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. 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.

  7. Geographic information system in marine biology: Way for sustainable utilization of living resources

    Digital Repository Service at National Institute of Oceanography (India)

    Chavan, V.S.; Sreepada, R.A.

    Sustainable utilization of aquatic living resources needs accurate assessment. This stress the need for use of Geographic Information System (GIS). In the recent past interest has been generated for use of GIS in various areas of biological...

  8. 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.

  9. 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...

  10. Computational Systems Chemical Biology

    OpenAIRE

    Oprea, Tudor I.; May, Elebeoba E.; Leitão, Andrei; Tropsha, Alexander

    2011-01-01

    There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically-based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology, SCB (Oprea et al., 2007).

  11. Systems Biology

    Indian Academy of Sciences (India)

    IAS Admin

    study and understand the function of biological systems, particu- larly, the response of such .... understand the organisation and behaviour of prokaryotic sys- tems. ... relationship of the structure of a target molecule to its ability to bind a certain ...

  12. Novel Developments of the MetaCrop Information System for Facilitating Systems Biological Approaches

    Directory of Open Access Journals (Sweden)

    Hippe Klaus

    2010-12-01

    Full Text Available Crop plants play a major role in human and animal nutrition and increasingly contribute to chemical or pharmaceutical industry and renewable resources. In order to achieve important goals, such as the improvement of growth or yield, it is indispensable to understand biological processes on a detailed level. Therefore, the well-structured management of fine-grained information about metabolic pathways is of high interest. Thus, we developed the MetaCrop information system, a manually curated repository of high quality information concerning the metabolism of crop plants. However, the data access to and flexible export of information of MetaCrop in standard exchange formats had to be improved. To automate and accelerate the data access we designed a set of web services to be integrated into external software. These web services have already been used by an add-on for the visualisation toolkit VANTED. Furthermore, we developed an export feature for the MetaCrop web interface, thus enabling the user to compose individual metabolic models using SBML.

  13. 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

  14. 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 .

  15. 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)

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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…

  1. Natural Information Processing Systems

    OpenAIRE

    John Sweller; Susan Sweller

    2006-01-01

    Natural information processing systems such as biological evolution and human cognition organize information used to govern the activities of natural entities. When dealing with biologically secondary information, these systems can be specified by five common principles that we propose underlie natural information processing systems. The principles equate: (1) human long-term memory with a genome; (2) learning from other humans with biological reproduction; (3) problem solving through random ...

  2. 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.

  3. The value of mechanistic biophysical information for systems-level understanding of complex biological processes such as cytokinesis.

    Science.gov (United States)

    Pollard, Thomas D

    2014-12-02

    This review illustrates the value of quantitative information including concentrations, kinetic constants and equilibrium constants in modeling and simulating complex biological processes. Although much has been learned about some biological systems without these parameter values, they greatly strengthen mechanistic accounts of dynamical systems. The analysis of muscle contraction is a classic example of the value of combining an inventory of the molecules, atomic structures of the molecules, kinetic constants for the reactions, reconstitutions with purified proteins and theoretical modeling to account for the contraction of whole muscles. A similar strategy is now being used to understand the mechanism of cytokinesis using fission yeast as a favorable model system. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  4. Information theory in molecular biology

    OpenAIRE

    Adami, Christoph

    2004-01-01

    This article introduces the physics of information in the context of molecular biology and genomics. Entropy and information, the two central concepts of Shannon's theory of information and communication, are often confused with each other but play transparent roles when applied to statistical ensembles (i.e., identically prepared sets) of symbolic sequences. Such an approach can distinguish between entropy and information in genes, predict the secondary structure of ribozymes, and detect the...

  5. 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.

  6. 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....

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

    International Nuclear Information System (INIS)

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

    2011-01-01

    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

  8. 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.

  9. 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....

  10. Translational environmental biology: cell biology informing conservation.

    Science.gov (United States)

    Traylor-Knowles, Nikki; Palumbi, Stephen R

    2014-05-01

    Typically, findings from cell biology have been beneficial for preventing human disease. However, translational applications from cell biology can also be applied to conservation efforts, such as protecting coral reefs. Recent efforts to understand the cell biological mechanisms maintaining coral health such as innate immunity and acclimatization have prompted new developments in conservation. Similar to biomedicine, we urge that future efforts should focus on better frameworks for biomarker development to protect coral reefs. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. Analyzing the Biology on the System Level

    OpenAIRE

    Tong, Wei

    2016-01-01

    Although various genome projects have provided us enormous static sequence information, understanding of the sophisticated biology continues to require integrating the computational modeling, system analysis, technology development for experiments, and quantitative experiments all together to analyze the biology architecture on various levels, which is just the origin of systems biology subject. This review discusses the object, its characteristics, and research attentions in systems biology,...

  12. 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

  13. Pragmatic Information as a Unifying Biological Concept

    Directory of Open Access Journals (Sweden)

    Reza Maleeh

    2014-09-01

    Full Text Available This paper aims to introduce a developed reading of Roederer’s interpretation of pragmatic information as a good candidate for a Unifying Information Concept required for an as-yet-unavailable Science of Information. According to pragmatic information, information and information processing are exclusive attributes of biological systems related to the very definition of life. I will apply the notion to give new accounts in the following areas: (1 quantum interpretation: based on a modified version of David Bohm’s interpretation of quantum mechanics, I propose an ontological, information-based interpretation of quantum mechanics which, unlike Roederer’s interpretation, satisfies all conditions of pragmatic information; (2 artificial intelligence: the notion successfully distinguishes natural living systems from artifacts and natural non-living systems, providing a context to pose an information-based argument against the thesis of Strong Artificial Intelligence; (3 phenomenal consciousness: I will use pragmatic information to modify and update Chalmers’s Double-aspect Theory of Information to be explanatorily more powerful regarding the physical aspect of his theory; (4 causation: based on pragmatic information, I pose a new account of causation which differentiates causation in biology from causation in natural abiotic world.

  14. 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...

  15. Heuristic Strategies in Systems Biology

    Directory of Open Access Journals (Sweden)

    Fridolin Gross

    2016-06-01

    Full Text Available Systems biology is sometimes presented as providing a superior approach to the problem of biological complexity. Its use of ‘unbiased’ methods and formal quantitative tools might lead to the impression that the human factor is effectively eliminated. However, a closer look reveals that this impression is misguided. Systems biologists cannot simply assemble molecular information and compute biological behavior. Instead, systems biology’s main contribution is to accelerate the discovery of mechanisms by applying models as heuristic tools. These models rely on a variety of idealizing and simplifying assumptions in order to be efficient for this purpose. The strategies of systems biologists are similar to those of experimentalists in that they attempt to reduce the complexity of the discovery process. Analyzing and comparing these strategies, or ‘heuristics’, reveals the importance of the human factor in computational approaches and helps to situate systems biology within the epistemic landscape of the life sciences.

  16. 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

  17. 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...

  18. 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).

  19. 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

  20. 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 ‘‘...

  1. Biophysics and systems biology.

    Science.gov (United States)

    Noble, Denis

    2010-03-13

    Biophysics at the systems level, as distinct from molecular biophysics, acquired its most famous paradigm in the work of Hodgkin and Huxley, who integrated their equations for the nerve impulse in 1952. Their approach has since been extended to other organs of the body, notably including the heart. The modern field of computational biology has expanded rapidly during the first decade of the twenty-first century and, through its contribution to what is now called systems biology, it is set to revise many of the fundamental principles of biology, including the relations between genotypes and phenotypes. Evolutionary theory, in particular, will require re-assessment. To succeed in this, computational and systems biology will need to develop the theoretical framework required to deal with multilevel interactions. While computational power is necessary, and is forthcoming, it is not sufficient. We will also require mathematical insight, perhaps of a nature we have not yet identified. This article is therefore also a challenge to mathematicians to develop such insights.

  2. 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."

  3. Answering biological questions: Querying a systems biology database for nutrigenomics

    NARCIS (Netherlands)

    Evelo, C.T.; Bochove, K. van; Saito, J.T.

    2011-01-01

    The requirement of systems biology for connecting different levels of biological research leads directly to a need for integrating vast amounts of diverse information in general and of omics data in particular. The nutritional phenotype database addresses this challenge for nutrigenomics. A

  4. 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

  5. Integrating systems biology models and biomedical ontologies.

    Science.gov (United States)

    Hoehndorf, Robert; Dumontier, Michel; Gennari, John H; Wimalaratne, Sarala; de Bono, Bernard; Cook, Daniel L; Gkoutos, Georgios V

    2011-08-11

    Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology. We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models. We establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms.

  6. 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.

  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. 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....

  9. Physical models of biological information and adaptation.

    Science.gov (United States)

    Stuart, C I

    1985-04-07

    The bio-informational equivalence asserts that biological processes reduce to processes of information transfer. In this paper, that equivalence is treated as a metaphor with deeply anthropomorphic content of a sort that resists constitutive-analytical definition, including formulation within mathematical theories of information. It is argued that continuance of the metaphor, as a quasi-theoretical perspective in biology, must entail a methodological dislocation between biological and physical science. It is proposed that a general class of functions, drawn from classical physics, can serve to eliminate the anthropomorphism. Further considerations indicate that the concept of biological adaptation is central to the general applicability of the informational idea in biology; a non-anthropomorphic treatment of adaptive phenomena is suggested in terms of variational principles.

  10. 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.

  11. 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...

  12. 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

  13. 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.

  14. 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 ...

  15. 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.

  16. Systems biology and medicine

    Indian Academy of Sciences (India)

    work could potentially provide us with ways to identify drug ... appropriately balance cause, effect, and context of a given clinical ... would not provide answers/solutions to multitude of tasks that were ... a major challenge of contemporary biology is to embark on an ... nificantly govern the life and responsiveness of cells.

  17. Integrating phosphoproteomics in systems biology

    Directory of Open Access Journals (Sweden)

    Yu Liu

    2014-07-01

    Full Text Available Phosphorylation of serine, threonine and tyrosine plays significant roles in cellular signal transduction and in modifying multiple protein functions. Phosphoproteins are coordinated and regulated by a network of kinases, phosphatases and phospho-binding proteins, which modify the phosphorylation states, recognize unique phosphopeptides, or target proteins for degradation. Detailed and complete information on the structure and dynamics of these networks is required to better understand fundamental mechanisms of cellular processes and diseases. High-throughput technologies have been developed to investigate phosphoproteomes in model organisms and human diseases. Among them, mass spectrometry (MS-based technologies are the major platforms and have been widely applied, which has led to explosive growth of phosphoproteomic data in recent years. New bioinformatics tools are needed to analyze and make sense of these data. Moreover, most research has focused on individual phosphoproteins and kinases. To gain a more complete knowledge of cellular processes, systems biology approaches, including pathways and networks modeling, have to be applied to integrate all components of the phosphorylation machinery, including kinases, phosphatases, their substrates, and phospho-binding proteins. This review presents the latest developments of bioinformatics methods and attempts to apply systems biology to analyze phosphoproteomics data generated by MS-based technologies. Challenges and future directions in this field will be also discussed.

  18. 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.

  19. 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),...

  20. 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

  1. 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...

  2. 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.

  3. Compartmental study of biological systems

    International Nuclear Information System (INIS)

    Moretti, J.L.

    1975-01-01

    The compartmental analysis of biological system is dealt with on several chapters devoted successively to: terminology; a mathematical and symbolic account of a system at equilibrium; different compartment systems; analysis of the experimental results. For this it is pointed out that the application of compartmental systems to biological phenomena is not always without danger. Sometimes the compartmental system established in a reference subject fails to conform in the patient. The compartments can divide into two or join together, completely changing the aspect of the system so that parameters calculated with the old model become entirely false. The conclusion is that the setting up of a compartmental system to represent a biological phenomenon is a tricky undertaking and the results must be constantly criticized and questioned [fr

  4. Integration of genomic information with biological networks using Cytoscape.

    Science.gov (United States)

    Bauer-Mehren, Anna

    2013-01-01

    Cytoscape is an open-source software for visualizing, analyzing, and modeling biological networks. This chapter explains how to use Cytoscape to analyze the functional effect of sequence variations in the context of biological networks such as protein-protein interaction networks and signaling pathways. The chapter is divided into five parts: (1) obtaining information about the functional effect of sequence variation in a Cytoscape readable format, (2) loading and displaying different types of biological networks in Cytoscape, (3) integrating the genomic information (SNPs and mutations) with the biological networks, and (4) analyzing the effect of the genomic perturbation onto the network structure using Cytoscape built-in functions. Finally, we briefly outline how the integrated data can help in building mathematical network models for analyzing the effect of the sequence variation onto the dynamics of the biological system. Each part is illustrated by step-by-step instructions on an example use case and visualized by many screenshots and figures.

  5. 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...

  6. Ten questions about systems biology

    DEFF Research Database (Denmark)

    Joyner, Michael J; Pedersen, Bente K

    2011-01-01

    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......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...

  7. 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.

  8. 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)

  9. A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language.

    Science.gov (United States)

    Nguyen, Tramy; Roehner, Nicholas; Zundel, Zach; Myers, Chris J

    2016-06-17

    Standards are important to synthetic biology because they enable exchange and reproducibility of genetic designs. This paper describes a procedure for converting between two standards: the Systems Biology Markup Language (SBML) and the Synthetic Biology Open Language (SBOL). SBML is a standard for behavioral models of biological systems at the molecular level. SBOL describes structural and basic qualitative behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent connection between behavioral and structural information for a biological design. The conversion process described in this paper leverages Systems Biology Ontology (SBO) annotations to enable inference of a designs qualitative function.

  10. 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.

  11. 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.

  12. From systems biology to systems biomedicine.

    Science.gov (United States)

    Antony, Paul M A; Balling, Rudi; Vlassis, Nikos

    2012-08-01

    Systems Biology is about combining theory, technology, and targeted experiments in a way that drives not only data accumulation but knowledge as well. The challenge in Systems Biomedicine is to furthermore translate mechanistic insights in biological systems to clinical application, with the central aim of improving patients' quality of life. The challenge is to find theoretically well-chosen models for the contextually correct and intelligible representation of multi-scale biological systems. In this review, we discuss the current state of Systems Biology, highlight the emergence of Systems Biomedicine, and highlight some of the topics and views that we think are important for the efficient application of Systems Theory in Biomedicine. Copyright © 2011 Elsevier Ltd. All rights reserved.

  13. 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)

  14. 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...

  15. 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

  16. 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...

  17. Workshop Introduction: Systems Biology and Biological Models

    Science.gov (United States)

    As we consider the future of toxicity testing, the importance of applying biological models to this problem is clear. Modeling efforts exist along a continuum with respect to the level of organization (e.g. cell, tissue, organism) linked to the resolution of the model. Generally,...

  18. 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’.

  19. 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.

  20. 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

  1. 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.

  2. Experience representation in information systems

    OpenAIRE

    Kaczmarek, Jan

    2014-01-01

    This thesis looks into the ways subjective dimension of experience could be represented in artificial, non-biological systems, in particular information systems. The pivotal assumption is that experience as opposed to mainstream thinking in information science is not equal to knowledge, so that experience is a broader term which encapsulates both knowledge and subjective, affective component of experience, which so far has not been properly embraced by knowledge representation theories. This ...

  3. Experience representation in information systems

    OpenAIRE

    Kaczmarek, Jan

    2014-01-01

    This thesis looks into the ways subjective dimension of experience could be represented in artificial, non-biological systems, in particular information systems. The pivotal assumption is that experience as opposed to mainstream thinking in information science is not equal to knowledge, so that experience is a broader term which encapsulates both knowledge and subjective, affective component of experience, which so far has not been properly embraced by knowledge representation theories. Th...

