WorldWideScience

Sample records for center systems biology

  1. Advancing Cancer Systems Biology: Introducing the Center for the Development of a Virtual Tumor, CViT

    Directory of Open Access Journals (Sweden)

    Sean Martin

    2007-01-01

    Full Text Available Integrative cancer biology research relies on a variety of data-driven computational modeling and simulation methods and techniques geared towards gaining new insights into the complexity of biological processes that are of critical importance for cancer research. These include the dynamics of gene-protein interaction networks, the percolation of subcellular perturbations across scales and the impact they may have on tumorigenesis in both experiments and clinics. Such innovative ‘systems’ research will greatly benefi t from enabling Information Technology that is currently under development, including an online collaborative environment, a Semantic Web based computing platform that hosts data and model repositories as well as high-performance computing access. Here, we present one of the National Cancer Institute’s recently established Integrative Cancer Biology Programs, i.e. the Center for the Development of a Virtual Tumor, CViT, which is charged with building a cancer modeling community, developing the aforementioned enabling technologies and fostering multi-scale cancer modeling and simulation.

  2. Biological Semiconductors | NCI Technology Transfer Center | TTC

    Science.gov (United States)

    The National Cancer Institute's Cancer Diagnostic Program and the Food and Drug Administration's Center for Devices and Radiological Health is seeking statements of capability or interest from parties interested in collaborative research to further develop, evaluate, or commercialize biological semiconductors as diagnostic sensors.

  3. 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).

  4. Systems interface biology

    OpenAIRE

    Francis J Doyle; Stelling, Jörg

    2006-01-01

    The field of systems biology has attracted the attention of biologists, engineers, mathematicians, physicists, chemists and others in an endeavour to create systems-level understanding of complex biological networks. In particular, systems engineering methods are finding unique opportunities in characterizing the rich behaviour exhibited by biological systems. In the same manner, these new classes of biological problems are motivating novel developments in theoretical systems approaches. Henc...

  5. Computational systems chemical biology.

    Science.gov (United States)

    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) (Nat Chem Biol 3: 447-450, 2007).The overarching goal of computational SCB is to develop tools for integrated chemical-biological data acquisition, filtering and processing, by taking into account relevant information related to interactions between proteins and small molecules, possible metabolic transformations of small molecules, as well as associated information related to genes, networks, small molecules, and, where applicable, mutants and variants of those proteins. There is yet an unmet need to develop an integrated in silico pharmacology/systems biology continuum that embeds drug-target-clinical outcome (DTCO) triplets, a capability that is vital to the future of chemical biology, pharmacology, and systems biology. Through the development of the SCB approach, scientists will be able to start addressing, in an integrated simulation environment, questions that make the best use of our ever-growing chemical and biological data repositories at the system-wide level. This chapter reviews some of the major research concepts and describes key components that constitute the emerging area of computational systems chemical biology.

  6. Engineering scalable biological systems

    OpenAIRE

    Lu, Timothy K.

    2010-01-01

    Synthetic biology is focused on engineering biological organisms to study natural systems and to provide new solutions for pressing medical, industrial, and environmental problems. At the core of engineered organisms are synthetic biological circuits that execute the tasks of sensing inputs, processing logic, and performing output functions. In the last decade, significant progress has been made in developing basic designs for a wide range of biological circuits in bacteria, yeast, and mammal...

  7. [Systems biology of cancer].

    Science.gov (United States)

    Barillot, Emmanuel; Calzone, Laurence; Zinovyev, Andrei

    2009-01-01

    Cancer Systems Biology is now accepted and recognized as a promising field both in biological and clinical research. It relies on a rigorous formalization of regulation networks into precise and unambiguous languages. It provides both detailed and modular views of the complex biological system of interest (which in cancer research is typically an interaction network governing essential cellular events such as proliferation, differentiation, cell death...) in order to facilitate the interpretation of molecular profiles of tumors. The translation of these networks into mathematical models allows prediction of the evolution of the system in time and under certain perturbations. As a result, it can not only propose specific target points for pharmaceutical purposes, but also anticipate the evolution of tumors as well as their classifications. These characteristics emphasize the important role of Systems Biology of Cancer in the future of biomedical research.

  8. Systems cell biology.

    Science.gov (United States)

    Mast, Fred D; Ratushny, Alexander V; Aitchison, John D

    2014-09-15

    Systems cell biology melds high-throughput experimentation with quantitative analysis and modeling to understand many critical processes that contribute to cellular organization and dynamics. Recently, there have been several advances in technology and in the application of modeling approaches that enable the exploration of the dynamic properties of cells. Merging technology and computation offers an opportunity to objectively address unsolved cellular mechanisms, and has revealed emergent properties and helped to gain a more comprehensive and fundamental understanding of cell biology.

  9. CSMB | Center For Structural Molecular Biology

    Data.gov (United States)

    Federal Laboratory Consortium — The Center for Structural Molecular Biologyat ORNL is dedicated to developing instrumentation and methods for determining the 3-dimensional structures of proteins,...

  10. 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 ‘‘...

  11. 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."

  12. Integrative radiation systems biology.

    Science.gov (United States)

    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. PMID:24411063

  13. Integrative radiation systems biology

    International Nuclear Information System (INIS)

    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

  14. 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...

  15. Systems biology, emergence and antireductionism.

    Science.gov (United States)

    Kesić, Srdjan

    2016-09-01

    This study explores the conceptual history of systems biology and its impact on philosophical and scientific conceptions of reductionism, antireductionism and emergence. Development of systems biology at the beginning of 21st century transformed biological science. Systems biology is a new holistic approach or strategy how to research biological organisms, developed through three phases. The first phase was completed when molecular biology transformed into systems molecular biology. Prior to the second phase, convergence between applied general systems theory and nonlinear dynamics took place, hence allowing the formation of systems mathematical biology. The second phase happened when systems molecular biology and systems mathematical biology, together, were applied for analysis of biological data. Finally, after successful application in science, medicine and biotechnology, the process of the formation of modern systems biology was completed. Systems and molecular reductionist views on organisms were completely opposed to each other. Implications of systems and molecular biology on reductionist-antireductionist debate were quite different. The analysis of reductionism, antireductionism and emergence issues, in the era of systems biology, revealed the hierarchy between methodological, epistemological and ontological antireductionism. Primarily, methodological antireductionism followed from the systems biology. Only after, epistemological and ontological antireductionism could be supported.

  16. Systems biology in animal sciences

    NARCIS (Netherlands)

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

    2011-01-01

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

  17. 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....

  18. ECO-BIOLOGICAL SYSTEM MODELING

    Directory of Open Access Journals (Sweden)

    T. I. Burak

    2015-01-01

    Full Text Available The methodology for computer modeling of complex eco-biological models is presented in this paper. It is based on system approach of J. Forrester. Developed methodology is universal for complex ecological and biological systems. Modeling algorithm considers specialties of eco-biological systems and shows adequate and accurate results in practice. 

  19. Protein microarrays for systems biology

    Institute of Scientific and Technical Information of China (English)

    Lina Yang; Shujuan Guo; Yang Li; Shumin Zhou; Shengce Tao

    2011-01-01

    Systems biology holds the key for understanding biological systems on a system level. It eventually holds the key for the treatment and cure of complex diseases such as cancer,diabetes, obesity, mental disorders, and many others. The '-omics' technologies, such as genomics, transcriptomics,proteomics, and metabonomics, are among the major driving forces of systems biology. Featured as highthroughput, miniaturized, and capable of parallel analysis,protein microarrays have already become an important technology platform for systems biology, In this review, we will focus on the system level or global analysis of biological systems using protein microarrays. Four major types of protein microarrays will be discussed: proteome microarrays, antibody microarrays, reverse-phase protein arrays,and lectin microarrays. We will also discuss the challenges and future directions of protein microarray technologies and their applications for systems biology. We strongly believe that protein microarrays will soon become an indispensable and invaluable tool for systems biology.

  20. Data acquisition and analysis at the Structural Biology Center

    International Nuclear Information System (INIS)

    The Structural Biology Center (SBC), a national user facility for macromolecular crystallography located at Argonne National Laboratory's Advanced Photon Source, is currently being built and commissioned. SBC facilities include a bending-magnet beamline, an insertion-device beamline, laboratory and office space adjacent to the beamlines, and associated instrumentation, experimental apparatus, and facilities. SBC technical facilities will support anomalous dispersion phasing experiments, data collection from microcrystals, data collection from crystals with large molecular structures and rapid data collection from multiple related crystal structures for protein engineering and drug design. The SBC Computing Systems and Software Engineering Group is tasked with developing the SBC Control System, which includes computing systems, network, and software. The emphasis of SBC Control System development has been to provide efficient and convenient beamline control, data acquisition, and data analysis for maximal facility and experimenter productivity. This paper describes the SBC Control System development, specifically data acquisition and analysis at the SBC, and the development methods used to meet this goal

  1. UC Merced Center for Computational Biology Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Colvin, Michael; Watanabe, Masakatsu

    2010-11-30

    Final report for the UC Merced Center for Computational Biology. The Center for Computational Biology (CCB) was established to support multidisciplinary scientific research and academic programs in computational biology at the new University of California campus in Merced. In 2003, the growing gap between biology research and education was documented in a report from the National Academy of Sciences, Bio2010 Transforming Undergraduate Education for Future Research Biologists. We believed that a new type of biological sciences undergraduate and graduate programs that emphasized biological concepts and considered biology as an information science would have a dramatic impact in enabling the transformation of biology. UC Merced as newest UC campus and the first new U.S. research university of the 21st century was ideally suited to adopt an alternate strategy - to create a new Biological Sciences majors and graduate group that incorporated the strong computational and mathematical vision articulated in the Bio2010 report. CCB aimed to leverage this strong commitment at UC Merced to develop a new educational program based on the principle of biology as a quantitative, model-driven science. Also we expected that the center would be enable the dissemination of computational biology course materials to other university and feeder institutions, and foster research projects that exemplify a mathematical and computations-based approach to the life sciences. As this report describes, the CCB has been successful in achieving these goals, and multidisciplinary computational biology is now an integral part of UC Merced undergraduate, graduate and research programs in the life sciences. The CCB began in fall 2004 with the aid of an award from U.S. Department of Energy (DOE), under its Genomes to Life program of support for the development of research and educational infrastructure in the modern biological sciences. This report to DOE describes the research and academic programs

  2. The biology of Phytophthora infestans at its center of origin

    NARCIS (Netherlands)

    Grünwald, N.J.; Flier, W.G.

    2005-01-01

    The central highlands of Mexico are considered to be a center of genetic diversity for both the potato late blight pathogen and for tuber-bearing Solanum spp. Recent work conducted in Mexico and South America sheds new light on the biology and evolution of Phytophthora infestans and other related Ph

  3. 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 ...

  4. 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.

  5. Telemetry System of Biological Parameters

    OpenAIRE

    2005-01-01

    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 consum...

  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. Learning System Center App Controller

    CERN Document Server

    Naeem, Nasir

    2015-01-01

    This book is intended for IT professionals working with Hyper-V, Azure cloud, VMM, and private cloud technologies who are looking for a quick way to get up and running with System Center 2012 R2 App Controller. To get the most out of this book, you should be familiar with Microsoft Hyper-V technology. Knowledge of Virtual Machine Manager is helpful but not mandatory.

  8. 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),...

  9. 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...... of nutritional research is, therefore, to borrow methods that are well established in medical and pharmacological research. In this thesis, we use advanced data-mining tools for the construction of a database with available, state-of-the-art information concerning the interaction of food and its molecular...

  10. Aging and computational systems biology.

    Science.gov (United States)

    Mooney, Kathleen M; Morgan, Amy E; Mc Auley, Mark T

    2016-01-01

    Aging research is undergoing a paradigm shift, which has led to new and innovative methods of exploring this complex phenomenon. The systems biology approach endeavors to understand biological systems in a holistic manner, by taking account of intrinsic interactions, while also attempting to account for the impact of external inputs, such as diet. A key technique employed in systems biology is computational modeling, which involves mathematically describing and simulating the dynamics of biological systems. Although a large number of computational models have been developed in recent years, these models have focused on various discrete components of the aging process, and to date no model has succeeded in completely representing the full scope of aging. Combining existing models or developing new models may help to address this need and in so doing could help achieve an improved understanding of the intrinsic mechanisms which underpin aging.

  11. Modelling coordination in biological systems

    OpenAIRE

    Clarke, David; Oliveira Costa, de, David; Arbab, Farhad

    2004-01-01

    We present an application of the Reo coordination paradigm to provide a compositional formal model for describing and reasoning about the behaviour of biological systems, such as regulatory gene networks. Reo governs the interaction and flow of data between components by allowing the construction of connector circuits which have a precise formal semantics. When applied to systems biology, the result is a graphical model, which is comprehensible, mathematically precise, and flexible

  12. Optimization in computational systems biology

    OpenAIRE

    Banga Julio R

    2008-01-01

    Abstract Optimization aims to make a system or design as effective or functional as possible. Mathematical optimization methods are widely used in engineering, economics and science. This commentary is focused on applications of mathematical optimization in computational systems biology. Examples are given where optimization methods are used for topics ranging from model building and optimal experimental design to metabolic engineering and synthetic biology. Finally, several perspectives for ...

  13. Ten questions about systems biology

    DEFF Research Database (Denmark)

    Joyner, Michael J; Pedersen, Bente K

    2011-01-01

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

  14. Informing Biological Design by Integration of Systems and Synthetic Biology

    OpenAIRE

    Smolke, Christina D.; Silver, Pamela A.

    2011-01-01

    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.

  15. Kinetic Modeling of Biological Systems

    Energy Technology Data Exchange (ETDEWEB)

    Resat, Haluk; Petzold, Linda; Pettigrew, Michel F.

    2009-04-21

    The dynamics of how its constituent components interact define the spatio-temporal response of a natural system to stimuli. Modeling the kinetics of the processes that represent a biophysical system has long been pursued with the aim of improving our understanding of the studied system. Due to the unique properties of biological systems, in addition to the usual difficulties faced in modeling the dynamics of physical or chemical systems, biological simulations encounter difficulties that result from intrinsic multiscale and stochastic nature of the biological processes. This chapter discusses the implications for simulation of models involving interacting species with very low copy numbers, which often occur in biological systems and give rise to significant relative fluctuations. The conditions necessitating the use of stochastic kinetic simulation methods and the mathematical foundations of the stochastic simulation algorithms are presented. How the well-organized structural hierarchies often seen in biological systems can lead to multiscale problems, and possible ways to address the encountered computational difficulties are discussed. We present the details of the existing kinetic simulation methods, and discuss their strengths and shortcomings. A list of the publicly available kinetic simulation tools and our reflections for future prospects are also provided.

  16. Circadian systems biology in Metazoa.

    Science.gov (United States)

    Lin, Li-Ling; Huang, Hsuan-Cheng; Juan, Hsueh-Fen

    2015-11-01

    Systems biology, which can be defined as integrative biology, comprises multistage processes that can be used to understand components of complex biological systems of living organisms and provides hierarchical information to decoding life. Using systems biology approaches such as genomics, transcriptomics and proteomics, it is now possible to delineate more complicated interactions between circadian control systems and diseases. The circadian rhythm is a multiscale phenomenon existing within the body that influences numerous physiological activities such as changes in gene expression, protein turnover, metabolism and human behavior. In this review, we describe the relationships between the circadian control system and its related genes or proteins, and circadian rhythm disorders in systems biology studies. To maintain and modulate circadian oscillation, cells possess elaborative feedback loops composed of circadian core proteins that regulate the expression of other genes through their transcriptional activities. The disruption of these rhythms has been reported to be associated with diseases such as arrhythmia, obesity, insulin resistance, carcinogenesis and disruptions in natural oscillations in the control of cell growth. This review demonstrates that lifestyle is considered as a fundamental factor that modifies circadian rhythm, and the development of dysfunctions and diseases could be regulated by an underlying expression network with multiple circadian-associated signals.

  17. Photosynthetic system as a biological functional element

    International Nuclear Information System (INIS)

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

  18. 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

  19. Systems biology and cancer, [Editorial

    OpenAIRE

    Soto, A M; Sonnenschein, C; Maini, P.K.

    2011-01-01

    The systems approach to complex biological problems has rapidly gained ground during the first decade of this century. There are several reasons for this development. An important one is that while the achievement of sequencing the complete human genome, and those of other species, has been of great benefit to fundamental science, for example in comparative genomics and evolutionary biology, it has not led to the expected quick and simple solutions to multifactorial diseases (2010). On the co...

  20. Sulfur-centered reactive intermediates derived from the oxidation of sulfur compounds of biological interest

    Energy Technology Data Exchange (ETDEWEB)

    Abedinzadeh, Z. [Lab. de Chimie Physique, UMR, Univ. Rene Descartes, Paris (France)

    2001-02-01

    Sulphur compounds play a central role in the structure and activity of many vital systems. In the living cell, sulfur constitutes an essential part of the defense against oxidative damage and is transformed into a variety of sulfur free radical species. Many studies of the chemistry of sulfur-centered radicals using pulse radiolysis and photolysis techniques to detect and measure the kinetics of these radicals have been published and reviewed. This paper discusses the present state of research on the formation and reactivity of certain sulfur-centered radicals [RS{sup .}, RSS{sup .}, RS{sup .+}, (RSSR){sup .+}] and their implications for biological systems. (author)

  1. Ten questions about systems biology

    DEFF Research Database (Denmark)

    Joyner, Michael J; Pedersen, Bente K

    2011-01-01

    In this paper we raise 'ten questions' broadly related to 'omics', the term systems biology, and why the new biology has failed to deliver major therapeutic advances for many common diseases, especially diabetes and cardiovascular disease. We argue that a fundamentally narrow and reductionist...... perspective about the contribution of genes and genetic variants to disease is a key reason 'omics' has failed to deliver the anticipated breakthroughs. We then point out the critical utility of key concepts from physiology like homeostasis, regulated systems and redundancy as major intellectual tools...... 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...

  2. Bridging the gap between systems biology and synthetic biology

    OpenAIRE

    Liu, Di; Hoynes-O’Connor, Allison; Zhang, Fuzhong

    2013-01-01

    Systems biology is an inter-disciplinary science that studies the complex interactions and the collective behavior of a cell or an organism. Synthetic biology, as a technological subject, combines biological science and engineering, allowing the design and manipulation of a system for certain applications. Both systems and synthetic biology have played important roles in the recent development of microbial platforms for energy, materials, and environmental applications. More importantly, syst...

  3. 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’.

  4. Modelling coordination in biological systems

    NARCIS (Netherlands)

    Clarke, D.G.; Oliveira Costa, D.F. de; Arbab, F.

    2004-01-01

    We present an application of the Reo coordination paradigm to provide a compositional formal model for describing and reasoning about the behaviour of biological systems, such as regulatory gene networks. Reo governs the interaction and flow of data between components by allowing the construction of

  5. 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...

  6. 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.

  7. Records Center Program Billing System

    Data.gov (United States)

    National Archives and Records Administration — RCPBS supports the Records center programs (RCP) in producing invoices for the storage (NARS-5) and servicing of National Archives and Records Administration’s...

  8. Evaluation of a fungal collection as certified reference material producer and as a biological resource center.

    Science.gov (United States)

    Forti, Tatiana; Souto, Aline da S S; do Nascimento, Carlos Roberto S; Nishikawa, Marilia M; Hubner, Marise T W; Sabagh, Fernanda P; Temporal, Rosane Maria; Rodrigues, Janaína M; da Silva, Manuela

    2016-01-01

    Considering the absence of standards for culture collections and more specifically for biological resource centers in the world, in addition to the absence of certified biological material in Brazil, this study aimed to evaluate a Fungal Collection from Fiocruz, as a producer of certified reference material and as Biological Resource Center (BRC). For this evaluation, a checklist based on the requirements of ABNT ISO GUIA34:2012 correlated with the ABNT NBR ISO/IEC17025:2005, was designed and applied. Complementing the implementation of the checklist, an internal audit was performed. An evaluation of this Collection as a BRC was also conducted following the requirements of the NIT-DICLA-061, the Brazilian internal standard from Inmetro, based on ABNT NBR ISO/IEC 17025:2005, ABNT ISO GUIA 34:2012 and OECD Best Practice Guidelines for BRCs. This was the first time that the NIT DICLA-061 was applied in a culture collection during an internal audit. The assessments enabled the proposal for the adequacy of this Collection to assure the implementation of the management system for their future accreditation by Inmetro as a certified reference material producer as well as its future accreditation as a Biological Resource Center according to the NIT-DICLA-061. PMID:26991280

  9. Evaluation of a fungal collection as certified reference material producer and as a biological resource center

    Directory of Open Access Journals (Sweden)

    Tatiana Forti

    2016-06-01

    Full Text Available Abstract Considering the absence of standards for culture collections and more specifically for biological resource centers in the world, in addition to the absence of certified biological material in Brazil, this study aimed to evaluate a Fungal Collection from Fiocruz, as a producer of certified reference material and as Biological Resource Center (BRC. For this evaluation, a checklist based on the requirements of ABNT ISO GUIA34:2012 correlated with the ABNT NBR ISO/IEC17025:2005, was designed and applied. Complementing the implementation of the checklist, an internal audit was performed. An evaluation of this Collection as a BRC was also conducted following the requirements of the NIT-DICLA-061, the Brazilian internal standard from Inmetro, based on ABNT NBR ISO/IEC 17025:2005, ABNT ISO GUIA 34:2012 and OECD Best Practice Guidelines for BRCs. This was the first time that the NIT DICLA-061 was applied in a culture collection during an internal audit. The assessments enabled the proposal for the adequacy of this Collection to assure the implementation of the management system for their future accreditation by Inmetro as a certified reference material producer as well as its future accreditation as a Biological Resource Center according to the NIT-DICLA-061.

  10. System biology of gene regulation.

    Science.gov (United States)

    Baitaluk, Michael

    2009-01-01

    ) questions of biological relevance. Thus systems biology could be treated as such a socioscientific phenomenon and a new approach to both experiments and theory that is defined by the strategy of pursuing integration of complex data about the interactions in biological systems from diverse experimental sources using interdisciplinary tools and personnel. PMID:19623486

  11. Robust Design of Biological Circuits: Evolutionary Systems Biology Approach

    OpenAIRE

    Bor-Sen Chen; Chih-Yuan Hsu; Jing-Jia Liou

    2011-01-01

    Artificial gene circuits have been proposed to be embedded into microbial cells that function as switches, timers, oscillators, and the Boolean logic gates. Building more complex systems from these basic gene circuit components is one key advance for biologic circuit design and synthetic biology. However, the behavior of bioengineered gene circuits remains unstable and uncertain. In this study, a nonlinear stochastic system is proposed to model the biological systems with intrinsic parameter ...

  12. 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.

  13. Bridging the gaps in systems biology

    OpenAIRE

    Marija Cvijovic; Joachim Almquist; Jonas Hagmar; Stefan Hohmann; Hans\\u2011Michael Kaltenbach; Edda Klipp; Marcus Krantz; Pedro Mendes; Sven Nelander; Jens Nielsen; Andrea Pagnani; Natasa Przulj; Andreas Raue; J\\xf6rg Stelling; Szymon Stoma

    2014-01-01

    International audience Systems biology aims at creating mathematical models, i.e., computational reconstructions of biological systems and processes that will result in a new level of understanding-the elucidation of the basic and presumably conserved "design" and "engineering" principles of biomolecular systems. Thus, systems biology will move biology from a phenomenological to a predictive science. Mathematical modeling of biological networks and processes has already greatly improved ou...

  14. 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.

  15. 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.

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

    OpenAIRE

    Bor-Sen Chen; Chia-Chou Wu

    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...

  17. Microsoft System Center 2012 Orchestrator cookbook

    CERN Document Server

    Erskine, Samuel

    2013-01-01

    This book is written in a practical, Cookbook style with numerous chapters and recipes focusing on creating runbooks to automate mission critical and everyday administration tasks.System Center 2012 Orchestrator is for administrators who wish to simplify the process of automating systems administration tasks. This book assumes that you have a basic knowledge of Windows Server 2008 Administration, Active Directory, Network Systems, and Microsoft System Center technologies.

  18. Cell biology: at the center of modern biomedicine.

    Science.gov (United States)

    Budde, Priya Prakash; Williams, Elizabeth H; Misteli, Tom

    2012-10-01

    How does basic cell biology contribute to biomedicine? A new series of Features in JCB provides a cross section of compelling examples of how basic cell biology findings can lead to therapeutics. These articles highlight the fruitful, essential, and increasingly prominent bridge that exists between cell biology and the clinic.

  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. 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.

  1. 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.

  2. 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.

  3. Analyzing the Biology on the System Level

    Institute of Scientific and Technical Information of China (English)

    Wei Tong

    2004-01-01

    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, and summarizes the analysis methods, experimental technologies, research developments, and so on in the four key fields of systems biology-systemic structures, dynamics, control methods, and design principles.

  4. Data Center Equipment Location and Monitoring System

    DEFF Research Database (Denmark)

    2013-01-01

    Abstract: Data center equipment location systems include hardware and software to provide information on the location, monitoring, and security of servers and other equipment in equipment racks. The systems provide a wired alternative to the wireless RFID tag system by using electronic ID tags...

  5. 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.

  6. Modeling biological systems with Answer Set Programming

    OpenAIRE

    Thiele, Sven

    2012-01-01

    Biology has made great progress in identifying and measuring the building blocks of life. The availability of high-throughput methods in molecular biology has dramatically accelerated the growth of biological knowledge for various organisms. The advancements in genomic, proteomic and metabolomic technologies allow for constructing complex models of biological systems. An increasing number of biological repositories is available on the web, incorporating thousands of biochemical reactions and ...

  7. Integrating systems biology models and biomedical ontologies

    Directory of Open Access Journals (Sweden)

    de Bono Bernard

    2011-08-01

    Full Text Available Abstract Background 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. Results 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. Conclusions 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.

  8. Principles of Systems Biology, No. 8.

    Science.gov (United States)

    2016-08-01

    Advances in biological engineering headline this month's Cell Systems call (Cell Systems 1, 307), alongside intriguing applications of modeling from the Elf, Goentoro, and Wolf groups. Check out our recent blogpost: http://crosstalk.cell.com/blog/a-call-for-papers-on-biological-engineering-and-synthetic-biology. PMID:27559920

  9. Spatial Aspects in Biological System Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Resat, Haluk; Costa, Michelle N.; Shankaran, Harish

    2011-01-30

    Mathematical models of the dynamical properties of biological systems aim to improve our understanding of the studied system with the ultimate goal of being able to predict system responses in the absence of experimentation. Despite the enormous advances that have been made in biological modeling and simulation, the inherently multiscale character of biological systems and the stochasticity of biological processes continue to present significant computational and conceptual challenges. Biological systems often consist of well-organized structural hierarchies, which inevitably lead to multiscale problems. This chapter introduces and discusses the advantages and shortcomings of several simulation methods that are being used by the scientific community to investigate the spatio-temporal properties of model biological systems. We first describe the foundations of the methods and then describe their relevance and possible application areas with illustrative examples from our own research. Possible ways to address the encountered computational difficulties are also discussed.

  10. 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...

  11. Resonances in the two centers Coulomb system

    Energy Technology Data Exchange (ETDEWEB)

    Seri, Marcello

    2012-09-14

    In this work we investigate the existence of resonances for two-centers Coulomb systems with arbitrary charges in two and three dimensions, defining them in terms of generalized complex eigenvalues of a non-selfadjoint deformation of the two-center Schroedinger operator. After giving a description of the bifurcation of the classical system for positive energies, we construct the resolvent kernel of the operators and we prove that they can be extended analytically to the second Riemann sheet. The resonances are then defined and studied with numerical methods and perturbation theory.

  12. Tritium Exchange in Biological Systems

    International Nuclear Information System (INIS)

    Whenever tritium-labelled water is employed as a test solute or tracer in biological systems, an appreciable exchange between tritium and labile hydrogen atoms occurs that frequently affects the nature and interpretation of experimental results. The studies reported here are concerned with the magnitude of the effect that tritium exchange introduces into measurements of total body water and water metabolism in animals and humans. Direct measurements of exchange were made in rats, guinea pigs, pigeons, and rabbits. Tritium-labelled water was administered intravenously or by mouth, and tritium space and turnover determined from the concentration of tritium in blood. The animals were then desiccated to constant weight in vacuo. The specific activity of water collected periodically during desiccation increased by 50% as a result of isotope effects. Water from combustion of dried rabbit tissues contained about 2% of the tritium originally given to the animal. Adipose tissue alone contained little or no exchange tritium. The dried tissues of the other animals were rehydrated with inactive water and the appearance of tritium in the water observed. The specific activity of the water increased in exponential fashion, i.e., 1-exp. (kt), with about 90% of exchange occurring with a half-time of 1 h, and the remaining 10% with a half-time of 10 h. The total tritium extracted accounted for 1.5 to 3.5% of the dose given to the animal, which agrees with the difference between the tritium space and total body water determined by desiccation. An indirect estimate of exchange in humans was derived from concurrent measurements of tritium and antipyrene spaces. The average difference of about 2% in water volume agrees with the direct estimates of exchanges in animals. It is evident that tritium space should be reduced by about 2% to identify it with total body water. The magnitude and relatively slow rate of exchange may also influence the interpretation of metabolic studies with

  13. Learner-Centered Inquiry in Undergraduate Biology: Positive Relationships with Long-Term Student Achievement

    Science.gov (United States)

    Derting, Terry L.; Ebert-May, Diane

    2010-01-01

    We determined short- and long-term correlates of a revised introductory biology curriculum on understanding of biology as a process of inquiry and learning of content. In the original curriculum students completed two traditional lecture-based introductory courses. In the revised curriculum students completed two new learner-centered,…

  14. Telemetry Computer System at Wallops Flight Center

    Science.gov (United States)

    Bell, H.; Strock, J.

    1980-01-01

    This paper describes the Telemetry Computer System in operation at NASA's Wallops Flight Center for real-time or off-line processing, storage, and display of telemetry data from rockets and aircraft. The system accepts one or two PCM data streams and one FM multiplex, converting each type of data into computer format and merging time-of-day information. A data compressor merges the active streams, and removes redundant data if desired. Dual minicomputers process data for display, while storing information on computer tape for further processing. Real-time displays are located at the station, at the rocket launch control center, and in the aircraft control tower. The system is set up and run by standard telemetry software under control of engineers and technicians. Expansion capability is built into the system to take care of possible future requirements.

  15. Network systems biology for targeted cancer therapies

    Institute of Scientific and Technical Information of China (English)

    Ting-Ting Zhou

    2012-01-01

    The era of targeted cancer therapies has arrived.However,due to the complexity of biological systems,the current progress is far from enough.From biological network modeling to structural/dynamic network analysis,network systems biology provides unique insight into the potential mechanisms underlying the growth and progression of cancer cells.It has also introduced great changes into the research paradigm of cancer-associated drug discovery and drug resistance.

  16. 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...

  17. Genomes, Phylogeny, and Evolutionary Systems Biology

    Energy Technology Data Exchange (ETDEWEB)

    Medina, Monica

    2005-03-25

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

  18. Systems Medicine: Evolution of Systems Biology From Bench To Bedside

    OpenAIRE

    Wang, Rui-Sheng; Maron, Bradley A.; Loscalzo, Joseph

    2015-01-01

    High-throughput experimental techniques for generating genomes, transcriptomes, proteomes, metabolomes, and interactomes have provided unprecedented opportunities to interrogate biological systems and human diseases on a global level. Systems biology integrates the mass of heterogeneous high-throughput data and predictive computational modeling to understand biological functions as system-level properties. Most human diseases are biological states caused by multiple components of perturbed pa...

  19. Biological control in greenhouse systems.

    Science.gov (United States)

    Paulitz, T C; Bélanger, R R

    2001-01-01

    The controlled environment of greenhouses, the high value of the crops, and the limited number of registered fungicides offer a unique niche for the biological control of plant diseases. During the past ten years, over 80 biocontrol products have been marketed worldwide. A large percentage of these have been developed for greenhouse crops. Products to control soilborne pathogens such as Sclerotinia, Pythium, Rhizoctonia and Fusarium include Coniothyrium minitans, species of Gliocladium, Trichoderma, Streptomyces, and Bacillus, and nonpathogenic Fusarium. Products containing Trichoderma, Ampelomyces quisqualis, Bacillus, and Ulocladium are being developed to control the primary foliar diseases, Botrytis and powdery mildew. The development of Pseudomonas for the control of Pythium diseases in hydroponics and Pseudozyma flocculosa for the control of powdery mildew by two Canadian research programs is presented. In the future, biological control of diseases in greenhouses could predominate over chemical pesticides, in the same way that biological control of greenhouse insects predominates in the United Kingdom. The limitations in formulation, registration, and commercialization are discussed, along with suggested future research priorities. PMID:11701861

  20. Genomes, phylogeny, and evolutionary systems biology

    OpenAIRE

    Medina, Monica

    2005-01-01

    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 c...

  1. Developmental systems biology flourishing on new technologies

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Organism development is a systems level process. It has benefited greatly from the recent technological advances in the field of systems biology. DNA microarray, phenome, interactome and transcriptome mapping, the new generation of deep sequencing technologies,and faster and better computational and modeling approaches have opened new frontiers for both systems biologists and developmental biologists to reexamine the old developmental biology questions, such as pattern formation, and to tackle new problems, such as stem cell reprogramming. As showcased in the International Developmental Systems Biology Symposium organized by Chinese Academy of Sciences, developmental systems biology is flourishing in many perspectives, from the evolution of developmental systems, to the underlying genetic and molecular pathways and networks, to the genomic, epigenomic and noncoding levels, to the computational analysis and modeling. We believe that the field will continue to reap rewards into the future with these new approaches.

  2. Developmental systems biology flourishing on new technologies.

    Science.gov (United States)

    Han, Jing-Dong J; Liu, Yi; Xue, Huiling; Xia, Kai; Yu, Hong; Zhu, Shanshan; Chen, Zhang; Zhang, Wei; Huang, Zheng; Jin, Chunyu; Xian, Bo; Li, Jing; Hou, Lei; Han, Yixing; Niu, Chaoqun; Alcon, Timothy C

    2008-10-01

    Organism development is a systems level process. It has benefited greatly from the recent technological advances in the field of systems biology. DNA microarray, phenome, interactome and transcriptome mapping, the new generation of deep sequencing technologies, and faster and better computational and modeling approaches have opened new frontiers for both systems biologists and developmental biologists to reexamine the old developmental biology questions, such as pattern formation, and to tackle new problems, such as stem cell reprogramming. As showcased in the International Developmental Systems Biology Symposium organized by Chinese Academy of Sciences, developmental systems biology is flourishing in many perspectives, from the evolution of developmental systems, to the underlying genetic and molecular pathways and networks, to the genomic, epigenomic and noncoding levels, to the computational analysis and modeling. We believe that the field will continue to reap rewards into the future with these new approaches. PMID:18937914

  3. Applicability of computational systems biology in toxicology.

    Science.gov (United States)

    Kongsbak, Kristine; Hadrup, Niels; Audouze, Karine; Vinggaard, Anne Marie

    2014-07-01

    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. However, computational systems biology offers more advantages than providing a high-throughput literature search; it may form the basis for establishment of hypotheses on potential links between environmental chemicals and human diseases, which would be very difficult to establish experimentally. This is possible due to the existence of comprehensive databases containing information on networks of human protein-protein interactions and protein-disease associations. Experimentally determined targets of the specific chemical of interest can be fed into these networks to obtain additional information that can 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 in the hypothesis-generating phase of toxicological research.

  4. Systems Biology Analysis of Heterocellular Signaling.

    Science.gov (United States)

    Tape, Christopher J

    2016-08-01

    Tissues comprise multiple heterotypic cell types (e.g., epithelial, mesenchymal, and immune cells). Communication between heterotypic cell types is essential for biological cohesion and is frequently dysregulated in disease. Despite the importance of heterocellular communication, most systems biology techniques do not report cell-specific signaling data from mixtures of cells. As a result, our existing perspective of cellular behavior under-represents the influence of heterocellular signaling. Recent technical advances now permit the resolution of systems-level cell-specific signaling data. This review discusses how new physical, spatial, and isotopic resolving methods are facilitating unique systems biology studies of heterocellular communication. PMID:27087613

  5. Mastering System Center 2012 Configuration Manager

    CERN Document Server

    Rachui, Steve; Martinez, Santos; Daalmans, Peter

    2012-01-01

    Expert coverage of Microsoft's highly anticipated network software deployment tool The latest version of System Center Configuration Manager (SCCM) is a dramatic update of its predecessor Configuration Manager 2007, and this book offers intermediate-to-advanced coverage of how the new SCCM boasts a simplified hierarchy, role-based security, a new console, flexible application deployment, and mobile management. You'll explore planning and installation, migrating from SCCM 2007, deploying software and operating systems, security, monitoring and troubleshooting, and automating and customizing SCC

  6. Contextual design defining customer-centered systems

    CERN Document Server

    Beyer, Hugh

    1997-01-01

    This book introduces a customer-centered approach to business by showing how data gathered from people while they work can drive the definition of a product or process while supporting the needs of teams and their organizations. This is a practical, hands-on guide for anyone trying to design systems that reflect the way customers want to do their work. The authors developed Contextual Design, the method discussed here, through their work with teams struggling to design products and internal systems. In this book, you'll find the underlying principles of the method and how to apply them to diff

  7. Bioferroelectricity and optical properties of biological systems

    Science.gov (United States)

    Bystrov, Vladimir; Bystrova, Natalia

    2003-08-01

    A bioferroelectric approach to analysis of ferroelectric behavior of biological systems is presented. The optical properties of nerve fibers, biomembrane ion channels, and purple membrane films containing bacteriorhodopsin are analyzed. The features, influence of the proton subsystem and proton transfer on the hydrogen-bonded biomolecular structures are analyzed within the ferroelectric liquid-crystal model and possible biomedical applications discussed. The ferroelectric behavior of biological systems and the set of various bioferroelectric effects are considered within the limits of phenomenological theory of ferroelectrics. The nonlinear response to weak actions under conditions critical to human organism is one of specific features characterizing biological objects on molecular, cell and organism levels.

  8. Learner-Centered Inquiry in Undergraduate Biology: Positive Relationships with Long-Term Student Achievement

    OpenAIRE

    Derting, Terry L.; Ebert-May, Diane

    2010-01-01

    We determined short- and long-term correlates of a revised introductory biology curriculum on understanding of biology as a process of inquiry and learning of content. In the original curriculum students completed two traditional lecture-based introductory courses. In the revised curriculum students completed two new learner-centered, inquiry-based courses. The new courses differed significantly from those of the original curriculum through emphases on critical thinking, collaborative work, a...

  9. 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...

  10. Systems biology: leading the revolution in ecotoxicology.

    Science.gov (United States)

    Garcia-Reyero, Natàlia; Perkins, Edward J

    2011-02-01

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

  11. Sino-Dutch joint center for systematic chemical biology opens in Dalian

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    @@ The inaugural ceremony for the Sino-Dutch Joint Research Center for Systematic Chemical Biology was held during the "Chinese-Dutch Workshop on Personalized Medicine and Preventive Diagnostics" convened on 10 July at the CAS Dalian Institute of Chemical Physics (DICP).

  12. 75 FR 6401 - Medical Devices Regulated by the Center for Biologics Evaluation and Research; Availability of...

    Science.gov (United States)

    2010-02-09

    ... Evaluation and Research; Availability of Summaries of Safety and Effectiveness Data for Premarket Approval... safety and effectiveness data to the Division of Dockets Management (HFA-305), Food and Drug... the Center for Biologics Evaluation and Research (CBER). This list is intended to inform the public...

  13. 76 FR 59407 - Center for Biologics Evaluation and Research Report of Scientific and Medical Literature and...

    Science.gov (United States)

    2011-09-26

    ... Scientific and Medical Literature and Information on Non-Standardized Allergenic Extracts in the Diagnosis... scientific and medical literature and information concerning the use of non-standardized allergenic extracts... ``Center for Biologics Evaluation and Research Report of Scientific and Medical Literature and...

  14. 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...

  15. Computational systems biology in cancer brain metastasis.

    Science.gov (United States)

    Peng, Huiming; Tan, Hua; Zhao, Weiling; Jin, Guangxu; Sharma, Sambad; Xing, Fei; Watabe, Kounosuke; Zhou, Xiaobo

    2016-01-01

    Brain metastases occur in 20-40% of patients with advanced malignancies. A better understanding of the mechanism of this disease will help us to identify novel therapeutic strategies. In this review, we will discuss the systems biology approaches used in this area, including bioinformatics and mathematical modeling. Bioinformatics has been used for identifying the molecular mechanisms driving brain metastasis and mathematical modeling methods for analyzing dynamics of a system and predicting optimal therapeutic strategies. We will illustrate the strategies, procedures, and computational techniques used for studying systems biology in cancer brain metastases. We will give examples on how to use a systems biology approach to analyze a complex disease. Some of the approaches used to identify relevant networks, pathways, and possibly biomarkers in metastasis will be reviewed into details. Finally, certain challenges and possible future directions in this area will also be discussed.

  16. Statistical Model Checking for Biological Systems

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  17. Stennis Space Center Environmental Geographic Information System

    Science.gov (United States)

    Lovely, Janette; Cohan, Tyrus

    2000-01-01

    As NASA's lead center for rocket propulsion testing, the John C. Stennis Space Center (SSC) monitors and assesses the off-site impacts of such testing through its Environmental Office (SSC-EO) using acoustical models and ancillary data. The SSC-EO has developed a geographical database, called the SSC Environmental Geographic Information System (SSC-EGIS), that covers an eight-county area bordering the NASA facility. Through the SSC-EGIS, the Enivronmental Office inventories, assesses, and manages the nearly 139,000 acres that comprise Stennis Space Center and its surrounding acoustical buffer zone. The SSC-EGIS contains in-house data as well as a wide range of data obtained from outside sources, including private agencies and local, county, state, and U.S. government agencies. The database comprises cadastral/geodetic, hydrology, infrastructure, geo-political, physical geography, and socio-economic vector and raster layers. The imagery contained in the database is varied, including low-resolution imagery, such as Landsat TM and SPOT; high-resolution imagery, such as IKONOS and AVIRIS; and aerial photographs. The SSC-EGIS has been an integral part of several major projects and the model upon which similar EGIS's will be developed for other NASA facilities. The Corps of Engineers utilized the SSC-EGIS in a plan to establish wetland mitigation sites within the SSC buffer zone. Mississippi State University employed the SSC-EGIS in a preliminary study to evaluate public access points within the buffer zone. The SSC-EO has also expressly used the SSC-EGIS to assess noise pollution modeling, land management/wetland mitigation assessment, environmental hazards mapping, and protected areas mapping for archaeological sites and for threatened and endangered species habitats. The SSC-EO has several active and planned projects that will also make use of the SSC-EGIS during this and the coming fiscal year.

  18. 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...

  19. Holarchical Systems and Emotional Holons : Biologically-Inspired System Designs for Control of Autonomous Aerial Vehicles

    Science.gov (United States)

    Ippolito, Corey; Plice, Laura; Pisanich, Greg

    2003-01-01

    The BEES (Bio-inspired Engineering for Exploration Systems) for Mars project at NASA Ames Research Center has the goal of developing bio-inspired flight control strategies to enable aerial explorers for Mars scientific investigations. This paper presents a summary of our ongoing research into biologically inspired system designs for control of unmanned autonomous aerial vehicle communities for Mars exploration. First, we present cooperative design considerations for robotic explorers based on the holarchical nature of biological systems and communities. Second, an outline of an architecture for cognitive decision making and control of individual robotic explorers is presented, modeled after the emotional nervous system of cognitive biological systems. Keywords: Holarchy, Biologically Inspired, Emotional UAV Flight Control

  20. Data driven computing for Biological Systems

    Energy Technology Data Exchange (ETDEWEB)

    Samatova, Nagiza F.; Gorin, Andrey; Uberbacher, Edward; Karpinets, Tatiana V.; Park, Byung H.; Pan, Chongle; Straatsma, TP; Cannon, William R.; Resat, Haluk; Lins, Roberto D.; Oehmen, Christopher S.

