutionary theory and current systems biology. Understanding robustness by analysing distributions of mutational effects and epistasis is pivotal for drug design, cancer research, responsible genetic engineering in synthetic biology and many other practical applications.

  15. Geographic information systems: introduction.

    Science.gov (United States)

    Calistri, Paolo; Conte, Annamaria; Freier, Jerome E; Ward, Michael P

    2007-01-01

    The recent exponential growth of the science and technology of geographic information systems (GIS) has made a tremendous contribution to epidemiological analysis and has led to the development of new powerful tools for the surveillance of animal diseases. GIS, spatial analysis and remote sensing provide valuable methods to collect and manage information for epidemiological surveys. Spatial patterns and trends of disease can be correlated with climatic and environmental information, thus contributing to a better understanding of the links between disease processes and explanatory spatial variables. Until recently, these tools were underexploited in the field of veterinary public health, due to the prohibitive cost of hardware and the complexity of GIS software that required a high level of expertise. The revolutionary developments in computer performance of the last decade have not only reduced the costs of equipment but have made available easy-to-use Web-based software which in turn have meant that GIS are more widely accessible by veterinary services at all levels. At the same time, the increased awareness of the possibilities offered by these tools has created new opportunities for decision-makers to enhance their planning, analysis and monitoring capabilities. These technologies offer a new way of sharing and accessing spatial and non-spatial data across groups and institutions. The series of papers included in this compilation aim to: - define the state of the art in the use of GIS in veterinary activities - identify priority needs in the development of new GIS tools at the international level for the surveillance of animal diseases and zoonoses - define practical proposals for their implementation. The topics addressed are presented in the following order in this book: - importance of GIS for the monitoring of animal diseases and zoonoses - GIS application in surveillance activities - spatial analysis in veterinary epidemiology - data collection and remote

  16. Biologi Komunikasi melalui Implementasi “Information Communications Technology”

    Directory of Open Access Journals (Sweden)

    Deni Darmawan

    2010-12-01

    Full Text Available The Biological communication Behavior has been constructed through the explanation of  the phenomena of their specific part of activies encompassing: Prefrontal, Frontal, Parietal, Central, Occipital and Parasagital which have been significantly tested in terms of their impacts in learning acceleration starting from Elementary School to College level. This study is conducted by means of constructive approach, meaning that it employs both the Quantitative and Qualitative techniques.The study outcomes show that: (1 designing of learning information with instructional model of communication and information  technology based their significant impacts on the learning acceleration controlled by the communication biology; (2 The biological communication behaviors that take place between the left brain and the right one is done by the specific parts as can be observed in such of learning activities; (3 Biological Communication is reliably tested scientifically from the  science point of view, especially from the intrapersonal and interpersonal perspective study.

  17. Information systems process and practice

    CERN Document Server

    Urquhart, Christine; Tbaishat, Dina; Yeoman, Alison

    2017-01-01

    This book adopts a holistic interpretation of information architecture, to offer a variety of methods, tools, and techniques that may be used when designing websites and information systems that support workflows and what people require when 'managing information'.

  18. A Philosophical Perspective on Evolutionary Systems Biology.

    Science.gov (United States)

    O'Malley, Maureen A; Soyer, Orkun S; Siegal, Mark L

    2015-03-01

    Evolutionary systems biology (ESB) is an emerging hybrid approach that integrates methods, models, and data from evolutionary and systems biology. Drawing on themes that arose at a cross-disciplinary meeting on ESB in 2013, we discuss in detail some of the explanatory friction that arises in the interaction between evolutionary and systems biology. These tensions appear because of different modeling approaches, diverse explanatory aims and strategies, and divergent views about the scope of the evolutionary synthesis. We locate these discussions in the context of long-running philosophical deliberations on explanation, modeling, and theoretical synthesis. We show how many of the issues central to ESB's progress can be understood as general philosophical problems. The benefits of addressing these philosophical issues feed back into philosophy too, because ESB provides excellent examples of scientific practice for the development of philosophy of science and philosophy of biology.

  19. Reasonable Accommodation Information Tracking System

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Reasonable Accommodation Information Tracking System (RAITS) is a case management system that allows the National Reasonable Accommodation Coordinator (NRAC) and...

  20. Security Information System Digital Simulation

    OpenAIRE

    Tao Kuang; Shanhong Zhu

    2015-01-01

    The study built a simulation model for the study of food security information system relay protection. MATLAB-based simulation technology can support the analysis and design of food security information systems. As an example, the food security information system fault simulation, zero-sequence current protection simulation and transformer differential protection simulation are presented in this study. The case studies show that the simulation of food security information system relay protect...

  1. Information Literacy in Biology Education: An Example from an Advanced Cell Biology Course

    Science.gov (United States)

    Porter, John R.

    2005-01-01

    Information literacy skills are critically important for the undergraduate biology student. The ability to find, understand, evaluate, and use information, whether from the scientific literature or from Web resources, is essential for a good understanding of a topic and for the conduct of research. A project in which students receive information…

  2. Towards Engineering Biological Systems in a Broader Context.

    Science.gov (United States)

    Venturelli, Ophelia S; Egbert, Robert G; Arkin, Adam P

    2016-02-27

    Significant advances have been made in synthetic biology to program information processing capabilities in cells. While these designs can function predictably in controlled laboratory environments, the reliability of these devices in complex, temporally changing environments has not yet been characterized. As human society faces global challenges in agriculture, human health and energy, synthetic biology should develop predictive design principles for biological systems operating in complex environments. Natural biological systems have evolved mechanisms to overcome innumerable and diverse environmental challenges. Evolutionary design rules should be extracted and adapted to engineer stable and predictable ecological function. We highlight examples of natural biological responses spanning the cellular, population and microbial community levels that show promise in synthetic biology contexts. We argue that synthetic circuits embedded in host organisms or designed ecologies informed by suitable measurement of biotic and abiotic environmental parameters could be used as engineering substrates to achieve target functions in complex environments. Successful implementation of these methods will broaden the context in which synthetic biological systems can be applied to solve important problems. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Interactive analysis of systems biology molecular expression data

    Directory of Open Access Journals (Sweden)

    Prabhakar Sunil

    2008-02-01

    Full Text Available Abstract Background Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular correlations and comparative studies of molecular expression are crucial to establishing interdependent connections in systems biology. The existing software packages provide limited data mining capability. The user must first generate visualization data with a preferred data mining algorithm and then upload the resulting data into the visualization package for graphic visualization of molecular relations. Results Presented is a novel interactive visual data mining application, SysNet that provides an interactive environment for the analysis of high data volume molecular expression information of most any type from biological systems. It integrates interactive graphic visualization and statistical data mining into a single package. SysNet interactively presents intermolecular correlation information with circular and heatmap layouts. It is also applicable to comparative analysis of molecular expression data, such as time course data. Conclusion The SysNet program has been utilized to analyze elemental profile changes in response to an increasing concentration of iron (Fe in growth media (an ionomics dataset. This study case demonstrates that the SysNet software is an effective platform for interactive analysis of molecular expression information in systems biology.

  4. The IAGOS Information System

    Science.gov (United States)

    Boulanger, Damien; Thouret, Valérie; Brissebrat, Guillaume

    2017-04-01

    IAGOS (In-service Aircraft for a Global Observing System) is a European Research Infrastructure which aims at the provision of long-term, regular and spatially resolved in situ observations of the atmospheric composition. IAGOS observation systems are deployed on a fleet of commercial aircraft and do measurements of aerosols, cloud particles, greenhouse gases, ozone, water vapor and nitrogen oxides from the surface to the lower stratosphere. The IAGOS database is an essential part of the global atmospheric monitoring network. It contains IAGOS-core data and IAGOS-CARIBIC (Civil Aircraft for the Regular Investigation of the Atmosphere Based on an Instrument Container) data. The IAGOS Data Portal http://www.iagos.org, damien.boulanger@obs-mip.fr) is part of the French atmospheric chemistry data center AERIS (http://www.aeris-data.fr). In 2016 the new IAGOS Data Portal has been released. In addition to the data download the portal provides improved and new services such as download in NetCDF or NASA Ames formats and plotting tools (maps, time series, vertical profiles, etc.). New added value products are or will be soon available through the portal: back trajectories, origin of air masses, co-location with satellite data, etc. Web services allow to download IAGOS metadata such as flights and airports information. Administration tools have been implemented for users management and instruments monitoring. A major improvement is the interoperability with international portals or other databases in order to improve IAGOS data discovery. In the frame of the IGAS project (IAGOS for the Copernicus Atmospheric Service), a data network has been setup. It is composed of three data centers: the IAGOS database in Toulouse, the HALO research aircraft database at DLR (https://halo-db.pa.op.dlr.de) and the CAMS (Copernicus Atmosphere Monitoring Service) data center in Jülich (http://join.iek.fz-juelich.de). The link with the CAMS data center, through the JOIN interface, allows to

  5. Systems Biology and Stem Cell Pluripotency

    DEFF Research Database (Denmark)

    Mashayekhi, Kaveh; Hall, Vanessa Jane; Freude, Kristine

    2016-01-01

    Recent breakthroughs in stem cell biology have accelerated research in the area of regenerative medicine. Over the past years, it has become possible to derive patient-specific stem cells which can be used to generate different cell populations for potential cell therapy. Systems biological...... improve systems biology and its uses in the field. In this chapter, we first give a general background on stem cell biology and regenerative medicine. Stem cell potency is introduced together with the hierarchy of stem cells ranging from pluripotent embryonic stem cells (ESCs) and induced pluripotent stem...... modeling of stem cell pluripotency and differentiation have largely been based on prior knowledge of signaling pathways, gene regulatory networks, and epigenetic factors. However, there is a great need to extend the complexity of the modeling and to integrate different types of data, which would further...

  6. Statistical Model Checking for Biological Systems

    DEFF Research Database (Denmark)

    David, Alexandre; Larsen, Kim Guldstrand; Legay, Axel

    2014-01-01

    Statistical Model Checking (SMC) is a highly scalable simulation-based verification approach for testing and estimating the probability that a stochastic system satisfies a given linear temporal property. The technique has been applied to (discrete and continuous time) Markov chains, stochastic...... timed automata and most recently hybrid systems using the tool Uppaal SMC. In this paper we enable the application of SMC to complex biological systems, by combining Uppaal SMC with ANIMO, a plugin of the tool Cytoscape used by biologists, as well as with SimBiology®, a plugin of Matlab to simulate...

  7. Lehrman's dictum: information and explanation in developmental biology.

    Science.gov (United States)

    Griffiths, Paul E

    2013-01-01

    The integration of concepts from evolutionary developmental biology, such as the homology concept, into developmental psychobiology has great potential. However, evolutionary developmental biology is an attempt to integrate evolutionary and developmental explanation and developmental psychobiology has traditionally been concerned to avoid conflating these two kinds of explanation. This article examines a recent attempt to explain development in terms of "inherited information." The resulting explanation is an evolutionary explanation of development of a kind typical of evolutionary developmental biology. But its proponent mistakes it for an actual developmental explanation. Any integration of evolutionary developmental biology and developmental psychobiology should pay close attention to longstanding concerns about conflating evolutionary and developmental explanations. Copyright © 2012 Wiley Periodicals, Inc.

  8. Informational system. Documents management

    Directory of Open Access Journals (Sweden)

    Vladut Iacob

    2009-12-01

    Full Text Available Productivity growing, as well as reducing of operational costs in a company can be achieved by adopting a document management solutions. Such application will allow management and structured and efficient transmission of information within the organization.

  9. National oceanographic information system

    Digital Repository Service at National Institute of Oceanography (India)

    Desai, B.N.; Kunte, P.D.; Bhargava, R.M.S.

    Ocean study is inherently interdisciplinary and therefore calls for a controlled and integrated approach for information generation, processing and decision making. In this context, Indian National Oceanographic Data Centre (INODC) of National...

  10. Nanophotonics for information systems

    International Nuclear Information System (INIS)

    Fainman, Y; Ikeda, K; Abashin, M; Tan, D

    2010-01-01

    The field of photonics finds applications in information technology, health care, lighting, and sensing. This paper explores the role of nanotechnology with focus on nanophotonics in dielectric and inhomogeneous metamaterials.

  11. Infobiotics information in biotic systems

    CERN Document Server

    Manca, Vincenzo

    2013-01-01

    The book presents topics in discrete biomathematics. Mathematics has been widely used in modeling biological phenomena. However, the molecular and discrete nature of basic life processes suggests that their logic follow principles that are intrinsically based on discrete and informational mechanisms. The ultimate reason of  polymers, as key element of life, is directly based on the computational power of strings, and the intrinsic necessity of metabolism is related to the mathematical notion of multiset.   The switch of the two roots of bioinformatics suggests a change of perspective. In bioinformatics, the biologists ask computer scientists to assist them in processing biological data. Conversely, in infobiotics mathematicians and computer scientists investigate principles and theories yielding new interpretation keys of biological phenomena. Life is too important to be investigated by biologists alone, and though computers are essential to process data from biological laboratories, many fundamental questi...

  12. Car insurance information management system

    OpenAIRE

    Sun, Yu

    2015-01-01

    A customer information system is a typical information management system. It involves three aspects, the backstage database establishment, the application development and the system maintenance. A car insurance information management system is based on browser/server structure. Microsoft SQL Server establishes the backstage database. Active Server Pages, from Microsoft as well is used as the interface layer. The objective of this thesis was to apply ASP to the dynamic storage of a web page...

  13. Entropy in Corporate Information Systems

    Directory of Open Access Journals (Sweden)

    Victor Y. Tsvetkov

    2014-03-01

    Full Text Available This paper describes the stages of entropy formation. It depicts the basic definitions of the corporate information systems. This paper describes the quality of entropy, the duration of the entropy in the corporate information system. The article also gives a paradigmatic description of the action of information entropy in time.

  14. Ins and outs of systems biology vis-à-vis molecular biology: continuation or clear cut?

    Science.gov (United States)

    De Backer, Philippe; De Waele, Danny; Van Speybroeck, Linda

    2010-03-01

    The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology 'revolutionizes' molecular biology and 'transcends' its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology's use of modelling and bioinformatics, and by its scale enlargement.

  15. Photosynthetic system as a biological functional element

    International Nuclear Information System (INIS)

    Zakhidov, E.A.; Zakhidova, M.A.; Kasymdzhanov, M.A.; Kurbanov, S.S.; Nematov, Sh.K.; Khabibullaev, P.K.

    2005-01-01

    Photosynthetic apparatus of high plants and photosynthetic bacteria is essentially autonomic system in terms of genetics and structural -functional properties located in specific medium, a bio-membrane. Processes of light absorption and exciton migration in light harvesting antenna, separation and further transfer of charges in reaction centers have specific features, which may be used for application of these objects as key elements in construction of future biological functional elements. Progress in study and genetic modification of photosynthetic membranes achieved during the last decade opens great prospects in development biological functional elements and systems. The main characteristics of photosynthetic system for these purposes are: (i) energy conversion processes in the first light phase of the photosynthesis have very short periods, up to picoseconds, which indicates possibility of creation of ultrafast functional elements on their basis; (ii) characteristics sizes of photosynthetic units, 10-100 nm, and possibility to arrange regularly disposed elements in relevant membranes could be prospective point for creation of nano structures and on their basis relevant biologic functional elements; (iii) elements based on modified photosynthetic apparatus and bio-membranes might be efficiently created by methods of gene engineering and manipulation, that open huge opportunities for development of read biological functional systems. In the paper structural-functional properties and characteristics of high plants and purple photosynthetic bacteria, which may be useful for creation of future biological functional elements are considered. (author)

  16. Biocellion: accelerating computer simulation of multicellular biological system models.

    Science.gov (United States)

    Kang, Seunghwa; Kahan, Simon; McDermott, Jason; Flann, Nicholas; Shmulevich, Ilya

    2014-11-01

    Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming. We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies. Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  17. Cardiovascular Biology of the Incretin System

    Science.gov (United States)

    Ussher, John R.; Drucker, Daniel J.

    2012-01-01

    Glucagon-like peptide-1 (GLP-1) is an incretin hormone that enhances glucose-stimulated insulin secretion and exerts direct and indirect actions on the cardiovascular system. GLP-1 and its related incretin hormone, glucose-dependent insulinotropic polypeptide (GIP), are rapidly inactivated by the enzyme dipeptidyl peptidase 4 (DPP-4), a key determinant of incretin bioactivity. Two classes of medications that enhance incretin action, GLP-1R agonists and DPP-4 inhibitors, are used for the treatment of type 2 diabetes mellitus (T2DM). We review herein the cardiovascular biology of GLP-1R agonists and DPP-4 inhibitors, including direct and indirect effects on cardiomyocytes, blood vessels, adipocytes, the control of blood pressure and postprandial lipoprotein secretion. Both GLP-1R activation and DPP-4 inhibition exert multiple cardioprotective actions in preclinical models of cardiovascular dysfunction, and short term studies in human subjects appear to demonstrate modest yet beneficial actions on cardiac function in subjects with ischemic heart disease. Incretin-based agents control body weight, improve glycemic control with a low risk of hypoglycemia, decrease blood pressure, inhibit the secretion of intestinal chylomicrons, and reduce inflammation in preclinical studies. Nevertheless, there is limited information on the cardiovascular actions of these agents in patients with diabetes and established cardiovascular disease. Hence, a more complete understanding of the cardiovascular risk:benefit ratio of incretin-based therapies will require completion of long term cardiovascular outcome studies currently underway in patients with T2DM. PMID:22323472

  18. The visual information system

    Science.gov (United States)

    Merlyn J. Paulson

    1979-01-01

    This paper outlines a project level process (V.I.S.) which utilizes very accurate and flexible computer algorithms in combination with contemporary site analysis and design techniques for visual evaluation, design and management. The process provides logical direction and connecting bridges through problem identification, information collection and verification, visual...

  19. Employee Information Management System (EIMS)

    Data.gov (United States)

    US Agency for International Development — The EIMS is the Office of Human Resources' web-based employee information system. Direct-hire employees can access and review their USAID personnel information, such...

  20. JPL Tropical Cyclone Information System

    Data.gov (United States)

    National Aeronautics and Space Administration — The JPL Tropical Cyclone Information System (TCIS) brings together satellite and in situ data sets from various sources to help you find information for a particular...

  1. On the analysis of complex biological supply chains: From Process Systems Engineering to Quantitative Systems Pharmacology.

    Science.gov (United States)

    Rao, Rohit T; Scherholz, Megerle L; Hartmanshenn, Clara; Bae, Seul-A; Androulakis, Ioannis P

    2017-12-05

    The use of models in biology has become particularly relevant as it enables investigators to develop a mechanistic framework for understanding the operating principles of living systems as well as in quantitatively predicting their response to both pathological perturbations and pharmacological interventions. This application has resulted in a synergistic convergence of systems biology and pharmacokinetic-pharmacodynamic modeling techniques that has led to the emergence of quantitative systems pharmacology (QSP). In this review, we discuss how the foundational principles of chemical process systems engineering inform the progressive development of more physiologically-based systems biology models.

  2. A lung function information system

    NARCIS (Netherlands)

    A.F.M. Verbraak (Anton); E.J. Hoorn (Ewout); J. de Vries (Julius); J.M. Bogaard (Jan); A. Versprille (Adrian)

    1991-01-01

    markdownabstractAbstract A lung function information system (LFIS) was developed for the data analysis of pulmonary function tests at different locations. This system was connected to the hospital information system (HIS) for the retrieval of patient data and the storage of the lung function

  3. Evolutionary Information System Development

    DEFF Research Database (Denmark)

    Kristensen, Jan

    This paper offers advice to companies and professionals that implement e-commerce systems in business organizations. Implementing e-commerce systems is different from traditional IT implementation and thus requires a new set of tools and skills. The need for a novel approach is illustrated...... and necessary items that must be taken into account are pointed out by narrating two stories of e-commerce implementation processes in wholesale companies. The empirical evidence suggests the following: Managing the continued development on an operational level requires operational insight and understanding...... of business priorities. On a more theoretical level this suggests that we must revise our current understanding of systems development to cope....

  4. Modeling of biological intelligence for SCM system optimization.

    Science.gov (United States)

    Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

    2012-01-01

    This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms.

  5. Modeling of Biological Intelligence for SCM System Optimization

    Directory of Open Access Journals (Sweden)

    Shengyong Chen

    2012-01-01

    Full Text Available This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms.

  6. Modeling of Biological Intelligence for SCM System Optimization

    Science.gov (United States)

    Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

    2012-01-01

    This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms. PMID:22162724

  7. Discovery of Chemical Toxicity via Biological Networks and Systems Biology

    Energy Technology Data Exchange (ETDEWEB)

    Perkins, Edward; Habib, Tanwir; Guan, Xin; Escalon, Barbara; Falciani, Francesco; Chipman, J.K.; Antczak, Philipp; Edwards, Stephen; Taylor, Ronald C.; Vulpe, Chris; Loguinov, Alexandre; Van Aggelen, Graham; Villeneuve, Daniel L.; Garcia-Reyero, Natalia

    2010-09-30

    Both soldiers and animals are exposed to many chemicals as the result of military activities. Tools are needed to understand the hazards and risks that chemicals and new materials pose to soldiers and the environment. We have investigated the potential of global gene regulatory networks in understanding the impact of chemicals on reproduction. We characterized effects of chemicals on ovaries of the model animal system, the Fathead minnow (Pimopheles promelas) connecting chemical impacts on gene expression to circulating blood levels of the hormones testosterone and estradiol in addition to the egg yolk protein vitellogenin. We describe the application of reverse engineering complex interaction networks from high dimensional gene expression data to characterize chemicals that disrupt the hypothalamus-pituitary-gonadal endocrine axis that governs reproduction in fathead minnows. The construction of global gene regulatory networks provides deep insights into how drugs and chemicals effect key organs and biological pathways.

  8. Science information systems: Visualization

    Science.gov (United States)

    Wall, Ray J.

    1991-01-01

    Future programs in earth science, planetary science, and astrophysics will involve complex instruments that produce data at unprecedented rates and volumes. Current methods for data display, exploration, and discovery are inadequate. Visualization technology offers a means for the user to comprehend, explore, and examine complex data sets. The goal of this program is to increase the effectiveness and efficiency of scientists in extracting scientific information from large volumes of instrument data.

  9. Information System Quality Assessment Methods

    OpenAIRE

    Korn, Alexandra

    2014-01-01

    This thesis explores challenging topic of information system quality assessment and mainly process assessment. In this work the term Information System Quality is defined as well as different approaches in a quality definition for different domains of information systems are outlined. Main methods of process assessment are overviewed and their relationships are described. Process assessment methods are divided into two categories: ISO standards and best practices. The main objective of this w...

  10. Medical Information Management System (MIMS): A generalized interactive information system

    Science.gov (United States)

    Alterescu, S.; Friedman, C. A.; Hipkins, K. R.

    1975-01-01

    An interactive information system is described. It is a general purpose, free format system which offers immediate assistance where manipulation of large data bases is required. The medical area is a prime area of application. Examples of the system's operation, commentary on the examples, and a complete listing of the system program are included.

  11. Health Research Information Tracking System

    Data.gov (United States)

    US Agency for International Development — The Health Research Information Tracking System (HRIT) is an expansion of the Child Health Research database that collects and maintains categorization, description,...

  12. Radiological/biological/aerosol removal system

    Science.gov (United States)

    Haslam, Jeffery J

    2015-03-17

    An air filter replacement system for existing buildings, vehicles, arenas, and other enclosed airspaces includes a replacement air filter for replacing a standard air filter. The replacement air filter has dimensions and air flow specifications that allow it to replace the standard air filter. The replacement air filter includes a filter material that removes radiological or biological or aerosol particles.

  13. Studies on Semantic Systems Chemical Biology

    Science.gov (United States)

    Chen, Bin

    2012-01-01

    Current "one disease, one target and one drug" drug development paradigm is under question as relatively few drugs have reached the market in the last two decades. Increasingly research focus is being placed on the study of drug action against biological systems as a whole rather than against a single component (called "Systems…

  14. Modular microfluidic system for biological sample preparation

    Science.gov (United States)

    Rose, Klint A.; Mariella, Jr., Raymond P.; Bailey, Christopher G.; Ness, Kevin Dean

    2015-09-29

    A reconfigurable modular microfluidic system for preparation of a biological sample including a series of reconfigurable modules for automated sample preparation adapted to selectively include a) a microfluidic acoustic focusing filter module, b) a dielectrophoresis bacteria filter module, c) a dielectrophoresis virus filter module, d) an isotachophoresis nucleic acid filter module, e) a lyses module, and f) an isotachophoresis-based nucleic acid filter.

  15. Nutritional Systems Biology: Definitions and Approaches

    DEFF Research Database (Denmark)

    Panagiotou, Gianni; Nielsen, Jens

    2009-01-01

    waiting for a predictive knowledge of genetic variation. It is widely recognized that systems and network biology has the potential to increase our understanding of how nutrition influences metabolic pathways and homeostasis, how this regulation is disturbed in a diet-related disease, and to what extent...... individual genotypes contribute to such diseases....

  16. How do biological systems escape 'chaotic' state?

    Indian Academy of Sciences (India)

    B J Rao

    2018-02-13

    Feb 13, 2018 ... triggering 'escape from homeostasis' (Nijhout et al. 2014) where phenotypes begin to become less stable and eventually turn into fully unstable state, the start of 'chaos' in a system. Therefore, the key to biological designs is to stay close to or within the 'homeostatic plateau' and resist drifting into 'chaos'.

  17. Notions of radiation chemistry in biological systems

    International Nuclear Information System (INIS)

    Mastro, N.L. del.

    1989-10-01

    The present paper examines some aspects of the direct and indirect biological radiation effects: pair formation, free radicals, superoxide ion, hydrogen peroxide, hydroxyl radical, oxygen singlet together with the endogen radioprotector mechanisms of organisms and the ways in which an improved radioresistance of biochemical systems can be achieved. (author) [pt

  18. Quantifying electron transfer reactions in biological systems

    DEFF Research Database (Denmark)

    Sjulstok, Emil Sjulstok; Olsen, Jógvan Magnus Haugaard; Solov'yov, Ilia A

    2015-01-01

    to deduce the driving force for the electron transfer reaction and to establish those interactions that play the major role in propelling the electron. The suggested approach is seen as a general recipe to treat electron transfer events in biological systems computationally, and we utilize it to describe...

  19. Micromechanics of engineered and biological systems

    Indian Academy of Sciences (India)

    Microsystems are good examples of integrated engineered systems of small size. Although this .... In develop- mental biology, the application of controlled forces on growing embryos is shown to help in under- standing ..... Optimization is a useful tool for synthesis. Many optimal synthesis methods have been developed for.

  20. The Information Systems Artifact

    DEFF Research Database (Denmark)

    Chatterjee, Surtirtha; Xiao, Xiao; Elbanna, Amany

    2017-01-01

    Passionate debates regarding the defining characteristic of the “IT artifact” continue. Such debates, and also the lack of explicit consideration of the “information” element in the IT artifact, motivate us to propose a revised conception, drawing upon concepts from General Systems Theory (GST...

  1. Fluid Information Systems

    DEFF Research Database (Denmark)

    Probst, Christian W.; Hansen, René Rydhof

    2009-01-01

    Networked communication systems and the data they make available have, over the last decades, made their way to the very core of both society and business. Not only do they support everyday life and day-to-day operations, in many cases they enable them in the first place, and often are among...