  4. Conference: Statistical Physics and Biological Information

    International Nuclear Information System (INIS)

    Gross, David J.; Hwa, Terence

    2001-01-01

    In the spring of 2001, the Institute for Theoretical Physics ran a 6 month scientific program on Statistical Physics and Biological Information. This program was organized by Walter Fitch (UC Irvine), Terence Hwa (UC San Diego), Luca Peliti (University Federico II), Naples Gary Stormo (Washington University School of Medicine) and Chao Tang (NEC). Overall scientific supervision was provided by David Gross, Director, ITP. The ITP has an online conference/program proceeding which consists of audio and transparencies of almost all of the talks held during this program. Over 100 talks are available on the site at http://online.kitp.ucsb.edu/online/infobio01/

  5. Conference: Statistical Physics and Biological Information; F

    International Nuclear Information System (INIS)

    Gross, David J.; Hwa, Terence

    2001-01-01

    In the spring of 2001, the Institute for Theoretical Physics ran a 6 month scientific program on Statistical Physics and Biological Information. This program was organized by Walter Fitch (UC Irvine), Terence Hwa (UC San Diego), Luca Peliti (University Federico II), Naples Gary Stormo (Washington University School of Medicine) and Chao Tang (NEC). Overall scientific supervision was provided by David Gross, Director, ITP. The ITP has an online conference/program proceeding which consists of audio and transparencies of almost all of the talks held during this program. Over 100 talks are available on the site at http://online.kitp.ucsb.edu/online/infobio01/

  6. 2007 Chemical Biological Information Systems

    Science.gov (United States)

    2007-01-11

    Chris Wasser , Northrop Grumman Data and Decision Support Tools – San Marcos Room (3:30 – 5:30 PM): “Decision Support Using Mission Simulation and...hazards in air, water , on land, on personnel, equipment or facilities. This capability includes detecting, identifying, and quantifying those CBRN...min X Day of Year 3/21, 6/20, 12/20 X Photochemistry (Cloud Cover) 0 – 8 Eighths X Temperature 230 – 310 K X Water Concentration 100 – 40000 PPM

  7. 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...

  8. 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.

  9. 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

  10. Systems Biology-an interdisciplinary approach.

    Science.gov (United States)

    Friboulet, Alain; Thomas, Daniel

    2005-06-15

    System-level approaches in biology are not new but foundations of "Systems Biology" are achieved only now at the beginning of the 21st century [Kitano, H., 2001. Foundations of Systems Biology. MIT Press, Cambridge, MA]. The renewed interest for a system-level approach is linked to the progress in collecting experimental data and to the limits of the "reductionist" approach. System-level understanding of native biological and pathological systems is needed to provide potential therapeutic targets. Examples of interdisciplinary approach in Systems Biology are described in U.S., Japan and Europe. Robustness in biology, metabolic engineering and idiotypic networks are discussed in the framework of Systems Biology.

  11. Mathematical methods in systems biology.

    Science.gov (United States)

    Kashdan, Eugene; Duncan, Dominique; Parnell, Andrew; Schattler, Heinz

    2016-12-01

    The editors of this Special Issue of Mathematical Biosciences and Engineering were the organizers for the Third International Workshop "Mathematical Methods in System Biology" that took place on June 15-18, 2015 at the University College Dublin in Ireland. As stated in the workshop goals, we managed to attract a good mix of mathematicians and statisticians working on biological and medical applications with biologists and clinicians interested in presenting their challenging problems and looking to find mathematical and statistical tools for their solutions.

  12. 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...

  13. 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

  14. 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.

  15. 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

  16. Geographic Information Systems: A Primer

    Science.gov (United States)

    1990-10-01

    Albert Bargeski Page Building 1 2001 Wisconsin Ave., N.W. Washington, DC 20235 (202) 673-5594 DATA: Physical Biological Chemical National Technical...Information Systems Proceedings. ’an Francisco, CA, Oct. 26-30. ASPRS and ACSM. Vol. 1. pp. 1’ - 147. John, N. 1982. Megatrends - Ten New Directions

  17. 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....

  18. 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....

  19. 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)

  20. Systems Biology of the Fluxome

    Directory of Open Access Journals (Sweden)

    Miguel A. Aon

    2015-07-01

    Full Text Available The advent of high throughput -omics has made the accumulation of comprehensive data sets possible, consisting of changes in genes, transcripts, proteins and metabolites. Systems biology-inspired computational methods for translating metabolomics data into fluxomics provide a direct functional, dynamic readout of metabolic networks. When combined with appropriate experimental design, these methods deliver insightful knowledge about cellular function under diverse conditions. The use of computational models accounting for detailed kinetics and regulatory mechanisms allow us to unravel the control and regulatory properties of the fluxome under steady and time-dependent behaviors. This approach extends the analysis of complex systems from description to prediction, including control of complex dynamic behavior ranging from biological rhythms to catastrophic lethal arrhythmias. The powerful quantitative metabolomics-fluxomics approach will help our ability to engineer unicellular and multicellular organisms evolve from trial-and-error to a more predictable process, and from cells to organ and organisms.

  1. 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)

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. On the limitations of standard statistical modeling in biological systems: a full Bayesian approach for biology.

    Science.gov (United States)

    Gomez-Ramirez, Jaime; Sanz, Ricardo

    2013-09-01

    One of the most important scientific challenges today is the quantitative and predictive understanding of biological function. Classical mathematical and computational approaches have been enormously successful in modeling inert matter, but they may be inadequate to address inherent features of biological systems. We address the conceptual and methodological obstacles that lie in the inverse problem in biological systems modeling. We introduce a full Bayesian approach (FBA), a theoretical framework to study biological function, in which probability distributions are conditional on biophysical information that physically resides in the biological system that is studied by the scientist. Copyright © 2013 Elsevier Ltd. All rights reserved.

  8. Towards the understanding of network information processing in biology

    Science.gov (United States)

    Singh, Vijay

    Living organisms perform incredibly well in detecting a signal present in the environment. This information processing is achieved near optimally and quite reliably, even though the sources of signals are highly variable and complex. The work in the last few decades has given us a fair understanding of how individual signal processing units like neurons and cell receptors process signals, but the principles of collective information processing on biological networks are far from clear. Information processing in biological networks, like the brain, metabolic circuits, cellular-signaling circuits, etc., involves complex interactions among a large number of units (neurons, receptors). The combinatorially large number of states such a system can exist in makes it impossible to study these systems from the first principles, starting from the interactions between the basic units. The principles of collective information processing on such complex networks can be identified using coarse graining approaches. This could provide insights into the organization and function of complex biological networks. Here I study models of biological networks using continuum dynamics, renormalization, maximum likelihood estimation and information theory. Such coarse graining approaches identify features that are essential for certain processes performed by underlying biological networks. We find that long-range connections in the brain allow for global scale feature detection in a signal. These also suppress the noise and remove any gaps present in the signal. Hierarchical organization with long-range connections leads to large-scale connectivity at low synapse numbers. Time delays can be utilized to separate a mixture of signals with temporal scales. Our observations indicate that the rules in multivariate signal processing are quite different from traditional single unit signal processing.

  9. 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

  10. Systems Biology — the Broader Perspective

    Directory of Open Access Journals (Sweden)

    Jonathan Bard

    2013-06-01

    Full Text Available Systems biology has two general aims: a narrow one, which is to discover how complex networks of proteins work, and a broader one, which is to integrate the molecular and network data with the generation and function of organism phenotypes. Doing all this involves complex methodologies, but underpinning the subject are more general conceptual problems about upwards and downwards causality, complexity and information storage, and their solutions provide the constraints within which these methodologies can be used. This essay considers these general aspects and the particular role of protein networks; their functional outputs are often the processes driving phenotypic change and physiological function—networks are, in a sense, the units of systems biology much as proteins are for molecular biology. It goes on to argue that the natural language for systems-biological descriptions of biological phenomena is the mathematical graph (a set of connected facts of the general form [process] (e.g., [activates] . Such graphs not only integrate events at different levels but emphasize the distributed nature of control as well as displaying a great deal of data. The implications and successes of these ideas for physiology, pharmacology, development and evolution are briefly considered. The paper concludes with some challenges for the future.

  11. 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...

  12. 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.

  13. 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)

  14. 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

  15. Community Information Systems.

    Science.gov (United States)

    Freeman, Andrew

    Information is provided on technological and social trends as background for a workshop designed to heighten the consciousness of workers in community information systems. Initially, the basic terminology is considered in its implications for an integrated perspective of community information systems, with particular attention given to the meaning…

  16. 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…

  17. 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

  18. 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...

  19. [Network structures in biological systems].

    Science.gov (United States)

    Oleskin, A V

    2013-01-01

    Network structures (networks) that have been extensively studied in the humanities are characterized by cohesion, a lack of a central control unit, and predominantly fractal properties. They are contrasted with structures that contain a single centre (hierarchies) as well as with those whose elements predominantly compete with one another (market-type structures). As far as biological systems are concerned, their network structures can be subdivided into a number of types involving different organizational mechanisms. Network organization is characteristic of various structural levels of biological systems ranging from single cells to integrated societies. These networks can be classified into two main subgroups: (i) flat (leaderless) network structures typical of systems that are composed of uniform elements and represent modular organisms or at least possess manifest integral properties and (ii) three-dimensional, partly hierarchical structures characterized by significant individual and/or intergroup (intercaste) differences between their elements. All network structures include an element that performs structural, protective, and communication-promoting functions. By analogy to cell structures, this element is denoted as the matrix of a network structure. The matrix includes a material and an immaterial component. The material component comprises various structures that belong to the whole structure and not to any of its elements per se. The immaterial (ideal) component of the matrix includes social norms and rules regulating network elements' behavior. These behavioral rules can be described in terms of algorithms. Algorithmization enables modeling the behavior of various network structures, particularly of neuron networks and their artificial analogs.

  20. 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...

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Management Information Systems Research.

    Science.gov (United States)

    Research on management information systems is illusive in many respects. Part of the basic research problem in MIS stems from the absence of standard...decision making. But the transition from these results to the realization of ’satisfactory’ management information systems remains difficult indeed. The...paper discusses several aspects of research on management information systems and reviews a selection of efforts that appear significant for future progress. (Author)

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. 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...

  13. 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

  14. Institute for Genomics and Systems Biology

    Science.gov (United States)

    Institute for Genomics and Systems Biology Discover. Predict. Improve. Advancing Human and , 2015 See all Research Papers Featured Video Introduction to Systems Biology Video: Introduction to Systems Biology News Jack Gilbert Heading UChicago Startup that Aims to Predict Behavior of Trillions of

  15. Information retrieval system

    Science.gov (United States)

    Berg, R. F.; Holcomb, J. E.; Kelroy, E. A.; Levine, D. A.; Mee, C., III

    1970-01-01

    Generalized information storage and retrieval system capable of generating and maintaining a file, gathering statistics, sorting output, and generating final reports for output is reviewed. File generation and file maintenance programs written for the system are general purpose routines.

  16. 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...

  17. National Emission Information System

    International Nuclear Information System (INIS)

    Sajtakova, E.; Spisakova, K.

    2005-01-01

    In this presentation the Slovak National Emission Information System (NEIS) is presented. The NEIS represents hierarchical oriented modular system of acquisition, verification, saving and reporting of data about annual emissions and payments for pollution of atmosphere

  18. 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.

  19. 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

  20. 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 th...

  1. 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.

  2. Management Information Systems

    OpenAIRE

    Furduescu Bogdan-Alexandru

    2017-01-01

    Technology is the science that studies processes, methods and operations run or applied onto raw materials, matters or data, in order to obtain a certain product. Information is the material signal able to launch a material reaction of a dynamic auto-tuning system for which the system is conditioned and finalized. Information Technology is the technology needed for handling (procuring, processing, storing converting and transmitting) information, in particular, with the use of computers [Long...

  3. Computer information systems framework

    International Nuclear Information System (INIS)

    Shahabuddin, S.

    1989-01-01

    Management information systems (MIS) is a commonly used term in computer profession. The new information technology has caused management to expect more from computer. The process of supplying information follows a well defined procedure. MIS should be capable for providing usable information to the various areas and levels of organization. MIS is different from data processing. MIS and business hierarchy provides a good framework for many organization which are using computers. (A.B.)

  4. 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.

  5. Next generation information systems

    Energy Technology Data Exchange (ETDEWEB)

    Limback, Nathan P [Los Alamos National Laboratory; Medina, Melanie A [Los Alamos National Laboratory; Silva, Michelle E [Los Alamos National Laboratory

    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

  6. Tourism information system

    OpenAIRE

    Ulevičius, Žygimantas

    2017-01-01

    The goal of this project is to create responsive design portal with the tools for its administration which lets users to access tourist relevant information. In order to achieve the goal certain tasks were formulated, few technical analysis were done and similar systems which already exist were reviewed. The result is creation of information system with administrative tools, which can be used by several user types which have rights to take adequate actions. The system has account control modu...

  7. Quantum Dynamics in Biological Systems

    Science.gov (United States)

    Shim, Sangwoo

    In the first part of this dissertation, recent efforts to understand quantum mechanical effects in biological systems are discussed. Especially, long-lived quantum coherences observed during the electronic energy transfer process in the Fenna-Matthews-Olson complex at physiological condition are studied extensively using theories of open quantum systems. In addition to the usual master equation based approaches, the effect of the protein structure is investigated in atomistic detail through the combined application of quantum chemistry and molecular dynamics simulations. To evaluate the thermalized reduced density matrix, a path-integral Monte Carlo method with a novel importance sampling approach is developed for excitons coupled to an arbitrary phonon bath at a finite temperature. In the second part of the thesis, simulations of molecular systems and applications to vibrational spectra are discussed. First, the quantum dynamics of a molecule is simulated by combining semiclassical initial value representation and density funcitonal theory with analytic derivatives. A computationally-tractable approximation to the sum-of-states formalism of Raman spectra is subsequently discussed.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. HOPE information system review

    Science.gov (United States)

    Suzuki, Yoshiaki; Nishiyama, Kenji; Ono, Shuuji; Fukuda, Kouin

    1992-08-01

    An overview of the review conducted on H-2 Orbiting Plane (HOPE) is presented. A prototype model was constructed by inputting various technical information proposed by related laboratories. Especially operation flow which enables understanding of correlation between various analysis items, judgement criteria, technical data, and interfaces with others was constructed. Technical information data base and retrieval systems were studied. A Macintosh personal computer was selected for information shaping because of its excellent function, performance, operability, and software completeness.

  15. Health Information Systems

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

    the technology and expertise to process and share ... services. GEHS supports efforts that reach beyond healthcare institutions to capture evidence ... Health information systems are a foundation for quality care, and can increase accountability ...

  16. Energy Information Systems

    Science.gov (United States)

    Home > Building Energy Information Systems and Performance Monitoring (EIS-PM) Building Energy evaluate and improve performance monitoring tools for energy savings in commercial buildings. Within the and visualization capabilities to energy and facility managers. As an increasing number of

  17. 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...

  18. 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...

  19. 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...

  20. 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...

  1. Management Information Systems

    Directory of Open Access Journals (Sweden)

    Furduescu Bogdan-Alexandru

    2017-12-01

    Full Text Available Technology is the science that studies processes, methods and operations run or applied onto raw materials, matters or data, in order to obtain a certain product. Information is the material signal able to launch a material reaction of a dynamic auto-tuning system for which the system is conditioned and finalized. Information Technology is the technology needed for handling (procuring, processing, storing converting and transmitting information, in particular, with the use of computers [Longley, D. & Shain, M. (1985, p. 164]. The importance of IT in the economic growth and development is widely known, taking into account the impact that technology can have on the success and survival, or the failure of the economic activity of enterprises/organizations, IT offering various management information systems (MIS, executive and feedback segments, which all have important and beneficial implications in management and control.