    2007-11-01

    Biological breakthroughs that can lead to improved diagnosis and treatment of diseases, generation of clean energy, and solutions to other critical societal problems require high performance, data-intensive computational tools that have the ability to process, analyze and cohesively integrate massive amounts of data and information in real time. Biological computing problems are typically data-intensive and must share very large sets of data effectively across many processors. However, the various components of biological systems, composed of complex networks and pathways, must be integrated to gain a coherent understanding of the system. The more different types of data that can be integrated, the deeper the insights into the biology of the system being studied. Conventional analysis software, however, hasn’t been able to efficiently deal with such massive data set. The goal of the Data-Intensive Computing for Complex Biological Systems (BioPilot) project, a multiyear project funded by the U.S. Department of Energy’s Office of Advanced Scientific Computing Research (ASCR), is to create an integrated suite of highly flexible, highly adaptable pipelines of computational tools for analyzing large-scale data sets that will be used to address specific challenges facing the U.S. Department of Energy (DOE) and our society.

  1. Ohjelmistolisenssien hallinta Microsoft System Center Configuration Managerilla

    OpenAIRE

    Kalliomäki, Jukka

    2012-01-01

    Tässä työssä pyritään selvittämään, miten hyvin ohjelmistolisenssien hallinta onnistuu Microsoft System Center Configuration Managerin (SCCM) Asset Intelligence -ominaisuudella. Lisäksi tavoitteena on selvittää, miten ominaisuus sopisi Seinäjoen koulutuskuntayhtymän kaltaiseen ympäristöön. Työn edetessä käydään läpi päätyypit erilaisista lisensseistä ja kerrotaan tärkeimmät seikat käytettävästä ohjelmistosta ja sen toiminnasta. Lisäksi työssä opastetaan, miten Asset Intelligence otetaan k...

  2. Stochastic Physics, Complex Systems and Biology

    CERN Document Server

    Qian, Hong

    2012-01-01

    In complex systems, the interplay between nonlinear and stochastic dynamics gives rise to an evolution process in Darwinian sense with punctuated equilibrium, random "mutations" and "adaptations". The emergent discrete states in such a system, i.e., attractors, have natural robustness against both internal and external perturbations. Epigenetic states of a biological cell, a mesoscopic nonlinear stochastic open biochemical system, could be understood through such a framework.

  3. 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.

  4. 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.

  5. Semantic annotation for biological information retrieval system.

    Science.gov (United States)

    Oshaiba, Mohamed Marouf Z; El Houby, Enas M F; Salah, Akram

    2015-01-01

    Online literatures are increasing in a tremendous rate. Biological domain is one of the fast growing domains. Biological researchers face a problem finding what they are searching for effectively and efficiently. The aim of this research is to find documents that contain any combination of biological process and/or molecular function and/or cellular component. This research proposes a framework that helps researchers to retrieve meaningful documents related to their asserted terms based on gene ontology (GO). The system utilizes GO by semantically decomposing it into three subontologies (cellular component, biological process, and molecular function). Researcher has the flexibility to choose searching terms from any combination of the three subontologies. Document annotation is taking a place in this research to create an index of biological terms in documents to speed the searching process. Query expansion is used to infer semantically related terms to asserted terms. It increases the search meaningful results using the term synonyms and term relationships. The system uses a ranking method to order the retrieved documents based on the ranking weights. The proposed system achieves researchers' needs to find documents that fit the asserted terms semantically.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-09-30

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

  7. INTERNATIONAL CONFERENCE ON INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY (ISMB)

    Energy Technology Data Exchange (ETDEWEB)

    Debra Goldberg; Matthew Hibbs; Lukas Kall; Ravikumar Komandurglayavilli; Shaun Mahony; Voichita Marinescu; Itay Mayrose; Vladimir Minin; Yossef Neeman; Guy Nimrod; Marian Novotny; Stephen Opiyo; Elon Portugaly; Tali Sadka; Noboru Sakabe; Indra Sarkar; Marc Schaub; Paul Shafer; Olena Shmygelska; Gregory Singer; Yun Song; Bhattacharya Soumyaroop; Michael Stadler; Pooja Strope; Rong Su; Yuval Tabach; Hongseok Tae; Todd Taylor; Michael Terribilini; Asha Thomas; Nam Tran; Tsai-Tien Tseng; Akshay Vashist; Parthiban Vijaya; Kai Wang; Ting Wang; Lai Wei; Yong Woo; Chunlei Wu; Yoshihiro Yamanishi; Changhui Yan; Jack Yang; Mary Yang; Ping Ye; Miao Zhang

    2009-12-29

    The Intelligent Systems for Molecular Biology (ISMB) conference has provided a general forum for disseminating the latest developments in bioinformatics on an annual basis for the past 13 years. ISMB is a multidisciplinary conference that brings together scientists from computer science, molecular biology, mathematics and statistics. The goal of the ISMB meeting is to bring together biologists and computational scientists in a focus on actual biological problems, i.e., not simply theoretical calculations. The combined focus on “intelligent systems” and actual biological data makes ISMB a unique and highly important meeting, and 13 years of experience in holding the conference has resulted in a consistently well organized, well attended, and highly respected annual conference. The ISMB 2005 meeting was held June 25-29, 2005 at the Renaissance Center in Detroit, Michigan. The meeting attracted over 1,730 attendees. The science presented was exceptional, and in the course of the five-day meeting, 56 scientific papers, 710 posters, 47 Oral Abstracts, 76 Software demonstrations, and 14 tutorials were presented. The attendees represented a broad spectrum of backgrounds with 7% from commercial companies, over 28% qualifying for student registration, and 41 countries were represented at the conference, emphasizing its important international aspect. The ISMB conference is especially important because the cultures of computer science and biology are so disparate. ISMB, as a full-scale technical conference with refereed proceedings that have been indexed by both MEDLINE and Current Contents since 1996, bridges this cultural gap.

  8. Global biology - An interdisciplinary scientific research program at NASA, Ames Research Center

    Science.gov (United States)

    Lawless, J. G.; Colin, L.

    1983-01-01

    NASA has initiated new effort in Global Biology, the primary focus of which is to understand biogeochemical cycles. As part of this effort, an interdisciplinary team of scientists has formed at Ames Research Center to investigate the cycling of sulfur in the marine coastal zone and to study the cycling of nitrogen in terrestrial ecosystems. Both studies will use remotely sensed data, coupled with ground-based research, to identify and measure the transfer of major and minor biologically produced gases between these ecosystems and global reservoirs.

  9. Global Biology: An Interdisciplinary Scientific Research Program at NASA Ames Research Center

    Science.gov (United States)

    Lawless, James G.; Colin, Lawrence

    1984-01-01

    NASA has initiated new effort in Global Biology, the primary focus of which is to understand biogeochemical cycles. As part of this effort, an interdisciplinary team of scientists has formed at Ames Research Center to investigate the cycling of sulfur in the marine coastal zone and to study the cycling of nitrogen in terrestrial ecosystems. Both studies will use remotely sensed data, coupled with ground-based research, to identify and measure the transfer of major and minor biologically produced gases between these ecosystems and global reservoirs.

  10. 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.

  11. Modular microfluidic system for biological sample preparation

    Energy Technology Data Exchange (ETDEWEB)

    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.

  12. Language Based Techniques for Systems Biology

    DEFF Research Database (Denmark)

    Pilegaard, Henrik

    calculi have similarly been used for the study of bio-chemical reactive systems. In this dissertation it is argued that techniques rooted in the theory and practice of programming languages, language based techniques if you will, constitute a strong basis for the investigation of models of biological......Process calculus is the common denominator for a class of compact, idealised, domain-specific formalisms normally associated with the study of reactive concurrent systems within Computer Science. With the rise of the interactioncentred science of Systems Biology a number of bio-inspired process...... systems as formalised in a process calculus. In particular it is argued that Static Program Analysis provides a useful approach to the study of qualitative properties of such models. In support of this claim a number of static program analyses are developed for Regev’s BioAmbients – a bio-inspired variant...

  13. Active Learning and Student-centered Pedagogy Improve Student Attitudes and Performance in Introductory Biology

    OpenAIRE

    Armbruster, Peter; Patel, Maya; Johnson, Erika; Weiss, Martha

    2009-01-01

    We describe the development and implementation of an instructional design that focused on bringing multiple forms of active learning and student-centered pedagogies to a one-semester, undergraduate introductory biology course for both majors and nonmajors. Our course redesign consisted of three major elements: 1) reordering the presentation of the course content in an attempt to teach specific content within the context of broad conceptual themes, 2) incorporating active and problem-based lea...

  14. Center for Efficiency in Sustainable Energy Systems

    Energy Technology Data Exchange (ETDEWEB)

    Abraham, Martin [Youngstown State Univ., OH (United States)

    2016-01-31

    The main goal of the Center for Efficiency in Sustainable Energy Systems is to produce a methodology that evaluates a variety of energy systems. Task I. Improved Energy Efficiency for Industrial Processes: This task, completed in partnership with area manufacturers, analyzes the operation of complex manufacturing facilities to provide flexibilities that allow them to improve active-mode power efficiency, lower standby-mode power consumption, and use low cost energy resources to control energy costs in meeting their economic incentives; (2) Identify devices for the efficient transformation of instantaneous or continuous power to different devices and sections of industrial plants; and (3) use these manufacturing sites to demonstrate and validate general principles of power management. Task II. Analysis of a solid oxide fuel cell operating on landfill gas: This task consists of: (1) analysis of a typical landfill gas; (2) establishment of a comprehensive design of the fuel cell system (including the SOFC stack and BOP), including durability analysis; (3) development of suitable reforming methods and catalysts that are tailored to the specific SOFC system concept; and (4) SOFC stack fabrication with testing to demonstrate the salient operational characteristics of the stack, including an analysis of the overall energy conversion efficiency of the system. Task III. Demonstration of an urban wind turbine system: This task consists of (1) design and construction of two side-by-side wind turbine systems on the YSU campus, integrated through power control systems with grid power; (2) preliminary testing of aerodynamic control effectors (provided by a small business partner) to demonstrate improved power control, and evaluation of the system performance, including economic estimates of viability in an urban environment; and (3) computational analysis of the wind turbine system as an enabling activity for development of smart rotor blades that contain integrated sensor

  15. Computational systems biology for aging research.

    Science.gov (United States)

    Mc Auley, Mark T; Mooney, Kathleen M

    2015-01-01

    Computational modelling is a key component of systems biology and integrates with the other techniques discussed thus far in this book by utilizing a myriad of data that are being generated to quantitatively represent and simulate biological systems. This chapter will describe what computational modelling involves; the rationale for using it, and the appropriateness of modelling for investigating the aging process. How a model is assembled and the different theoretical frameworks that can be used to build a model are also discussed. In addition, the chapter will describe several models which demonstrate the effectiveness of each computational approach for investigating the constituents of a healthy aging trajectory. Specifically, a number of models will be showcased which focus on the complex age-related disorders associated with unhealthy aging. To conclude, we discuss the future applications of computational systems modelling to aging research.

  16. Effects of Pesticides on Biological Systems

    Directory of Open Access Journals (Sweden)

    Ergul Belge Kurutas

    2003-06-01

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

  17. Integrated physiology and systems biology of PPARα.

    Science.gov (United States)

    Kersten, Sander

    2014-07-01

    The Peroxisome Proliferator Activated Receptor alpha (PPARα) is a transcription factor that plays a major role in metabolic regulation. This review addresses the functional role of PPARα in intermediary metabolism and provides a detailed overview of metabolic genes targeted by PPARα, with a focus on liver. A distinction is made between the impact of PPARα on metabolism upon physiological, pharmacological, and nutritional activation. Low and high throughput gene expression analyses have allowed the creation of a comprehensive map illustrating the role of PPARα as master regulator of lipid metabolism via regulation of numerous genes. The map puts PPARα at the center of a regulatory hub impacting fatty acid uptake, fatty acid activation, intracellular fatty acid binding, mitochondrial and peroxisomal fatty acid oxidation, ketogenesis, triglyceride turnover, lipid droplet biology, gluconeogenesis, and bile synthesis/secretion. In addition, PPARα governs the expression of several secreted proteins that exert local and endocrine functions.

  18. 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. PMID:26696234

  19. Computer structures perspective on switching dynamics of simple biological systems

    OpenAIRE

    Moškon, Miha

    2012-01-01

    Synthetic biology is a rapidly evolving discipline that copes with the modifications of existent and with the construction of new biological systems with novel functionalities. Its interdisciplinarity arises from combining of engineering and biological sciences. Biological computing is a relatively new research field that is analyzing the possibilities of constructing a biological computer. Synthetic biology approaches can also be used in order to build biological computer. Certain levels of ...

  20. Graphical Modelling in Genetics and Systems Biology

    OpenAIRE

    Scutari, Marco

    2012-01-01

    Graphical modelling has a long history in statistics as a tool for the analysis of multivariate data, starting from Wright's path analysis and Gibbs' applications to statistical physics at the beginning of the last century. In its modern form, it was pioneered by Lauritzen and Wermuth and Pearl in the 1980s, and has since found applications in fields as diverse as bioinformatics, customer satisfaction surveys and weather forecasts. Genetics and systems biology are unique among these fields in...

  1. Systems Biology from a Yeast Omics Perspective

    OpenAIRE

    Snyder, Michael; Gallagher, Jennifer E.G.

    2009-01-01

    Systems biology represents a paradigm shift from the study of individual genes, proteins or other components to that of the analysis of entire pathways, cellular, developmental, or organismal processes. Large scale studies, primarily initiated in S. cerevisiae, have allowed the identification and characterization of components on an unprecedented level. Large scale interaction, transcription factor binding and phosphorylation data have enabled the elucidation of global regulatory networks. Th...

  2. Systems biology of cancer biomarker detection.

    Science.gov (United States)

    Mitra, Sanga; Das, Smarajit; Chakrabarti, Jayprokas

    2013-01-01

    Cancer systems-biology is an ever-growing area of research due to explosion of data; how to mine these data and extract useful information is the problem. To have an insight on carcinogenesis one need to systematically mine several resources, such as databases, microarray and next-generation sequences. This review encompasses management and analysis of cancer data, databases construction and data deposition, whole transcriptome and genome comparison, analysing results from high throughput experiments to uncover cellular pathways and molecular interactions, and the design of effective algorithms to identify potential biomarkers. Recent technical advances such as ChIP-on-chip, ChIP-seq and RNA-seq can be applied to get epigenetic information transformed into a high-throughput endeavour to which systems biology and bioinformatics are making significant inroads. The data from ENCODE and GENCODE projects available through UCSC genome browser can be considered as benchmark for comparison and meta-analysis. A pipeline for integrating next generation sequencing data, microarray data, and putting them together with the existing database is discussed. The understanding of cancer genomics is changing the way we approach cancer diagnosis and treatment. To give a better understanding of utilizing available resources' we have chosen oral cancer to show how and what kind of analysis can be done. This review is a computational genomic primer that provides a bird's eye view of computational and bioinformatics' tools currently available to perform integrated genomic and system biology analyses of several carcinoma.

  3. Center for Efficiency in Sustainable Energy Systems

    Energy Technology Data Exchange (ETDEWEB)

    Abraham, Martin [Youngstown State Univ., OH (United States)

    2016-01-31

    The main goal of the Center for Efficiency in Sustainable Energy Systems is to produce a methodology that evaluates a variety of energy systems. Task I. Improved Energy Efficiency for Industrial Processes: This task, completed in partnership with area manufacturers, analyzes the operation of complex manufacturing facilities to provide flexibilities that allow them to improve active-mode power efficiency, lower standby-mode power consumption, and use low cost energy resources to control energy costs in meeting their economic incentives; (2) Identify devices for the efficient transformation of instantaneous or continuous power to different devices and sections of industrial plants; and (3) use these manufacturing sites to demonstrate and validate general principles of power management. Task II. Analysis of a solid oxide fuel cell operating on landfill gas: This task consists of: (1) analysis of a typical landfill gas; (2) establishment of a comprehensive design of the fuel cell system (including the SOFC stack and BOP), including durability analysis; (3) development of suitable reforming methods and catalysts that are tailored to the specific SOFC system concept; and (4) SOFC stack fabrication with testing to demonstrate the salient operational characteristics of the stack, including an analysis of the overall energy conversion efficiency of the system. Task III. Demonstration of an urban wind turbine system: This task consists of (1) design and construction of two side-by-side wind turbine systems on the YSU campus, integrated through power control systems with grid power; (2) preliminary testing of aerodynamic control effectors (provided by a small business partner) to demonstrate improved power control, and evaluation of the system performance, including economic estimates of viability in an urban environment; and (3) computational analysis of the wind turbine system as an enabling activity for development of smart rotor blades that contain integrated sensor

  4. 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

  5. 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.

  6. [Systems theory in medicine and biology].

    Science.gov (United States)

    Feigl, W; Bonet, E M

    1989-03-15

    We try to determinate, that systems theory has to be introduced into modern medicine. The biological roots as well as the cybernetic ones are outlined. Among various concepts about systems theory the evaluation by Riedl seems to be the most efficient to explain medical procedures. His basic informations refer to von Bertalanffy, the additional introduction of a 4-cause-principle, Aristoteles, permits the explanation of complex relations. The examples of tumor and inflammation are used to demonstrate the basic idea of the formal cause as well as the final cause. The latter should also become an important fact in the solution of other medical problems.

  7. Center for Advanced Biofuel Systems (CABS) Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Kutchan, Toni M. [Donald Danforth Plant Science Center, St. Louis, MO (United States)

    2015-12-02

    One of the great challenges facing current and future generations is how to meet growing energy demands in an environmentally sustainable manner. Renewable energy sources, including wind, geothermal, solar, hydroelectric, and biofuel energy systems, are rapidly being developed as sustainable alternatives to fossil fuels. Biofuels are particularly attractive to the U.S., given its vast agricultural resources. The first generation of biofuel systems was based on fermentation of sugars to produce ethanol, typically from food crops. Subsequent generations of biofuel systems, including those included in the CABS project, will build upon the experiences learned from those early research results and will have improved production efficiencies, reduced environmental impacts and decreased reliance on food crops. Thermodynamic models predict that the next generations of biofuel systems will yield three- to five-fold more recoverable energy products. To address the technological challenges necessary to develop enhanced biofuel systems, greater understanding of the non-equilibrium processes involved in solar energy conversion and the channeling of reduced carbon into biofuel products must be developed. The objective of the proposed Center for Advanced Biofuel Systems (CABS) was to increase the thermodynamic and kinetic efficiency of select plant- and algal-based fuel production systems using rational metabolic engineering approaches grounded in modern systems biology. The overall strategy was to increase the efficiency of solar energy conversion into oils and other specialty biofuel components by channeling metabolic flux toward products using advanced catalysts and sensible design:1) employing novel protein catalysts that increase the thermodynamic and kinetic efficiencies of photosynthesis and oil biosynthesis; 2) engineering metabolic networks to enhance acetyl-CoA production and its channeling towards lipid synthesis; and 3) engineering new metabolic networks for the

  8. 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.

  9. Engineering biological systems toward a sustainable bioeconomy.

    Science.gov (United States)

    Lopes, Mateus Schreiner Garcez

    2015-06-01

    The nature of our major global risks calls for sustainable innovations to decouple economic growth from greenhouse gases emission. The development of sustainable technologies has been negatively impacted by several factors including sugar production costs, production scale, economic crises, hydraulic fracking development and the market inability to capture externality costs. However, advances in engineering of biological systems allow bridging the gap between exponential growth of knowledge about biology and the creation of sustainable value chains for a broad range of economic sectors. Additionally, industrial symbiosis of different biobased technologies can increase competitiveness and sustainability, leading to the development of eco-industrial parks. Reliable policies for carbon pricing and revenue reinvestments in disruptive technologies and in the deployment of eco-industrial parks could boost the welfare while addressing our major global risks toward the transition from a fossil to a biobased economy. PMID:25845304

  10. Biological Therapy in Systemic Lupus Erythematosus

    Directory of Open Access Journals (Sweden)

    Mariana Postal

    2012-01-01

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

  11. 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.

  12. A Free Energy Principle for Biological Systems

    Directory of Open Access Journals (Sweden)

    Friston Karl

    2012-10-01

    Full Text Available This paper describes a free energy principle that tries to explain the ability of biological systems to resist a natural tendency to disorder. It appeals to circular causality of the sort found in synergetic formulations of self-organization (e.g., the slaving principle and models of coupled dynamical systems, using nonlinear Fokker Planck equations. Here, circular causality is induced by separating the states of a random dynamical system into external and internal states, where external states are subject to random fluctuations and internal states are not. This reduces the problem to finding some (deterministic dynamics of the internal states that ensure the system visits a limited number of external states; in other words, the measure of its (random attracting set, or the Shannon entropy of the external states is small. We motivate a solution using a principle of least action based on variational free energy (from statistical physics and establish the conditions under which it is formally equivalent to the information bottleneck method. This approach has proved useful in understanding the functional architecture of the brain. The generality of variational free energy minimisation and corresponding information theoretic formulations may speak to interesting applications beyond the neurosciences; e.g., in molecular or evolutionary biology.

  13. Design of automatic leveling and centering system of theodolite

    Science.gov (United States)

    Liu, Chun-tong; He, Zhen-Xin; Huang, Xian-xiang; Zhan, Ying

    2012-09-01

    To realize the theodolite automation and improve the azimuth Angle measurement instrument, the theodolite automatic leveling and centering system with the function of leveling error compensation is designed, which includes the system solution, key components selection, the mechanical structure of leveling and centering, and system software solution. The redesigned leveling feet are driven by the DC servo motor; and the electronic control center device is installed. Using high precision of tilt sensors as horizontal skew detection sensors ensures the effectiveness of the leveling error compensation. Aiming round mark center is located using digital image processing through surface array CCD; and leveling measurement precision can reach the pixel level, which makes the theodolite accurate centering possible. Finally, experiments are conducted using the automatic leveling and centering system of the theodolite. The results show the leveling and centering system can realize automatic operation with high centering accuracy of 0.04mm.The measurement precision of the orientation angle after leveling error compensation is improved, compared with that of in the traditional method. Automatic leveling and centering system of theodolite can satisfy the requirements of the measuring precision and its automation.

  14. 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…

  15. 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…

  16. Microsoft System Center 2012 R2 compliance management cookbook

    CERN Document Server

    Baumgarten, Andreas; Roesner, Susan

    2014-01-01

    Whether you are an IT manager, an administrator, or security professional who wants to learn how Microsoft Security Compliance Manager and Microsoft System Center can help fulfil compliance and security requirements, this is the book for you. Prior knowledge of Microsoft System Center is required.

  17. National Finance Center Personnel/Payroll System

    Data.gov (United States)

    US Agency for International Development — The NFC system is an USDA system used for processing transactions for payroll/personnel systems. Personnel processing is done through EPIC/HCUP, which is web-based....

  18. 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.

  19. 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.; Putten, van der W.H.; Ruiter, de P.C.; Struik, P.C.; Thomma, B.

    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 agricultura

  20. 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....

  1. A Comparison of Organization-Centered and Agent-Centered Multi-Agent Systems

    DEFF Research Database (Denmark)

    Jensen, Andreas Schmidt; Villadsen, Jørgen

    2013-01-01

    Whereas most classical multi-agent systems have the agent in center, there has recently been a development towards focusing more on the organization of the system, thereby allowing the designer to focus on what the system goals are, without considering how the goals should be fulfilled. We have d...

  2. Human Centered Autonomous and Assistant Systems Testbed for Exploration Operations

    Science.gov (United States)

    Malin, Jane T.; Mount, Frances; Carreon, Patricia; Torney, Susan E.

    2001-01-01

    The Engineering and Mission Operations Directorates at NASA Johnson Space Center are combining laboratories and expertise to establish the Human Centered Autonomous and Assistant Systems Testbed for Exploration Operations. This is a testbed for human centered design, development and evaluation of intelligent autonomous and assistant systems that will be needed for human exploration and development of space. This project will improve human-centered analysis, design and evaluation methods for developing intelligent software. This software will support human-machine cognitive and collaborative activities in future interplanetary work environments where distributed computer and human agents cooperate. We are developing and evaluating prototype intelligent systems for distributed multi-agent mixed-initiative operations. The primary target domain is control of life support systems in a planetary base. Technical approaches will be evaluated for use during extended manned tests in the target domain, the Bioregenerative Advanced Life Support Systems Test Complex (BIO-Plex). A spinoff target domain is the International Space Station (ISS) Mission Control Center (MCC). Prodl}cts of this project include human-centered intelligent software technology, innovative human interface designs, and human-centered software development processes, methods and products. The testbed uses adjustable autonomy software and life support systems simulation models from the Adjustable Autonomy Testbed, to represent operations on the remote planet. Ground operations prototypes and concepts will be evaluated in the Exploration Planning and Operations Center (ExPOC) and Jupiter Facility.

  3. 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.

  4. An Integrated Biological Control System At Hanford

    International Nuclear Information System (INIS)

    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.

  5. Non-Equilibrium Quantum Entanglement in Biological Systems

    Institute of Scientific and Technical Information of China (English)

    LI Hong-Rong; ZHANG Pei; GAO Hong; BI Wen-Ting; ALAMRI M. D.; LI Fu-Li

    2012-01-01

    A non-equilibrium model of a classically driven quantum harmonic oscillator is proposed to explain persistent quantum entanglement in biological systems at ambient temperature. The conditions for periodic entanglement generation are derived. Our results support the evidence that biological systems may have quantum entanglement at biological temperatures.%A non-equilibrium model of a classically driven quantum harmonic oscillator is proposed to explain persistent quantum entanglement in biological systems at ambient temperature.The conditions for periodic entanglement generation are derived.Our results support the evidence that biological systems may have quantum entanglement at biological temperatures.

  6. 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...

  7. Computer based human-centered display system

    Science.gov (United States)

    Still, David L. (Inventor); Temme, Leonard A. (Inventor)

    2002-01-01

    A human centered informational display is disclosed that can be used with vehicles (e.g. aircraft) and in other operational environments where rapid human centered comprehension of an operational environment is required. The informational display integrates all cockpit information into a single display in such a way that the pilot can clearly understand with a glance, his or her spatial orientation, flight performance, engine status and power management issues, radio aids, and the location of other air traffic, runways, weather, and terrain features. With OZ the information is presented as an integrated whole, the pilot instantaneously recognizes flight path deviations, and is instinctively drawn to the corrective maneuvers. Our laboratory studies indicate that OZ transfers to the pilot all of the integrated display information in less than 200 milliseconds. The reacquisition of scan can be accomplished just as quickly. Thus, the time constants for forming a mental model are near instantaneous. The pilot's ability to keep up with rapidly changing and threatening environments is tremendously enhanced. OZ is most easily compatible with aircraft that has flight path information coded electronically. With the correct sensors (which are currently available) OZ can be installed in essentially all current aircraft.

  8. Biological Systems for Hydrogen Photoproduction (Presentation)

    Energy Technology Data Exchange (ETDEWEB)

    Ghirardi, M. L.

    2012-05-01

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

  9. Are Biological Systems Poised at Criticality?

    Science.gov (United States)

    Mora, Thierry; Bialek, William

    2011-07-01

    Many of life's most fascinating phenomena emerge from interactions among many elements—many amino acids determine the structure of a single protein, many genes determine the fate of a cell, many neurons are involved in shaping our thoughts and memories. Physicists have long hoped that these collective behaviors could be described using the ideas and methods of statistical mechanics. In the past few years, new, larger scale experiments have made it possible to construct statistical mechanics models of biological systems directly from real data. We review the surprising successes of this "inverse" approach, using examples from families of proteins, networks of neurons, and flocks of birds. Remarkably, in all these cases the models that emerge from the data are poised near a very special point in their parameter space—a critical point. This suggests there may be some deeper theoretical principle behind the behavior of these diverse systems.

  10. Strategies for structuring interdisciplinary education in Systems Biology

    DEFF Research Database (Denmark)

    Cvijovic, Marija; Höfer, Thomas; Aćimović, Jure;

    2016-01-01

    Systems Biology is an approach to biology and medicine that has the potential to lead to a better understanding of how biological properties emerge from the interaction of genes, proteins, molecules, cells and organisms. The approach aims at elucidating how these interactions govern biological fu...

  11. Development and Testing of the Glenn Research Center Visitor's Center Grid-Tied Photovoltaic Power System

    Science.gov (United States)

    Eichenberg, Dennis J.

    2009-01-01

    The NASA Glenn Research Center (GRC) has developed, installed, and tested a 12 kW DC grid-tied photovoltaic (PV) power system at the GRC Visitor s Center. This system utilizes a unique ballast type roof mount for installing the photovoltaic panels on the roof of the Visitor s Center with no alterations or penetrations to the roof. The PV system has generated in excess of 15000 kWh since operation commenced in August 2008. The PV system is providing power to the GRC grid for use by all. Operation of the GRC Visitor s Center PV system has been completely trouble free. A grid-tied PV power system is connected directly to the utility distribution grid. Facility power can be obtained from the utility system as normal. The PV system is synchronized with the utility system to provide power for the facility, and excess power is provided to the utility. The project transfers space technology to terrestrial use via nontraditional partners. GRC personnel glean valuable experience with PV power systems that are directly applicable to various space power systems, and provides valuable space program test data. PV power systems help to reduce harmful emissions and reduce the Nation s dependence on fossil fuels. Power generated by the PV system reduces the GRC utility demand, and the surplus power aids the community. Present global energy concerns reinforce the need for the development of alternative energy systems. Modern PV panels are readily available, reliable, efficient, and economical with a life expectancy of at least 25 years. Modern electronics has been the enabling technology behind grid-tied power systems, making them safe, reliable, efficient, and economical with a life expectancy of at least 25 years. Based upon the success of the GRC Visitor s Center PV system, additional PV power system expansion at GRC is under consideration. The GRC Visitor s Center grid-tied PV power system was successfully designed and developed which served to validate the basic principles

  12. Integrated Design of Antibodies for Systems Biology Using Ab Designer

    OpenAIRE

    Pisitkun, Trairak; Dummer, Patrick; Somparn, Poorichaya; Hirankarn, Nattiya; Kopp, Jeffrey B.; Knepper, Mark A.

    2014-01-01

    In the current era of large-scale biology, systems biology has evolved as a powerful approach to identify complex interactions within biological systems. In addition to high throughput identification and quantification techniques, methods based on high-quality mono-specific antibodies remain an essential element of the approach. To assist the large-scale design and production of peptide-directed antibodies for systems biology studies, we developed a fully integrated online application, AbDesi...

  13. 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.

  14. Quantum integrable systems. Quantitative methods in biology

    CERN Document Server

    Feverati, Giovanni

    2011-01-01

    Quantum integrable systems have very strong mathematical properties that allow an exact description of their energetic spectrum. From the Bethe equations, I formulate the Baxter "T-Q" relation, that is the starting point of two complementary approaches based on nonlinear integral equations. The first one is known as thermodynamic Bethe ansatz, the second one as Kl\\"umper-Batchelor-Pearce-Destri- de Vega. I show the steps toward the derivation of the equations for some of the models concerned. I study the infrared and ultraviolet limits and discuss the numerical approach. Higher rank integrals of motion can be obtained, so gaining some control on the eigenvectors. After, I discuss the Hubbard model in relation to the N = 4 supersymmetric gauge theory. The Hubbard model describes hopping electrons on a lattice. In the second part, I present an evolutionary model based on Turing machines. The goal is to describe aspects of the real biological evolution, or Darwinism, by letting evolve populations of algorithms. ...

  15. The start of systems biology in Ukraine

    Directory of Open Access Journals (Sweden)

    Obolenskaya M. Yu.

    2014-01-01

    Full Text Available The first laboratory of Systems Biology in Ukraine (IMBIG NASU represents a track record of its scientific results. They include the pioneered development of a web-based tool for genome-wide surveys of eukaryotic promoters for the presence of transcription factors binding sites (COTRASIF; the deciphered mechanisms of the fine-tuned and balanced response of primary hepatocytes to interferon alpha levels recorded after partial hepatectomy; the elaboration of a novel method of gene regulatory network inference compatible with GRID environment and the development of a stoichiometric model of folate-related one carbon unit metabolism in human placenta and its application for the characteristics of the system’s behavior as a whole at different human pathologies.

  16. 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...... that were in concordance with their effects in experimental animals. In project II, I profiled the effects on rat liver gene expression levels following exposure to a 14-chemical mixture ± the presence of an endocrine disrupting chemical. This project helped us shed light on the mechanism of action...... of the 14-chemical mixture and the endocrine disrupting chemical. In project III, I modeled a predictive signature for an in vivo endpoint that is sensitive to endocrine disruption. I used publicly available data generated for the purpose of modeling predictive signatures for various in vivo endpoints. From...

  17. Nutritional Systems Biology: Definitions and Approaches

    DEFF Research Database (Denmark)

    Panagiotou, Gianni; Nielsen, Jens

    2009-01-01

    Nutrigenetics and nutrigenomics are nascent areas that are evolving quickly and riding on the wave of “personalized medicine” that is providing opportunities in the discovery and development of nutraceutical compounds. The human genome sequence and sequences of model organisms provide...... will benefit most from, or be placed at risk by, intervention strategies. More accurate assessment of the inputs to human health and the consequences of those inputs measured as accurate transcriptomic, proteomic, and metabolomic analyses would bring personalized health/diet to practice far faster than would...... waiting for a predictive knowledge of genetic variation. It is widely recognized that systems and network biology has the potential to increase our understanding of how nutrition influences metabolic pathways and homeostasis, how this regulation is disturbed in a diet-related disease, and to what extent...

  18. The effect of student-centered and teacher-centered instruction with and without conceptual advocacy on biology students' misconceptions, achievement, attitudes toward science, and cognitive retention

    Science.gov (United States)

    Gallop, Roger Graham

    The purpose of this study was to investigate the effect of student-centered and teacher-centered instructional strategies with and without conceptual advocacy (CA) on ninth-grade biology students' misconceptions (MIS), biology achievement (ACH), attitudes toward science (ATT), and cognitive retention of scientific method and measurement, spontaneous generation, and characteristics of living things. Students were purposively selected using intact classes and assigned to one of four treatment groups (i.e., student-centered instruction without CA, student-centered instruction with CA, teacher-centered instruction with CA, and teacher-centered instruction without CA). A modified quasi-experimental design was used in which students were not matched in the conventional sense but instead, groups were shown to be equivalent on the dependent measure via a pretest. A 5-day treatment implementation period addressed science conceptions under investigation. The treatment period was based on the number of class periods teachers at the target school actually spend teaching the biological concepts under investigation using traditional instruction. At the end of the treatment period, students were posttested using the Concepts in Biology instrument and Science Questionnaire. Eight weeks after the posttest, these instruments were administered again as a delayed posttest to determine cognitive retention of the correct biological conceptions and attitudes toward science. MANCOVA and follow-up univariate ANCOVA results indicated that student-centered instruction without CA (i.e., Group 1) did not have a significant effect on students' MIS, ACH, and ATT (F = .029, p = .8658; F = .002, p =.9688, F = .292, p = .5897, respectively). On the other hand, student-centered instruction with CA (i.e., Group 2) had a significant effect on students' MIS and ACH (F =10.33, p = .0016 and F = 10.17, p = .0017, respectively), but did not on ATT (F = .433, p = .5117). Teacher-centered instruction with

  19. Microbial systems biology: New frontiers open to predictive microbiology

    NARCIS (Netherlands)

    S. Brul; F.I.C. Mensonides; K.J. Hellingwerf; M.J. Teixeira De Mattos

    2008-01-01

    The field of Systems Biology is a rapidly evolving area of research. It follows on from the previous experimental and theoretical ‘omics’ revolution in biology. Now that we have through the use of these tools many ‘indices’ of biological systems available the next step is to actually start composing

  20. Center for Information Systems Research Research Briefings 2002

    OpenAIRE

    Ross, Jeanne W.

    2003-01-01

    This paper is comprised of research briefings from the MIT Sloan School of Management's Center for Information Systems Research (CISR). CISR's mission is to perform practical empirical research on how firms generate business value from IT.

  1. Microsoft System Center 2012 R2 Operations Manager cookbook

    CERN Document Server

    Beaumont (MVP), Steve; Odika, Chiyo; Ryan, Robert

    2015-01-01

    If you are tasked with monitoring the IT infrastructure within your organization, this book demonstrates how System Center 2012 R2 Operations Manager offers a radical and exciting solution to modern administration.

  2. Expert systems guide biological phosphorus removal

    Energy Technology Data Exchange (ETDEWEB)

    Krichten, D.J.; Wilson, K.D.; Tracy, K.D. (Air Products and Chemicals, Inc., Allentown, PA (United States))

    1991-10-01

    There is a large body of knowledge regarding optimum control strategies for new secondary wastewater treatment technology using an anaerobic selector to provide biological phosphorus removal. However, because the selector technology is new and the concepts differ somewhat from those used in conventional activated sludge wastewater treatment, a method of communicating this knowledge to plant operators is needed. Traditional methods such as classroom training and operating manuals are of limited effectiveness. The commonplace availability and low cost of the personal computer (PC) makes it practical to use a computer program to communicate the type of information required to control a wastewater treatment plant. Knowledge-based systems technology, commonly referred to as expert systems (ES) technology, is easy to use, provides useful information regarding a consistent control strategy, relieves the anxiety associated with learning a new process,' and provides instruction for inexperienced personnel. ES technology does not require special formatted input and is therefore easily accessible. All information required by the program is readily available through routine laboratory analysis, common plant instrumentation, or direct user observation. The program was designed for all levels of computer users and will run on all IBM-compatible or Apple MacIntosh systems.

  3. Biological robustness: paradigms, mechanisms, and systems principles.

    Science.gov (United States)

    Whitacre, James Michael

    2012-01-01

    Robustness has been studied through the analysis of data sets, simulations, and a variety of experimental techniques that each have their own limitations but together confirm the ubiquity of biological robustness. Recent trends suggest that different types of perturbation (e.g., mutational, environmental) are commonly stabilized by similar mechanisms, and system sensitivities often display a long-tailed distribution with relatively few perturbations representing the majority of sensitivities. Conceptual paradigms from network theory, control theory, complexity science, and natural selection have been used to understand robustness, however each paradigm has a limited scope of applicability and there has been little discussion of the conditions that determine this scope or the relationships between paradigms. Systems properties such as modularity, bow-tie architectures, degeneracy, and other topological features are often positively associated with robust traits, however common underlying mechanisms are rarely mentioned. For instance, many system properties support robustness through functional redundancy or through response diversity with responses regulated by competitive exclusion and cooperative facilitation. Moreover, few studies compare and contrast alternative strategies for achieving robustness such as homeostasis, adaptive plasticity, environment shaping, and environment tracking. These strategies share similarities in their utilization of adaptive and self-organization processes that are not well appreciated yet might be suggestive of reusable building blocks for generating robust behavior. PMID:22593762

  4. Biological Robustness: Paradigms, Mechanisms, and Systems Principles

    Directory of Open Access Journals (Sweden)

    James Michael Whitacre

    2012-05-01

    Full Text Available Robustness has been studied through the analysis of data sets, simulations, and a variety of experimental techniques that each have their own limitations but together confirm the ubiquity of biological robustness. Recent trends suggest that different types of perturbation (e.g. mutational, environmental are commonly stabilized by similar mechanisms, and system sensitivities often display a long-tailed distribution with relatively few perturbations representing the majority of sensitivities. Conceptual paradigms from network theory, control theory, complexity science, and natural selection have been used to understand robustness, however each paradigm has a limited scope of applicability and there has been little discussion of the conditions that determine this scope or the relationships between paradigms. Systems properties such as modularity, bow-tie architectures, degeneracy, and other topological features are often positively associated with robust traits, however common underlying mechanisms are rarely mentioned. For instance, many system properties support robustness through functional redundancy or through response diversity with responses regulated by competitive exclusion and cooperative facilitation. Moreover, few studies compare and contrast alternative strategies for achieving robustness such as homeostasis, adaptive plasticity, environment shaping, and environment tracking. These strategies share similarities in their utilization of adaptive and self-organization processes that are not well appreciated yet might be suggestive of reusable building blocks for generating robust behavior.

  5. Microsoft System Center Data Protection Manager 2012

    CERN Document Server

    Buchannan, Steve; Gomaa, Islam

    2013-01-01

    This book is a Packt tutorial, walking the administrator through the steps needed to create real solutions to the problems and tasks faced when ensuring that their data is protected. This book is for network administrators, system administrators, backup administrators, or IT consultants who are looking to expand their knowledge on how to utilize DPM to protect their organization's data.

  6. [Investigation of the microstructure of biological systems by triplet label].

    Science.gov (United States)

    Kotel'niko, A I; Kuznetsov, S N; Fogel', V R; Likhtenshteĭn, G I

    1979-01-01

    A method for investigating the microstruct and dynamics of biological systems by means of triplet-excited molecules is suggested. The method is based on the phenomenon of triplet excitation disactivation by exchange-resonance triplet-triplet energy transfer to the acceptor or by intercombination conversion induced by interaction of an excited molecule with a paramagnetic center. The disactivation efficiency was measured by registrating the phosphorescense decay kinetics. The interaction of the triplet label eosin isothiocyanate, covalently coupled with albumine, lysozyme, sarcoplasmic reticulum membrane and Ca-Mg-dependent sarcoplasmic reticulum ATPase, with O2, the stable nitroxide radicals and ions of Mn2+ was investigated to analyse the potentialities of this method. As a model system the eosin phosphorescence quenching by the same quenchers in glycerine-aguaous solutions was studied. The method permits to investigate the microviscosity and microstructure of biological objects in the label attached region on interaction of the label with a sound-quencher with constants being 10(4) divided by 10(9) M-1 sec-1 and to measure the lateral diffusion of molecules in highly viscosity media (10 divided by 10(5) santypuas). PMID:223037

  7. Active learning and student-centered pedagogy improve student attitudes and performance in introductory biology.

    Science.gov (United States)

    Armbruster, Peter; Patel, Maya; Johnson, Erika; Weiss, Martha

    2009-01-01

    We describe the development and implementation of an instructional design that focused on bringing multiple forms of active learning and student-centered pedagogies to a one-semester, undergraduate introductory biology course for both majors and nonmajors. Our course redesign consisted of three major elements: 1) reordering the presentation of the course content in an attempt to teach specific content within the context of broad conceptual themes, 2) incorporating active and problem-based learning into every lecture, and 3) adopting strategies to create a more student-centered learning environment. Assessment of our instructional design consisted of a student survey and comparison of final exam performance across 3 years-1 year before our course redesign was implemented (2006) and during two successive years of implementation (2007 and 2008). The course restructuring led to significant improvement of self-reported student engagement and satisfaction and increased academic performance. We discuss the successes and ongoing challenges of our course restructuring and consider issues relevant to institutional change. PMID:19723815

  8. A SYSTEMIC VISION OF BIOLOGY: OVERCOMING LINEARITY

    Directory of Open Access Journals (Sweden)

    M. Mayer

    2005-07-01

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

  9. 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 ...