  2. Computer-Supported Information Systems.

    Science.gov (United States)

    Mayhew, William H.

    1983-01-01

    The planning and implementation of a computerized management information system at a fictional small college is described. Nine key points are made regarding department involvement, centralization, gradual program implementation, lowering costs, system documentation, and upper-level administrative support. (MSE)

  3. Systematic integration of experimental data and models in systems biology.

    Science.gov (United States)

    Li, Peter; Dada, Joseph O; Jameson, Daniel; Spasic, Irena; Swainston, Neil; Carroll, Kathleen; Dunn, Warwick; Khan, Farid; Malys, Naglis; Messiha, Hanan L; Simeonidis, Evangelos; Weichart, Dieter; Winder, Catherine; Wishart, Jill; Broomhead, David S; Goble, Carole A; Gaskell, Simon J; Kell, Douglas B; Westerhoff, Hans V; Mendes, Pedro; Paton, Norman W

    2010-11-29

    The behaviour of biological systems can be deduced from their mathematical models. However, multiple sources of data in diverse forms are required in the construction of a model in order to define its components and their biochemical reactions, and corresponding parameters. Automating the assembly and use of systems biology models is dependent upon data integration processes involving the interoperation of data and analytical resources. Taverna workflows have been developed for the automated assembly of quantitative parameterised metabolic networks in the Systems Biology Markup Language (SBML). A SBML model is built in a systematic fashion by the workflows which starts with the construction of a qualitative network using data from a MIRIAM-compliant genome-scale model of yeast metabolism. This is followed by parameterisation of the SBML model with experimental data from two repositories, the SABIO-RK enzyme kinetics database and a database of quantitative experimental results. The models are then calibrated and simulated in workflows that call out to COPASIWS, the web service interface to the COPASI software application for analysing biochemical networks. These systems biology workflows were evaluated for their ability to construct a parameterised model of yeast glycolysis. Distributed information about metabolic reactions that have been described to MIRIAM standards enables the automated assembly of quantitative systems biology models of metabolic networks based on user-defined criteria. Such data integration processes can be implemented as Taverna workflows to provide a rapid overview of the components and their relationships within a biochemical system.

  4. Mathematical Modeling of Complex Biological Systems

    OpenAIRE

    Fischer, Hans Peter

    2008-01-01

    To understand complex biological systems such as cells, tissues, or even the human body, it is not sufficient to identify and characterize the individual molecules in the system. It also is necessary to obtain a thorough understanding of the interaction between molecules and pathways. This is even truer for understanding complex diseases such as cancer, Alzheimer’s disease, or alcoholism. With recent technological advances enabling researchers to monitor complex cellular processes on the mole...

  5. Visualizing dimensionality reduction of systems biology data

    OpenAIRE

    Lehrmann, Andreas; Huber, Michael; Polatkan, Aydin C.; Pritzkau, Albert; Nieselt, Kay

    2012-01-01

    One of the challenges in analyzing high-dimensional expression data is the detection of important biological signals. A common approach is to apply a dimension reduction method, such as principal component analysis. Typically, after application of such a method the data is projected and visualized in the new coordinate system, using scatter plots or profile plots. These methods provide good results if the data have certain properties which become visible in the new coordinate system and which...

  6. Tropical Cyclone Information System

    Science.gov (United States)

    Li, P. Peggy; Knosp, Brian W.; Vu, Quoc A.; Yi, Chao; Hristova-Veleva, Svetla M.

    2009-01-01

    The JPL Tropical Cyclone Infor ma tion System (TCIS) is a Web portal (http://tropicalcyclone.jpl.nasa.gov) that provides researchers with an extensive set of observed hurricane parameters together with large-scale and convection resolving model outputs. It provides a comprehensive set of high-resolution satellite (see figure), airborne, and in-situ observations in both image and data formats. Large-scale datasets depict the surrounding environmental parameters such as SST (Sea Surface Temperature) and aerosol loading. Model outputs and analysis tools are provided to evaluate model performance and compare observations from different platforms. The system pertains to the thermodynamic and microphysical structure of the storm, the air-sea interaction processes, and the larger-scale environment as depicted by ocean heat content and the aerosol loading of the environment. Currently, the TCIS is populated with satellite observations of all tropical cyclones observed globally during 2005. There is a plan to extend the database both forward in time till present as well as backward to 1998. The portal is powered by a MySQL database and an Apache/Tomcat Web server on a Linux system. The interactive graphic user interface is provided by Google Map.

  7. Methods of information theory and algorithmic complexity for network biology.

    Science.gov (United States)

    Zenil, Hector; Kiani, Narsis A; Tegnér, Jesper

    2016-03-01

    We survey and introduce concepts and tools located at the intersection of information theory and network biology. We show that Shannon's information entropy, compressibility and algorithmic complexity quantify different local and global aspects of synthetic and biological data. We show examples such as the emergence of giant components in Erdös-Rényi random graphs, and the recovery of topological properties from numerical kinetic properties simulating gene expression data. We provide exact theoretical calculations, numerical approximations and error estimations of entropy, algorithmic probability and Kolmogorov complexity for different types of graphs, characterizing their variant and invariant properties. We introduce formal definitions of complexity for both labeled and unlabeled graphs and prove that the Kolmogorov complexity of a labeled graph is a good approximation of its unlabeled Kolmogorov complexity and thus a robust definition of graph complexity. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Information technology equipment cooling system

    Science.gov (United States)

    Schultz, Mark D.

    2014-06-10

    According to one embodiment, a system for removing heat from a rack of information technology equipment may include a sidecar indoor air to liquid heat exchanger that cools warm air generated by the rack of information technology equipment. The system may also include a liquid to liquid heat exchanger and an outdoor heat exchanger. The system may further include configurable pathways to connect and control fluid flow through the sidecar heat exchanger, the liquid to liquid heat exchanger, the rack of information technology equipment, and the outdoor heat exchanger based upon ambient temperature and/or ambient humidity to remove heat from the rack of information technology equipment.

  9. Information Literacy in Biology Education: An Example from an Advanced Cell Biology Course

    Science.gov (United States)

    2005-01-01

    Information literacy skills are critically important for the undergraduate biology student. The ability to find, understand, evaluate, and use information, whether from the scientific literature or from Web resources, is essential for a good understanding of a topic and for the conduct of research. A project in which students receive information literacy instruction and then proceed to select, update, and write about a current research topic in an upper-level cell biology course is described. Students research the chosen topic using paper and electronic resources, generate a list of relevant articles, prepare abstracts based on papers read, and, finally, prepare a “state-of-the-art” paper on the topic. This approach, which extends over most of one semester, has resulted in a number of well-researched and well-written papers that incorporate some of the latest research in cell biology. The steps in this project have also led to students who are prepared to address future projects on new and complex topics. The project is part of an undergraduate course in cell biology, but parts of the assignments can be modified to fit a variety of subject areas and levels. PMID:16341261

  10. INFORMATION SYSTEM SECURITY THREATS CLASSIFICATIONS

    Directory of Open Access Journals (Sweden)

    Sandro Gerić

    2007-06-01

    Full Text Available Information systems are exposed to different types of security risks. Theconsequences of information systems security (ISS breaches can vary from e.g. damaging the data base integrity to physical "destruction" of entire information system facilities, and can result with minor disruptions in less important segments of information systems, or with significant interruptions in information systems functionality. The sources of security risks are different, and can origin from inside or outside of information system facility, and can be intentional or unintentional. The precise calculation of loses caused by such incidents is often not possible because a number of small scale ISS incidents are never detected, or detected with a significant time delay, a part of incidents are interpreted as an accidental mistakes, and all that results with an underestimation of ISS risks. This paper addresses the different types and criteria of information system security risks (threats classification and gives an overview of most common classifications used in literature and in practice. We define a common set of criteria that can be used for information system security threats classification, which will enable the comparison and evaluation of different security threats from different security threats classifications.

  11. Astro-WISE information system

    NARCIS (Netherlands)

    Valentijn, E. A.; Belikov, A. N.; Kleijn, G. A. Verdoes; Williams, O.R.; Radziwill, NM; Chiozzi, G

    2012-01-01

    Astro-WISE is the first information system in astronomy which covers all aspects of data processing, storage and visualization. We show the various concepts behind the Astro-WISE, their realization and use, migration of Astro-WISE to other astronomical and non-astronomical information systems.

  12. Legislative and Judicial Information Systems.

    Science.gov (United States)

    Becker, Louise Giovane

    1983-01-01

    Reviews computer applications in judicial, legal, and legislative information activities being used to support litigation and court administration, assist in searching for legislation and laws, aid criminal justice information systems, and provide appropriate bibliographic and reference assistance. Management issues in automating systems are…

  13. Systems Biology Knowledgebase for a New Era in Biology A Genomics:GTL Report from the May 2008 Workshop

    Energy Technology Data Exchange (ETDEWEB)

    Gregurick, S.; Fredrickson, J. K.; Stevens, R.

    2009-03-01

    Biology has entered a systems-science era with the goal to establish a predictive understanding of the mechanisms of cellular function and the interactions of biological systems with their environment and with each other. Vast amounts of data on the composition, physiology, and function of complex biological systems and their natural environments are emerging from new analytical technologies. Effectively exploiting these data requires developing a new generation of capabilities for analyzing and managing the information. By revealing the core principles and processes conserved in collective genomes across all biology and by enabling insights into the interplay between an organism's genotype and its environment, systems biology will allow scientific breakthroughs in our ability to project behaviors of natural systems and to manipulate and engineer managed systems. These breakthroughs will benefit Department of Energy (DOE) missions in energy security, climate protection, and environmental remediation.

  14. Systems biology of vaccination in the elderly.

    Science.gov (United States)

    Duraisingham, Sai S; Rouphael, Nadine; Cavanagh, Mary M; Nakaya, Helder I; Goronzy, Jorg J; Pulendran, Bali

    2013-01-01

    Aging population demographics, combined with suboptimal vaccine responses in the elderly, make the improvement of vaccination strategies in the elderly a developing public health issue. The immune system changes with age, with innate and adaptive cell components becoming increasingly dysfunctional. As such, vaccine responses in the elderly are impaired in ways that differ depending on the type of vaccine (e.g., live attenuated, polysaccharide, conjugate, or subunit) and the mediators of protection (e.g., antibody and/or T cell). The rapidly progressing field of systems biology has been shown to be useful in predicting immunogenicity and offering insights into potential mechanisms of protection in young adults. Future application of systems biology to vaccination in the elderly may help to identify gene signatures that predict suboptimal responses and help to identify more accurate correlates of protection. Moreover, the identification of specific defects may be used to target novel vaccination strategies that improve efficacy in elderly populations.

  15. Information in individual quantum systems

    International Nuclear Information System (INIS)

    Brukner, C.

    1999-09-01

    A new measure of information in quantum mechanics is proposed which takes into account that for quantum systems, the only feature known before an experiment is performed are the probabilities for various events to occur. The sum of the individual measures of information for mutually complementary observations is invariant under the choice of the particular set of complementary observations and conserved in time if there is no information exchange with an environment unitary transformation. This operational quantum information invariant results in k bits of information for a system consisting of $k$ qubits. For a composite system, maximal entanglement results if the total information carried by the system is exhausted in specifying joint properties, with no individual qubit carrying any information on its own. We interpret our results as implying that information is the most fundamental notion in quantum mechanics. Based on this observation we suggest ideas for a foundational principle for quantum theory. It is proposed here that the foundational principle for quantum theory may be identified through the assumption that the most elementary system carries one bit of information only. Therefore an elementary system can only give a definite answer in one specific measurement. The irreducible randomness of individual outcomes in other measurements and quantum complementarity are then necessary consequences. The most natural function between probabilities for outcomes to occur and the experimental parameters, consistent with the foundational principle proposed, is the well-known sinusoidal dependence. (author)

  16. Medical-Information-Management System

    Science.gov (United States)

    Alterescu, Sidney; Friedman, Carl A.; Frankowski, James W.

    1989-01-01

    Medical Information Management System (MIMS) computer program interactive, general-purpose software system for storage and retrieval of information. Offers immediate assistance where manipulation of large data bases required. User quickly and efficiently extracts, displays, and analyzes data. Used in management of medical data and handling all aspects of data related to care of patients. Other applications include management of data on occupational safety in public and private sectors, handling judicial information, systemizing purchasing and procurement systems, and analyses of cost structures of organizations. Written in Microsoft FORTRAN 77.

  17. Information security management system planning for CBRN facilities

    Energy Technology Data Exchange (ETDEWEB)

    Lenaeu, Joseph D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); O' Neil, Lori Ross [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Leitch, Rosalyn M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Glantz, Clifford S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Landine, Guy P. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Bryant, Janet L. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Lewis, John [National Nuclear Lab., Workington (United Kingdom); Mathers, Gemma [National Nuclear Lab., Workington (United Kingdom); Rodger, Robert [National Nuclear Lab., Workington (United Kingdom); Johnson, Christopher [National Nuclear Lab., Workington (United Kingdom)

    2015-12-01

    The focus of this document is to provide guidance for the development of information security management system planning documents at chemical, biological, radiological, or nuclear (CBRN) facilities. It describes a risk-based approach for planning information security programs based on the sensitivity of the data developed, processed, communicated, and stored on facility information systems.

  18. IAEA Safeguards Information System (ISIS)

    International Nuclear Information System (INIS)

    1984-10-01

    Publication of this technical document should serve for better understanding of the technical and functional features of the IAEA Safeguards Information System (ISIS) within the Agency, as well as in the National Systems of accounting for and control of nuclear material. It will also serve as a foundation for further development and improvement of the design and modifications of the Safeguards Information System and its services as a function of Safeguards implementation

  19. Effects of Pesticides on Biological Systems

    Directory of Open Access Journals (Sweden)

    Ergul Belge Kurutas

    2003-06-01

    Full Text Available The use of pesticid both in Turkey and other contries is widespread in order to combat against many pests which cause economical damages. However, pesticides in human pass through skin, respiratory or digestive systems and is metabolized by monooxygenase system dependent upon cytocrome P450 in liver. They also give rise to severe decreases cytochrome P450 and amount of "hem" enzyme activites of glucose-6-phosphatase, pyrophosphatase by stimulating lipid peroxidation on hepatic microsomes. In this study effects of pesticides on biological systems will be presented in genaral terms. [Archives Medical Review Journal 2003; 12(3.000: 215-228

  20. Integrated risk information system (IRIS)

    Energy Technology Data Exchange (ETDEWEB)

    Tuxen, L. [Environmental Protection Agency, Washington, DC (United States)

    1990-12-31

    The Integrated Risk Information System (IRIS) is an electronic information system developed by the US Environmental Protection Agency (EPA) containing information related to health risk assessment. IRIS is the Agency`s primary vehicle for communication of chronic health hazard information that represents Agency consensus following comprehensive review by intra-Agency work groups. The original purpose for developing IRIS was to provide guidance to EPA personnel in making risk management decisions. This original purpose for developing IRIS was to guidance to EPA personnel in making risk management decisions. This role has expanded and evolved with wider access and use of the system. IRIS contains chemical-specific information in summary format for approximately 500 chemicals. IRIS is available to the general public on the National Library of Medicine`s Toxicology Data Network (TOXNET) and on diskettes through the National Technical Information Service (NTIS).

  1. Optoelectronic system and apparatus for connection to biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Okandan, Murat; Nielson, Gregory N.

    2018-03-06

    The present invention relates to a biological probe structure, as well as apparatuses, systems, and methods employing this structure. In particular embodiments, the structure includes a hermetically sealed unit configured to receive and transmit one or more optical signals. Furthermore, the structure can be implanted subcutaneously and interrogated externally. In this manner, a minimally invasive method can be employed to detect, treat, and/or assess the biological target. Additional methods and systems are also provided.

  2. Geographic information system and marine biology

    Digital Repository Service at National Institute of Oceanography (India)

    Kunte, P.D.

    stream_size 8 stream_content_type text/plain stream_name Workshop_Databases_Networking_Mar_Biol_1994_76.pdf.txt stream_source_info Workshop_Databases_Networking_Mar_Biol_1994_76.pdf.txt Content-Encoding ISO-8859-1 Content...-Type text/plain; charset=ISO-8859-1 ...

  3. Inverse Problems in Systems Biology: A Critical Review.

    Science.gov (United States)

    Guzzi, Rodolfo; Colombo, Teresa; Paci, Paola

    2018-01-01

    Systems Biology may be assimilated to a symbiotic cyclic interplaying between the forward and inverse problems. Computational models need to be continuously refined through experiments and in turn they help us to make limited experimental resources more efficient. Every time one does an experiment we know that there will be some noise that can disrupt our measurements. Despite the noise certainly is a problem, the inverse problems already involve the inference of missing information, even if the data is entirely reliable. So the addition of a certain limited noise does not fundamentally change the situation but can be used to solve the so-called ill-posed problem, as defined by Hadamard. It can be seen as an extra source of information. Recent studies have shown that complex systems, among others the systems biology, are poorly constrained and ill-conditioned because it is difficult to use experimental data to fully estimate their parameters. For these reasons was born the concept of sloppy models, a sequence of models of increasing complexity that become sloppy in the limit of microscopic accuracy. Furthermore the concept of sloppy models contains also the concept of un-identifiability, because the models are characterized by many parameters that are poorly constrained by experimental data. Then a strategy needs to be designed to infer, analyze, and understand biological systems. The aim of this work is to provide a critical review to the inverse problems in systems biology defining a strategy to determine the minimal set of information needed to overcome the problems arising from dynamic biological models that generally may have many unknown, non-measurable parameters.

  4. Control Evaluation Information System Savings

    Directory of Open Access Journals (Sweden)

    Eddy Sutedjo

    2011-05-01

    Full Text Available The purpose of this research is to evaluate the control of information system savings in the banking and to identify the weaknesses and problem happened in those saving systems. Research method used are book studies by collecting data and information needed and field studies by interview, observation, questioner, and checklist using COBIT method as a standard to assess the information system control of the company. The expected result about the evaluation result that show in the problem happened and recommendation given as the evaluation report and to give a view about the control done by the company. Conclusion took from this research that this banking company has met standards although some weaknesses still exists in the system.Index Terms - Control Information System, Savings

  5. Earth Science Information System (ESIS)

    Science.gov (United States)

    ,

    1982-01-01

    The Earth Science Information System (ESIS) was developed in 1981 by the U.S. Geological Survey's Office of the Data Administrator. ESIS serves as a comprehensive data management facility designed to support the coordination, integration, and standardization of scientific, technical, and bibliographic data of the U.S. Geological Survey (USGS). ESIS provides, through an online interactive computer system, referral to information about USGS data bases, data elements which are fields in the records of data bases, and systems. The data bases contain information about many subjects from several scientific disciplines such as: geology, geophysics, geochemistry, hydrology, cartography, oceanography, geography, minerals exploration and conservation, and satellite data sensing.

  6. Market opening and information systems

    International Nuclear Information System (INIS)

    Dardevet, G.; Dardoise, P.; Dreyer, P.; Flahaut, P.

    2007-01-01

    The opening of energy markets to competition requires relevant information systems accessible to all end-users in concern without any discrimination. So, how existing information systems can be changed to become conformable with the requested requirements? Concerning the last step of the opening of energy markets which concerns several millions of clients, how this problem will be overcome considering the huge volume of processing needed? Who will decide or pay the forthcoming upgrades of the information system with respect to the evolution of actors' needs? Four participants were invited to this round table to answer these questions. Their answers are reported in this article. (J.S.)

  7. Design Theory in Information Systems

    Directory of Open Access Journals (Sweden)

    Shirley Gregor

    2002-11-01

    Full Text Available The aim of this paper is to explore an important category of information systems knowledge that is termed “design theory”. This knowledge is distinguished as the fifth of five types of theory: (i theory for analysing and describing, (ii theory for understanding, (iii theory for predicting, (iv theory for explaining and predicting, and (v theory for design and action. Examples of design theory in information systems are provided, with associated research methods. The limited understanding and recognition of this type of theory in information systems indicates that further debate concerning its nature and role in our discipline is needed.

  8. The Impact of Systems Biology on Bioprocessing

    DEFF Research Database (Denmark)

    Campbell, Kate; Xia, Jianye; Nielsen, Jens

    2017-01-01

    alongside mathematical modeling to characterize and predict cellular physiology. This approach can drive cycles of design, build, test, and learn implemented by metabolic engineers to optimize the cell factory performance. Streamlining of the design phase requires a clearer understanding of metabolism...... and its regulation, which can be achieved using quantitative and integrated omic characterization, alongside more advanced analytical methods. We discuss here the current impact of systems biology and challenges of closing the gap between bioprocessing and more traditional methods of chemical production....

  9. Nutritional systems biology of type 2 diabetes

    OpenAIRE

    Zhao, Y; Barrere-Cain, RE; Yang, X

    2015-01-01

    © 2015, The Author(s). Type 2 diabetes (T2D) has become an increasingly challenging health burden due to its high morbidity, mortality, and heightened prevalence worldwide. Although dietary and nutritional imbalances have long been recognized as key risk factors for T2D, the underlying mechanisms remain unclear. The advent of nutritional systems biology, a field that aims to elucidate the interactions between dietary nutrients and endogenous molecular entities in disease-related tissues, offe...

  10. Modelling and Inference Strategies for Biological Systems

    OpenAIRE

    Palmisano, Alida

    2010-01-01

    For many years, computers have played an important role in helping scientists to store, manipulate, and analyze data coming from many different disciplines. In recent years, however, new technological capabilities and new ways of thinking about the usefulness of computer science is extending the reach of computers from simple analysis of collected data to hypothesis generation. The aim of this work is to provide a contribution in the Computational Systems Biology field. The main purpose of...

  11. Systems biology solutions for biochemical production challenges

    DEFF Research Database (Denmark)

    Hansen, Anne Sofie Lærke; Lennen, Rebecca M; Sonnenschein, Nikolaus

    2017-01-01

    characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions. This additional complexity......There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics...

  12. World-wide information systems

    International Nuclear Information System (INIS)

    1974-01-01

    The three international organizations, IAEA, FAO, and UNESCO, which jointly sponsored the Symposium, share an active interest and involvement in information systems development. The extent of their interest was explained by the Director General of the IAEA, Dr. Sigvard Eklund, when he opened the meeting on behalf of the three co-sponsors: UNESCO in conjunction with the International Council of Scientific Unions (ICSU), took initiatives in 1966 which led to the establishment of its UNISIST programme. Its aims are to co-ordinate existing trends towards international co-operation in the collection, storage and dissemination of information and to act as a catalyst. Its ultimate goal is to establish 'a flexible and loosely connected network of information services based on voluntary co-operation'. A particular concern of UNISIST is to ensure co-ordination of the information activities of the United Nations organizations. The Symposium provided an opportunity for the science information community to assess the progress already made in creating links between diverse national, international, intergovernmental and non-governmental information systems and services. Papers were presented describing current developments in the national information systems of a number of countries, with special emphasis on how these developments were furthering harmonization of national information policies and facilitating interconnection with international systems. INIS and AGRIS figured prominently amongst the international systems discussed. In addition, proposals for two new international systems, to be known as DEVSIS and SPINIS, were outlined. The former will deal with development science information; the latter will cover the information on the administrative, scientific and legal aspects of science policy. There was also discussion of international co-operation in information handling within such international organizations as the CMEA, the Commission of the European Communities and

  13. Exploring the Possible Use of Information Barriers for future Biological Weapons Verification Regimes

    Energy Technology Data Exchange (ETDEWEB)

    Luke, S J

    2011-12-20

    This report describes a path forward for implementing information barriers in a future generic biological arms-control verification regime. Information barriers have become a staple of discussion in the area of arms control verification approaches for nuclear weapons and components. Information barriers when used with a measurement system allow for the determination that an item has sensitive characteristics without releasing any of the sensitive information. Over the last 15 years the United States (with the Russian Federation) has led on the development of information barriers in the area of the verification of nuclear weapons and nuclear components. The work of the US and the Russian Federation has prompted other states (e.g., UK and Norway) to consider the merits of information barriers for possible verification regimes. In the context of a biological weapons control verification regime, the dual-use nature of the biotechnology will require protection of sensitive information while allowing for the verification of treaty commitments. A major question that has arisen is whether - in a biological weapons verification regime - the presence or absence of a weapon pathogen can be determined without revealing any information about possible sensitive or proprietary information contained in the genetic materials being declared under a verification regime. This study indicates that a verification regime could be constructed using a small number of pathogens that spans the range of known biological weapons agents. Since the number of possible pathogens is small it is possible and prudent to treat these pathogens as analogies to attributes in a nuclear verification regime. This study has determined that there may be some information that needs to be protected in a biological weapons control verification regime. To protect this information, the study concludes that the Lawrence Livermore Microbial Detection Array may be a suitable technology for the detection of the

  14. Specifications of Standards in Systems and Synthetic Biology.

    Science.gov (United States)

    Schreiber, Falk; Bader, Gary D; Golebiewski, Martin; Hucka, Michael; Kormeier, Benjamin; Le Novère, Nicolas; Myers, Chris; Nickerson, David; Sommer, Björn; Waltemath, Dagmar; Weise, Stephan

    2015-09-04

    Standards shape our everyday life. From nuts and bolts to electronic devices and technological processes, standardised products and processes are all around us. Standards have technological and economic benefits, such as making information exchange, production, and services more efficient. However, novel, innovative areas often either lack proper standards, or documents about standards in these areas are not available from a centralised platform or formal body (such as the International Standardisation Organisation). Systems and synthetic biology is a relatively novel area, and it is only in the last decade that the standardisation of data, information, and models related to systems and synthetic biology has become a community-wide effort. Several open standards have been established and are under continuous development as a community initiative. COMBINE, the ‘COmputational Modeling in BIology’ NEtwork has been established as an umbrella initiative to coordinate and promote the development of the various community standards and formats for computational models. There are yearly two meeting, HARMONY (Hackathons on Resources for Modeling in Biology), Hackathon-type meetings with a focus on development of the support for standards, and COMBINE forums, workshop-style events with oral presentations, discussion, poster, and breakout sessions for further developing the standards. For more information see http://co.mbine.org/. So far the different standards were published and made accessible through the standards’ web- pages or preprint services. The aim of this special issue is to provide a single, easily accessible and citable platform for the publication of standards in systems and synthetic biology. This special issue is intended to serve as a central access point to standards and related initiatives in systems and synthetic biology, it will be published annually to provide an opportunity for standard development groups to communicate updated specifications.

  15. Clinical Information Support System (CISS)

    Data.gov (United States)

    Department of Veterans Affairs — Clinical Information Support System (CISS) is a web-based portal application that provides a framework of services for the VA enterprise and supplies an integration...

  16. Integrated Risk Information System (IRIS)

    Data.gov (United States)

    U.S. Environmental Protection Agency — EPA?s Integrated Risk Information System (IRIS) is a compilation of electronic reports on specific substances found in the environment and their potential to cause...

  17. Map projections cartographic information systems

    CERN Document Server

    Grafarend, Erik W

    2006-01-01

    In the context of Geographical Information Systems (GIS) the book offers a timely review of map projections (sphere, ellipsoid, rotational surfaces) and geodetic datum transformations. For the needs of photogrammetry, computer vision, and remote sensing space projective mappings are reviewed.