  2. 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...

  3. Management information systems

    Energy Technology Data Exchange (ETDEWEB)

    Crump, K.

    1978-01-01

    An Australian university architect studying management information systems programs at academic institutions in the United States visited 26 universities and colleges and nine educational and professional associations, including extended visits at the University of Wisconsin and the National Center of Higher Education Management Systems. During these visits, he investigated university and college space utilization programs, gained operational and developmental experience at institutions with education philosophies similar to those in Australia, and examined trends in low cost student housing. This report of his observations focusses on management information systems projects throughout the academic community, resource accountability, energy conservation, facilities planning for the handicapped, student housing, and interdisciplinary approaches to education.

  4. 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 generic products, instead of custom made software. We discuss how the move away from traditional in-house development and the increasing use of generic software is likely to transform IS development in the near future. We conclude that these developments will make new demands on the information systems...

  5. Metabolomics: Definitions and Significance in Systems Biology.

    Science.gov (United States)

    Klassen, Aline; Faccio, Andréa Tedesco; Canuto, Gisele André Baptista; da Cruz, Pedro Luis Rocha; Ribeiro, Henrique Caracho; Tavares, Marina Franco Maggi; Sussulini, Alessandra

    2017-01-01

    Nowadays, there is a growing interest in deeply understanding biological mechanisms not only at the molecular level (biological components) but also the effects of an ongoing biological process in the organism as a whole (biological functionality), as established by the concept of systems biology. Within this context, metabolomics is one of the most powerful bioanalytical strategies that allow obtaining a picture of the metabolites of an organism in the course of a biological process, being considered as a phenotyping tool. Briefly, metabolomics approach consists in identifying and determining the set of metabolites (or specific metabolites) in biological samples (tissues, cells, fluids, or organisms) under normal conditions in comparison with altered states promoted by disease, drug treatment, dietary intervention, or environmental modulation. The aim of this chapter is to review the fundamentals and definitions used in the metabolomics field, as well as to emphasize its importance in systems biology and clinical studies.

  6. JINR information retrieval system

    International Nuclear Information System (INIS)

    Arnaudov, D.D.; Govorun, N.N.

    1975-01-01

    The organization of the main files of the JINR Information Retrieval System is described. There are four main files in the System. They are as follows: MD file that consists of abstracts of documents; OMPOD file where the index records of documents are gathered; MZD file that consists of list heads, and OMD file- the file of descriptors. The last three files are considered in some detail. The System is realized in the COBOL language on the CDC computer

  7. Anesthesia information management systems

    OpenAIRE

    Feri Štivan; Janez Benedik; Tomaž Lužar

    2014-01-01

    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...

  8. 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

  9. Advanced radiology information system.

    Science.gov (United States)

    Kolovou, L; Vatousi, M; Lymperopoulos, D; Koukias, M

    2005-01-01

    The innovative features of an advanced Radiology Information System (RIS) are presented in this paper. The interoperability of RIS with the other Intra-hospital Information Systems that interacts with, dealing with the compatibility and open architecture issues, are accomplished by two novel mechanisms [1]. The first one is the particular message handling system that is applied for the exchange of information, according to the Health Level Seven (HL7) protocol's specifications and serves the transfer of medical and administrative data among the RIS applications and data store unit. The same mechanism allows the secure and HL7-compatible interactions with the Hospital Information System (HIS) too. The second one implements the translation of information between the formats that HL7 and Digital Imaging and Communication in Medicine (DICOM) protocols specify, providing the communication between RIS and Picture and Archive Communication System (PACS). The whole structure ensures the automation of the every-day procedures that the ;medical protocol' specifies and provides its services through a friendly and easy to manage graphical user interface.

  10. Systems biology of personalized nutrition

    NARCIS (Netherlands)

    Ommen, B. van; Broek, T. van den; Hoogh, I. de; Erk, M. van; Someren, E. van; Rouhani-Rankouhi, T.; Anthony, J.C.; Hogenelst, K.; Pasman, W.; Boorsma, A.; Wopereis, S.

    2017-01-01

    Personalized nutrition is fast becoming a reality due to a number of technological, scientific, and societal developments that complement and extend current public health nutrition recommendations. Personalized nutrition tailors dietary recommendations to specific biological requirements on the

  11. Hierarchical structure of biological systems: a bioengineering approach.

    Science.gov (United States)

    Alcocer-Cuarón, Carlos; Rivera, Ana L; Castaño, Victor M

    2014-01-01

    A general theory of biological systems, based on few fundamental propositions, allows a generalization of both Wierner and Berthalanffy approaches to theoretical biology. Here, a biological system is defined as a set of self-organized, differentiated elements that interact pair-wise through various networks and media, isolated from other sets by boundaries. Their relation to other systems can be described as a closed loop in a steady-state, which leads to a hierarchical structure and functioning of the biological system. Our thermodynamical approach of hierarchical character can be applied to biological systems of varying sizes through some general principles, based on the exchange of energy information and/or mass from and within the systems.

  12. Information Management and the Biological Warfare Threat

    National Research Council Canada - National Science Library

    Martinez, Antonio

    2002-01-01

    ...: the scientific paradigm, the business paradigm and the security paradigm. The findings of this thesis demonstrate an information sharing paradigm favoring full and open access to scientific data currently being practiced by the U.S...

  13. Materials management information systems.

    Science.gov (United States)

    1996-01-01

    The hospital materials management function--ensuring that goods and services get from a source to an end user--encompasses many areas of the hospital and can significantly affect hospital costs. Performing this function in a manner that will keep costs down and ensure adequate cash flow requires effective management of a large amount of information from a variety of sources. To effectively coordinate such information, most hospitals have implemented some form of materials management information system (MMIS). These systems can be used to automate or facilitate functions such as purchasing, accounting, inventory management, and patient supply charges. In this study, we evaluated seven MMISs from seven vendors, focusing on the functional capabilities of each system and the quality of the service and support provided by the vendor. This Evaluation is intended to (1) assist hospitals purchasing an MMIS by educating materials managers about the capabilities, benefits, and limitations of MMISs and (2) educate clinical engineers and information system managers about the scope of materials management within a healthcare facility. Because software products cannot be evaluated in the same manner as most devices typically included in Health Devices Evaluations, our standard Evaluation protocol was not applicable for this technology. Instead, we based our ratings on our observations (e.g., during site visits), interviews we conducted with current users of each system, and information provided by the vendor (e.g., in response to a request for information [RFI]). We divided the Evaluation into the following sections: Section 1. Responsibilities and Information Requirements of Materials Management: Provides an overview of typical materials management functions and describes the capabilities, benefits, and limitations of MMISs. Also includes the supplementary article, "Inventory Cost and Reimbursement Issues" and the glossary, "Materials Management Terminology." Section 2. The

  14. 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)

  15. 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.

  16. PROLOGUE : Health Information System

    OpenAIRE

    Tomar, Shivanjali

    2013-01-01

    Prologue is a health information system developed for underserved communities in Bihar, India. It is aimed at helping people living in poverty and with low literacy to take the right steps to manage their and their family’s health. Bihar suffers from one of the worst healthcare records in the country. This is as much due to the lack of access to the right information as it is due to the economic condition of the region. The inaccessibility of information is aggravated by the complex social se...

  17. 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

  18. 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...... 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...... that goes beyond the scope of molecular biology and genetic engineering, respectively. With the emphasis on systems and interaction networks, the approaches explicitly engage in one of the oldest philosophical discussions on the relationship between parts and wholes, or between reductionism and holism...

  19. Safety Information System Guide

    International Nuclear Information System (INIS)

    Bullock, M.G.

    1977-03-01

    This Guide provides guidelines for the design and evaluation of a working safety information system. For the relatively few safety professionals who have already adopted computer-based programs, this Guide may aid them in the evaluation of their present system. To those who intend to develop an information system, it will, hopefully, inspire new thinking and encourage steps towards systems safety management. For the line manager who is working where the action is, this Guide may provide insight on the importance of accident facts as a tool for moving ideas up the communication ladder where they will be heard and acted upon; where what he has to say will influence beneficial changes among those who plan and control his operations. In the design of a safety information system, it is suggested that the safety manager make friends with a computer expert or someone on the management team who has some feeling for, and understanding of, the art of information storage and retrieval as a new and better means for communication

  20. 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

  1. Micro-separation toward systems biology.

    Science.gov (United States)

    Liu, Bi-Feng; Xu, Bo; Zhang, Guisen; Du, Wei; Luo, Qingming

    2006-02-17

    Current biology is experiencing transformation in logic or philosophy that forces us to reevaluate the concept of cell, tissue or entire organism as a collection of individual components. Systems biology that aims at understanding biological system at the systems level is an emerging research area, which involves interdisciplinary collaborations of life sciences, computational and mathematical sciences, systems engineering, and analytical technology, etc. For analytical chemistry, developing innovative methods to meet the requirement of systems biology represents new challenges as also opportunities and responsibility. In this review, systems biology-oriented micro-separation technologies are introduced for comprehensive profiling of genome, proteome and metabolome, characterization of biomolecules interaction and single cell analysis such as capillary electrophoresis, ultra-thin layer gel electrophoresis, micro-column liquid chromatography, and their multidimensional combinations, parallel integrations, microfabricated formats, and nano technology involvement. Future challenges and directions are also suggested.

  2. 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.

  3. 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. 

  4. 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.

  5. Impact of Thermodynamic Principles in Systems Biology

    NARCIS (Netherlands)

    Heijnen, J.J.

    2010-01-01

    It is shown that properties of biological systems which are relevant for systems biology motivated mathematical modelling are strongly shaped by general thermodynamic principles such as osmotic limit, Gibbs energy dissipation, near equilibria and thermodynamic driving force. Each of these aspects

  6. Aspergilli: Systems biology and industrial applications

    DEFF Research Database (Denmark)

    Knuf, Christoph; Nielsen, Jens

    2012-01-01

    possible to implement systems biology tools to advance metabolic engineering. These tools include genome-wide transcription analysis and genome-scale metabolic models. Herein, we review achievements in the field and highlight the impact of Aspergillus systems biology on industrial biotechnology....

  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. Outage information system

    International Nuclear Information System (INIS)

    Svengren, Haakan; Meyer, Brita Diskerud

    2005-09-01

    Today's control room systems are designed to operate during power operation, and there is clearly a need for a system to support control room personnel in automatically supervising the status of the plant during the outage period. In order to improve the supervision of Nuclear Power Plants during outages, three prototypes of the Outage Information system have been designed by the Halden Project, one for PWR and two for BWR. The Outage Information System is presented on a large screen, centrally placed in the control room. There will be a PC connected to manage the system. By using signals from the process as input to logic diagrams reflecting the plant's Safety Technical Specifications, the system automatically is supervising that requirements in Safety Technical Specifications are fulfilled during all plant states of the outage period. The system also automatically gives an overview of the status of safety systems and electrical bus bars. Alarm will occur if a requirement in the Safety Technical Specifications is not fulfilled or if a component planned to be ready for operation, is inoperable. In addition, selected measurements being important during the outage period are presented on the large screen. Which measurements and in which way the values will be presented, depends on the plant's control room design and work practice. (Author)

  9. Insect barcode information system.

    Science.gov (United States)

    Pratheepa, Maria; Jalali, Sushil Kumar; Arokiaraj, Robinson Silvester; Venkatesan, Thiruvengadam; Nagesh, Mandadi; Panda, Madhusmita; Pattar, Sharath

    2014-01-01

    Insect Barcode Information System called as Insect Barcode Informática (IBIn) is an online database resource developed by the National Bureau of Agriculturally Important Insects, Bangalore. This database provides acquisition, storage, analysis and publication of DNA barcode records of agriculturally important insects, for researchers specifically in India and other countries. It bridges a gap in bioinformatics by integrating molecular, morphological and distribution details of agriculturally important insects. IBIn was developed using PHP/My SQL by using relational database management concept. This database is based on the client- server architecture, where many clients can access data simultaneously. IBIn is freely available on-line and is user-friendly. IBIn allows the registered users to input new information, search and view information related to DNA barcode of agriculturally important insects.This paper provides a current status of insect barcode in India and brief introduction about the database IBIn. http://www.nabg-nbaii.res.in/barcode.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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...

  16. 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

  17. 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

  18. Enterprise Information Systems Outsourcing

    DEFF Research Database (Denmark)

    Svejvig, Per; Pries.Heje, Jan

    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-tech organiz......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...... the rational cost saving explanation; but then with a more careful analysis focusing on institutional factors, other explanations "behind the curtain" were revealed, such as management consultants with a "best practice" agenda, people promoting outsourcing thereby being promoted themselves, and outside...

  19. 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-tech organ......  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...... the rational cost saving explanation; but then with a more careful analysis focusing on institutional factors, other explanations "behind the curtain" were revealed, such as management consultants with a "best practice" agenda, people promoting outsourcing thereby being promoted themselves, and outside...

  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. Management information systems

    Energy Technology Data Exchange (ETDEWEB)

    1991-01-01

    This contract was for the development of a new range of colliery information computer systems (CIS) using a VAX 11/730 computer. The report details the selection of the system and the set-up of the hardware and software. The first application of these systems was to monitor production and delays from longwall faces. A trial installation was implemented at Shirebrook Colliery and this proved so successful that British Coal are now installing many similar systems. The key features of the production monitoring application are that delays are automatically detected in real time and the operator is prompted for the root cause of the delay. This is done through a linked series of questions and answere from a linked set of possible delay causes. Ad hoc and regular reports are produced giving local colliery management visibility of coal face performance, thus enabling informed decisions and corrective action to be taken. Following the successful application to production monitoring, the system was extended to heading/drivages, coal clearance/conveyors, mine air environment and fixed plant. Those applications were operational during the contract but have since been extended.

  2. 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.

  3. Multi-level and hybrid modelling approaches for systems biology.

    Science.gov (United States)

    Bardini, R; Politano, G; Benso, A; Di Carlo, S

    2017-01-01

    During the last decades, high-throughput techniques allowed for the extraction of a huge amount of data from biological systems, unveiling more of their underling complexity. Biological systems encompass a wide range of space and time scales, functioning according to flexible hierarchies of mechanisms making an intertwined and dynamic interplay of regulations. This becomes particularly evident in processes such as ontogenesis, where regulative assets change according to process context and timing, making structural phenotype and architectural complexities emerge from a single cell, through local interactions. The information collected from biological systems are naturally organized according to the functional levels composing the system itself. In systems biology, biological information often comes from overlapping but different scientific domains, each one having its own way of representing phenomena under study. That is, the different parts of the system to be modelled may be described with different formalisms. For a model to have improved accuracy and capability for making a good knowledge base, it is good to comprise different system levels, suitably handling the relative formalisms. Models which are both multi-level and hybrid satisfy both these requirements, making a very useful tool in computational systems biology. This paper reviews some of the main contributions in this field.

  4. 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.

  5. 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)

  6. 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

  7. 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.

  8. 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...

  9. 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.

  10. 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 ...

  11. 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

  12. 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.