  10. Biological Visualization, Imaging and Simulation(Bio-VIS) at NASA Ames Research Center: Developing New Software and Technology for Astronaut Training and Biology Research in Space

    Science.gov (United States)

    Smith, Jeffrey

    2003-01-01

    The Bio- Visualization, Imaging and Simulation (BioVIS) Technology Center at NASA's Ames Research Center is dedicated to developing and applying advanced visualization, computation and simulation technologies to support NASA Space Life Sciences research and the objectives of the Fundamental Biology Program. Research ranges from high resolution 3D cell imaging and structure analysis, virtual environment simulation of fine sensory-motor tasks, computational neuroscience and biophysics to biomedical/clinical applications. Computer simulation research focuses on the development of advanced computational tools for astronaut training and education. Virtual Reality (VR) and Virtual Environment (VE) simulation systems have become important training tools in many fields from flight simulation to, more recently, surgical simulation. The type and quality of training provided by these computer-based tools ranges widely, but the value of real-time VE computer simulation as a method of preparing individuals for real-world tasks is well established. Astronauts routinely use VE systems for various training tasks, including Space Shuttle landings, robot arm manipulations and extravehicular activities (space walks). Currently, there are no VE systems to train astronauts for basic and applied research experiments which are an important part of many missions. The Virtual Glovebox (VGX) is a prototype VE system for real-time physically-based simulation of the Life Sciences Glovebox where astronauts will perform many complex tasks supporting research experiments aboard the International Space Station. The VGX consists of a physical display system utilizing duel LCD projectors and circular polarization to produce a desktop-sized 3D virtual workspace. Physically-based modeling tools (Arachi Inc.) provide real-time collision detection, rigid body dynamics, physical properties and force-based controls for objects. The human-computer interface consists of two magnetic tracking devices

  11. Systems Biology in Aging: Linking the Old and the Young

    OpenAIRE

    HOU, LEI; Huang, Jialiang; Green, Christopher D.; Boyd-Kirkup, Jerome; Zhang, Wei; Yu, Xiaoming; Gong, Wenxuan; Zhou, Bing; Jing-Dong J Han

    2012-01-01

    Aging can be defined as a process of progressive decline in the physiological capacity of an organism, manifested by accumulated alteration and destabilization at the whole system level. Systems biology approaches offer a promising new perspective to examine the old problem of aging. We begin this review by introducing the concepts of systems biology, and then illustrate the application of systems biology approaches to aging research, from gene expression profiling to network analysis. We the...

  12. Marshall Space Flight Center Ground Systems Development and Integration

    Science.gov (United States)

    Wade, Gina

    2016-01-01

    Ground Systems Development and Integration performs a variety of tasks in support of the Mission Operations Laboratory (MOL) and other Center and Agency projects. These tasks include various systems engineering processes such as performing system requirements development, system architecture design, integration, verification and validation, software development, and sustaining engineering of mission operations systems that has evolved the Huntsville Operations Support Center (HOSC) into a leader in remote operations for current and future NASA space projects. The group is also responsible for developing and managing telemetry and command configuration and calibration databases. Personnel are responsible for maintaining and enhancing their disciplinary skills in the areas of project management, software engineering, software development, software process improvement, telecommunications, networking, and systems management. Domain expertise in the ground systems area is also maintained and includes detailed proficiency in the areas of real-time telemetry systems, command systems, voice, video, data networks, and mission planning systems.

  13. Apparatus and Methods for Manipulation and Optimization of Biological Systems

    Science.gov (United States)

    Ho, Chih-Ming (Inventor); Wong, Pak Kin (Inventor); Sun, Ren (Inventor); Yu, Fuqu (Inventor)

    2014-01-01

    The invention provides systems and methods for manipulating biological systems, for example to elicit a more desired biological response from a biological sample, such as a tissue, organ, and/or a cell. In one aspect, the invention operates by efficiently searching through a large parametric space of stimuli and system parameters to manipulate, control, and optimize the response of biological samples sustained in the system. In one aspect, the systems and methods of the invention use at least one optimization algorithm to modify the actuator's control inputs for stimulation, responsive to the sensor's output of response signals. The invention can be used, e.g., to optimize any biological system, e.g., bioreactors for proteins, and the like, small molecules, polysaccharides, lipids, and the like. Another use of the apparatus and methods includes is for the discovery of key parameters in complex biological systems.

  14. 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.

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

    Science.gov (United States)

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

    2016-01-01

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

  16. Exploring Synthetic and Systems Biology at the University of Edinburgh.

    Science.gov (United States)

    Fletcher, Liz; Rosser, Susan; Elfick, Alistair

    2016-06-15

    The Centre for Synthetic and Systems Biology ('SynthSys') was originally established in 2007 as the Centre for Integrative Systems Biology, funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and the Engineering and Physical Sciences Research Council (EPSRC). Today, SynthSys embraces an extensive multidisciplinary community of more than 200 researchers from across the University with a common interest in synthetic and systems biology. Our research is broad and deep, addressing a diversity of scientific questions, with wide ranging impact. We bring together the power of synthetic biology and systems approaches to focus on three core thematic areas: industrial biotechnology, agriculture and the environment, and medicine and healthcare. In October 2015, we opened a newly refurbished building as a physical hub for our new U.K. Centre for Mammalian Synthetic Biology funded by the BBSRC/EPSRC/MRC as part of the U.K. Research Councils' Synthetic Biology for Growth programme.

  17. 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...

  18. Resonances in the two-center Coulomb systems

    Science.gov (United States)

    Seri, Marcello; Knauf, Andreas; Esposti, Mirko Degli; Jecko, Thierry

    2016-09-01

    We investigate the existence of resonances for two-center Coulomb systems with arbitrary charges in two dimensions, defining them in terms of generalized complex eigenvalues of a non-selfadjoint deformation of the two-center Schrödinger operator. We construct the resolvent kernels of the operators and prove that they can be extended analytically to the second Riemann sheet. The resonances are then analyzed by means of perturbation theory and numerical methods.

  19. Micrasterias as a model system in plant cell biology

    Directory of Open Access Journals (Sweden)

    Ursula Luetz-Meindl

    2016-07-01

    Full Text Available The unicellular freshwater alga Micrasterias denticulata is an exceptional organism due to its extraordinary star-shaped, highly symmetric morphology and has thus attracted the interest of researchers for many decades. As a member of the Streptophyta, Micrasterias is not only genetically closely related to higher land plants but shares common features with them in many physiological and cell biological aspects. These facts, together with its considerable cell size of about 200 µm, its modest cultivation conditions and the uncomplicated accessibility particularly to any microscopic techniques, make Micrasterias a very well suited cell biological plant model system. The review focuses particularly on cell wall formation and composition, dictyosomal structure and function, cytoskeleton control of growth and morphogenesis as well as on ionic regulation and signal transduction. It has been also shown in the recent years that Micrasterias is a highly sensitive indicator for environmental stress impact such as heavy metals, high salinity, oxidative stress or starvation. Stress induced organelle degradation, autophagy, adaption and detoxification mechanisms have moved in the center of interest and have been investigated with modern microscopic techniques such as 3-D- and analytical electron microscopy as well as with biochemical, physiological and molecular approaches. This review is intended to summarize and discuss the most important results obtained in Micrasterias in the last 20 years and to compare the results to similar processes in higher plant cells.

  20. Micrasterias as a Model System in Plant Cell Biology

    Science.gov (United States)

    Lütz-Meindl, Ursula

    2016-01-01

    The unicellular freshwater alga Micrasterias denticulata is an exceptional organism due to its complex star-shaped, highly symmetric morphology and has thus attracted the interest of researchers for many decades. As a member of the Streptophyta, Micrasterias is not only genetically closely related to higher land plants but shares common features with them in many physiological and cell biological aspects. These facts, together with its considerable cell size of about 200 μm, its modest cultivation conditions and the uncomplicated accessibility particularly to any microscopic techniques, make Micrasterias a very well suited cell biological plant model system. The review focuses particularly on cell wall formation and composition, dictyosomal structure and function, cytoskeleton control of growth and morphogenesis as well as on ionic regulation and signal transduction. It has been also shown in the recent years that Micrasterias is a highly sensitive indicator for environmental stress impact such as heavy metals, high salinity, oxidative stress or starvation. Stress induced organelle degradation, autophagy, adaption and detoxification mechanisms have moved in the center of interest and have been investigated with modern microscopic techniques such as 3-D- and analytical electron microscopy as well as with biochemical, physiological and molecular approaches. This review is intended to summarize and discuss the most important results obtained in Micrasterias in the last 20 years and to compare the results to similar processes in higher plant cells. PMID:27462330

  1. The experimental teaching reform in biochemistry and molecular biology for undergraduate students in Peking University Health Science Center.

    Science.gov (United States)

    Yang, Xiaohan; Sun, Luyang; Zhao, Ying; Yi, Xia; Zhu, Bin; Wang, Pu; Lin, Hong; Ni, Juhua

    2015-01-01

    Since 2010, second-year undergraduate students of an eight-year training program leading to a Doctor of Medicine degree or Doctor of Philosophy degree in Peking University Health Science Center (PKUHSC) have been required to enter the "Innovative talent training project." During that time, the students joined a research lab and participated in some original research work. There is a critical educational need to prepare these students for the increasing accessibility of research experience. The redesigned experimental curriculum of biochemistry and molecular biology was developed to fulfill such a requirement, which keeps two original biochemistry experiments (Gel filtration and Enzyme kinetics) and adds a new two-experiment component called "Analysis of anti-tumor drug induced apoptosis." The additional component, also known as the "project-oriented experiment" or the "comprehensive experiment," consists of Western blotting and a DNA laddering assay to assess the effects of etoposide (VP16) on the apoptosis signaling pathways. This reformed laboratory teaching system aims to enhance the participating students overall understanding of important biological research techniques and the instrumentation involved, and to foster a better understanding of the research process all within a classroom setting. Student feedback indicated that the updated curriculum helped them improve their operational and self-learning capability, and helped to increase their understanding of theoretical knowledge and actual research processes, which laid the groundwork for their future research work.

  2. Commentary: Systems Biology and Its Relevance to Alcohol Research

    OpenAIRE

    Guo, Q. Max; Zakhari, Sam

    2008-01-01

    Systems biology, a new scientific discipline, aims to study the behavior of a biological organization or process in order to understand the function of a dynamic system. This commentary will put into perspective topics discussed in this issue of Alcohol Research & Health, provide insight into why alcohol-induced disorders exemplify the kinds of conditions for which a systems biological approach would be fruitful, and discuss the opportunities and challenges facing alcohol researchers.

  3. Interactive analysis of systems biology molecular expression data

    OpenAIRE

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

    2008-01-01

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

  4. Influence of low intensity laser radiation on different biological systems

    OpenAIRE

    Tsivunchyk, Olga S.

    2004-01-01

    Abstract There are a lot of examples and contradictory results concerning influence of low intensity laser irradiation (LILI) on biological objects. In this work with a number of experiments the influence of LILI on different biological systems was investigated. For the carried out experiments the following biological objects and systems were used: * different enzymes of anti-oxidant system of animals (i.e. catalase, superoxide-di...

  5. Advanced Systems Biology Methods in Drug Discovery and Translational Biomedicine

    OpenAIRE

    Jun Zou; Ming-Wu Zheng; Gen Li; Zhi-Guang Su

    2013-01-01

    Systems biology is in an exponential development stage in recent years and has been widely utilized in biomedicine to better understand the molecular basis of human disease and the mechanism of drug action. Here, we discuss the fundamental concept of systems biology and its two computational methods that have been commonly used, that is, network analysis and dynamical modeling. The applications of systems biology in elucidating human disease are highlighted, consisting of human disease networ...

  6. Human-centered design of a distributed knowledge management system.

    Science.gov (United States)

    Rinkus, Susan; Walji, Muhammad; Johnson-Throop, Kathy A; Malin, Jane T; Turley, James P; Smith, Jack W; Zhang, Jiajie

    2005-02-01

    Many healthcare technology projects fail due to the lack of consideration of human issues, such as workflow, organizational change, and usability, during the design and implementation stages of a project's development process. Even when human issues are considered, the consideration is typically on designing better user interfaces. We argue that human-centered computing goes beyond a better user interface: it should include considerations of users, functions and tasks that are fundamental to human-centered computing. From this perspective, we integrated a previously developed human-centered methodology with a Project Design Lifecycle, and we applied this integration in the design of a complex distributed knowledge management system for the Biomedical Engineer (BME) domain in the Mission Control Center at NASA Johnson Space Center. We analyzed this complex system, identified its problems, generated systems requirements, and provided specifications of a replacement prototype for effective organizational memory and knowledge management. We demonstrated the value provided by our human-centered approach and described the unique properties, structures, and processes discovered using this methodology and how they contributed in the design of the prototype. PMID:15694881

  7. Developing Performance-Centered Systems for Higher Education

    Directory of Open Access Journals (Sweden)

    2007-01-01

    Full Text Available The experience in developing performance-centered systems for higher education has improved significantly, and practitioners have made considerable progress in elaborating a methodology. This paper discusses the convergence of thinking among various disciplines in analysis and design methodologies, and describes the key elements of the new-emerged performance support engineering development methodology. These are important for designing web-based systems, information systems, and knowledge management systems in higher education.

  8. MEMBRANE COMPUTING AS THE PARADIGM FOR MODELING SYSTEMS BIOLOGY

    Directory of Open Access Journals (Sweden)

    Ravie Chandren Muniyandi

    2013-01-01

    Full Text Available Membrane computing is a field in computer science that is inspired from the structure and the processes of living cells and is being considered as an alternative in solving the limitations in conventional mathematical approaches by taking into consideration its essential features that are of interest for research in systems biology. Advancements in computability make it feasible to handle huge volumes of data in biology and propose a new and better approach using a discreet computer science model, such as membrane computing. In this respect, membrane-computing abilities, to enhance the understanding of the system level of biological systems, have been explored. This study discusses experiences in applying membrane computing in modeling biological systems as well as possibilities of incorporating membrane computing into other computer science paradigms to enhance the use of membrane computing in systems biology. Experiences in modeling aspects of systems biology with membrane computing demonstrate additional advantages and possibilities compared with conventional methods. However, they are not yet used widely to model or simulate biological processes or systems. A general framework of modeling and verifying biological systems using membrane computing is essential as a guideline for biologists in their research in systems biology.

  9. Peroxisystem: harnessing systems cell biology to study peroxisomes.

    Science.gov (United States)

    Schuldiner, Maya; Zalckvar, Einat

    2015-04-01

    In recent years, high-throughput experimentation with quantitative analysis and modelling of cells, recently dubbed systems cell biology, has been harnessed to study the organisation and dynamics of simple biological systems. Here, we suggest that the peroxisome, a fascinating dynamic organelle, can be used as a good candidate for studying a complete biological system. We discuss several aspects of peroxisomes that can be studied using high-throughput systematic approaches and be integrated into a predictive model. Such approaches can be used in the future to study and understand how a more complex biological system, like a cell and maybe even ultimately a whole organism, works.

  10. A guide to numerical modelling in systems biology

    CERN Document Server

    Deuflhard, Peter

    2015-01-01

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

  11. 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.

  12. BASIN-CENTERED GAS SYSTEMS OF THE U.S.

    Energy Technology Data Exchange (ETDEWEB)

    Marin A. Popov; Vito F. Nuccio; Thaddeus S. Dyman; Timothy A. Gognat; Ronald C. Johnson; James W. Schmoker; Michael S. Wilson; Charles Bartberger

    2000-11-01

    The USGS is re-evaluating the resource potential of basin-centered gas accumulations in the U.S. because of changing perceptions of the geology of these accumulations, and the availability of new data since the USGS 1995 National Assessment of United States oil and gas resources (Gautier et al., 1996). To attain these objectives, this project used knowledge of basin-centered gas systems and procedures such as stratigraphic analysis, organic geochemistry, modeling of basin thermal dynamics, reservoir characterization, and pressure analysis. This project proceeded in two phases which had the following objectives: Phase I (4/1998 through 5/1999): Identify and describe the geologic and geographic distribution of potential basin-centered gas systems, and Phase II (6/1999 through 11/2000): For selected systems, estimate the location of those basin-centered gas resources that are likely to be produced over the next 30 years. In Phase I, we characterize thirty-three (33) potential basin-centered gas systems (or accumulations) based on information published in the literature or acquired from internal computerized well and reservoir data files. These newly defined potential accumulations vary from low to high risk and may or may not survive the rigorous geologic scrutiny leading towards full assessment by the USGS. For logistical reasons, not all basins received the level of detail desired or required.

  13. A unified biological modeling and simulation system for analyzing biological reaction networks

    Science.gov (United States)

    Yu, Seok Jong; Tung, Thai Quang; Park, Junho; Lim, Jongtae; Yoo, Jaesoo

    2013-12-01

    In order to understand the biological response in a cell, a researcher has to create a biological network and design an experiment to prove it. Although biological knowledge has been accumulated, we still don't have enough biological models to explain complex biological phenomena. If a new biological network is to be created, integrated modeling software supporting various biological models is required. In this research, we design and implement a unified biological modeling and simulation system, called ezBioNet, for analyzing biological reaction networks. ezBioNet designs kinetic and Boolean network models and simulates the biological networks using a server-side simulation system with Object Oriented Parallel Accelerator Library framework. The main advantage of ezBioNet is that a user can create a biological network by using unified modeling canvas of kinetic and Boolean models and perform massive simulations, including Ordinary Differential Equation analyses, sensitivity analyses, parameter estimates and Boolean network analysis. ezBioNet integrates useful biological databases, including the BioModels database, by connecting European Bioinformatics Institute servers through Web services Application Programming Interfaces. In addition, we employ Eclipse Rich Client Platform, which is a powerful modularity framework to allow various functional expansions. ezBioNet is intended to be an easy-to-use modeling tool and a simulation system for understanding the control mechanism by monitoring the change of each component in a biological network. The simulation result can be managed and visualized on ezBioNet, which is available free of charge at http://ezbionet.sourceforge.net or http://ezbionet.cbnu.ac.kr.

  14. Optimal maintenance center inventories for fault-tolerant repairable systems

    Science.gov (United States)

    Lawrence, S. H.; Schaefer, M. K.

    1984-01-01

    A probabilistic approach is taken to determine the optimal repairable parts inventory for a maintenance center, servicing machines which contain several m-out-of-n systems of different parts, with a constraint on the total inventory investment. A model, based on the discrete Markov process, accounts for a typical ultrareliable avionics system, such as one presently being developed by NASA. The dynamic programming algorithm for minimizing the stockout and holding costs is applied to an exemplary maintenance center, and solutions for single-item and multi-item cases are given. The computational burden is noted to be reasonable and a computer program is used to generate optimal solutions.

  15. 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

  16. Dynamics and kinetics of model biological systems

    Science.gov (United States)

    Mirigian, Stephen

    In this work we study three systems of biological interest: the translocation of a heterogeneously charged polymer through an infinitely thin pore, the wrapped of a rigid particle by a soft vesicle and the modification of the dynamical properties of a gel due to the presence of rigid inclusions. We study the kinetics of translocation for a heterogeneously charged polyelectrolyte through an infinitely narrow pore using the Fokker-Planck formalism to compute mean first passage times, the probability of successful translocation, and the mean successful translocation time for a diblock copolymer. We find, in contrast to the homopolymer result, that details of the boundary conditions lead to qualitatively different behavior. Under experimentally relevant conditions for a diblock copolymer we find that there is a threshold length of the charged block, beyond which the probability of successful translocation is independent of charge fraction. Additionally, we find that mean successful translocation time exhibits non-monotonic behavior with increasing length of the charged fraction; there is an optimum length of the charged block where the mean successful translocation time is slowest and there can be a substantial range of charge fraction where it is slower than a minimally charged chain. For a fixed total charge on the chain, we find that finer distributions of the charge along the chain leads to a significant reduction in mean translocation time compared to the diblock distribution. Endocytosis is modeled using a simple geometrical model from the literature. We map the process of wrapping a rigid spherical bead onto a one-dimensional stochastic process described by the Fokker-Planck equation to compute uptake rates as a function of membrane properties and system geometry. We find that simple geometrical considerations pick an optimal particle size for uptake and a corresponding maximal uptake rate, which can be controlled by altering the material properties of the

  17. 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.

  18. 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.

  19. Developing Performance-Centered Systems for Higher Education

    OpenAIRE

    Ioan I. ANDONE; Vasile Daniel PAVALOAIA

    2007-01-01

    The experience in developing performance-centered systems for higher education has improved significantly, and practitioners have made considerable progress in elaborating a methodology. This paper discusses the convergence of thinking among various disciplines in analysis and design methodologies, and describes the key elements of the new-emerged performance support engineering development methodology. These are important for designing web-based systems, information systems, and knowledge ma...

  20. Approximate bayesian parameter inference for dynamical systems in systems biology

    International Nuclear Information System (INIS)

    This paper proposes to use approximate instead of exact stochastic simulation algorithms for approximate Bayesian parameter inference of dynamical systems in systems biology. It first presents the mathematical framework for the description of systems biology models, especially from the aspect of a stochastic formulation as opposed to deterministic model formulations based on the law of mass action. In contrast to maximum likelihood methods for parameter inference, approximate inference method- share presented which are based on sampling parameters from a known prior probability distribution, which gradually evolves toward a posterior distribution, through the comparison of simulated data from the model to a given data set of measurements. The paper then discusses the simulation process, where an over- view is given of the different exact and approximate methods for stochastic simulation and their improvements that we propose. The exact and approximate simulators are implemented and used within approximate Bayesian parameter inference methods. Our evaluation of these methods on two tasks of parameter estimation in two different models shows that equally good results are obtained much faster when using approximate simulation as compared to using exact simulation. (Author)

  1. Building momentum for systems and synthetic biology in India

    OpenAIRE

    Krishnan, Remya; Manjaly-Antony, Lijo Anto; Dhar, Pawan K.

    2010-01-01

    Biological systems are inherently noisy. Predicting the outcome of a perturbation is extremely challenging. Traditional reductionist approach of describing properties of parts, vis-a-vis higher level behaviour has led to enormous understanding of fundamental molecular level biology. This approach typically consists of converting genes into junk (knock-down) and garbage (knock-out) and observe how a system responds. To enable broader understanding of biological dynamics, an integrated computat...

  2. Global optimization in systems biology: stochastic methods and their applications

    OpenAIRE

    Balsa-Canto, Eva; Banga, Julio R.; Egea, José A.; Villaverde, A. F.; Hijas-Liste, G. M.

    2012-01-01

    Mathematical optimization is at the core of many problems in systems biology: (1) as the underlying hypothesis for model development, (2) in model identification, or (3) in the computation of optimal stimulation procedures to synthetically achieve a desired biological behavior. These problems are usually formulated as nonlinear programing problems (NLPs) with dynamic and algebraic constraints. However the nonlinear and highly constrained nature of systems biology models, together with the usu...

  3. Systems biology in aging: linking the old and the young.

    Science.gov (United States)

    Hou, Lei; Huang, Jialiang; Green, Christopher D; Boyd-Kirkup, Jerome; Zhang, Wei; Yu, Xiaoming; Gong, Wenxuan; Zhou, Bing; Han, Jing-Dong J

    2012-11-01

    Aging can be defined as a process of progressive decline in the physiological capacity of an organism, manifested by accumulated alteration and destabilization at the whole system level. Systems biology approaches offer a promising new perspective to examine the old problem of aging. We begin this review by introducing the concepts of systems biology, and then illustrate the application of systems biology approaches to aging research, from gene expression profiling to network analysis. We then introduce the network that can be constructed using known lifespan and aging regulators, and conclude with a look forward to the future of systems biology in aging research. In summary, systems biology is not only a young field that may help us understand aging at a higher level, but also an important platform that can link different levels of knowledge on aging, moving us closer to a more comprehensive control of systematic decline during aging. PMID:23633915

  4. Systems biology of neutrophil differentiation and immune response

    DEFF Research Database (Denmark)

    Theilgaard-Mönch, Kim; Porse, Bo T; Borregaard, Niels

    2005-01-01

    Systems biology has emerged as a new scientific field, which aims at investigating biological processes at the genomic and proteomic levels. Recent studies have unravelled aspects of neutrophil differentiation and immune responses at the systems level using high-throughput technologies...

  5. Biological oceanography of the red oceanic system

    Science.gov (United States)

    Theil, Hjalmar; Weikert, Horst

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

  6. Biologic

    CERN Document Server

    Kauffman, L H

    2002-01-01

    In this paper we explore the boundary between biology and the study of formal systems (logic). In the end, we arrive at a summary formalism, a chapter in "boundary mathematics" where there are not only containers but also extainers ><, entities open to interaction and distinguishing the space that they are not. The boundary algebra of containers and extainers is to biologic what boolean algebra is to classical logic. We show how this formalism encompasses significant parts of the logic of DNA replication, the Dirac formalism for quantum mechanics, formalisms for protein folding and the basic structure of the Temperley Lieb algebra at the foundations of topological invariants of knots and links.

  7. The Current State and Perspectives of Systems Biology

    Institute of Scientific and Technical Information of China (English)

    Tielui Shi; Yixue Li

    2006-01-01

    Emerging as a new field in biology recently, Systems Biology provides a branch new way to study the biological activities in organisms. In order to decode the complexity of life systematically,systems biology integrates the "-omics" and uses the high throughput methods from transcriptomics,protomics and metabonomics to detect the dynamic activities in cell; and then, it incorporates bioinformatics methods to integrate and analyze those data, and simulate the biological processes based on the model built from those integrated data. In this paper, the current state, the research field and the methods for the Systems Biology are introduced briefly, and then, several ideas about future development in this field are also proposed.

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

    DEFF Research Database (Denmark)

    Green, Sara; Wolkenhauer, Olaf

    2014-01-01

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

  9. Mathematical modeling of the evolution of a simple biological system

    Digital Repository Service at National Institute of Oceanography (India)

    Gonsalves, M.J.B.D.; Neetu, S.; Krishnan, K.P.; Attri, K.; LokaBharathi, P.A.

    physical system, where a model usually can be developed from well established fundamental principles, in case of biological systems such principles are not always available offering an opportunity for innovation. The success of the innovation, of course...

  10. World Key Information Service System Designed For EPCOT Center

    Science.gov (United States)

    Kelsey, J. A.

    1984-03-01

    An advanced Bell Laboratories and Western Electric designed electronic information retrieval system utilizing the latest Information Age technologies, and a fiber optic transmission system is featured at the Walt Disney World Resort's newest theme park - The Experimental Prototype Community of Tomorrow (EPCOT Center). The project is an interactive audio, video and text information system that is deployed at key locations within the park. The touch sensitive terminals utilizing the ARIEL (Automatic Retrieval of Information Electronically) System is interconnected by a Western Electric designed and manufactured lightwave transmission system.

  11. Power-reduction techniques for data-center storage systems

    NARCIS (Netherlands)

    Bostoen, Tom; Mullender, Sape; Berbers, Yolande

    2013-01-01

    As data-intensive, network-based applications proliferate, the power consumed by the data-center storage subsystem surges. This survey summarizes, organizes, and integrates a decade of research on power-aware enterprise storage systems. All of the existing power-reduction techniques are classified a

  12. Geographic information systems at the Goddard Space Flight Center

    Science.gov (United States)

    Goldberg, M.

    1982-01-01

    The basic functions of a Geographic Information System (GIS) and the different ways that a GIS may be implemented are described. It surveys that GIS software packages that are currently in operation at the Goddard Space Flight Center and discusses the types of applications for which they are best suited. Future plans for in-house GIS research and development are outlined.

  13. Microsoft System Center Data Protection Manager 2012 R2 cookbook

    CERN Document Server

    Hedblom, Robert

    2015-01-01

    If you are a DPM administrator, this book will help you verify your knowledge and provide you with everything you need to know about the 2012 R2 release. No prior knowledge about System Center DPM is required, however some experience of running backups will come in handy.

  14. Human-centered text mining: a new software system

    NARCIS (Netherlands)

    J. Poelmans; P. Elzinga; A.A. Neznanov; G. Dedene; S. Viaene; S. Kuznetsov

    2012-01-01

    In this paper we introduce a novel human-centered data mining software system which was designed to gain intelligence from unstructured textual data. The architecture takes its roots in several case studies which were a collaboration between the Amsterdam-Amstelland Police, GasthuisZusters Antwerpen

  15. Performance evaluation of a center pivot variable rate irrigation system

    Science.gov (United States)

    Variable Rate Irrigation (VRI) for center pivots offers potential to match specific application rates to non-uniform soil conditions along the length of the lateral. The benefit of such systems is influenced by the areal extent of these variations and the smallest scale to which the irrigation syste...

  16. 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.

  17. Machine learning in systems biology at different scales : from molecular biology to ecology

    OpenAIRE

    Aderhold, Andrej

    2015-01-01

    Machine learning has been a source for continuous methodological advances in the field of computational learning from data. Systems biology has profited in various ways from machine learning techniques but in particular from network inference, i.e. the learning of interactions given observed quantities of the involved components or data that stem from interventional experiments. Originally this domain of system biology was confined to the inference of gene regulation networks but ...

  18. Application of a reliability centered maintenence on a drilling system

    OpenAIRE

    Langlo, Frank

    2014-01-01

    The first part of the thesis is an introduction of the drilling system where the theoretical background of the drilling system is described. Then the reliability centered maintenance (RCM) methodology is described. RCM is a logic way of identifying what equipment that needs to be maintained with a preventative maintenance basis rather than letting it fail and then fix it basis, commonly referred to as the run to failure (RTF). The maintenance strategies are described in 3.2 Reliability cen...

  19. NASA Space Engineering Research Center for VLSI systems design

    Science.gov (United States)

    1991-01-01

    This annual review reports the center's activities and findings on very large scale integration (VLSI) systems design for 1990, including project status, financial support, publications, the NASA Space Engineering Research Center (SERC) Symposium on VLSI Design, research results, and outreach programs. Processor chips completed or under development are listed. Research results summarized include a design technique to harden complementary metal oxide semiconductors (CMOS) memory circuits against single event upset (SEU); improved circuit design procedures; and advances in computer aided design (CAD), communications, computer architectures, and reliability design. Also described is a high school teacher program that exposes teachers to the fundamentals of digital logic design.

  20. Integrative systems biology for data-driven knowledge discovery.

    Science.gov (United States)

    Greene, Casey S; Troyanskaya, Olga G

    2010-09-01

    Integrative systems biology is an approach that brings together diverse high-throughput experiments and databases to gain new insights into biological processes or systems at molecular through physiological levels. These approaches rely on diverse high-throughput experimental techniques that generate heterogeneous data by assaying varying aspects of complex biological processes. Computational approaches are necessary to provide an integrative view of these experimental results and enable data-driven knowledge discovery. Hypotheses generated from these approaches can direct definitive molecular experiments in a cost-effective manner. By using integrative systems biology approaches, we can leverage existing biological knowledge and large-scale data to improve our understanding of as yet unknown components of a system of interest and how its malfunction leads to disease.

  1. Introducing Bioinformatics into the Biology Curriculum: Exploring the National Center for Biotechnology Information.

    Science.gov (United States)

    Smith, Thomas M.; Emmeluth, Donald S.

    2002-01-01

    Explains the potential of computer technology in science education and argues for integrating bioinformatics into the biology curriculum. Describes three modules designed to introduce students to technological advancements in biology. Aims to develop a better understanding of molecular biology among students. (YDS)

  2. Classification of Recombinant Biologics in the EU: Divergence between National Pharmacovigilance Centers

    NARCIS (Netherlands)

    Klein, Kevin; De Bruin, Marie L.; Broekmans, Andre W.; Stolk, Pieter

    2015-01-01

    Background and Objective: Biological medicinal products (biologics) are subject to specific pharmacovigilance requirements to ensure that biologics are identifiable by brand name and batch number in adverse drug reaction (ADR) reports. Since Member States collect ADR data at the national level befor

  3. 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.

  4. Measuring cell identity in noisy biological systems

    OpenAIRE

    Birnbaum, Kenneth D; Kussell, Edo

    2011-01-01

    Global gene expression measurements are increasingly obtained as a function of cell type, spatial position within a tissue and other biologically meaningful coordinates. Such data should enable quantitative analysis of the cell-type specificity of gene expression, but such analyses can often be confounded by the presence of noise. We introduce a specificity measure Spec that quantifies the information in a gene's complete expression profile regarding any given cell type, and an uncertainty me...

  5. Towards systems thinking in cell biology education

    OpenAIRE

    Verhoeff, Roald Pieter

    2003-01-01

    Students are taught a large variety of life structures and processes at the cellular level. The concepts used to describe them are mainly drawn from the sub-cellular level, but this knowledge seems to be fragmentary if its integration at the cellular and organismic level remains undone. As a consequence, many students fail to acquire coherent conceptual understanding of the cell as a basic and functional unit of the organism. To enhance the coherence in students’ cell biological knowledge we ...

  6. Systems for Detection and Identification of Biological Aerosols (Review Paper)

    OpenAIRE

    Eva Švabenska

    2012-01-01

    Easy and inexpensive manufacturing of biological weapons, their complicated detection, expensive protection, difficult treating of affected individuals, selective impact only for people, animals or plants, are all factors making an effective defense against biological warfare agents very difficult. The aim of this study is an introduction to the systems for the detection and identification of biological aerosols containing dangerous bioagents. The basic techniques used for detection and ident...

  7. Digital optical computers at the optoelectronic computing systems center

    Science.gov (United States)

    Jordan, Harry F.

    1991-01-01

    The Digital Optical Computing Program within the National Science Foundation Engineering Research Center for Opto-electronic Computing Systems has as its specific goal research on optical computing architectures suitable for use at the highest possible speeds. The program can be targeted toward exploiting the time domain because other programs in the Center are pursuing research on parallel optical systems, exploiting optical interconnection and optical devices and materials. Using a general purpose computing architecture as the focus, we are developing design techniques, tools and architecture for operation at the speed of light limit. Experimental work is being done with the somewhat low speed components currently available but with architectures which will scale up in speed as faster devices are developed. The design algorithms and tools developed for a general purpose, stored program computer are being applied to other systems such as optimally controlled optical communication networks.

  8. Evolutionary Tradeoffs between Economy and Effectiveness in Biological Homeostasis Systems

    OpenAIRE

    Pablo Szekely; Hila Sheftel; Avi Mayo; Uri Alon

    2013-01-01

    Biological regulatory systems face a fundamental tradeoff: they must be effective but at the same time also economical. For example, regulatory systems that are designed to repair damage must be effective in reducing damage, but economical in not making too many repair proteins because making excessive proteins carries a fitness cost to the cell, called protein burden. In order to see how biological systems compromise between the two tasks of effectiveness and economy, we applied an approach ...

  9. Systems-biology dissection of eukaryotic cell growth

    OpenAIRE

    Andrews Justen; Przytycka Teresa M

    2010-01-01

    Abstract A recent article in BMC Biology illustrates the use of a systems-biology approach to integrate data across the transcriptome, proteome and metabolome of budding yeast in order to dissect the relationship between nutrient conditions and cell growth. See research article http://jbiol.com/content/6/2/4 and http://www.biomedcentral.com/1741-7007/8/68

  10. Systems Biology: The elements and principles of Life

    NARCIS (Netherlands)

    Westerhoff, H.V.; Winder, C.; Messiha, H.; Simeonidis, E.; Adamczyk, M.; Verma, M.; Bruggeman, F.J.; Dunn, W.

    2009-01-01

    Systems Biology has a mission that puts it at odds with traditional paradigms of physics and molecular biology, such as the simplicity requested by Occam’s razor and minimum energy/maximal efficiency. By referring to biochemical experiments on control and regulation, and on flux balancing in yeast,

  11. Directed evolution and synthetic biology applications to microbial systems.

    Science.gov (United States)

    Bassalo, Marcelo C; Liu, Rongming; Gill, Ryan T

    2016-06-01

    Biotechnology applications require engineering complex multi-genic traits. The lack of knowledge on the genetic basis of complex phenotypes restricts our ability to rationally engineer them. However, complex phenotypes can be engineered at the systems level, utilizing directed evolution strategies that drive whole biological systems toward desired phenotypes without requiring prior knowledge of the genetic basis of the targeted trait. Recent developments in the synthetic biology field accelerates the directed evolution cycle, facilitating engineering of increasingly complex traits in biological systems. In this review, we summarize some of the most recent advances in directed evolution and synthetic biology that allows engineering of complex traits in microbial systems. Then, we discuss applications that can be achieved through engineering at the systems level. PMID:27054950

  12. Block Fusion Systems and the Center of the Group Ring

    DEFF Research Database (Denmark)

    Jacobsen, Martin Wedel

    This thesis develops some aspects of the theory of block fusion systems. Chapter 1 contains a brief introduction to the group algebra and some simple results about algebras over a field of positive characteristic. In chapter 2 we define the concept of a fusion system and the fundamental property ...... algebra is one-dimensional. Chapter 4 consists of a proof that block fusion systems of symmetric groups are always group fusion systems of symmetric groups, and an analogous result holds for the alternating groups.......This thesis develops some aspects of the theory of block fusion systems. Chapter 1 contains a brief introduction to the group algebra and some simple results about algebras over a field of positive characteristic. In chapter 2 we define the concept of a fusion system and the fundamental property...... of saturation. We also define block fusion systems and prove that they are saturated. Chapter 3 develops some tools for relating block fusion systems to the structure of the center of the group algebra. In particular, it is proven that a block has trivial defect group if and only if the center of the block...

  13. Control Systems Security Test Center - FY 2004 Program Summary

    Energy Technology Data Exchange (ETDEWEB)

    Robert E. Polk; Alen M. Snyder

    2005-04-01

    In May 2004, the US-CERT Control Systems Security Center (CSSC) was established at Idaho National Laboratory to execute assessment activities to reduce the vulnerability of the nation’s critical infrastructure control systems to terrorist attack. The CSSC implements a program to accomplish the five goals presented in the US-CERT National Strategy for Control Systems Security. This report summarizes the first year funding of startup activities and program achievements that took place in FY 2004 and early FY 2005. This document was prepared for the US-CERT Control Systems Security Center of the National Cyber Security Division of the Department of Homeland Security (DHS). DHS has been tasked under the Homeland Security Act of 2002 to coordinate the overall national effort to enhance the protection of the national critical infrastructure. Homeland Security Presidential Directive HSPD-7 directs federal departments to identify and prioritize the critical infrastructure and protect it from terrorist attack. The US-CERT National Strategy for Control Systems Security was prepared by the National Cyber Security Division to address the control system security component addressed in the National Strategy to Secure Cyberspace and the National Strategy for the Physical Protection of Critical Infrastructures and Key Assets. The US-CERT National Strategy for Control Systems Security identified five high-level strategic goals for improving cyber security of control systems.

  14. Search for organising principles: understanding in systems biology.

    Science.gov (United States)

    Mesarovic, M D; Sreenath, S N; Keene, J D

    2004-06-01

    Due in large measure to the explosive progress in molecular biology, biology has become arguably the most exciting scientific field. The first half of the 21st century is sometimes referred to as the 'era of biology', analogous to the first half of the 20th century, which was considered to be the 'era of physics'. Yet, biology is facing a crisis--or is it an opportunity--reminiscent of the state of biology in pre-double-helix time. The principal challenge facing systems biology is complexity. According to Hood, 'Systems biology defines and analyses the interrelationships of all of the elements in a functioning system in order to understand how the system works.' With 30000+ genes in the human genome the study of all relationships simultaneously becomes a formidably complex problem. Hanahan and Weinberg raised the question as to whether progress will consist of 'adding further layers of complexity to a scientific literature that is already complex almost beyond measure' or whether the progress will lead to a 'science with a conceptual structure and logical coherence that rivals that of chemistry or physics.' At the core of the challenge is the need for a new approach, a shift from reductionism to a holistic perspective. However, more than just a pronouncement of a new approach is needed. We suggest that what is needed is to provide a conceptual framework for systems biology research. We propose that the concept of a complex system, i.e. a system of systems as defined in mathematical general systems theory (MGST), is central to provide such a framework. We further argue that for a deeper understanding in systems biology investigations should go beyond building numerical mathematical or computer models--important as they are. Biological phenomena cannot be predicted with the level of numerical precision as in classical physics. Explanations in terms of how the categories of systems are organised to function in ever changing conditions are more revealing. Non

  15. Search for organising principles: understanding in systems biology.

    Science.gov (United States)

    Mesarovic, M D; Sreenath, S N; Keene, J D

    2004-06-01

    Due in large measure to the explosive progress in molecular biology, biology has become arguably the most exciting scientific field. The first half of the 21st century is sometimes referred to as the 'era of biology', analogous to the first half of the 20th century, which was considered to be the 'era of physics'. Yet, biology is facing a crisis--or is it an opportunity--reminiscent of the state of biology in pre-double-helix time. The principal challenge facing systems biology is complexity. According to Hood, 'Systems biology defines and analyses the interrelationships of all of the elements in a functioning system in order to understand how the system works.' With 30000+ genes in the human genome the study of all relationships simultaneously becomes a formidably complex problem. Hanahan and Weinberg raised the question as to whether progress will consist of 'adding further layers of complexity to a scientific literature that is already complex almost beyond measure' or whether the progress will lead to a 'science with a conceptual structure and logical coherence that rivals that of chemistry or physics.' At the core of the challenge is the need for a new approach, a shift from reductionism to a holistic perspective. However, more than just a pronouncement of a new approach is needed. We suggest that what is needed is to provide a conceptual framework for systems biology research. We propose that the concept of a complex system, i.e. a system of systems as defined in mathematical general systems theory (MGST), is central to provide such a framework. We further argue that for a deeper understanding in systems biology investigations should go beyond building numerical mathematical or computer models--important as they are. Biological phenomena cannot be predicted with the level of numerical precision as in classical physics. Explanations in terms of how the categories of systems are organised to function in ever changing conditions are more revealing. Non

  16. A system for success: BMC Systems Biology, a new open access journal

    OpenAIRE

    Webb Penelope A; Hodgkinson Matt J

    2007-01-01

    Abstract BMC Systems Biology is the first open access journal spanning the growing field of systems biology from molecules up to ecosystems. The journal has launched as more and more institutes are founded that are similarly dedicated to this new approach. BMC Systems Biology builds on the ongoing success of the BMC series, providing a venue for all sound research in the systems-level analysis of biology.

  17. A system for success: BMC Systems Biology, a new open access journal

    Directory of Open Access Journals (Sweden)

    Webb Penelope A

    2007-09-01

    Full Text Available Abstract BMC Systems Biology is the first open access journal spanning the growing field of systems biology from molecules up to ecosystems. The journal has launched as more and more institutes are founded that are similarly dedicated to this new approach. BMC Systems Biology builds on the ongoing success of the BMC series, providing a venue for all sound research in the systems-level analysis of biology.

  18. New lidar systems at the German Aerospace Center

    OpenAIRE

    Kaifler, Bernd; Kaifler, Natalie; Büdenbender, Christian; Witschas, Benjamin; Gomez Kabelka, Pau; Rapp, Markus; Mahnke, Peter; Sauder, Daniel; Geyer, Gerhard; Speiser, Jochen

    2015-01-01

    This work gives an overview of the lower-, middle and upper atmosphere lidar projects at the German Aerospace Center (DLR). The Temperature Lidar for Middle Atmosphere research (TELMA) is a combined sodium/Rayleigh/Brillouin-lidar integrated into an 8-foot container. It will provide temperature profiles with high temporal and spatial resolution from near ground level up to approximately 110 km altitude. The lidar system is designed for remote/autonomous operation. First observations with the...

  19. Managing IT infrastructure using Microsoft System Center Configuration Manager

    OpenAIRE

    Tkavc, Peter

    2010-01-01

    The thesis deals with the issue of effective management of information infrastructure in the enterprise. Three software products are presented as a solution: Symantec Altiris IT Management Suite 7.0, LanDesk Management Suite 9.0 and Microsoft System Center Configuration Manager 2007 (SCCM). Their main features and options are described and then a comparison between them is made. Since the Trimo d.d. decided to use SCCM, the following chapters describe the procedures required to start using...

  20. The Center-TRACON Automation System: Simulation and field testing

    Science.gov (United States)

    Denery, Dallas G.; Erzberger, Heinz

    1995-01-01

    A new concept for air traffic management in the terminal area, implemented as the Center-TRACON Automation System, has been under development at NASA Ames in a cooperative program with the FAA since 1991. The development has been strongly influenced by concurrent simulation and field site evaluations. The role of simulation and field activities in the development process will be discussed. Results of recent simulation and field tests will be presented.