  18. System Wide Information Management (SWIM)

    Science.gov (United States)

    Hritz, Mike; McGowan, Shirley; Ramos, Cal

    2004-01-01

    This viewgraph presentation lists questions regarding the implementation of System Wide Information Management (SWIM). Some of the questions concern policy issues and strategies, technology issues and strategies, or transition issues and strategies.

  19. Life: An Introduction to Complex Systems Biology

    CERN Document Server

    Kaneko, Kunihiko

    2006-01-01

    What is life? Has molecular biology given us a satisfactory answer to this question? And if not, why, and how to carry on from there? This book examines life not from the reductionist point of view, but rather asks the question: what are the universal properties of living systems and how can one construct from there a phenomenological theory of life that leads naturally to complex processes such as reproductive cellular systems, evolution and differentiation? The presentation has been deliberately kept fairly non-technical so as to address a broad spectrum of students and researchers from the natural sciences and informatics.

  20. Humanitarian information management and systems

    NARCIS (Netherlands)

    van de Walle, B.A.; van den Eede, G.G.P.; Muhren, W.J.; Loffler, J.; Klann, M.

    2009-01-01

    In times of major disasters such as hurricane Katrina or the Sichuan earthquake, the need for accurate and timely information is as crucial as is rapid and coherent coordination among the responding humanitarian community. Effective humanitarian information systems that provide timely access to

  1. In-Vehicle Information Systems

    Directory of Open Access Journals (Sweden)

    Gordana Štefančić

    2012-10-01

    Full Text Available The work considers different information systems, includingthe infonnation ~ystems with autonomous units, whichcany all their intelligence around with them, and those withcommunicating units, which infonn the motorist about the currentsituation of the road system by radio or other means. Thesymbols of various messages have three main objectives: to provideinstruction, to warn of oncoming dange1~ or to give adviceregarding parking or looking for altemative routes. When notused for these pwposes, they are used to provide general informationabout the weathe1~ temperature or possible attractions.The in-vehicle information systems fly to assist the motorist indriving, and they are promoted as part of the comprehensive intelligenttransport system.

  2. RIMS: Resource Information Management System

    Science.gov (United States)

    Symes, J.

    1983-01-01

    An overview is given of the capabilities and functions of the resource management system (RIMS). It is a simple interactive DMS tool which allows users to build, modify, and maintain data management applications. The RIMS minimizes programmer support required to develop/maintain small data base applications. The RIMS also assists in bringing the United Information Services (UIS) budget system work inhouse. Information is also given on the relationship between the RIMS and the user community.

  3. Information system revives materials management

    International Nuclear Information System (INIS)

    Hansen, T.

    1995-01-01

    Through a change in philosophy and the development of a new, more efficient information management system, Arizona Public Service Co. (APSW) has, in less than two years, reduced material and service costs by 10 percent. The utility plans to cut these costs form 1993 figures by 25 percent before 2000. The utility is breaking new ground with ongoing implementation of new business processes and the new Materials Logistics Information System (MLIS), which has been co-developed with Texas Instruments Software Division (TISD)

  4. BIMS: Biomedical Information Management System

    OpenAIRE

    Mora Pérez, Oscar

    2009-01-01

    This final year project presents the design principles and prototype implementation of BIMS (Biomedical Information Management System), a flexible software system which provides an infrastructure to manage all information required by biomedical research projects.The BIMS project was initiated with the motivation to solve several limitations in medical data acquisition of some research projects, in which Universitat Pompeu Fabra takes part. These limitations,based on the lack of control mechan...

  5. Management Information System & Computer Applications

    OpenAIRE

    Sreeramana Aithal

    2017-01-01

    The book contains following Chapters : Chapter 1 : Introduction to Management Information Systems, Chapter 2 : Structure of MIS, Chapter 3 : Planning for MIS, Chapter 4 : Introduction to Computers Chapter 5 : Decision Making Process in MIS Chapter 6 : Approaches for System Development Chapter 7 : Form Design Chapter 8 : Charting Techniques Chapter 9 : System Analysis & Design Chapter 10 : Applications of MIS in Functional Areas Chapter 11 : System Implement...

  6. GPSR: A Resource for Genomics Proteomics and Systems Biology

    Indian Academy of Sciences (India)

    GPSR: A Resource for Genomics Proteomics and Systems Biology · Simple Calculation Programs for Biology Immunological Methods · Simple Calculation Programs for Biology Methods in Molecular Biology · Simple Calculation Programs for Biology Other Methods · PowerPoint Presentation · Slide 6 · Slide 7 · Prediction of ...

  7. Marine data and information management system for the Indian Ocean

    Digital Repository Service at National Institute of Oceanography (India)

    Sarupria, J.S.

    The user friendly computer system for the management of marine data/information has been developed for processing of physical, chemical, biological, geological and geophysical data sets with a common inventory database. It provides geographical...

  8. The role of mechanics in biological and bio-inspired systems.

    Science.gov (United States)

    Egan, Paul; Sinko, Robert; LeDuc, Philip R; Keten, Sinan

    2015-07-06

    Natural systems frequently exploit intricate multiscale and multiphasic structures to achieve functionalities beyond those of man-made systems. Although understanding the chemical make-up of these systems is essential, the passive and active mechanics within biological systems are crucial when considering the many natural systems that achieve advanced properties, such as high strength-to-weight ratios and stimuli-responsive adaptability. Discovering how and why biological systems attain these desirable mechanical functionalities often reveals principles that inform new synthetic designs based on biological systems. Such approaches have traditionally found success in medical applications, and are now informing breakthroughs in diverse frontiers of science and engineering.

  9. Engineering biological systems toward a sustainable bioeconomy.

    Science.gov (United States)

    Lopes, Mateus Schreiner Garcez

    2015-06-01

    The nature of our major global risks calls for sustainable innovations to decouple economic growth from greenhouse gases emission. The development of sustainable technologies has been negatively impacted by several factors including sugar production costs, production scale, economic crises, hydraulic fracking development and the market inability to capture externality costs. However, advances in engineering of biological systems allow bridging the gap between exponential growth of knowledge about biology and the creation of sustainable value chains for a broad range of economic sectors. Additionally, industrial symbiosis of different biobased technologies can increase competitiveness and sustainability, leading to the development of eco-industrial parks. Reliable policies for carbon pricing and revenue reinvestments in disruptive technologies and in the deployment of eco-industrial parks could boost the welfare while addressing our major global risks toward the transition from a fossil to a biobased economy.

  10. Biological Therapy in Systemic Lupus Erythematosus

    Directory of Open Access Journals (Sweden)

    Mariana Postal

    2012-01-01

    Full Text Available Systemic lupus erythematosus (SLE is a prototypic inflammatory autoimmune disorder characterized by multisystem involvement and fluctuating disease activity. Symptoms range from rather mild manifestations such as rash or arthritis to life-threatening end-organ manifestations. Despite new and improved therapy having positively impacted the prognosis of SLE, a subgroup of patients do not respond to conventional therapy. Moreover, the risk of fatal outcomes and the damaging side effects of immunosuppressive therapies in SLE call for an improvement in the current therapeutic management. New therapeutic approaches are focused on B-cell targets, T-cell downregulation and costimulatory blockade, cytokine inhibition, and the modulation of complement. Several biological agents have been developed, but this encouraging news is associated with several disappointments in trials and provide a timely moment to reflect on biologic therapy in SLE.

  11. Hanford Environmental Information System (HEIS)

    International Nuclear Information System (INIS)

    Schreck, R.I.

    1994-01-01

    The Hanford Environmental Information System (HEIS) Subject Area manuals are designed as reference guides, that is, each chapter provides the information needed to make best use of each subject area, its tables, and reporting capabilities. Each subject area is documented in a chapter in one of the subject area manuals. Because these are reference manuals, most of the information is also available in the online help system as well. See Section 5.4.2 of the HEIS User's Guide (DOE-RL 1994a) for a detailed description of the online help

  12. Radiation exposure information record system

    International Nuclear Information System (INIS)

    Murphy, D.W.; Fix, J.J.; Murphy, B.L.

    1983-01-01

    The proposed alternative information system to provide DOE with a radiation exposure data base that could be used to assess the impacts of proposed changes in radiation protection practices and regulations. Although the data base would contain dose information on all DOE employees who are monitored for compliance, no personal identifiers would be maintained with this information. The proposed system includes a DOE employee locator file and a badged visitor file. The primary purpose of the locator file is to provide an up-to-date list of all current employees at DOE and DOE contractor sites

  13. The IAEA safeguards information system

    International Nuclear Information System (INIS)

    Gmelin, W.R.; Parsick, R.

    1976-01-01

    The IAEA safeguards under the Non-Proliferation Treaty is meant to follow the model agreement developed by the Safeguards Committee in 1970 and formulated in document INFCIRC/153, which contains provisions that Member States, having concluded Safeguards Agreements with the Agency, should provide design information and reports on initial inventories, changes in the inventories and material balances in respect of each nuclear facility and material balance area for all nuclear materials subject to safeguards. The Agency, on the other hand, should establish and maintain an accountancy system which would provide the data on the location and the movements of all nuclear material subject to safeguards on the basis of the reported information and information obtained during inspections in order to support the Agency's verification activities in the field, to enable the preparation of safeguards statements and to adjust the inspection intensity. Following these requirements, a computer-based information system has been developed and is being implemented and used routinely for input manipulations and queries on a limited scale. This information system comprises two main parts: Part 1 for processing the information as provided by the States, and Part 2 (still under development) for processing the inspection data obtained during verification. This paper describes the characteristics of the Agency information system for processing data under the Non-Proliferation Treaty as well as recent operational experience. (author)

  14. Emergency management information system (EMINS)

    International Nuclear Information System (INIS)

    Desonier, L.M.

    1987-01-01

    In a time of crisis or in an emergency, a manager is required to make many decisions to facilitate the proper solution and conclusion to the emergency or crisis. In order to make these decisions, it is necessary for the manager to have correct up-to-date information on the situation, which calls for an automated information display and entry process. The information handling needs are identified in terms of data, video, and voice. Studies of existing Emergency Operations Centers and evaluations of hardware and software have been completed. The result of these studies and investigations is the design and implementation of an automated Emergency Management Information System. Not only is the system useful for Emergency Management but for any information management requirement

  15. MIMS - MEDICAL INFORMATION MANAGEMENT SYSTEM

    Science.gov (United States)

    Frankowski, J. W.

    1994-01-01

    MIMS, Medical Information Management System is an interactive, general purpose information storage and retrieval system. It was first designed to be used in medical data management, and can be used to handle all aspects of data related to patient care. Other areas of application for MIMS include: managing occupational safety data in the public and private sectors; handling judicial information where speed and accuracy are high priorities; systemizing purchasing and procurement systems; and analyzing organizational cost structures. Because of its free format design, MIMS can offer immediate assistance where manipulation of large data bases is required. File structures, data categories, field lengths and formats, including alphabetic and/or numeric, are all user defined. The user can quickly and efficiently extract, display, and analyze the data. Three means of extracting data are provided: certain short items of information, such as social security numbers, can be used to uniquely identify each record for quick access; records can be selected which match conditions defined by the user; and specific categories of data can be selected. Data may be displayed and analyzed in several ways which include: generating tabular information assembled from comparison of all the records on the system; generating statistical information on numeric data such as means, standard deviations and standard errors; and displaying formatted listings of output data. The MIMS program is written in Microsoft FORTRAN-77. It was designed to operate on IBM Personal Computers and compatibles running under PC or MS DOS 2.00 or higher. MIMS was developed in 1987.

  16. Multilayer network modeling of integrated biological systems. Comment on "Network science of biological systems at different scales: A review" by Gosak et al.

    Science.gov (United States)

    De Domenico, Manlio

    2018-03-01

    Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several studies are highlighting how simple networks - obtained by aggregating or neglecting temporal or categorical description of biological data - are not able to account for the richness of information characterizing biological systems. More complex models, namely multilayer networks, are needed to account for interdependencies, often varying across time, of biological interacting units within a cell, a tissue or parts of an organism.

  17. Management Information Systems at CERN

    OpenAIRE

    Ferguson, J

    1986-01-01

    The specific areas addressed in the study are 1.Management decision support (data presentation, data base management systems â" DBMS, modeling) 2.Text processing, 3.Electronic communication for management purposes, 4.Office automation, 5.Administrative use of Management Information Systems (MIS) and in particular Administrative Data Processing (ADP).

  18. It's the System, Stupid: How Systems Biology Is Transforming.

    Science.gov (United States)

    2010-01-01

    So far, little is known about systems biology and its potential for changing how we diagnose and treat disease. That will change soon, say the systems experts, who advise payers to begin learning now about how it could make healthcare efficient.

  19. PREFACE: Complex Networks: from Biology to Information Technology

    Science.gov (United States)

    Barrat, A.; Boccaletti, S.; Caldarelli, G.; Chessa, A.; Latora, V.; Motter, A. E.

    2008-06-01

    The field of complex networks is one of the most active areas in contemporary statistical physics. Ten years after seminal work initiated the modern study of networks, interest in the field is in fact still growing, as indicated by the ever increasing number of publications in network science. The reason for such a resounding success is most likely the simplicity and broad significance of the approach that, through graph theory, allows researchers to address a variety of different complex systems within a common framework. This special issue comprises a selection of contributions presented at the workshop 'Complex Networks: from Biology to Information Technology' held in July 2007 in Pula (Cagliari), Italy as a satellite of the general conference STATPHYS23. The contributions cover a wide range of problems that are currently among the most important questions in the area of complex networks and that are likely to stimulate future research. The issue is organised into four sections. The first two sections describe 'methods' to study the structure and the dynamics of complex networks, respectively. After this methodological part, the issue proceeds with a section on applications to biological systems. The issue closes with a section concentrating on applications to the study of social and technological networks. The first section, entitled Methods: The Structure, consists of six contributions focused on the characterisation and analysis of structural properties of complex networks: The paper Motif-based communities in complex networks by Arenas et al is a study of the occurrence of characteristic small subgraphs in complex networks. These subgraphs, known as motifs, are used to define general classes of nodes and their communities by extending the mathematical expression of the Newman-Girvan modularity. The same line of research, aimed at characterising network structure through the analysis of particular subgraphs, is explored by Bianconi and Gulbahce in Algorithm

  20. The decommissioning information management system

    International Nuclear Information System (INIS)

    Park, Seung-Kook; Moon, Jei-Kwon

    2015-01-01

    At the Korea Atomic Energy Research Institute (KAERI), the Korea Research Reactor (KRR-2) and one uranium conversion plant (UCP) were decommissioned. A project was launched in 1997, for the decommissioning of KRR-2 reactor with the goal of completion by 2008. Another project for the decommissioning of the UCP was launched in 2001. The physical dismantling works were started in August 2003 and the entire project was completed by the end of 2010. KAERI has developed a computer information system, named DECOMMIS, for an information management with an increased effectiveness for decommissioning projects and for record keeping for the future decommissioning projects. This decommissioning information system consists of three sub-systems; code management system, data input system (DDIS) and data processing and output system (DDPS). Through the DDIS, the data can be directly inputted at sites to minimize the time gap between the dismantling activities and the evaluation of the data by the project staff. The DDPS provides useful information to the staff for more effective project management and this information includes several fields, such as project progress management, man power management, waste management, and radiation dose control of workers and so on. The DECOMMIS was applied to the decommissioning projects of the KRR-2 and the UCP, and was utilized to give information to the staff for making decisions regarding the progress of projects. It is also to prepare the reference data for the R and D program which is for the development of the decommissioning engineering system tools and to maintain the decommissioning data for the next projects. In this paper, the overall system will be explained and the several examples of its utilization, focused on waste management and manpower control, will be introduced. (author)

  1. Information requirements for enterprise systems

    OpenAIRE

    Sommerville, Ian; Lock, Russell; Storer, Tim

    2012-01-01

    In this paper, we discuss an approach to system requirements engineering, which is based on using models of the responsibilities assigned to agents in a multi-agency system of systems. The responsibility models serve as a basis for identifying the stakeholders that should be considered in establishing the requirements and provide a basis for a structured approach, described here, for information requirements elicitation. We illustrate this approach using a case study drawn from civil emergenc...

  2. Laboratory information management system proposal

    Energy Technology Data Exchange (ETDEWEB)

    Brown, B.; Schweitzer, S.; Adams, C.; White, S. [Tennessee Univ., Knoxville, TN (United States)

    1992-08-01

    The objectives of this paper is design a user friendly information management system using a relational database in order to: allow customers direct access to the system; provide customers with direct sample tracking capabilities; provide customers with more timely, consistent reporting; better allocate costs for analyses to appropriate customers; eliminate cumbersome and costly papertrails; and enhance facility utilization by laboratory personnel. The resultant savings through increased efficiency provided by this system should more than offset its cost in the long-term.

  3. Laboratory information management system proposal

    Energy Technology Data Exchange (ETDEWEB)

    Brown, B.; Schweitzer, S.; Adams, C.; White, S. (Tennessee Univ., Knoxville, TN (United States))

    1992-01-01

    The objectives of this paper is design a user friendly information management system using a relational database in order to: allow customers direct access to the system; provide customers with direct sample tracking capabilities; provide customers with more timely, consistent reporting; better allocate costs for analyses to appropriate customers; eliminate cumbersome and costly papertrails; and enhance facility utilization by laboratory personnel. The resultant savings through increased efficiency provided by this system should more than offset its cost in the long-term.

  4. Systems Biology: Impressions from a Newcomer Graduate Student in 2016

    Science.gov (United States)

    Simpson, Melanie Rae

    2016-01-01

    As a newcomer, the philosophical basis of systems biology seems intuitive and appealing, the underlying philosophy being that the whole of a living system cannot be completely understood by the study of its individual parts. Yet answers to the questions "What is systems biology?" and "What constitutes a systems biology approach in…

  5. System for determining sizes of biological macromolecules

    International Nuclear Information System (INIS)

    Nelson, R.M.; Danby, P.C.

    1987-01-01

    An electrophoresis system for determining the sizes of radiolabelled biological macromolecules is described. It comprises a cell containing an electrophoresis gel and having at least one lane, a voltage source connected across the gel for effecting the movement of macromolecules in the lane, a detector fixed relative to the moving molecules for generating electrical pulses responsive to signals emitted by the radiolabelled molecules; a pulse processor for counting the pulse rate, and a computational device for comparing the pulse rate to a predetermined value. (author)

  6. Integrative Systems Biology Applied to Toxicology

    DEFF Research Database (Denmark)

    Kongsbak, Kristine Grønning

    associated with combined exposure to multiple chemicals. Testing all possible combinations of the tens of thousands environmental chemicals is impractical. This PhD project was launched to apply existing computational systems biology methods to toxicological research. In this thesis, I present in three...... projects three different approaches to using computational toxicology to aid classical toxicological investigations. In project I, we predicted human health effects of five pesticides using publicly available data. We obtained a grouping of the chemical according to their potential human health effects...

  7. Development of logistics information systems

    Directory of Open Access Journals (Sweden)

    Milan Ž. Dronjak

    2012-10-01

    Full Text Available An adequate logistics information system provides real time automated data processing, distribution and of information according to Terrain Commander's requirements, which leads to timely fulfillment of logistic demands of units. SAP ERP The SAP ERP application is the integrated (ERP software capable of working with complex organisational structures, personnel, equipment, and finance. It enables planning and combining forces for every type of operations. The system also enables the determination of the readiness status of modelled forces. ISL The Information System for Logistics (ISL is a comprehensive information system of the Ministry of Defence (MoD and the Army of the Czech Republic that covers many areas: acquisition, supply, ammunition and equipment maintenance, logistics, etc. The ISL provides support for military logistics in all important areas of consumer and acquisition logistics, satisfaying all kinds of Defence Forces needs in the country and abroad. LOGFAS The information system LOGFAS comprises Logistics Database (LOGBASE, Movement and Transportation software (M&T, Allied Command Europe Resource Optimisation Software System (ACROSS and Logistic Reporting System (LOGREP. The Logistics Database LOGBASE represents a logistics information source and also a database related to assets, forces, geography, infrastructure, targets, supplies, movements and medical data. The main software tools which rely on the LOGBASE are M&T, ACROSS and LOGREP. GCSS-Army The original impetus to create the SALE came in the mid-90s when the United States Department of Defense (DoD started a logistics modernisation programme. One of tasks was to build The Single Army Logistics Enterprise (SALE for the purpose of covering the whole organisational structure of the DoD. There are three components of the SALE: GCSS-Army, PLM+ and LMP. Each of them uses the commercial Enterprise Resource Planning SAP Software with a Web access. The main component, GCSS

  8. Biological Information Document, Radioactive Liquid Waste Treatment Facility

    International Nuclear Information System (INIS)

    Biggs, J.

    1995-01-01

    This document is intended to act as a baseline source material for risk assessments which can be used in Environmental Assessments and Environmental Impact Statements. The current Radioactive Liquid Waste Treatment Facility (RLWTF) does not meet current General Design Criteria for Non-reactor Nuclear Facilities and could be shut down affecting several DOE programs. This Biological Information Document summarizes various biological studies that have been conducted in the vicinity of new Proposed RLWTF site and an Alternative site. The Proposed site is located on Mesita del Buey, a mess top, and the Alternative site is located in Mortandad Canyon. The Proposed Site is devoid of overstory species due to previous disturbance and is dominated by a mixture of grasses, forbs, and scattered low-growing shrubs. Vegetation immediately adjacent to the site is a pinyon-juniper woodland. The Mortandad canyon bottom overstory is dominated by ponderosa pine, willow, and rush. The south-facing slope was dominated by ponderosa pine, mountain mahogany, oak, and muhly. The north-facing slope is dominated by Douglas fir, ponderosa pine, and oak. Studies on wildlife species are limited in the vicinity of the proposed project and further studies will be necessary to accurately identify wildlife populations and to what extent they utilize the project area. Some information is provided on invertebrates, amphibians and reptiles, and small mammals. Additional species information from other nearby locations is discussed in detail. Habitat requirements exist in the project area for one federally threatened wildlife species, the peregrine falcon, and one federal candidate species, the spotted bat. However, based on surveys outside of the project area but in similar habitats, these species are not expected to occur in either the Proposed or Alternative RLWTF sites. Habitat Evaluation Procedures were used to evaluate ecological functioning in the project area

  9. Biological Information Document, Radioactive Liquid Waste Treatment Facility

    Energy Technology Data Exchange (ETDEWEB)

    Biggs, J.

    1995-12-31

    This document is intended to act as a baseline source material for risk assessments which can be used in Environmental Assessments and Environmental Impact Statements. The current Radioactive Liquid Waste Treatment Facility (RLWTF) does not meet current General Design Criteria for Non-reactor Nuclear Facilities and could be shut down affecting several DOE programs. This Biological Information Document summarizes various biological studies that have been conducted in the vicinity of new Proposed RLWTF site and an Alternative site. The Proposed site is located on Mesita del Buey, a mess top, and the Alternative site is located in Mortandad Canyon. The Proposed Site is devoid of overstory species due to previous disturbance and is dominated by a mixture of grasses, forbs, and scattered low-growing shrubs. Vegetation immediately adjacent to the site is a pinyon-juniper woodland. The Mortandad canyon bottom overstory is dominated by ponderosa pine, willow, and rush. The south-facing slope was dominated by ponderosa pine, mountain mahogany, oak, and muhly. The north-facing slope is dominated by Douglas fir, ponderosa pine, and oak. Studies on wildlife species are limited in the vicinity of the proposed project and further studies will be necessary to accurately identify wildlife populations and to what extent they utilize the project area. Some information is provided on invertebrates, amphibians and reptiles, and small mammals. Additional species information from other nearby locations is discussed in detail. Habitat requirements exist in the project area for one federally threatened wildlife species, the peregrine falcon, and one federal candidate species, the spotted bat. However, based on surveys outside of the project area but in similar habitats, these species are not expected to occur in either the Proposed or Alternative RLWTF sites. Habitat Evaluation Procedures were used to evaluate ecological functioning in the project area.

  10. BIMS: Biomedical Information Management System

    OpenAIRE

    Mora, Oscar; Bisbal, Jesús

    2013-01-01

    In this paper, we present BIMS (Biomedical Information Management System). BIMS is a software architecture designed to provide a flexible computational framework to manage the information needs of a wide range of biomedical research projects. The main goal is to facilitate the clinicians' job in data entry, and researcher's tasks in data management, in high data quality biomedical research projects. The BIMS architecture has been designed following the two-level modeling paradigm, a promising...

  11. Introduction to Management Information system

    OpenAIRE

    Mishra, Umakant

    2013-01-01

    A Management Information System (MIS) is a systematic organization and presentation of information that is generally required by the management of an organization for taking better decisions for the organization. The MIS data may be derived from various units of the organization or from other sources. However it is very difficult to say the exact structure of MIS as the structure and goals of different types of organizations are different. Hence both the data and structure of MIS is dependent...

  12. Evolution of toxicology information systems

    Energy Technology Data Exchange (ETDEWEB)

    Wassom, J.S.; Lu, P.Y. [Oak Ridge National Laboratory, TN (United States)

    1990-12-31

    Society today is faced with new health risk situations that have been brought about by recent scientific and technical advances. Federal and state governments are required to assess the many potential health risks to exposed populations from the products (chemicals) and by-products (pollutants) of these advances. Because a sound analysis of any potential health risk should be based on the use of relevant information, it behooves those individuals responsible for making the risk assessments to know where to obtain needed information. This paper reviews the origins of toxicology information systems and explores the specialized information center concept that was proposed in 1963 as a means of providing ready access to scientific and technical information. As a means of illustrating this concept, the operation of one specialized information center (the Environmental Mutagen Information Center at Oak Ridge National Laboratory) will be discussed. Insights into how toxicological information resources came into being, their design and makeup, will be of value to those seeking to acquire information for risk assessment purposes. 7 refs., 1 fig., 4 tabs.

  13. AN INTEGRATED BIOLOGICAL CONTROL SYSTEM AT HANFORD

    Energy Technology Data Exchange (ETDEWEB)

    JOHNSON AR; CAUDILL JG; GIDDINGS RF; RODRIGUEZ JM; ROOS RC; WILDE JW

    2010-02-11

    In 1999 an integrated biological control system was instituted at the U.S. Department of Energy's Hanford Site. Successes and changes to the program needed to be communicated to a large and diverse mix of organizations and individuals. Efforts at communication are directed toward the following: Hanford Contractors (Liquid or Tank Waste, Solid Waste, Environmental Restoration, Science and Technology, Site Infrastructure), General Hanford Employees, and Hanford Advisory Board (Native American Tribes, Environmental Groups, Local Citizens, Washington State and Oregon State regulatory agencies). Communication was done through direct interface meetings, individual communication, where appropriate, and broadly sharing program reports. The objectives of the communication efforts was to have the program well coordinated with Hanford contractors, and to have the program understood well enough that all stakeholders would have confidence in the work performed by the program to reduce or elimated spread of radioactive contamination by biotic vectors. Communication of successes and changes to an integrated biological control system instituted in 1999 at the Department of Energy's Hanford Site have required regular interfaces with not only a diverse group of Hanford contractors (i.e., those responsible for liquid or tank waste, solid wastes, environmental restoration, science and technology, and site infrastructure), and general Hanford employees, but also with a consortium of designated stake holders organized as the Hanford Advisory Board (i.e., Native American tribes, various environmental groups, local citizens, Washington state and Oregon regulatory agencies, etc.). Direct interface meetings, individual communication where appropriate, and transparency of the biological control program were the methods and outcome of this effort.