  13. 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

  14. The AMMA information system

    Science.gov (United States)

    Fleury, Laurence; Brissebrat, Guillaume; Boichard, Jean-Luc; Cloché, Sophie; Eymard, Laurence; Mastrorillo, Laurence; Moulaye, Oumarou; Ramage, Karim; Favot, Florence; Roussot, Odile

    2014-05-01

    In the framework of the African Monsoon Multidisciplinary Analyses (AMMA) programme, several tools have been developed in order to facilitate and speed up data and information exchange between researchers from different disciplines. The AMMA information system includes (i) a multidisciplinary user-friendly data management and dissemination system, (ii) report and chart archives associated with display websites and (iii) a scientific paper exchange system. The AMMA information system is enriched by several previous (IMPETUS...) and following projects (FENNEC, ESCAPE, QweCI, DACCIWA…) and is becoming a reference information system about West Africa monsoon. (i) The AMMA project includes airborne, ground-based and ocean measurements, satellite data use, modelling studies and value-added product development. Therefore, the AMMA database user interface 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 from 1850 to present, long term monitoring research networks (CATCH, IDAF, PIRATA...) or 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. All the data are documented in compliance with metadata international standards, and delivered into standard formats. The data request user interface takes full advantage of the data and metadata base relational structure and enables users to elaborate easily multicriteria data requests (period, area, property, property value…). The AMMA data portal counts around 800 registered users and process about 50 data requests every month. The AMMA databases and data portal have been developed and are operated jointly by SEDOO and ESPRI in France

  15. 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…

  16. Omics/systems biology and cancer cachexia.

    Science.gov (United States)

    Gallagher, Iain J; Jacobi, Carsten; Tardif, Nicolas; Rooyackers, Olav; Fearon, Kenneth

    2016-06-01

    Cancer cachexia is a complex syndrome generated by interaction between the host and tumour cells with a background of treatment effects and toxicity. The complexity of the physiological pathways likely involved in cancer cachexia necessitates a holistic view of the relevant biology. Emergent properties are characteristic of complex systems with the result that the end result is more than the sum of its parts. Recognition of the importance of emergent properties in biology led to the concept of systems biology wherein a holistic approach is taken to the biology at hand. Systems biology approaches will therefore play an important role in work to uncover key mechanisms with therapeutic potential in cancer cachexia. The 'omics' technologies provide a global view of biological systems. Genomics, transcriptomics, proteomics, lipidomics and metabolomics approaches all have application in the study of cancer cachexia to generate systems level models of the behaviour of this syndrome. The current work reviews recent applications of these technologies to muscle atrophy in general and cancer cachexia in particular with a view to progress towards integration of these approaches to better understand the pathology and potential treatment pathways in cancer cachexia. Copyright © 2016. Published by Elsevier Ltd.

  17. Decision Making in Biological Systems

    DEFF Research Database (Denmark)

    Tian, Chengzhe

    This thesis consists of five projects in three topics with a shared theme of understanding cellular decision-making processes with mathematical modeling. In the first topic, we address the possible interaction between bacterial Toxin-Antitoxin (TA) systems and stringent response alarmone guanosin...

  18. Iowa Flood Information System

    Science.gov (United States)

    Demir, I.; Krajewski, W. F.; Goska, R.; Mantilla, R.; Weber, L. J.; Young, N.

    2011-12-01

    The Iowa Flood Information System (IFIS) is a web-based platform developed by the Iowa Flood Center (IFC) to provide access to flood inundation maps, real-time flood conditions, flood forecasts both short-term and seasonal, flood-related data, information and interactive visualizations for communities in Iowa. The key element of the system's architecture is the notion of community. Locations of the communities, those near streams and rivers, define basin boundaries. The IFIS provides community-centric watershed and river characteristics, weather (rainfall) conditions, and streamflow data and visualization tools. Interactive interfaces allow access to inundation maps for different stage and return period values, and flooding scenarios with contributions from multiple rivers. Real-time and historical data of water levels, gauge heights, and rainfall conditions are available in the IFIS by streaming data from automated IFC bridge sensors, USGS stream gauges, NEXRAD radars, and NWS forecasts. Simple 2D and 3D interactive visualizations in the IFIS make the data more understandable to general public. Users are able to filter data sources for their communities and selected rivers. The data and information on IFIS is also accessible through web services and mobile applications. The IFIS is optimized for various browsers and screen sizes to provide access through multiple platforms including tablets and mobile devices. The IFIS includes a rainfall-runoff forecast model to provide a five-day flood risk estimate for around 500 communities in Iowa. Multiple view modes in the IFIS accommodate different user types from general public to researchers and decision makers by providing different level of tools and details. River view mode allows users to visualize data from multiple IFC bridge sensors and USGS stream gauges to follow flooding condition along a river. The IFIS will help communities make better-informed decisions on the occurrence of floods, and will alert communities

  19. 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.

  20. Genome Scale Modeling in Systems Biology: Algorithms and Resources

    Science.gov (United States)

    Najafi, Ali; Bidkhori, Gholamreza; Bozorgmehr, Joseph H.; Koch, Ina; Masoudi-Nejad, Ali

    2014-01-01

    In recent years, in silico studies and trial simulations have complemented experimental procedures. A model is a description of a system, and a system is any collection of interrelated objects; an object, moreover, is some elemental unit upon which observations can be made but whose internal structure either does not exist or is ignored. Therefore, any network analysis approach is critical for successful quantitative modeling of biological systems. This review highlights some of most popular and important modeling algorithms, tools, and emerging standards for representing, simulating and analyzing cellular networks in five sections. Also, we try to show these concepts by means of simple example and proper images and graphs. Overall, systems biology aims for a holistic description and understanding of biological processes by an integration of analytical experimental approaches along with synthetic computational models. In fact, biological networks have been developed as a platform for integrating information from high to low-throughput experiments for the analysis of biological systems. We provide an overview of all processes used in modeling and simulating biological networks in such a way that they can become easily understandable for researchers with both biological and mathematical backgrounds. Consequently, given the complexity of generated experimental data and cellular networks, it is no surprise that researchers have turned to computer simulation and the development of more theory-based approaches to augment and assist in the development of a fully quantitative understanding of cellular dynamics. PMID:24822031

  1. LIBRARY MANAGEMNT INFORMATION SYSTEM

    Directory of Open Access Journals (Sweden)

    Magnolia Tilca

    2013-06-01

    Full Text Available The focus of any educational institution is the content and services of the university library. The mission of the library is to obtain, organize, preserve and update the information with the greatest possible accuracy, minimum effort and time. This requires automation of the library’s operations. This paper presents a software application for managing the activity of the territorial "Vasile Goldiş" West University library. The application is developed using Visual Basic for Application programming language and using the database management system Microsoft Access 2010. The goal of this application is to optimize the inner workings of local library and to meet the requests of the institution and of the readers.

  2. 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...... 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...... 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...

  3. 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...

  4. 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...

  5. 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...... for accomplishing such altered gene expression levels are discussed here along with examples of their use, and ideas for new tools are described. The road ahead looks very promising for synthetic and systems biologists as tools to achieve just about anything in terms of tuning and timing multiple gene expression...

  6. Biological indicators for monitoring water quality of MTF canals system

    Science.gov (United States)

    Sethi, S. L.

    1975-01-01

    Biological models, diversity indexes, were developed to predict environmental effects of NASA's Mississippi test facility (MTF) chemical operations on canal systems in the area. To predict the effects on local streams, a physical model of unpolluted streams was established. The model is fed by artesian well water free of background levels of pollutants. The species diversity and biota composition of unpolluted MTF stream was determined; resulting information will be used to form baseline data for future comparisons. Biological modeling was accomplished by adding controlled quantities or kinds of chemical pollutants and evaluating the effects of these chemicals on the biological life of the stream.

  7. Design of the RFID for Storage of Biological Information

    OpenAIRE

    Sang-Hee Son; Seok-Man Kim; Yu-Lee Choi; Kyoung-Rok Cho

    2009-01-01

    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 stor...

  8. 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.

  9. Does “quorum sensing” imply a new type of biological information?

    DEFF Research Database (Denmark)

    Bruni, Luis Emilio

    2002-01-01

    When dealing with biological communication and information, unifying concepts are necessary in order to couple the different “codes” that are being inductively “cracked” and defined at different emergent and “de-emergent” levels of the biological hierarchy. In this paper I compare the type...... of biological information implied by genetic information with that implied in the concept of “quorum sensing” (which refers to a prokaryotic cell-to-cell communication system) in order to explore if such integration is being achieved. I use the Lux operon paradigm and the Vibrio fischeri – Euprymna scolopes...... symbiotic partnership to exemplify the emergence of informational contexts along the biological hierarchy (from molecules to ecologies). I suggest that the biosemiotic epistemological framework can play an integra¬tive role to overcome the limits of dyadic mechanistic descriptions when relating...

  10. Phylogenetically informed logic relationships improve detection of biological network organization

    Science.gov (United States)

    2011-01-01

    Background A "phylogenetic profile" refers to the presence or absence of a gene across a set of organisms, and it has been proven valuable for understanding gene functional relationships and network organization. Despite this success, few studies have attempted to search beyond just pairwise relationships among genes. Here we search for logic relationships involving three genes, and explore its potential application in gene network analyses. Results Taking advantage of a phylogenetic matrix constructed from the large orthologs database Roundup, we invented a method to create balanced profiles for individual triplets of genes that guarantee equal weight on the different phylogenetic scenarios of coevolution between genes. When we applied this idea to LAPP, the method to search for logic triplets of genes, the balanced profiles resulted in significant performance improvement and the discovery of hundreds of thousands more putative triplets than unadjusted profiles. We found that logic triplets detected biological network organization and identified key proteins and their functions, ranging from neighbouring proteins in local pathways, to well separated proteins in the whole pathway, and to the interactions among different pathways at the system level. Finally, our case study suggested that the directionality in a logic relationship and the profile of a triplet could disclose the connectivity between the triplet and surrounding networks. Conclusion Balanced profiles are superior to the raw profiles employed by traditional methods of phylogenetic profiling in searching for high order gene sets. Gene triplets can provide valuable information in detection of biological network organization and identification of key genes at different levels of cellular interaction. PMID:22172058

  11. 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

  12. 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'.

  13. Systems biology solutions for biochemical production challenges

    DEFF Research Database (Denmark)

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

    2017-01-01

    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...... 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...... compared to basic science research requires pushing systems biology strategies to their limits and often spurs innovative developments that benefit fields outside metabolic engineering. Here we survey recent advanced applications of systems biology methods in engineering microbial production strains...

  14. Systems biology solutions for biochemical production challenges.

    Science.gov (United States)

    Hansen, Anne Sofie Lærke; Lennen, Rebecca M; Sonnenschein, Nikolaus; Herrgård, Markus J

    2017-06-01

    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 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 compared to basic science research requires pushing systems biology strategies to their limits and often spurs innovative developments that benefit fields outside metabolic engineering. Here we survey recent advanced applications of systems biology methods in engineering microbial production strains for biofuels and -chemicals. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  15. Audit for Information Systems Security

    Directory of Open Access Journals (Sweden)

    Ana-Maria SUDUC

    2010-01-01

    Full Text Available The information and communication technologies advances made available enormous and vast amounts of information. This availability generates also significant risks to computer systems, information and to the critical operations and infrastructures they support. In spite of significant advances in the information security area many information systems are still vulnerable to inside or outside attacks. The existence of an internal audit for information system security increases the probability of adopting adequate security measures and preventing these attacks or lowering the negative consequences. The paper presents an exploratory study on informatics audit for information systems security.

  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. Synthetic Biology: Advancing Biological Frontiers by Building Synthetic Systems

    OpenAIRE

    Chen, Yvonne Yu-Hsuan; Galloway, Kate E; Smolke, Christina D

    2012-01-01

    Advances in synthetic biology are contributing to diverse research areas, from basic biology to biomanufacturing and disease therapy. We discuss the theoretical foundation, applications, and potential of this emerging field.

  18. 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...

  19. 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...

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. Apoptosis Gene Information System--AGIS.

    Science.gov (United States)

    Sakharkar, Kishore R; Clement, Marie V; Chow, Vincent T K; Pervaiz, Shazib

    2006-05-01

    Genes implicated in apoptosis have great relevance to biology, medicine and oncology. Here, we describe a unique resource, Apoptosis Gene Information System (AGIS) that provides data for over 2400 genes involved directly or indirectly, in apoptotic pathways of more than 350 different organisms. The organization of this information system is based on the principle of one-gene, one record. AGIS will be updated on a six monthly basis as new information becomes available. AGIS can be accessed at: http://www.cellfate.org/AGIS/.

  5. Promoting Systems Thinking through Biology Lessons

    Science.gov (United States)

    Riess, Werner; Mischo, Christoph

    2010-01-01

    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…

  6. Systems Biology of Glucocorticoids in Muscle Disease

    Science.gov (United States)

    2010-10-01

    Introduction Duchenne muscular dystrophy (DMD) is the most common and incurable muscular dystrophy of childhood. Muscle regeneration fails with...SUBJECT TERMS Duchenne Muscular dystrophy , Glucocorticoids, Systems biology, Drug mechanism 16. SECURITY CLASSIFICATION OF: U 17. LIMITATION...better targeted and more effective therapies for Duchenne muscular dystrophy dynamically. This MDA grant proposal is led by Dr. Eric Hoffman, and it

  7. 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.

  8. 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.

  9. 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

  10. 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...

  11. CEFR information management system solution

    International Nuclear Information System (INIS)

    Lu Fei; Zhao Jia'ning

    2011-01-01

    Based on finished information resources planning scheme for China sodium cooled experimental fast breeder reactor and the advanced information resources management solution concepts were applied, we got the building solution of CEFR information management systems. At the same time, the technical solutions of systems structures, logic structures, physical structures, development platforms and operation platforms for information resources management system in fast breeder reactors were developed, which provided programmatic introductions for development works in future. (authors)

  12. 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.

  13. 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...... of a system thereby suggesting new ways of thinking specific toxicological endpoints. Furthermore, computational methods can serve as valuable input for the hypothesis generating phase of the preparations of a research project....

  14. 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.

  15. 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...

  16. 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...

  17. 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.

  18. 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...

  19. 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...

  20. Sequencing Genetics Information: Integrating Data into Information Literacy for Undergraduate Biology Students

    Science.gov (United States)

    MacMillan, Don

    2010-01-01

    This case study describes an information literacy lab for an undergraduate biology course that leads students through a range of resources to discover aspects of genetic information. The lab provides over 560 students per semester with the opportunity for hands-on exploration of resources in steps that simulate the pathways of higher-level…

  1. Information Systems for University Planning.

    Science.gov (United States)

    Robinson, Robert J.

    This paper proposes construction of a separate data base environment for university planning information, distinct from data bases and systems supporting operational functioning and management. The data base would receive some of its input from the management information systems (MIS)/transactional data bases and systems through a process of…

  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. Engineering Information System (EIS)

    Science.gov (United States)

    1992-01-31

    be availabe and usefu for creating powerful tailored contro and mangeen functions. Mode and Framwork Wirth further elaboration of the EIS portio of...control data and activities of the engineering process. The EIM is a conceptual model of administrative and electroic design information. It records...of the access opeations are derived from the instance variable name and type. An attribute conceptually holds one or more instances of a basic type

  4. Information systems in Nuclenor

    International Nuclear Information System (INIS)

    Garcia Sanchez, M.

    2013-01-01

    In the 1989s in Nuclenor a large number of application programs were developed, this spread of software was based on the use of the new incoming machine in those years: the PC. The most severe consequences of having such an amount of isolated programs was the breaking up of corporate data and the loss of coherence between applications. The objective since then has been to unify and consolidate the stored information to increase its quality. (Author)

  5. Intelligent Information Systems Institute

    National Research Council Canada - National Science Library

    Gomes, Carla

    2004-01-01

    ...) at Cornell during the first three years of operation. IISI's mandate is threefold: To perform and stimulate research in computational and data-intensive methods for intelligent decision making systems...