  1. System Center 2012 R2 Virtual Machine Manager cookbook

    CERN Document Server

    Cardoso, Edvaldo Alessandro

    2014-01-01

    This book is a step-by-step guide packed with recipes that cover architecture design and planning. The book is also full of deployment tips, techniques, and solutions. If you are a solutions architect, technical consultant, administrator, or any other virtualization enthusiast who needs to use Microsoft System Center Virtual Machine Manager in a real-world environment, then this is the book for you. We assume that you have previous experience with Windows 2012 R2 and Hyper-V.

  2. Evaluation models for contaminated sites – biological system at risk

    OpenAIRE

    Golomeova, Mirjana; Krstev, Boris; Golomeov, Blagoj; Zendelska, Afrodita; Krstev, Aleksandar

    2009-01-01

    The paper presents the different methods that can be used correspond to three types of approaches, testing, monitoring, and modeling: experimental models, in situ indicators and mathematical models, and choice of model for contaminated sites – biological system at risk.

  3. Yeast systems biology to unravel the network of life

    DEFF Research Database (Denmark)

    Mustacchi, Roberta; Hohmann, S; Nielsen, Jens

    2006-01-01

    of advanced cell factories for production of fuels, chemicals, food ingredients and pharmaceuticals. The yeast Saccharomyces cerevisiae represents an excellent model system; the density of biological information available on this organism allows it to serve as a eukaryotic model for studying human diseases....... 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...... appropriate guidelines, establish an appropriate infrastructure for the network and organize courses, meetings and conferences that will consolidate the network and promote systems biology. This paper discusses the impacts of systems biology and how YSBN may play a role in the future development of the field...

  4. Advancing metabolic engineering through systems biology of industrial microorganisms.

    Science.gov (United States)

    Dai, Zongjie; Nielsen, Jens

    2015-12-01

    Development of sustainable processes to produce bio-based compounds is necessary due to the severe environmental problems caused by the use of fossil resources. Metabolic engineering can facilitate the development of highly efficient cell factories to produce these compounds from renewable resources. The objective of systems biology is to gain a comprehensive and quantitative understanding of living cells and can hereby enhance our ability to characterize and predict cellular behavior. Systems biology of industrial microorganisms is therefore valuable for metabolic engineering. Here we review the application of systems biology tools for the identification of metabolic engineering targets which may lead to reduced development time for efficient cell factories. Finally, we present some perspectives of systems biology for advancing metabolic engineering further.

  5. Advancing metabolic engineering through systems biology of industrial microorganisms

    DEFF Research Database (Denmark)

    Dai, Zongjie; Nielsen, Jens

    2015-01-01

    resources. The objective of systems biology is to gain a comprehensive and quantitative understanding of living cells and can hereby enhance our ability to characterize and predict cellular behavior. Systems biology of industrial microorganisms is therefore valuable for metabolic engineering. Here we review......Development of sustainable processes to produce bio-based compounds is necessary due to the severe environmental problems caused by the use of fossil resources. Metabolic engineering can facilitate the development of highly efficient cell factories to produce these compounds from renewable...... the application of systems biology tools for the identification of metabolic engineering targets which may lead to reduced development time for efficient cell factories. Finally, we present some perspectives of systems biology for advancing metabolic engineering further....

  6. Network benchmarking: a happy marriage between systems and synthetic biology.

    Science.gov (United States)

    Minty, Jeremy J; Varedi K, S Marjan; Nina Lin, Xiaoxia

    2009-03-27

    In their new Cell paper, Cantone et al. (2009) present exciting results on constructing and utilizing a small synthetic gene regulatory network in yeast that draws from two rapidly developing fields of systems and synthetic biology.

  7. Increasing the Use of Student-Centered Pedagogies from Moderate to High Improves Student Learning and Attitudes about Biology.

    Science.gov (United States)

    Connell, Georgianne L; Donovan, Deborah A; Chambers, Timothy G

    2016-01-01

    Student-centered strategies are being incorporated into undergraduate classrooms in response to a call for reform. We tested whether teaching in an extensively student-centered manner (many active-learning pedagogies, consistent formative assessment, cooperative groups; the Extensive section) was more effective than teaching in a moderately student-centered manner (fewer active-learning pedagogies, less formative assessment, without groups; the Moderate section) in a large-enrollment course. One instructor taught both sections of Biology 101 during the same quarter, covering the same material. Students in the Extensive section had significantly higher mean scores on course exams. They also scored significantly higher on a content postassessment when accounting for preassessment score and student demographics. Item response theory analysis supported these results. Students in the Extensive section had greater changes in postinstruction abilities compared with students in the Moderate section. Finally, students in the Extensive section exhibited a statistically greater expert shift in their views about biology and learning biology. We suggest our results are explained by the greater number of active-learning pedagogies experienced by students in cooperative groups, the consistent use of formative assessment, and the frequent use of explicit metacognition in the Extensive section. PMID:26865643

  8. Increasing the Use of Student-Centered Pedagogies from Moderate to High Improves Student Learning and Attitudes about Biology.

    Science.gov (United States)

    Connell, Georgianne L; Donovan, Deborah A; Chambers, Timothy G

    2016-01-01

    Student-centered strategies are being incorporated into undergraduate classrooms in response to a call for reform. We tested whether teaching in an extensively student-centered manner (many active-learning pedagogies, consistent formative assessment, cooperative groups; the Extensive section) was more effective than teaching in a moderately student-centered manner (fewer active-learning pedagogies, less formative assessment, without groups; the Moderate section) in a large-enrollment course. One instructor taught both sections of Biology 101 during the same quarter, covering the same material. Students in the Extensive section had significantly higher mean scores on course exams. They also scored significantly higher on a content postassessment when accounting for preassessment score and student demographics. Item response theory analysis supported these results. Students in the Extensive section had greater changes in postinstruction abilities compared with students in the Moderate section. Finally, students in the Extensive section exhibited a statistically greater expert shift in their views about biology and learning biology. We suggest our results are explained by the greater number of active-learning pedagogies experienced by students in cooperative groups, the consistent use of formative assessment, and the frequent use of explicit metacognition in the Extensive section.

  9. [Community health centers: an alternative for the health system

    Science.gov (United States)

    Fernandes; Monteiro

    1997-01-01

    Reflecting on the current reorganization of the relationship between the state and civil society, the health care field is involved in an intense debate over the organization and use of government and private health services. The authors propose an alternative, consisting of the implementation of primary health care clinics, managed by local institutions and funded by the Unified Health System. To support this proposition, they report on the current experience at the Rocinha slum in Rio de Janeiro, where a community health center was built by the neighborhood association 12 years ago and has been managed by the community since then. The hospital referral rate at the clinic, requests for laboratory tests, and use of precriptions have been considerably limited, although these services are available. These low rates are attributed to the possibility of closer social control by the community, as well as to the geographical features of the center, favoring a broader perception of both health problems and treatment. In order to provide more substantial support to the proposed centers, some suggestions are presented, like the implementation of direct agreements between the government and neighborhood associations (not allowed under current legislation) and expanding potential sources of funding for the health centers, currently restricted to government programs. PMID:10886837

  10. Effects of abiotic stress on plants: a systems biology perspective

    OpenAIRE

    Cramer Grant R; Urano Kaoru; Delrot Serge; Pezzotti Mario; Shinozaki Kazuo

    2011-01-01

    Abstract The natural environment for plants is composed of a complex set of abiotic stresses and biotic stresses. Plant responses to these stresses are equally complex. Systems biology approaches facilitate a multi-targeted approach by allowing one to identify regulatory hubs in complex networks. Systems biology takes the molecular parts (transcripts, proteins and metabolites) of an organism and attempts to fit them into functional networks or models designed to describe and predict the dynam...

  11. Stochastic chemical kinetics theory and (mostly) systems biological applications

    CERN Document Server

    Érdi, Péter

    2014-01-01

    This volume reviews the theory and simulation methods of stochastic kinetics by integrating historical and recent perspectives, presents applications, mostly in the context of systems biology and also in combustion theory. In recent years, due to the development in experimental techniques, such as optical imaging, single cell analysis, and fluorescence spectroscopy, biochemical kinetic data inside single living cells have increasingly been available. The emergence of systems biology brought renaissance in the application of stochastic kinetic methods.

  12. Reproductive biology of the biofuel plant Jatropha curcas in its center of origin.

    Science.gov (United States)

    Rincón-Rabanales, Manuel; Vargas-López, Laura I; Adriano-Anaya, Lourdes; Vázquez-Ovando, Alfredo; Salvador-Figueroa, Miguel; Ovando-Medina, Isidro

    2016-01-01

    In this work, we studied the main characteristics of flowering, reproductive system and diversity of pollinators for the biofuel plant Jatropha curcas (L.) in a site of tropical southeastern Mexico, within its center of origin. The plants were monoecious with inflorescences of unisexual flowers. The male flowers produced from 3062-5016 pollen grains (266-647 per anther). The plants produced fruits with both geitonogamy and xenogamy, although insect pollination significantly increased the number and quality of fruits. A high diversity of flower visiting insects (36 species) was found, of which nine were classified as efficient pollinators. The native stingless bees Scaptotrigona mexicana (Guérin-Meneville) and Trigona (Tetragonisca) angustula (Latreille) were the most frequent visitors and their presence coincided with the hours when the stigma was receptive. It is noteworthy that the female flowers open before the male flowers, favoring xenogamy, which may explain the high genetic variability reported in J. curcas for this region of the world. PMID:26989640

  13. New computer system for the Japan Tier-2 center

    CERN Multimedia

    Hiroyuki Matsunaga

    2007-01-01

    The ICEPP (International Center for Elementary Particle Physics) of the University of Tokyo has been operating an LCG Tier-2 center dedicated to the ATLAS experiment, and is going to switch over to the new production system which has been recently installed. The system will be of great help to the exciting physics analyses for coming years. The new computer system includes brand-new blade servers, RAID disks, a tape library system and Ethernet switches. The blade server is DELL PowerEdge 1955 which contains two Intel dual-core Xeon (WoodCrest) CPUs running at 3GHz, and a total of 650 servers will be used as compute nodes. Each of the RAID disks is configured to be RAID-6 with 16 Serial ATA HDDs. The equipment as well as the cooling system is placed in a new large computer room, and both are hooked up to UPS (uninterruptible power supply) units for stable operation. As a whole, the system has been built with redundant configuration in a cost-effective way. The next major upgrade will take place in thre...

  14. Mathematical aspects of pattern formation in biological systems

    CERN Document Server

    Wei, Juncheng

    2013-01-01

    This monograph is concerned with the mathematical analysis of patterns which are encountered in biological systems. It summarises, expands and relates results obtained in the field during the last fifteen years. It also links the results to biological applications and highlights their relevance to phenomena in nature. Of particular concern are large-amplitude patterns far from equilibrium in biologically relevant models.The approach adopted in the monograph is based on the following paradigms:• Examine the existence of spiky steady states in reaction-diffusion systems and select as observabl

  15. Engineering system dynamics a unified graph-centered approach

    CERN Document Server

    Brown, Forbes T

    2006-01-01

    For today's students, learning to model the dynamics of complex systems is increasingly important across nearly all engineering disciplines. First published in 2001, Forbes T. Brown's Engineering System Dynamics: A Unified Graph-Centered Approach introduced students to a unique and highly successful approach to modeling system dynamics using bond graphs. Updated with nearly one-third new material, this second edition expands this approach to an even broader range of topics. What's New in the Second Edition? In addition to new material, this edition was restructured to build students' competence in traditional linear mathematical methods before they have gone too far into the modeling that still plays a pivotal role. New topics include magnetic circuits and motors including simulation with magnetic hysteresis; extensive new material on the modeling, analysis, and simulation of distributed-parameter systems; kinetic energy in thermodynamic systems; and Lagrangian and Hamiltonian methods. MATLAB(R) figures promi...

  16. Primary energy-transformations in biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Lehninger, A.L.

    1980-10-01

    In this paper I shall review the main outlines of current research on the molecular aspects of the primary energy-coupling mechanisms in cells, those carried out by energy-transducing membranes. They include the capture of solar energy by the chloroplast membranes of green plants, used to generate carbohydrates and molecular oxygen from carbon dioxide and water, and the counterpart of photosynthesis, the process of respiration in heterotrophic organisms, in which reduced organic products generated by photosynthesis are oxidized at the expense of dioxygen to form carbon dioxide and water. Although the cycling of dioxygen, carbon dioxide, and organic matter between the plant and animal worlds is well known, it is not generally appreciated that the magnitude of biological energy flux in these cycles is huge compared to the total energy flux in man-made devices. A major consequence is that the concentration of carbon dioxide in the atmosphere has been increasing at a significant rate, at a time when there is also a decrease, at least in some parts of the world, in the counterbalancing utilization of CO/sub 2/ by green plants, due to deforestation. The greenhouse effect of increased atmospheric CO/sub 2/ may not only change the earth's climate, but also may influence the rate of photosynthesis. It is also not generally appreciated that energy flow in the biosphere leads to production of enormous amounts of organic matter potentially useful in furnishing man's energy requirements.

  17. Virtual Tissues and Developmental Systems Biology

    Science.gov (United States)

    Computational modeling of embryonic systems to analyze how 'core development processes' are wired together. Has the potential to address environmental and human health factors with broad scientific and economic impacts.

  18. System chemical biology studies of endocrine disruptors

    DEFF Research Database (Denmark)

    Taboureau, Olivier; Oprea, Tudor I.

    Endocrine disrupting chemicals (EDCs) alter hormonal balance and other physiological systems through inappropriate developmental or adult exposure, perturbing the reproductive function of further generations. While disruption of key receptors (e.g., estrogen, androgen, and thyroid) at the ligand...

  19. Effects of Pesticides on Biological Systems

    OpenAIRE

    Ergul Belge Kurutas; Metin Kilinc

    2003-01-01

    The use of pesticid both in Turkey and other contries is widespread in order to combat against many pests which cause economical damages. However, pesticides in human pass through skin, respiratory or digestive systems and is metabolized by monooxygenase system dependent upon cytocrome P450 in liver. They also give rise to severe decreases cytochrome P450 and amount of "hem" enzyme activites of glucose-6-phosphatase, pyrophosphatase by stimulating lipid peroxidation on hepatic microsomes. In ...

  20. Computational Modeling, Formal Analysis, and Tools for Systems Biology.

    Directory of Open Access Journals (Sweden)

    Ezio Bartocci

    2016-01-01

    Full Text Available As the amount of biological data in the public domain grows, so does the range of modeling and analysis techniques employed in systems biology. In recent years, a number of theoretical computer science developments have enabled modeling methodology to keep pace. The growing interest in systems biology in executable models and their analysis has necessitated the borrowing of terms and methods from computer science, such as formal analysis, model checking, static analysis, and runtime verification. Here, we discuss the most important and exciting computational methods and tools currently available to systems biologists. We believe that a deeper understanding of the concepts and theory highlighted in this review will produce better software practice, improved investigation of complex biological processes, and even new ideas and better feedback into computer science.

  1. Application of Bioinformatics and Systems Biology in Medicinal Plant Studies

    Institute of Scientific and Technical Information of China (English)

    DENG You-ping; AI Jun-mei; XIAO Pei-gen

    2010-01-01

    One important purpose to investigate medicinal plants is to understand genes and enzymes that govern the biological metabolic process to produce bioactive compounds.Genome wide high throughput technologies such as genomics,transcriptomics,proteomics and metabolomics can help reach that goal.Such technologies can produce a vast amount of data which desperately need bioinformatics and systems biology to process,manage,distribute and understand these data.By dealing with the"omics"data,bioinformatics and systems biology can also help improve the quality of traditional medicinal materials,develop new approaches for the classification and authentication of medicinal plants,identify new active compounds,and cultivate medicinal plant species that tolerate harsh environmental conditions.In this review,the application of bioinformatics and systems biology in medicinal plants is briefly introduced.

  2. Computational Modeling, Formal Analysis, and Tools for Systems Biology.

    Science.gov (United States)

    Bartocci, Ezio; Lió, Pietro

    2016-01-01

    As the amount of biological data in the public domain grows, so does the range of modeling and analysis techniques employed in systems biology. In recent years, a number of theoretical computer science developments have enabled modeling methodology to keep pace. The growing interest in systems biology in executable models and their analysis has necessitated the borrowing of terms and methods from computer science, such as formal analysis, model checking, static analysis, and runtime verification. Here, we discuss the most important and exciting computational methods and tools currently available to systems biologists. We believe that a deeper understanding of the concepts and theory highlighted in this review will produce better software practice, improved investigation of complex biological processes, and even new ideas and better feedback into computer science.

  3. A Real-Time and Dynamic Biological Information Retrieval and Analysis System (BIRAS)

    Institute of Scientific and Technical Information of China (English)

    Qi Zhou; Hong Zhang; Meiying Geng; Chenggang Zhang

    2003-01-01

    The aim of this study is to design a biological information retrieval and analysis system (BIRAS) based on the Internet. Using the specific network protocol, BIRAS system could send and receive information from the Entrez search and retrieval system maintained by National Center for Biotechnology Information (NCBI) in USA. The literatures, nucleotide sequence, protein sequences, and other resources according to the user-defined term could then be retrieved and sent to the user by pop up message or by E-mail informing automatically using BIRAS system.All the information retrieving and analyzing processes are done in real-time. As a robust system for intelligently and dynamically retrieving and analyzing on the user-defined information, it is believed that BIRAS would be extensively used to retrieve specific information from large amount of biological databases in now days.The program is available on request from the corresponding author.

  4. Towards Engineering Biological Systems in a Broader Context.

    Science.gov (United States)

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

    2016-02-27

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

  5. PathSys: integrating molecular interaction graphs for systems biology

    Directory of Open Access Journals (Sweden)

    Raval Alpan

    2006-02-01

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

  6. Towards Engineering Biological Systems in a Broader Context.

    Science.gov (United States)

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

    2016-02-27

    Significant advances have been made in synthetic biology to program information processing capabilities in cells. While these designs can function predictably in controlled laboratory environments, the reliability of these devices in complex, temporally changing environments has not yet been characterized. As human society faces global challenges in agriculture, human health and energy, synthetic biology should develop predictive design principles for biological systems operating in complex environments. Natural biological systems have evolved mechanisms to overcome innumerable and diverse environmental challenges. Evolutionary design rules should be extracted and adapted to engineer stable and predictable ecological function. We highlight examples of natural biological responses spanning the cellular, population and microbial community levels that show promise in synthetic biology contexts. We argue that synthetic circuits embedded in host organisms or designed ecologies informed by suitable measurement of biotic and abiotic environmental parameters could be used as engineering substrates to achieve target functions in complex environments. Successful implementation of these methods will broaden the context in which synthetic biological systems can be applied to solve important problems. PMID:26546279

  7. Biologically-Inspired Water Propulsion System

    Institute of Scientific and Technical Information of China (English)

    Andrzej Sioma

    2013-01-01

    Most propulsion systems of vehicles travelling in the aquatic environment are equipped with propellers.Observations of nature,however,show that the absolute majority of organisms travel through water using wave motion,paddling or using water jet power.Inspired by these observations of nature,an innovative propulsion system working in aquatic environment was developed.This paper presents the design of the water propulsion system.Particular attention was paid to the use of paddling techniques and water jet power.A group of organisms that use those mechanisms to travel through water was selected and analysed.The results of research were used in the design of a propulsion system modelled simultaneously on two methods of movement in the aquatic environment.A method for modelling a propulsion system using a combination of the two solutions and the result were described.A conceptual design and a prototype constructed based on the solution were presented.With respect to the solution developed,studies and analyses of selected parameters of the prototype were described.

  8. Computational Proteomics: High-throughput Analysis for Systems Biology

    Energy Technology Data Exchange (ETDEWEB)

    Cannon, William R.; Webb-Robertson, Bobbie-Jo M.

    2007-01-03

    High-throughput (HTP) proteomics is a rapidly developing field that offers the global profiling of proteins from a biological system. The HTP technological advances are fueling a revolution in biology, enabling analyses at the scales of entire systems (e.g., whole cells, tumors, or environmental communities). However, simply identifying the proteins in a cell is insufficient for understanding the underlying complexity and operating mechanisms of the overall system. Systems level investigations are relying more and more on computational analyses, especially in the field of proteomics generating large-scale global data.

  9. 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.

  10. Analysis on Failure Mode Severity of Machining Center Spindle System

    Institute of Scientific and Technical Information of China (English)

    Guixiang Shen; Shuguang Sun; Yingzhi Zhang; Xiaoyan Qi; Bingkun Chen

    2015-01-01

    According to the subjectivity and fuzziness of analysis on failure mode severity about spindle system of machining center, an analysis model of the failure mode severity of such a system is proposed based on the new fault severity index system, improved analytic hierarchy process ( IAHP ) and entropy⁃based fuzzy comprehensive evaluation. IAHP and entropy methods are adopted to determine the comprehensive failure severity index weight. The evaluation result is obtained after the factor set, comment set, weight set, and other parameters are determined, and then the level of risk degree and numerical value order of every spindle system failure mode is given. By taking an example, we verify that the proposed method can quantify the qualitative problem comprehensively, obtain more accurate analysis results, and provide the theoretical reference for mechanization and sequencing of failure mode effect analysis in reliability analysis. The calculation results can also serve as the basis of failure mode, effects, and criticality analysis in the subsequent step.

  11. System Engineering Processes at Kennedy Space Center for Development of SLS and Orion Launch Systems

    Science.gov (United States)

    Schafer, Eric; Stambolian, Damon; Henderson, Gena

    2013-01-01

    There are over 40 subsystems being developed for the future SLS and Orion Launch Systems at Kennedy Space Center. These subsystems are developed at the Kennedy Space Center Engineering Directorate. The Engineering Directorate at Kennedy Space Center follows a comprehensive design process which requires several different product deliverables during each phase of each of the subsystems. This Presentation describes this process with examples of where the process has been applied.

  12. Biologic Therapy in Inflammatory Immunomediated Systemic Diseases: Safety Profile.

    Science.gov (United States)

    Moroncini, Gianluca; Albani, Lisa; Nobili, Lorenzo; Gabrielli, Armando

    2016-01-01

    The discovery of some key molecular mechanisms underlying the dysregulation of the immune system responsible for inflammatory systemic diseases as severe as Systemic Lupus Erythematosus (SLE), Systemic Sclerosis (SSc), and Systemic Vasculitides, led to the development and subsequent introduction into clinical practice of biological drugs which are significantly improving the management of such complex disorders. This novel molecular targeted therapeutics represents in fact a valid alternative or complementary treatment to conventional immunosuppressive strategies, characterized by broad, unspecific actions and severe adverse effects. Main advantages of the use of biologic drugs reside in their steroid-sparing effect and in the ability of inducing remission of refractory disease states or curing specific organ involvements. Aim of this article is to review and briefly discuss the scientific evidence supporting the use of biologics in these diseases, with a particular emphasis on their efficacy and safety profile compared to the canonical drugs.

  13. Modern power systems control centers: From EMS to AEMS

    Institute of Scientific and Technical Information of China (English)

    HE GuangYu; SUN YingYun; RUAN QianTu; WANG Wei; DONG ShuFeng

    2009-01-01

    Traditional energy management system (EMS) plays an indispensable role in control centers of electric power systems. However, it also has several shortcomings, including lack of real-time closed-loop control, unreliable functional modules, and difficult to exchange data. The electric hybrid control theory (EHCT) has been proposed as an innovative and effective means to overcome these shortcomings. This paper argues that the EHCT provides a theoretical foundation for the advanced energy manage-ment system (AEMS) that can achieve multi-objective, near-optimal, and closed-loop control of electric power grids. This paper also discusses the significance for control centers to evolve from the tradi-tional EMS to the AEMS. Furthermore, this paper points out that the traditional EMS can be considered as an integral part of the AEMS and that the AEMS can be built upon the traditional EMS. Thus, the re-sources that are currently available can be fully utilized to achieve near-optimal and closed-loop con-trol of power system operations.

  14. Modern power systems control centers:From EMS to AEMS

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Traditional energy management system (EMS) plays an indispensable role in control centers of electric power systems. However, it also has several shortcomings, including lack of real-time closed-loop control, unreliable functional modules, and difficult to exchange data. The electric hybrid control theory (EHCT) has been proposed as an innovative and effective means to overcome these shortcomings. This paper argues that the EHCT provides a theoretical foundation for the advanced energy management system (AEMS) that can achieve multi-objective, near-optimal, and closed-loop control of electric power grids. This paper also discusses the significance for control centers to evolve from the traditional EMS to the AEMS. Furthermore, this paper points out that the traditional EMS can be considered as an integral part of the AEMS and that the AEMS can be built upon the traditional EMS. Thus, the resources that are currently available can be fully utilized to achieve near-optimal and closed-loop control of power system operations.

  15. Circadian systems biology: When time matters

    Directory of Open Access Journals (Sweden)

    Luise Fuhr

    2015-01-01

    In this manuscript we review the combination of experimental methodologies, bioinformatics and theoretical models that have been essential to explore this remarkable timing-system. Such an integrative and interdisciplinary approach may provide new strategies with regard to chronotherapeutic treatment and new insights concerning the restoration of the circadian timing in clock-associated diseases.

  16. Metagenomic Systems Biology of the Human Microbiome

    DEFF Research Database (Denmark)

    Bonde, Ida

    in the system. Applying the CAG clustering method to data from the human gut microbiome, we identified dependency-associations between plasmids, phages and clone-specific gene sets to their bacterial host. Connections between CRISPR-elements and phages were also observed. Additionally, the persistence of some...

  17. Using the Unified Modelling Language (UML) to guide the systemic description of biological processes and systems.

    Science.gov (United States)

    Roux-Rouquié, Magali; Caritey, Nicolas; Gaubert, Laurent; Rosenthal-Sabroux, Camille

    2004-07-01

    One of the main issues in Systems Biology is to deal with semantic data integration. Previously, we examined the requirements for a reference conceptual model to guide semantic integration based on the systemic principles. In the present paper, we examine the usefulness of the Unified Modelling Language (UML) to describe and specify biological systems and processes. This makes unambiguous representations of biological systems, which would be suitable for translation into mathematical and computational formalisms, enabling analysis, simulation and prediction of these systems behaviours.

  18. Stochastic Physics, Complex Systems and Biology

    OpenAIRE

    Qian, Hong

    2012-01-01

    In complex systems, the interplay between nonlinear and stochastic dynamics, e.g., J. Monod's necessity and chance, gives rise to an evolutionary process in Darwinian sense, in terms of discrete jumps among attractors, with punctuated equilibrium, spontaneous random "mutations" and "adaptations". On an evlutionary time scale it produces sustainable diversity among individuals in a homogeneous population rather than convergence as usually predicted by a deterministic dynamics. The emergent dis...

  19. Systems Biology of the Vervet Monkey

    OpenAIRE

    Jasinska, Anna J.; Schmitt, Christopher A.; Susan K Service; Cantor, Rita M.; Dewar, Ken; James D. Jentsch; Kaplan, Jay R; Turner, Trudy R.; Warren, Wesley C.; George M Weinstock; Woods, Roger P.; Freimer, Nelson B.

    2013-01-01

    Nonhuman primates (NHP) provide crucial biomedical model systems intermediate between rodents and humans. The vervet monkey (also called the African green monkey) is a widely used NHP model that has unique value for genetic and genomic investigations of traits relevant to human diseases. This article describes the phylogeny and population history of the vervet monkey and summarizes the use of both captive and wild vervet monkeys in biomedical research. It also discusses the effort of an inter...

  20. Integrative systems biology approaches in asthma pharmacogenomics

    OpenAIRE

    Dahlin, Amber; Tantisira, Kelan G.

    2012-01-01

    In order to improve therapeutic outcomes, there is a tremendous need to identify patients who are likely to respond to a given asthma treatment. Pharmacogenomic studies have explained a portion of the variability in drug response and provided an increasing list of candidate genes and SNPs. However, as phenotypic variation arises from a network of complex interactions among genetic and environmental factors, rather than individual genes or SNPs, a multidisciplinary, systems-level approach is r...

  1. Applications of dynamical systems in biology and medicine

    CERN Document Server

    Radunskaya, Ami

    2015-01-01

    This volume highlights problems from a range of biological and medical applications that can be interpreted as questions about system behavior or control.  Topics include drug resistance in cancer and malaria, biological fluid dynamics, auto-regulation in the kidney, anti-coagulation therapy, evolutionary diversification and photo-transduction.  Mathematical techniques used to describe and investigate these biological and medical problems include ordinary, partial and stochastic differentiation equations, hybrid discrete-continuous approaches, as well as 2 and 3D numerical simulation. .

  2. Systems Biology Brings Life Sciences Closer--Report on the China-UK Systems Biology Workshop 2005

    Institute of Scientific and Technical Information of China (English)

    Ming Chen

    2005-01-01

    @@ The China-UK Systems Biology Workshop 2005 was held during June 20-21 in the National Science Park of Zhejiang University, Hangzhou, China. It was organized by the Institute of Bioinformatics, Zhejiang University, and was initiated by Prof. Dr. Jun Zhu (Zhejiang University) and Prof. Dr. John Findlay (University of Leeds, UK). The workshop was part of the program called UK-China Partners in Science, a one-year campaign that was initiated by the British government to explore more collaborations between UK and China on science and technology. It was attended also by a representative of this program, Mr.Frank Yuan, senior science & innovation officer. The idea of the workshop was to bring together experts with specialists in systems biology in order to promote the "natural partnership" between scientists from the two countries. The most important items of systems biology considered at the workshop were: (1) New technologies and advances in systems biology; (2) Research developments in genomics and proteomics; (3) New methodologies and software in computational biology; (4) Research collaboration on systems biology between China and UK.

  3. Differential Neuroproteomic and Systems Biology Analysis of Spinal Cord Injury.

    Science.gov (United States)

    Moghieb, Ahmed; Bramlett, Helen M; Das, Jyotirmoy H; Yang, Zhihui; Selig, Tyler; Yost, Richard A; Wang, Michael S; Dietrich, W Dalton; Wang, Kevin K W

    2016-07-01

    Acute spinal cord injury (SCI) is a devastating condition with many consequences and no known effective treatment. Although it is quite easy to diagnose traumatic SCI, the assessment of injury severity and projection of disease progression or recovery are often challenging, as no consensus biomarkers have been clearly identified. Here rats were subjected to experimental moderate or severe thoracic SCI. At 24h and 7d postinjury, spinal cord segment caudal to injury center versus sham samples was harvested and subjected to differential proteomic analysis. Cationic/anionic-exchange chromatography, followed by 1D polyacrylamide gel electrophoresis, was used to reduce protein complexity. A reverse phase liquid chromatography-tandem mass spectrometry proteomic platform was then utilized to identify proteome changes associated with SCI. Twenty-two and 22 proteins were up-regulated at 24 h and 7 day after SCI, respectively; whereas 19 and 16 proteins are down-regulated at 24 h and 7 day after SCI, respectively, when compared with sham control. A subset of 12 proteins were identified as candidate SCI biomarkers - TF (Transferrin), FASN (Fatty acid synthase), NME1 (Nucleoside diphosphate kinase 1), STMN1 (Stathmin 1), EEF2 (Eukaryotic translation elongation factor 2), CTSD (Cathepsin D), ANXA1 (Annexin A1), ANXA2 (Annexin A2), PGM1 (Phosphoglucomutase 1), PEA15 (Phosphoprotein enriched in astrocytes 15), GOT2 (Glutamic-oxaloacetic transaminase 2), and TPI-1 (Triosephosphate isomerase 1), data are available via ProteomeXchange with identifier PXD003473. In addition, Transferrin, Cathepsin D, and TPI-1 and PEA15 were further verified in rat spinal cord tissue and/or CSF samples after SCI and in human CSF samples from moderate/severe SCI patients. Lastly, a systems biology approach was utilized to determine the critical biochemical pathways and interactome in the pathogenesis of SCI. Thus, SCI candidate biomarkers identified can be used to correlate with disease progression or

  4. System Engineering Processes at Kennedy Space Center for Development of the SLS and Orion Launch Systems

    Science.gov (United States)

    Schafer, Eric J.

    2012-01-01

    There are over 40 subsystems being developed for the future SLS and Orion Launch Systems at Kennedy Space Center. These subsystems developed at the Kennedy Space Center Engineering Directorate follow a comprehensive design process which requires several different product deliverables during each phase of each of the subsystems. This Paper describes this process and gives an example of where the process has been applied.

  5. New data acquisition system for the lujan center

    International Nuclear Information System (INIS)

    To meet the data acquisition requirements for six new neutron scattering instruments at the Los Alamos Science Center (LANSCE), we are building systems using Web tools, commercial hardware and software, software developed by the controls community, and custom hardware developed by the neutron scattering community. To service these new instruments as well as seven existing instruments, our data acquisition system needs common software and hardware core capabilities and the means to flexibly integrate them while differentiating the needs of the diverse instrument suite. Neutron events are captured and processed in VXI modules while controls for sample environment and beam line setup are processed with PCs. Typically users access the system through web browsers. (author)

  6. CCSDS telemetry systems experience at the Goddard Space Flight Center

    Science.gov (United States)

    Carper, Richard D.; Stallings, William H., III

    1990-09-01

    NASA Goddard Space Flight Center (GSFC) designs, builds, manages, and operates science and applications spacecraft in near-earth orbit, and provides data capture, data processing, and flight control services for these spacecraft. In addition, GSFC has the responsibility of providing space-ground and ground-ground communications for near-earth orbiting spacecraft, including those of the manned spaceflight programs. The goal of reducing both the developmental and operating costs of the end-to-end information system has led the GSFC to support and participate in the standardization activities of the Consultative Committee for Space Data Systems (CCSDS), including those for packet telemetry. The environment in which such systems function is described, and the GSFC experience with CCSDS packet telemetry in the context of the Gamma-Ray Observatory project is discussed.

  7. Improving Collaboration by Standardization Efforts in Systems Biology

    OpenAIRE

    Dräger, Andreas; Palsson, Bernhard Ø.

    2014-01-01

    Collaborative genome-scale reconstruction endeavors of metabolic networks would not be possible without a common, standardized formal representation of these systems. The ability to precisely define biological building blocks together with their dynamic behavior has even been considered a prerequisite for upcoming synthetic biology approaches. Driven by the requirements of such ambitious research goals, standardization itself has become an active field of research on nearly all levels of gran...

  8. Enterobacter aerogenes Needle Stick Leads to Improved Biological Management System

    Energy Technology Data Exchange (ETDEWEB)

    Johanson, Richard E.

    2004-08-01

    A laboratory worker who received a needle stick from a contaminated needle while working with a culture containing Enterobactor aerogenes developed a laboratory acquired infection. Although this organism has been shown to cause community and nosocomial infections, there have been no documented cases of a laboratory acquired infections. Lessons learned from the event led to corrective actions which included modification of lab procedures, development of a biological inventory tracking and risk identification system and the establishment of an effective biological safety program.

  9. Learning (from) the errors of a systems biology model

    OpenAIRE

    Benjamin Engelhardt; Holger Frőhlich; Maik Kschischo

    2016-01-01

    Mathematical modelling is a labour intensive process involving several iterations of testing on real data and manual model modifications. In biology, the domain knowledge guiding model development is in many cases itself incomplete and uncertain. A major problem in this context is that biological systems are open. Missed or unknown external influences as well as erroneous interactions in the model could thus lead to severely misleading results. Here we introduce the dynamic elastic-net, a dat...

  10. Systems-biology dissection of eukaryotic cell growth

    Directory of Open Access Journals (Sweden)

    Andrews Justen

    2010-05-01

    Full Text Available Abstract A recent article in BMC Biology illustrates the use of a systems-biology approach to integrate data across the transcriptome, proteome and metabolome of budding yeast in order to dissect the relationship between nutrient conditions and cell growth. See research article http://jbiol.com/content/6/2/4 and http://www.biomedcentral.com/1741-7007/8/68

  11. Phase transitions in fluids and biological systems

    Science.gov (United States)

    Sipos, Maksim

    In this thesis, I consider systems from two seemingly different fields: fluid dynamics and microbial ecology. In these systems, the unifying features are the existences of global non-equilibrium steady states. I consider generic and statistical models for transitions between these global states, and I relate the model results with experimental data. A theme of this thesis is that these rather simple, minimal models are able to capture a lot of functional detail about complex dynamical systems. In Part I, I consider the transition between laminar and turbulent flow. I find that quantitative and qualitative features of pipe flow experiments, the superexponential lifetime and the splitting of turbulent puffs, and the growth rate of turbulent slugs, can all be explained by a coarse-grained, phenomenological model in the directed percolation universality class. To relate this critical phenomena approach closer to the fluid dynamics, I consider the transition to turbulence in the Burgers equation, a simplified model for Navier-Stokes equations. Via a transformation to a model of directed polymers in a random medium, I find that the transition to Burgers turbulence may also be in the directed percolation universality class. This evidence implies that the turbulent-to-laminar transition is statistical in nature and does not depend on details of the Navier-Stokes equations describing the fluid flow. In Part II, I consider the disparate subject of microbial ecology where the complex interactions within microbial ecosystems produce observable patterns in microbe abundance, diversity and genotype. In order to be able to study these patterns, I develop a bioinformatics pipeline to multiply align and quickly cluster large microbial metagenomics datasets. I also develop a novel metric that quantifies the degree of interactions underlying the assembly of a microbial ecosystem, particularly the transition between neutral (random) and niche (deterministic) assembly. I apply this

  12. Decoherence and Spin Echo in Biological Systems

    CERN Document Server

    Nesterov, Alexander I

    2015-01-01

    The spin echo approach is extended to include bio-complexes for which the interaction with dynamical noise is strong. Significant restoration of the free induction decay signal due to homogeneous (decoherence) and inhomogeneous (dephasing) broadening is demonstrated analytically and numerically, for both an individual dimer of interacting chlorophylls and for an ensemble of dimers. This approach is based on an exact and closed system of ordinary differential equations that can be easily solved for a wide range of parameters that are relevant for bio-applications.

  13. Object-centered reference systems and human spatial memory.

    Science.gov (United States)

    Chen, Xiaoli; McNamara, Timothy

    2011-10-01

    The present study investigated the role of object-centered reference systems in memories of objects' locations. Participants committed to memory the locations and orientations of either 11 human avatars (Experiment 1) or 11 animal models (Experiment 2) displayed in a desktop virtual environment and then completed judgments of relative directions, in which they pointed to objects from imagined vantage points corresponding to the locations of the objects. Results showed that, with avatars, performance was better when the imagined heading was congruent with the facing direction of the avatar located at the imagined vantage point. With animal models, no such facilitation was found. For both types of stimuli, performance was better for the learning view than for the novel 135° view. Results demonstrate that memories of the locations of objects are affected by object-centered reference systems and are consistent with conjectures that spatial memories are hierarchies of spatial reference systems, with higher levels corresponding to larger scales of space. PMID:21786070

  14. GATE Center for Automotive Fuel Cell Systems at Virginia Tech

    Energy Technology Data Exchange (ETDEWEB)

    Nelson, Douglas [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States)

    2011-09-30

    The Virginia Tech GATE Center for Automotive Fuel Cell Systems (CAFCS) achieved the following objectives in support of the domestic automotive industry: Expanded and updated fuel cell and vehicle technologies education programs; Conducted industry directed research in three thrust areas development and characterization of materials for PEM fuel cells; performance and durability modeling for PEM fuel cells; and fuel cell systems design and optimization, including hybrid and plug-in hybrid fuel cell vehicles; Developed MS and Ph.D. engineers and scientists who are pursuing careers related to fuel cells and automotive applications; Published research results that provide industry with new knowledge which contributes to the advancement of fuel cell and vehicle systems commercialization. With support from the Dept. of Energy, the CAFCS upgraded existing graduate course offerings; introduced a hands-on laboratory component that make use of Virginia Tech's comprehensive laboratory facilities, funded 15 GATE Fellowships over a five year period; and expanded our program of industry interaction to improve student awareness of challenges and opportunities in the automotive industry. GATE Center graduate students have a state-of-the-art research experience preparing them for a career to contribute to the advancement fuel cell and vehicle technologies.

  15. Assessment center energy collector system of crude Puerto Escondido

    International Nuclear Information System (INIS)

    In this paper the results of the evaluation of the energy system Collector Crude Center of Puerto Escondido in the first half of 2014. By implementing the overall strategy presented Process Analysis developed and implemented an energy assessment procedure allowed characterize current plant conditions, and raise a number of measures and recommendations that lead to improved energy use and reduced environmental impact. It also presents the computational tools used for both process simulation (Hysys v 3.2) as for technical analysis - economic and environmental (Microsoft Excel). (full text)

  16. 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.

  17. Biologically Inspired Execution Framework for Vulnerable Workflow Systems

    CERN Document Server

    Safdar, Sohail; Qureshi, Muhammad Aasim; Akbar, Rehan

    2009-01-01

    The main objective of the research is to introduce a biologically inspired execution framework for workflow systems under threat due to some intrusion attack. Usually vulnerable systems need to be stop and put into wait state, hence to insure the data security and privacy while being recovered. This research ensures the availability of services and data to the end user by keeping the data security, privacy and integrity intact. To achieve the specified goals, the behavior of chameleons and concept of hibernation has been considered in combination. Hence the workflow systems become more robust using biologically inspired methods and remain available to the business consumers safely even in a vulnerable state.

  18. Using Entropy Leads to a Better Understanding of Biological Systems

    Directory of Open Access Journals (Sweden)

    Chih-Yuan Tseng

    2010-12-01

    Full Text Available In studying biological systems, conventional approaches based on the laws of physics almost always require introducing appropriate approximations. We argue that a comprehensive approach that integrates the laws of physics and principles of inference provides a better conceptual framework than these approaches to reveal emergence in such systems. The crux of this comprehensive approach hinges on entropy. Entropy is not merely a physical quantity. It is also a reasoning tool to process information with the least bias. By reviewing three distinctive examples from protein folding dynamics to drug design, we demonstrate the developments and applications of this comprehensive approach in the area of biological systems.

  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. What's behind the Biological Classification System in Use Today?

    Science.gov (United States)

    Robertson, William C.

    2010-01-01

    Whether students should memorize classification schemes (taxonomies) is a column in itself, but the author can address the role that this system plays in the study of biology. To that end, it will help to address how the system developed over time. And toward "that" end, you will do a simple activity to start. (Contains 3 figures.)

  1. 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 ...

  2. Chemical imaging of biological systems with the scanning electrochemical microscope.

    Science.gov (United States)

    Gyurcsányi, Róbert E; Jágerszki, Gyula; Kiss, Gergely; Tóth, Klára

    2004-06-01

    A brief overview on recent advances in the application of scanning electrochemical microscopy (SECM) to the investigation of biological systems is presented. Special emphasis is given to the mapping of local enzyme activity by SECM, which is exemplified by relevant original systems. PMID:15110274

  3. 3D Modelling of Biological Systems for Biomimetics

    Institute of Scientific and Technical Information of China (English)

    Shujun Zhang; Kevin Hapeshi; Ashok K. Bhattacharya

    2004-01-01

    With the advanced development of computer-based enabling technologies, many engineering, medical, biology,chemistry, physics and food science etc have developed to the unprecedented levels, which lead to many research and development interests in various multi-discipline areas. Among them, biomimetics is one of the most promising and attractive branches of study. Biomimetics is a branch of study that uses biological systems as a model to develop synthetic systems.To learn from nature, one of the fundamental issues is to understand the natural systems such animals, insects, plants and human beings etc. The geometrical characterization and representation of natural systems is an important fundamental work for biomimetics research. 3D modeling plays a key role in the geometrical characterization and representation, especially in computer graphical visualization. This paper firstly presents the typical procedure of 3D modelling methods and then reviews the previous work of 3D geometrical modelling techniques and systems developed for industrial, medical and animation applications. Especially the paper discusses the problems associated with the existing techniques and systems when they are applied to 3D modelling of biological systems. Based upon the discussions, the paper proposes some areas of research interests in 3D modelling of biological systems and for Biomimetics.