  14. An Integrated Biological Control System At Hanford

    International Nuclear Information System (INIS)

    Johnson, A.R.; Caudill, J.G.; Giddings, R.F.; Rodriguez, J.M.; Roos, R.C.; Wilde, J.W.

    2010-01-01

    In 1999 an integrated biological control system was instituted at the U.S. Department of Energy's Hanford Site. Successes and changes to the program needed to be communicated to a large and diverse mix of organizations and individuals. Efforts at communication are directed toward the following: Hanford Contractors (Liquid or Tank Waste, Solid Waste, Environmental Restoration, Science and Technology, Site Infrastructure), General Hanford Employees, and Hanford Advisory Board (Native American Tribes, Environmental Groups, Local Citizens, Washington State and Oregon State regulatory agencies). Communication was done through direct interface meetings, individual communication, where appropriate, and broadly sharing program reports. The objectives of the communication efforts was to have the program well coordinated with Hanford contractors, and to have the program understood well enough that all stakeholders would have confidence in the work performed by the program to reduce or elimate spread of radioactive contamination by biotic vectors. Communication of successes and changes to an integrated biological control system instituted in 1999 at the Department of Energy's Hanford Site have required regular interfaces with not only a diverse group of Hanford contractors (i.e., those responsible for liquid or tank waste, solid wastes, environmental restoration, science and technology, and site infrastructure), and general Hanford employees, but also with a consortium of designated stake holders organized as the Hanford Advisory Board (i.e., Native American tribes, various environmental groups, local citizens, Washington state and Oregon regulatory agencies, etc.). Direct interface meetings, individual communication where appropriate, and transparency of the biological control program were the methods and outcome of this effort.

  15. 77 FR 40090 - Proposed Collection of Information; Comment Request: Biological Sciences Proposal Classification...

    Science.gov (United States)

    2012-07-06

    ... NATIONAL SCIENCE FOUNDATION Proposed Collection of Information; Comment Request: Biological Sciences Proposal Classification Form AGENCY: National Science Foundation. ACTION: Notice. SUMMARY: The... Biological Sciences has a continuing commitment to monitor its information collection in order to preserve...

  16. Film home "taurapilis" information system

    OpenAIRE

    Dumskis, Algirdas

    2017-01-01

    Topic of bachelor thesis is - Film Home “Taurapilis” Information System. The main goal of this work is to create a web site that allows users to buy tickets to the films house “Taurapilis” movies showings, also movies house’s staff to administrate website content. To achieve this, was analyzed other websites of Lithuanian cinemas with simular features required by movies house. The result of this work is a system that allow users get information about the movies showing, buy tickets on interne...

  17. Information Systems in University Learning

    Directory of Open Access Journals (Sweden)

    Gheorghe SABAU

    2010-01-01

    Full Text Available The authors of this article are going to bring into light the significance, the place and the role of information systems in the university education process. At the same time they define the objectives and the target group of the subject named Economic Information Systems and state the competence gained by students by studying this subject. Special attention is given to the curriculum to be taught to students and to a suggestive enumeration of a series of economic applications that can be themes for laboratory practice and for students’ dissertation (graduation thesis.

  18. Collaborative Systems Biology Projects for the Military Medical Community.

    Science.gov (United States)

    Zalatoris, Jeffrey J; Scheerer, Julia B; Lebeda, Frank J

    2017-09-01

    This pilot study was conducted to examine, for the first time, the ongoing systems biology research and development projects within the laboratories and centers of the U.S. Army Medical Research and Materiel Command (USAMRMC). The analysis has provided an understanding of the breadth of systems biology activities, resources, and collaborations across all USAMRMC subordinate laboratories. The Systems Biology Collaboration Center at USAMRMC issued a survey regarding systems biology research projects to the eight U.S.-based USAMRMC laboratories and centers in August 2016. This survey included a data call worksheet to gather self-identified project and programmatic information. The general topics focused on the investigators and their projects, on the project's research areas, on omics and other large data types being collected and stored, on the analytical or computational tools being used, and on identifying intramural (i.e., USAMRMC) and extramural collaborations. Among seven of the eight laboratories, 62 unique systems biology studies were funded and active during the final quarter of fiscal year 2016. Of 29 preselected medical Research Task Areas, 20 were associated with these studies, some of which were applicable to two or more Research Task Areas. Overall, studies were categorized among six general types of objectives: biological mechanisms of disease, risk of/susceptibility to injury or disease, innate mechanisms of healing, diagnostic and prognostic biomarkers, and host/patient responses to vaccines, and therapeutic strategies including host responses to therapies. We identified eight types of omics studies and four types of study subjects. Studies were categorized on a scale of increasing complexity from single study subject/single omics technology studies (23/62) to studies integrating results across two study subject types and two or more omics technologies (13/62). Investigators at seven USAMRMC laboratories had collaborations with systems biology experts

  19. Advancing metabolic engineering through systems biology of industrial microorganisms

    DEFF Research Database (Denmark)

    Dai, Zongjie; Nielsen, Jens

    2015-01-01

    resources. The objective of systems biology is to gain a comprehensive and quantitative understanding of living cells and can hereby enhance our ability to characterize and predict cellular behavior. Systems biology of industrial microorganisms is therefore valuable for metabolic engineering. Here we review...... the application of systems biology tools for the identification of metabolic engineering targets which may lead to reduced development time for efficient cell factories. Finally, we present some perspectives of systems biology for advancing metabolic engineering further....

  20. Biological Systems for Hydrogen Photoproduction (Presentation)

    Energy Technology Data Exchange (ETDEWEB)

    Ghirardi, M. L.

    2012-05-01

    This presentation summarizes NREL biological systems for hydrogen photoproduction work for the DOE Hydrogen and Fuel Cells Program Annual Merit Review and Peer Evaluation Meeting, May 14-18, 2012. General goal is develop photobiological systems for large-scale, low cost and efficient H{sub 2} production from water (barriers AH, AI and AJ). Specific tasks are: (1) Address the O{sub 2} sensitivity of hydrogenases that prevent continuity of H{sub 2} photoproduction under aerobic, high solar-to-hydrogen (STH) light conversion efficiency conditions; and (2) Utilize a limited STH H{sub 2}-producing method (sulfur deprivation) as a platform to address or test other factors limiting commercial algal H{sub 2} photoproduction, including low rates due to biochemical and engineering mechanisms.

  1. Language Based Techniques for Systems Biology

    DEFF Research Database (Denmark)

    Pilegaard, Henrik

    Process calculus is the common denominator for a class of compact, idealised, domain-specific formalisms normally associated with the study of reactive concurrent systems within Computer Science. With the rise of the interactioncentred science of Systems Biology a number of bio-inspired process......), is context insensitive, while the other, a poly-variant analysis (2CFA), is context-sensitive. These analyses compute safe approximations to the set of spatial configurations that are reachable according to a given model. This is useful in the qualitative study of cellular self-organisation and, e.......g., the effects of receptor defects or drug delivery mechanisms. The property of sequential realisability. which is closely related to the function of biochemical pathways, is addressed by a variant of traditional Data Flow Analysis (DFA). This so-called ‘Pathway Analysis’ computes safe approximations to the set...

  2. Spatial Structures and Regulation in Biological Systems

    DEFF Research Database (Denmark)

    Yde, Pernille

    , and the other is the spatial regulation of biological systems, here related to different aspects of the inflammatory response. All systems are studied using computational modelling and mathematical analysis. The first part of the thesis explores different protein aggregation scenarios. In Chapter 1, we consider...... a previously studied and very general aggregation model describing frangible linear filaments. This model is especially relevant for the growth of amyloid fibres, that have been related to a number of serious human diseases, and which are known to grow in an accelerated self-enhanced manner.We derive...... model of the tissue and show how coupled cells are able to function as an excitable medium and propagate waves of high cytokine concentration through the tissue. If the internal regulation in the cells is over-productive, the model predicts a continuous amplification of cytokines, which spans the entire...

  3. Microbial stress tolerance for biofuels. Systems biology

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Zonglin Lewis (ed.) [National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL (United States)

    2012-07-01

    The development of sustainable and renewable biofuels is attracting growing interest. It is vital to develop robust microbial strains for biocatalysts that are able to function under multiple stress conditions. This Microbiology Monograph provides an overview of methods for studying microbial stress tolerance for biofuels applications using a systems biology approach. Topics covered range from mechanisms to methodology for yeast and bacteria, including the genomics of yeast tolerance and detoxification; genetics and regulation of glycogen and trehalose metabolism; programmed cell death; high gravity fermentations; ethanol tolerance; improving biomass sugar utilization by engineered Saccharomyces; the genomics on tolerance of Zymomonas mobilis; microbial solvent tolerance; control of stress tolerance in bacterial host organisms; metabolomics for ethanologenic yeast; automated proteomics work cell systems for strain improvement; and unification of gene expression data for comparable analyses under stress conditions. (orig.)

  4. Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity

    DEFF Research Database (Denmark)

    Green, Sara; Serban, Maria; Scholl, Raphael

    2018-01-01

    The increasing application of network models to interpret biological systems raises a number of important methodological and epistemological questions. What novel insights can network analysis provide in biology? Are network approaches an extension of or in conflict with mechanistic research...

  5. Systems biology approaches and pathway tools for investigating cardiovascular disease

    NARCIS (Netherlands)

    Wheelock, C.E.; Wheelock, A.M.; Kawashima, S.; Diez, D.; Kanehisa, M.; Erk, M. van; Kleemann, R.; Haeggström, J.Z.; Goto, S.

    2009-01-01

    Systems biology aims to understand the nonlinear interactions of multiple biomolecular components that characterize a living organism. One important aspect of systems biology approaches is to identify the biological pathways or networks that connect the differing elements of a system, and examine

  6. [Electronic poison information management system].

    Science.gov (United States)

    Kabata, Piotr; Waldman, Wojciech; Kaletha, Krystian; Sein Anand, Jacek

    2013-01-01

    We describe deployment of electronic toxicological information database in poison control center of Pomeranian Center of Toxicology. System was based on Google Apps technology, by Google Inc., using electronic, web-based forms and data tables. During first 6 months from system deployment, we used it to archive 1471 poisoning cases, prepare monthly poisoning reports and facilitate statistical analysis of data. Electronic database usage made Poison Center work much easier.

  7. Promoting Systems Thinking through Biology Lessons

    Science.gov (United States)

    Riess, Werner; Mischo, Christoph

    2010-04-01

    This study's goal was to analyze various teaching approaches within the context of natural science lessons, especially in biology. The main focus of the paper lies on the effectiveness of different teaching methods in promoting systems thinking in the field of Education for Sustainable Development. The following methods were incorporated into the study: special lessons designed to promote systems thinking, a computer-simulated scenario on the topic "ecosystem forest," and a combination of both special lessons and the computer simulation. These groups were then compared to a control group. A questionnaire was used to assess systems thinking skills of 424 sixth-grade students of secondary schools in Germany. The assessment differentiated between a conceptual understanding (measured as achievement score) and a reflexive justification (measured as justification score) of systems thinking. The following control variables were used: logical thinking, grades in school, memory span, and motivational goal orientation. Based on the pretest-posttest control group design, only those students who received both special instruction and worked with the computer simulation showed a significant increase in their achievement scores. The justification score increased in the computer simulation condition as well as in the combination of computer simulation and lesson condition. The possibilities and limits of promoting various forms of systems thinking by using realistic computer simulations are discussed.

  8. Molecular profiles to biology and pathways: a systems biology approach.

    Science.gov (United States)

    Van Laere, Steven; Dirix, Luc; Vermeulen, Peter

    2016-06-16

    Interpreting molecular profiles in a biological context requires specialized analysis strategies. Initially, lists of relevant genes were screened to identify enriched concepts associated with pathways or specific molecular processes. However, the shortcoming of interpreting gene lists by using predefined sets of genes has resulted in the development of novel methods that heavily rely on network-based concepts. These algorithms have the advantage that they allow a more holistic view of the signaling properties of the condition under study as well as that they are suitable for integrating different data types like gene expression, gene mutation, and even histological parameters.

  9. Addressing Semantic Geographic Information Systems

    Directory of Open Access Journals (Sweden)

    Salvatore F. Pileggi

    2013-11-01

    Full Text Available The progressive consolidation of information technologies on a large scale has been facilitating and progressively increasing the production, collection, and diffusion of geographic data, as well as facilitating the integration of a large amount of external information into geographic information systems (GIS. Traditional GIS is transforming into a consolidated information infrastructure. This consolidated infrastructure is affecting more and more aspects of internet computing and services. Most popular systems (such as social networks, GPS, and decision support systems involve complex GIS and significant amounts of information. As a web service, GIS is affected by exactly the same problems that affect the web as a whole. Therefore, next generation GIS solutions have to address further methodological and data engineering challenges in order to accommodate new applications’ extended requirements (in terms of scale, interoperability, and complexity. The conceptual and semantic modeling of GIS, as well as the integration of semantics into current GIS, provide highly expressive environments that are capable of meeting the needs and requirements of a wide range of applications.

  10. The ideal laboratory information system.

    Science.gov (United States)

    Sepulveda, Jorge L; Young, Donald S

    2013-08-01

    Laboratory information systems (LIS) are critical components of the operation of clinical laboratories. However, the functionalities of LIS have lagged significantly behind the capacities of current hardware and software technologies, while the complexity of the information produced by clinical laboratories has been increasing over time and will soon undergo rapid expansion with the use of new, high-throughput and high-dimensionality laboratory tests. In the broadest sense, LIS are essential to manage the flow of information between health care providers, patients, and laboratories and should be designed to optimize not only laboratory operations but also personalized clinical care. To list suggestions for designing LIS with the goal of optimizing the operation of clinical laboratories while improving clinical care by intelligent management of laboratory information. Literature review, interviews with laboratory users, and personal experience and opinion. Laboratory information systems can improve laboratory operations and improve patient care. Specific suggestions for improving the function of LIS are listed under the following sections: (1) Information Security, (2) Test Ordering, (3) Specimen Collection, Accessioning, and Processing, (4) Analytic Phase, (5) Result Entry and Validation, (6) Result Reporting, (7) Notification Management, (8) Data Mining and Cross-sectional Reports, (9) Method Validation, (10) Quality Management, (11) Administrative and Financial Issues, and (12) Other Operational Issues.

  11. Systems Biology in Immunology – A Computational Modeling Perspective

    Science.gov (United States)

    Germain, Ronald N.; Meier-Schellersheim, Martin; Nita-Lazar, Aleksandra; Fraser, Iain D. C.

    2011-01-01

    Systems biology is an emerging discipline that combines high-content, multiplexed measurements with informatic and computational modeling methods to better understand biological function at various scales. Here we present a detailed review of the methods used to create computational models and conduct simulations of immune function, We provide descriptions of the key data gathering techniques employed to generate the quantitative and qualitative data required for such modeling and simulation and summarize the progress to date in applying these tools and techniques to questions of immunological interest, including infectious disease. We include comments on what insights modeling can provide that complement information obtained from the more familiar experimental discovery methods used by most investigators and why quantitative methods are needed to eventually produce a better understanding of immune system operation in health and disease. PMID:21219182

  12. Database, expert systems, information retrieval

    International Nuclear Information System (INIS)

    Fedele, P.; Grandoni, G.; Mammarella, M.C.

    1989-12-01

    The great debate concerning the Italian high-school reform has induced a ferment of activity among the most interested and sensible of people. This was clearly demonstrated by the course 'Innovazione metodologico-didattica e tecnologie informatiche' organized for the staff of the 'lstituto Professionale L. Einaudi' of Lamezia Terme. The course was an interesting opportunity for discussions and interaction between the world of School and computer technology used in the Research field. This three day course included theoretical and practical lessons, showing computer facilities that could be useful for teaching. During the practical lessons some computer tools were presented from the very simple Electronic Sheets to the more complicated information Retrieval on CD-ROM interactive realizations. The main topics will be discussed later. They are: Modelling, Data Base, Integrated Information Systems, Expert Systems, Information Retrieval. (author)

  13. Executive Information Systems' Multidimensional Models

    Directory of Open Access Journals (Sweden)

    2007-01-01

    Full Text Available Executive Information Systems are design to improve the quality of strategic level of management in organization through a new type of technology and several techniques for extracting, transforming, processing, integrating and presenting data in such a way that the organizational knowledge filters can easily associate with this data and turn it into information for the organization. These technologies are known as Business Intelligence Tools. But in order to build analytic reports for Executive Information Systems (EIS in an organization we need to design a multidimensional model based on the business model from the organization. This paper presents some multidimensional models that can be used in EIS development and propose a new model that is suitable for strategic business requests.

  14. Managing Sustainable Information Systems Development

    DEFF Research Database (Denmark)

    Kautz, Karlheinz

    2013-01-01

    Sustainable information systems development (ISD) in the context of this paper is not about products that support sustainability at large with its environmental, economic and social dimensions and little about the development of sustainable products, which are both without doubt important topics...

  15. INIS - International Nuclear Information System

    International Nuclear Information System (INIS)

    1995-01-01

    The paper presents International Nuclear Information System (INIS): history of its development; INIS support products (INIS Reference Series, Friendly Inputting of Bibliographic Records software); INIS output products (INIS Atomindex, magnetic tapes, online service, database on CD-ROM, microfiche service); INIS philosophy; input of INIS database by subject areas; and examples of INIS input

  16. Geographic Information Systems: A Primer

    Science.gov (United States)

    1990-10-01

    821787 Symposium. American society for Photogrammetry and Remote Sensing. Falls Church, VA. pp. 396-409. Lillesand, T. M. and R. W. Kiefer . 1987. Remote...Geographic Information System Using Symbolic Models and Hierarchical Data Structures. PhD Dissertation, University of California, Santa Barbara

  17. Grenada Education Management Information System

    OpenAIRE

    Porta, Emilio; Klein, Jennifer; Arcia, Gustavo; Nannyonjo, Harriet

    2012-01-01

    The Education Management Information System (EMIS) country report for Grenada includes the following headings: background which includes education data in Grenada, EMIS staff, facilities and equipment, EMIS data, and publications; prerequisites of quality; assurances of integrity; methodological soundness; accuracy and reliability; serviceability; and accessibility.

  18. Qualitative Studies in Information Systems

    DEFF Research Database (Denmark)

    Sarker, Suprateek; Xiao, Xiao; Beaulieu, Tanya

    2013-01-01

    The authors discuss a review of qualitative papers on information systems (IS) published in various journals between 2001 and 2012. They explain trends related to qualitative research in the chosen journals and the key anatomical components of a qualitative research manuscript, including...

  19. Teaching RFID Information Systems Security

    Science.gov (United States)

    Thompson, Dale R.; Di, Jia; Daugherty, Michael K.

    2014-01-01

    The future cyber security workforce needs radio frequency identification (RFID) information systems security (INFOSEC) and threat modeling educational materials. A complete RFID security course with new learning materials and teaching strategies is presented here. A new RFID Reference Model is used in the course to organize discussion of RFID,…

  20. Radiology information management system, TOSRIM

    Energy Technology Data Exchange (ETDEWEB)

    Tani, Yuichiro; Uchiyama, Akira; Kimura, Hirohito (Toshiba Corp., Kawasaki, Kanagawa (Japan))

    1991-02-01

    This is a report on a new type of distributed computer system for radiology departments named 'TOSRIM' (Toshiba radiology information management system), which is designed to be installed between medical diagnosis equipment and a host computer system in a hospital. Recently, a new type of host computer system has been developed which enables doctors to order any of the hospital's entire activities using terminals. By connecting 'TOSRIM' to this type of host computer system, many of the activities of a radiology department can be carried out via terminals without the use of examination requirement forms. As well as being connected to medical diagnosis equipment, 'TOSRIM' can also be connected to a medical imaging system which stores and displays medical images. By means of these connections, doctors will be able to diagnose medical images using display terminals without the need for films. (author).

  1. Radiology information management system, TOSRIM

    International Nuclear Information System (INIS)

    Tani, Yuichiro; Uchiyama, Akira; Kimura, Hirohito

    1991-01-01

    This is a report on a new type of distributed computer system for radiology departments named 'TOSRIM' (Toshiba radiology information management system), which is designed to be installed between medical diagnosis equipment and a host computer system in a hospital. Recently, a new type of host computer system has been developed which enables doctors to order any of the hospital's entire activities using terminals. By connecting 'TOSRIM' to this type of host computer system, many of the activities of a radiology department can be carried out via terminals without the use of examination requirement forms. As well as being connected to medical diagnosis equipment, 'TOSRIM' can also be connected to a medical imaging system which stores and displays medical images. By means of these connections, doctors will be able to diagnose medical images using display terminals without the need for films. (author)

  2. 3S - Systematic, systemic, and systems biology and toxicology.

    Science.gov (United States)

    Smirnova, Lena; Kleinstreuer, Nicole; Corvi, Raffaella; Levchenko, Andre; Fitzpatrick, Suzanne C; Hartung, Thomas

    2018-01-01

    A biological system is more than the sum of its parts - it accomplishes many functions via synergy. Deconstructing the system down to the molecular mechanism level necessitates the complement of reconstructing functions on all levels, i.e., in our conceptualization of biology and its perturbations, our experimental models and computer modelling. Toxicology contains the somewhat arbitrary subclass "systemic toxicities"; however, there is no relevant toxic insult or general disease that is not systemic. At least inflammation and repair are involved that require coordinated signaling mechanisms across the organism. However, the more body components involved, the greater the challenge to reca-pitulate such toxicities using non-animal models. Here, the shortcomings of current systemic testing and the development of alternative approaches are summarized. We argue that we need a systematic approach to integrating existing knowledge as exemplified by systematic reviews and other evidence-based approaches. Such knowledge can guide us in modelling these systems using bioengineering and virtual computer models, i.e., via systems biology or systems toxicology approaches. Experimental multi-organ-on-chip and microphysiological systems (MPS) provide a more physiological view of the organism, facilitating more comprehensive coverage of systemic toxicities, i.e., the perturbation on organism level, without using substitute organisms (animals). The next challenge is to establish disease models, i.e., micropathophysiological systems (MPPS), to expand their utility to encompass biomedicine. Combining computational and experimental systems approaches and the chal-lenges of validating them are discussed. The suggested 3S approach promises to leverage 21st century technology and systematic thinking to achieve a paradigm change in studying systemic effects.

  3. GEOGRAPHIC NAMES INFORMATION SYSTEM (GNIS) ...

    Science.gov (United States)

    The Geographic Names Information System (GNIS), developed by the U.S. Geological Survey in cooperation with the U.S. Board on Geographic Names (BGN), contains information about physical and cultural geographic features in the United States and associated areas, both current and historical, but not including roads and highways. The database also contains geographic names in Antarctica. The database holds the Federally recognized name of each feature and defines the location of the feature by state, county, USGS topographic map, and geographic coordinates. Other feature attributes include names or spellings other than the official name, feature designations, feature class, historical and descriptive information, and for some categories of features the geometric boundaries. The database assigns a unique feature identifier, a random number, that is a key for accessing, integrating, or reconciling GNIS data with other data sets. The GNIS is our Nation's official repository of domestic geographic feature names information.

  4. In-Vehicle Information Systems

    Directory of Open Access Journals (Sweden)

    Gordana Štefančić

    2002-03-01

    Full Text Available The paper considers different systems, including thesystems with autonomous units, which cany all their knowledgewith them, and those with communication units, which informthe driver about the current situation of the road system byradio or other means. The symbols of various messageshave three main goals: to provide instruction, to warn ofoncoming danger, or to give advice regarding parking or lookingfor alternative routes. When not used for these purposes,they are used to provide general information about/he weathe1;temperature or possible attractions. The in-vehicle informationsystems try to assist the motorist in driving, and they arepromoted as part of the comprehensive intelligent transport system.

  5. Hydrogen production from biomass by biological systems

    International Nuclear Information System (INIS)

    Sharifan, H.R.; Qader, S.

    2009-01-01

    Hydrogen gas is seen as a future energy carrier, not involved in 'greenhouse' gas and its released energy in combustion can be converted to electric power. Biological system with low energy can produce hydrogen compared to electrochemical hydrogen production via solar battery-based water splitting which requires the use of solar batteries with high energy requirements. The biological hydrogen production occurs in microalgae and cyanobacteria by photosynthesis. They consume biochemical energy to produce molecular hydrogen. Hydrogen in some algae is an anaerobic production in the absence of light. In cyanobacteria the hydrogen production simultaneously happens with nitrogen fixation, and also catalyzed by nitrogenase as a side reaction. Hydrogen production by photosynthetic bacteria is mediated by nitrogenase activity, although hydrogenases may be active for both hydrogen production and hydrogen uptake under some conditions. Genetic studies on photosynthetic microorganisms have markedly increased in recent times, relatively few genetic engineering studies have focused on altering the characteristics of these microorganisms, particularly with respect to enhancing the hydrogen-producing capabilities of photosynthetic bacteria and cyanobacteria. (author)

  6. The Information Tekhnology Share In Management Information System

    Directory of Open Access Journals (Sweden)

    Nur Zeina Maya Sari

    2015-08-01

    Full Text Available Abstract Management Information System growth cause change of role from all manager in decision making the information technology. While prima facie reason for the usage of information technology in business to support such a manner so that information system may operate better OBrienamp Marakas 2004. Its meaning with existence of information tekhnology in management information system SIM company management decision making which initially often pursued by many factor of non technical become accurately is relevant complete and on schedule

  7. PROMIS (Procurement Management Information System)

    Science.gov (United States)

    1987-01-01

    The PROcurement Management Information System (PROMIS) provides both detailed and summary level information on all procurement actions performed within NASA's procurement offices at Marshall Space Flight Center (MSFC). It provides not only on-line access, but also schedules procurement actions, monitors their progress, and updates Forecast Award Dates. Except for a few computational routines coded in FORTRAN, the majority of the systems is coded in a high level language called NATURAL. A relational Data Base Management System called ADABAS is utilized. Certain fields, called descriptors, are set up on each file to allow the selection of records based on a specified value or range of values. The use of like descriptors on different files serves as the link between the falls, thus producing a relational data base. Twenty related files are currently being maintained on PROMIS.