  6. Implementing Student Information Systems

    Science.gov (United States)

    Sullivan, Laurie; Porter, Rebecca

    2006-01-01

    Implementing an enterprise resource planning system is a complex undertaking. Careful planning, management, communication, and staffing can make the difference between a successful and unsuccessful implementation. (Contains 3 tables.)

  7. 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...

  8. Information systems for risk management

    OpenAIRE

    Michael S. Gibson

    1997-01-01

    Risk management information systems are designed to overcome the problem of aggregating data across diverse trading units. The design of an information system depends on the risk measurement methodology that a firm chooses. Inherent in the design of both a risk management information system and a risk measurement methodology is a tradeoff between the accuracy of the resulting measures of risk and the burden of computing them. Technical progress will make this tradeoff more favorable over time...

  9. 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.

  10. Optoelectronic system and apparatus for connection to biological systems

    Science.gov (United States)

    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.

  11. 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.

  12. Aviation Safety Hotline Information System -

    Data.gov (United States)

    Department of Transportation — The Aviation Safety Hotline Information System (ASHIS) collects, stores, and retrieves reports submitted by pilots, mechanics, cabin crew, passengers, or the public...

  13. Decline traffic information system

    Energy Technology Data Exchange (ETDEWEB)

    Du Plessis, K [Computer Sciences Corporation (CSC), Sydney (Australia)

    2007-09-06

    BHP Billion (BHPB) Cannington has experienced problems in regards to their traffic flow in the decline at the mine. The problems related to reports on near misses of vehicles moving towards each other in the decline. The decline is also to narrow for trucks to pass each other and the operators need to be aware of oncoming traffic in the decline to ensure they could take early evasive steps to ensure the rules of right of way in the decline are adhered to. BHPB Cannington requested CSC to conduct a problem analysis and to provide a solutions proposal to Cannington. The solution was put forward as an augmentation of their current safety procedures used with in the decline. During this phase of the project CSC developed a solutions architecture which involved the use of Active (Radio Frequency Identification) RFID tagging which will enable vehicle movement tracking on a real time basis after which the appropriate traffic movement can be relayed to the operators in the decline. The primary objective of the DTIS is to provide accurate information of traffic movement in the decline and present that information to the operators of the decline IN THE DECLINE upon which they would make their decisions. (orig.)

  14. 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). ...

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

    International Nuclear Information System (INIS)

    Luke, S.J.

    2011-01-01

    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

  16. 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

  17. Geographic information system and marine biology

    Digital Repository Service at National Institute of Oceanography (India)

    Kunte

    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 ...

  18. 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)

  19. 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.

  20. Optical Biosensors to Explore Biological Systems

    DEFF Research Database (Denmark)

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

    2016-01-01

    their capability to work in biosensor devices. For example, Raman spectroscopy can be non-invasive and can provide 1 μm of spatial resolution in 1 second of collection time, well suited for sensing. Moreover, it may give information at the single cell and even approaching the single molecule scale. Here we present...... 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...

  1. 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.

  2. 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 ...

  3. 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.

  4. Information security management system planning for CBRN facilities

    International Nuclear Information System (INIS)

    Lenaeu, Joseph D.; O'Neil, Lori Ross; Leitch, Rosalyn M.; Glantz, Clifford S.; Landine, Guy P.; Bryant, Janet L.; Lewis, John; Mathers, Gemma; Rodger, Robert; Johnson, Christopher

    2015-01-01

    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.

  5. 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.

  6. 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.

  7. 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.

  8. 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…

  9. Underground risk management information systems

    Energy Technology Data Exchange (ETDEWEB)

    Matsuyama, S.; Inoue, M.; Sakai, T.

    2006-03-15

    JCOAL has conducted Joint Research on an Underground Communication and Risk Management Information System with CSIRO of Australia under a commissioned study project for the promotion of coal use starting in fiscal 2002. The goal of this research project is the establishment of a new Safety System focusing on the comprehensive risk management information system by the name of Nexsys. The main components of the system are the Ethernet type underground communication system that represents the data communication base, and the risk management information system that permits risk analysis in real-time and provides decision support based on the collected data. The Nexsys is an open system and is a core element of the underground monitoring system. Using a vast amount of underground data, it is capable of accommodating a wide range of functions that were not available in the past. Because of it, it is possible to construct an advanced underground safety system. 14 figs., 4 tabs.

  10. A Distributed User Information System

    Science.gov (United States)

    1990-03-01

    NOE08 Department of Computer Science NOVO 8 1990 University of Maryland S College Park, MD 20742 D Abstract Current user information database technology ...Transactions on Computer Systems, May 1988. [So189] K. Sollins. A plan for internet directory services. Technical report, DDN Network Information Center...2424 A Distributed User Information System DTiC Steven D. Miller, Scott Carson, and Leo Mark DELECTE Institute for Advanced Computer Studies and

  11. System biology and the project Encode

    Directory of Open Access Journals (Sweden)

    M. Yu. Obolenskaya

    2014-08-01

    Full Text Available The goal of this review is to give an incipient knowledge on the background of system biology, the premises to its assignment as a new branch of biology, its principles, methodology and its great achievements in identification of functional elements of human genome and regulation of their concordant­ and differential activity. The short characteristics of functional elements including the protein-coding sequences and those coding noncoding RNAs, the DNAse 1 hypersensitivity sites and methylated CpG islets, modified histones and specific 3D structure of chromatin, are represented. The topology of transcription factors network with its main motifs, hierar­chy, combination and association of transcription factors and their allelic specificity are highlighted­.

  12. 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.

  13. 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.

  14. Information Security Management System toolkit

    OpenAIRE

    Καραμανλής, Μάνος; Karamanlis, Manos

    2016-01-01

    Secure management of information is becoming critical for any organization because information is one of the most valuable assets in organization’s business operations. An Information security management system (ISMS) consists of the policies, procedures, guidelines, and associated resources and activities, collectively managed by an organization, in the pursuit of protecting its information assets. An ISMS is a systematic approach for establishing, implementing, operating, mon...

  15. 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.

  16. 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.

  17. Information-theoretic analysis of the dynamics of an executable biological model.

    Directory of Open Access Journals (Sweden)

    Avital Sadot

    Full Text Available To facilitate analysis and understanding of biological systems, large-scale data are often integrated into models using a variety of mathematical and computational approaches. Such models describe the dynamics of the biological system and can be used to study the changes in the state of the system over time. For many model classes, such as discrete or continuous dynamical systems, there exist appropriate frameworks and tools for analyzing system dynamics. However, the heterogeneous information that encodes and bridges molecular and cellular dynamics, inherent to fine-grained molecular simulation models, presents significant challenges to the study of system dynamics. In this paper, we present an algorithmic information theory based approach for the analysis and interpretation of the dynamics of such executable models of biological systems. We apply a normalized compression distance (NCD analysis to the state representations of a model that simulates the immune decision making and immune cell behavior. We show that this analysis successfully captures the essential information in the dynamics of the system, which results from a variety of events including proliferation, differentiation, or perturbations such as gene knock-outs. We demonstrate that this approach can be used for the analysis of executable models, regardless of the modeling framework, and for making experimentally quantifiable predictions.

  18. 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.

  19. 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

  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. [Habitability and biological life support systems for man].

    Science.gov (United States)

    Gazenko, O G; Grigor'ev, A I; Meleshko, G I; Shepelev, E Ia

    1990-01-01

    This paper discusses general concepts and specific details of the habitability of space stations and planetary bases completely isolated from the Earth for long periods of time. It emphasizes inadequacy of the present-day knowledge about natural conditions that provide a biologically acceptable environment on the Earth as well as lack of information about life support systems as a source of consumables (oxygen, water, food) and a tool for waste management. The habitability of advanced space vehicles is closely related to closed bioregenerative systems used as life support systems.

  2. Understanding genetic variation - the value of systems biology.

    Science.gov (United States)

    Hütt, Marc-Thorsten

    2014-04-01

    Pharmacology is currently transformed by the vast amounts of genome-associated information available for system-level interpretation. Here I review the potential of systems biology to facilitate this interpretation, thus paving the way for the emerging field of systems pharmacology. In particular, I will show how gene regulatory and metabolic networks can serve as a framework for interpreting high throughput data and as an interface to detailed dynamical models. In addition to the established connectivity analyses of effective networks, I suggest here to also analyze higher order architectural properties of effective networks. © 2013 The British Pharmacological Society.

  3. 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.

  4. 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

  5. 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…

  6. The Feasibility of Systems Thinking in Biology Education

    Science.gov (United States)

    Boersma, Kerst; Waarlo, Arend Jan; Klaassen, Kees

    2011-01-01

    Systems thinking in biology education is an up and coming research topic, as yet with contrasting feasibility claims. In biology education systems thinking can be understood as thinking backward and forward between concrete biological objects and processes and systems models representing systems theoretical characteristics. Some studies claim that…

  7. Disposal Site Information Management System

    International Nuclear Information System (INIS)

    Larson, R.A.; Jouse, C.A.; Esparza, V.

    1986-01-01

    An information management system for low-level waste shipped for disposal has been developed for the Nuclear Regulatory Commission (NRC). The Disposal Site Information Management System (DSIMS) was developed to provide a user friendly computerized system, accessible through NRC on a nationwide network, for persons needing information to facilitate management decisions. This system has been developed on NOMAD VP/CSS, and the data obtained from the operators of commercial disposal sites are transferred to DSIMS semiannually. Capabilities are provided in DSIMS to allow the user to select and sort data for use in analysis and reporting low-level waste. The system also provides means for describing sources and quantities of low-level waste exceeding the limits of NRC 10 CFR Part 61 Class C. Information contained in DSIMS is intended to aid in future waste projections and economic analysis for new disposal sites

  8. 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

  9. Nuclear magnetic resonance applications in biological systems

    International Nuclear Information System (INIS)

    Jiang Ling; Liu Maili

    2011-01-01

    Nuclear magnetic resonance (NMR) spectroscopy is a state-of-the-art technology which has been widely applied in biological systems over the past decades. It is a powerful tool for macromolecular structure determination in solution, and has the unique advantage of being capable of elucidating the structure and dynamic behavior of proteins during vital biomedical processes. In this review, we introduce the recent progress in NMR techniques for studying the structure, interaction and dynamics of proteins. The methods for NMR based drug discovery and metabonomics are also briefly introduced. (authors)

  10. 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)

  11. Information Systems Outsourcing Relationship Model

    Directory of Open Access Journals (Sweden)

    Richard Flemming

    2007-09-01

    Full Text Available Increasing attention is being paid to what determines the success of an information systems outsourcing arrangement. The current research aims to provide an improved understanding of the factors influencing the outcome of an information systems outsourcing relationship and to provide a preliminary validation of an extended outsourcing relationship model by interviews with information systems outsourcing professionals in both the client and vendor of a major Australian outsourcing relationship. It also investigates whether the client and the vendor perceive the relationship differently and if so, how they perceive it differently and whether the two perspectives are interrelated.

  12. 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.)

  13. 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

  14. 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...

  15. 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

  16. 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.

  17. Distribution and Biological Effects of Nanoparticles in the Reproductive System.

    Science.gov (United States)

    Liu, Ying; Li, Hongxia; Xiao, Kai

    2016-01-01

    Nanoparticles have shown great potential in biomedical applications such as imaging probes and drug delivery. However, the increasing use of nanoparticles has raised concerns about their adverse effects on human health and environment. Reproductive tissues and gametes represent highly delicate biological systems with the essential function of transmitting genetic information to the offspring, which is highly sensitive to environmental toxicants. This review aims to summarzie the penetration of physiological barriers (blood-testis barrier and placental barrier), distribution and biological effects of nanoparticles in the reproductive system, which is essential to control the beneficial effects of nanoparticles applications and to avoid their adverse effects on the reproductive system. We referred to a large number of relevant peer-reviewed research articles about the reproductive toxicity of nanoparticles. The comprehensive information was summarized into two parts: physiological barrier penetration and biological effects of nanoparticles in male or female reproductive system; distribution and metabolism of nanoparticles in the reproductive system. The representative examples were also presented in four tables. The in vitro and in vivo studies imply that some nanoparticles are able to cross the blood-testis barrier or placental barrier, and their penetration depends on the physicochemical characteristics of nanoparticles (e.g., composition, shape, particle size and surface coating). The toxicity assays indicate that nanoparticles might induce adverse physiological effects and impede fertility or embryogenesis. The barrier penetration, adverse physiological effects, distribution and metabolism are closely related to physicochemical characteristics of nanoparticles. Further systematic and mechanistic studies using well-characterized nanoparticles, relevant administration routes, and doses relevant to the expected exposure level are required to improve our

  18. Developing Information Systems for Competitive Intelligence Support.

    Science.gov (United States)

    Hohhof, Bonnie

    1994-01-01

    Discusses issues connected with developing information systems for competitive intelligence support; defines the elements of an effective competitive information system; and summarizes issues affecting system design and implementation. Highlights include intelligence information; information needs; information sources; decision making; and…

  19. Dielectric relaxation in biological systems physical principles, methods, and applications

    CERN Document Server

    Feldman, Yuri

    2015-01-01

    This title covers the theoretical basis and practical aspects of the study of dielectric properties of biological systems, such as water, electrolyte and polyelectrolytes, solutions of biological macromolecules, cells suspensions and cellular systems.

  20. 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.

  1. 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.

  2. 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...

  3. 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.

  4. 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...

  5. 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.

  6. 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

  7. Structural Identifiability of Dynamic Systems Biology Models.

    Science.gov (United States)

    Villaverde, Alejandro F; Barreiro, Antonio; Papachristodoulou, Antonis

    2016-10-01

    A powerful way of gaining insight into biological systems is by creating a nonlinear differential equation model, which usually contains many unknown parameters. Such a model is called structurally identifiable if it is possible to determine the values of its parameters from measurements of the model outputs. Structural identifiability is a prerequisite for parameter estimation, and should be assessed before exploiting a model. However, this analysis is seldom performed due to the high computational cost involved in the necessary symbolic calculations, which quickly becomes prohibitive as the problem size increases. In this paper we show how to analyse the structural identifiability of a very general class of nonlinear models by extending methods originally developed for studying observability. We present results about models whose identifiability had not been previously determined, report unidentifiabilities that had not been found before, and show how to modify those unidentifiable models to make them identifiable. This method helps prevent problems caused by lack of identifiability analysis, which can compromise the success of tasks such as experiment design, parameter estimation, and model-based optimization. The procedure is called STRIKE-GOLDD (STRuctural Identifiability taKen as Extended-Generalized Observability with Lie Derivatives and Decomposition), and it is implemented in a MATLAB toolbox which is available as open source software. The broad applicability of this approach facilitates the analysis of the increasingly complex models used in systems biology and other areas.

  8. Model checking biological systems described using ambient calculus

    DEFF Research Database (Denmark)

    Mardare, Radu Iulian; Priami, Corrado; Qualia, Paola

    2005-01-01

    Model checking biological systems described using ambient calculus. In Proc. of the second International Workshop on Computational Methods in Systems Biology (CMSB04), Lecture Notes in Bioinformatics 3082:85-103, Springer, 2005.......Model checking biological systems described using ambient calculus. In Proc. of the second International Workshop on Computational Methods in Systems Biology (CMSB04), Lecture Notes in Bioinformatics 3082:85-103, Springer, 2005....