  4. The Use of an Electronic Response System in Teaching Biology

    Science.gov (United States)

    Bessler, William C.; Nisbet, Jerry J.

    1971-01-01

    An electronic student response system was used in teaching college biology to non-science students. Achievement of this treatment group was compared with that of the control group (not utilizing the response system). The only statistical significant difference found in an analysis of covariance was an interaction between treatment group and time…

  5. A Calculus for Modelling, Simulating and Analysing Compartmentalized Biological Systems

    DEFF Research Database (Denmark)

    Mardare, Radu Iulian; Ihekwaba, Adoha

    2007-01-01

    A. Ihekwaba, R. Mardare. A Calculus for Modelling, Simulating and Analysing Compartmentalized Biological Systems. Case study: NFkB system. In Proc. of International Conference of Computational Methods in Sciences and Engineering (ICCMSE), American Institute of Physics, AIP Proceedings, N 2...

  6. Systems Biology: The Role of Engineering in the Reverse Engineering of Biological Signaling

    OpenAIRE

    Iglesias, Pablo A.

    2013-01-01

    One of the principle tasks of systems biology has been the reverse engineering of signaling networks. Because of the striking similarities to engineering systems, a number of analysis and design tools from engineering disciplines have been used in this process. This review looks at several examples including the analysis of homeostasis using control theory, the attenuation of noise using signal processing, statistical inference and the use of information theory to understand both binary decis...

  7. Computational approaches to metabolic engineering utilizing systems biology and synthetic biology.

    Science.gov (United States)

    Fong, Stephen S

    2014-08-01

    Metabolic engineering modifies cellular function to address various biochemical applications. Underlying metabolic engineering efforts are a host of tools and knowledge that are integrated to enable successful outcomes. Concurrent development of computational and experimental tools has enabled different approaches to metabolic engineering. One approach is to leverage knowledge and computational tools to prospectively predict designs to achieve the desired outcome. An alternative approach is to utilize combinatorial experimental tools to empirically explore the range of cellular function and to screen for desired traits. This mini-review focuses on computational systems biology and synthetic biology tools that can be used in combination for prospective in silico strain design.

  8. Hepatocellular carcinoma: a systems biology perspective

    Directory of Open Access Journals (Sweden)

    Lorenza Alice D'alessandro

    2013-02-01

    Full Text Available Hepatocellular carcinomas (HCC have different etiology and heterogenic genomic alterations lead to high complexity. The molecular features of HCC have largely been studied by gene expression and proteome profiling focusing on the correlations between the expression of specific markers and clinical data. Integration of the increasing amounts of data in databases has facilitated the link of genomic and proteomic profiles of HCC to disease state and clinical outcome. Despite the current knowledge, specific molecular markers remain to be identified and new strategies are required to establish novel targeted therapies. In the last years, mathematical models reconstructing gene and protein networks based on experimental data of HCC have been developed providing powerful tools to predict candidate interactions and potential targets for therapy. Furthermore, the combination of dynamic and logical mathematical models with quantitative data allows detailed mechanistic insights into system properties. To address effects at the organ level, mathematical models reconstructing the three-dimensional organization of liver lobules were developed. In the future, integration of different modeling approaches capturing the effects at the cellular up to the organ level is required to address the complex properties of HCC and to enable the discovery of new targets for HCC prevention or treatment.

  9. Implementation of a virtual link between power system testbeds at Marshall Spaceflight Center and Lewis Research Center

    Science.gov (United States)

    Doreswamy, Rajiv

    1990-01-01

    The Marshall Space Flight Center (MSFC) owns and operates a space station module power management and distribution (SSM-PMAD) testbed. This system, managed by expert systems, is used to analyze and develop power system automation techniques for Space Station Freedom. The Lewis Research Center (LeRC), Cleveland, Ohio, has developed and implemented a space station electrical power system (EPS) testbed. This system and its power management controller are representative of the overall Space Station Freedom power system. A virtual link is being implemented between the testbeds at MSFC and LeRC. This link would enable configuration of SSM-PMAD as a load center for the EPS testbed at LeRC. This connection will add to the versatility of both systems, and provide an environment of enhanced realism for operation of both testbeds.

  10. Systems Biology Approaches to a Rational Drug Discovery Paradigm.

    Science.gov (United States)

    Prathipati, Philip; Mizuguchi, Kenji

    2016-01-01

    Ligand- and structure-based drug design approaches complement phenotypic and target screens, respectively, and are the two major frameworks for guiding early-stage drug discovery efforts. Since the beginning of this century, the advent of the genomic era has presented researchers with a myriad of high throughput biological data (parts lists and their interaction networks) to address efficacy and toxicity, augmenting the traditional ligand- and structure-based approaches. This data rich era has also presented us with challenges related to integrating and analyzing these multi-platform and multi-dimensional datasets and translating them into viable hypotheses. Hence in the present paper, we review these existing approaches to drug discovery research and argue the case for a new systems biology based approach. We present the basic principles and the foundational arguments/underlying assumptions of the systems biology based approaches to drug design. Also discussed are systems biology data types (key entities, their attributes and their relationships with each other, and data models/representations), software and tools used for both retrospective and prospective analysis, and the hypotheses that can be inferred. In addition, we summarize some of the existing resources for a systems biology based drug discovery paradigm (open TG-GATEs, DrugMatrix, CMap and LINCs) in terms of their strengths and limitations. PMID:26306988

  11. Systems Biology Approaches to a Rational Drug Discovery Paradigm.

    Science.gov (United States)

    Prathipati, Philip; Mizuguchi, Kenji

    2016-01-01

    Ligand- and structure-based drug design approaches complement phenotypic and target screens, respectively, and are the two major frameworks for guiding early-stage drug discovery efforts. Since the beginning of this century, the advent of the genomic era has presented researchers with a myriad of high throughput biological data (parts lists and their interaction networks) to address efficacy and toxicity, augmenting the traditional ligand- and structure-based approaches. This data rich era has also presented us with challenges related to integrating and analyzing these multi-platform and multi-dimensional datasets and translating them into viable hypotheses. Hence in the present paper, we review these existing approaches to drug discovery research and argue the case for a new systems biology based approach. We present the basic principles and the foundational arguments/underlying assumptions of the systems biology based approaches to drug design. Also discussed are systems biology data types (key entities, their attributes and their relationships with each other, and data models/representations), software and tools used for both retrospective and prospective analysis, and the hypotheses that can be inferred. In addition, we summarize some of the existing resources for a systems biology based drug discovery paradigm (open TG-GATEs, DrugMatrix, CMap and LINCs) in terms of their strengths and limitations.

  12. Model-Based Systems Engineering in Concurrent Engineering Centers

    Science.gov (United States)

    Iwata, Curtis; Infeld, Samatha; Bracken, Jennifer Medlin; McGuire, Melissa; McQuirk, Christina; Kisdi, Aron; Murphy, Jonathan; Cole, Bjorn; Zarifian, Pezhman

    2015-01-01

    Concurrent Engineering Centers (CECs) are specialized facilities with a goal of generating and maturing engineering designs by enabling rapid design iterations. This is accomplished by co-locating a team of experts (either physically or virtually) in a room with a narrow design goal and a limited timeline of a week or less. The systems engineer uses a model of the system to capture the relevant interfaces and manage the overall architecture. A single model that integrates other design information and modeling allows the entire team to visualize the concurrent activity and identify conflicts more efficiently, potentially resulting in a systems model that will continue to be used throughout the project lifecycle. Performing systems engineering using such a system model is the definition of model-based systems engineering (MBSE); therefore, CECs evolving their approach to incorporate advances in MBSE are more successful in reducing time and cost needed to meet study goals. This paper surveys space mission CECs that are in the middle of this evolution, and the authors share their experiences in order to promote discussion within the community.

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

    DEFF Research Database (Denmark)

    Nielsen, Jens; Jewett, Michael Christopher

    2008-01-01

    Saccharomyces cerevisiae is extremely well suited for this objective. As one of the most intensely studied eukaryotic model organisms, a rich density of knowledge detailing its genetics, biochemistry, physiology, and large-scale fermentation performance can be capitalized upon to enable a substantial increase...... 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....

  14. Learning (from) the errors of a systems biology model

    Science.gov (United States)

    Engelhardt, Benjamin; Frőhlich, Holger; Kschischo, Maik

    2016-02-01

    Mathematical modelling is a labour intensive process involving several iterations of testing on real data and manual model modifications. In biology, the domain knowledge guiding model development is in many cases itself incomplete and uncertain. A major problem in this context is that biological systems are open. Missed or unknown external influences as well as erroneous interactions in the model could thus lead to severely misleading results. Here we introduce the dynamic elastic-net, a data driven mathematical method which automatically detects such model errors in ordinary differential equation (ODE) models. We demonstrate for real and simulated data, how the dynamic elastic-net approach can be used to automatically (i) reconstruct the error signal, (ii) identify the target variables of model error, and (iii) reconstruct the true system state even for incomplete or preliminary models. Our work provides a systematic computational method facilitating modelling of open biological systems under uncertain knowledge.

  15. Continuum analysis of biological systems conserved quantities, fluxes and forces

    CERN Document Server

    Suraishkumar, G K

    2014-01-01

    This book addresses the analysis, in the continuum regime, of biological systems at various scales, from the cellular level to the industrial one. It presents both fundamental conservation principles (mass, charge, momentum and energy) and relevant fluxes resulting from appropriate driving forces, which are important for the analysis, design and operation of biological systems. It includes the concept of charge conservation, an important principle for biological systems that is not explicitly covered in any other book of this kind. The book is organized in five parts: mass conservation; charge conservation; momentum conservation; energy conservation; and multiple conservations simultaneously applied. All mathematical aspects are presented step by step, allowing any reader with a basic mathematical background (calculus, differential equations, linear algebra, etc.) to follow the text with ease. The book promotes an intuitive understanding of all the relevant principles and in so doing facilitates their applica...

  16. Biologically erodable microspheres as potential oral drug delivery systems

    Science.gov (United States)

    Mathiowitz, Edith; Jacob, Jules S.; Jong, Yong S.; Carino, Gerardo P.; Chickering, Donald E.; Chaturvedi, Pravin; Santos, Camilla A.; Vijayaraghavan, Kavita; Montgomery, Sean; Bassett, Michael; Morrell, Craig

    1997-03-01

    Biologically adhesive delivery systems offer important advantages1-5 over conventional drug delivery systems6. Here we show that engineered polymer microspheres made of biologically erodable polymers, which display strong adhesive interactions with gastrointestinal mucus and cellular linings, can traverse both the mucosal absorptive epithelium and the follicle-associated epithelium covering the lymphoid tissue of Peyer's patches. The polymers maintain contact with intestinal epithelium for extended periods of time and actually penetrate it, through and between cells. Thus, once loaded with compounds of pharmacological interest, the microspheres could be developed as delivery systems to transfer biologically active molecules to the circulation. We show that these microspheres increase the absorption of three model substances of widely different molecular size: dicumarol, insulin and plasmid DNA.

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

    Directory of Open Access Journals (Sweden)

    Roberto Luzzi

    2012-10-01

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

  18. Investigation of bacterial populations in a biological nutrient removal system

    OpenAIRE

    Kavanaugh, Rathi G.

    1991-01-01

    Bacterial populations proliferating in a pilot scale biological nutrient removal system (BNR) were studied. The objective of the research was to develop media and methods to identify bacterial populations in BNR systems. Samples were obtained from the last aerobic zone of a University of Cape Town (UCT)-type system. The most probable numbers (MPN) of bacteria in the samples were analyzed in liquid media containing volatile fatty acids as sole sources of carbon. Samples...

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

    OpenAIRE

    Wright Jeremiah; Wagner Andreas

    2008-01-01

    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 calle...

  20. Controlled biological and biomimetic systems for landmine detection.

    Science.gov (United States)

    Habib, Maki K

    2007-08-30

    Humanitarian demining requires to accurately detect, locate and deactivate every single landmine and other buried mine-like objects as safely and as quickly as possible, and in the most non-invasive manner. The quality of landmine detection affects directly the efficiency and safety of this process. Most of the available methods to detect explosives and landmines are limited by their sensitivity and/or operational complexities. All landmines leak with time small amounts of their explosives that can be found on surrounding ground and plant life. Hence, explosive signatures represent the robust primary indicator of landmines. Accordingly, developing innovative technologies and efficient techniques to identify in real-time explosives residue in mined areas represents an attractive and promising approach. Biological and biologically inspired detection technology has the potential to compete with or be used in conjunction with other artificial technology to complement performance strengths. Biological systems are sensitive to many different scents concurrently, a property that has proven difficult to replicate artificially. Understanding biological systems presents unique opportunities for developing new capabilities through direct use of trained bio-systems, integration of living and non-living components, or inspiring new design by mimicking biological capabilities. It is expected that controlled bio-systems, biotechnology and microbial techniques will contribute to the advancement of mine detection and other application domains. This paper provides directions, evaluation and analysis on the progress of controlled biological and biomimetic systems for landmine detection. It introduces and discusses different approaches developed, underlining their relative advantages and limitations, and highlighting trends, safety and ecology concern, and possible future directions. PMID:17662594

  1. The Integrated Ocean Observing System Data Assembly Center

    Science.gov (United States)

    Bouchard, R. H.; Henderson, D.; Burnett, W.; Hervey, R. V.; Crout, R.

    2008-05-01

    The Integrated Ocean Observing System (IOOS) is the U.S. contribution to the Global Ocean Observing System and the Global Earth Observing System of Systems (GEOSS). As the Integrated Ocean Observing System Data Assembly Center (IOOS DAC), the National Oceanic and Atmospheric Administration`s (NOAA) National Data Buoy Center (NDBC) collects data from ocean observing systems and performs quality control on the data. Once the IOOS DAC performs the quality control, it distributes them in real-time: (1) in World Meteorological Organization alphanumeric data formats via the Global Telecommunications System (GTS) that provides instant availability to national and international users (2) in text files via its website (http://www.ndbc.noaa.gov) that provide easy access and use, and (3) in netCDF format via its OPeNDAP/DODS Server (http://dods.ndbc.noaa.gov) that provides higher resolution data than available in WMO alphanumeric or text file formats. The IOOS DAC routinely checks and distributes data from about 200 NDBC stations that include meteorological and oceanographic observations from buoys and coastal stations, water-level estimations from tsunameters (DART), and climate monitoring from buoys (Tropical Atmosphere Ocean array (TAO)). The IOOS DAC operates continuously - 24 hours per day, 7 days per week. In addition to data from NDBC`s platforms, the IOOS DAC applies its scientific expertise and data management and communications capabilities to facilitate partnerships for the exchange and application of data and to coordinate and leverage regional assets and resources from about 350 IOOS Partner stations. The IOOS DAC through its quality control process provides feedback to its partners on the quality of their observation that can lead to improved quality of the observations. The NDBC-IOOS Data Partnerships span the Western Hemisphere with data collection from the Beaufort Sea to the Peru Current, from the International Date Line to the central Atlantic Ocean, and

  2. Scientific and educational center "space systems and technology"

    Science.gov (United States)

    Kovalev, I. V.; Loginov, Y. Y.; Zelenkov, P. V.

    2015-10-01

    The issues of engineers training in the aerospace university on the base of Scientific and Educational Center "Space Systems and Technology" are discussed. In order to improve the quality of education in the Siberian State Aerospace University the research work of students, as well as the practice- oriented training of engineers are introduced in the educational process. It was made possible as a result of joint efforts of university with research institutes of the Russian Academy of Science and industrial enterprises. The university experience in this area promotes the development of a new methods and forms of educational activities, including the project-oriented learning technologies, identifying promising areas of specialization and training of highly skilled engineers for aerospace industry and other institutions. It also allows you to coordinate the work of departments and other units of the university to provide the educational process in workshops and departments of the industrial enterprises in accordance with the needs of the target training. Within the framework of scientific and education center the students perform researches, diploma works and master's theses; the postgraduates are trained in advanced scientific and technical areas of enterprise development.

  3.  Biological therapies in systemic lupus erythematosus

    Directory of Open Access Journals (Sweden)

    Dorota Suszek

    2012-08-01

    Full Text Available  The prevention of chronic organic damage and complete inhibition of inflammatory activity of the disease are the main goals in the treatment of systemic lupus erythematosus (SLE. Current therapies of SLE are not effective enough and they may cause various serious side effects. Biological therapies, affecting important pathogenetic disturbances in the immunological system of SLE patients, give hope for the development of a new treatment for SLE. Currently the most advanced clinical trials are being conducted with anti-lymphocyte B drugs, such as rituximab, belimumab and epratuzumab. Belimumab as the first biological agent was registered for treatment of the active, seropositive form of SLE. The advances in immunology and rheumatology nowadays raise the hope of finding effective and safe treatment for SLE. In our article we present an overview of data concerning perspectives of biological treatment in SLE.

  4. Evolutionary tradeoffs between economy and effectiveness in biological homeostasis systems.

    Directory of Open Access Journals (Sweden)

    Pablo Szekely

    Full Text Available Biological regulatory systems face a fundamental tradeoff: they must be effective but at the same time also economical. For example, regulatory systems that are designed to repair damage must be effective in reducing damage, but economical in not making too many repair proteins because making excessive proteins carries a fitness cost to the cell, called protein burden. In order to see how biological systems compromise between the two tasks of effectiveness and economy, we applied an approach from economics and engineering called Pareto optimality. This approach allows calculating the best-compromise systems that optimally combine the two tasks. We used a simple and general model for regulation, known as integral feedback, and showed that best-compromise systems have particular combinations of biochemical parameters that control the response rate and basal level. We find that the optimal systems fall on a curve in parameter space. Due to this feature, even if one is able to measure only a small fraction of the system's parameters, one can infer the rest. We applied this approach to estimate parameters in three biological systems: response to heat shock and response to DNA damage in bacteria, and calcium homeostasis in mammals.

  5. Final report for Conference Support Grant "From Computational Biophysics to Systems Biology - CBSB12"

    Energy Technology Data Exchange (ETDEWEB)

    Hansmann, Ulrich H.E.

    2012-07-02

    This report summarizes the outcome of the international workshop “From Computational Biophysics to Systems Biology (CBSB12)” which was held June 3-5, 2012, at the University of Tennessee Conference Center in Knoxville, TN, and supported by DOE through the Conference Support Grant 120174. The purpose of CBSB12 was to provide a forum for the interaction between a data-mining interested systems biology community and a simulation and first-principle oriented computational biophysics/biochemistry community. CBSB12 was the sixth in a series of workshops of the same name organized in recent years, and the second that has been held in the USA. As in previous years, it gave researchers from physics, biology, and computer science an opportunity to acquaint each other with current trends in computational biophysics and systems biology, to explore venues of cooperation, and to establish together a detailed understanding of cells at a molecular level. The conference grant of $10,000 was used to cover registration fees and provide travel fellowships to selected students and postdoctoral scientists. By educating graduate students and providing a forum for young scientists to perform research into the working of cells at a molecular level, the workshop adds to DOE's mission of paving the way to exploit the abilities of living systems to capture, store and utilize energy.

  6. Final report for Conference Support Grant "From Computational Biophysics to Systems Biology - CBSB12"

    Energy Technology Data Exchange (ETDEWEB)

    Hansmann, Ulrich H.E.

    2012-07-02

    This report summarizes the outcome of the international workshop From Computational Biophysics to Systems Biology (CBSB12) which was held June 3-5, 2012, at the University of Tennessee Conference Center in Knoxville, TN, and supported by DOE through the Conference Support Grant 120174. The purpose of CBSB12 was to provide a forum for the interaction between a data-mining interested systems biology community and a simulation and first-principle oriented computational biophysics/biochemistry community. CBSB12 was the sixth in a series of workshops of the same name organized in recent years, and the second that has been held in the USA. As in previous years, it gave researchers from physics, biology, and computer science an opportunity to acquaint each other with current trends in computational biophysics and systems biology, to explore venues of cooperation, and to establish together a detailed understanding of cells at a molecular level. The conference grant of $10,000 was used to cover registration fees and provide travel fellowships to selected students and postdoctoral scientists. By educating graduate students and providing a forum for young scientists to perform research into the working of cells at a molecular level, the workshop adds to DOE's mission of paving the way to exploit the abilities of living systems to capture, store and utilize energy.

  7. Heat-pump-centered integrated community energy systems. Final report

    Energy Technology Data Exchange (ETDEWEB)

    1979-11-01

    A Heat Pump Centered-Integrated Community Energy System (HP-ICES) concept was explored and developed that is based on use of privately owned ice-making heat pumps in each building or complex within a community. These heat pumps will provide all of the space heating, space cooling and domestic hot water needs. All of the community input energy required is provided by electrical power, thereby eliminating a community's dependence on gas or oil supplies. The heat pumps will operate in both air and water source modes, deriving performance advantages of both. The possible forms of an HP-ICES system, the technical and economic limitations, environmental impacts and other factors are discussed from a general viewpoint. The concept is applied to a specific planned community and its performance and economic features are examined in detail. It is concluded that the HP-ICES concept is technically viable, but that its economic desirability as compared with conventional heat pump systems is hampered by much higher initial costs, and that the economic feasibility of HP-ICES systems will depend on future fuel source costs and supply and on electric power rates. (LCL)

  8. Information System Success Model for Customer Relationship Management System in Health Promotion Centers

    Science.gov (United States)

    Choi, Wona; Rho, Mi Jung; Park, Jiyun; Kim, Kwang-Jum; Kwon, Young Dae

    2013-01-01

    Objectives Intensified competitiveness in the healthcare industry has increased the number of healthcare centers and propelled the introduction of customer relationship management (CRM) systems to meet diverse customer demands. This study aimed to develop the information system success model of the CRM system by investigating previously proposed indicators within the model. Methods The evaluation areas of the CRM system includes three areas: the system characteristics area (system quality, information quality, and service quality), the user area (perceived usefulness and user satisfaction), and the performance area (personal performance and organizational performance). Detailed evaluation criteria of the three areas were developed, and its validity was verified by a survey administered to CRM system users in 13 nationwide health promotion centers. The survey data were analyzed by the structural equation modeling method, and the results confirmed that the model is feasible. Results Information quality and service quality showed a statistically significant relationship with perceived usefulness and user satisfaction. Consequently, the perceived usefulness and user satisfaction had significant influence on individual performance as well as an indirect influence on organizational performance. Conclusions This study extends the research area on information success from general information systems to CRM systems in health promotion centers applying a previous information success model. This lays a foundation for evaluating health promotion center systems and provides a useful guide for successful implementation of hospital CRM systems. PMID:23882416

  9. Operating The Central Process Systems At Glenn Research Center

    Science.gov (United States)

    Weiler, Carly P.

    2004-01-01

    As a research facility, the Glenn Research Center (GRC) trusts and expects all the systems, controlling their facilities to run properly and efficiently in order for their research and operations to occur proficiently and on time. While there are many systems necessary for the operations at GRC, one of those most vital systems is the Central Process Systems (CPS). The CPS controls operations used by GRC's wind tunnels, propulsion systems lab, engine components research lab, and compressor, turbine and combustor test cells. Used widely throughout the lab, it operates equipment such as exhausters, chillers, cooling towers, compressors, dehydrators, and other such equipment. Through parameters such as pressure, temperature, speed, flow, etc., it performs its primary operations on the major systems of Electrical Dispatch (ED), Central Air Dispatch (CAD), Central Air Equipment Building (CAEB), and Engine Research Building (ERB). In order for the CPS to continue its operations at Glenn, a new contract must be awarded. Consequently, one of my primary responsibilities was assisting the Source Evaluation Board (SEB) with the process of awarding the recertification contract of the CPS. The job of the SEB was to evaluate the proposals of the contract bidders and then to present their findings to the Source Selecting Official (SSO). Before the evaluations began, the Center Director established the level of the competition. For this contract, the competition was limited to those companies classified as a small, disadvantaged business. After an industry briefing that explained to qualified companies the CPS and type of work required, each of the interested companies then submitted proposals addressing three components: Mission Suitability, Cost, and Past Performance. These proposals were based off the Statement of Work (SOW) written by the SEB. After companies submitted their proposals, the SEB reviewed all three components and then presented their results to the SSO. While the

  10. Common front end systems for Space Shuttle and Space Station control centers at Johnson Space Center

    Science.gov (United States)

    Uljon, Linda; Muratore, John

    1993-03-01

    In the beginning of the fiscal year 1992, the development organizations of Johnson Space Center (JSC) were poised to begin two major projects: the Space Station Control Center and the refurbishment of the telemetry processing area of the Space Shuttle Mission Control Center. A study team established that a common front end concept could be used and could reduce development costs for both projects. A standard processor was defined to support most of the front end functions of both control centers and supports a consolidation of control positions which effectively reduces operations cost. This paper defines that common concept and describes the progress that has been made in development of the Consolidated Communications Facility (CCF) during the past year.

  11. Request for Travel Funds for Systems Radiation Biology Workshop

    Energy Technology Data Exchange (ETDEWEB)

    Barcellos-Hoff, Mary Helen [NYU School of Medicine

    2014-03-22

    The 3rd International Systems Radiation Biology Workshop brought together the major European, US and Japanese research programs on radiation risk as well as selected experts representing systems biological approaches to discuss how the new methodologies could be best exploited for low dose research. A significant part of the workshop was devoted to discussions organised as breakout group sessions. To facilitate discussions number of participants was limited to 60 persons. To achieve the goals of this symposium in this international conference, support from DOE is vital. Hence, this proposal requested support in the amount of $15,000 to cover the travel expenses of international experts and radiation biology scientists from the United States. This supporting mechanism was clearly identified to the selected US participants as a conference support award from the DOE (See attached PDF). The workshop was an outstanding opportunity to strengthen interactions between leading experts in the emerging areas of radiation sciences, and will also provide opportunities for younger scientists to meet with experts and discuss their results. This workshop was designed to endorse active engagement in international collaboration. A major objective of this conference was to effectively communicate research results, in order to ensure that current thinking reflects sound science of radiation biology. Further, this international event addressed the use and success of scientific initiatives in radiation biology for policymakers, standard-setters, and the general public.

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

    OpenAIRE

    He, Fei; Murabito, Ettore; Westerhoff, Hans 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 through in silico theoretical studies with the aim to guide and complement further in vitro and in vivo experimental efforts. Clearly, what counts is the result in vivo, not only in terms of maximal productivity but also robustness against environmental perturbations. Engineering an organism towards an increased...

  13. Cancer systems biology: signal processing for cancer research

    Institute of Scientific and Technical Information of China (English)

    Olli Yli-Harja; Antti Ylip(a)(a); Matti Nykter; Wei Zhang

    2011-01-01

    In this editorial we introduce the research paradigms of signal processing in the era of systems biology. Signal processing is a field of science traditionally focused on modeling electronic and communications systems, but recently it has turned to biological applications with astounding results. The essence of signal processing is to describe the natural world by mathematical models and then, based on these models, develop efficient computational tools for solving engineering problems. Here, we underline, with examples, the endless possibilities which arise when the battle-hardened tools of engineering are applied to solve the problems that have tormented cancer researchers. Based on this approach, a new field has emerged, called cancer systems biology. Despite its short history, cancer systems biology has already produced several success stories tackling previously impracticable problems. Perhaps most importantly, it has been accepted as an integral part of the major endeavors of cancer research, such as analyzing the genomic and epigenomic data produced by The Cancer Genome Atlas (TCGA) project. Finally, we show that signal processing and cancer research, two fields that are seemingly distant from each other, have merged into a field that is indeed more than the sum of its parts.

  14. System as metaphor in the psychology and biology of shame.

    Science.gov (United States)

    Maunder, R

    1996-01-01

    Biological theories of brain and psychological theories of mind are two systems of explanation that seem related to one another. The nature of the relationship is problematic and constitutes the age-old mind-body problem. The most prominent solutions currently are variations of materialism. While psychological theories can be consistent with materialism, there remains a difficulty in comprehending nonphysical (social, psychological) causes of physical effects. This difficulty is an obstacle to integration in psychiatry, where we routinely assume that illnesses that include or depend on biological dysfunction are caused multifactorially by causal agents such as perceived parental warmth, parental loss, stressful life events, genetics, and personality (Hammen et al. 1992; Kendler et al. 1993). Unity theory adopts the stance that neurobiological theories and psychological theories are essentially disparate explanations of the same psychobiological events; thus the relationship of mind to brain is one of shared reference (Goodman 1991; Maunder 1995). In Goodman's model the gap between biological and psychological systems is not bridgeable. Different conceptual categories refer to the same referents but cannot interact with each other. Stepping into the breach, systems theory has been presented as offering a language that can bridge the gap between psychological and biological theories of causation (Schwartz 1981; Weiner 1989). Thus, there is a controversy about the applicability of systems theory for integration in psychiatry. PMID:8837180

  15. Cancer systems biology: signal processing for cancer research.

    Science.gov (United States)

    Yli-Harja, Olli; Ylipää, Antti; Nykter, Matti; Zhang, Wei

    2011-04-01

    In this editorial we introduce the research paradigms of signal processing in the era of systems biology. Signal processing is a field of science traditionally focused on modeling electronic and communications systems, but recently it has turned to biological applications with astounding results. The essence of signal processing is to describe the natural world by mathematical models and then, based on these models, develop efficient computational tools for solving engineering problems. Here, we underline, with examples, the endless possibilities which arise when the battle-hardened tools of engineering are applied to solve the problems that have tormented cancer researchers. Based on this approach, a new field has emerged, called cancer systems biology. Despite its short history, cancer systems biology has already produced several success stories tackling previously impracticable problems. Perhaps most importantly, it has been accepted as an integral part of the major endeavors of cancer research, such as analyzing the genomic and epigenomic data produced by The Cancer Genome Atlas (TCGA) project. Finally, we show that signal processing and cancer research, two fields that are seemingly distant from each other, have merged into a field that is indeed more than the sum of its parts.

  16. Environmental Noise and Nonlinear Relaxation in Biological Systems

    CERN Document Server

    Spagnolo, B; Spezia, S; Curcio, L; Pizzolato, N; Dubkov, A A; Fiasconaro, A; Adorno, D Persano; Bue, P Lo; Peri, E; Colazza, S

    2011-01-01

    We analyse the effects of environmental noise in three different biological systems: (i) mating behaviour of individuals of \\emph{Nezara viridula} (L.) (Heteroptera Pentatomidae); (ii) polymer translocation in crowded solution; (iii) an ecosystem described by a Verhulst model with a multiplicative L\\'{e}vy noise.

  17. FIELD INVESTIGATION OF BIOLOGICAL TOILET SYSTEMS AND GREY WATER TREATMENT

    Science.gov (United States)

    The objective of the field program was to determine the operational characteristics and overall acceptability of popular models of biological toilets and a few select grey water systems. A field observation scheme was devised to take advantage of in-use sites throughout the State...

  18. Integration of proteomics into systems biology of cancer

    OpenAIRE

    Hanash, S; Schliekelman, M.; Q. Zhang; Taguchi, A

    2012-01-01

    Deciphering the complexity and heterogeneity of cancer benefits from integration of proteomic level data into systems biology efforts. The opportunities available as a result of advances in proteomic technologies, the successes to date and the challenges involved in integrating diverse datasets are addressed in this review.

  19. System as metaphor in the psychology and biology of shame.

    Science.gov (United States)

    Maunder, R

    1996-01-01

    Biological theories of brain and psychological theories of mind are two systems of explanation that seem related to one another. The nature of the relationship is problematic and constitutes the age-old mind-body problem. The most prominent solutions currently are variations of materialism. While psychological theories can be consistent with materialism, there remains a difficulty in comprehending nonphysical (social, psychological) causes of physical effects. This difficulty is an obstacle to integration in psychiatry, where we routinely assume that illnesses that include or depend on biological dysfunction are caused multifactorially by causal agents such as perceived parental warmth, parental loss, stressful life events, genetics, and personality (Hammen et al. 1992; Kendler et al. 1993). Unity theory adopts the stance that neurobiological theories and psychological theories are essentially disparate explanations of the same psychobiological events; thus the relationship of mind to brain is one of shared reference (Goodman 1991; Maunder 1995). In Goodman's model the gap between biological and psychological systems is not bridgeable. Different conceptual categories refer to the same referents but cannot interact with each other. Stepping into the breach, systems theory has been presented as offering a language that can bridge the gap between psychological and biological theories of causation (Schwartz 1981; Weiner 1989). Thus, there is a controversy about the applicability of systems theory for integration in psychiatry.

  20. Catalytic mechanisms by biological systems : Special issue introduction

    NARCIS (Netherlands)

    Fraaije, Marco W; Scrutton, Nigel S

    2013-01-01

    Research on enzyme mechanisms is advancing knowledge of the chemistry and biochemistry of catalytic mechanisms by biological systems. The structural-dynamical properties of enzymes are of key importance. Advanced methodological approaches and new insights into enzyme functioning, and new emerging ap

  1. Integration of proteomics into systems biology of cancer.

    Science.gov (United States)

    Hanash, S; Schliekelman, M; Zhang, Q; Taguchi, A

    2012-01-01

    Deciphering the complexity and heterogeneity of cancer, benefits from integration of proteomic level data into systems biology efforts. The opportunities available as a result of advances in proteomic technologies, the successes to date, and the challenges involved in integrating diverse datasets are addressed in this review.

  2. Beyond standardization : dynamic software infrastructures for systems biology

    NARCIS (Netherlands)

    Swertz, Morris A.; Jansen, Ritsert C.

    2007-01-01

    Progress in systems biology is seriously hindered by slow production of suitable software infrastructures. Biologists need infrastructure that easily connects to work that is done in other laboratories, for which standardization is helpful. However, the infrastructure must also accommodate the speci

  3. Molecular biology of the renin-angiotensin system

    Energy Technology Data Exchange (ETDEWEB)

    Dzau, V.J.; Burt, D.W.; Pratt, R.E. (Harvard Medical School, Boston, MA (USA))

    1988-10-01

    This paper reviews the molecular biology of the renin-angiotensin system. The renin gene structure is analyzed in detail, including an examination of the putative regulatory regions. The combined action of these regulatory sequences would result in the complex, tissue-specific expression and regulation observed in vivo. The expression of the tissue renin-angiotensin systems, which may have important physiological functions, is also described. In addition, the pathway of renin biosynthesis and secretion is reviewed. This includes speculation on the fate of circulating prorenin and the physiological role of multiple renin forms and secretory pathways. The molecular approaches described in this paper have greatly advanced our knowledge of the biology of the renin-angiotensin system. Future studies using these and other approaches should provide further insight into this complex system.

  4. Applications of membrane computing in systems and synthetic biology

    CERN Document Server

    Gheorghe, Marian; Pérez-Jiménez, Mario

    2014-01-01

    Membrane Computing was introduced as a computational paradigm in Natural Computing. The models introduced, called Membrane (or P) Systems, provide a coherent platform to describe and study living cells as computational systems. Membrane Systems have been investigated for their computational aspects and employed to model problems in other fields, like: Computer Science, Linguistics, Biology, Economy, Computer Graphics, Robotics, etc. Their inherent parallelism, heterogeneity and intrinsic versatility allow them to model a broad range of processes and phenomena, being also an efficient means to solve and analyze problems in a novel way. Membrane Computing has been used to model biological systems, becoming with time a thorough modeling paradigm comparable, in its modeling and predicting capabilities, to more established models in this area. This book is the result of the need to collect, in an organic way, different facets of this paradigm. The chapters of this book, together with the web pages accompanying th...

  5. Predicting biological system objectives de novo from internal state measurements

    Directory of Open Access Journals (Sweden)

    Maranas Costas D

    2008-01-01

    Full Text Available Abstract Background Optimization theory has been applied to complex biological systems to interrogate network properties and develop and refine metabolic engineering strategies. For example, methods are emerging to engineer cells to optimally produce byproducts of commercial value, such as bioethanol, as well as molecular compounds for disease therapy. Flux balance analysis (FBA is an optimization framework that aids in this interrogation by generating predictions of optimal flux distributions in cellular networks. Critical features of FBA are the definition of a biologically relevant objective function (e.g., maximizing the rate of synthesis of biomass, a unit of measurement of cellular growth and the subsequent application of linear programming (LP to identify fluxes through a reaction network. Despite the success of FBA, a central remaining challenge is the definition of a network objective with biological meaning. Results We present a novel method called Biological Objective Solution Search (BOSS for the inference of an objective function of a biological system from its underlying network stoichiometry as well as experimentally-measured state variables. Specifically, BOSS identifies a system objective by defining a putative stoichiometric "objective reaction," adding this reaction to the existing set of stoichiometric constraints arising from known interactions within a network, and maximizing the putative objective reaction via LP, all the while minimizing the difference between the resultant in silico flux distribution and available experimental (e.g., isotopomer flux data. This new approach allows for discovery of objectives with previously unknown stoichiometry, thus extending the biological relevance from earlier methods. We verify our approach on the well-characterized central metabolic network of Saccharomyces cerevisiae. Conclusion We illustrate how BOSS offers insight into the functional organization of biochemical networks

  6. Fort Collins Science Center- Policy Analysis and Science Assistance Branch : Integrating social, behavioral, economic and biological sciences

    Science.gov (United States)

    2010-01-01

    The Fort Collins Science Center's Policy Analysis and Science Assistance (PASA) Branch is a team of approximately 22 scientists, technicians, and graduate student researchers. PASA provides unique capabilities in the U.S. Geological Survey by leading projects that integrate social, behavioral, economic, and biological analyses in the context of human-natural resource interactions. Resource planners, managers, and policymakers in the U.S. Departments of the Interior (DOI) and Agriculture (USDA), State and local agencies, as well as international agencies use information from PASA studies to make informed natural resource management and policy decisions. PASA scientists' primary functions are to conduct both theoretical and applied social science research, provide technical assistance, and offer training to advance performance in policy relevant research areas. Management and research issues associated with human-resource interactions typically occur in a unique context, involve difficult to access populations, require knowledge of both natural/biological science in addition to social science, and require the skill to integrate multiple science disciplines. In response to these difficult contexts, PASA researchers apply traditional and state-of-the-art social science methods drawing from the fields of sociology, demography, economics, political science, communications, social-psychology, and applied industrial organization psychology. Social science methods work in concert with our rangeland/agricultural management, wildlife, ecology, and biology capabilities. The goal of PASA's research is to enhance natural resource management, agency functions, policies, and decision-making. Our research is organized into four broad areas of study.

  7. Leakage from biological shield cooling system in Pickering NGS A

    International Nuclear Information System (INIS)

    Over the past eight years, a number of leaks have developed in the Biological Shield Cooling (BSC) system of the Pickering NGS A reactors. The highest leak rate exists in Unit 4. The failure mechanism is not known, but corrosion and/or weld failure are suspected. This paper summarizes the concerns associated with the leaks and possible solutions. It should be noted that the BSC system is peculiar to Pickering A reactors only

  8. Facile: a command-line network compiler for systems biology

    OpenAIRE

    Ollivier Julien F; Siso-Nadal Fernando; Swain Peter S

    2007-01-01

    Abstract Background A goal of systems biology is the quantitative modelling of biochemical networks. Yet for many biochemical systems, parameter values and even the existence of interactions between some chemical species are unknown. It is therefore important to be able to easily investigate the effects of adding or removing reactions and to easily perform a bifurcation analysis, which shows the qualitative dynamics of a model for a range of parameter values. Results We present Facile, a Perl...

  9. The solar system: Importance of research to the biological sciences

    Science.gov (United States)

    Klein, Harold P.

    1992-01-01

    An attempt is made to describe the scope of scientific areas that comprise the current field of exobiology in the United States. From investigations of astrophysical phenomena that deal with the birth of stars and planetary systems to questions of molecular biology involving phylogenetic relationships among organisms, from attempts to simulate the synthesis of biological precursor molecules in the chemistry laboratory to making measurements of the organic constituents of Titan's atmosphere, these researches all converge toward a common objective--answering the question of how life came about in the universe.

  10. Joint Space Operations Center (JSpOC) Mission System (JMS)

    Science.gov (United States)

    Morton, M.; Roberts, T.

    2011-09-01

    US space capabilities benefit the economy, national security, international relationships, scientific discovery, and our quality of life. Realizing these space responsibilities is challenging not only because the space domain is increasingly congested, contested, and competitive but is further complicated by the legacy space situational awareness (SSA) systems approaching end of life and inability to provide the breadth of SSA and command and control (C2) of space forces in this challenging domain. JMS will provide the capabilities to effectively employ space forces in this challenging domain. Requirements for JMS were developed based on regular, on-going engagement with the warfighter. The use of DoD Architecture Framework (DoDAF) products facilitated requirements scoping and understanding and transferred directly to defining and documenting the requirements in the approved Capability Development Document (CDD). As part of the risk reduction efforts, the Electronic System Center (ESC) JMS System Program Office (SPO) fielded JMS Capability Package (CP) 0 which includes an initial service oriented architecture (SOA) and user defined operational picture (UDOP) along with force status, sensor management, and analysis tools. Development efforts are planned to leverage and integrate prototypes and other research projects from Defense Advanced Research Projects Agency, Air Force Research Laboratories, Space Innovation and Development Center, and Massachusetts Institute of Technology/Lincoln Laboratories. JMS provides a number of benefits to the space community: a reduction in operational “transaction time” to accomplish key activities and processes; ability to process the increased volume of metric observations from new sensors (e.g., SBSS, SST, Space Fence), as well as owner/operator ephemerides thus enhancing the high accuracy near-real-time catalog, and greater automation of SSA data sharing supporting collaboration with government, civil, commercial, and foreign

  11. Exogenous control of biological and ecological systems through evolutionary modelling

    Directory of Open Access Journals (Sweden)

    Alessandro Ferrarini

    2013-09-01

    Full Text Available The controllability of network-like systems is a topical issue in ecology and biology. It relies on the ability to lead a system's behaviour towards the desired state through the appropriate handling of input variables. Up to now, controllability of networks is based on the permanent control of a set of driver nodes that can guide the system's dynamics. This assumption seems motivated by real-world networks observation, where a decentralized control is often applied only to part of the nodes. While in a previous paper I showed that ecological and biological networks can be efficaciously controlled from the inside, here I further introduce a new framework for network controllability based on the employment of exogenous controllers and evolutionary modelling, and provide an exemplification of its application.

  12. Complex fluids in biological systems experiment, theory, and computation

    CERN Document Server

    2015-01-01

    This book serves as an introduction to the continuum mechanics and mathematical modeling of complex fluids in living systems. The form and function of living systems are intimately tied to the nature of surrounding fluid environments, which commonly exhibit nonlinear and history dependent responses to forces and displacements. With ever-increasing capabilities in the visualization and manipulation of biological systems, research on the fundamental phenomena, models, measurements, and analysis of complex fluids has taken a number of exciting directions. In this book, many of the world’s foremost experts explore key topics such as: Macro- and micro-rheological techniques for measuring the material properties of complex biofluids and the subtleties of data interpretation Experimental observations and rheology of complex biological materials, including mucus, cell membranes, the cytoskeleton, and blood The motility of microorganisms in complex fluids and the dynamics of active suspensions Challenges and solut...

  13. RNA Systems Biology for Cancer: From Diagnosis to Therapy.

    Science.gov (United States)

    Amirkhah, Raheleh; Farazmand, Ali; Wolkenhauer, Olaf; Schmitz, Ulf

    2016-01-01

    It is due to the advances in high-throughput omics data generation that RNA species have re-entered the focus of biomedical research. International collaborate efforts, like the ENCODE and GENCODE projects, have spawned thousands of previously unknown functional non-coding RNAs (ncRNAs) with various but primarily regulatory roles. Many of these are linked to the emergence and progression of human diseases. In particular, interdisciplinary studies integrating bioinformatics, systems biology, and biotechnological approaches have successfully characterized the role of ncRNAs in different human cancers. These efforts led to the identification of a new tool-kit for cancer diagnosis, monitoring, and treatment, which is now starting to enter and impact on clinical practice. This chapter is to elaborate on the state of the art in RNA systems biology, including a review and perspective on clinical applications toward an integrative RNA systems medicine approach. The focus is on the role of ncRNAs in cancer.