  8. European Marine Information System. Eumaris; European Marine Information System. Eumaris

    Energy Technology Data Exchange (ETDEWEB)

    Caiaffa, E. [ENEA, Centro Ricerche Casaccia, Rome (Italy). Dipt. Ambiente

    1999-07-01

    The present paper summarises the activities developed by ETC/MCE, under European Environment Agency (EEA) contract, on the Geographic Information System. The aim of present paper is to introduce some general concepts about the Geographic Information Systems and to investigate the potential of G.I.S. as tool for the assessment of the European seas. Care has also been taken to explain the main technical and educational reasons that led to EUMARIS GIS birth, its evolution in the last year, till to its presentation at the Inter-Regional Forum of the European Conventions held in Venice. GIS is a technological tool phenomenon involving various aspects and different issues; many examples of thematic maps involving that different subjects are shown in the paper. [Italian] Il presente articolo riassume le attivita' svolte, nell'ambito del Geographic Information System, dall'ETC/MCE sotto contratto con l'Agenzia Europea per l'Ambiente (EEA) che ha sede a Copenhagen. Scopo del presente articolo e' quello di introdurre alcuni concetti generali sui Geographic Information System (GIS) e di dimostrare la possibilita' di utilizzare il GIS stesso come strumento per la valutazione dello stato dei mari dell'Europa. Si e' cercato di spiegare le principali ragioni tecniche che hanno portato alla nascita del progeto del GIS EUMARIS, alla sua realizzazione fino alla sua presentazione all'Inter-Regional Forum of European Conventions tenutosi a Venezia. Si e' cercato anche di mostrare come un GIS per sua natura e' uno strumento che coinvolge vari aspetti tecnologici e differenti tipi di dati; nell'articolo vengono mostrati diversi esempi di mappe tematiche che contengono tali differenti argomenti.

  9. [Systems biology applications to explore secondary metabolites in medicinal plants].

    Science.gov (United States)

    Huang, Luqi; Gao, Wei; Zhou, Jie; Wang, Ruiting

    2010-01-01

    Secondary metabolites are produced during the growth and development of plants along with the adaptation of outer environment, as a rule they are the main active ingredients in medicinal plants and ensure the quality of crude drugs. Since biogenesis is quite complex, the production and accumulation of secondary metabolites are influenced by various biotic and abiotic factors either from gene or environments, the complexity may affect quality control of crude drugs and utilization of the active ingredients. The thought and approach adopted in systems biology is a powerful tool to explore biology fully, along with the development of modern molecular biology and information biology, omics integration like genomics, transcriptomics, proteomics, and metabolomics will bring new opportunities for the study of secondary metabolites of medicinal plant. It has great significance to apply this holistic and systematic method in researches on biosynthetic pathway, signal transduction, ecological environment and metabolic engineering of the formation of the secondary metabolites of medicinal plants, and in building secondary metabolite biosynthesis gene expression and regulation system model, in order to explain the origin of the active ingredients of medicinal plants, formation mechanism of the Chinese herbs, metabolic engineering effecting active ingredients of medicinal plants, and the rational exploitation and utilization of resources of medicinal plants systematically.

  10. EnviroTRADE information system

    International Nuclear Information System (INIS)

    Harlan, C.; Harrington, M.W.

    1993-01-01

    Environmental Technologies for Remedial Actions Data Exchange (EnviroTRADE) is a graphical/textual information management system being developed for the cleanup program of the U.S. Department of Energy's (DOE) Weapons Complex. Its principal purpose is to provide a single, powerful, interactive database that addresses environmental restoration and waste management (ER/WM) problems and the technologies currently under development or already available to resolve them. Because the volume and complexity of the information is so large, a sophisticated Relational Database Management System (RDBMS) is employed in EnviroTRADE. EnviroTRADE will be a multi-purpose, multi-user system capable of addressing a broad range of environmental assessment and cleanup issues. An early focus for the Beta version of EnviroTRADE has been to find matches between specific environmental problems at particular sites (e.g., in terms of waste composition and form) and available and new technologies suited to solve problems. The current prototype EnviroTRADE database includes both U.S. and foreign problems and technologies. A Beta version was developed and demonstrated during FY92 and was expanded in FY93. This system was delivered to EM-523 as a stand-alone resident system for demonstration and feedback purposes. The resident system demonstrates the feasibility of this kind of multi-purpose system and also provides a test bed for refining the system architecture. As the architecture and database grow, an increasing range of possible applications is envisioned. The ability to import very large quantities of graphical, textual, and numerical information into the database is of particular importance. Since a great deal of appropriate data already exists in various electronic formats, a rapid expansion into EnviroTRADE-accessible data is possible without relying on manual entry methods

  11. Systems Biology of Metabolism: Annual Review of Biochemistry

    DEFF Research Database (Denmark)

    Nielsen, Jens

    2017-01-01

    Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology......, the application of systems biology for analyzing global regulatory structures, engineering the metabolism of cell factories, and analyzing human diseases is discussed....

  12. Computational Modeling of Biological Systems From Molecules to Pathways

    CERN Document Server

    2012-01-01

    Computational modeling is emerging as a powerful new approach for studying and manipulating biological systems. Many diverse methods have been developed to model, visualize, and rationally alter these systems at various length scales, from atomic resolution to the level of cellular pathways. Processes taking place at larger time and length scales, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. Computational Modeling of Biological Systems: From Molecules to Pathways provides an overview of established computational methods for the modeling of biologically and medically relevant systems. It is suitable for researchers and professionals working in the fields of biophysics, computational biology, systems biology, and molecular medicine.

  13. Integrative Systems Biology: Elucidating Complex Traits

    DEFF Research Database (Denmark)

    Pers, Tune Hannes

    Risk-phenotypes and diseases are oen caused by perturbed cellular networks, as biological processes depend on an overwhelming number of heavily intertwined components. e impact of a genetically altered gene may ripple through its molecular neighborhood instead of being confined to the gene...... product itself. My doctoral studies have been focused on the development of integrative approaches to identify systemic risk-modifying and disease-causing patterns. ey have been rooted in the hypothesis that data integration of complementary data sets may yield additional etiologic insights compared...... to analyses conducted within a single type of data. e first line of research presented here outlines two integrative methodologies designed to identify etiological pathways and susceptibility genes. In Paper I, my coworkers and I present an integrative approach that interrogates protein complexes...

  14. Human Development V: Biochemistry Unable to Explain the Emergence of Biological Form (Morphogenesis and Therefore a New Principle as Source of Biological Information is Needed

    Directory of Open Access Journals (Sweden)

    Søren Ventegodt

    2006-01-01

    Full Text Available Today's biomedicine builds on the conviction that biochemistry can explain the creation of the body, its anatomy and physiology. Unfortunately there are still deep mysteries strangely “fighting back” when we try to define and understand the organism and its creation in the ontogenesis as emerging from biochemistry. In analysing this from a theoretical perspective using a mathematical model focusing on the noise in complex chemical systems we argue that evolving biological structure cannot in principle be a product of chemistry. In this paper we go through the chemical gradient model and argue that this is not able to explain the ontogenesis. We discuss the used gradients as information carriers in chemical self-organizing systems and argue that by use of the “Turing structures” we are only able to modelling the mostly simple biological systems. The bio-chemical model is only able to model simple organization but not to explain the complexity of biological phenomena. We conclude that we seemingly have presented a formal proof (a NO-GO theorem that the self-organizing chemical systems that are using chemical gradients are not able to explain complex biological matters as the ontogenesis. We need a fundamentally new, information-carrying principle to understand biological information and biological order.

  15. Systems Biology and Ecology of Streamlined Bacterioplankton

    Science.gov (United States)

    Giovannoni, S. J.

    2014-12-01

    complex questions hinge on translating gene frequencies into trait based ecological models that reflect the systems biology of cells.

  16. Study of the effects of radon in three biological systems

    International Nuclear Information System (INIS)

    Tavera, L.; Balcazar, M.; Lopez, A.; Brena, M.; Rosa, M.E. De la; Villalobos P, R.

    2002-01-01

    The radon and its decay products are responsible of the 3/4 parts of the exposure of the persons to the environmental radiation. The discovery at the end of XIX Century of the illnesses, mainly of cancer, which appeared in the presence of radon, lead to an accelerated growing of the radon studies: monitoring, dosimetry, effects on the persons, etc. Several epidemiological studies of radon in miners and population in general have been realized; advancing in the knowledge about the concentration-lung cancer risk relationship, but with discrepancies in the results depending on the concentration levels. Therefor, studies which consuming time, efforts and money go on doing. The research of the radon effects in biological systems different to human, allows to realize studies in less time, in controlled conditions and generally at lower cost, generating information about the alpha radiation effects in the cellular field. Therefor it was decided to study the response of three biological systems exposed to radon: an unicellular bacteria Escherichia Coli which was exposed directly to alpha particles from an electrodeposited source for determining the sensitivity limit of the chose technique. A plant, Tradescantia, for studying the cytogenetic effect of the system exposed to controlled concentrations of radon. An insect, Drosophila Melanogaster, for studying the genetic effects and the accumulated effects in several generations exposed to radon. In this work the experimental settlements are presented for the expositions of the systems and the biological results commenting the importance of these. (Author)

  17. Hanford Environmental Information System (HEIS)

    International Nuclear Information System (INIS)

    1994-01-01

    The Hanford Environmental Information System (HEIS) is a consolidated set of automated resources that effectively manage the data gathered during environmental monitoring and restoration of the Hanford Site. HEIS includes an integrated database that provides consistent and current data to all users and promotes sharing of data by the entire user community. HEIS is an information system with an inclusive database. Although the database is the nucleus of the system, HEIS also provides user access software: query-by-form data entry, extraction, and browsing facilities; menu-driven reporting facilities; an ad hoc query facility; and a geographic information system (GIS). These features, with the exception of the GIS, are described in this manual set. Because HEIS contains data from the entire Hanford Site, many varieties of data are included and have.been divided into subject areas. Related subject areas comprise several volumes of the manual set. The manual set includes a data dictionary that lists all of the fields in the HEIS database, with their definitions and a cross reference of their locations in the database; definitions of data qualifiers for analytical results; and a mapping between the HEIS software functions and the keyboard keys for each of the supported terminals or terminal emulators

  18. Automated Information System (AIS) Alarm System

    Energy Technology Data Exchange (ETDEWEB)

    Hunteman, W.

    1997-05-01

    The Automated Information Alarm System is a joint effort between Los Alamos National Laboratory, Lawrence Livermore National Laboratory, and Sandia National Laboratory to demonstrate and implement, on a small-to-medium sized local area network, an automated system that detects and automatically responds to attacks that use readily available tools and methodologies. The Alarm System will sense or detect, assess, and respond to suspicious activities that may be detrimental to information on the network or to continued operation of the network. The responses will allow stopping, isolating, or ejecting the suspicious activities. The number of sensors, the sensitivity of the sensors, the assessment criteria, and the desired responses may be set by the using organization to meet their local security policies.

  19. Automated Information System (AIS) Alarm System

    International Nuclear Information System (INIS)

    Hunteman, W.

    1997-01-01

    The Automated Information Alarm System is a joint effort between Los Alamos National Laboratory, Lawrence Livermore National Laboratory, and Sandia National Laboratory to demonstrate and implement, on a small-to-medium sized local area network, an automated system that detects and automatically responds to attacks that use readily available tools and methodologies. The Alarm System will sense or detect, assess, and respond to suspicious activities that may be detrimental to information on the network or to continued operation of the network. The responses will allow stopping, isolating, or ejecting the suspicious activities. The number of sensors, the sensitivity of the sensors, the assessment criteria, and the desired responses may be set by the using organization to meet their local security policies

  20. 75 FR 23834 - Occupational Information System

    Science.gov (United States)

    2010-05-04

    ... SOCIAL SECURITY ADMINISTRATION [Docket No. SSA-2010-0018] Occupational Information System AGENCY... Administration Occupational Information System, September 2009.'' The complete Panel report (including appendices... to provide independent advice and recommendations on creating an occupational information system...

  1. Systems biology in practice: concepts, implementation and application

    National Research Council Canada - National Science Library

    Klipp, E

    2005-01-01

    ... approaching systems biology from a different discipline. We see the origin and the methodological foundations for systems biology (1) in the accumulation of detailed biological knowledge with the prospect of utilization in biotechnology and health care, (2) in the emergence of new experimental techniques in genomics and proteomics, (3) in the traditio...

  2. Regulatory authority information system RAIS

    International Nuclear Information System (INIS)

    Ortiz, P.; Mrabit, K.; Miaw, S.

    2000-01-01

    In this lecture the principles of the regulatory authority information system (RAIS) are presented. RAIS is a tool currently being developed by the IAEA for the Regulatory Authorities. It is a part of a set of supporting actions designed to assist member states in achieving the objectives of the Model project on radiation and waste safety infrastructure. RAIS is a tool that provides the management of the Regulatory Authority with the key information needed for the planning and implementation of activities and to ensure confidence that resources are optimally used. The RAIS contains five modules: Inventory of installations and radiation sources; Authorization process; Inspection and follow-up actions; Information on personal dosimetry; Assessment of effectiveness by means of performance indicators

  3. Information Systems for Enterprise Architecture

    Directory of Open Access Journals (Sweden)

    Oswaldo Moscoso Zea

    2014-03-01

    Full Text Available (Received: 2014/02/14 - Accepted: 2014/03/25Enterprise Architecture (EA has emerged as one of the most important topics to consider in Information System studies and has grown to become an essential business management activity to visualize and evaluate the future direction of a company. Nowadays in the market there are several software tools that support Enterprise Architects to work with EA. In order to decrease the risk of purchasing software tools that do not fulfill stakeholder´s needs is important to assess the software before making an investment. In this paper a literature review of the state of the art of EA will be done. Furthermore evaluation initiatives and existing information systems are analyzed which can support decision makers in the appropriate software tools for their companies.

  4. Image and information management system

    Science.gov (United States)

    Robertson, Tina L. (Inventor); Raney, Michael C. (Inventor); Dougherty, Dennis M. (Inventor); Kent, Peter C. (Inventor); Brucker, Russell X. (Inventor); Lampert, Daryl A. (Inventor)

    2009-01-01

    A system and methods through which pictorial views of an object's configuration, arranged in a hierarchical fashion, are navigated by a person to establish a visual context within the configuration. The visual context is automatically translated by the system into a set of search parameters driving retrieval of structured data and content (images, documents, multimedia, etc.) associated with the specific context. The system places ''hot spots'', or actionable regions, on various portions of the pictorials representing the object. When a user interacts with an actionable region, a more detailed pictorial from the hierarchy is presented representing that portion of the object, along with real-time feedback in the form of a popup pane containing information about that region, and counts-by-type reflecting the number of items that are available within the system associated with the specific context and search filters established at that point in time.

  5. NRPB emergency response information system

    International Nuclear Information System (INIS)

    Higgins, N.A.; Casey, K.

    1993-01-01

    To enhance emergency response management NRPB has introduced an advanced information handling and map display facility. The NRPB Emergency Response Information System (NERIS) provides a central resource which holds, displays and analyses the available information on an accidental release of radioactivity. The bringing together of the commercial tools of computerised map display and database technology, capable of storing geographically referenced information, provided the initial building blocks for the development of NERIS. The rapid manipulation of the large amounts of data used by NERIS is achieved by the use of complex software on powerful computers and a substantial investment of both staff time and resources. The synthesis of these products with the analysis tools under development by NRPB staff will provide a system which will greatly enhance the organisation's emergency response capability. The need to assess the consequences of an accident and give advice on countermeasure strategies and actions will inevitably place high demands on NRPB staff. NERIS will enable a more complete understanding of the situation to be gained and give staff the time and tools to cope effectively with all exigencies. (Author)

  6. Power reactor information system (PRIS)

    International Nuclear Information System (INIS)

    1989-06-01

    Since the very beginning of commercial operation of nuclear power plants, the nuclear power industry worldwide has accumulated more than 5000 reactor years of experience. The IAEA has been collecting Operating Experience data for Nuclear Power Plants since 1970 which were computerized in 1980. The Agency has undertaken to make Power Reactor Information System (PRIS) available on-line to its Member States. The aim of this publication is to provide the users of PRIS from their terminals with description of data base and communication systems and to show the methods of accessing the data

  7. Hanford Environmental Information System (HEIS)

    International Nuclear Information System (INIS)

    1994-01-01

    The purpose of the Biota subject area of the Hanford Environmental Information System (HEIS) is to manage the data collected from samples of plants and animals. This includes both samples taken from the plant or animal or samples related to the plant or animal. Related samples include animal feces and animal habitat. Data stored in the Biota subject area include data about the biota samples taken, analysis results counts from population studies, and species distribution maps

  8. A SYSTEMIC VISION OF BIOLOGY: OVERCOMING LINEARITY

    Directory of Open Access Journals (Sweden)

    M. Mayer

    2005-07-01

    Full Text Available Many  authors have proposed  that contextualization of reality  is necessary  to teach  Biology, empha- sizing students´ social and  economic realities.   However, contextualization means  more than  this;  it is related  to working with  different kinds of phenomena  and/or objects  which enable  the  expression of scientific concepts.  Thus,  contextualization allows the integration of different contents.  Under this perspective,  the  objectives  of this  work were to articulate different  biology concepts  in order  to de- velop a systemic vision of biology; to establish  relationships with other areas of knowledge and to make concrete the  cell molecular  structure and organization as well as their  implications  on living beings´ environment, using  contextualization.  The  methodology  adopted  in this  work  was based  on three aspects:  interdisciplinarity, contextualization and development of competences,  using energy:  its flux and transformations as a thematic axis and  an approach  which allowed the  interconnection between different situations involving  these  concepts.   The  activities developed  were:  1.   dialectic exercise, involving a movement around  micro and macroscopic aspects,  by using questions  and activities,  sup- ported  by the use of alternative material  (as springs, candles on the energy, its forms, transformations and  implications  in the  biological way (microscopic  concepts;  2, Construction of molecular  models, approaching the concepts of atom,  chemical bonds and bond energy in molecules; 3. Observations de- veloped in Manguezal¨(mangrove swamp  ecosystem (Itapissuma, PE  were used to work macroscopic concepts  (as  diversity  and  classification  of plants  and  animals,  concerning  to  energy  flow through food chains and webs. A photograph register of all activities  along the course plus texts

  9. Programmable temperature control system for biological materials

    Science.gov (United States)

    Anselmo, V. J.; Harrison, R. G.; Rinfret, A. P.

    1982-01-01

    A system was constructed which allows programmable temperature-time control for a 5 cu cm sample volume of arbitrary biological material. The system also measures the parameters necessary for the determination of the sample volume specific heat and thermal conductivity as a function of temperature, and provides a detailed measurement of the temperature during phase change and a means of calculating the heat of the phase change. Steady-state and dynamic temperature control is obtained by supplying heat to the sample volume through resistive elements constructed as an integral part of the sample container. For cooling purposes, this container is totally immersed into a cold heat sink. Using a mixture of dry ice and alcohol at 79 C, the sample volume can be controlled from +40 to -60 C at rates from steady state to + or - 65 C/min. Steady-state temperature precision is better than 0.2 C, while the dynamic capability depends on the temperature rate of change as well as the mass of both the sample and the container.

  10. Drawing inspiration from biological optical systems

    Science.gov (United States)

    Wolpert, H. D.

    2009-08-01

    Bio-Mimicking/Bio-Inspiration: How can we not be inspired by Nature? Life has evolved on earth over the last 3.5 to 4 billion years. Materials formed during this time were not toxic; they were created at low temperatures and low pressures unlike many of the materials developed today. The natural materials formed are self-assembled, multifunctional, nonlinear, complex, adaptive, self-repairing and biodegradable. The designs that failed are fossils. Those that survived are the success stories. Natural materials are mostly formed from organics, inorganic crystals and amorphous phases. The materials make economic sense by optimizing the design of the structures or systems to meet multiple needs. We constantly "see" many similar strategies in approaches, between man and nature, but we seldom look at the details of natures approaches. The power of image processing, in many of natures creatures, is a detail that is often overlooked. Seldon does the engineer interact with the biologist and learn what nature has to teach us. The variety and complexity of biological materials and the optical systems formed should inspire us.

  11. 78 FR 33846 - Agency Information Collection Activities; Proposed Collection; Comment Request; Biological...

    Science.gov (United States)

    2013-06-05

    ...; Biological Products: Reporting of Biological Product Deviations and Human Cells, Tissues, and Cellular and... biological product deviations in manufacturing and human cells, tissues, and cellular and tissue- based... techniques, when appropriate, and other forms of information technology. Biological Products: Reporting of...

  12. Fire Effects Information System: New engine, remodeled interior, added options

    Science.gov (United States)

    Jane Kapler Smith

    2010-01-01

    Some of today's firefighters weren't even born when the Fire Effects Information System (FEIS) (Web site ) "hit the streets" in 1986. Managers might remember using a dial-up connection in the early 1990s to access information on biology, ecology, and fire offered by FEIS.

  13. Application of computational systems biology to explore environmental toxicity hazards

    DEFF Research Database (Denmark)

    Audouze, Karine Marie Laure; Grandjean, Philippe

    2011-01-01

    Background: Computer-based modeling is part of a new approach to predictive toxicology.Objectives: We investigated the usefulness of an integrated computational systems biology approach in a case study involving the isomers and metabolites of the pesticide dichlorodiphenyltrichloroethane (DDT......) to ascertain their possible links to relevant adverse effects.Methods: We extracted chemical-protein association networks for each DDT isomer and its metabolites using ChemProt, a disease chemical biology database that includes both binding and gene expression data, and we explored protein-protein interactions...... diseases were linked to the two DDT isomers. Asthma was uniquely linked with p,p´-DDT, and autism with o,p´-DDT. Several reproductive and neurobehavioral outcomes and cancer types were linked to all three compounds.Conclusions: Computer-based modeling relies on available information. Although differences...

  14. Large-Scale Information Systems

    Energy Technology Data Exchange (ETDEWEB)

    D. M. Nicol; H. R. Ammerlahn; M. E. Goldsby; M. M. Johnson; D. E. Rhodes; A. S. Yoshimura

    2000-12-01

    Large enterprises are ever more dependent on their Large-Scale Information Systems (LSLS), computer systems that are distinguished architecturally by distributed components--data sources, networks, computing engines, simulations, human-in-the-loop control and remote access stations. These systems provide such capabilities as workflow, data fusion and distributed database access. The Nuclear Weapons Complex (NWC) contains many examples of LSIS components, a fact that motivates this research. However, most LSIS in use grew up from collections of separate subsystems that were not designed to be components of an integrated system. For this reason, they are often difficult to analyze and control. The problem is made more difficult by the size of a typical system, its diversity of information sources, and the institutional complexities associated with its geographic distribution across the enterprise. Moreover, there is no integrated approach for analyzing or managing such systems. Indeed, integrated development of LSIS is an active area of academic research. This work developed such an approach by simulating the various components of the LSIS and allowing the simulated components to interact with real LSIS subsystems. This research demonstrated two benefits. First, applying it to a particular LSIS provided a thorough understanding of the interfaces between the system's components. Second, it demonstrated how more rapid and detailed answers could be obtained to questions significant to the enterprise by interacting with the relevant LSIS subsystems through simulated components designed with those questions in mind. In a final, added phase of the project, investigations were made on extending this research to wireless communication networks in support of telemetry applications.

  15. Complexity, Analysis and Control of Singular Biological Systems

    CERN Document Server

    Zhang, Qingling; Zhang, Xue

    2012-01-01

    Complexity, Analysis and Control of Singular Biological Systems follows the control of real-world biological systems at both ecological and phyisological levels concentrating on the application of now-extensively-investigated singular system theory. Much effort has recently been dedicated to the modelling and analysis of developing bioeconomic systems and the text establishes singular examples of these, showing how proper control can help to maintain sustainable economic development of biological resources. The book begins from the essentials of singular systems theory and bifurcations before tackling  the use of various forms of control in singular biological systems using examples including predator-prey relationships and viral vaccination and quarantine control. Researchers and graduate students studying the control of complex biological systems are shown how a variety of methods can be brought to bear and practitioners working with the economics of biological systems and their control will also find the ...

  16. Script, code, information: how to differentiate analogies in the "prehistory" of molecular biology.

    Science.gov (United States)

    Kogge, Werner

    2012-01-01

    The remarkable fact that twentieth-century molecular biology developed its conceptual system on the basis of sign-like terms has been the object of numerous studies and debates. Throughout these, the assumption is made that this vocabulary's emergence should be seen in the historical context of mathematical communication theory and cybernetics. This paper, in contrast, sets out the need for a more differentiated view: whereas the success of the terms "code" and "information" would probably be unthinkable outside that historical context, general semiotic and especially scriptural concepts arose far earlier in the "prehistory" of molecular biology, and in close association with biological research and phenomena. This distinction, established through a reconstruction of conceptual developments between 1870 and 1950, makes it possible to separate off a critique of the reductive implications of particular information-based concepts from the use of semiotic and scriptural concepts, which is fundamental to molecular biology. Gene-centrism and determinism are not implications of semiotic and scriptural analogies, but arose only when the vocabulary of information was superimposed upon them.

  17. Information system development activities and inquiring systems

    DEFF Research Database (Denmark)

    Carugati, Andrea

    2008-01-01

    This article presents a framework that maps information system development (ISD) activities on systems for the creation of knowledge. This work addresses the relevant and persisting problem of improving the chances of ISD success. The article builds upon previous research on knowledge aspects...... provides a new way to see the development of a system in terms of the knowledge created in the process. The main practical implication of the framework is that it improves the managers' ability to guide ISD activities as knowledge activities embedded in a knowledge process, a crucial element in development...... of ISD, abandoning the idea of a monolithic approach to knowledge and presenting a pluralistic approach based on the idea that different inquiring systems can support micro-level ISD activities. The article is divided into two parts. The first part presents the theoretical development of the framework...

  18. A complex systems approach to computational molecular biology

    Energy Technology Data Exchange (ETDEWEB)

    Lapedes, A. [Los Alamos National Lab., NM (United States)]|[Santa Fe Inst., NM (United States)

    1993-09-01

    We report on the containing research program at Santa Fe Institute that applies complex systems methodology to computational molecular biology. Two aspects are stressed here are the use of co-evolving adaptive neutral networks for determining predictable protein structure classifications, and the use of information theory to elucidate protein structure and function. A ``snapshot`` of the current state of research in these two topics is presented, representing the present state of two major research thrusts in the program of Genetic Data and Sequence Analysis at the Santa Fe Institute.

  19. Network Reconstruction of Dynamic Biological Systems

    OpenAIRE

    Asadi, Behrang

    2013-01-01

    Inference of network topology from experimental data is a central endeavor in biology, since knowledge of the underlying signaling mechanisms a requirement for understanding biological phenomena. As one of the most important tools in bioinformatics area, development of methods to reconstruct biological networks has attracted remarkable attention in the current decade. Integration of different data types can lead to remarkable improvements in our ability to identify the connectivity of differe...

  20. Generalized lattice graphs for 2D-visualization of biological information.

    Science.gov (United States)

    González-Díaz, H; Pérez-Montoto, L G; Duardo-Sanchez, A; Paniagua, E; Vázquez-Prieto, S; Vilas, R; Dea-Ayuela, M A; Bolas-Fernández, F; Munteanu, C R; Dorado, J; Costas, J; Ubeira, F M

    2009-11-07

    Several graph representations have been introduced for different data in theoretical biology. For instance, complex networks based on Graph theory are used to represent the structure and/or dynamics of different large biological systems such as protein-protein interaction networks. In addition, Randic, Liao, Nandy, Basak, and many others developed some special types of graph-based representations. This special type of graph includes geometrical constrains to node positioning in space and adopts final geometrical shapes that resemble lattice-like patterns. Lattice networks have been used to visually depict DNA and protein sequences but they are very flexible. However, despite the proved efficacy of new lattice-like graph/networks to represent diverse systems, most works focus on only one specific type of biological data. This work proposes a generalized type of lattice and illustrates how to use it in order to represent and compare biological data from different sources. We exemplify the following cases: protein sequence; mass spectra (MS) of protein peptide mass fingerprints (PMF); molecular dynamic trajectory (MDTs) from structural studies; mRNA microarray data; single nucleotide polymorphisms (SNPs); 1D or 2D-Electrophoresis study of protein polymorphisms and protein-research patent and/or copyright information. We used data available from public sources for some examples but for other, we used experimental results reported herein for the first time. This work may break new ground for the application of Graph theory in theoretical biology and other areas of biomedical sciences.