  9. Calculating life? Duelling discourses in interdisciplinary systems biology.

    Science.gov (United States)

    Calvert, Jane; Fujimura, Joan H

    2011-06-01

    A high profile context in which physics and biology meet today is in the new field of systems biology. Systems biology is a fascinating subject for sociological investigation because the demands of interdisciplinary collaboration have brought epistemological issues and debates front and centre in discussions amongst systems biologists in conference settings, in publications, and in laboratory coffee rooms. One could argue that systems biologists are conducting their own philosophy of science. This paper explores the epistemic aspirations of the field by drawing on interviews with scientists working in systems biology, attendance at systems biology conferences and workshops, and visits to systems biology laboratories. It examines the discourses of systems biologists, looking at how they position their work in relation to previous types of biological inquiry, particularly molecular biology. For example, they raise the issue of reductionism to distinguish systems biology from molecular biology. This comparison with molecular biology leads to discussions about the goals and aspirations of systems biology, including epistemic commitments to quantification, rigor and predictability. Some systems biologists aspire to make biology more similar to physics and engineering by making living systems calculable, modelable and ultimately predictable-a research programme that is perhaps taken to its most extreme form in systems biology's sister discipline: synthetic biology. Other systems biologists, however, do not think that the standards of the physical sciences are the standards by which we should measure the achievements of systems biology, and doubt whether such standards will ever be applicable to 'dirty, unruly living systems'. This paper explores these epistemic tensions and reflects on their sociological dimensions and their consequences for future work in the life sciences. Copyright © 2010 Elsevier Ltd. All rights reserved.

  10. 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

  11. 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.

  12. 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)

  13. 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.

  14. Environmental monitoring and information systems

    International Nuclear Information System (INIS)

    Gibbert, R.

    1998-01-01

    Environmental monitoring and information systems installed by Dornier are summarized. A broad spectrum of environmental areas from air quality and water to radioactivity is covered. Nuclear power plant monitoring systems, either as remote or plant-internal monitoring systems, form an important element of the work undertaken. The systems delivered covered local, regional or national areas. The range of services provided, and hardware and software platforms are listed. (R.P.)

  15. 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.)

  16. 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...

  17. 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.

  18. 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

  19. Developing Scalable Information Security Systems

    Directory of Open Access Journals (Sweden)

    Valery Konstantinovich Ablekov

    2013-06-01

    Full Text Available Existing physical security systems has wide range of lacks, including: high cost, a large number of vulnerabilities, problems of modification and support system. This paper covers an actual problem of developing systems without this list of drawbacks. The paper presents the architecture of the information security system, which operates through the network protocol TCP/IP, including the ability to connect different types of devices and integration with existing security systems. The main advantage is a significant increase in system reliability, scalability, both vertically and horizontally, with minimal cost of both financial and time resources.

  20. 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)

  1. 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

  2. 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.

  3. Correlation Between Information Technology And Management Information Systems Quality

    Directory of Open Access Journals (Sweden)

    Annisa Fitri Anggraeni

    2015-08-01

    Full Text Available The aim of this research is to find out the correlation between Information Technology and Management Information System Quality. This research applies literature review from various theories and previously conducted research where controversies between Information Technology and Management Information Systems. The result of this research shows that Information Technology is a part of Management Information System and supports the performance of Management Information Systems.

  4. Management Information Systems at CERN

    CERN Document Server

    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).

  5. Krsko NPP ecological information system

    International Nuclear Information System (INIS)

    Kovac, A.; Breznik, B.

    1996-01-01

    The Ecological Information System was developed and is used for continuous data collecting from different measuring points as well as for dose calculation in case of emergency. The system collects all the data which are continuously measured in the environment or might have influence to the environment or are necessary for evaluation of impact to the environment. (author)

  6. International Nuclear Information System (INIS)

    International Nuclear Information System (INIS)

    1987-01-01

    Depicts the nature and operations of the first truly international, decentralized and computerized information processing and dissemination system, INIS. The products of the system, consisting of various literature indexes issued in both printed form and on magnetic tapes are described and their utility to scientists is demonstrated

  7. Information Systems and Management Training.

    Science.gov (United States)

    Curry, B.; Smith, D. G.

    1991-01-01

    A case study of a South Wales manufacturer illustrates the need for companies to adopt an integrated strategy for computerization and information systems. Lack of management training blending computing and business skills can have a crippling effect on system development and organizational health. (SK)

  8. Notions of similarity for systems biology models.

    Science.gov (United States)

    Henkel, Ron; Hoehndorf, Robert; Kacprowski, Tim; Knüpfer, Christian; Liebermeister, Wolfram; Waltemath, Dagmar

    2018-01-01

    Systems biology models are rapidly increasing in complexity, size and numbers. When building large models, researchers rely on software tools for the retrieval, comparison, combination and merging of models, as well as for version control. These tools need to be able to quantify the differences and similarities between computational models. However, depending on the specific application, the notion of 'similarity' may greatly vary. A general notion of model similarity, applicable to various types of models, is still missing. Here we survey existing methods for the comparison of models, introduce quantitative measures for model similarity, and discuss potential applications of combined similarity measures. To frame model comparison as a general problem, we describe a theoretical approach to defining and computing similarities based on a combination of different model aspects. The six aspects that we define as potentially relevant for similarity are underlying encoding, references to biological entities, quantitative behaviour, qualitative behaviour, mathematical equations and parameters and network structure. We argue that future similarity measures will benefit from combining these model aspects in flexible, problem-specific ways to mimic users' intuition about model similarity, and to support complex model searches in databases. © The Author 2016. Published by Oxford University Press.

  9. 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)

  10. HTR-10 management information system

    International Nuclear Information System (INIS)

    Liu Ruoxiao; Wu Zhongwang; Xi Shuren

    2000-01-01

    The HTR-10 Management information system (REMIS) strengthens the managerial level and usage of the information of HTR-10, thereby enhances the ability and efficiency of the design and management work. REMIS is designed based on the Client/Server framework. Database management system is SQL Server 6.5 for NT, While the client side is developed by Borland C ++ Builder, and it is based on Windows 95/98. The network protocol is TCP/IP. REMIS collects date of the HTR-10 at four parameters: Reactor properties, Design parameters, Equipment properties Reactor system flow charts. Final discussing extended prospect of REMIS

  11. Personalized Mobile Information Retrieval System

    Directory of Open Access Journals (Sweden)

    Okkyung Choi

    2012-04-01

    Full Text Available Building a global Network Relations with the internet has made huge changes in personal information system and even comments left on a webpage of SNS(Social Network Services are appreciated as important elements that would provide valuable information for someone. Social Network is a relation between individuals or groups, represented in a graph model, which converts the concept of psychological and social relations into a logical structure by using node and link. But, most of the current personalized systems on the basis of Social Network are built and constructed mainly in the PC environment, and the systems are neither designed nor implemented in mobile environment. Hence, the objective of this study is to propose methods of providing Personalized Mobile Information Retrieval System using NFC (Near Field Communication Smartphone, which will be then used for Smartphone users. Besides, this study aims to verify its efficiency through a comparative analysis of existing studies.

  12. Databases and information systems: Applications in biogeography

    International Nuclear Information System (INIS)

    Escalante E, Tania; Llorente B, Jorge; Espinoza O, David N; Soberon M, Jorge

    2000-01-01

    Some aspects of the new instrumentalization and methodological elements that make up information systems in biodiversity (ISB) are described. The use of accurate geographically referenced data allows a broad range of available sources: natural history collections and scientific literature require the use of databases and geographic information systems (GIS). The conceptualization of ISB and GIS, based in the use of extensive data bases, has implied detailed modeling and the construction of authoritative archives: exhaustive catalogues of nomenclature and synonymies, complete bibliographic lists, list of names proposed, historical-geographic gazetteers with localities and their synonyms united under a global positioning system which produces a geospheric conception of the earth and its biota. Certain difficulties in the development of the system and the construction of the biological databases are explained: quality control of data, for example. The use of such systems is basic in order to respond to many questions at the frontier of current studies of biodiversity and conservation. In particular, some applications in biogeography and their importance for modeling distributions, to identify and contrast areas of endemism and biological richness for conservation, and their use as tools in what we identify as predictive and experimental faunistics are detailed. Lastly, the process as well as its relevance is emphasized at national and regional levels

  13. 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.

  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. 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)

  16. 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.

  17. A Magnetic Sensor System for Biological Detection

    KAUST Repository

    Li, Fuquan

    2015-01-01

    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

  18. 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.

  19. 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.

  20. 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...

  1. A comprehensive radiology information system

    International Nuclear Information System (INIS)

    Jost, R.G.

    1985-01-01

    DECrad version II was recently tested by members of the Radiology Information System Consortium (RISC) and was found to meet the specifications prepared by the consortium. It is a comprehensive tailorable system that can be interfaced to practically any HIS. This paper provides an overall view of the major functions of the system which include registration, scheduling, tracking, film library management, reporting, statistics, and teaching modules. The evolution of the specification and user experiences is reported

  2. Hologenomics: Systems-Level Host Biology.

    Science.gov (United States)

    Theis, Kevin R

    2018-01-01

    The hologenome concept of evolution is a hypothesis explaining host evolution in the context of the host microbiomes. As a hypothesis, it needs to be evaluated, especially with respect to the extent of fidelity of transgenerational coassociation of host and microbial lineages and the relative fitness consequences of repeated associations within natural holobiont populations. Behavioral ecologists are in a prime position to test these predictions because they typically focus on animal phenotypes that are quantifiable, conduct studies over multiple generations within natural animal populations, and collect metadata on genetic relatedness and relative reproductive success within these populations. Regardless of the conclusion on the hologenome concept as an evolutionary hypothesis, a hologenomic perspective has applied value as a systems-level framework for host biology, including in medicine. Specifically, it emphasizes investigating the multivarious and dynamic interactions between patient genomes and the genomes of their diverse microbiota when attempting to elucidate etiologies of complex, noninfectious diseases.

  3. 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)

  4. Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project.

    Science.gov (United States)

    Hucka, M; Finney, A; Bornstein, B J; Keating, S M; Shapiro, B E; Matthews, J; Kovitz, B L; Schilstra, M J; Funahashi, A; Doyle, J C; Kitano, H

    2004-06-01

    Biologists are increasingly recognising that computational modelling is crucial for making sense of the vast quantities of complex experimental data that are now being collected. The systems biology field needs agreed-upon information standards if models are to be shared, evaluated and developed cooperatively. Over the last four years, our team has been developing the Systems Biology Markup Language (SBML) in collaboration with an international community of modellers and software developers. SBML has become a de facto standard format for representing formal, quantitative and qualitative models at the level of biochemical reactions and regulatory networks. In this article, we summarise the current and upcoming versions of SBML and our efforts at developing software infrastructure for supporting and broadening its use. We also provide a brief overview of the many SBML-compatible software tools available today.

  5. 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

  6. Biomarkers of Nanoparticles Impact on Biological Systems

    Science.gov (United States)

    Mikhailenko, V.; Ieleiko, L.; Glavin, A.; Sorochinska, J.

    Studies of nanoscale mineral fibers have demonstrated that the toxic and carcinogenic effects are related to the surface area and surface activity of inhaled particles. Particle surface characteristics are considered to be key factors in the generation of free radicals and reactive oxygen species and are related to the development of apoptosis or cancer. Existing physico-chemical methods do not always allow estimation of the nanoparticles impact on organismal and cellular levels. The aim of this study was to develop marker system for evaluation the toxic and carcinogenic effects of nanoparticles on cells. The markers are designed with respect to important nanoparticles characteristics for specific and sensitive assessment of their impact on biological system. We have studied DNA damage, the activity of xanthine oxidoreductase influencing the level of free radicals, bioenergetic status, phospholipids profile and formation of 1H-NMR-visible mobile lipid domains in Ehrlich carcinoma cells. The efficiency of the proposed marker system was tested in vivo and in vitro with the use of C60 fullerene nanoparticles and multiwalled carbon nanotubes. Our data suggest that multiwalled carbon nanotubes and fullerene C60 may pose genotoxic effect, change energy metabolism and membrane structure, alter free radical level via xanthine oxidase activation and cause mobile lipid domains formation as determined in vivo and in vitro studies on Ehrlich carcinoma cells.

  7. 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.

  8. 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...

  9. 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 are descr...

  10. 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.

  11. Advanced Information Processing System (AIPS)

    Science.gov (United States)

    Pitts, Felix L.

    1993-01-01

    Advanced Information Processing System (AIPS) is a computer systems philosophy, a set of validated hardware building blocks, and a set of validated services as embodied in system software. The goal of AIPS is to provide the knowledgebase which will allow achievement of validated fault-tolerant distributed computer system architectures, suitable for a broad range of applications, having failure probability requirements of 10E-9 at 10 hours. A background and description is given followed by program accomplishments, the current focus, applications, technology transfer, FY92 accomplishments, and funding.

  12. 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

  13. Ecological and biological systems under extreme conditions

    Energy Technology Data Exchange (ETDEWEB)

    Zlobin, V S; Nenishkiene, V B

    1989-01-01

    The behaviour of biological and ecological systems under extreme conditions (high and low temperatures, electromagnetic fields of different frequencies, ultraviolet. X-ray and gamma radiation) is analyzed. The ecosystems of macro- and microalgae living in salt, brackinsh and fresh waters are considered in the evolutional aspect basing on their chemical and biochemical composition taking into account the mechanism of radionuclide uptake by water plant cells, osmotic regulation, water and ice structures, combined water in a living organism. The problems of life-support in cosmic flights and of mastering the planets of the Solar system, for instance Mars and Venus, utilizing some microalgae and bacteria with high adaptive properties are discussed. Abnormal water points and their role in the metabolism of a water plant cell are estimated. The 'life niches' are determined at the temperatures exceeding 100 deg C and the possibility of existence for living organisms in high pressure and temperature is grounded. Attempts are made to change the metabolism of the plant and animal cell by subjecting it to the action of electromagnetic and thermal fields, heavy water, chemical and pharmocological substances changing the structure of bound water. 333 refs.; 79 tabs.

  14. 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.

  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. [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.

  17. 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.

  18. 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.

  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. 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.

  1. 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)

  2. 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...

  3. 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,…

  4. 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

  5. Information interchange system and apparatus

    NARCIS (Netherlands)

    2013-01-01

    To overcome the drawback of difficulties when interchanging a patient's health record among different health information management systems and yet keep the patient's privacy, this invention proposes a method comprising the steps of: extracting, from a certificate, a signature of a first service

  6. 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.

  7. DEVELOPMENT OF MANAGEMENT INFORMATION SYSTEMS

    OpenAIRE

    Wiesław Samitowski

    2016-01-01

    On the basis of many years of experience in providing consulting services in the area of management, the author presents the issues regarding the development of information systems to be applied in business. The analysis is conducted within the framework of a field of study introduced by the author and referred to as infornomics.

  8. 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)

  9. 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).

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. Respiratory care management information systems.

    Science.gov (United States)

    Ford, Richard M

    2004-04-01

    Hospital-wide computerized information systems evolved from the need to capture patient information and perform billing and other financial functions. These systems, however, have fallen short of meeting the needs of respiratory care departments regarding work load assessment, productivity management, and the level of outcome reporting required to support programs such as patient-driven protocols. The respiratory care management information systems (RCMIS) of today offer many advantages over paper-based systems and hospital-wide computer systems. RCMIS are designed to facilitate functions specific to respiratory care, including assessing work demand, assigning and tracking resources, charting, billing, and reporting results. RCMIS incorporate mobile, point-of-care charting and are highly configurable to meet the specific needs of individual respiratory care departments. Important and substantial benefits can be realized with an RCMIS and mobile, wireless charting devices. The initial and ongoing costs of an RCMIS are justified by increased charge capture and reduced costs, by way of improved productivity and efficiency. It is not unusual to recover the total cost of an RCMIS within the first year of its operation. In addition, such systems can facilitate and monitor patient-care protocols and help to efficiently manage the vast amounts of information encountered during the practitioner's workday. Respiratory care departments that invest in RCMIS have an advantage in the provision of quality care and in reducing expenses. A centralized respiratory therapy department with an RCMIS is the most efficient and cost-effective way to monitor work demand and manage the hospital-wide allocation of respiratory care services.