  14. Data management in systems biology I - Overview and bibliography

    CERN Document Server

    Mayer, Gerhard

    2009-01-01

    Large systems biology projects can encompass several workgroups often located in different countries. An overview about existing data standards in systems biology and the management, storage, exchange and integration of the generated data in large distributed research projects is given, the pros and cons of the different approaches are illustrated from a practical point of view, the existing software - open source as well as commercial - and the relevant literature is extensively overview, so that the reader should be enabled to decide which data management approach is the best suited for his special needs. An emphasis is laid on the use of workflow systems and of TAB-based formats. The data in this format can be viewed and edited easily using spreadsheet programs which are familiar to the working experimental biologists. The use of workflows for the standardized access to data in either own or publicly available databanks and the standardization of operation procedures is presented. The use of ontologies and...

  15. Systems biology: A tool for charting the antiviral landscape.

    Science.gov (United States)

    Bowen, James R; Ferris, Martin T; Suthar, Mehul S

    2016-06-15

    The host antiviral programs that are initiated following viral infection form a dynamic and complex web of responses that we have collectively termed as "the antiviral landscape". Conventional approaches to studying antiviral responses have primarily used reductionist systems to assess the function of a single or a limited subset of molecules. Systems biology is a holistic approach that considers the entire system as a whole, rather than individual components or molecules. Systems biology based approaches facilitate an unbiased and comprehensive analysis of the antiviral landscape, while allowing for the discovery of emergent properties that are missed by conventional approaches. The antiviral landscape can be viewed as a hierarchy of complexity, beginning at the whole organism level and progressing downward to isolated tissues, populations of cells, and single cells. In this review, we will discuss how systems biology has been applied to better understand the antiviral landscape at each of these layers. At the organismal level, the Collaborative Cross is an invaluable genetic resource for assessing how genetic diversity influences the antiviral response. Whole tissue and isolated bulk cell transcriptomics serves as a critical tool for the comprehensive analysis of antiviral responses at both the tissue and cellular levels of complexity. Finally, new techniques in single cell analysis are emerging tools that will revolutionize our understanding of how individual cells within a bulk infected cell population contribute to the overall antiviral landscape.

  16. Scalable DDoS Mitigation System for Data Centers

    Directory of Open Access Journals (Sweden)

    Zdenek Martinasek

    2015-01-01

    Full Text Available Distributed Denial of Service attacks (DDoS have been used by attackers for over two decades because of their effectiveness. This type of the cyber-attack is one of the most destructive attacks in the Internet. In recent years, the intensity of DDoS attacks has been rapidly increasing and the attackers combine more often different techniques of DDoS to bypass the protection. Therefore, the main goal of our research is to propose a DDoS solution that allows to increase the filtering capacity linearly and allows to protect against the combination of attacks. The main idea is to develop the DDoS defense system in the form of a portable software image that can be installed on the reserve hardware capacities. During a DDoS attack, these servers will be used as filters of this DDoS attack. Our solution is suitable for data centers and eliminates some lacks of commercial solutions. The system employs modular DDoS filters in the form of special grids containing specific protocol parameters and conditions.

  17. 77 FR 37025 - Final Priority: Disability Rehabilitation Research Project-Burn Model Systems Centers

    Science.gov (United States)

    2012-06-20

    ... the NIDRR-funded Model Systems Knowledge Translation Center (MSKT Center). The commenters asked NIDRR... evidence-based knowledge translation process are allowable research activities for which grant funds under.... (d) Coordinating with the NIDRR-funded Model Systems Knowledge Translation Center (MSKTC) (...

  18. Systems biology in the frontier of cancer research:a report of the Second International Workshop of Cancer Systems Biology

    Institute of Scientific and Technical Information of China (English)

    Juan Cui; Yan-Chun Liang; Ying Xu

    2012-01-01

    The report summarizes the Second International Workshop of Cancer Systems Biology held on July 5-6,2012 in Changchun,China.The goal of the workshop was to bring together cancer researchers with different backgrounds to share their views about cancer and their experiences in fighting against cancer,and to gain new and systems-level understanding about cancer formation,progression,diagnosis,and treatment through exchanging ideas.

  19. Systems biology in the frontier of cancer research: a report of the Second International Workshop of Cancer Systems Biology

    OpenAIRE

    Ying Xu; Yan-Chun Liang; Juan Cui

    2012-01-01

    The report summarizes the Second International Workshop of Cancer Systems Biology held on July 5-6, 2012 in Changchun, China. The goal of the workshop was to bring together cancer researchers with different backgrounds to share their views about cancer and their experiences in fighting against cancer, and to gain new and systems-level understanding about cancer formation, progression, diagnosis, and treatment through exchanging ideas.

  20. 78 FR 74163 - Harrison Medical Center, a Subsidiary of Franciscan Health System Bremerton, Washington; Notice...

    Science.gov (United States)

    2013-12-10

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF LABOR Employment and Training Administration Harrison Medical Center, a Subsidiary of Franciscan Health System... Adjustment Assistance (TAA), applicable to workers and former workers of Harrison Medical Center,...

  1. Improving collaboration by standardization efforts in systems biology.

    Science.gov (United States)

    Dräger, Andreas; Palsson, Bernhard Ø

    2014-01-01

    Collaborative genome-scale reconstruction endeavors of metabolic networks would not be possible without a common, standardized formal representation of these systems. The ability to precisely define biological building blocks together with their dynamic behavior has even been considered a prerequisite for upcoming synthetic biology approaches. Driven by the requirements of such ambitious research goals, standardization itself has become an active field of research on nearly all levels of granularity in biology. In addition to the originally envisaged exchange of computational models and tool interoperability, new standards have been suggested for an unambiguous graphical display of biological phenomena, to annotate, archive, as well as to rank models, and to describe execution and the outcomes of simulation experiments. The spectrum now even covers the interaction of entire neurons in the brain, three-dimensional motions, and the description of pharmacometric studies. Thereby, the mathematical description of systems and approaches for their (repeated) simulation are clearly separated from each other and also from their graphical representation. Minimum information definitions constitute guidelines and common operation protocols in order to ensure reproducibility of findings and a unified knowledge representation. Central database infrastructures have been established that provide the scientific community with persistent links from model annotations to online resources. A rich variety of open-source software tools thrives for all data formats, often supporting a multitude of programing languages. Regular meetings and workshops of developers and users lead to continuous improvement and ongoing development of these standardization efforts. This article gives a brief overview about the current state of the growing number of operation protocols, mark-up languages, graphical descriptions, and fundamental software support with relevance to systems biology. PMID:25538939

  2. Improving collaboration by standardization efforts in systems biology

    Directory of Open Access Journals (Sweden)

    Andreas eDräger

    2014-12-01

    Full Text Available Collaborative genome-scale reconstruction endeavors of metabolic networks would not be possible without a common, standardized formal representation of these systems. The ability to precisely define biological building blocks together with their dynamic behavior has even been considered a prerequisite for upcoming synthetic biology approaches.Driven by the requirements of such ambitious research goals, standardization itself has become an active field of research on nearly all levels of granularity in biology.In addition to the originally envisaged exchange of computational models and tool interoperability, new standards have been suggested for an unambiguous graphical display of biological phenomena, to annotate, archive, as well as to rank models, and to describe execution and the outcomes of simulation experiments. The spectrum now even covers the interaction of entire neurons in the brain, three-dimensional motions, and the description of pharmacometric studies.Thereby, the mathematical description of systems and approaches for their (repeated simulation are clearly separated from each other and also from their graphical representation. Minimum information definitions constitute guidelines and common operation protocols in order to ensure reproducibility of findings and a unified knowledge representation.Central database infrastructures have been established that provide the scientific community with persistent links from model annotations to on-line resources. A rich variety of open-source software tools thrives for all data formats, often supporting a multitude of programming languages. Regular meetings and workshops of developers and users lead to continuous improvement and ongoing development of these standardization efforts.This article gives a brief overview about the current state of the growing number of operation protocols, markup languages, graphical descriptions, and fundamental software support with relevance to systems biology.

  3. Chemical and biological interactions in the Rose Garden hydrothermal vent field, Galapagos spreading center

    Science.gov (United States)

    Johnson, Kenneth S.; Childress, James J.; Hessler, Robert R.; Sakamoto-Arnold, Carole M.; Beehler, Carl L.

    1988-10-01

    The concentrations of a suite of redox reactive chemicals were measured in the Rose Garden hydrothermal vent field of the Galapagos spreading center. Sulfide, silicate, oxygen and temperature distributions were measured in situ with a submersible chemical analyser. In addition, 15 chemical species were measured in discrete samples. Variability in the slope of the temperature-silicate plots indicates that heat is lost from these relatively low temperatures (<15°C) solutions by conduction to the solid phase. Consumption of oxygen, sulfide and nitrate from the hydrothermal solution as it flows past the vent animals is apparent from the distributions measured in situ and in the discrete samples. The fraction of sulfide and nitrate removed from the solution by consumption appears to have increased between 1979-1985. Sulfide and oxygen appear to be consumed under different conditions: sulfide is removed primarily from the warmest solutions, and oxygen is consumed only from the cold seawater. This separation may be driven primarily by the increased gradients of each chemical under these conditions. There is no evidence for the consumption of significant amounts of manganese(II) by the vent organisms. The analysis of other data sets from this vent field indicate no significant consumption of methane by the vent organisms, as well.

  4. Marshall Space Flight Center Propulsion Systems Department (PSD) KM Initiative

    Science.gov (United States)

    Caraccioli, Paul; Varnadoe, Tom; McCarter, Mike

    2006-01-01

    NASA Marshall Space Flight Center s Propulsion Systems Department (PSD) is four months into a fifteen month Knowledge Management (KM) initiative to support enhanced engineering decision making and analyses, faster resolution of anomalies (near-term) and effective, efficient knowledge infused engineering processes, reduced knowledge attrition, and reduced anomaly occurrences (long-term). The near-term objective of this initiative is developing a KM Pilot project, within the context of a 3-5 year KM strategy, to introduce and evaluate the use of KM within PSD. An internal NASA/MSFC PSD KM team was established early in project formulation to maintain a practitioner, user-centric focus throughout the conceptual development, planning and deployment of KM technologies and capabilities with in the PSD. The PSD internal team is supported by the University of Alabama's Aging Infrastructure Systems Center Of Excellence (AISCE), Intergraph Corporation, and The Knowledge Institute. The principle product of the initial four month effort has been strategic planning of PSD KM implementation by first determining the "as is" state of KM capabilities and developing, planning and documenting the roadmap to achieve the desired "to be" state. Activities undertaken to support the planning phase have included data gathering; cultural surveys, group work-sessions, interviews, documentation review, and independent research. Assessments and analyses have been performed including industry benchmarking, related local and Agency initiatives, specific tools and techniques used and strategies for leveraging existing resources, people and technology to achieve common KM goals. Key findings captured in the PSD KM Strategic Plan include the system vision, purpose, stakeholders, prioritized strategic objectives mapped to the top ten practitioner needs and analysis of current resource usage. Opportunities identified from research, analyses, cultural/KM surveys and practitioner interviews include

  5. The advantages of reliability centered maintenance for standby safety systems

    International Nuclear Information System (INIS)

    On standby safety systems, nuclear plants have to balance the requirements of demonstrating the reliability of each system, while maintaining the system and plant availability. With the goal of demonstrating statistical reliability, these systems have extensive testing programs, which often makes the system unavailable and this can impact plant capacity. The inputs to the process are often safety and regulatory related, resulting in programs that provide a high level of scrutiny on the systems being considered. In such cases, the value of the application of a maintenance optimization strategy, such as Reliability Centered Maintenance (RCM), is questioned. Part of the question stems from the use of the word 'Reliability' in RCM. When RCM is applied to a system maintenance program driven by reliability requirements, there appears to be redundancy. A deeper look at the RCM process, however, shows that the RCM goal is to ensure that the system operates 'reliably' through the application of an integrated maintenance strategy. This is a subtle, but important distinction. Although the system reliability requirements are an important part of the strategy evaluation, RCM provides a broader context where testing is only one part of an overall strategy focused on ensuring that component function is maintained through a combination of monitoring technologies (including testing), predictive techniques, and intrusive maintenance strategies. Each strategy is targeted to identify known component degradation mechanisms. The conclusion is that a maintenance program driven by reliability requirements will tend to have testing defined at a frequency intended to support the needed statistics. The testing demonstrates that the desired function is available today. Maintenance driven by functional requirements and known failure causes, as developed through a maintenance optimization assessment, will have frequencies tied to industry experience with components and rely on a higher degree

  6. The advantages of reliability centered maintenance for standby safety systems

    International Nuclear Information System (INIS)

    Full text: On standby safety systems, nuclear plants have to balance the requirements of demonstrating the reliability of each system, while maintaining the system and plant availability. With the goal of demonstrating statistical reliability, these systems have extensive testing programs, which often makes the system unavailable and this can impact the plant capacity. The inputs to the process are often safety and regulatory related, resulting in programs that provide a high level of scrutiny on the systems being considered. In such cases, the value of the application of a maintenance optimization strategy, such as Reliability Centered Maintenance (RCM), is questioned. Part of the question stems from the use of the word 'Reliability' in RCM, which implies a level of redundancy when applied to a system maintenance program driven by reliability requirements. A deeper look at the RCM process, however, shows that RCM has the goal of ensuring that the system operates 'reliably' through the application of an integrated maintenance strategy. This is a subtle, but important distinction. Although the system reliability requirements are an important part of the strategy evaluation, RCM provides a broader context where testing is only one part of an overall strategy focused on ensuring that component function is maintained through a combination of monitoring technologies (including testing), predictive techniques, and intrusive maintenance strategies. Each strategy is targeted to identify known component degradation mechanisms. The conclusion is that a maintenance program driven by reliability requirements will tend to have testing defined at a frequency intended to support the needed statistics. The testing demonstrates that the desired function is available today. Maintenance driven by functional requirements and known failure causes, as developed through an RCM assessment, will have frequencies tied to industry experience with components and rely on a higher degree of

  7. National Verification System of National Meteorological Center , China

    Science.gov (United States)

    Zhang, Jinyan; Wei, Qing; Qi, Dan

    2016-04-01

    Product Quality Verification Division for official weather forecasting of China was founded in April, 2011. It is affiliated to Forecast System Laboratory (FSL), National Meteorological Center (NMC), China. There are three employees in this department. I'm one of the employees and I am in charge of Product Quality Verification Division in NMC, China. After five years of construction, an integrated realtime National Verification System of NMC, China has been established. At present, its primary roles include: 1) to verify official weather forecasting quality of NMC, China; 2) to verify the official city weather forecasting quality of Provincial Meteorological Bureau; 3) to evaluate forecasting quality for each forecasters in NMC, China. To verify official weather forecasting quality of NMC, China, we have developed : • Grid QPF Verification module ( including upascale) • Grid temperature, humidity and wind forecast verification module • Severe convective weather forecast verification module • Typhoon forecast verification module • Disaster forecast verification • Disaster warning verification module • Medium and extend period forecast verification module • Objective elements forecast verification module • Ensemble precipitation probabilistic forecast verification module To verify the official city weather forecasting quality of Provincial Meteorological Bureau, we have developed : • City elements forecast verification module • Public heavy rain forecast verification module • City air quality forecast verification module. To evaluate forecasting quality for each forecasters in NMC, China, we have developed : • Off-duty forecaster QPF practice evaluation module • QPF evaluation module for forecasters • Severe convective weather forecast evaluation module • Typhoon track forecast evaluation module for forecasters • Disaster warning evaluation module for forecasters • Medium and extend period forecast evaluation module The further

  8. From globally coupled maps to complex-systems biology

    Energy Technology Data Exchange (ETDEWEB)

    Kaneko, Kunihiko, E-mail: kaneko@complex.c.u-tokyo.ac.jp [Research Center for Complex Systems Biology, Graduate School of Arts and Sciences, The University of Tokyo 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan)

    2015-09-15

    Studies of globally coupled maps, introduced as a network of chaotic dynamics, are briefly reviewed with an emphasis on novel concepts therein, which are universal in high-dimensional dynamical systems. They include clustering of synchronized oscillations, hierarchical clustering, chimera of synchronization and desynchronization, partition complexity, prevalence of Milnor attractors, chaotic itinerancy, and collective chaos. The degrees of freedom necessary for high dimensionality are proposed to equal the number in which the combinatorial exceeds the exponential. Future analysis of high-dimensional dynamical systems with regard to complex-systems biology is briefly discussed.

  9. From globally coupled maps to complex-systems biology

    Science.gov (United States)

    Kaneko, Kunihiko

    2015-09-01

    Studies of globally coupled maps, introduced as a network of chaotic dynamics, are briefly reviewed with an emphasis on novel concepts therein, which are universal in high-dimensional dynamical systems. They include clustering of synchronized oscillations, hierarchical clustering, chimera of synchronization and desynchronization, partition complexity, prevalence of Milnor attractors, chaotic itinerancy, and collective chaos. The degrees of freedom necessary for high dimensionality are proposed to equal the number in which the combinatorial exceeds the exponential. Future analysis of high-dimensional dynamical systems with regard to complex-systems biology is briefly discussed.

  10. Biological Computation as the Revolution of Complex Engineered Systems

    CERN Document Server

    Gómez-Cruz, Nelson Alfonso

    2011-01-01

    Provided that there is no theoretical frame for complex engineered systems (CES) as yet, this paper claims that bio-inspired engineering can help provide such a frame. Within CES bio-inspired systems play a key role. The disclosure from bio-inspired systems and biological computation has not been sufficiently worked out, however. Biological computation is to be taken as the processing of information by living systems that is carried out in polynomial time, i.e., efficiently; such processing however is grasped by current science and research as an intractable problem (for instance, the protein folding problem). A remark is needed here: P versus NP problems should be well defined and delimited but biological computation problems are not. The shift from conventional engineering to bio-inspired engineering needs bring the subject (or problem) of computability to a new level. Within the frame of computation, so far, the prevailing paradigm is still the Turing-Church thesis. In other words, conventional engineering...

  11. Integrative biological systems modeling:challenges and opportunities

    Institute of Scientific and Technical Information of China (English)

    Jialiang WU; Eberhard VOIT

    2009-01-01

    Most biological systems are by nature hybrids consist of interacting discrete and continuous components,which may even operate on different time scales. Therefore," it is desirable to establish modeling frameworks that are capable of combining deterministic and stochastic, discrete and continuous, as well as multi-timescale features. In the context of molecular systems biology, an example for the need of such a combination is the investigation of integrated biological pathways that contain gene regulatory, metabolic and signaling components, which may operate on different time scales and involve on-off switches as well as stochastic effects. The implementation of integrated hybrid systems is not trivial because most software is limited to one or the other of the dichotomies above. In this study, we first review the motivation for hybrid modeling. Secondly, by using the example of a toggle switch model, we illustrate a recently developed modeling framework that is based on the combination of biochemical systems theory (BST) and hybrid functional Petri nets (HFPN). Finally, we discuss remaining challenges and future opportunities.

  12. 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.

  13. The effects of a visualization-centered curriculum on conceptual understanding and representational competence in high school biology

    Science.gov (United States)

    Wilder, Anna

    The purpose of this study was to investigate the effects of a visualization-centered curriculum, Hemoglobin: A Case of Double Identity, on conceptual understanding and representational competence in high school biology. Sixty-nine students enrolled in three sections of freshman biology taught by the same teacher participated in this study. Online Chemscape Chime computer-based molecular visualizations were incorporated into the 10-week curriculum to introduce students to fundamental structure and function relationships. Measures used in this study included a Hemoglobin Structure and Function Test, Mental Imagery Questionnaire, Exam Difficulty Survey, the Student Assessment of Learning Gains, the Group Assessment of Logical Thinking, the Attitude Toward Science in School Assessment, audiotapes of student interviews, students' artifacts, weekly unit activity surveys, informal researcher observations and a teacher's weekly questionnaire. The Hemoglobin Structure and Function Test, consisting of Parts A and B, was administered as a pre and posttest. Part A used exclusively verbal test items to measure conceptual understanding, while Part B used visual-verbal test items to measure conceptual understanding and representational competence. Results of the Hemoglobin Structure and Function pre and posttest revealed statistically significant gains in conceptual understanding and representational competence, suggesting the visualization-centered curriculum implemented in this study was effective in supporting positive learning outcomes. The large positive correlation between posttest results on Part A, comprised of all-verbal test items, and Part B, using visual-verbal test items, suggests this curriculum supported students' mutual development of conceptual understanding and representational competence. Evidence based on student interviews, Student Assessment of Learning Gains ratings and weekly activity surveys indicated positive attitudes toward the use of Chemscape Chime

  14. Fingerprint Identification System in library and Information Center

    Directory of Open Access Journals (Sweden)

    Raju Rajkumar

    2011-12-01

    Full Text Available AFIS is dramatically improving in the last decade. It can use in Library and Information Center for providing better security. The application of AFIS in Library and Information Center will protectfrom thief, mutilation of library materials and other unethical losses.

  15. Systems biology of IL-6, IL-12 family cytokines.

    Science.gov (United States)

    Dittrich, Anna; Hessenkemper, Wiebke; Schaper, Fred

    2015-10-01

    Interleukin-6-type cytokines play important roles in the communication between cells of multicellular organisms. They are involved in the regulation of complex cellular processes such as proliferation and differentiation and act as key player during inflammation and immune response. A major challenge is to understand how these complex non-linear processes are connected and regulated. Systems biology approaches are used to tackle this challenge in an iterative process of quantitative experimental and mathematical analyses. Here we review quantitative experimental studies and systems biology approaches dealing with the function of Interleukin-6-type cytokines in physiological and pathophysiological conditions. These approaches cover the analyses of signal transduction on a cellular level up to pharmacokinetic and pharmacodynamic studies on a whole organism level.

  16. Cellular systems biology profiling applied to cellular models of disease.

    Science.gov (United States)

    Giuliano, Kenneth A; Premkumar, Daniel R; Strock, Christopher J; Johnston, Patricia; Taylor, Lansing

    2009-11-01

    Building cellular models of disease based on the approach of Cellular Systems Biology (CSB) has the potential to improve the process of creating drugs as part of the continuum from early drug discovery through drug development and clinical trials and diagnostics. This paper focuses on the application of CSB to early drug discovery. We discuss the integration of protein-protein interaction biosensors with other multiplexed, functional biomarkers as an example in using CSB to optimize the identification of quality lead series compounds.

  17. Systems Biology Approaches to Epidemiological Studies of Complex Diseases

    OpenAIRE

    Li, Hongzhe

    2013-01-01

    Systems biology approaches to epidemiological studies of complex diseases include collection of genetic, genomic, epigenomic and metagenomic data in large-scale epidemiological studies of complex phenotypes. Designs and analyses of such studies raise many statistical challenges. This paper reviews some issues related to integrative analysis of such high dimensional and inter-related data sets and outline some possible solutions. I focus my review on integrative approaches for genome-wide gene...

  18. The Structural Biology of CRISPR-Cas Systems

    OpenAIRE

    Jiang, Fuguo; Doudna, Jennifer A.

    2015-01-01

    Prokaryotic CRISPR-Cas genomic loci encode RNA-mediated adaptive immune systems that bear some functional similarities with eukaryotic RNA interference. Acquired and heritable immunity against bacteriophage and plasmids begins with integration of ~30 base pair foreign DNA sequences into the host genome. CRISPR-derived transcripts assemble with CRISPR-associated (Cas) proteins to target complementary nucleic acids for degradation. Here we review recent advances in the structural biology of the...

  19. Assessing Current Instructional Practices in General Biology One (BIO1010) and Arguing for a Model-Centered Curriculum

    Science.gov (United States)

    Manthey, Seth

    This collected papers dissertation focused on the argument for the need to adapt and develop a model-centered General Biology I course through the analyses of current instructional practices at a large, public, Hispanic-serving university. This dissertation included a comparison of General Biology I course sections taught in two differing formats, one is a traditional lecture with face-to-face meetings and the other is an online instruction setting. The comparison of these sections was accomplished through the use of a conceptual inventory, student attitude survey, drop-fail-withdraw (DFW) rates, and Social Network Analysis. This comparison found that there was no detectible significant difference between course type for both the conceptual understanding and formation of student-to-student networks. It was also found that there was a significant difference between course type when looking at students' attitudes towards Biology and success in the two course types. Additionally in a second study the project used a phenomoenographic analysis of student interviews that explored the students' use of scientific models when asked about plant cells and animal cells. It was found that during the analysis of students' ideas that students predominantly used a single model function. The cell types of focus in the second study were two models that were identified, in a third study, through a coded analysis of faculty interviews and textbook analysis. These models are viewed as essential for students to possess an understanding of upon completion of General Biology I. The model-based course that this study argued for is based on a curricular framework initially developed for use in introductory physics courses. University Modeling Instruction courses in physics (UMI-P) have been linked to improved student conceptual understanding positive attitudinal shifts, and decreased DFW rates. UMI, however, has not been expanded for implementation within the other science disciplines

  20. Systems Biology - A Pivotal Research Methodology for Understanding the Mechanisms of Traditional Medicine

    OpenAIRE

    Soojin Lee

    2015-01-01

    Objectives: Systems biology is a novel subject in the field of life science that aims at a systems’ level understanding of biological systems. Because of the significant progress in high-throughput technologies and molecular biology, systems biology occupies an important place in research during the post-genome era. Methods: The characteristics of systems biology and its applicability to traditional medicine research have been discussed from three points of view: data and databases, network a...

  1. Systems Biology for Mapping Genotype-Phenotype Relations in Yeast

    KAUST Repository

    Nielsen, Jens

    2016-01-25

    The yeast Saccharomyces cerevisiae is widely used for production of fuels, chemicals, pharmaceuticals and materials. Through metabolic engineering of this yeast a number of novel new industrial processes have been developed over the last 10 years. Besides its wide industrial use, S. cerevisiae serves as an eukaryal model organism, and many systems biology tools have therefore been developed for this organism. Among these genome-scale metabolic models have shown to be most successful as they easy integrate with omics data and at the same time have been shown to have excellent predictive power. Despite our extensive knowledge of yeast metabolism and its regulation we are still facing challenges when we want to engineer complex traits, such as improved tolerance to toxic metabolites like butanol and elevated temperatures or when we want to engineer the highly complex protein secretory pathway. In this presentation it will be demonstrated how we can combine directed evolution with systems biology analysis to identify novel targets for rational design-build-test of yeast strains that have improved phenotypic properties. In this lecture an overview of systems biology of yeast will be presented together with examples of how genome-scale metabolic modeling can be used for prediction of cellular growth at different conditions. Examples will also be given on how adaptive laboratory evolution can be used for identifying targets for improving tolerance towards butanol, increased temperature and low pH and for improving secretion of heterologous proteins.

  2. Macroscopic Quantum-Type Potentials in Theoretical Systems Biology

    Directory of Open Access Journals (Sweden)

    Laurent Nottale

    2013-12-01

    Full Text Available We review in this paper the use of the theory of scale relativity and fractal space-time as a tool particularly well adapted to the possible development of a future genuine systems theoretical biology. We emphasize in particular the concept of quantum-type potentials, since, in many situations, the effect of the fractality of space—or of the underlying medium—can be reduced to the addition of such a potential energy to the classical equations of motion. Various equivalent representations—geodesic, quantum-like, fluid mechanical, stochastic—of these equations are given, as well as several forms of generalized quantum potentials. Examples of their possible intervention in high critical temperature superconductivity and in turbulence are also described, since some biological processes may be similar in some aspects to these physical phenomena. These potential extra energy contributions could have emerged in biology from the very fractal nature of the medium, or from an evolutive advantage, since they involve spontaneous properties of self-organization, morphogenesis, structuration and multi-scale integration. Finally, some examples of applications of the theory to actual biological-like processes and functions are also provided.

  3. On Mechanical Transitions in Biologically Motivated Soft Matter Systems

    Science.gov (United States)

    Fogle, Craig

    The notion of phase transitions as a characterization of a change in physical properties pervades modern physics. Such abrupt and fundamental changes in the behavior of physical systems are evident in condensed matter system and also occur in nuclear and subatomic settings. While this concept is less prevalent in the field of biology, recent advances have pointed to its relevance in a number of settings. Recent studies have modeled both the cell cycle and cancer as phase transition in physical systems. In this dissertation we construct simplified models for two biological systems. As described by those models, both systems exhibit phase transitions. The first model is inspired by the shape transition in the nuclei of neutrophils during differentiation. During differentiation the nucleus transitions from spherical to a shape often described as "beads on a string." As a simplified model of this system, we investigate the spherical-to-wrinkled transition in an elastic core bounded to a fluid shell system. We find that this model exhibits a first-order phase transition, and the shape that minimizes the energy of the system scales as (micror3/kappa). . The second system studied is motivated by the dynamics of globular proteins. These proteins may undergoes conformational changes with large displacements relative to their size. Transitions between conformational states are not possible if the dynamics are governed strictly by linear elasticity. We construct a model consisting of an predominantly elastic region near the energetic minimum of the system and a non-linear softening of the system at a critical displacement. We find that this simple model displays very rich dynamics include a sharp dynamical phase transition and driving-force-dependent symmetry breaking.

  4. Human Metabolic Network: Reconstruction, Simulation, and Applications in Systems Biology

    Science.gov (United States)

    Wu, Ming; Chan, Christina

    2012-01-01

    Metabolism is crucial to cell growth and proliferation. Deficiency or alterations in metabolic functions are known to be involved in many human diseases. Therefore, understanding the human metabolic system is important for the study and treatment of complex diseases. Current reconstructions of the global human metabolic network provide a computational platform to integrate genome-scale information on metabolism. The platform enables a systematic study of the regulation and is applicable to a wide variety of cases, wherein one could rely on in silico perturbations to predict novel targets, interpret systemic effects, and identify alterations in the metabolic states to better understand the genotype-phenotype relationships. In this review, we describe the reconstruction of the human metabolic network, introduce the constraint based modeling approach to analyze metabolic networks, and discuss systems biology applications to study human physiology and pathology. We highlight the challenges and opportunities in network reconstruction and systems modeling of the human metabolic system. PMID:24957377

  5. Model Checking the Biological Model of Membrane Computing with Probabilistic Symbolic Model Checker by Using Two Biological Systems

    Directory of Open Access Journals (Sweden)

    Ravie c. Muniyandi

    2010-01-01

    Full Text Available Problem statement: Membrane computing formalism has provided better modeling capabilities for biological systems in comparison to conventional mathematical models. Model checking could be used to reason about the biological system in detail and with precision by verifying formally whether membrane computing model meets the properties of the system. Approach: This study was carried to investigate the preservation of properties of two biological systems that had been modeled and simulated in membrane computing by a method of model checking using PRISM. The two biological systems were prey-predator population and signal processing in the legend-receptor networks of protein TGF-ß. Results: The model checking of membrane computing model of the biological systems with five different properties showed that the properties of the biological systems could be preserved in the membrane computing model. Conclusion: Membrane computing model not only provides a better approach in representing and simulating a biological system but also able to sustain the basic properties of the system.

  6. 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

  7. Wearable System for Acquisition and Monitoring of Biological Signals

    Science.gov (United States)

    Piccinini, D. J.; Andino, N. B.; Ponce, S. D.; Roberti, MA; López, y. N.

    2016-04-01

    This paper presents a modular, wearable system for acquisition and wireless transmission of biological signals. Configurable slaves for different signals (such as ECG, EMG, inertial sensors, and temperature) based in the ADS1294 Medical Analog Front End are connected to a Master, based in the CC3200 microcontroller, both from Texas Instruments. The slaves are configurable according to the specific application, providing versatility to the wearable system. The battery consumption is reduced, through a couple of Li-ion batteries and the circuit has also a battery charger. A custom made box was designed and fabricated in a 3D printer, preserving the requirements of low cost, low weight and safety recommendations.

  8. Algebraic Systems Biology: A Case Study for the Wnt Pathway.

    Science.gov (United States)

    Gross, Elizabeth; Harrington, Heather A; Rosen, Zvi; Sturmfels, Bernd

    2016-01-01

    Steady-state analysis of dynamical systems for biological networks gives rise to algebraic varieties in high-dimensional spaces whose study is of interest in their own right. We demonstrate this for the shuttle model of the Wnt signaling pathway. Here, the variety is described by a polynomial system in 19 unknowns and 36 parameters. It has degree 9 over the parameter space. This case study explores multistationarity, model comparison, dynamics within regions of the state space, identifiability, and parameter estimation, from a geometric point of view. We employ current methods from computational algebraic geometry, polyhedral geometry, and combinatorics.

  9. Nearly Closed Loops in Biological Systems as Electromagnetic Receptors

    CERN Document Server

    Eichler, D

    1997-01-01

    It is noted here that when a nearly closed loop in a biological system, such as a self-synapsing (autapsing) neuron or mutually synapsing pair, is exposed to an AC magnetic field, the induced electric fields in the insulating gaps can be many orders of magnitude larger than the average values typically discussed in the literature.$^{1,2}$ It is suggested that animal nervous systems might possibly be affected in selected spots by man-made alternating magnetic fields at weaker levels than previously supposed. Radio and microwave radiation should be considered particularly suspect.

  10. Algebraic Systems Biology: A Case Study for the Wnt Pathway.

    Science.gov (United States)

    Gross, Elizabeth; Harrington, Heather A; Rosen, Zvi; Sturmfels, Bernd

    2016-01-01

    Steady-state analysis of dynamical systems for biological networks gives rise to algebraic varieties in high-dimensional spaces whose study is of interest in their own right. We demonstrate this for the shuttle model of the Wnt signaling pathway. Here, the variety is described by a polynomial system in 19 unknowns and 36 parameters. It has degree 9 over the parameter space. This case study explores multistationarity, model comparison, dynamics within regions of the state space, identifiability, and parameter estimation, from a geometric point of view. We employ current methods from computational algebraic geometry, polyhedral geometry, and combinatorics. PMID:26645985

  11. An Intuitive Automated Modelling Interface for Systems Biology

    Directory of Open Access Journals (Sweden)

    Ozan Kahramanoğulları

    2009-11-01

    Full Text Available We introduce a natural language interface for building stochastic pi calculus models of biological systems. In this language, complex constructs describing biochemical events are built from basic primitives of association, dissociation and transformation. This language thus allows us to model biochemical systems modularly by describing their dynamics in a narrative-style language, while making amendments, refinements and extensions on the models easy. We demonstrate the language on a model of Fc-gamma receptor phosphorylation during phagocytosis. We provide a tool implementation of the translation into a stochastic pi calculus language, Microsoft Research's SPiM.

  12. Environmental Geographic Information Systems (EGIS) at Stennis Space Center (SSC)

    Science.gov (United States)

    Carr, Hugh; Smoot, James; Parikh, Joy

    2004-01-01

    This viewgraph presentation includes: 1) Background of SSC Environmental GIS (EGIS); 2) Principal Center Activities; 3) SSC's GIS Applications: a) Environmental Emergency Response Tool, b) CERCLA, c) Facilities Master Planning, d) Natural Resource Management and Site Assessment.

  13. Modeling drug- and chemical- induced hepatotoxicity with systems biology approaches

    Directory of Open Access Journals (Sweden)

    Sudin eBhattacharya

    2012-12-01

    Full Text Available We provide an overview of computational systems biology approaches as applied to the study of chemical- and drug-induced toxicity. The concept of ‘toxicity pathways’ is described in the context of the 2007 US National Academies of Science report, Toxicity testing in the 21st Century: A Vision and A Strategy. Pathway mapping and modeling based on network biology concepts are a key component of the vision laid out in this report for a more biologically-based analysis of dose-response behavior and the safety of chemicals and drugs. We focus on toxicity of the liver (hepatotoxicity – a complex phenotypic response with contributions from a number of different cell types and biological processes. We describe three case studies of complementary multi-scale computational modeling approaches to understand perturbation of toxicity pathways in the human liver as a result of exposure to environmental contaminants and specific drugs. One approach involves development of a spatial, multicellular virtual tissue model of the liver lobule that combines molecular circuits in individual hepatocytes with cell-cell interactions and blood-mediated transport of toxicants through hepatic sinusoids, to enable quantitative, mechanistic prediction of hepatic dose-response for activation of the AhR toxicity pathway. Simultaneously, methods are being developing to extract quantitative maps of intracellular signaling and transcriptional regulatory networks perturbed by environmental contaminants, using a combination of gene expression and genome-wide protein-DNA interaction data. A predictive physiological model (DILIsymTM to understand drug-induced liver injury (DILI, the most common adverse event leading to termination of clinical development programs and regulatory actions on drugs, is also described. The model initially focuses on reactive metabolite-induced DILI in response to administration of acetaminophen, and spans multiple biological scales.

  14. Systems analysis of biological networks in skeletal muscle function.

    Science.gov (United States)

    Smith, Lucas R; Meyer, Gretchen; Lieber, Richard L

    2013-01-01

    Skeletal muscle function depends on the efficient coordination among subcellular systems. These systems are composed of proteins encoded by a subset of genes, all of which are tightly regulated. In the cases where regulation is altered because of disease or injury, dysfunction occurs. To enable objective analysis of muscle gene expression profiles, we have defined nine biological networks whose coordination is critical to muscle function. We begin by describing the expression of proteins necessary for optimal neuromuscular junction function that results in the muscle cell action potential. That action potential is transmitted to proteins involved in excitation-contraction coupling enabling Ca(2+) release. Ca(2+) then activates contractile proteins supporting actin and myosin cross-bridge cycling. Force generated by cross-bridges is transmitted via cytoskeletal proteins through the sarcolemma and out to critical proteins that support the muscle extracellular matrix. Muscle contraction is fueled through many proteins that regulate energy metabolism. Inflammation is a common response to injury that can result in alteration of many pathways within muscle. Muscle also has multiple pathways that regulate size through atrophy or hypertrophy. Finally, the isoforms associated with fast muscle fibers and their corresponding isoforms in slow muscle fibers are delineated. These nine networks represent important biological systems that affect skeletal muscle function. Combining high-throughput systems analysis with advanced networking software will allow researchers to use these networks to objectively study skeletal muscle systems. PMID:23188744

  15. Limit Cycles and Isochronous Centers in a Class of Ninth Degree System

    Directory of Open Access Journals (Sweden)

    Li Hongwei

    2013-01-01

    Full Text Available A class of ninth degree system is studied and the conditions ensuring that its five singular points can be centers and isochronous centers (or linearizable centers at the same time by exact calculation and strict proof are obtained. What is more, the expressions of Lyapunov constants and periodic constants are simplified, and 21 limit circles could be bifurcated at least.

  16. Review of neutron radiographic applications in industrial and biological systems

    International Nuclear Information System (INIS)

    Neutron radiography is a non-destructive testing technique and is being used worldwide for the design and the development of reactor fuels for research and power reactors. It is also being used for non-destructive examination of nuclear industrial products. In addition to its explosives and other industrial sectors. In addition to its applications in industrial sectors, the technique is widely used for research and development activities in biological systems. A review of technical applications of neutron radiography in different fields particularly in nuclear fuel management, aerospace industry, explosives and biology is presented. The methodology of neutron radiography is also discussed in detail along with the advantages of the technique. In addition, the potential of the neutron radiography facility at PINSTECH has been described. (author)

  17. Application of enriched stable isotopes as tracers in biological systems

    DEFF Research Database (Denmark)

    Stürup, Stefan; Hansen, Helle Rüsz; Gammelgaard, Bente

    2008-01-01

    The application of enriched stable isotopes of minerals and trace elements as tracers in biological systems is a rapidly growing research field that benefits from the many new developments in inorganic mass spectrometric instrumentation, primarily within inductively coupled plasma mass spectrometry...... (ICP-MS) instrumentation, such as reaction/collision cell ICP-MS and multicollector ICP-MS with improved isotope ratio measurement and interference removal capabilities. Adaptation and refinement of radioisotope tracer experiment methodologies for enriched stable isotope experiments......, and the development of new methodologies coupled with more advanced compartmental and mathematical models for the distribution of elements in living organisms has enabled a broader use of enriched stable isotope experiments in the biological sciences. This review discusses the current and future uses of enriched...

  18. Local therapy, systemic benefit: challenging the paradigm of biological predeterminism.

    Science.gov (United States)

    Kurtz, J M

    2006-04-01

    This paper briefly reviews the historical evolution of paradigms that have been purported to characterise the clinical behaviour of breast cancer, with the intention of guiding treatment approaches. Results from randomised clinical trials and the explosion of knowledge in the area of cancer biology have discredited the monolithic paradigms that had dominated thinking about breast cancer in the past. Contemporary notions of breast cancer biology recognise that, although some cancers disseminate well before becoming clinically detectable, acquisition of a metastatic phenotype can occur at any point (or not at all) in the local evolution of the tumour. As a consequence, both systemic and timely local--regional therapies can be expected to influence disease dissemination and patient survival. This is consistent with results observed in clinical trials, overviews of which indicate that prevention of four local recurrences will, on the average, prevent one death from breast cancer. Optimisation of local-regional treatment is an important goal in breast cancer management. PMID:16605046

  19. Genetically engineered biological agents in therapy for systemic lupus erythematosus

    Directory of Open Access Journals (Sweden)

    Elena Aleksandrovna Aseeva

    2013-01-01

    Full Text Available Systemic lupus erythematosus (SLE is a prototype for chronic autoimmune disease. Its prevalence is 20 to 70 cases per 100,000 women and varies by race and ethnicity. Despite considerable progress in traditional therapy, many problems associated with the management of these patients need to be immediately solved: thus, 50-80% are found to have activity signs and/or frequent exacerbations and about 30% of the patients have to stop work; Class IV lupus nephritis increases the risk of terminalrenal failure. In the past 20 years great progress has been made in studying the pathogenesis of SLE: biological targets to affect drugs have been sought and fundamentally new therapeutic goals defined. Belimumab is the first genetically biological agent specially designed to treat SLE, which is rightly regarded as one of the most important achievements of rheumatology in the past 50 years.

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

    Directory of Open Access Journals (Sweden)

    Flores Ricardo J

    2012-05-01

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

  1. Physical and biological studies with protons and HZE particles in a NASA supported research center in radiation health

    Science.gov (United States)

    Chatterjee, A.; Borak, T. H.

    2001-01-01

    NASA has established and supports a specialized center for research and training (NSCORT) to specifically address the potential deleterious effects of HZE particles on human health. The NSCORT in radiation health is a joint effort between Lawrence Berkeley National Laboratory (LBNL) and Colorado State University (CSU). The overall scope of research encompasses a broad range of subjects from microdosimetric studies to cellular and tissue responses to initial damage produced by highly energetic protons and heavy charged particles of the type found in galactic cosmic rays (GCR) spectrum. The objectives of the microdosimetry studies are to determine the response of Tissue Equivalent Proportional Counter (TEPC) to cosmic rays using ground based accelerators. This includes evaluation of energy loss due to the escape of high-energy delta rays and increased energy deposition due to the enhanced delta ray production in the wall of the detector. In this report major results are presented for 56Fe at 1000, 740, 600 and 400 MeV/nucleon. An assessment of DNA repair and early development of related chromosomal changes is extremely important to our overall understanding of enhanced biological effectiveness of high LET particle radiation. Results are presented with respect to the fidelity of the rejoining of double strand breaks and the implications of misrejoining. The relationship between molecular and cytogenetic measurements is presented by studying damage processing in highly heterochromatic supernumerary (correction of sypernumerary) X chromosomes and the active X-chromosome. One of the important consequences of cell's inability to handle DNA damage can be evaluated through mutation studies. Part of our goal is the assessment of potential radioprotectors to reduce the mutation yield following HZE exposures, and some promising results are presented on one compound. A second goal is the integration of DNA repair and mutation studies. Results are presented on a direct

  2. Process-based design of dynamical biological systems

    Science.gov (United States)

    Tanevski, Jovan; Todorovski, Ljupčo; Džeroski, Sašo

    2016-09-01

    The computational design of dynamical systems is an important emerging task in synthetic biology. Given desired properties of the behaviour of a dynamical system, the task of design is to build an in-silico model of a system whose simulated be- haviour meets these properties. We introduce a new, process-based, design methodology for addressing this task. The new methodology combines a flexible process-based formalism for specifying the space of candidate designs with multi-objective optimization approaches for selecting the most appropriate among these candidates. We demonstrate that the methodology is general enough to both formulate and solve tasks of designing deterministic and stochastic systems, successfully reproducing plausible designs reported in previous studies and proposing new designs that meet the design criteria, but have not been previously considered.