  1. Systems biology of microbial exopolysaccharides production

    Directory of Open Access Journals (Sweden)

    Ozlem eAtes

    2015-12-01

    Full Text Available Exopolysaccharides (EPS produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture and medicine. EPSs are mainly associated with high-value applications and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore a systems-based approach constitutes an important step towards understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan and dextran.

  2. Systems Biology of Microbial Exopolysaccharides Production.

    Science.gov (United States)

    Ates, Ozlem

    2015-01-01

    Exopolysaccharides (EPSs) produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture, and medicine. EPSs are mainly associated with high-value applications, and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However, only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover, a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore, a systems-based approach constitutes an important step toward understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism, and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan, and dextran.

  3. Modeling and Simulation Tools: From Systems Biology to Systems Medicine.

    Science.gov (United States)

    Olivier, Brett G; Swat, Maciej J; Moné, Martijn J

    2016-01-01

    Modeling is an integral component of modern biology. In this chapter we look into the role of the model, as it pertains to Systems Medicine, and the software that is required to instantiate and run it. We do this by comparing the development, implementation, and characteristics of tools that have been developed to work with two divergent methodologies: Systems Biology and Pharmacometrics. From the Systems Biology perspective we consider the concept of "Software as a Medical Device" and what this may imply for the migration of research-oriented, simulation software into the domain of human health.In our second perspective, we see how in practice hundreds of computational tools already accompany drug discovery and development at every stage of the process. Standardized exchange formats are required to streamline the model exchange between tools, which would minimize translation errors and reduce the required time. With the emergence, almost 15 years ago, of the SBML standard, a large part of the domain of interest is already covered and models can be shared and passed from software to software without recoding them. Until recently the last stage of the process, the pharmacometric analysis used in clinical studies carried out on subject populations, lacked such an exchange medium. We describe a new emerging exchange format in Pharmacometrics which covers the non-linear mixed effects models, the standard statistical model type used in this area. By interfacing these two formats the entire domain can be covered by complementary standards and subsequently the according tools.

  4. Toxicity of silver nanoparticles in biological systems: Does the complexity of biological systems matter?

    Science.gov (United States)

    Vazquez-Muñoz, Roberto; Borrego, Belen; Juárez-Moreno, Karla; García-García, Maritza; Mota Morales, Josué D; Bogdanchikova, Nina; Huerta-Saquero, Alejandro

    2017-07-05

    Currently, nanomaterials are more frequently in our daily life, specifically in biomedicine, electronics, food, textiles and catalysis just to name a few. Although nanomaterials provide many benefits, recently their toxicity profiles have begun to be explored. In this work, the toxic effects of silver nanoparticles (35nm-average diameter and Polyvinyl-Pyrrolidone-coated) on biological systems of different levels of complexity was assessed in a comprehensive and comparatively way, through a variety of viability and toxicological assays. The studied organisms included viruses, bacteria, microalgae, fungi, animal and human cells (including cancer cell lines). It was found that biological systems of different taxonomical groups are inhibited at concentrations of silver nanoparticles within the same order of magnitude. Thus, the toxicity of nanomaterials on biological/living systems, constrained by their complexity, e.g. taxonomic groups, resulted contrary to the expected. The fact that cells and virus are inhibited with a concentration of silver nanoparticles within the same order of magnitude could be explained considering that silver nanoparticles affects very primitive cellular mechanisms by interacting with fundamental structures for cells and virus alike. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Systems biology: properties of reconstructed networks

    National Research Council Canada - National Science Library

    Palsson, Bernhard

    2006-01-01

    ... between the mathematical ideas and biological processes are made clear, the book reflects the irreversible trend of increasing mathematical content in biology education. Therefore to assist both teacher and student, Palsson provides problem sets, projects, and PowerPoint slides in an associated web site and keeps the presentation in the book concrete with illustrat...

  6. Stochastic modelling of dynamical systems in biology

    NARCIS (Netherlands)

    Pellin, Danilo

    2017-01-01

    In this thesis two relevant biological problems will be addressed from a statistical modelling perspective. The first regards the study of hematopoiesis, a still not well understood biological process rarely observable in humans due to technical and ethical reasons. Hematopoiesis is responsible for

  7. Isotopic fractionation of tritium in biological systems.

    Science.gov (United States)

    Le Goff, Pierre; Fromm, Michel; Vichot, Laurent; Badot, Pierre-Marie; Guétat, Philippe

    2014-04-01

    Isotopic fractionation of tritium is a highly relevant issue in radiation protection and requires certain radioecological considerations. Sound evaluation of this factor is indeed necessary to determine whether environmental compartments are enriched/depleted in tritium or if tritium is, on the contrary, isotopically well-distributed in a given system. The ubiquity of tritium and the standard analytical methods used to assay it may induce biases in both the measurement and the signification that is accorded to the so-called fractionation: based on an exhaustive review of the literature, we show how, sometimes large deviations may appear. It is shown that when comparing the non-exchangeable fraction of organically bound tritium (neOBT) to another fraction of tritium (e.g. tritiated water) the preparation of samples and the measurement of neOBT reported frequently led to underestimation of the ratio of tritium to hydrogen (T/H) in the non-exchangeable compartment by a factor of 5% to 50%. In the present study, corrections are proposed for most of the biological matrices studied so far. Nevertheless, the values of isotopic fractionation reported in the literature remain difficult to compare with each other, especially since the physical quantities and units often vary between authors. Some improvements are proposed to better define what should encompass the concepts of exchangeable and non-exchangeable fractions. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. Toward mechanical systems biology in bone.

    Science.gov (United States)

    Trüssel, Andreas; Müller, Ralph; Webster, Duncan

    2012-11-01

    Cyclic mechanical loading is perhaps the most important physiological factor regulating bone mass and shape in a way which balances optimal strength with minimal weight. This bone adaptation process spans multiple length and time scales. Forces resulting from physiological exercise at the organ scale are sensed at the cellular scale by osteocytes, which reside inside the bone matrix. Via biochemical pathways, osteocytes orchestrate the local remodeling action of osteoblasts (bone formation) and osteoclasts (bone resorption). Together these local adaptive remodeling activities sum up to strengthen bone globally at the organ scale. To resolve the underlying mechanisms it is required to identify and quantify both cause and effect across the different scales. Progress has been made at the different scales experimentally. Computational models of bone adaptation have been developed to piece together various experimental observations at the different scales into coherent and plausible mechanisms. However additional quantitative experimental validation is still required to build upon the insights which have already been achieved. In this review we discuss emerging as well as state of the art experimental and computational techniques and how they might be used in a mechanical systems biology approach to further our understanding of the mechanisms governing load induced bone adaptation, i.e., ways are outlined in which experimental and computational approaches could be coupled, in a quantitative manner to create more reliable multiscale models of bone.

  9. Amoxicillin in a biological water recovery system

    Energy Technology Data Exchange (ETDEWEB)

    Morse, A.; Jackson, A.; Rainwater, K. [Texas Tech Univ., Water Resources Center, Lubbock, Texas (United States); Pickering, K. [Johnson Space Center, NASA, Houston, Texas (United States)

    2002-06-15

    Pharmaceuticals are new contaminants of concern in the aquatic environment, having been identified in groundwater, surface water, and residential tap water. Possible sources of pharmaceuticals include household wastewaters, runoff from feedlots, or waste discharges from pharmaceutical manufacturing plants. When surface water or groundwater supplies impacted by pharmaceuticals are used in drinking water production, the contaminants may reduce drinking water quality. Many pharmaceuticals, such as amoxicillin, pass through the body largely unmetabolized and directly enter wastewater collection systems. Pharmaceuticals are designed to persist in the body long enough to have the desired therapeutic effect. Therefore, they may also have the ability to persist in the environment (Seiler et al, 1999). The purpose of this work is to determine the overall transformation potential of a candidate pharmaceutical in wastewater treatment with specific emphasis on recycle systems. Amoxicillin is the selected pharmaceutical agent, an orally absorbed broad-spectrum antibiotic with a variety of clinical uses including ear, nose, and throat infections and lower respiratory tract infections. Experiments were conducted using an anaerobic reactor (with NO{sub 3}{sup -} and NO{sub 2}{sup -} as the e{sup -} acceptors) followed by a two-phase nitrifying tubular reactor. Influent composed of water, urine and surfactant was spiked with amoxicillin and fed into the wastewater recycle system. The concentration of amoxicillin in the feed and effluent was quantified using an HPLC. Results from this study include potential for long-term buildup in recycled systems, accumulation of breakdown products and possible transfer of antibiotic resistance to microorganisms in the system effluent. In addition, the results of this study may provide information on contamination potential for communities that are considering supplementing drinking water supplies with recovered wastewater or for entities

  10. Amoxicillin in a biological water recovery system

    International Nuclear Information System (INIS)

    Morse, A.; Jackson, A.; Rainwater, K.; Pickering, K.

    2002-01-01

    Pharmaceuticals are new contaminants of concern in the aquatic environment, having been identified in groundwater, surface water, and residential tap water. Possible sources of pharmaceuticals include household wastewaters, runoff from feedlots, or waste discharges from pharmaceutical manufacturing plants. When surface water or groundwater supplies impacted by pharmaceuticals are used in drinking water production, the contaminants may reduce drinking water quality. Many pharmaceuticals, such as amoxicillin, pass through the body largely unmetabolized and directly enter wastewater collection systems. Pharmaceuticals are designed to persist in the body long enough to have the desired therapeutic effect. Therefore, they may also have the ability to persist in the environment (Seiler et al, 1999). The purpose of this work is to determine the overall transformation potential of a candidate pharmaceutical in wastewater treatment with specific emphasis on recycle systems. Amoxicillin is the selected pharmaceutical agent, an orally absorbed broad-spectrum antibiotic with a variety of clinical uses including ear, nose, and throat infections and lower respiratory tract infections. Experiments were conducted using an anaerobic reactor (with NO 3 - and NO 2 - as the e - acceptors) followed by a two-phase nitrifying tubular reactor. Influent composed of water, urine and surfactant was spiked with amoxicillin and fed into the wastewater recycle system. The concentration of amoxicillin in the feed and effluent was quantified using an HPLC. Results from this study include potential for long-term buildup in recycled systems, accumulation of breakdown products and possible transfer of antibiotic resistance to microorganisms in the system effluent. In addition, the results of this study may provide information on contamination potential for communities that are considering supplementing drinking water supplies with recovered wastewater or for entities considering a closed loop

  11. An Evaluation of Information Consistency in Grid Information Systems

    CERN Document Server

    Field, Laurence

    2016-01-01

    A Grid information system resolves queries that may need to consider all information sources (Grid services), which are widely distributed geographically, in order to enable efficient Grid functions that may utilise multiple cooperating services. Fundamentally this can be achieved by either moving the query to the data (query shipping) or moving the data to the query (data shipping). Existing Grid information system implementations have adopted one of the two approaches. This paper explores the two approaches in further detail by evaluating them to the best possible extent with respect to Grid information system benchmarking metrics. A Grid information system that follows the data shipping approach based on the replication of information that aims to improve the currency for highly-mutable information is presented. An implementation of this, based on an Enterprise Messaging System, is evaluated using the benchmarking method and the consequence of the results for the design of Grid information systems is discu...

  12. Hanford Environmental Information System (HEIS)

    International Nuclear Information System (INIS)

    1994-01-01

    This report discusses the procedures that establish the configuration control processes for the Hanford Environmental Information System (HEIS) software. The procedures also provide the charter and function of the HEIS Configuration Control Board (CCB) for maintaining software. The software configuration control items covered under these procedures include the HEIS software and database structure. The configuration control processes include both administrative and audit functions. The administrative role includes maintaining the overall change schedule, ensuring consistency of proposed changes, negotiating change plan adjustments, setting priorities, and tracking the status of changes. The configuration control process audits to ensure that changes are performed to applicable standards

  13. Power Reactor Information System (PRIS)

    International Nuclear Information System (INIS)

    Spiegelberg, R.

    1992-01-01

    The IAEA has been collecting Operating Experience data for Nuclear Power Plants of the IAEA Member States since 1970. In order to facilitate an analysis of nuclear power plant performance as well as to produce relevant publications, all previously collected data supplied from the questionnaires were computerized in 1980 and the Power Reactor Information System was implemented. PRIS currently contains production records for the years up to and including 1990 and about 98% of the reactors-years operating experience in the world is contained in PRIS. (orig.)

  14. Radionuclide Imaging Technologies for Biological Systems

    Energy Technology Data Exchange (ETDEWEB)

    Howell, Calvin R. [Duke Univ., Durham, NC (United States); Reid, Chantal D. [Duke Univ., Durham, NC (United States); Weisenberger, Andrew G. [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States)

    2014-05-14

    The main objective of this project is to develop technologies and experimental techniques for studying the dynamics of physiological responses of plants to changes in their interface with the local environment and to educate a new generation of scientists in an interdisciplinary environment of biology, physics and engineering. Also an important goal is to perform measurements to demonstrate the new data that can be produced and made available to the plant-biology community using the imaging technologies and experimental techniques developed in this project. The study of the plant-environment interface includes a wide range of topics in plant physiology, e.g., the root-soil interface, resource availability, impact of herbivores, influence of microbes on root surface, and responses to toxins in the air and soil. The initial scientific motivation for our work is to improve understanding of the mechanisms for physiological responses to abrupt changes in the local environment, in particular, the responses that result in short-term adjustments in resource (e.g., sugars, nutrients and water) allocations. Data of time-dependent responses of plants to environmental changes are essential in developing mechanistic models for substance intake and resource allocation. Our approach is to use radioisotope tracing techniques to study whole-plant and plant organ (e.g., leaves, stems, roots) dynamical responses to abrupt changes in environmental conditions such as concentration of CO2 in the atmosphere, nutrient availability and lighting. To this aim we are collaborating with the Radiation Detector and Imaging Group at the Thomas Jefferson National Laboratory Facility (JLab) to develop gamma-ray and beta particle imaging systems optimized for plant studies. The radioisotope tracing measurements are conducted at the Phytotron facility at Duke University. The Phytotron is a controlled environment plant research facility with a variety of plant growth chambers. One chamber

  15. The Co-Creation of Information Systems

    Science.gov (United States)

    Gomillion, David

    2013-01-01

    In information systems development, end-users have shifted in their role: from consumers of information to informants for requirements to developers of systems. This shift in the role of users has also changed how information systems are developed. Instead of systems developers creating specifications for software or end-users creating small…

  16. Systems for the management of pharmacogenomic information.

    Science.gov (United States)

    Sturn, Alexander; Maurer, Michael; Molidor, Robert; Trajanoski, Zlatko

    2005-01-01

    Recent breakthroughs in biological research have been made possible by remarkable advances in high-performance computing and the establishment of a highly sophisticated information technology infrastructure. This chapter gives an overview of the main and most important technologies needed for the management of pharmacogenomic information, namely database management systems and software and hardware architectures. Because pharmacogenomics deals with a great many of public and/or proprietary data, the most prominent ways for easy storage, retrieval, analysis, and exchange are presented. Processing these data requires the use of sophisticated software architectures. Several most recent practices useful for a pharmacogenomic environment are explained. Multitiered application design and web services are discussed and described independent of the major enterprise development platforms. Because life sciences are becoming increasingly quantitative and because state-of-the-art software architectures use many system resources, this chapter presents the most recent and powerful systems for parallel data processing and data storage. Finally, shared and distributed memory systems and combinations of them as well as different storage architectures such as directly attached storage, network-attached storage, and storage-area network are explained in detail.

  17. Systems biology in physiology: the vasopressin signaling network in kidney.

    Science.gov (United States)

    Knepper, Mark A

    2012-12-01

    Over the past 80 years, physiological research has moved progressively in a reductionist direction, providing mechanistic information on a smaller and smaller scale. This trend has culminated in the present focus on "molecular physiology," which deals with the function of single molecules responsible for cellular function. There is a need to assemble the information from the molecular level into models that explain physiological function at cellular, tissue, organ, and whole organism levels. Such integration is the major focus of an approach called "systems biology." The genome sequencing projects provide a basis for a new kind of systems biology called "data-rich" systems biology that is based on large-scale data acquisition methods including protein mass spectrometry, DNA microarrays, and deep sequencing of nucleic acids. These techniques allow investigators to measure thousands of variables simultaneously in response to an external stimulus. My laboratory is applying such an approach to the question: "How does the peptide hormone vasopressin regulate water permeability in the renal collecting duct?" We are using protein mass spectrometry to identify and quantify the phosphoproteome of collecting duct cells. The response to vasopressin, presented in the form of a network model, includes a general downregulation of proline-directed kinases (MAP kinases and cyclin-dependent kinases) and upregulation of basophilic kinases (ACG kinases and calmodulin-dependent kinases). Further progress depends on characterization and localization of candidate protein kinases in these families. The ultimate goal is to use multivariate statistical techniques and differential equations to obtain predictive models describing vasopressin signaling in the renal collecting duct.

  18. The economics of information systems and software

    CERN Document Server

    Veryard, Richard

    2014-01-01

    The Economics of Information Systems and Software focuses on the economic aspects of information systems and software, including advertising, evaluation of information systems, and software maintenance. The book first elaborates on value and values, software business, and scientific information as an economic category. Discussions focus on information products and information services, special economic properties of information, culture and convergence, hardware and software products, materiality and consumption, technological progress, and software flexibility. The text then takes a look at a

  19. Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Nielsen, Jens; Jewett, Michael Christopher

    2008-01-01

    in the industrial application of this yeast. Developments in genomics and high-throughput systems biology tools are enhancing one's ability to rapidly characterize cellular behaviour, which is valuable in the field of metabolic engineering where strain characterization is often the bottleneck in strain development...... programmes. Here, the impact of systems biology on metabolic engineering is reviewed and perspectives on the role of systems biology in the design of cell factories are given....

  20. Interactive analysis of systems biology molecular expression data

    OpenAIRE

    Prabhakar Sunil; Salt David E; Kane Michael D; Stephenson Alan; Ouyang Qi; Zhang Mingwu; Burgner John; Buck Charles; Zhang Xiang

    2008-01-01

    Abstract Background Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular correlations and comparative studies of molecular expression are crucial to establishing interdependent connections in systems biology. The existing software packages provide limited data mining capability. The user must first generate visualization data with a preferr...

  1. Application of integrative genomics and systems biology to conventional and in vitro reproductive traits in cattle

    DEFF Research Database (Denmark)

    Mazzoni, Gianluca; Pedersen, Hanne S.; de Oliveira Junior, Gerson A.

    2017-01-01

    by both conventional and ARTs such as OPU-IVP. The integration of systems biology information across different biological layers generates a complete view of the different molecular networks that control complex traits and can provide a strong contribution to the understanding of traits related to ARTs....

  2. System parameter identification information criteria and algorithms

    CERN Document Server

    Chen, Badong; Hu, Jinchun; Principe, Jose C

    2013-01-01

    Recently, criterion functions based on information theoretic measures (entropy, mutual information, information divergence) have attracted attention and become an emerging area of study in signal processing and system identification domain. This book presents a systematic framework for system identification and information processing, investigating system identification from an information theory point of view. The book is divided into six chapters, which cover the information needed to understand the theory and application of system parameter identification. The authors' research pr

  3. Adapting to Biology: Maintaining Container-Closure System Compatibility with the Therapeutic Biologic Revolution.

    Science.gov (United States)

    Degrazio, Dominick

    Many pharmaceutical companies are transitioning their research and development drug product pipeline from traditional small-molecule injectables to the dimension of evolving therapeutic biologics. Important concerns associated with this changeover are becoming forefront, as challenges develop of varying complexity uncommon with the synthesis and production of traditional drugs. Therefore, alternative measures must be established that aim to preserve the efficacy and functionality of a biologic that might not be implemented for small molecules. Conserving protein stability is relative to perpetuating a net equilibrium of both intrinsic and extrinsic factors. Key to sustaining this balance is the ability of container-closure systems to maintain their compatibility with the ever-changing dynamics of therapeutic biologics. Failure to recognize and adjust the material properties of packaging components to support compatibility with therapeutic biologics can compromise patient safety, drug productivity, and biological stability. This review will examine the differences between small-molecule drugs and therapeutic biologics, lay a basic foundation for understanding the stability of therapeutic biologics, and demonstrate potential sources of container-closure systems' incompatibilities with therapeutic biologics at a mechanistic level. Many pharmaceutical companies are transitioning their research and development drug product pipeline from traditional small-molecule injectables to recombinantly derived therapeutic biologics. Concerns associated with this transformation are becoming prominent, as therapeutic biologics are uncharacteristic to small-molecule drugs. Maintaining the stability of a therapeutic biologic is a combination of balancing intrinsic factors and external elements within the biologic's microenvironment. An important aspect of this balance is relegated to the overall compatibility of primary, parenteral container-closure systems with therapeutic biologics

  4. Seasonal allergic rhinitis and systems biology-oriented biomarker discovery

    NARCIS (Netherlands)

    Baars, E.W.; Nierop, A.F.M.; Savelkoul, H.F.J.

    2015-01-01

    There is an increasing interest in science and medicine in the systems approach. Instead of the reductionist approach that focuses on the physical and chemical properties of the individual components, systems biology aims to describe, understand, and explain from the complex biological systems

  5. Sulfur K-edge absorption spectroscopy on selected biological systems

    International Nuclear Information System (INIS)

    Lichtenberg, Henning

    2008-07-01

    Sulfur is an essential element in organisms. In this thesis investigations of sulfur compounds in selected biological systems by XANES (X-ray Absorption Near Edge Structure) spectroscopy are reported. XANES spectroscopy at the sulfur K-edge provides an excellent tool to gain information about the local environments of sulfur atoms in intact biological samples - no extraction processes are required. Spatially resolved measurements using a Kirkpatrick-Baez mirror focusing system were carried out to investigate the infection of wheat leaves by rust fungi. The results give information about changes in the sulfur metabolism of the host induced by the parasite and about the extension of the infection into visibly uninfected plant tissue. Furthermore, XANES spectra of microbial mats from sulfidic caves were measured. These mats are dominated by microbial groups involved in cycling sulfur. Additionally, the influence of sulfate deprivation and H 2 S exposure on sulfur compounds in onion was investigated. To gain an insight into the thermal degradation of organic material the influence of roasting of sulfur compounds in coffee beans was studied. (orig.)

  6. Breeding system and pollination biology of the semidomesticated ...

    African Journals Online (AJOL)

    Breeding system and pollination biology of the semidomesticated fruit tree, Tamarindus indica L. (Leguminosae: Caesalpinioideae ): Implications for fruit production, selective breeding, and conservation of genetic resources.

  7. A guide to numerical modelling in systems biology

    CERN Document Server

    Deuflhard, Peter

    2015-01-01

    This book is intended for students of computational systems biology with only a limited background in mathematics. Typical books on systems biology merely mention algorithmic approaches, but without offering a deeper understanding. On the other hand, mathematical books are typically unreadable for computational biologists. The authors of the present book have worked hard to fill this gap. The result is not a book on systems biology, but on computational methods in systems biology. This book originated from courses taught by the authors at Freie Universität Berlin. The guiding idea of the courses was to convey those mathematical insights that are indispensable for systems biology, teaching the necessary mathematical prerequisites by means of many illustrative examples and without any theorems. The three chapters cover the mathematical modelling of biochemical and physiological processes, numerical simulation of the dynamics of biological networks, and identification of model parameters by means of comparisons...

  8. 'Information Seeking in Context' and the development of information systems

    Directory of Open Access Journals (Sweden)

    Irina Gaslikova

    1999-01-01

    Full Text Available This paper reports on some findings of the explorations represented at the conference "Information Seeking in Context" (ISIC’98. These findings are investigated with the aim to evaluate their practical usefulness for the design of information computer systems. The paper discusses some common problems connected with the conceptual approaches to the information system development.

  9. Two applications of information extraction to biological science journal articles: enzyme interactions and protein structures.

    Science.gov (United States)

    Humphreys, K; Demetriou, G; Gaizauskas, R

    2000-01-01

    Information extraction technology, as defined and developed through the U.S. DARPA Message Understanding Conferences (MUCs), has proved successful at extracting information primarily from newswire texts and primarily in domains concerned with human activity. In this paper we consider the application of this technology to the extraction of information from scientific journal papers in the area of molecular biology. In particular, we describe how an information extraction system designed to participate in the MUC exercises has been modified for two bioinformatics applications: EMPathIE, concerned with enzyme and metabolic pathways; and PASTA, concerned with protein structure. Progress to date provides convincing grounds for believing that IE techniques will deliver novel and effective ways for scientists to make use of the core literature which defines their disciplines.

  10. Management information systems software evaluation

    International Nuclear Information System (INIS)

    Al-Tunisi, N.; Ghazzawi, A.; Gruyaert, F.; Clarke, D.

    1995-01-01

    In November 1993, Saudi Aramco management endorsed a proposal to coordinate the development of the Management Information Systems (MISs) of four concurrent projects for its facilities Controls Modernization Program. The affected projects were the Ras Tanura Refinery Upgrade Project, the Abqaiq Plant Controls Modernization and the Shedgum and Uthmaniyah Gas plants Control Upgrade Projects. All of these projects had a significant requirement of MISs in their scope. Under the leadership of the Process and Control Systems Department, and MIS Coordination Team was formed with representatives of several departments. An MIS Applications Evaluation procedure was developed based on the Kepner Tregoe Decisions Analysis Process and general questionnaires were sent to over a hundred potential Vendors. The applications were divided into several categories, such as: Data Capture and Historization, Human User Interface, Trending, Reporting, Graphic Displays, Data Reconciliation, Statistical Analysis, Expert Systems, Maintenance Applications, Document Management and Operations Planning and Scheduling. For each of the MIS Application areas, detailed follow-up questionnaires were used to short list the candidate products. In May and June 1994, selected Vendors were invited to Saudi Arabia for an Exhibition which was open to all Saudi Aramco employees. In conjunction with this, the Vendors were subjected to a rigorous product testing exercise by independent teams of testers. The paper will describe the methods used and the lessons learned in this extensive software evaluation phase, which was a first for Saudi Aramco

  11. Management information systems software evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Al-Tunisi, N.; Ghazzawi, A.; Gruyaert, F.; Clarke, D. [Saudi Aramco, Dhahran (Saudi Arabia). Process and Control Systems Dept.