  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

    which for example occur in photosynthesis, cellular respiration, DNA repair, and possibly magnetic field sensing. Quantum biology uses computation to model biological interactions in light of quantum mechanical effects and has primarily developed over the past decade as a result of convergence between...

  19. 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...

  20. 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

  1. Precision medicine driven by cancer systems biology.

    Science.gov (United States)

    Filipp, Fabian V

    2017-03-01

    Molecular insights from genome and systems biology are influencing how cancer is diagnosed and treated. We critically evaluate big data challenges in precision medicine. The melanoma research community has identified distinct subtypes involving chronic sun-induced damage and the mitogen-activated protein kinase driver pathway. In addition, despite low mutation burden, non-genomic mitogen-activated protein kinase melanoma drivers are found in membrane receptors, metabolism, or epigenetic signaling with the ability to bypass central mitogen-activated protein kinase molecules and activating a similar program of mitogenic effectors. Mutation hotspots, structural modeling, UV signature, and genomic as well as non-genomic mechanisms of disease initiation and progression are taken into consideration to identify resistance mutations and novel drug targets. A comprehensive precision medicine profile of a malignant melanoma patient illustrates future rational drug targeting strategies. Network analysis emphasizes an important role of epigenetic and metabolic master regulators in oncogenesis. Co-occurrence of driver mutations in signaling, metabolic, and epigenetic factors highlights how cumulative alterations of our genomes and epigenomes progressively lead to uncontrolled cell proliferation. Precision insights have the ability to identify independent molecular pathways suitable for drug targeting. Synergistic treatment combinations of orthogonal modalities including immunotherapy, mitogen-activated protein kinase inhibitors, epigenetic inhibitors, and metabolic inhibitors have the potential to overcome immune evasion, side effects, and drug resistance.

  2. 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.

  3. 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.

  4. Interactomes, manufacturomes and relational biology: analogies between systems biology and manufacturing systems

    Science.gov (United States)

    2011-01-01

    Background We review and extend the work of Rosen and Casti who discuss category theory with regards to systems biology and manufacturing systems, respectively. Results We describe anticipatory systems, or long-range feed-forward chemical reaction chains, and compare them to open-loop manufacturing processes. We then close the loop by discussing metabolism-repair systems and describe the rationality of the self-referential equation f = f (f). This relationship is derived from some boundary conditions that, in molecular systems biology, can be stated as the cardinality of the following molecular sets must be about equal: metabolome, genome, proteome. We show that this conjecture is not likely correct so the problem of self-referential mappings for describing the boundary between living and nonliving systems remains an open question. We calculate a lower and upper bound for the number of edges in the molecular interaction network (the interactome) for two cellular organisms and for two manufacturomes for CMOS integrated circuit manufacturing. Conclusions We show that the relevant mapping relations may not be Abelian, and that these problems cannot yet be resolved because the interactomes and manufacturomes are incomplete. PMID:21689427

  5. Marketing in Admissions: The Information System Approach.

    Science.gov (United States)

    Wofford, O. Douglas; Timmerman, Ed

    1982-01-01

    A marketing information system approach for college admissions is outlined that includes objectives, information needs and sources, a data collection format, and information evaluation. Coordination with other institutional information systems is recommended. (MSE)

  6. INIS - International Nuclear Information System

    International Nuclear Information System (INIS)

    Nevyjel, A.

    1983-10-01

    The International Nuclear Information System is operated by the IAEA in close cooperation with its participating countries. Each country is responsible for the acquisition of the literature published within its boundaries. These data are collected by the INIS secretariat in Vienna and the resulting comprehensive data base is available for all member states. On behalf of Austrian Federal Chancellor's Office the Austrian Research Centre Seibersdorf operates the Austrian INIS-Center, which offers information services in form of retrospective searches and current awareness services. (Author) [de

  7. 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....... This paper is about a prerequisite for such products, namely, a sustainable ISD process, a process which exhibits reasonable and responsible stewardship and utilisation of the existing resources for ISD—people and information in the context of scope, time/schedule, budget/cost, quality and risk....

  8. 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

  9. 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

  10. The National Biological Information Infrastructure as an E-Government tool

    Science.gov (United States)

    Sepic, R.; Kase, K.

    2002-01-01

    Coordinated by the U.S. Geological Survey (USGS), the National Biological Information Infrastructure (NBII) is a Web-based system that provides access to data and information on the nation's biological resources. Although it was begun in 1993, predating any formal E-Government initiative, the NBII typifies the E-Government concepts outlined in the President's Management Agenda, as well as in the proposed E-Government Act of 2002. This article-an individual case study and not a broad survey with extensive references to the literature-explores the structure and operation of the NBII in relation to several emerging trends in E-Government: end-user focus, defined and scalable milestones, public-private partnerships, alliances with stakeholders, and interagency cooperation. ?? 2002 Elsevier Science Inc. All rights reserved.

  11. 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

  12. Management information systems. [United Kingdom

    Energy Technology Data Exchange (ETDEWEB)

    Hartley, D.; Spence, A.C.

    1985-02-01

    The successful application in the United Kingdom of the real time monitoring and control systems (MINOS) for underground mining operations, particularly in coal transport and the development of coalface monitoring (FIDO) in 1980 led naturally to the design of an operational data base for management. A User Group of experienced colliery managers produced a Management Information System (MIS) requirements specification and began the evolution of the systems of today. Twenty-four mines operate MIS in different ways from total dependency to a means of checking their manual reporting system. MIS collects useful data from all the major MINOS applications and provides a means of manually inputting other, relevant information. A wide variety of displays and reports are available to management, adjusted to meet individual requirements. The benefits from the use of MIS are difficult to quantify, since they become part of the management process. Further developments are taking place based on operational experience and requirements and taking advantage of the recent advances in computer technology. MIS is the modern management tool in British coal mining, collecting, storing, analysing and presenting accurate information upon which management decision making is based.

  13. 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

  14. 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...... based on ISD literature and on Churchman's (1971) inquiring systems. The second part presents the use of the framework in an ISD project. The case is used to show the applicability of the framework and to highlight the advantages of this approach. The main theoretical implication is that the framework...

  15. 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....

  16. 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.

  17. 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

  18. 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....

  19. 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.

  20. Information systems for materials performance

    International Nuclear Information System (INIS)

    Roberge, P.

    1999-01-01

    The rapid development of accessible computing power in the 1980s has led to the use of machine intelligence in every sphere of engineering. The incredible progress in computing power and availability has also created a tremendous wealth of information available at the touch of few buttons. However, such wealth can easily provoke what is commonly described as 'information overload'. The massive number of connections produced by a single search of the web, for example, can greatly overwhelm users of this new technology. The rapidity of Web searches is due to the synergy between progress made in network connectivity protocols, intelligent search strategies and supporting hardware. This paper will attempt to define the basic elements of machine intelligence in the context of corrosion engineering and examine what has been done or could be done to introduce artificial thinking into daily operations. This paper will also review some modem software systems commonly used for information processing and internet searches. (author)

  1. 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

  2. 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

    of biological networks using tools from graph theory to the application of dynamical systems theory to understand the behavior of complex biological systems. We show how network approaches support and extend traditional mechanistic strategies but also offer novel strategies for dealing with biological...... strategies? When and how can network and mechanistic approaches interact in productive ways? In this paper we address these questions by focusing on how biological networks are represented and analyzed in a diverse class of case studies. Our examples span from the investigation of organizational properties...

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. Selecting practice management information systems.

    Science.gov (United States)

    Worley, R; Ciotti, V

    1997-01-01

    Despite enormous advances in information systems, the process by which most medical practices select them has remained virtually unchanged for decades: the request for proposal (RFP). Unfortunately, vendors have learned ways to minimize the value of RFP checklists to where purchasers now learn little about the system functionality. The authors describe a selection methodology that replaces the RFP with scored demos, reviews of vendor user manuals and mathematically structured reference checking. In a recent selection process at a major medical center, these techniques yielded greater user buy-in and favorable contract terms as well.

  9. 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

  10. Hanford Environmental Information System (HEIS)

    International Nuclear Information System (INIS)

    1994-01-01

    The purpose of the Soil subject area of the Hanford Environmental Information System (HEIS) is to manage the data acquired from soil samples, both geologic and surface, and sediment samples. Stored in the Soil subject area are data relevant to the soil samples, laboratory analytical results, and field measurements. The two major types of data make up the Soil subject area are data concerning the samples and data about the chemical and/or radiologic analyses of soil samples

  11. Scottish Nuclear's information systems strategy

    International Nuclear Information System (INIS)

    Inglis, P.

    1991-01-01

    Scottish Nuclear, the company which has owned and operated Scotland's nuclear power generating capacity since privatization, inherited a substantial amount of computer hardware and software from its predecessor, the South of Scotland Electricity Board. Each of the two power stations, Torness and Hunterston, were using Digital Vax clusters as the Scottish Nuclear company was formed. This had a major influence on the information systems strategy which has subsequently been adopted. (UK)

  12. 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.)

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

    Indian Academy of Sciences (India)

    B J Rao

    2018-02-13

    Feb 13, 2018 ... Lorencova 2016), sociology, physics, computer science, economics and even biology ... dynamic complexity associated with them at multiple levels? .... Social anthropology and the science of chaos (Oxford: Berghahn Books).

  14. Multiway modeling and analysis in stem cell systems biology

    Directory of Open Access Journals (Sweden)

    Vandenberg Scott L

    2008-07-01

    Full Text Available Abstract Background Systems biology refers to multidisciplinary approaches designed to uncover emergent properties of biological systems. Stem cells are an attractive target for this analysis, due to their broad therapeutic potential. A central theme of systems biology is the use of computational modeling to reconstruct complex systems from a wealth of reductionist, molecular data (e.g., gene/protein expression, signal transduction activity, metabolic activity, etc.. A number of deterministic, probabilistic, and statistical learning models are used to understand sophisticated cellular behaviors such as protein expression during cellular differentiation and the activity of signaling networks. However, many of these models are bimodal i.e., they only consider row-column relationships. In contrast, multiway modeling techniques (also known as tensor models can analyze multimodal data, which capture much more information about complex behaviors such as cell differentiation. In particular, tensors can be very powerful tools for modeling the dynamic activity of biological networks over time. Here, we review the application of systems biology to stem cells and illustrate application of tensor analysis to model collagen-induced osteogenic differentiation of human mesenchymal stem cells. Results We applied Tucker1, Tucker3, and Parallel Factor Analysis (PARAFAC models to identify protein/gene expression patterns during extracellular matrix-induced osteogenic differentiation of human mesenchymal stem cells. In one case, we organized our data into a tensor of type protein/gene locus link × gene ontology category × osteogenic stimulant, and found that our cells expressed two distinct, stimulus-dependent sets of functionally related genes as they underwent osteogenic differentiation. In a second case, we organized DNA microarray data in a three-way tensor of gene IDs × osteogenic stimulus × replicates, and found that application of tensile strain to a

  15. Technical Literature Review Concerning Management Information Systems.

    Science.gov (United States)

    interrelationships of the many aspects of management information systems (MIS); that is, with how analysis, design, operation, evaluation, and user considerations affect management information systems . (Author)

  16. Industrial systems biology and its impact on synthetic biology of yeast cell factories.

    Science.gov (United States)

    Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

    2016-06-01

    Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal of developing improved yeast cell factories. Biotechnol. Bioeng. 2016;113: 1164-1170. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  17. Industrial systems biology and its impact on synthetic biology of yeast cell factories

    DEFF Research Database (Denmark)

    Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

    2016-01-01

    Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools......, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex...... regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal...

  18. Structure, function, and behaviour of computational models in systems biology.

    Science.gov (United States)

    Knüpfer, Christian; Beckstein, Clemens; Dittrich, Peter; Le Novère, Nicolas

    2013-05-31

    Systems Biology develops computational models in order to understand biological phenomena. The increasing number and complexity of such "bio-models" necessitate computer support for the overall modelling task. Computer-aided modelling has to be based on a formal semantic description of bio-models. But, even if computational bio-models themselves are represented precisely in terms of mathematical expressions their full meaning is not yet formally specified and only described in natural language. We present a conceptual framework - the meaning facets - which can be used to rigorously specify the semantics of bio-models. A bio-model has a dual interpretation: On the one hand it is a mathematical expression which can be used in computational simulations (intrinsic meaning). On the other hand the model is related to the biological reality (extrinsic meaning). We show that in both cases this interpretation should be performed from three perspectives: the meaning of the model's components (structure), the meaning of the model's intended use (function), and the meaning of the model's dynamics (behaviour). In order to demonstrate the strengths of the meaning facets framework we apply it to two semantically related models of the cell cycle. Thereby, we make use of existing approaches for computer representation of bio-models as much as possible and sketch the missing pieces. The meaning facets framework provides a systematic in-depth approach to the semantics of bio-models. It can serve two important purposes: First, it specifies and structures the information which biologists have to take into account if they build, use and exchange models. Secondly, because it can be formalised, the framework is a solid foundation for any sort of computer support in bio-modelling. The proposed conceptual framework establishes a new methodology for modelling in Systems Biology and constitutes a basis for computer-aided collaborative research.

  19. 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

  20. Information Security and Integrity Systems

    Science.gov (United States)

    1990-01-01

    Viewgraphs from the Information Security and Integrity Systems seminar held at the University of Houston-Clear Lake on May 15-16, 1990 are presented. A tutorial on computer security is presented. The goals of this tutorial are the following: to review security requirements imposed by government and by common sense; to examine risk analysis methods to help keep sight of forest while in trees; to discuss the current hot topic of viruses (which will stay hot); to examine network security, now and in the next year to 30 years; to give a brief overview of encryption; to review protection methods in operating systems; to review database security problems; to review the Trusted Computer System Evaluation Criteria (Orange Book); to comment on formal verification methods; to consider new approaches (like intrusion detection and biometrics); to review the old, low tech, and still good solutions; and to give pointers to the literature and to where to get help. Other topics covered include security in software applications and development; risk management; trust: formal methods and associated techniques; secure distributed operating system and verification; trusted Ada; a conceptual model for supporting a B3+ dynamic multilevel security and integrity in the Ada runtime environment; and information intelligence sciences.

  1. The aims of systems biology: between molecules and organisms.

    Science.gov (United States)

    Noble, D

    2011-05-01

    The systems approach to biology has a long history. Its recent rapid resurgence at the turn of the century reflects the problems encountered in interpreting the sequencing of the genome and the failure of that immense achievement to provide rapid and direct solutions to major multi-factorial diseases. This paper argues that systems biology is necessarily multilevel and that there is no privileged level of causality in biological systems. It is an approach rather than a separate discipline. Functionality arises from biological networks that interact with the genome, the environment and the phenotype. This view of biology is very different from the gene-centred views of neo-Darwinism and molecular biology. In neuroscience, the systems approach leads naturally to 2 important conclusions: first, that the idea of 'programs' in the brain is confusing, and second, that the self is better interpreted as a process than as an object. © Georg Thieme Verlag KG Stuttgart · New York.