  3. Microbial diversity of biological filters in recirculating aquaculture systems.

    Science.gov (United States)

    Schreier, Harold J; Mirzoyan, Natella; Saito, Keiko

    2010-06-01

    Development of environmentally sustainable farming of marine and freshwater species using recirculating aquaculture systems (RASs) requires a complete understanding of the biological component involved in wastewater treatment. This component integrates biofilters composed of microbial communities whose structure, dynamics, and activities are responsible for system success. Engineering highly efficient, environmentally sound, disease-free, and economically viable systems necessitates a thorough knowledge of microbial processes involved in all facets of RAS biofilters and has only recently been the focus of comprehensive studies. These studies have included the application of molecular tools to characterize community diversity and have identified key processes useful for improving system performance. In this paper we summarize the current understanding of the microbial diversity and physiology of RAS biofilters and discuss directions for future studies. PMID:20371171

  4. An easy iris center detection method for eye gaze tracking system

    OpenAIRE

    Yu, Mingxin; Lin, Yingzi; Tang, Xiaoying; Xu, Jing; Schmidt, David; Wang, Xiangzhou; Guo, Yikang

    2015-01-01

    Iris center detection accuracy has great impact on eye gaze tracking system performance. This paper proposes an easy and efficient iris center detection method based on modeling the geometric relationship between the detected rough iris center and the two corners of the eye. The method fully considers four states of iris within the eye region, i.e. center, left, right, and upper. The proposed active edge detection algorithm is utilized to extract iris edge points for ellipse fitting. In addit...

  5. Community control of health services. Dr. Martin Luther King, Jr. Health Center's community management system.

    Science.gov (United States)

    Tichy, N M; Taylor, J I

    1976-01-01

    This article presents the case of Dr. Martin Luther King Jr. Health Center's unique community management system in which neighborhood workers have been developed to assume managerial responsibilities and are directing the Center. The Martin Luther King Center experience is instructive because the Center was able to achieve significant community control by focusing primarily on the internal dimension of control, namely, management, without experiencing destructive conflicts and the deterioration of health services.

  6. 23 CFR 752.8 - Privately operated information centers and systems.

    Science.gov (United States)

    2010-04-01

    ...) The State shall have title to the information center or system upon completion of construction or... national origin. (7) The center or system shall be adequately maintained and kept clean and sanitary. (8... system in the interests of the public. (9) The State may terminate the lease or agreement for...

  7. It is time to talk about people: a human-centered healthcare system

    Directory of Open Access Journals (Sweden)

    Borgi Lea

    2010-11-01

    Full Text Available Abstract Examining vulnerabilities within our current healthcare system we propose borrowing two tools from the fields of engineering and design: a Reason's system approach 1 and b User-centered design 23. Both approaches are human-centered in that they consider common patterns of human behavior when analyzing systems to identify problems and generate solutions. This paper examines these two human-centered approaches in the context of healthcare. We argue that maintaining a human-centered orientation in clinical care, research, training, and governance is critical to the evolution of an effective and sustainable healthcare system.

  8. Low angle neutron data acquisition system for molecular biology

    International Nuclear Information System (INIS)

    The low angle spectrometer system utilizing a 2-dimensional position sensitive counter was designed to accommodate a variety of experiments in molecular biology requiring good low angle resolution. Biological structures requiring low angle analysis techniques fall into two groups: non-ordered systems (proteins or protein complexes in solution) and ordered systems with large spacings like muscle, collagen, and membranes. For structural investigations into such systems, data are ideally needed to a low scattering angle of 0.20 at 4.5 A or a minimum Q of 0.005 A-1 (Q = theta . 2π/lambda). Depending on the type of structure, data often extend to the high angle region, say 300. Apart from the low angle requirements, the spectrometer has to have good resolution to resolve diffraction peaks from samples with crystal spacings up to 1000 A or even larger. While it is desirable to build a spectrometer to such scattering conditions, given reactor conditions might not permit this and compromises have to be made between flux, resolution and lowest angle. The low angle spectrometer described here was designed to be used at the HFBR neutron beam pipe working at approximately 4.2 A or at the H4 satellite station working at 2.4 A

  9. Systems Biology and P4 Medicine: Past, Present, and Future

    Directory of Open Access Journals (Sweden)

    Leroy Hood

    2013-04-01

    Full Text Available Studying complex biological systems in a holistic rather than a “one gene or one protein” at a time approach requires the concerted effort of scientists from a wide variety of disciplines. The Institute for Systems Biology (ISB has seamlessly integrated these disparate fields to create a cross-disciplinary platform and culture in which “biology drives technology drives computation.” To achieve this platform/culture, it has been necessary for cross-disciplinary ISB scientists to learn one another’s languages and work together effectively in teams. The focus of this “systems” approach on disease has led to a discipline denoted systems medicine. The advent of technological breakthroughs in the fields of genomics, proteomics, and, indeed, the other “omics” is catalyzing striking advances in systems medicine that have and are transforming diagnostic and therapeutic strategies. Systems medicine has united genomics and genetics through family genomics to more readily identify disease genes. It has made blood a window into health and disease. It is leading to the stratification of diseases (division into discrete subtypes for proper impedance match against drugs and the stratification of patients into subgroups that respond to environmental challenges in a similar manner (e.g. response to drugs, response to toxins, etc.. The convergence of patient-activated social networks, big data and their analytics, and systems medicine has led to a P4 medicine that is predictive, preventive, personalized, and participatory. Medicine will focus on each individual. It will become proactive in nature. It will increasingly focus on wellness rather than disease. For example, in 10 years each patient will be surrounded by a virtual cloud of billions of data points, and we will have the tools to reduce this enormous data dimensionality into simple hypotheses about how to optimize wellness and avoid disease for each individual. P4 medicine will be able to

  10. Multimode lasers as analogs of complex biological systems (a survey)

    Science.gov (United States)

    Danilov, O. B.; Rosanov, N. N.; Solov'ev, N. A.; Soms, L. N.

    2016-04-01

    Simulating the activity of complex biological systems, in particular, the human brain, is a topical problem the solution of which is necessary both for understanding their functioning and for developing new classes of computational system based on operating principles of the brain. Some features and analogies that can be found in the operation of laser systems and brain and used for developing new generation computational systems are discussed. The appropriateness of such analogies is justified by the fact that both laser systems and the brain are open (interacting with the environment) dissipative spatially distributed nonlinear systems. Therefore, laser optical systems and, in particular, systems with dissipative optical solitons offer an opportunity to experimentally and theoretically model some important cognitive brain functions. One of particularities of the brain operation is the ability to manipulate images. Proceeding from this, in this work, problems related to generation and amplification with laser of spatial structures (images), as well as to amplification of signals coming to it from outside are discussed.

  11. External noise control in inherently stochastic biological systems.

    Science.gov (United States)

    Zheng, Likun; Chen, Meng; Nie, Qing

    2012-11-01

    Biological systems are often subject to external noise from signal stimuli and environmental perturbations, as well as noises in the intracellular signal transduction pathway. Can different stochastic fluctuations interact to give rise to new emerging behaviors? How can a system reduce noise effects while still being capable of detecting changes in the input signal? Here, we study analytically and computationally the role of nonlinear feedback systems in controlling external noise with the presence of large internal noise. In addition to noise attenuation, we analyze derivatives of Fano factor to study systems' capability of differentiating signal inputs. We find effects of internal noise and external noise may be separated in one slow positive feedback loop system; in particular, the slow loop can decrease external noise and increase robustness of signaling with respect to fluctuations in rate constants, while maintaining the signal output specific to the input. For two feedback loops, we demonstrate that the influence of external noise mainly depends on how the fast loop responds to fluctuations in the input and the slow loop plays a limited role in determining the signal precision. Furthermore, in a dual loop system of one positive feedback and one negative feedback, a slower positive feedback always leads to better noise attenuation; in contrast, a slower negative feedback may not be more beneficial. Our results reveal interesting stochastic effects for systems containing both extrinsic and intrinsic noises, suggesting novel noise filtering strategies in inherently stochastic systems. PMID:23213267

  12. Modeling biological systems with delays in Bio-PEPA

    CERN Document Server

    Caravagna, Giulio; 10.4204/EPTCS.40.7

    2010-01-01

    Delays in biological systems may be used to model events for which the underlying dynamics cannot be precisely observed, or to provide abstraction of some behavior of the system resulting more compact models. In this paper we enrich the stochastic process algebra Bio-PEPA, with the possibility of assigning delays to actions, yielding a new non-Markovian process algebra: Bio-PEPAd. This is a conservative extension meaning that the original syntax of Bio-PEPA is retained and the delay specification which can now be associated with actions may be added to existing Bio-PEPA models. The semantics of the firing of the actions with delays is the delay-as-duration approach, earlier presented in papers on the stochastic simulation of biological systems with delays. These semantics of the algebra are given in the Starting-Terminating style, meaning that the state and the completion of an action are observed as two separate events, as required by delays. Furthermore we outline how to perform stochastic simulation of Bio...

  13. Casual Games and Casual Learning About Human Biological Systems

    Science.gov (United States)

    Price, C. Aaron; Gean, Katherine; Christensen, Claire G.; Beheshti, Elham; Pernot, Bryn; Segovia, Gloria; Person, Halcyon; Beasley, Steven; Ward, Patricia

    2016-02-01

    Casual games are everywhere. People play them throughout life to pass the time, to engage in social interactions, and to learn. However, their simplicity and use in distraction-heavy environments can attenuate their potential for learning. This experimental study explored the effects playing an online, casual game has on awareness of human biological systems. Two hundred and forty-two children were given pretests at a Museum and posttests at home after playing either a treatment or control game. Also, 41 children were interviewed to explore deeper meanings behind the test results. Results show modest improvement in scientific attitudes, ability to identify human biological systems and in the children's ability to describe how those systems work together in real-world scenarios. Interviews reveal that children drew upon their prior school learning as they played the game. Also, on the surface they perceived the game as mainly entertainment but were easily able to discern learning outcomes when prompted. Implications for the design of casual games and how they can be used to enhance transfer of knowledge from the classroom to everyday life are discussed.

  14. StochKit-FF: Efficient Systems Biology on Multicore Architectures

    CERN Document Server

    Aldinucci, Marco; Liò, Pietro; Sorathiya, Anil; Torquati, Massimo

    2010-01-01

    The stochastic modelling of biological systems is an informative, and in some cases, very adequate technique, which may however result in being more expensive than other modelling approaches, such as differential equations. We present StochKit-FF, a parallel version of StochKit, a reference toolkit for stochastic simulations. StochKit-FF is based on the FastFlow programming toolkit for multicores and exploits the novel concept of selective memory. We experiment StochKit-FF on a model of HIV infection dynamics, with the aim of extracting information from efficiently run experiments, here in terms of average and variance and, on a longer term, of more structured data.

  15. Text mining and its potential applications in systems biology.

    Science.gov (United States)

    Ananiadou, Sophia; Kell, Douglas B; Tsujii, Jun-ichi

    2006-12-01

    With biomedical literature increasing at a rate of several thousand papers per week, it is impossible to keep abreast of all developments; therefore, automated means to manage the information overload are required. Text mining techniques, which involve the processes of information retrieval, information extraction and data mining, provide a means of solving this. By adding meaning to text, these techniques produce a more structured analysis of textual knowledge than simple word searches, and can provide powerful tools for the production and analysis of systems biology models. PMID:17045684

  16. The Search for Covalently Ligandable Proteins in Biological Systems.

    Science.gov (United States)

    Badshah, Syed Lal; Mabkhot, Yahia Nasser

    2016-01-01

    This commentary highlights the recent article published in Nature, June 2016, titled: "Proteome-wide covalent ligand discovery in native biological systems". They screened the whole proteome of different human cell lines and cell lysates. Around 700 druggable cysteines in the whole proteome were found to bind the electrophilic fragments in both active and inactive states of the proteins. Their experiment and computational docking results agreed with one another. The usefulness of this study in terms of bringing a change in medicinal chemistry is highlighted here. PMID:27598117

  17. Caenorhabditis elegans - A model system for space biology studies

    Science.gov (United States)

    Johnson, Thomas E.; Nelson, Gregory A.

    1991-01-01

    The utility of the nematode Caenorhabditis elegans in studies spanning aspects of development, aging, and radiobiology is reviewed. These topics are interrelated via cellular and DNA repair processes especially in the context of oxidative stress and free-radical metabolism. The relevance of these research topics to problems in space biology is discussed and properties of the space environment are outlined. Exposure to the space-flight environment can induce rapid changes in living systems that are similar to changes occurring during aging; manipulation of these environmental parameters may represent an experimental strategy for studies of development and senescence. The current and future opportunities for such space-flight experimentation are presented.

  18. Rigid Biological Systems as Models for Synthetic Composites

    Science.gov (United States)

    Mayer, George

    2005-11-01

    Advances that have been made in understanding the mechanisms underlying the mechanical behavior of a number of biological materials (namely mollusk shells and sponge spicules) are discussed here. Attempts at biomimicry of the structure of a nacreous layer of a mollusk shell have shown reasonable success. However, they have revealed additional issues that must be addressed if new synthetic composite materials that are based on natural systems are to be constructed. Some of the important advantages and limitations of copying from nature are also described here.

  19. A complex systems approach to computational molecular biology

    Energy Technology Data Exchange (ETDEWEB)

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

    1993-09-01

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

  20. From experimental systems to evolutionary biology: an impossible journey?

    Science.gov (United States)

    Morange, Michel

    2013-01-01

    The historical approach to the sciences has undergone a sea change during recent decades. Maybe the major contribution of Hans-Jörg Rheinberger to this movement was his demonstration of the importance of experimental systems, and of their transformations, in the development of the sciences. To describe these transformations, Hans-Jörg borrows metaphors from evolutionary biology. I want to argue that evolutionary biologists can find in these recent historical studies plenty of models and concepts to address unresolved issues in their discipline. At a time when transdisciplinarity is highly praised, it is useful to provide a precise description of the obstacles that have so far prevented this exchange.

  1. TissueCypher™: A systems biology approach to anatomic pathology

    Directory of Open Access Journals (Sweden)

    Jeffrey W Prichard

    2015-01-01

    Full Text Available Background: Current histologic methods for diagnosis are limited by intra- and inter-observer variability. Immunohistochemistry (IHC methods are frequently used to assess biomarkers to aid diagnoses, however, IHC staining is variable and nonlinear and the manual interpretation is subjective. Furthermore, the biomarkers assessed clinically are typically biomarkers of epithelial cell processes. Tumors and premalignant tissues are not composed only of epithelial cells but are interacting systems of multiple cell types, including various stromal cell types that are involved in cancer development. The complex network of the tissue system highlights the need for a systems biology approach to anatomic pathology, in which quantification of system processes is combined with informatics tools to produce actionable scores to aid clinical decision-making. Aims: Here, we describe a quantitative, multiplexed biomarker imaging approach termed TissueCypher™ that applies systems biology to anatomic pathology. Applications of TissueCypher™ in understanding the tissue system of Barrett's esophagus (BE and the potential use as an adjunctive tool in the diagnosis of BE are described. Patients and Methods: The TissueCypher™ Image Analysis Platform was used to assess 14 epithelial and stromal biomarkers with known diagnostic significance in BE in a set of BE biopsies with nondysplastic BE with reactive atypia (RA, n = 22 and Barrett's with high-grade dysplasia (HGD, n = 17. Biomarker and morphology features were extracted and evaluated in the confirmed BE HGD cases versus the nondysplastic BE cases with RA. Results: Multiple image analysis features derived from epithelial and stromal biomarkers, including immune biomarkers and morphology, showed significant differences between HGD and RA. Conclusions: The assessment of epithelial cell abnormalities combined with an assessment of cellular changes in the lamina propria may serve as an adjunct to conventional

  2. Computational Systems Biology of Psoriasis: Are We Ready for the Age of Omics and Systems Biomarkers?

    Science.gov (United States)

    Sevimoglu, Tuba; Arga, Kazim Yalcin

    2015-11-01

    Computational biology and 'omics' systems sciences are greatly impacting research on common diseases such as cancer. By contrast, dermatology covering an array of skin diseases with high prevalence in society, has received relatively less attention from 'omics' and computational biosciences. We are focusing on psoriasis, a common and debilitating autoimmune disease involving skin and joints. Using computational systems biology and reconstruction, topological, modular, and a novel correlational analyses (based on fold changes) of biological and transcriptional regulatory networks, we analyzed and integrated data from a total of twelve studies from the Gene Expression Omnibus (sample size = 534). Samples represented a comprehensive continuum from lesional and nonlesional skin, as well as bone marrow and dermal mesenchymal stem cells. We identified and propose here a JAK/STAT signaling pathway significant for psoriasis. Importantly, cytokines, interferon-stimulated genes, antimicrobial peptides, among other proteins, were involved in intrinsic parts of the proposed pathway. Several biomarker and therapeutic candidates such as SUB1 are discussed for future experimental studies. The integrative systems biology approach presented here illustrates a comprehensive perspective on the molecular basis of psoriasis. This also attests to the promise of systems biology research in skin diseases, with psoriasis as a systemic component. The present study reports, to the best of our knowledge, the largest set of microarray datasets on psoriasis, to offer new insights into the disease mechanisms with a proposal of a disease pathway. We call for greater computational systems biology research and analyses in dermatology and skin diseases in general.

  3. Human-centered design of the human-system interfaces of medical equipment: thyroid uptake system

    Energy Technology Data Exchange (ETDEWEB)

    Monteiro, Jonathan K.R.; Farias, Marcos S.; Santos, Isaac J.A. Luquetti, E-mail: luquetti@ien.gov.br [Instituto de Engenharia Nuclear (IEN/CNEN-RJ), Rio de Janeiro, RJ (Brazil); Monteiro, Beany G. [Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ (Brazil). Dept. de Desenho Industrial

    2013-07-01

    Technology plays an important role in modern medical centers, making healthcare increasingly complex, relying on complex technical equipment. This technical complexity is particularly noticeable in the nuclear medicine. Poorly design human-system interfaces can increase the risks for human error. The human-centered approach emphasizes the development of the equipment with a deep understanding of the users activities, current work practices, needs and abilities of the users. An important concept of human-centered design is that the ease-of-use of the equipment can be ensured only if users are actively incorporated in all phases of the life cycle of design process. Representative groups of users are exposed to the equipment at various stages in development, in a variety of testing, evaluation and interviewing situations. The users feedback obtained is then used to refine the design, with the result serving as input to the next interaction of design process. The limits of the approach are that the users cannot address any particular future needs without prior experience or knowledge about the equipment operation. The aim of this paper is to present a methodological framework that contributes to the design of the human-system interfaces, through an approach related to the users and their activities. A case study is described in which the methodological framework is being applied in development of new human-system interfaces of the thyroid uptake system. (author)

  4. Staff roster for 1979: National Center for Analysis of Energy Systems

    Energy Technology Data Exchange (ETDEWEB)

    1980-01-01

    This publication is a compilation of resumes from the current staff of the National Center for Analysis of Energy Systems. The Center, founded in January 1976, is one of four areas within the Department of Energy and Environment at Brookhaven National Laboratory. The emphasis of programs at the Center is on energy policy and planning studies at the regional, national, and international levels, involving quantitative, interdisciplinary studies of the technological, economic, social, and environmental aspects of energy systems. To perform these studies the Center has assembled a staff of experts in the areas of science, technology, economics planning, health and safety, information systems, and quantitative analysis.

  5. Recent insights into the biological activities and drug delivery systems of tanshinones

    Directory of Open Access Journals (Sweden)

    Cai Y

    2016-01-01

    Full Text Available Yuee Cai,1,* Wenji Zhang,2,* Zirong Chen,3 Zhi Shi,1,2 Chengwei He,1 Meiwan Chen1 1State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, People’s Republic of China; 2Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, People’s Republic of China; 3Department of Molecular Genetics and Microbiology, Shands Cancer Center, University of Florida, Gainesville, FL, USA *These authors contributed equally to this work Abstract: Tanshinones, the major lipid-soluble pharmacological constituents of the Chinese medicinal herb Tanshen (Salvia miltiorrhiza, have attracted growing scientific attention because of the prospective biomedical applications of these compounds. Numerous pharmacological activities, including anti-inflammatory, anticancer, and cardio-cerebrovascular protection activities, are exhibited by the three primary bioactive constituents among the tanshinones, ie, tanshinone I (TNI, tanshinone IIA (TNIIA, and cryptotanshinone (CPT. However, due to their poor solubility and low dissolution rate, the clinical applications of TNI, TNIIA, and CPT are limited. To solve these problems, many studies have focused on loading tanshinones into liposomes, nanoparticles, microemulsions, cyclodextrin inclusions, solid dispersions, and so on. In this review, we aim to offer an updated summary of the biological activities and drug delivery systems of tanshinones to provide a reference for these constituents in clinical applications. Keywords: tanshinones, biological activities, drug delivery systems, bioavailability, solubility

  6. Systems biology applied to vaccine and immunotherapy development

    Directory of Open Access Journals (Sweden)

    Marincola Francesco M

    2011-09-01

    Full Text Available Abstract Immunotherapies, including vaccines, represent a potent tool to prevent or contain disease with high morbidity or mortality such as infections and cancer. However, despite their widespread use, we still have a limited understanding of the mechanisms underlying the induction of protective immune responses. Immunity is made of a multifaceted set of integrated responses involving a dynamic interaction of thousands of molecules; among those is a growing appreciation for the role the innate immunity (i.e. pathogen recognition receptors - PRRs plays in determining the nature and duration (immune memory of adaptive T and B cell immunity. The complex network of interactions between immune manipulation of the host (immunotherapy on one side and innate and adaptive responses on the other might be fully understood only employing the global level of investigation provided by systems biology. In this framework, the advancement of high-throughput technologies, together with the extensive identification of new genes, proteins and other biomolecules in the "omics" era, facilitate large-scale biological measurements. Moreover, recent development of new computational tools enables the comprehensive and quantitative analysis of the interactions between all of the components of immunity over time. Here, we review recent progress in using systems biology to study and evaluate immunotherapy and vaccine strategies for infectious and neoplastic diseases. Multi-parametric data provide novel and often unsuspected mechanistic insights while enabling the identification of common immune signatures relevant to human investigation such as the prediction of immune responsiveness that could lead to the improvement of the design of future immunotherapy trials. Thus, the paradigm switch from "empirical" to "knowledge-based" conduct of medicine and immunotherapy in particular, leading to patient-tailored treatment.

  7. Strategies for the reduction of Legionella in biological treatment systems.

    Science.gov (United States)

    Nogueira, R; Utecht, K-U; Exner, M; Verstraete, W; Rosenwinkel, K-H

    2016-01-01

    A community-wide outbreak of Legionnaire's disease occurred in Warstein, Germany, in August 2013. The epidemic strain, Legionella pneumophila Serogruppe 1, was isolated from an industrial wastewater stream entering the municipal wastewater treatment plant (WWTP) in Wartein, the WWTP itself, the river Wäster and air/water samples from an industrial cooling system 3 km downstream of the WWTP. The present study investigated the effect of physical-chemical disinfection methods on the reduction of the concentration of Legionella in the biological treatment and in the treated effluent entering the river Wäster. Additionally, to gain insight into the factors that promote the growth of Legionella in biological systems, growth experiments were made with different substrates and temperatures. The dosage rates of silver micro-particles, hydrogen peroxide, chlorine dioxide and ozone and pH stress to the activated sludge were not able to decrease the number of culturable Legionella spp. in the effluent. Nevertheless, the UV treatment of secondary treated effluent reduced Legionella spp. on average by 1.6-3.4 log units. Laboratory-scale experiments and full-scale measurements suggested that the aerobic treatment of warm wastewater (30-35 °C) rich in organic nitrogen (protein) is a possible source of Legionella infection. PMID:27533856

  8. Mathematical and Statistical Modeling in Cancer Systems Biology

    Directory of Open Access Journals (Sweden)

    Rachael eHageman Blair

    2012-06-01

    Full Text Available Cancer is a major health problem with high mortality rates. In the post-genome era, investigators have access to massive amounts of rapidly accumulating high-throughput data in publicly available databases, some of which are exclusively devoted to housing Cancer data. However, data interpretation efforts have not kept pace with data collection, and gained knowledge is not necessarily translating into better diagnoses and treatments. A fundamental problem is to integrate and interpret data to further our understanding in Cancer Systems Biology. Viewing cancer as a network provides insights into the complex mechanisms underlying the disease. Mathematical and statistical models provide an avenue for cancer network modeling. In this article, we review two widely used modeling paradigms: deterministic metabolic models and statistical graphical models. The strength of these approaches lies in their flexibility and predictive power. Once a model has been validated, it can be used to make predictions and generate hypotheses. We describe a number of diverse applications to Cancer Biology, including, the system-wide effects of drug-treatments, disease prognosis, tumor classification, forecasting treatment outcomes, and survival predictions.

  9. 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.

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

    International Nuclear Information System (INIS)

    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 H2S 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.)

  11. First Steps in Computational Systems Biology: A Practical Session in Metabolic Modeling and Simulation

    Science.gov (United States)

    Reyes-Palomares, Armando; Sanchez-Jimenez, Francisca; Medina, Miguel Angel

    2009-01-01

    A comprehensive understanding of biological functions requires new systemic perspectives, such as those provided by systems biology. Systems biology approaches are hypothesis-driven and involve iterative rounds of model building, prediction, experimentation, model refinement, and development. Developments in computer science are allowing for ever…

  12. 20 CFR 670.535 - Are Job Corps centers required to establish behavior management systems?

    Science.gov (United States)

    2010-04-01

    ... behavior management systems? 670.535 Section 670.535 Employees' Benefits EMPLOYMENT AND TRAINING... Activities and Center Operations § 670.535 Are Job Corps centers required to establish behavior management... behavior management system, according to procedures established by the Secretary. The behavior...

  13. Strategies for structuring interdisciplinary education in Systems Biology: an European perspective

    NARCIS (Netherlands)

    Cvijovic, Marija; Höfer, Thomas; Acimovic, Jure; Alberghina, Lilia; Almaas, Eivind; Besozzi, Daniela; Blomberg, Anders; Bretschneider, Till; Cascante, Marta; Collin, Olivier; Atauri, de Pedro; Depner, Cornelia; Dickinson, Robert; Dobrzynski, Maciej; Fleck, C.; Garcia-Ojalvo, Jordi; Gonze, Didier; Hahn, Jens; Hess, Heide Marie; Hollmann, Susanne; Krantz, Marcus; Kummer, Ursula; Lundh, Torbjörn; Martial, Gifta; Martins dos Santos, V.A.P.; Mauer-Oberthür, Angela; Regierer, Babette; Skene, Barbara; Stalidzans, Egils; Stelling, Jörg; Teusink, Bas; Workman, Christopher T.; Hohmann, Stefan

    2016-01-01

    Systems Biology is an approach to biology and medicine that has the potential to lead to a better understanding of how biological properties emerge from the interaction of genes, proteins, molecules, cells and organisms. The approach aims at elucidating how these interactions govern biological funct

  14. Internal communications program expands at Salina Regional Health Center as the health system grows.

    Science.gov (United States)

    Herreria, J

    1999-01-01

    The e-mail system is evolving into one of Salina, Kan., Regional Health Center's primary sources of communications for its 1,350 employees and physicians. Check out how the health system uses other internal communication tools. PMID:10387297

  15. Complex systems of biological interest stability under ionising radiations

    International Nuclear Information System (INIS)

    This PhD work presents the study of stability of molecular systems of biological interest in the gas phase after interaction with ionising radiations. The use of ionising radiation can probe the physical chemistry of complex systems at the molecular scale and thus consider their intrinsic properties. Beyond the fundamental aspect, this work is part of the overall understanding of radiation effects on living organisms and in particular the use of ionizing radiation in radiotherapy. Specifically, this study focused on the use of low-energy multiply charged ions (tens of keV) provided by the GANIL (Caen), which includes most of the experiments presented. In addition, experiments using VUV photons were also conducted at synchrotron ELETTRA (Trieste, Italy). The bio-molecular systems studied are amino acids and nucleic acid constituents. Using an experimental crossed beams device allows interaction between biomolecules and ionising radiation leads mainly to the ionization and fragmentation of the system. The study of its relaxation dynamics is by time-of-flight mass spectrometry coupled to a coincidences measurements method. It is shown that an approach combining experiment and theory allows a detailed study of the fragmentation dynamics of complex systems. The results indicate that fragmentation is generally governed by the Coulomb repulsion but the intramolecular rearrangements involve specific relaxation mechanisms. (author)

  16. Bridging Mechanistic and Phenomenological Models of Complex Biological Systems

    Science.gov (United States)

    Transtrum, Mark K.; Qiu, Peng

    2016-01-01

    The inherent complexity of biological systems gives rise to complicated mechanistic models with a large number of parameters. On the other hand, the collective behavior of these systems can often be characterized by a relatively small number of phenomenological parameters. We use the Manifold Boundary Approximation Method (MBAM) as a tool for deriving simple phenomenological models from complicated mechanistic models. The resulting models are not black boxes, but remain expressed in terms of the microscopic parameters. In this way, we explicitly connect the macroscopic and microscopic descriptions, characterize the equivalence class of distinct systems exhibiting the same range of collective behavior, and identify the combinations of components that function as tunable control knobs for the behavior. We demonstrate the procedure for adaptation behavior exhibited by the EGFR pathway. From a 48 parameter mechanistic model, the system can be effectively described by a single adaptation parameter τ characterizing the ratio of time scales for the initial response and recovery time of the system which can in turn be expressed as a combination of microscopic reaction rates, Michaelis-Menten constants, and biochemical concentrations. The situation is not unlike modeling in physics in which microscopically complex processes can often be renormalized into simple phenomenological models with only a few effective parameters. The proposed method additionally provides a mechanistic explanation for non-universal features of the behavior. PMID:27187545

  17. Comparison of Three Systems for Biological Greywater Treatment

    Directory of Open Access Journals (Sweden)

    Lucía Hernández Leal

    2010-04-01

    Full Text Available Greywater consists of household wastewater excluding toilet discharges. Three systems were compared for the biological treatment of greywater at a similar hydraulic retention time of approximately 12–13 hours. These systems were aerobic treatment in a sequencing batch reactor, anaerobic treatment in an up-flow anaerobic blanket reactor and combined anaerobic-aerobic treatment (up-flow anaerobic blanket reactor + sequencing batch reactor. Aerobic conditions resulted in a COD removal of 90%, which was significantly higher than 51% removal by anaerobic treatment. The low removal in the anaerobic reactor may have been caused by high concentration of anionic surfactants in the influent (43.5 mg/L and a poor removal of the colloidal fraction of the COD in up-flow anaerobic sludge blanket reactors. Combined aerobic-anaerobic treatment accomplished a COD removal of 89%, similar to the aerobic treatment alone. Greywater methanization was 32% for the anaerobic system and 25% for the anaerobic-aerobic system, yielding a small amount of energy. Therefore, anaerobic pre-treatment is not feasible and an aerobic system is preferred for the treatment of greywater.

  18. Bridging Mechanistic and Phenomenological Models of Complex Biological Systems.

    Directory of Open Access Journals (Sweden)

    Mark K Transtrum

    2016-05-01

    Full Text Available The inherent complexity of biological systems gives rise to complicated mechanistic models with a large number of parameters. On the other hand, the collective behavior of these systems can often be characterized by a relatively small number of phenomenological parameters. We use the Manifold Boundary Approximation Method (MBAM as a tool for deriving simple phenomenological models from complicated mechanistic models. The resulting models are not black boxes, but remain expressed in terms of the microscopic parameters. In this way, we explicitly connect the macroscopic and microscopic descriptions, characterize the equivalence class of distinct systems exhibiting the same range of collective behavior, and identify the combinations of components that function as tunable control knobs for the behavior. We demonstrate the procedure for adaptation behavior exhibited by the EGFR pathway. From a 48 parameter mechanistic model, the system can be effectively described by a single adaptation parameter τ characterizing the ratio of time scales for the initial response and recovery time of the system which can in turn be expressed as a combination of microscopic reaction rates, Michaelis-Menten constants, and biochemical concentrations. The situation is not unlike modeling in physics in which microscopically complex processes can often be renormalized into simple phenomenological models with only a few effective parameters. The proposed method additionally provides a mechanistic explanation for non-universal features of the behavior.

  19. Systems of organic farming in spring vetch I: Biological response of sucking insect pests

    OpenAIRE

    Ivelina Nikolova; Natalia Georgieva

    2015-01-01

    Four systems of organic farming and a conventional farming system were studied over the period 2012-2014. The organic system trial variants included: I - an organic farming system without any biological products used (growth under natural soil fertility) - Control; II - an organic farming system involving the use of a biological foliar fertilizer and a biological plant growth regulator (Polyversum+Biofa); III - an organic farming system in which a biologica...

  20. Evolutionary systems biology of amino acid biosynthetic cost in yeast.

    Directory of Open Access Journals (Sweden)

    Michael D Barton

    Full Text Available Every protein has a biosynthetic cost to the cell based on the synthesis of its constituent amino acids. In order to optimise growth and reproduction, natural selection is expected, where possible, to favour the use of proteins whose constituents are cheaper to produce, as reduced biosynthetic cost may confer a fitness advantage to the organism. Quantifying the cost of amino acid biosynthesis presents challenges, since energetic requirements may change across different cellular and environmental conditions. We developed a systems biology approach to estimate the cost of amino acid synthesis based on genome-scale metabolic models and investigated the effects of the cost of amino acid synthesis on Saccharomyces cerevisiae gene expression and protein evolution. First, we used our two new and six previously reported measures of amino acid cost in conjunction with codon usage bias, tRNA gene number and atomic composition to identify which of these factors best predict transcript and protein levels. Second, we compared amino acid cost with rates of amino acid substitution across four species in the genus Saccharomyces. Regardless of which cost measure is used, amino acid biosynthetic cost is weakly associated with transcript and protein levels. In contrast, we find that biosynthetic cost and amino acid substitution rates show a negative correlation, but for only a subset of cost measures. In the economy of the yeast cell, we find that the cost of amino acid synthesis plays a limited role in shaping transcript and protein expression levels compared to that of translational optimisation. Biosynthetic cost does, however, appear to affect rates of amino acid evolution in Saccharomyces, suggesting that expensive amino acids may only be used when they have specific structural or functional roles in protein sequences. However, as there appears to be no single currency to compute the cost of amino acid synthesis across all cellular and environmental

  1. Molecular eco-systems biology: towards an understanding of community function

    OpenAIRE

    Raes, J.; Bork, P.

    2008-01-01

    Systems-biology approaches, which are driven by genome sequencing and high-throughput functional genomics data, are revolutionizing single-cell-organism biology. With the advent of various high-throughput techniques that aim to characterize complete microbial ecosystems (metagenomics, meta-transcriptomics and meta-metabolomics), we propose that the time is ripe to consider molecular systems biology at the ecosystem level (eco-systems biology). Here, we discuss the necessary data types that ar...

  2. SENVM: Server Environment Monitoring and Controlling System for a Small Data Center Using Wireless Sensor Network

    CERN Document Server

    Choochaisri, Supasate; Jenjaturong, Saran; Intanagonwiwat, Chalermek; Ratanamahatana, Chotirat Ann

    2011-01-01

    In recent years, efficient energy utilization becomes an essential requirement for data centers, especially in data centers of world-leading companies, where "Green Data Center" defines a new term for an environment-concerned data center. Solutions to change existing a data center to the green one may vary. In the big company, high-cost approaches including re-planning server rooms, changing air-conditioners, buying low-powered servers, and equipping sophisticating environmental control equipments are possible, but not for small to medium enterprises (SMEs) and academic sectors which have limited budget. In this paper, we propose a novel system, SENVM, used to monitor and control air temperature in a server room to be in appropriate condition, not too cold, where very unnecessary cooling leads to unnecessary extra electricity expenses, and also inefficient in energy utilization. With implementing on an emerging technology, Wireless Sensor Network (WSN), Green Data Center is feasible to every small data center...

  3. Entity grammar systems: a grammatical tool for studying the hierarchical structures of biological systems.

    Science.gov (United States)

    Wang, Yun

    2004-05-01

    The hierarchical structures of biological systems are the typical complex hierarchical dynamical structures in the physical world, the effective investigations on which could not be performed with the existing formal grammar systems. To meet the needs of the investigation on these kinds of systems, especially the emerging field of system biology, a grammatical tool was proposed in the present article. Because the grammatical tool mainly deals with the systems composed of structured entities, they are called entity grammar systems (EGSs). The structure of entities in EGSs have the general form of the objects in the physical world, which means EGSs could be used as a tool to study the complex system composed of many objects with different structures, just like the biological systems. The article contains the formal definition of EGSs and the hierarchy of EGSs, which is congruent with the Chomsky hierarchy. The relationship between EGSs and array grammar systems, graph grammar systems, tree grammar systems, multi-set grammar systems are discussed to show the generative power of EGSs. At the end of the present article, the steps to define new grammar systems with the form of EGS are provided and the possible applicable fields of EGSs are discussed. PMID:15006443

  4. From product centered design to value centered design: understanding the value-system

    DEFF Research Database (Denmark)

    Randmaa, Merili; Howard, Thomas J.; Otto, T.

    more value for the customer for less eford. Value and understanding the value-system needs to be in the focus of business strategy. Value can be created, exchanged and perceived. It can be tangible (physical products, money) or intangible (information, experience, relationships, service). Creating......Product design has focused on different parameters through history- design for usability, design for manufacturing, design for assembly etc. Today, as the products get bundled with service, it is important to interconnect product, service and business model design to create synergy effect and offer...

  5. Nutritional Systems Biology Modeling: From Molecular Mechanisms to Physiology

    Science.gov (United States)

    de Graaf, Albert A.; Freidig, Andreas P.; De Roos, Baukje; Jamshidi, Neema; Heinemann, Matthias; Rullmann, Johan A.C.; Hall, Kevin D.; Adiels, Martin; van Ommen, Ben

    2009-01-01

    The use of computational modeling and simulation has increased in many biological fields, but despite their potential these techniques are only marginally applied in nutritional sciences. Nevertheless, recent applications of modeling have been instrumental in answering important nutritional questions from the cellular up to the physiological levels. Capturing the complexity of today's important nutritional research questions poses a challenge for modeling to become truly integrative in the consideration and interpretation of experimental data at widely differing scales of space and time. In this review, we discuss a selection of available modeling approaches and applications relevant for nutrition. We then put these models into perspective by categorizing them according to their space and time domain. Through this categorization process, we identified a dearth of models that consider processes occurring between the microscopic and macroscopic scale. We propose a “middle-out” strategy to develop the required full-scale, multilevel computational models. Exhaustive and accurate phenotyping, the use of the virtual patient concept, and the development of biomarkers from “-omics” signatures are identified as key elements of a successful systems biology modeling approach in nutrition research—one that integrates physiological mechanisms and data at multiple space and time scales. PMID:19956660

  6. Nutritional systems biology modeling: from molecular mechanisms to physiology.

    Directory of Open Access Journals (Sweden)

    Albert A de Graaf

    2009-11-01

    Full Text Available The use of computational modeling and simulation has increased in many biological fields, but despite their potential these techniques are only marginally applied in nutritional sciences. Nevertheless, recent applications of modeling have been instrumental in answering important nutritional questions from the cellular up to the physiological levels. Capturing the complexity of today's important nutritional research questions poses a challenge for modeling to become truly integrative in the consideration and interpretation of experimental data at widely differing scales of space and time. In this review, we discuss a selection of available modeling approaches and applications relevant for nutrition. We then put these models into perspective by categorizing them according to their space and time domain. Through this categorization process, we identified a dearth of models that consider processes occurring between the microscopic and macroscopic scale. We propose a "middle-out" strategy to develop the required full-scale, multilevel computational models. Exhaustive and accurate phenotyping, the use of the virtual patient concept, and the development of biomarkers from "-omics" signatures are identified as key elements of a successful systems biology modeling approach in nutrition research--one that integrates physiological mechanisms and data at multiple space and time scales.

  7. Gene gymnastics: Synthetic biology for baculovirus expression vector system engineering.

    Science.gov (United States)

    Vijayachandran, Lakshmi S; Thimiri Govinda Raj, Deepak B; Edelweiss, Evelina; Gupta, Kapil; Maier, Josef; Gordeliy, Valentin; Fitzgerald, Daniel J; Berger, Imre

    2013-01-01

    Most essential activities in eukaryotic cells are catalyzed by large multiprotein assemblies containing up to ten or more interlocking subunits. The vast majority of these protein complexes are not easily accessible for high resolution studies aimed at unlocking their mechanisms, due to their low cellular abundance and high heterogeneity. Recombinant overproduction can resolve this bottleneck and baculovirus expression vector systems (BEVS) have emerged as particularly powerful tools for the provision of eukaryotic multiprotein complexes in high quality and quantity. Recently, synthetic biology approaches have begun to make their mark in improving existing BEVS reagents by de novo design of streamlined transfer plasmids and by engineering the baculovirus genome. Here we present OmniBac, comprising new custom designed reagents that further facilitate the integration of heterologous genes into the baculovirus genome for multiprotein expression. Based on comparative genome analysis and data mining, we herein present a blueprint to custom design and engineer the entire baculovirus genome for optimized production properties using a bottom-up synthetic biology approach. PMID:23328086

  8. Ultrasensitive Force Detection and Applications to Biological Systems

    Science.gov (United States)

    Kenny, Thomas

    2001-03-01

    For many years, researchers have developed a variety of micromechanical devices for a range of applications. The majority of these devices are based on micromechanical force transducers to convert external physical signals into electrical signals. The force sensing capabilities of these devices are remarkable - it is possible to design devices with force resolution ranging from milli-N to atto-N within this technology. In addition to the conventional applications for MEMS devices, it is possible to tailor these designs to allow interesting scientific measurements on biological systems. For example, there are active research communities investigating cellular adhesion, protein folding, and animal locomotion. In all of these cases, the basic questions are mechanical in nature, and direct force measurements can provide new insight. This talk will review some ongoing biological research that makes use of MEMS devices, and discuss opportunities for new directions. Collaborators on this research include : Yiching Liang, Robert Rudnitsky, Michael Bartsch, Robert Full, Kellar Autumn, James Nelson, Jim Spudich, and Mark Cutkosky This work is funded by NSF (XYZ on a Chip) and ONR MURI (Biomimetic Robots).

  9. Yeast prions: structure, biology, and prion-handling systems.

    Science.gov (United States)

    Wickner, Reed B; Shewmaker, Frank P; Bateman, David A; Edskes, Herman K; Gorkovskiy, Anton; Dayani, Yaron; Bezsonov, Evgeny E

    2015-03-01

    A prion is an infectious protein horizontally transmitting a disease or trait without a required nucleic acid. Yeast and fungal prions are nonchromosomal genes composed of protein, generally an altered form of a protein that catalyzes the same alteration of the protein. Yeast prions are thus transmitted both vertically (as genes composed of protein) and horizontally (as infectious proteins, or prions). Formation of amyloids (linear ordered β-sheet-rich protein aggregates with β-strands perpendicular to the long axis of the filament) underlies most yeast and fungal prions, and a single prion protein can have any of several distinct self-propagating amyloid forms with different biological properties (prion variants). Here we review the mechanism of faithful templating of protein conformation, the biological roles of these prions, and their interactions with cellular chaperones, the Btn2 and Cur1 aggregate-handling systems, and other cellular factors governing prion generation and propagation. Human amyloidoses include the PrP-based prion conditions and many other, more common amyloid-based diseases, several of which show prion-like features. Yeast prions increasingly are serving as models for the understanding and treatment of many mammalian amyloidoses. Patients with different clinical pictures of the same amyloidosis may be the equivalent of yeasts with different prion variants.