    1995-11-01

    In November 1993, Saudi Aramco management endorsed a proposal to coordinate the development of the Management Information Systems (MISs) of four concurrent projects for its facilities Controls Modernization Program. The affected projects were the Ras Tanura Refinery Upgrade Project, the Abqaiq Plant Controls Modernization and the Shedgum and Uthmaniyah Gas plants Control Upgrade Projects. All of these projects had a significant requirement of MISs in their scope. Under the leadership of the Process and Control Systems Department, and MIS Coordination Team was formed with representatives of several departments. An MIS Applications Evaluation procedure was developed based on the Kepner Tregoe Decisions Analysis Process and general questionnaires were sent to over a hundred potential Vendors. The applications were divided into several categories, such as: Data Capture and Historization, Human User Interface, Trending, Reporting, Graphic Displays, Data Reconciliation, Statistical Analysis, Expert Systems, Maintenance Applications, Document Management and Operations Planning and Scheduling. For each of the MIS Application areas, detailed follow-up questionnaires were used to short list the candidate products. In May and June 1994, selected Vendors were invited to Saudi Arabia for an Exhibition which was open to all Saudi Aramco employees. In conjunction with this, the Vendors were subjected to a rigorous product testing exercise by independent teams of testers. The paper will describe the methods used and the lessons learned in this extensive software evaluation phase, which was a first for Saudi Aramco.

  12. A Magnetic Sensor System for Biological Detection

    KAUST Repository

    Li, Fuquan

    2015-05-01

    Magnetic biosensors detect biological targets through sensing the stray field of magnetic beads which label the targets. Commonly, magnetic biosensors employ the “sandwich” method to immobilize biological targets, i.e., the targets are sandwiched between a bio-functionalized sensor surface and bio-functionalized magnetic beads. This method has been used very successfully in different application, but its execution requires a rather elaborate procedure including several washing and incubation steps. This dissertation investigates a new magnetic biosensor concept, which enables a simple and effective detection of biological targets. The biosensor takes advantage of the size difference between bare magnetic beads and compounds of magnetic beads and biological targets. First, the detection of super-paramagnetic beads via magnetic tunnel junction (MTJ) sensors is implemented. Frequency modulation is used to enhance the signal-to-noise ratio, enabling the detection of a single magnetic bead. Second, the concept of the magnetic biosensor is investigated theoretically. The biosensor consists of an MTJ sensor, which detects the stray field of magnetic beads inside of a trap on top of the MTJ. A microwire between the trap and the MTJ is used to attract magnetic beads to the trapping well by applying a current to it. The MTJ sensor’s output depends on the number of beads inside the trap. If biological targets are in the sample solution, the beads will form bead compounds consisting of beads linked to the biological targets. Since bead compounds are larger than bare beads, the number of beads inside the trapping well will depend on the presence of biological targets. Hence, the output of the MTJ sensor will depend on the biological targets. The dependences of sensor signals on the sizes of the MTJ sensor, magnetic beads and biological targets are studied to find the optimum constellations for the detection of specific biological targets. The optimization is demonstrated

  13. Information in the system of state administration

    OpenAIRE

    Kalytych, G.; Litosh, G.

    2009-01-01

    The article analyses the approaches to the notions of "information", "state administration system", "administrative information". The article considers the importance of of information for the whole state administration system and reveals the criteria which provide the information with administrative status. Special attention is paid to making of administrative decisions on the level of the sate which are based on effective information management.

  14. Unmanned Aircraft Systems complement biologging in spatial ecology studies.

    Science.gov (United States)

    Mulero-Pázmány, Margarita; Barasona, Jose Ángel; Acevedo, Pelayo; Vicente, Joaquín; Negro, Juan José

    2015-11-01

    The knowledge about the spatial ecology and distribution of organisms is important for both basic and applied science. Biologging is one of the most popular methods for obtaining information about spatial distribution of animals, but requires capturing the animals and is often limited by costs and data retrieval. Unmanned Aircraft Systems (UAS) have proven their efficacy for wildlife surveillance and habitat monitoring, but their potential contribution to the prediction of animal distribution patterns and abundance has not been thoroughly evaluated. In this study, we assess the usefulness of UAS overflights to (1) get data to model the distribution of free-ranging cattle for a comparison with results obtained from biologged (GPS-GSM collared) cattle and (2) predict species densities for a comparison with actual density in a protected area. UAS and biologging derived data models provided similar distribution patterns. Predictions from the UAS model overestimated cattle densities, which may be associated with higher aggregated distributions of this species. Overall, while the particular researcher interests and species characteristics will influence the method of choice for each study, we demonstrate here that UAS constitute a noninvasive methodology able to provide accurate spatial data useful for ecological research, wildlife management and rangeland planning.

  15. Public Sector Information Systems (PSIS)

    DEFF Research Database (Denmark)

    Brooks, Laurence; Zinner Henriksen, Helle; Janssen, Marijn

    2014-01-01

    Policies are traditionally developed by experts with limited forms of stakeholder involvement. New technologies can change policy making practice through new methods of citizens’ engagement. As a result, the traditional boundaries between governments and the public are also changing. Policy makers...... face the challenge of advancing their policy-making practices to take advantage of these new developments. Many new tools and instruments are available that can help to improve policy-making, yet little is known about their costs, benefits, or contribution. The objective of this panel is to advance our...... understanding of how research in various disciplines can contribute to new ways of policy-making, in particular the role of information systems. The panelists represent various academic backgrounds and cultures and the audience will be challenged to share their experiences and contribute to the debate....

  16. A conceptual review on systems biology in health and diseases: from biological networks to modern therapeutics

    OpenAIRE

    Somvanshi, Pramod Rajaram; Venkatesh, K. V.

    2013-01-01

    Human physiology is an ensemble of various biological processes spanning from intracellular molecular interactions to the whole body phenotypic response. Systems biology endures to decipher these multi-scale biological networks and bridge the link between genotype to phenotype. The structure and dynamic properties of these networks are responsible for controlling and deciding the phenotypic state of a cell. Several cells and various tissues coordinate together to generate an organ level respo...

  17. A systems biology approach reveals common metastatic pathways in osteosarcoma

    Directory of Open Access Journals (Sweden)

    Flores Ricardo J

    2012-05-01

    Full Text Available Abstract Background Osteosarcoma (OS is the most common malignant bone tumor in children and adolescents. The survival rate of patients with metastatic disease remains very dismal. Nevertheless, metastasis is a complex process and a single-level analysis is not likely to identify its key biological determinants. In this study, we used a systems biology approach to identify common metastatic pathways that are jointly supported by both mRNA and protein expression data in two distinct human metastatic OS models. Results mRNA expression microarray and N-linked glycoproteomic analyses were performed on two commonly used isogenic pairs of human metastatic OS cell lines, namely HOS/143B and SaOS-2/LM7. Pathway analysis of the differentially regulated genes and glycoproteins separately revealed pathways associated to metastasis including cell cycle regulation, immune response, and epithelial-to-mesenchymal-transition. However, no common significant pathway was found at both genomic and proteomic levels between the two metastatic models, suggesting a very different biological nature of the cell lines. To address this issue, we used a topological significance analysis based on a “shortest-path” algorithm to identify topological nodes, which uncovered additional biological information with respect to the genomic and glycoproteomic profiles but remained hidden from the direct analyses. Pathway analysis of the significant topological nodes revealed a striking concordance between the models and identified significant common pathways, including “Cytoskeleton remodeling/TGF/WNT”, “Cytoskeleton remodeling/Cytoskeleton remodeling”, and “Cell adhesion/Chemokines and adhesion”. Of these, the “Cytoskeleton remodeling/TGF/WNT” was the top ranked common pathway from the topological analysis of the genomic and proteomic profiles in the two metastatic models. The up-regulation of proteins in the “Cytoskeleton remodeling/TGF/WNT” pathway in the Sa

  18. Information Systems Coordinate Emergency Management

    Science.gov (United States)

    2012-01-01

    -changing planet. This information can be captured, analyzed, and visualized by geographic information systems (GIS) to produce maps, charts, and other tools that can reveal information essential to a wide variety of applications including emergency management. Knowing precise, real-time information about the size, location, environmental conditions, and resulting damage of an event like a flood or wildfire as well as the location and numbers of emergency responders and other resources contributes directly to the effectiveness of disaster mitigation. The need for such information is also evident when responding to homeland security threats, such as a terrorist attack. Recognizing the value of its geospatial information resources for this and other purposes, in 1998 Stennis and the state of Mississippi partnered to form what became the Enterprise for Innovative Geospatial Solutions (EIGS) industry cluster, supporting the growth of remote sensing and GIS-based research and business. As part of EIGS, several companies partnered with NASA through dual use and Small Business Innovation Research (SBIR) contracts. Among those was NVision.

  19. A review of imaging techniques for systems biology

    Directory of Open Access Journals (Sweden)

    Po Ming J

    2008-08-01

    Full Text Available Abstract This paper presents a review of imaging techniques and of their utility in system biology. During the last decade systems biology has matured into a distinct field and imaging has been increasingly used to enable the interplay of experimental and theoretical biology. In this review, we describe and compare the roles of microscopy, ultrasound, CT (Computed Tomography, MRI (Magnetic Resonance Imaging, PET (Positron Emission Tomography, and molecular probes such as quantum dots and nanoshells in systems biology. As a unified application area among these different imaging techniques, examples in cancer targeting are highlighted.

  20. Automated information retrieval system for radioactivation analysis

    International Nuclear Information System (INIS)

    Lambrev, V.G.; Bochkov, P.E.; Gorokhov, S.A.; Nekrasov, V.V.; Tolstikova, L.I.

    1981-01-01

    An automated information retrieval system for radioactivation analysis has been developed. An ES-1022 computer and a problem-oriented software ''The description information search system'' were used for the purpose. Main aspects and sources of forming the system information fund, characteristics of the information retrieval language of the system are reported and examples of question-answer dialogue are given. Two modes can be used: selective information distribution and retrospective search [ru

  1. The Intelligent Technologies of Electronic Information System

    Science.gov (United States)

    Li, Xianyu

    2017-08-01

    Based upon the synopsis of system intelligence and information services, this paper puts forward the attributes and the logic structure of information service, sets forth intelligent technology framework of electronic information system, and presents a series of measures, such as optimizing business information flow, advancing data decision capability, improving information fusion precision, strengthening deep learning application and enhancing prognostic and health management, and demonstrates system operation effectiveness. This will benefit the enhancement of system intelligence.

  2. Morphogenesis and pattern formation in biological systems experiments and models

    CERN Document Server

    Noji, Sumihare; Ueno, Naoto; Maini, Philip

    2003-01-01

    A central goal of current biology is to decode the mechanisms that underlie the processes of morphogenesis and pattern formation. Concerned with the analysis of those phenomena, this book covers a broad range of research fields, including developmental biology, molecular biology, plant morphogenesis, ecology, epidemiology, medicine, paleontology, evolutionary biology, mathematical biology, and computational biology. In Morphogenesis and Pattern Formation in Biological Systems: Experiments and Models, experimental and theoretical aspects of biology are integrated for the construction and investigation of models of complex processes. This collection of articles on the latest advances by leading researchers not only brings together work from a wide spectrum of disciplines, but also provides a stepping-stone to the creation of new areas of discovery.

  3. Biological oceanography of the red oceanic system

    Science.gov (United States)

    Theil, Hjalmar; Weikert, Horst

    1. In 1977, 1979 and 1980-81, investigations were carried out which aimed at evaluating the potential risks from mining metalliferous muds precipating in the Atlantis II Deep of the central Red Sea. This environmental research was initiated by the Saudi Sudanese Red Sea Joint Commission in order to avoid any danger for the Red Sea ecosystem. The broad environmental research programme coherent studies in physical, chemical, biological, and geological oceanography as well as toxicological investigations in the oceanic and in reef zones. We summarise the results from our biological fiels studies in the open sea. 2. The biological investigations were concentrated on the area of the Atlantis II Deep. Benthos was sampled between 700-2000m. For comparison a few samples were also taken further north in the central Red Sea, and to east and west along the flanking deep terraces (500-1000m). Plankton studies covered the total water column above the Deep, and were extended along the axial through to north and south. 3. Benthos sampling was carried out using a heavy closing trawl, a large box grab (box size 50 × 50 cm), Van Veen grabs and traps; photographic surveys were made a phototrap and a photosled. Community respiration was measured with a ship-board method using grab subsamples. Nutrient concentrations, seston and phytoplankton standing stocks as well as in situ primary production were determined from hydrocast samples. Data on zooplankton and micronekton composition and standing stock were obtained from samples collected using different multiple opening-and-closing nets equipped with 100 μm, 300 μm, and 1000 μm mesh sizes. Daily and ontogenetical vertical migration patterns were studied by comparisons of data from midday and midnight tows. 4. Throughout the whole area the sediment is a pteropod ooze containing low contentrations of organic matter; measured organic carbon and nitrogen contents were 0.5 and 0.05% respectively, and chloroplastic pigment equivalents

  4. Programming Morphogenesis through Systems and Synthetic Biology.

    Science.gov (United States)

    Velazquez, Jeremy J; Su, Emily; Cahan, Patrick; Ebrahimkhani, Mo R

    2018-04-01

    Mammalian tissue development is an intricate, spatiotemporal process of self-organization that emerges from gene regulatory networks of differentiating stem cells. A major goal in stem cell biology is to gain a sufficient understanding of gene regulatory networks and cell-cell interactions to enable the reliable and robust engineering of morphogenesis. Here, we review advances in synthetic biology, single cell genomics, and multiscale modeling, which, when synthesized, provide a framework to achieve the ambitious goal of programming morphogenesis in complex tissues and organoids. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Reservoir Model Information System: REMIS

    Science.gov (United States)

    Lee, Sang Yun; Lee, Kwang-Wu; Rhee, Taehyun; Neumann, Ulrich

    2009-01-01

    We describe a novel data visualization framework named Reservoir Model Information System (REMIS) for the display of complex and multi-dimensional data sets in oil reservoirs. It is aimed at facilitating visual exploration and analysis of data sets as well as user collaboration in an easier way. Our framework consists of two main modules: the data access point module and the data visualization module. For the data access point module, the Phrase-Driven Grammar System (PDGS) is adopted for helping users facilitate the visualization of data. It integrates data source applications and external visualization tools and allows users to formulate data query and visualization descriptions by selecting graphical icons in a menu or on a map with step-by-step visual guidance. For the data visualization module, we implemented our first prototype of an interactive volume viewer named REMVR to classify and to visualize geo-spatial specific data sets. By combining PDGS and REMVR, REMIS assists users better in describing visualizations and exploring data so that they can easily find desired data and explore interesting or meaningful relationships including trends and exceptions in oil reservoir model data.

  6. Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites

    DEFF Research Database (Denmark)

    Hwang, Kyu-Sang; Kim, Hyun Uk; Charusanti, Pep

    2014-01-01

    have been more systematized with high-throughput techniques through inspections of correlations among components of the primary and secondary metabolisms at the genome scale. Moreover, up-to-date information on the genome of Streptomyces species with emphasis on their secondary metabolism has been...... collected in the form of databases and knowledgebases, providing predictive information and enabling one to explore experimentally unrecognized biological spaces of secondary metabolism. Herein, we review recent trends in the systems biology and biotechnology of Streptomyces species....

  7. INFORMATION SYSTEM SECURITY (CYBER SECURITY

    Directory of Open Access Journals (Sweden)

    Muhammad Siddique Ansari

    2016-03-01

    Full Text Available Abstract - Business Organizations and Government unequivocally relies on upon data to deal with their business operations. The most unfavorable impact on association is disappointment of friendship, goodness, trustworthiness, legitimacy and probability of data and administrations. There is an approach to ensure data and to deal with the IT framework's Security inside association. Each time the new innovation is made, it presents some new difficulties for the insurance of information and data. To secure the information and data in association is imperative on the grounds that association nowadays inside and remotely joined with systems of IT frameworks. IT structures are inclined to dissatisfaction and security infringement because of slips and vulnerabilities. These slips and vulnerabilities can be brought on by different variables, for example, quickly creating headway, human slip, poor key particulars, poor movement schedules or censuring the threat. Likewise, framework changes, new deserts and new strikes are a huge piece of the time displayed, which helpers augmented vulnerabilities, disappointments and security infringement all through the IT structure life cycle. The business went to the confirmation that it is essentially difficult to ensure a slip free, risk free and secure IT structure in perspective of the disfigurement of the disavowing security parts, human pass or oversight, and part or supplies frustration. Totally secure IT frameworks don't exist; just those in which the holders may have changing degrees of certainty that security needs of a framework are fulfilled do. The key viewpoints identified with security of data outlining are examined in this paper. From the start, the paper recommends pertinent legitimate structure and their duties including open association obligation, and afterward it returns to present and future time, system limits, structure security in business division. At long last, two key inadequacy markers

  8. 28 CFR 25.3 - System information.

    Science.gov (United States)

    2010-07-01

    ... 28 Judicial Administration 1 2010-07-01 2010-07-01 false System information. 25.3 Section 25.3 Judicial Administration DEPARTMENT OF JUSTICE DEPARTMENT OF JUSTICE INFORMATION SYSTEMS The National Instant Criminal Background Check System § 25.3 System information. (a) There is established at the FBI a...

  9. A system for managing information at ATLAS

    International Nuclear Information System (INIS)

    Tilbrook, I.R.

    1993-01-01

    In response to a need for better management of maintenance and document information at the Argonne Tandem-Linear Accelerating System (ATLAS), the ATLAS Information Management System (AIMS) has been created. The system is based on the relational database model. The system's applications use the Alpha-4 relational database management system, a commercially available software package. The system's function and design are described

  10. How Information Literate Are Junior and Senior Class Biology Students?

    Science.gov (United States)

    Schiffl, Iris

    2018-03-01

    Information literacy—i.e. obtaining, evaluating and using information—is a key element of scientific literacy. However, students are frequently equipped with poor information literacy skills—even at university level—as information literacy is often not explicitly taught in schools. Little is known about students' information skills in science at junior and senior class level, and about teachers' competences in dealing with information literacy in science class. This study examines the information literacy of Austrian 8th, 10th and 12th grade students. Information literacy is important for science education in Austria, because it is listed as a basic competence in Austria's science standards. Two different aspects of information literacy are examined: obtaining information and extracting information from texts. An additional research focus of this study is teachers' competences in diagnosing information skills. The results reveal that students mostly rely on online sources for obtaining information. However, they also use books and consult with people they trust. The younger the students, the more they rely on personal sources. Students' abilities to evaluate sources are poor, especially among younger students. Although teachers claim to use information research in class, their ability to assess their students' information competences is limited.

  11. Network science of biological systems at different scales: A review

    Science.gov (United States)

    Gosak, Marko; Markovič, Rene; Dolenšek, Jurij; Slak Rupnik, Marjan; Marhl, Marko; Stožer, Andraž; Perc, Matjaž

    2018-03-01

    Network science is today established as a backbone for description of structure and function of various physical, chemical, biological, technological, and social systems. Here we review recent advances in the study of complex biological systems that were inspired and enabled by methods of network science. First, we present

  12. Designing an oil spill information management system

    Energy Technology Data Exchange (ETDEWEB)

    Douligeris, C.; Collins, J.; Iakovou, E.; Sun, P.; Riggs, K.R. [Univ. of Miami, Coral Gables, FL (United States)

    1995-12-31

    This paper presents the architectural design of OSIMS, an Oil Spill Information Management System, which is an integrated information management tool that consists of an object-relational database management system, an adaptive decision support system, an advanced visualization system (AVS) and a geographic information system (GIS). OSIMS will handle large and diverse databases of environmental, ecological, geographical, engineering, and regulatory information and will be used for risk analysis and contingency planning.

  13. Optical Biosensors to Explore Biological Systems

    DEFF Research Database (Denmark)

    Palanco, Marta Espina; Mogensen, Klaus Bo; Andersen, Nils H. Skovgaard

    2016-01-01

    protein may be used as an efficient sensor in an organic environment via a biomimetic membrane model. The combination of both biomimetic membranes and protein membranes as a signal transduction medium has interesting applications in biology and medicine. It is crucial that the matrix where a protein...

  14. A Systems Approach to Biology (SAB).

    Science.gov (United States)

    Bush, Kenneth H.; And Others

    This pupil's study guide is intended to be used with audio-taped biology modules. Each of the units (on laboratory techniques, plant and animal diversity, chemistry, cells, energy, microbiology, genetics, and development) contains an abstract providing an overview of the unit, the rationale and performance objectives for each module, questions to…

  15. Systems Biology, Neuroimaging, Neuropsychology, Neuroconnectivity and Traumatic Brain Injury.

    Science.gov (United States)

    Bigler, Erin D

    2016-01-01

    The patient who sustains a traumatic brain injury (TBI) typically undergoes neuroimaging studies, usually in the form of computed tomography (CT) and magnetic resonance imaging (MRI). In most cases the neuroimaging findings are clinically assessed with descriptive statements that provide qualitative information about the presence/absence of visually identifiable abnormalities; though little if any of the potential information in a scan is analyzed in any quantitative manner, except in research settings. Fortunately, major advances have been made, especially during the last decade, in regards to image quantification techniques, especially those that involve automated image analysis methods. This review argues that a systems biology approach to understanding quantitative neuroimaging findings in TBI provides an appropriate framework for better utilizing the information derived from quantitative neuroimaging and its relation with neuropsychological outcome. Different image analysis methods are reviewed in an attempt to integrate quantitative neuroimaging methods with neuropsychological outcome measures and to illustrate how different neuroimaging techniques tap different aspects of TBI-related neuropathology. Likewise, how different neuropathologies may relate to neuropsychological outcome is explored by examining how damage influences brain connectivity and neural networks. Emphasis is placed on the dynamic changes that occur following TBI and how best to capture those pathologies via different neuroimaging methods. However, traditional clinical neuropsychological techniques are not well suited for interpretation based on contemporary and advanced neuroimaging methods and network analyses. Significant improvements need to be made in the cognitive and behavioral assessment of the brain injured individual to better interface with advances in neuroimaging-based network analyses. By viewing both neuroimaging and neuropsychological processes within a systems biology

  16. Yeast systems biology to unravel the network of life

    DEFF Research Database (Denmark)

    Mustacchi, Roberta; Hohmann, S; Nielsen, Jens

    2006-01-01

    Systems biology focuses on obtaining a quantitative description of complete biological systems, even complete cellular function. In this way, it will be possible to perform computer-guided design of novel drugs, advanced therapies for treatment of complex diseases, and to perform in silico design....... Furthermore, it serves as an industrial workhorse for production of a wide range of chemicals and pharmaceuticals. Systems biology involves the combination of novel experimental techniques from different disciplines as well as functional genomics, bioinformatics and mathematical modelling, and hence no single...... laboratory has access to all the necessary competences. For this reason the Yeast Systems Biology Network (YSBN) has been established. YSBN will coordinate research efforts, in yeast systems biology and, through the recently obtained EU funding for a Coordination Action, it will be possible to set...

  17. Tracing organizing principles: Learning from the history of systems biology

    DEFF Research Database (Denmark)

    Green, Sara; Wolkenhauer, Olaf

    2014-01-01

    With the emergence of systems biology, the identification of organizing principles is being highlighted as a key research aim. Researchers attempt to “reverse engineer” the functional organization of biological systems using methodologies from mathematics, engineering and computer science while...... taking advantage of data produced by new experimental techniques. While systems biology is a relatively new approach, the quest for general principles of biological organization dates back to systems theoretic approaches in early and mid-twentieth century. The aim of this paper is to draw...... on this historical background in order to increase the understanding of the motivation behind the search for general principles and to clarify different epistemic aims within systems biology. We pinpoint key aspects of earlier approaches that also underlie the current practice. These are i) the focus on relational...

  18. Modeling and simulation of biological systems using SPICE language

    Science.gov (United States)

    Lallement, Christophe; Haiech, Jacques

    2017-01-01

    The article deals with BB-SPICE (SPICE for Biochemical and Biological Systems), an extension of the famous Simulation Program with Integrated Circuit Emphasis (SPICE). BB-SPICE environment is composed of three modules: a new textual and compact description formalism for biological systems, a converter that handles this description and generates the SPICE netlist of the equivalent electronic circuit and NGSPICE which is an open-source SPICE simulator. In addition, the environment provides back and forth interfaces with SBML (System Biology Markup Language), a very common description language used in systems biology. BB-SPICE has been developed in order to bridge the gap between the simulation of biological systems on the one hand and electronics circuits on the other hand. Thus, it is suitable for applications at the interface between both domains, such as development of design tools for synthetic biology and for the virtual prototyping of biosensors and lab-on-chip. Simulation results obtained with BB-SPICE and COPASI (an open-source software used for the simulation of biochemical systems) have been compared on a benchmark of models commonly used in systems biology. Results are in accordance from a quantitative viewpoint but BB-SPICE outclasses COPASI by 1 to 3 orders of magnitude regarding the computation time. Moreover, as our software is based on NGSPICE, it could take profit of incoming updates such as the GPU implementation, of the coupling with powerful analysis and verification tools or of the integration in design automation tools (synthetic biology). PMID:28787027

  19. Systems biology for molecular life sciences and its impact in biomedicine.

    Science.gov (United States)

    Medina, Miguel Ángel

    2013-03-01

    Modern systems biology is already contributing to a radical transformation of molecular life sciences and biomedicine, and it is expected to have a real impact in the clinical setting in the next years. In this review, the emergence of systems biology is contextualized with a historic overview, and its present state is depicted. The present and expected future contribution of systems biology to the development of molecular medicine is underscored. Concerning the present situation, this review includes a reflection on the "inflation" of biological data and the urgent need for tools and procedures to make hidden information emerge. Descriptions of the impact of networks and models and the available resources and tools for applying them in systems biology approaches to molecular medicine are provided as well. The actual current impact of systems biology in molecular medicine is illustrated, reviewing two cases, namely, those of systems pharmacology and cancer systems biology. Finally, some of the expected contributions of systems biology to the immediate future of molecular medicine are commented.

  20. Nature's longest threads new frontiers in the mathematics and physics of information in biology

    CERN Document Server

    Sreekantan, B V

    2014-01-01

    Organisms endowed with life show a sense of awareness, interacting with and learning from the universe in and around them. Each level of interaction involves transfer of information of various kinds, and at different levels. Each thread of information is interlinked with the other, and woven together, these constitute the universe — both the internal self and the external world — as we perceive it. They are, figuratively speaking, Nature's longest threads. This volume reports inter-disciplinary research and views on information and its transfer at different levels of organization by reputed scientists working on the frontier areas of science. It is a frontier where physics, mathematics and biology merge seamlessly, binding together specialized streams such as quantum mechanics, dynamical systems theory, and mathematics. The topics would interest a broad cross-section of researchers in life sciences, physics, cognition, neuroscience, mathematics and computer science, as well as interested amateurs, familia...

  1. [From bioinformatics to systems biology: account of the 12th international conference on intelligent systems in molecular biology].

    Science.gov (United States)

    Ivakhno, S S

    2004-01-01

    The paper reviews the 12th International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004 that was held in Glasgow, UK, during July 31-August 4. A number of talks, papers and software demos from the conference in bioinformatics, genomics, proteomics, transcriptomics and systems biology are described. Recent applications of liquid chromatography - tandem mass spectrometry, comparative genomics and DNA microarrays are given along with the discussion of bioinformatics curricular in higher education.

  2. Partitioning of genomic variance using prior biological information

    DEFF Research Database (Denmark)

    Edwards, Stefan McKinnon; Janss, Luc; Madsen, Per

    of single nucleotide polymorphism (SNP) data and trait phenotypes and can account for a much larger fraction of the heritable component of the trait. A disadvantage is that this “black box” modelling approach does not provide any insight into the biological mechanisms underlying the trait. We propose...