  2. CIMS: The Cartographic Information Management System,

    Science.gov (United States)

    1981-01-01

    use. Large-scale information systems may cover large amounts of information such as the Land Identification and Information Management System (LIMS...small computer in managing the information holdings of a mapping institute. The result is the Cartographic Information Management System (CIMS), a...American countrie.s. 1 .- - _ _ _ _. = _ m m m THE CARTOGRAPHIC INFORMATION MANAGEMENT SYSTEM System Rationale Interactive computer-assisted cartography

  3. 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.

  4. 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.

  5. BIRS - Bioterrorism Information Retrieval System.

    Science.gov (United States)

    Tewari, Ashish Kumar; Rashi; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Jain, Chakresh Kumar

    2013-01-01

    Bioterrorism is the intended use of pathogenic strains of microbes to widen terror in a population. There is a definite need to promote research for development of vaccines, therapeutics and diagnostic methods as a part of preparedness to any bioterror attack in the future. BIRS is an open-access database of collective information on the organisms related to bioterrorism. The architecture of database utilizes the current open-source technology viz PHP ver 5.3.19, MySQL and IIS server under windows platform for database designing. Database stores information on literature, generic- information and unique pathways of about 10 microorganisms involved in bioterrorism. This may serve as a collective repository to accelerate the drug discovery and vaccines designing process against such bioterrorist agents (microbes). The available data has been validated from various online resources and literature mining in order to provide the user with a comprehensive information system. The database is freely available at http://www.bioterrorism.biowaves.org.

  6. On the interplay between mathematics and biology: hallmarks toward a new systems biology.

    Science.gov (United States)

    Bellomo, Nicola; Elaiw, Ahmed; Althiabi, Abdullah M; Alghamdi, Mohammed Ali

    2015-03-01

    This paper proposes a critical analysis of the existing literature on mathematical tools developed toward systems biology approaches and, out of this overview, develops a new approach whose main features can be briefly summarized as follows: derivation of mathematical structures suitable to capture the complexity of biological, hence living, systems, modeling, by appropriate mathematical tools, Darwinian type dynamics, namely mutations followed by selection and evolution. Moreover, multiscale methods to move from genes to cells, and from cells to tissue are analyzed in view of a new systems biology approach. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Hanford Environmental Information System (HEIS)

    International Nuclear Information System (INIS)

    1994-01-01

    The Well subject area of the Hanford Environmental Information System (HEIS) manages data relevant to wells, boreholes and test pits constructed at the Hanford Site for soil sampling, geologic analysis and/or ground-water monitoring, and sampling for hydrochemical and radiological analysis. Data stored in the Well subject area include information relevant to the construction of the wells and boreholes, structural modifications to existing wells and boreholes, the location of wells, boreholes and test pits, and the association of wells, boreholes and test pits with organization entities such as waste sites. Data resulting from ground-water sampling performed at wells are stored in tables in the Ground-Water subject area. Geologic data collected during drilling, including particle sizing and interpretative geologic summaries, are stored in tables in the Geologic subject area. Data from soil samples taken during the drilling or excavation and sent for chemical and/or radiological analysis are stored in the Soil subject area

  8. 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.

  9. 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

  10. SEEK: a systems biology data and model management platform.

    NARCIS (Netherlands)

    Wolstencroft, K.J.; Owen, S.; Krebs, O.; Nguyen, Q.; Stanford, N.J.; Golebiewski, M.; Weidemann, A.; Bittkowski, M.; An, L.; Shockley, D.; Snoep, J.L.; Mueller, W.; Goble, C.

    2015-01-01

    Background: Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources to facilitate the sharing and integration of data, and for linking of data to systems

  11. An Evaluation of Information Consistency in Grid Information Systems

    CERN Document Server

    Field, Laurence

    2017-01-01

    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. Novel approaches to the integration and analysis of systems biology data

    OpenAIRE

    Ramírez, Fidel

    2011-01-01

    The opportunity to investigate whole cellular systems using experimental and computational high-throughput methods leads to the generation of unprecedented amounts of data. Processing of these data often results in large lists of genes or proteins that need to be analyzed and interpreted in the context of all other biological information that is already available. To support such analyses, repositories aggregating and merging the biological information contained in different databases are req...

  13. 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

  14. Information System of Municipal Office

    OpenAIRE

    Surý, Jaroslav

    2009-01-01

    Bakalářská práce se zabývá problematikou návrhu a implementací informačního systému obecního úřadu. Pro práci byly použity tyto programovací jazyky: PHP, JavaScript, HTML, CSS a databáze MySQL. The Bachelor's Thesis is concerned with the dilemma of suggestion and implementation of information system for municipal office. The programming languages: PHP, JavaScript, HTML, CSS and database MySQL were used for this bachelor's thesis. E

  15. 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.)

  16. Plant Systems Biology at the Single-Cell Level.

    Science.gov (United States)

    Libault, Marc; Pingault, Lise; Zogli, Prince; Schiefelbein, John

    2017-11-01

    Our understanding of plant biology is increasingly being built upon studies using 'omics and system biology approaches performed at the level of the entire plant, organ, or tissue. Although these approaches open new avenues to better understand plant biology, they suffer from the cellular complexity of the analyzed sample. Recent methodological advances now allow plant scientists to overcome this limitation and enable biological analyses of single-cells or single-cell-types. Coupled with the development of bioinformatics and functional genomics resources, these studies provide opportunities for high-resolution systems analyses of plant phenomena. In this review, we describe the recent advances, current challenges, and future directions in exploring the biology of single-cells and single-cell-types to enhance our understanding of plant biology as a system. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. 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.

  18. 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…

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

    DEFF Research Database (Denmark)

    Green, Sara; Wolkenhauer, Olaf

    2014-01-01

    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......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...

  20. 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...

  1. Developing a knowledge system for information operations

    CSIR Research Space (South Africa)

    Leenen, L

    2011-03-01

    Full Text Available In this paper we describe a research project to develop an optimal information retrieval system in an Information Operations domain. Information Operations is the application and management of information to gain an advantage over an opponent...

  2. 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

  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. 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

  5. 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.

  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. The Systems Biology Research Tool: evolvable open-source software

    Directory of Open Access Journals (Sweden)

    Wright Jeremiah

    2008-06-01

    Full Text Available Abstract Background Research in the field of systems biology requires software for a variety of purposes. Software must be used to store, retrieve, analyze, and sometimes even to collect the data obtained from system-level (often high-throughput experiments. Software must also be used to implement mathematical models and algorithms required for simulation and theoretical predictions on the system-level. Results We introduce a free, easy-to-use, open-source, integrated software platform called the Systems Biology Research Tool (SBRT to facilitate the computational aspects of systems biology. The SBRT currently performs 35 methods for analyzing stoichiometric networks and 16 methods from fields such as graph theory, geometry, algebra, and combinatorics. New computational techniques can be added to the SBRT via process plug-ins, providing a high degree of evolvability and a unifying framework for software development in systems biology. Conclusion The Systems Biology Research Tool represents a technological advance for systems biology. This software can be used to make sophisticated computational techniques accessible to everyone (including those with no programming ability, to facilitate cooperation among researchers, and to expedite progress in the field of systems biology.

  9. 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...

  10. Information on black-footed ferret biology collected within the framework of ferret conservation

    Science.gov (United States)

    Biggins, Dean E.

    2012-01-01

    Once feared to be extinct, black-footed ferrets (Mustela nigripes) were rediscovered near Meeteetse, Wyoming, in 1981, resulting in renewed conservation and research efforts for this highly endangered species. A need for information directly useful to recovery has motivated much monitoring of ferrets since that time, but field activities have enabled collection of data relevant to broader biological themes. This special feature is placed in a context of similar books and proceedings devoted to ferret biology and conservation. Articles include general observations on ferrets, modeling of potential impacts of ferrets on prairie dogs (Cynomys spp.), discussions on relationships of ferrets to prairie dog habitats at several spatial scales (from individual burrows to patches of burrow systems) and a general treatise on the status of black-footed ferret recovery.

  11. '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.

  12. 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.

  13. 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.

  14. 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.

  15. Information Science and Information Systems: Conjunct Subjects Disjunct Disciplines.

    Science.gov (United States)

    Ellis, David; Allen, David; Wilson, Tom

    1999-01-01

    Examines the relationship between information science and information-systems (IS) research through analysis of the subject literature of each field and by citation and co-citation analysis of highly cited researchers in each field. Subfields of user studies and information-retrieval research were selected to represent information-science…

  16. Human Development VII: A Spiral Fractal Model of Fine Structure of Physical Energy Could Explain Central Aspects of Biological Information, Biological Organization and Biological Creativity

    Directory of Open Access Journals (Sweden)

    Søren Ventegodt

    2006-01-01

    Full Text Available In this paper we have made a draft of a physical fractal essence of the universe, a sketch of a new cosmology, which we believe to lay at the root of our new holistic biological paradigm. We present the fractal roomy spiraled structures and the energy-rich dancing “infinite strings” or lines of the universe that our hypothesis is based upon. The geometric language of this cosmology is symbolic and both pre-mathematical and pre-philosophical. The symbols are both text and figures, and using these we step by step explain the new model that at least to some extent is able to explain the complex informational system behind morphogenesis, ontogenesis, regeneration and healing. We suggest that it is from this highly dynamic spiraled structure that organization of cells, organs, and the wholeness of the human being including consciousness emerge. The model of ““dancing fractal spirals” carries many similarities to premodern cultures descriptions of the energy of the life and universe. Examples are the Native American shamanistic descriptions of their perception of energy and the old Indian Yogis descriptions of the life-energy within the body and outside. Similar ideas of energy and matter are found in the modern superstring theories. The model of the informational system of the organism gives new meaning to Bateson’s definition of information: “A difference that makes a difference”, and indicates how information-directed self-organization can exist on high structural levels in living organisms, giving birth to their subjectivity and consciousness.

  17. A computerized legal information management system | Ohiagu ...

    African Journals Online (AJOL)

    A computerized legal information management system. ... process through the filling system using the survey research methodology. ... A framework for the design and implementation of a legal information management system was presented.

  18. 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.

  19. Geo-scientific information system

    International Nuclear Information System (INIS)

    Gedeon, M.; De Soete, H.

    2010-01-01

    Document available in extended abstract form only. In the framework of the geological disposal of radioactive waste, the characterization of the Boom Clay and its environment has been going on for more than 30 years. During this time, a great quantity of data was collected to support the research on the reference host rock. A geo-scientific information system was built to store the data acquired in this framework,. The aim was to create a central place where all types of data could be looked up for further analyses and interpretation. All data stored in the system are geographically referenced. The GSIS database was created using PostgreSQL database with PostGIS spatial extension. PostgreSQL is an open-source object-relational database management system (ORDBMS) based on POSTGRES, developed at the University of California at Berkeley Computer Science Department. POSTGRES pioneered many concepts that only became available in some commercial database systems much later. PostgreSQL is an open-source descendant of this original Berkeley code. It supports SQL92 and SQL99 and offers many modern features: complex queries, foreign keys, triggers, views, transactional integrity, multi-version concurrency control. PostGIS is an extension to the PostgreSQL object-relational database system which allows GIS (Geographic Information Systems) objects to be stored in the database. PostGIS includes support for GiST-based R-Tree spatial indexes, and functions for analysis and processing of GIS objects. The GSIS database consists of three principal database domains, the objects database domain (ObjectsDB) and the data domain (DataDB). ObjectsDB includes the definitions (including the geometry/ position) and relative hierarchy of the objects. The objects are defined as structures, enclosed areas or scientific instruments with definable geometry (2D or 3D) including samples used to acquire data (boreholes, piezometers, sampling locations, galleries, sensors, etc.). DataDB includes

  20. 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.

  1. 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

  2. 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...

  3. 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.

  4. Hera : Development of semantic web information systems

    NARCIS (Netherlands)

    Houben, G.J.P.M.; Barna, P.; Frasincar, F.; Vdovják, R.; Cuella Lovelle, J.M.; et al., xx

    2003-01-01

    As a consequence of the success of the Web, methodologies for information system development need to consider systems that use the Web paradigm. These Web Information Systems (WIS) use Web technologies to retrieve information from the Web and to deliver information in a Web presentation to the

  5. LIFE CYCLE OF INFORMATION SYSTEMS

    Directory of Open Access Journals (Sweden)

    Y. S. Sennik

    2015-01-01

    Full Text Available This work is a generalization of the theoretical propositions related to the life cycle of information systems. There was given the definition of the life cycle, specify which items you should include every step of the cycle. Describes the methodology division of the life cycle on the main stage, including methodology Rational Unified Process. The description of the fundamental standards in this area. Special attention was paid to the work of the basic life cycle models. It was carried out their comparative characteristics. On the basis of the theoretical propositions, it was concluded that the preferred model of the life cycle for the corporate network is a spiral model and the use of international standards in the life cycle saves a lot of effort, time and material resources.

  6. Hanford Environmental Information System (HEIS)

    International Nuclear Information System (INIS)

    1994-01-01

    The purpose of the Tank Characterization Data subject area of the Hanford Environmental Information System (HEIS) is to manage data acquired from waste tank characterization efforts. Tank samples provide the data stored in this subject area. Also included are data from tank inventories. These data are analyzed to determine disposal requirements, such as suitability for grout or vitrification. The data provide the basis for developing safety analyses and closure plans, and for establishing and verifying compliance with waste acceptance specifications. Two major sources of data make up the tank characterization data subject area: Data from single-shell and double-shell tank core samples -- core sampling analytical results include physical properties, radionuclides, major chemicals, and hazardous components; and data from waste tank supernatant samples. Four types of data are stored in the TCD subject area. Qualifiers for TCD analytical result data are listed in Appendix A. Data loading and verification procedures are described in Appendix B

  7. 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.

  8. 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.)

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. Information fluency for undergraduate biology majors: applications of inquiry-based learning in a developmental biology course.

    Science.gov (United States)

    Gehring, Kathleen M; Eastman, Deborah A

    2008-01-01

    Many initiatives for the improvement of undergraduate science education call for inquiry-based learning that emphasizes investigative projects and reading of the primary literature. These approaches give students an understanding of science as a process and help them integrate content presented in courses. At the same time, general initiatives to promote information fluency are being promoted on many college and university campuses. Information fluency refers to discipline-specific processing of information, and it involves integration of gathered information with specific ideas to form logical conclusions. We have implemented the use of inquiry-based learning to enhance and study discipline-specific information fluency skills in an upper-level undergraduate Developmental Biology course. In this study, an information literacy tutorial and a set of linked assignments using primary literature analysis were integrated with two inquiry-based laboratory research projects. Quantitative analysis of student responses suggests that the abilities of students to identify and apply valid sources of information were enhanced. Qualitative assessment revealed a set of patterns by which students gather and apply information. Self-assessment responses indicated that students recognized the impact of the assignments on their abilities to gather and apply information and that they were more confident about these abilities for future biology courses and beyond.

  16. 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

  17. Internet security information system implement method

    International Nuclear Information System (INIS)

    Liu Baoxu; Mei Jie; Xu Rongsheng; An Dehai; Yu Mingjian; Chen Xiangyang; Zheng Peng

    1999-01-01

    On the basis of analysis of the key elements that will affect the Internet Security Information System, the author takes UNIX Operating System as an example, and provides the important stages that must be considered when implementing the Internet Security Information System. An implemental model of the Internet Security Information System is given

  18. 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...

  19. 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

  20. Designing an oil spill information management system

    International Nuclear Information System (INIS)

    Douligeris, C.; Collins, J.; Iakovou, E.; Sun, P.; Riggs, K.R.

    1995-01-01

    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