  3. Network biology: Describing biological systems by complex networks. Comment on "Network science of biological systems at different scales: A review" by M. Gosak et al.

    Science.gov (United States)

    Jalili, Mahdi

    2018-03-01

    I enjoyed reading Gosak et al. review on analysing biological systems from network science perspective [1]. Network science, first started within Physics community, is now a mature multidisciplinary field of science with many applications ranging from Ecology to biology, medicine, social sciences, engineering and computer science. Gosak et al. discussed how biological systems can be modelled and described by complex network theory which is an important application of network science. Although there has been considerable progress in network biology over the past two decades, this is just the beginning and network science has a great deal to offer to biology and medical sciences.

  4. Sandy Hook Traveler Information System

    Science.gov (United States)

    2010-09-01

    This report focuses on equipment and procedural solutions for gathering and disseminating a wide range of visitor information, including real-time traveler information data relating to traffic and parking at the Sandy Hook Unit of the Gateway Recreat...

  5. Tensegrity I. Cell structure and hierarchical systems biology

    Science.gov (United States)

    Ingber, Donald E.

    2003-01-01

    In 1993, a Commentary in this journal described how a simple mechanical model of cell structure based on tensegrity architecture can help to explain how cell shape, movement and cytoskeletal mechanics are controlled, as well as how cells sense and respond to mechanical forces (J. Cell Sci. 104, 613-627). The cellular tensegrity model can now be revisited and placed in context of new advances in our understanding of cell structure, biological networks and mechanoregulation that have been made over the past decade. Recent work provides strong evidence to support the use of tensegrity by cells, and mathematical formulations of the model predict many aspects of cell behavior. In addition, development of the tensegrity theory and its translation into mathematical terms are beginning to allow us to define the relationship between mechanics and biochemistry at the molecular level and to attack the larger problem of biological complexity. Part I of this two-part article covers the evidence for cellular tensegrity at the molecular level and describes how this building system may provide a structural basis for the hierarchical organization of living systems--from molecule to organism. Part II, which focuses on how these structural networks influence information processing networks, appears in the next issue.

  6. Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering

    NARCIS (Netherlands)

    He, F.; Murabito, E.; Westerhoff, H.V.

    2016-01-01

    Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out throughin silicotheoretical studies with the aim to guide and complement furtherin vitroandin vivoexperimental

  7. Biological Detection System Technologies Technology and Industrial Base Study. A Primer on Biological Detection Technologies

    National Research Council Canada - National Science Library

    2001-01-01

    .... and Canadian military personnel. In light of these concerns both defense departments have increased efforts to develop and field biological agent detection systems to help protect their military forces and fixed assets...

  8. Towards an Integrated Laboratory Information System

    OpenAIRE

    Boyarsky, M. William; Schneider, Dale E.; Lindbloom, Hali; Pickett, Michael P.; Schneider, Kenneth A.; Stead, William W.

    1989-01-01

    A pilot workstation in a project to integrate Laboratory Information System (LIS) function into an existing Hospital Information System is presented. The goal is to distribute local function while maintaining an integrated central database.

  9. Scaling for Dynamical Systems in Biology.

    Science.gov (United States)

    Ledder, Glenn

    2017-11-01

    Asymptotic methods can greatly simplify the analysis of all but the simplest mathematical models and should therefore be commonplace in such biological areas as ecology and epidemiology. One essential difficulty that limits their use is that they can only be applied to a suitably scaled dimensionless version of the original dimensional model. Many books discuss nondimensionalization, but with little attention given to the problem of choosing the right scales and dimensionless parameters. In this paper, we illustrate the value of using asymptotics on a properly scaled dimensionless model, develop a set of guidelines that can be used to make good scaling choices, and offer advice for teaching these topics in differential equations or mathematical biology courses.

  10. Magnetic biosensor system to detect biological targets

    KAUST Repository

    Li, Fuquan

    2012-09-01

    Magneto-resistive sensors in combination with magnetic beads provide sensing platforms, which are small in size and highly sensitive. These platforms can be fully integrated with microchannels and electronics to enable devices capable of performing complex tasks. Commonly, a sandwich method is used that requires a specific coating of the sensor\\'s surface to immobilize magnetic beads and biological targets on top of the sensor. This paper concerns a micro device to detect biological targets using magnetic concentration, magnetic as well as mechanical trapping and magnetic sensing. Target detection is based on the size difference between bare magnetic beads and magnetic beads with targets attached. This method remedies the need for a coating layer and reduces the number of steps required to run an experiment. © 2012 IEEE.

  11. Information management system for KNGR

    Energy Technology Data Exchange (ETDEWEB)

    Moon, Chankook; Yoo, Keunbae; Lee, Jinkie [Korea Electric Power Corporation, Seoul (Korea, Republic of); Park, Jaemoon [Korea Power Engineering Co., Inc., Daejeon (Korea, Republic of)

    1996-04-15

    Information management system(IMS) is under development by Korea Electric Power COrporation(KEPCO) joined with KOrea Power Engineering Company(KOPEC) since early 1993 in accordance with Korean Next Generation Reactor(KNGR) project schedule, which is divided into three phases: Phase I(1993-1994), Phase II(1995-Feb.1998), Phase III(1998-2001). Necessity of creating IMS comes from two main purposes: one is from client requirement as described on Electric Power Research Institute(EPRI) Utility Requirement Document(URD) top-tier, the other is from supplier's need to improve productivity whatever it is motivated by management or working group. To satisfy both consumer's and producer's requirements we have set up goals of IMS, to provide configuration management based on network and reliable integrated data base through KNGR's life cycle: i.e.,chronologically, siting, designing, construction, operation and maintenance, and decommissioning. This paper will show what we have done to make the concept during Phase I, and what is a current problem and what will be done through Phase II and III.

  12. Expert Systems and Intelligent Information Retrieval.

    Science.gov (United States)

    Brooks, H. M.

    1987-01-01

    Explores what an intelligent information retrieval system involves and why expert system techniques might interest system designers. Expert systems research is reviewed with emphasis on components, architecture, and computer interaction, and it is concluded that information retrieval is not an ideal problem domain for expert system application at…

  13. Synthetic Biology: Engineering Living Systems from Biophysical Principles.

    Science.gov (United States)

    Bartley, Bryan A; Kim, Kyung; Medley, J Kyle; Sauro, Herbert M

    2017-03-28

    Synthetic biology was founded as a biophysical discipline that sought explanations for the origins of life from chemical and physical first principles. Modern synthetic biology has been reinvented as an engineering discipline to design new organisms as well as to better understand fundamental biological mechanisms. However, success is still largely limited to the laboratory and transformative applications of synthetic biology are still in their infancy. Here, we review six principles of living systems and how they compare and contrast with engineered systems. We cite specific examples from the synthetic biology literature that illustrate these principles and speculate on their implications for further study. To fully realize the promise of synthetic biology, we must be aware of life's unique properties. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  14. Program Information System Auditing Theoritical Approach

    Directory of Open Access Journals (Sweden)

    Ahmadi Aidi

    2015-08-01

    Full Text Available Efficient information systems when using fewer resources or minimal in achieving organizational goals are expected. Effective information system capable of completing the organizations objectives. Audit information systems necessary to know the needs of users whether it is in line with the preparation of the decision-making process

  15. Biologi Komunikasi melalui Implementasi “Information Communications Technology”

    OpenAIRE

    Darmawan, Deni

    2010-01-01

    The Biological communication Behavior has been constructed through the explanation of  the phenomena of their specific part of activies encompassing: Prefrontal, Frontal, Parietal, Central, Occipital and Parasagital which have been significantly tested in terms of their impacts in learning acceleration starting from Elementary School to College level. This study is conducted by means of constructive approach, meaning that it employs both the Quantitative and Qualitative techniques.The study o...

  16. Using directed information for influence discovery in interconnected dynamical systems

    Science.gov (United States)

    Rao, Arvind; Hero, Alfred O.; States, David J.; Engel, James Douglas

    2008-08-01

    Structure discovery in non-linear dynamical systems is an important and challenging problem that arises in various applications such as computational neuroscience, econometrics, and biological network discovery. Each of these systems have multiple interacting variables and the key problem is the inference of the underlying structure of the systems (which variables are connected to which others) based on the output observations (such as multiple time trajectories of the variables). Since such applications demand the inference of directed relationships among variables in these non-linear systems, current methods that have a linear assumption on structure or yield undirected variable dependencies are insufficient. Hence, in this work, we present a methodology for structure discovery using an information-theoretic metric called directed time information (DTI). Using both synthetic dynamical systems as well as true biological datasets (kidney development and T-cell data), we demonstrate the utility of DTI in such problems.

  17. A systems biology approach to study systemic inflammation.

    Science.gov (United States)

    Chen, Bor-Sen; Wu, Chia-Chou

    2014-01-01

    Systemic inflammation needs a precise control on the sequence and magnitude of occurring events. The high throughput data on the host-pathogen interactions gives us an opportunity to have a glimpse on the systemic inflammation. In this article, a dynamic Candida albicans-zebrafish interactive infectious network is built as an example to demonstrate how systems biology approach can be used to study systematic inflammation. In particular, based on microarray data of C. albicans and zebrafish during infection, the hyphal growth, zebrafish, and host-pathogen intercellular PPI networks were combined to form an integrated infectious PPI network that helps us understand the systematic mechanisms underlying the pathogenicity of C. albicans and the immune response of the host. The signaling pathways for morphogenesis and hyphal growth of C. albicans were 2 significant interactions found in the intercellular PPI network. Two cellular networks were also developed corresponding to the different infection stages (adhesion and invasion), and then compared with each other to identify proteins to gain more insight into the pathogenic role of hyphal development in the C. albicans infection process. Important defense-related proteins in zebrafish were predicted using the same approach. This integrated network consisting of intercellular invasion and cellular defense processes during infection can improve medical therapies and facilitate development of new antifungal drugs.

  18. Reverse allostasis in biological systems: Minimal conditions and implications.

    Science.gov (United States)

    Rezaei-Ghaleh, Nasrollah; Bakhtiari, Davood; Rashidi, Armin

    2017-08-07

    Biological control systems regulate the behavior of biological systems in a constantly changing environment. Homeostasis is the most widely studied outcome of biological control systems. Homeostatic systems maintain the system in its desired state despite variations in system parameters or the externally-determined input rates of their constituents, i.e. they have zero or near zero steady state error. On the other hand, allostatic systems are not resistant against environmental changes and the steady state level of their controlled variables responds positively to the changes in their input rates. Little is known, however, on the existence and frequency of reverse allostatic systems, where the steady state value of the controlled variable correlates negatively with the input rate of that variable. In the present study, we derive the minimal conditions for the existence and local stability of reverse allostatic systems, and demonstrate in examples of metabolic, pharmacological, pathophysiological and ecological systems that the reverse allostasis requirements are relatively non-stringent and may be satisfied in biological systems more commonly than usually thought. The possible existence of reverse allostatic systems in nature and their counter-intuitive implications in physiological systems, drug treatment, ecosystem management, and biological control are explored and testable predictions are made. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Behaviors of tritium in terrestrial biological system

    International Nuclear Information System (INIS)

    Inomata, Tsuyako

    1983-01-01

    The in vivo behaviors of HTO- 3 H in food chain models in experimental animals were described. Of pregnant mice that had ingested HTO and drinking water alone for 19 days, the total 3 H content in the tissue/wet weight was greater by 20% in fetuses and newborns than in mothers, and the proportion of tissue-bound 3 H was 8-24% in mothers and 3% in fetuses. The mean 3 H concentration in the free water in tissues was about 36% of ingested HTO. When only 3 H foods were ingested for 18 days, the total 3 H content in the tissue/wet weight showed no marked difference among the mother, fetuses and newborns, nor did the bound 3 H level show great differences. With respect to the tissue distribution of 3 H, only the incorporation rate by the mother's brain from HTO was satisfactory, whereas in other organs, the mother, fetuses and newborns showed higher incorporation rates from 3 H foods. The ratio of specific radioactivity of soft tissue 3 H in mothers to HTO in drinking water exceeded 1 only for the spleen, but other tissues showed no biological concentration. Again, no biological concentration was observed with 3 H foods. Environmental HTO did not result in biological concentration of 3 H in mother mice that had ingested 3 H foods, but 3 H was rather diluted. Tissues other than the spleen showed similar values of 3 H ingestion from environmental HTO through all routes. However, the proportion of bound 3 H in the total 3 H in the soft tissue was about 1.4-1.6 times that on ingestion of HTO alone. (Chiba, N.)

  20. Overview of BioCreAtIvE: critical assessment of information extraction for biology

    Directory of Open Access Journals (Sweden)

    Hirschman Lynette

    2005-05-01

    Full Text Available Abstract Background The goal of the first BioCreAtIvE challenge (Critical Assessment of Information Extraction in Biology was to provide a set of common evaluation tasks to assess the state of the art for text mining applied to biological problems. The results were presented in a workshop held in Granada, Spain March 28–31, 2004. The articles collected in this BMC Bioinformatics supplement entitled "A critical assessment of text mining methods in molecular biology" describe the BioCreAtIvE tasks, systems, results and their independent evaluation. Results BioCreAtIvE focused on two tasks. The first dealt with extraction of gene or protein names from text, and their mapping into standardized gene identifiers for three model organism databases (fly, mouse, yeast. The second task addressed issues of functional annotation, requiring systems to identify specific text passages that supported Gene Ontology annotations for specific proteins, given full text articles. Conclusion The first BioCreAtIvE assessment achieved a high level of international participation (27 groups from 10 countries. The assessment provided state-of-the-art performance results for a basic task (gene name finding and normalization, where the best systems achieved a balanced 80% precision / recall or better, which potentially makes them suitable for real applications in biology. The results for the advanced task (functional annotation from free text were significantly lower, demonstrating the current limitations of text-mining approaches where knowledge extrapolation and interpretation are required. In addition, an important contribution of BioCreAtIvE has been the creation and release of training and test data sets for both tasks. There are 22 articles in this special issue, including six that provide analyses of results or data quality for the data sets, including a novel inter-annotator consistency assessment for the test set used in task 2.

  1. The evolution of information systems

    International Nuclear Information System (INIS)

    1970-01-01

    Man must dream to achieve progress. That this applies to the complex task of making scientific information easily and rapidly available to scientists was the clear message of rapporteurs summing up an Agency symposium held in Vienna during February on the handling of nuclear information. It was attended by more than 150 specialists in the work. (author)

  2. The common ground of genomics and systems biology

    Science.gov (United States)

    2014-01-01

    The rise of systems biology is intertwined with that of genomics, yet their primordial relationship to one another is ill-defined. We discuss how the growth of genomics provided a critical boost to the popularity of systems biology. We describe the parts of genomics that share common areas of interest with systems biology today in the areas of gene expression, network inference, chromatin state analysis, pathway analysis, personalized medicine, and upcoming areas of synergy as genomics continues to expand its scope across all biomedical fields. PMID:25033072

  3. Noninvasive biological sensor system for detection of drunk driving.

    Science.gov (United States)

    Murata, Kohji; Fujita, Etsunori; Kojima, Shigeyuki; Maeda, Shinitirou; Ogura, Yumi; Kamei, Tsutomu; Tsuji, Toshio; Kaneko, Shigehiko; Yoshizumi, Masao; Suzuki, Nobutaka

    2011-01-01

    Systems capable of monitoring the biological condition of a driver and issuing warnings during instances of drowsiness have recently been studied. Moreover, many researchers have reported that biological signals, such as brain waves, pulsation waves, and heart rate, are different between people who have and have not consumed alcohol. Currently, we are developing a noninvasive system to detect individuals driving under the influence of alcohol by measuring biological signals. We used the frequency time series analysis to attempt to distinguish between normal and intoxicated states of a person as the basis of the sensing system.

  4. Biochemical Space: A Framework for Systemic Annotation of Biological Models

    Czech Academy of Sciences Publication Activity Database

    Klement, M.; Děd, T.; Šafránek, D.; Červený, Jan; Müller, Stefan; Steuer, Ralf

    2014-01-01

    Roč. 306, JUL (2014), s. 31-44 ISSN 1571-0661 R&D Projects: GA MŠk(CZ) EE2.3.20.0256 Institutional support: RVO:67179843 Keywords : biological models * model annotation * systems biology * cyanobacteria Subject RIV: EH - Ecology, Behaviour

  5. Review of "Stochastic Modelling for Systems Biology" by Darren Wilkinson

    Directory of Open Access Journals (Sweden)

    Bullinger Eric

    2006-12-01

    Full Text Available Abstract "Stochastic Modelling for Systems Biology" by Darren Wilkinson introduces the peculiarities of stochastic modelling in biology. This book is particularly suited to as a textbook or for self-study, and for readers with a theoretical background.

  6. Interdisciplinary problem-solving: emerging modes in integrative systems biology

    NARCIS (Netherlands)

    MacLeod, Miles Alexander James; Nersessian, Nancy J.

    2016-01-01

    Integrative systems biology is an emerging field that attempts to integrate computation, applied mathematics, engineering concepts and methods, and biological experimentation in order to model large-scale complex biochemical networks. The field is thus an important contemporary instance of an

  7. Airport Information Retrieval System (AIRS) System Design

    Science.gov (United States)

    1974-07-01

    This report presents the system design for a prototype air traffic flow control automation system developed for the FAA's Systems Command Center. The design was directed toward the immediate automation of airport data for use in traffic load predicti...

  8. Science Information Systems Newsletter, issue 28

    Science.gov (United States)

    1993-01-01

    The purpose of the Information Systems Newsletter is to inform the space science and applications research community about information systems development and to promote coordination and collaboration by providing a forum for communication. This quarterly publication focuses on programs sponsored by the Information Systems Branch in support of NASA's Office of Space Science. Articles of interest for other programs and agencies are presented as well. The April 1993 issue is presented.

  9. Rethinking Information Systems in the Public Sector

    DEFF Research Database (Denmark)

    Medaglia, Rony

    2014-01-01

    This section of Information Polity consists of papers presented during the workshop “Rethinking Information Systems in the Public Sector: Bridging Academia and Public Service”. The workshop was held on 8 June 2014 in Tel Aviv, Israel, in conjunction with the European Conference on Information...... Systems (ECIS 2014), and it is part of the activities of the Special Interest Group for eGovernment (SIGeGov) of the Association for Information Systems (AIS)....

  10. Biologically inspired collision avoidance system for unmanned vehicles

    Science.gov (United States)

    Ortiz, Fernando E.; Graham, Brett; Spagnoli, Kyle; Kelmelis, Eric J.

    2009-05-01

    In this project, we collaborate with researchers in the neuroscience department at the University of Delaware to develop an Field Programmable Gate Array (FPGA)-based embedded computer, inspired by the brains of small vertebrates (fish). The mechanisms of object detection and avoidance in fish have been extensively studied by our Delaware collaborators. The midbrain optic tectum is a biological multimodal navigation controller capable of processing input from all senses that convey spatial information, including vision, audition, touch, and lateral-line (water current sensing in fish). Unfortunately, computational complexity makes these models too slow for use in real-time applications. These simulations are run offline on state-of-the-art desktop computers, presenting a gap between the application and the target platform: a low-power embedded device. EM Photonics has expertise in developing of high-performance computers based on commodity platforms such as graphic cards (GPUs) and FPGAs. FPGAs offer (1) high computational power, low power consumption and small footprint (in line with typical autonomous vehicle constraints), and (2) the ability to implement massively-parallel computational architectures, which can be leveraged to closely emulate biological systems. Combining UD's brain modeling algorithms and the power of FPGAs, this computer enables autonomous navigation in complex environments, and further types of onboard neural processing in future applications.

  11. Functional synchronization of biological rhythms in a tritrophic system.

    Science.gov (United States)

    Zhang, Sufang; Wei, Jianing; Guo, Xiaojiao; Liu, Tong-Xian; Kang, Le

    2010-06-10

    In a tritrophic system formed by a plant, an herbivore and a natural enemy, each component has its own biological rhythm. However, the rhythm correlations among the three levels and the underlying mechanisms in any tritrophic system are largely unknown. Here, we report that the rhythms exhibited bidirectional correlations in a model tritrophic system involving a lima bean, a pea leafminer and a parasitoid. From the bottom-up perspective, the rhythm was initiated from herbivore feeding, which triggered the rhythms of volatile emissions; then the rhythmic pattern of parasitoid activities was affected, and these rhythms were synchronized by a light switch signal. Increased volatile concentration can enhance the intensity of parasitoid locomotion and oviposition only under light. From the top-down perspective, naive and oviposition-experienced parasitoids were able to utilize the different volatile rhythm information from the damaged plant to locate host leafminers respectively. Our results indicated that the three interacting organisms in this system can achieve rhythmic functional synchronization under a natural light-dark photoperiod, but not under constant light or darkness. These findings provide new insight into the rhythm synchronization of three key players that contribute to the utilization of light and chemical signals, and our results may be used as potential approaches for manipulating natural enemies.

  12. Functional synchronization of biological rhythms in a tritrophic system.

    Directory of Open Access Journals (Sweden)

    Sufang Zhang

    Full Text Available In a tritrophic system formed by a plant, an herbivore and a natural enemy, each component has its own biological rhythm. However, the rhythm correlations among the three levels and the underlying mechanisms in any tritrophic system are largely unknown. Here, we report that the rhythms exhibited bidirectional correlations in a model tritrophic system involving a lima bean, a pea leafminer and a parasitoid. From the bottom-up perspective, the rhythm was initiated from herbivore feeding, which triggered the rhythms of volatile emissions; then the rhythmic pattern of parasitoid activities was affected, and these rhythms were synchronized by a light switch signal. Increased volatile concentration can enhance the intensity of parasitoid locomotion and oviposition only under light. From the top-down perspective, naive and oviposition-experienced parasitoids were able to utilize the different volatile rhythm information from the damaged plant to locate host leafminers respectively. Our results indicated that the three interacting organisms in this system can achieve rhythmic functional synchronization under a natural light-dark photoperiod, but not under constant light or darkness. These findings provide new insight into the rhythm synchronization of three key players that contribute to the utilization of light and chemical signals, and our results may be used as potential approaches for manipulating natural enemies.

  13. A data integration approach for cell cycle analysis oriented to model simulation in systems biology

    Directory of Open Access Journals (Sweden)

    Mosca Ettore

    2007-08-01

    Full Text Available Abstract Background The cell cycle is one of the biological processes most frequently investigated in systems biology studies and it involves the knowledge of a large number of genes and networks of protein interactions. A deep knowledge of the molecular aspect of this biological process can contribute to making cancer research more accurate and innovative. In this context the mathematical modelling of the cell cycle has a relevant role to quantify the behaviour of each component of the systems. The mathematical modelling of a biological process such as the cell cycle allows a systemic description that helps to highlight some features such as emergent properties which could be hidden when the analysis is performed only from a reductionism point of view. Moreover, in modelling complex systems, a complete annotation of all the components is equally important to understand the interaction mechanism inside the network: for this reason data integration of the model components has high relevance in systems biology studies. Description In this work, we present a resource, the Cell Cycle Database, intended to support systems biology analysis on the Cell Cycle process, based on two organisms, yeast and mammalian. The database integrates information about genes and proteins involved in the cell cycle process, stores complete models of the interaction networks and allows the mathematical simulation over time of the quantitative behaviour of each component. To accomplish this task, we developed, a web interface for browsing information related to cell cycle genes, proteins and mathematical models. In this framework, we have implemented a pipeline which allows users to deal with the mathematical part of the models, in order to solve, using different variables, the ordinary differential equation systems that describe the biological process. Conclusion This integrated system is freely available in order to support systems biology research on the cell cycle and

  14. Master information data acquisition system

    International Nuclear Information System (INIS)

    Stratton, R.C.

    1981-06-01

    MIDAS provides real-time work and component status as a function of the Work Control Log (WCL). Status is maintained and tracked with regard to Tag-Out status, Out-of-Service status, and document status. Component integration and technical and safety information is provided by the MIDAS Component Index (MCI). This information is provided directly to the user upon request. This information is also provided directly to the WCL as a function of component input to the WCL document prior to the documents release for execution

  15. Environmental information system for visualizing environmental impact assessment information.

    Science.gov (United States)

    Cserny, Angelika; Kovács, Zsófia; Domokos, Endre; Rédey, Akos

    2009-01-01

    The Institute of Environmental Engineering at the University of Pannonia has undertaken the challenge to develop an online environmental information system. This system is able to receive and process the collected environmental data via Internet. The authors have attached importance to the presentation of the data and have included other comprehensible information for laymen as well in order to work out visualisation techniques that are expressive and attract attention for environmental questions through the developed information system. The ways of visualizing physical and chemical parameters of surface water and the effects of motorway construction were examined.

  16. Genome modularity and synthetic biology: Engineering systems.

    Science.gov (United States)

    Mol, Milsee; Kabra, Ritika; Singh, Shailza

    2018-01-01

    Whole genome sequencing projects running in various laboratories around the world has generated immense data. A systematic phylogenetic analysis of this data shows that genome complexity goes on decreasing as it evolves, due to its modular nature. This modularity can be harnessed to minimize the genome further to reduce it with the bare minimum essential genes. A reduced modular genome, can fuel progress in the area of synthetic biology by providing a ready to use plug and play chassis. Advances in gene editing technology such as the use of tailor made synthetic transcription factors will further enhance the availability of synthetic devices to be applied in the fields of environment, agriculture and health. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Integrated Compliance Information System (ICIS)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The purpose of ICIS is to meet evolving Enforcement and Compliance business needs for EPA and State users by integrating information into a single integrated data...

  18. Consolidated Business Information System (CBIS)

    Data.gov (United States)

    Office of Personnel Management — Data from the U.S. Office of Personnel Management (OPM)'s core financial system. CBIS is the official OPM financial management system of record. Every agency must...

  19. Modelling biological and chemically induced precipitation of calcium phosphate in enhanced biological phosphorus removal systems.

    Science.gov (United States)

    Barat, R; Montoya, T; Seco, A; Ferrer, J

    2011-06-01

    The biologically induced precipitation processes can be important in wastewater treatment, in particular treating raw wastewater with high calcium concentration combined with Enhanced Biological Phosphorus Removal. Currently, there is little information and experience in modelling jointly biological and chemical processes. This paper presents a calcium phosphate precipitation model and its inclusion in the Activated Sludge Model No 2d (ASM2d). The proposed precipitation model considers that aqueous phase reactions quickly achieve the chemical equilibrium and that aqueous-solid change is kinetically governed. The model was calibrated using data from four experiments in a Sequencing Batch Reactor (SBR) operated for EBPR and finally validated with two experiments. The precipitation model proposed was able to reproduce the dynamics of amorphous calcium phosphate (ACP) formation and later crystallization to hydroxyapatite (HAP) under different scenarios. The model successfully characterised the EBPR performance of the SBR, including the biological, physical and chemical processes. Copyright © 2011 Elsevier Ltd. All rights reserved.

  20. Information Measures for Multisensor Systems

    Science.gov (United States)

    2013-12-11

    information theory to problems in analytical chemistry is not new. However, its inclusion in chemometrics for modeling large scale sets of multivariate... chemometrics subsequently developed analysis tools for multivariate spectral data6. The purpose of this report is to demonstrate how an information...set of 540 unique IR spectra. PCA is a standard data reduction technique in chemometrics that functions by projecting high-dimensional data onto a