  10. Methods of 15N tracer research in biological systems

    International Nuclear Information System (INIS)

    The application of the stable isotope 15N is of increasing importance in different scientific disciplines, especially in medicine, agriculture, and the biosciences. The close correlation between the growing interest and improvements of analytical procedures resulted in remarkable advances in the 15N tracer technique. On the basis of the latest results of 15N tracer research in life sciences and agriculture methods of 15N tracer research in biological systems are compiled. The 15N methodology is considered under three headings: Chemical analysis with a description of methods of sample preparation (including different separation and isolation methods for N-containing substances of biological and agricultural origin) and special procedures converting ammonia to molecular nitrogen. Isotopic analysis with a review on the most important methods of isotopic analysis of nitrogen: mass spectrometry (including the GC-MS technique), emission spectrometry, NMR spectroscopy, and other analytical procedures. 15N-tracer techniques with a consideration of the role of the isotope dilution analysis as well as different labelling techniques and the mathematical interpretation of tracer data (modelling, N turnover experiments). In these chapters also sources of errors in chemical and isotopic analysis, the accuracy of the different methods and its importance on tracer experiments are discussed. Procedures for micro scale 15N analysis and aspects of 15N analysis on the level of natural abundance are considered. Furthermore some remarks on isotope effects in 15N tracer experiments are made. (author)

  11. Large-scale violation of detailed balance in biological systems

    Science.gov (United States)

    Broedersz, Chase; Battle, Christopher; Fakhri, Nikta; Mackintosh, Fred; Schmidt, Christopher

    2015-03-01

    Living systems are out of equilibrium. A fundamental manifestation of non-equilibrium dynamics in biological systems is the violation of detailed balance: at the microscopic level, enzymatic processes such as kinetic proofreading or molecular motor activity clearly violate detailed balance. We study how such non-equilibrium dynamics emerge at macroscopic scales in cellular assemblies. We measure the steady-state dynamics of two systems, beating flagella of Chlamydomonas reinhardtii and mechanosensitive primary cilia protruding from epithelial kidney cells. The flagellum exhibits clear non-equilibrium driving, whereas fluctuations in the primary cilium are difficult to differentiate from Brownian motion. We parameterize the shapes of the flagellum and primary cilium using a low-dimensional representation of their configuration phase space, and use the measured dynamics to infer the steady-state probability distributions and probability currents. For both the flagellum and the primary cilium we find significant, coherent circulating probability currents, demonstrating that these systems violate detailed balance at the mesoscopic scale.

  12. Systems biology of recombinant protein production using Bacillus megaterium.

    Science.gov (United States)

    Biedendieck, Rebekka; Borgmeier, Claudia; Bunk, Boyke; Stammen, Simon; Scherling, Christian; Meinhardt, Friedhelm; Wittmann, Christoph; Jahn, Dieter

    2011-01-01

    The Gram-negative bacterium Escherichia coli is the most widely used production host for recombinant proteins in both academia and industry. The Gram-positive bacterium Bacillus megaterium represents an increasingly used alternative for high yield intra- and extracellular protein synthesis. During the past two decades, multiple tools including gene expression plasmids and production strains have been developed. Introduction of free replicating and integrative plasmids into B. megaterium is possible via protoplasts transformation or transconjugation. Using His(6)- and StrepII affinity tags, the intra- or extracellular produced proteins can easily be purified in one-step procedures. Different gene expression systems based on the xylose controlled promoter P(xylA) and various phage RNA polymerase (T7, SP6, K1E) driven systems enable B. megaterium to produce up to 1.25g of recombinant protein per liter. Biomass concentrations of up to 80g/l can be achieved by high cell density cultivations in bioreactors. Gene knockouts and gene replacements in B. megaterium are possible via an optimized gene disruption system. For a safe application in industry, sporulation and protease-deficient as well as UV-sensitive mutants are available. With the help of the recently published B. megaterium genome sequence, it is possible to characterize bottle necks in the protein production process via systems biology approaches based on transcriptome, proteome, metabolome, and fluxome data. The bioinformatical platform (Megabac, http://www.megabac.tu-bs.de) integrates obtained theoretical and experimental data. PMID:21943898

  13. Electrical Measurement of Biological Oscillations in Unicellular Systems.

    Science.gov (United States)

    Giaever, Ivar; Linton, Michael; Halvorsrud, Ragnhild; Male, Tone

    1997-03-01

    Many different rhythms or oscillations exists in biological systems; the circadian rhythm is probably the best known, but other oscillations are also common. The slimemold Physarum is a classical example of ultradian oscillations occurring in a single multinucleated cell, and the period is a few minutes long. It is also reasonable well known that oscillations occur in yeast with a periods of a few minutes These oscillations result from the action of a single allosteric enzyme in the glycolytic pathway. We have recently discovered a new oscillating system in the Madin-Darby Canine Kidney (MDCK) epithelial cells that have a period of 2-3 hours, and at present the origin of these oscillations is unknown. All these systems have been studied for the first time using a biosensor that measures impedance changes caused by mammalian cells and is referred to as Electrical Cell-surface Impedance Sensing or ECIS for short. The characteristic behavior of these three systems will be contrasted and discussed in detail. In particular we will focus on how the oscillations can be induced, how long they persists, and finally the stability of the observed frequencies.

  14. Heat pump centered integrated community energy systems: system development. Georgia Institute of Technology final report

    Energy Technology Data Exchange (ETDEWEB)

    Wade, D.W.; Trammell, B.C.; Dixit, B.S.; McCurry, D.C.; Rindt, B.A.

    1979-12-01

    Heat Pump Centered-Integrated Community Energy Systems (HP-ICES) show the promise of utilizing low-grade thermal energy for low-quality energy requirements such as space heating and cooling. The Heat Pump - Wastewater Heat Recovery (HP-WHR) scheme is one approach to an HP-ICES that proposes to reclaim low-grade thermal energy from a community's wastewater effluent. This report develops the concept of an HP-WHR system, evaluates the potential performance and economics of such a system, and examines the potential for application. A thermodynamic performance analysis of a hypothetical system projects an overall system Coefficient of Performance (C.O.P.) of from 2.181 to 2.264 for waste-water temperatures varying from 50/sup 0/F to 80/sup 0/F. Primary energy source savings from the nationwide implementation of this system is projected to be 6.0 QUADS-fuel oil, or 8.5 QUADS - natural gas, or 29.7 QUADS - coal for the period 1980 to 2000, depending upon the type and mix of conventional space conditioning systems which could be displaced with the HP-WHR system. Site-specific HP-WHR system designs are presented for two application communities in Georgia. Performance analyses for these systems project annual cycle system C.O.P.'s of 2.049 and 2.519. Economic analysis on the basis of a life cycle cost comparison shows one site-specific system design to be cost competitive in the immediate market with conventional residential and light commercial HVAC systems. The second site-specific system design is shown through a similar economic analysis to be more costly than conventional systems due mainly to the current low energy costs for natural gas. It is anticipated that, as energy costs escalate, this HP-WHR system will also approach the threshold of economic viability.

  15. Unifying Human Centered Design and Systems Engineering for Human Systems Integration

    Science.gov (United States)

    Boy, Guy A.; McGovernNarkevicius, Jennifer

    2013-01-01

    Despite the holistic approach of systems engineering (SE), systems still fail, and sometimes spectacularly. Requirements, solutions and the world constantly evolve and are very difficult to keep current. SE requires more flexibility and new approaches to SE have to be developed to include creativity as an integral part and where the functions of people and technology are appropriately allocated within our highly interconnected complex organizations. Instead of disregarding complexity because it is too difficult to handle, we should take advantage of it, discovering behavioral attractors and the emerging properties that it generates. Human-centered design (HCD) provides the creativity factor that SE lacks. It promotes modeling and simulation from the early stages of design and throughout the life cycle of a product. Unifying HCD and SE will shape appropriate human-systems integration (HSI) and produce successful systems.

  16. Systems biology studies of Aspergilli - from sequence to science

    DEFF Research Database (Denmark)

    Andersen, Mikael Rørdam

    2008-01-01

    sequence analysis, exo-metabolomics, transcriptomics and classical genetics. With a special focus on the traits making one strain a high-yield citric acid producer and the other an efficient glucoamylase producer, a surprising number of co-enhancing factors were found on multiple levels of cellular...... of citric acid. Furthermore, a detailed transcriptome profiling of all of the genes of A. niger predicted to code for extracellular enzymes was made using a new literature-based graphical tool for analysis of the degradation targets of the enzymes. In conclusion, the versatility of a systems biology...... metabolism. Transcriptome profiling coupled with metabolic modeling further allowed the charting of the genome-wide regulation of A. niger in response to ambient pH in the context of organic acid production and a plausible explanation for the evolution of the capabilities to be a high-yield producer...

  17. Systems biology and bioinformatics in aging research: a workshop report.

    Science.gov (United States)

    Fuellen, Georg; Dengjel, Jörn; Hoeflich, Andreas; Hoeijemakers, Jan; Kestler, Hans A; Kowald, Axel; Priebe, Steffen; Rebholz-Schuhmann, Dietrich; Schmeck, Bernd; Schmitz, Ulf; Stolzing, Alexandra; Sühnel, Jürgen; Wuttke, Daniel; Vera, Julio

    2012-12-01

    In an "aging society," health span extension is most important. As in 2010, talks in this series of meetings in Rostock-Warnemünde demonstrated that aging is an apparently very complex process, where computational work is most useful for gaining insights and to find interventions that counter aging and prevent or counteract aging-related diseases. The specific topics of this year's meeting entitled, "RoSyBA: Rostock Symposium on Systems Biology and Bioinformatics in Ageing Research," were primarily related to "Cancer and Aging" and also had a focus on work funded by the German Federal Ministry of Education and Research (BMBF). The next meeting in the series, scheduled for September 20-21, 2013, will focus on the use of ontologies for computational research into aging, stem cells, and cancer. Promoting knowledge formalization is also at the core of the set of proposed action items concluding this report.

  18. Abstract Interpretation for Probabilistic Termination of Biological Systems

    CERN Document Server

    Gori, Roberta; 10.4204/EPTCS.11.9

    2009-01-01

    In a previous paper the authors applied the Abstract Interpretation approach for approximating the probabilistic semantics of biological systems, modeled specifically using the Chemical Ground Form calculus. The methodology is based on the idea of representing a set of experiments, which differ only for the initial concentrations, by abstracting the multiplicity of reagents present in a solution, using intervals. In this paper, we refine the approach in order to address probabilistic termination properties. More in details, we introduce a refinement of the abstract LTS semantics and we abstract the probabilistic semantics using a variant of Interval Markov Chains. The abstract probabilistic model safely approximates a set of concrete experiments and reports conservative lower and upper bounds for probabilistic termination.

  19. Comparative Pathogenesis and Systems Biology for Biodefense Virus Vaccine Development

    Directory of Open Access Journals (Sweden)

    Gavin C. Bowick

    2010-01-01

    Full Text Available Developing vaccines to biothreat agents presents a number of challenges for discovery, preclinical development, and licensure. The need for high containment to work with live agents limits the amount and types of research that can be done using complete pathogens, and small markets reduce potential returns for industry. However, a number of tools, from comparative pathogenesis of viral strains at the molecular level to novel computational approaches, are being used to understand the basis of viral attenuation and characterize protective immune responses. As the amount of basic molecular knowledge grows, we will be able to take advantage of these tools not only to rationally attenuate virus strains for candidate vaccines, but also to assess immunogenicity and safety in silico. This review discusses how a basic understanding of pathogenesis, allied with systems biology and machine learning methods, can impact biodefense vaccinology.

  20. Biologically mediated transport of contaminants to aquatic systems.

    Science.gov (United States)

    Blais, Jules M; Macdonald, Robie W; Mackay, Donald; Webster, Eva; Harvey, Colin; Smol, John P

    2007-02-15

    The prevailing view is that long-range transport of semivolatile contaminants is primarily conducted by the physical system (e.g., winds, currents), and biological transport is typically ignored. Although this view may be correct in terms of bulk budgets and fluxes, it neglects the potential of animals to focus contaminants into foodwebs due to their behaviors and lifecycles. In particular, gregarious animals that biomagnify and bioaccumulate certain contaminants and then migrate and congregate can become the predominant pathway for contaminants in many circumstances. Fish and birds provide prominent examples for such behavior. This review examines the potential for biovector transport to expose populations to contaminants. In addition, we apply a modeling approach to compare the potential of biovector transport to other physical transport pathways for a hypothetical lake receiving large numbers of fish. We conclude that biovector transport should not be neglected when considering environmental risks of biomagnifying contaminants.

  1. SBR-Blood: systems biology repository for hematopoietic cells.

    Science.gov (United States)

    Lichtenberg, Jens; Heuston, Elisabeth F; Mishra, Tejaswini; Keller, Cheryl A; Hardison, Ross C; Bodine, David M

    2016-01-01

    Extensive research into hematopoiesis (the development of blood cells) over several decades has generated large sets of expression and epigenetic profiles in multiple human and mouse blood cell types. However, there is no single location to analyze how gene regulatory processes lead to different mature blood cells. We have developed a new database framework called hematopoietic Systems Biology Repository (SBR-Blood), available online at http://sbrblood.nhgri.nih.gov, which allows user-initiated analyses for cell type correlations or gene-specific behavior during differentiation using publicly available datasets for array- and sequencing-based platforms from mouse hematopoietic cells. SBR-Blood organizes information by both cell identity and by hematopoietic lineage. The validity and usability of SBR-Blood has been established through the reproduction of workflows relevant to expression data, DNA methylation, histone modifications and transcription factor occupancy profiles. PMID:26590403

  2. Gravitational biology and the mammalian circadian timing system.

    Science.gov (United States)

    Fuller, C A; Murakami, D M; Sulzman, F M

    1989-01-01

    Mammals have evolved under the influence of many selective pressures. Two of these pressures have been the static force of gravity and the daily variations in the environment due to the rotation of the earth. It is now clear that each of these pressures has led to specific adaptations which influence how organisms respond to changes in either gravity or daily time cues. However, several unpredicted responses to altered gravitational environments occur within the homeostatic and circadian control systems. These results may be particularly relevant to biological and medical issues related to spaceflight. This paper demonstrates that the homeostatic regulation of rat body temperature, heart rate, and activity become depressed following exposure to a 2 G hyperdynamic field, and recovers within 5-6 days. In addition, the circadian rhythms of these same variables exhibit a depression of rhythm amplitude; however, recovery required a minimum of 7 days. PMID:11537343

  3. Predicting Dynamic Behavior of a Biological System Using ANNs

    Science.gov (United States)

    Osman, Mohd Haniff; Ibrahim, Ratnawati; Hashim, Ishak; Yeun, Liong Choong; Bakar, Azuraliza Abu; Hussein, Zeti Azura Mohamed

    2008-01-01

    In this paper, artificial neural networks (ANNs) are applied to predict protein concentrations of a biological system. The input data are generated from a nonlinear mathematical model of the protein concentration. The protein concentrations from CDC6 data with actual kinetic parameter are taken as the target output. The data are then trained using multilayer perceptron (MLP) neural network with a 6-6-6 configuration. The allocation of the data will be distributed into 3 categories that are 80% as training data, 10% as validation data, and 10% as test data. The learning rules used in this work to determine the best model are gradient descent, conjugate gradient, scaled conjugate gradient. It is found that the MLP with scaled conjugate gradient learning rule gives the best prediction rate.

  4. Modular Verification of Interactive Systems with an Application to Biology

    Directory of Open Access Journals (Sweden)

    P. Milazzo

    2011-01-01

    Full Text Available We propose sync-programs, an automata-based formalism for the description of biological systems, and a modular verification technique for such a formalism that allows properties expressed in the universal fragment of CTL to be verified on suitably chosen fragments of models, rather than on whole models. As an application we show the modelling of the lac operon regulation process and the modular verification of some properties. Verification of properties is performed by using the NuSMV model checker and we show that by applying our modular verification technique we can verify properties in shorter times than those necessary to verify the same properties in the whole model.

  5. A new model of the microwave interaction with biological systems

    International Nuclear Information System (INIS)

    The interaction of 30-300 GHz electromagnetic field with biological media is studied . The refraction index and the extinction, reflection and transmission coefficients were shown to depend on concentration of coherent photons created by the biological objects and their dependence was studied on the biological medium excitation level, the non-linear character of this dependence being established. (authors)

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

    Science.gov (United States)

    Bigler, Erin D

    2016-01-01

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

  7. Systems Biology of Platelet-Vessel Wall Interactions.

    Directory of Open Access Journals (Sweden)

    Scott L. Diamond

    2013-08-01

    Full Text Available Blood Systems Biology seeks to quantify outside-in signaling as platelets respond to numerous external stimuli, typically under flow conditions. Platelets can activate via GPVI collagen receptor and numerous G-protein coupled receptors (GPCRs responsive to ADP, thromboxane, thrombin, and prostacyclin. A bottom-up ODE approach allowed prediction of platelet calcium and phosphoinositides following P2Y1 activation with ADP, either for a population average or single cell stochastic behavior. The homeostasis assumption (i.e. a resting platelet stays resting until activated was particularly useful in finding global steady states for these large metabolic networks. Alternatively, a top-down approach involving Pairwise Agonist Scanning allowed large data sets of measured calcium mobilization to predict an individual’s platelet responses. The data was used to train Neural Network (NN models of signaling to predict patient-specific responses to combinatorial stimulation. A kinetic description of platelet signaling then allows prediction of inside-out activation of platelets as they experience the complex biochemical milieu at the site of thrombosis. Multiscale lattice kinetic Monte Carlo (LKMC utilizes these detailed descriptions of platelet signaling under flow conditions where released soluble species are solved by finite element method and the flow field around the growing thrombus is updated using computational fluid dynamics or lattice Boltzmann method. Since hemodynamic effects are included in a multiscale approach, thrombosis can then be predicted under arterial and venous thrombotic conditions for various anatomical geometries. Such systems biology approaches accommodate the effect of anti-platelet pharmacological intervention where COX1 pathways or ADP signaling are modulated in a patient-specific manner.

  8. ERDA/Lewis research center photovoltaic systems test facility

    Science.gov (United States)

    Forestieri, A. F.; Johnson, J. A.; Knapp, W. D.; Rigo, H.; Stover, J.; Suhay, R.

    1977-01-01

    A national photovoltaic power systems test facility (of initial 10-kW peak power rating) is described. It consists of a solar array to generate electrical power, test-hardware for several alternate methods of power conversion, electrical energy storage systems, and an instrumentation and data acquisition system.

  9. A systems engineering perspective on the human-centered design of health information systems.

    Science.gov (United States)

    Samaras, George M; Horst, Richard L

    2005-02-01

    The discipline of systems engineering, over the past five decades, has used a structured systematic approach to managing the "cradle to grave" development of products and processes. While elements of this approach are typically used to guide the development of information systems that instantiate a significant user interface, it appears to be rare for the entire process to be implemented. In fact, a number of authors have put forth development lifecycle models that are subsets of the classical systems engineering method, but fail to include steps such as incremental hazard analysis and post-deployment corrective and preventative actions. In that most health information systems have safety implications, we argue that the design and development of such systems would benefit by implementing this systems engineering approach in full. Particularly with regard to bringing a human-centered perspective to the formulation of system requirements and the configuration of effective user interfaces, this classical systems engineering method provides an excellent framework for incorporating human factors (ergonomics) knowledge and integrating ergonomists in the interdisciplinary development of health information systems. PMID:15694886

  10. Tunnel radio communications system at Stanford Linear Accelerator Center

    Energy Technology Data Exchange (ETDEWEB)

    Struven, W.C.

    1980-07-01

    A unique single frequency, dual daisy chain tunnel radio communication system has been developed for use in our new Positron-Electron Storage Ring. Communications are possible between portables in the underground ring and between a portable in the ring and all control rooms on the site. The system is designed as a wide band facility and therefore can carry many simplex and duplex transmissions. This system utilizes TV twinlead as a distributed antenna and repeater amplifiers to cover more than 7000 feet of underground tunnel. The design philosophy, tests and initial design are discussed and contrasted with the final implementation of the system. Future uses of the system are discussed.

  11. Biological fouling of ethylene production water recycling system

    Energy Technology Data Exchange (ETDEWEB)

    Kurdish, I.K.; Khenkina, L.M.; Pavlenko, N.I.

    A study was made of biotic factors determining the intensity of biological overgrowth of ethylene as well as the distribution of sulfate-reducing bacteria in the system. The total quantity of microorganisms was determined by counting on membrane filters. The content of heterotrophic aerobic and anaerobic microorganisms was determined by inoculating specimens on meat-peptone agar and wort agar. The resistance of the microflora in the water supply system to high temperatures was studied by exposure of the specimens to various temperatures for one hour. The results indicated presence of large quantities of a number of biogenous substances in the water, including compounds of phosphorus and carbon. Large numbers of both aerobic and anaerobic microorganisms were present, consuming the oxygen absorbed by the water in the cooling tower, creating favorable conditions for development of both aerobic and anaerobic microorganisms. The sulfate-reducing bacteria present caused accumulation of hydrogen sulfide in the system, increasing corrosion. One possible means of controlling the fouling organisms might be to heat the water. Heating to 60C for sixty minutes significantly reduces the microorganism population, while 70C results in almost total elimination. 8 references, 4 figures.

  12. Using systems biology to simplify complex disease: immune cartography.

    Science.gov (United States)

    Polpitiya, Ashoka D; McDunn, Jonathan E; Burykin, Anton; Ghosh, Bijoy K; Cobb, J Perren

    2009-01-01

    What if there was a rapid, inexpensive, and accurate blood diagnostic that could determine which patients were infected, identify the organism(s) responsible, and identify patients who were not responding to therapy? We hypothesized that systems analysis of the transcriptional activity of circulating immune effector cells could be used to identify conserved elements in the host response to systemic inflammation, and furthermore, to discriminate between sterile and infectious etiologies. We review herein a validated, systems biology approach demonstrating that 1) abdominal and pulmonary sepsis diagnoses can be made in mouse models using microarray (RNA) data from circulating blood, 2) blood microarray data can be used to differentiate between the host response to Gram-negative and Gram-positive pneumonia, 3) the endotoxin response of normal human volunteers can be mapped at the level of gene expression, and 4) a similar strategy can be used in the critically ill to follow septic patients and quantitatively determine immune recovery. These findings provide the foundation of immune cartography and demonstrate the potential of this approach for rapidly diagnosing sepsis and identifying pathogens. Further, our data suggest a new approach to determine how specific pathogens perturb the physiology of circulating leukocytes in a cell-specific manner. Large, prospective clinical trails are needed to validate the clinical utility of leukocyte RNA diagnostics (e.g., the riboleukogram).

  13. Research on the Reliability Centered Maintenance Plan of a Launching System

    Institute of Scientific and Technical Information of China (English)

    XIE Chao; SUN Ming-fang; DU Jun-min

    2011-01-01

    Aiming at the shortcomings of the traditional maintenance plan of a launching system, an analysis was made on the development of the reliability centered maintenance methods (RCM) and the basic models for reliability centered maintenance of a launching system are presented in this paper. The common methods for functional impor- tant product determination, failure modes and effect analysis ( FMEA ) and logic decision analysis were illustrated and the basic methods for maintenance interval calculation models were studied based on availability. According to the research, the reliability centered maintenance plan of a certain launching system was given.

  14. Distributed Monitoring and Control System of Bearing Test and Inspection Center

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Distributed bearing test center monitoring and controlsystem based on CAN bus is designed in this paper. It canmonitor bearing test process, collect test data, analyze vibrationsignals, extract features of bearing failure and diagnose bearingfaults. The system has been used in a bearing test and inspec-tion center of a bearing plant successfully.

  15. Revision history aware repositories of computational models of biological systems

    Directory of Open Access Journals (Sweden)

    Nickerson David P

    2011-01-01

    Full Text Available Abstract Background Building repositories of computational models of biological systems ensures that published models are available for both education and further research, and can provide a source of smaller, previously verified models to integrate into a larger model. One problem with earlier repositories has been the limitations in facilities to record the revision history of models. Often, these facilities are limited to a linear series of versions which were deposited in the repository. This is problematic for several reasons. Firstly, there are many instances in the history of biological systems modelling where an 'ancestral' model is modified by different groups to create many different models. With a linear series of versions, if the changes made to one model are merged into another model, the merge appears as a single item in the history. This hides useful revision history information, and also makes further merges much more difficult, as there is no record of which changes have or have not already been merged. In addition, a long series of individual changes made outside of the repository are also all merged into a single revision when they are put back into the repository, making it difficult to separate out individual changes. Furthermore, many earlier repositories only retain the revision history of individual files, rather than of a group of files. This is an important limitation to overcome, because some types of models, such as CellML 1.1 models, can be developed as a collection of modules, each in a separate file. The need for revision history is widely recognised for computer software, and a lot of work has gone into developing version control systems and distributed version control systems (DVCSs for tracking the revision history. However, to date, there has been no published research on how DVCSs can be applied to repositories of computational models of biological systems. Results We have extended the Physiome Model

  16. ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis.

    Directory of Open Access Journals (Sweden)

    Michael Römer

    Full Text Available Bioinformatics analysis has become an integral part of research in biology. However, installation and use of scientific software can be difficult and often requires technical expert knowledge. Reasons are dependencies on certain operating systems or required third-party libraries, missing graphical user interfaces and documentation, or nonstandard input and output formats. In order to make bioinformatics software easily accessible to researchers, we here present a web-based platform. The Center for Bioinformatics Tuebingen (ZBIT Bioinformatics Toolbox provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics and proteomics studies. All tools are hosted on a customized Galaxy instance and run on a dedicated computation cluster. Users only need a web browser and an active internet connection in order to benefit from this service. The web platform is designed to facilitate the usage of the bioinformatics tools for researchers without advanced technical background. Users can combine tools for complex analyses or use predefined, customizable workflows. All results are stored persistently and reproducible. For each tool, we provide documentation, tutorials, and example data to maximize usability. The ZBIT Bioinformatics Toolbox is freely available at https://webservices.cs.uni-tuebingen.de/.

  17. ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis.

    Science.gov (United States)

    Römer, Michael; Eichner, Johannes; Dräger, Andreas; Wrzodek, Clemens; Wrzodek, Finja; Zell, Andreas

    2016-01-01

    Bioinformatics analysis has become an integral part of research in biology. However, installation and use of scientific software can be difficult and often requires technical expert knowledge. Reasons are dependencies on certain operating systems or required third-party libraries, missing graphical user interfaces and documentation, or nonstandard input and output formats. In order to make bioinformatics software easily accessible to researchers, we here present a web-based platform. The Center for Bioinformatics Tuebingen (ZBIT) Bioinformatics Toolbox provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics and proteomics studies. All tools are hosted on a customized Galaxy instance and run on a dedicated computation cluster. Users only need a web browser and an active internet connection in order to benefit from this service. The web platform is designed to facilitate the usage of the bioinformatics tools for researchers without advanced technical background. Users can combine tools for complex analyses or use predefined, customizable workflows. All results are stored persistently and reproducible. For each tool, we provide documentation, tutorials, and example data to maximize usability. The ZBIT Bioinformatics Toolbox is freely available at https://webservices.cs.uni-tuebingen.de/.

  18. ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis.

    Science.gov (United States)

    Römer, Michael; Eichner, Johannes; Dräger, Andreas; Wrzodek, Clemens; Wrzodek, Finja; Zell, Andreas

    2016-01-01

    Bioinformatics analysis has become an integral part of research in biology. However, installation and use of scientific software can be difficult and often requires technical expert knowledge. Reasons are dependencies on certain operating systems or required third-party libraries, missing graphical user interfaces and documentation, or nonstandard input and output formats. In order to make bioinformatics software easily accessible to researchers, we here present a web-based platform. The Center for Bioinformatics Tuebingen (ZBIT) Bioinformatics Toolbox provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics and proteomics studies. All tools are hosted on a customized Galaxy instance and run on a dedicated computation cluster. Users only need a web browser and an active internet connection in order to benefit from this service. The web platform is designed to facilitate the usage of the bioinformatics tools for researchers without advanced technical background. Users can combine tools for complex analyses or use predefined, customizable workflows. All results are stored persistently and reproducible. For each tool, we provide documentation, tutorials, and example data to maximize usability. The ZBIT Bioinformatics Toolbox is freely available at https://webservices.cs.uni-tuebingen.de/. PMID:26882475

  19. Networks as a Privileged Way to Develop Mesoscopic Level Approaches in Systems Biology

    OpenAIRE

    Alessandro Giuliani

    2014-01-01

    The methodologies advocated in computational biology are in many cases proper system-level approaches. These methodologies are variously connected to the notion of “mesosystem” and thus on the focus on relational structures that are at the basis of biological regulation. Here, I describe how the formalization of biological systems by means of graph theory constitutes an extremely fruitful approach to biology. I suggest the epistemological relevance of the notion of graph resides in its multil...

  20. Toward a learner-centered system for adult learning

    NARCIS (Netherlands)

    Hermans, Henry; Kalz, Marco; Koper, Rob

    2014-01-01

    This paper presents an e-learning system that integrates the use of concepts of virtual learning environments, personal learning environments, and social network sites. The system is based on a learning model which comprises and integrates three learning contexts for the adult learner: the formal, i

  1. NASA Johnson Space Center Life Sciences Data System

    Science.gov (United States)

    Rahman, Hasan; Cardenas, Jeffery

    1994-01-01

    The Life Sciences Project Division (LSPD) at JSC, which manages human life sciences flight experiments for the NASA Life Sciences Division, augmented its Life Sciences Data System (LSDS) in support of the Spacelab Life Sciences-2 (SLS-2) mission, October 1993. The LSDS is a portable ground system supporting Shuttle, Spacelab, and Mir based life sciences experiments. The LSDS supports acquisition, processing, display, and storage of real-time experiment telemetry in a workstation environment. The system may acquire digital or analog data, storing the data in experiment packet format. Data packets from any acquisition source are archived and meta-parameters are derived through the application of mathematical and logical operators. Parameters may be displayed in text and/or graphical form, or output to analog devices. Experiment data packets may be retransmitted through the network interface and database applications may be developed to support virtually any data packet format. The user interface provides menu- and icon-driven program control and the LSDS system can be integrated with other workstations to perform a variety of functions. The generic capabilities, adaptability, and ease of use make the LSDS a cost-effective solution to many experiment data processing requirements. The same system is used for experiment systems functional and integration tests, flight crew training sessions and mission simulations. In addition, the system has provided the infrastructure for the development of the JSC Life Sciences Data Archive System scheduled for completion in December 1994.

  2. Two-center-multipole expansion method: application to macromolecular systems

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Yakubovich, Alexander V.; Solov'yov, Andrey V.;

    2007-01-01

    We propose a theoretical method for the calculation of the interaction energy between macromolecular systems at large distances. The method provides a linear scaling of the computing time with the system size and is considered as an alternative to the well-known fast multipole method. Its efficie...

  3. Biological phosphorus and nitrogen removal in a single sludge system

    Energy Technology Data Exchange (ETDEWEB)

    Carlsson, Hans

    1996-05-01

    The primary aim of this thesis was to investigate the process stability of a single sludge activated system designed for the combined operation of enhanced biological phosphorus removal (EBPR) and nitrogen removal. A pilot plant at the Sjoelunda wastewater treatment plant in Malmoe, Sweden, has formed the basis for the investigation. The pilot plant study showed that the concentration of total phosphorus on average was low in the effluent, below 0.5 mg P/l. Simultaneously with the highest concentrations of phosphorus in the effluent, the lowest COD/P ratios in the effluent were recorded. A recurrent pattern of high concentrations of phosphorus was observed every year in July, which is the industrial holiday month in Sweden. Other instances of increased phosphorus concentrations in the secondary effluent illustrate the effect of prolonged periods of rain. Increasing flow rates due to rain lead to a dilution and a change in the composition of the COD in the influent wastewater. The COD/P and VFA/P ratios decrease with decreasing concentrations of COD. It was also shown that high removal ratios of both nitrogen and phosphorus during long periods are possible. The nitrogen removal was stable during the whole investigated period, whereas the phosphorus removal was unstable during prolonged periods with low concentrations of COD in the influent water. The combined biological phosphorus and nitrogen removal process implies that during these periods the risk of recirculating nitrate to the anaerobic reactor increases. Such a recirculation both stabilizes the nitrogen removal and withdraws some of the readily degradable organic material from the bio-P bacteria. The main conclusion of this study is that a phosphorus limited EBPR process can cope with the day to day variations, but occasionally, measures have to be taken if the demands for phosphorus removal are stringent. 49 refs, 8 figs, 1 tab

  4. Adaptive resistance to antibiotics in bacteria: a systems biology perspective.

    Science.gov (United States)

    Sandoval-Motta, Santiago; Aldana, Maximino

    2016-05-01

    Despite all the major breakthroughs in antibiotic development and treatment procedures, there is still no long-term solution to the bacterial antibiotic resistance problem. Among all the known types of resistance, adaptive resistance (AdR) is particularly inconvenient. This phenotype is known to emerge as a consequence of concentration gradients, as well as contact with subinhibitory concentrations of antibiotics, both known to occur in human patients and livestock. Moreover, AdR has been repeatedly correlated with the appearance of multidrug resistance, although the biological processes behind its emergence and evolution are not well understood. Epigenetic inheritance, population structure and heterogeneity, high mutation rates, gene amplification, efflux pumps, and biofilm formation have all been reported as possible explanations for its development. Nonetheless, these concepts taken independently have not been sufficient to prevent AdR's fast emergence or to predict its low stability. New strains of resistant pathogens continue to appear, and none of the new approaches used to kill them (mixed antibiotics, sequential treatments, and efflux inhibitors) are completely efficient. With the advent of systems biology and its toolsets, integrative models that combine experimentally known features with computational simulations have significantly improved our understanding of the emergence and evolution of the adaptive-resistant phenotype. Apart from outlining these findings, we propose that one of the main cornerstones of AdR in bacteria, is the conjunction of two types of mechanisms: one rapidly responding to transient environmental challenges but not very efficient, and another much more effective and specific, but developing on longer time scales. WIREs Syst Biol Med 2016, 8:253-267. doi: 10.1002/wsbm.1335 For further resources related to this article, please visit the WIREs website. PMID:27103502

  5. A Comprehensive Systems Biology Approach to Studying Zika Virus.

    Science.gov (United States)

    May, Meghan; Relich, Ryan F

    2016-01-01

    Zika virus (ZIKV) is responsible for an ongoing and intensifying epidemic in the Western Hemisphere. We examined the complete predicted proteomes, glycomes, and selectomes of 33 ZIKV strains representing temporally diverse members of the African lineage, the Asian lineage, and the current outbreak in the Americas. Derivation of the complete selectome is an 'omics' approach to identify distinct evolutionary pressures acting on different features of an organism. Employment of the M8 model did not show evidence of global diversifying selection acting on the ZIKV polyprotein; however, a mixed effect model of evolution showed strong evidence (P<0.05) for episodic diversifying selection acting on specific sites. Single nucleotide polymorphisms (SNPs) were predictably frequent across strains relative to the derived consensus sequence. None of the 9 published detection procedures utilize targets that share 100% identity across the 33 strains examined, indicating that ZIKV escape from molecular detection is predictable. The predicted O-linked glycome showed marked diversity across strains; however, the N-linked glycome was highly stable. All Asian and American strains examined were predicted to include glycosylation of E protein ASN154, a modification proposed to mediate neurotropism, whereas the modification was not predicted for African strains. SNP diversity, episodic diversifying selection, and differential glycosylation, particularly of ASN154, may have major biological implications for ZIKV disease. Taken together, the systems biology perspective of ZIKV indicates: a.) The recently emergent Asian/American N-glycotype is mediating the new and emerging neuropathogenic potential of ZIKV; and b.) further divergence at specific sites is predictable as endemnicity is established in the Americas. PMID:27584813

  6. Adaptive resistance to antibiotics in bacteria: a systems biology perspective.

    Science.gov (United States)

    Sandoval-Motta, Santiago; Aldana, Maximino

    2016-05-01

    Despite all the major breakthroughs in antibiotic development and treatment procedures, there is still no long-term solution to the bacterial antibiotic resistance problem. Among all the known types of resistance, adaptive resistance (AdR) is particularly inconvenient. This phenotype is known to emerge as a consequence of concentration gradients, as well as contact with subinhibitory concentrations of antibiotics, both known to occur in human patients and livestock. Moreover, AdR has been repeatedly correlated with the appearance of multidrug resistance, although the biological processes behind its emergence and evolution are not well understood. Epigenetic inheritance, population structure and heterogeneity, high mutation rates, gene amplification, efflux pumps, and biofilm formation have all been reported as possible explanations for its development. Nonetheless, these concepts taken independently have not been sufficient to prevent AdR's fast emergence or to predict its low stability. New strains of resistant pathogens continue to appear, and none of the new approaches used to kill them (mixed antibiotics, sequential treatments, and efflux inhibitors) are completely efficient. With the advent of systems biology and its toolsets, integrative models that combine experimentally known features with computational simulations have significantly improved our understanding of the emergence and evolution of the adaptive-resistant phenotype. Apart from outlining these findings, we propose that one of the main cornerstones of AdR in bacteria, is the conjunction of two types of mechanisms: one rapidly responding to transient environmental challenges but not very efficient, and another much more effective and specific, but developing on longer time scales. WIREs Syst Biol Med 2016, 8:253-267. doi: 10.1002/wsbm.1335 For further resources related to this article, please visit the WIREs website.

  7. A Comprehensive Systems Biology Approach to Studying Zika Virus

    Science.gov (United States)

    Relich, Ryan F.

    2016-01-01

    Zika virus (ZIKV) is responsible for an ongoing and intensifying epidemic in the Western Hemisphere. We examined the complete predicted proteomes, glycomes, and selectomes of 33 ZIKV strains representing temporally diverse members of the African lineage, the Asian lineage, and the current outbreak in the Americas. Derivation of the complete selectome is an ‘omics’ approach to identify distinct evolutionary pressures acting on different features of an organism. Employment of the M8 model did not show evidence of global diversifying selection acting on the ZIKV polyprotein; however, a mixed effect model of evolution showed strong evidence (P<0.05) for episodic diversifying selection acting on specific sites. Single nucleotide polymorphisms (SNPs) were predictably frequent across strains relative to the derived consensus sequence. None of the 9 published detection procedures utilize targets that share 100% identity across the 33 strains examined, indicating that ZIKV escape from molecular detection is predictable. The predicted O-linked glycome showed marked diversity across strains; however, the N-linked glycome was highly stable. All Asian and American strains examined were predicted to include glycosylation of E protein ASN154, a modification proposed to mediate neurotropism, whereas the modification was not predicted for African strains. SNP diversity, episodic diversifying selection, and differential glycosylation, particularly of ASN154, may have major biological implications for ZIKV disease. Taken together, the systems biology perspective of ZIKV indicates: a.) The recently emergent Asian/American N-glycotype is mediating the new and emerging neuropathogenic potential of ZIKV; and b.) further divergence at specific sites is predictable as endemnicity is established in the Americas. PMID:27584813

  8. Lessons learned from quantitative dynamical modeling in systems biology.

    Directory of Open Access Journals (Sweden)

    Andreas Raue

    Full Text Available Due to the high complexity of biological data it is difficult to disentangle cellular processes relying only on intuitive interpretation of measurements. A Systems Biology approach that combines quantitative experimental data with dynamic mathematical modeling promises to yield deeper insights into these processes. Nevertheless, with growing complexity and increasing amount of quantitative experimental data, building realistic and reliable mathematical models can become a challenging task: the quality of experimental data has to be assessed objectively, unknown model parameters need to be estimated from the experimental data, and numerical calculations need to be precise and efficient. Here, we discuss, compare and characterize the performance of computational methods throughout the process of quantitative dynamic modeling using two previously established examples, for which quantitative, dose- and time-resolved experimental data are available. In particular, we present an approach that allows to determine the quality of experimental data in an efficient, objective and automated manner. Using this approach data generated by different measurement techniques and even in single replicates can be reliably used for mathematical modeling. For the estimation of unknown model parameters, the performance of different optimization algorithms was compared systematically. Our results show that deterministic derivative-based optimization employing the sensitivity equations in combination with a multi-start strategy based on latin hypercube sampling outperforms the other methods by orders of magnitude in accuracy and speed. Finally, we investigated transformations that yield a more efficient parameterization of the model and therefore lead to a further enhancement in optimization performance. We provide a freely available open source software package that implements the algorithms and examples compared here.

  9. JobCenter: an open source, cross-platform, and distributed job queue management system optimized for scalability and versatility

    Directory of Open Access Journals (Sweden)

    Jaschob Daniel

    2012-07-01

    Full Text Available Abstract Background Laboratories engaged in computational biology or bioinformatics frequently need to run lengthy, multistep, and user-driven computational jobs. Each job can tie up a computer for a few minutes to several days, and many laboratories lack the expertise or resources to build and maintain a dedicated computer cluster. Results JobCenter is a client–server application and framework for job management and distributed job execution. The client and server components are both written in Java and are cross-platform and relatively easy to install. All communication with the server is client-driven, which allows worker nodes to run anywhere (even behind external firewalls or “in the cloud” and provides inherent load balancing. Adding a worker node to the worker pool is as simple as dropping the JobCenter client files onto any computer and performing basic configuration, which provides tremendous ease-of-use, flexibility, and limitless horizontal scalability. Each worker installation may be independently configured, including the types of jobs it is able to run. Executed jobs may be written in any language and may include multistep workflows. Conclusions JobCenter is a versatile and scalable distributed job management system that allows laboratories to very efficiently distribute all computational work among available resources. JobCenter is freely available at http://code.google.com/p/jobcenter/.

  10. Polymer biomaterial constructs for regenerative medicine and functional biological systems

    Science.gov (United States)

    Meng, Linghui

    The use of collagen as a biomaterial is currently undergoing a renaissance in the tissue engineering field. The excellent biocompatibility and safety due to its biological characteristics, such as biodegradability and weak antigenicity, make collagen a primary material resource in medical applications. Described herein is work towards the development of novel collagen-based matrices, with additional multi-functionality imparted through a novel in-situ crosslinking approach. The process of electrospinning has become a widely used technique for the creation of fibrous scaffolds for tissue engineering applications due to its ability to rapidly create structures composed of nano-scale polymer fibers closely resembling the architecture of the extracellular matrix (ECM). Collagen-PCL sheath-core bicomponent fibrous scaffolds were fabricated using a novel variation on traditional electrospinning, known as co-axial electrospinning. The results showed that the addition of a synthetic polymer core into collagen nanofibers remarkably increased the mechanical strength of collagen matrices spun from the benign solvent system. A novel single-step, in-situ collagen crosslink approach was developed in order to solve the problems dominating traditional collagen crosslinking methods, such as dimensional shrinking and loss of porous morphology, and to simplify the crosslinking procedure for electrospun collagen scaffolds. The excess amount of NHS present in the crosslinking mixture was found to delay the EDC/collagen coupling reaction in a controlled fashion. Fundamental investigations into the development and characterization of in-situ crosslinked collagen matrices such as fibrous scaffolds, gels and sponges, as well as their biomedical applications including cell culture substrates, wound dressings, drug delivery matrices and bone regeneration substitutes, were performed. The preliminary mice studies indicated that the in-situ crosslinked collagen matrices could be good candidates

  11. Nuclear Energy Center Site Survey, 1975. Part II. The U.S. electric power system and the potential role of nuclear energy centers

    International Nuclear Information System (INIS)

    Information related to Nuclear Energy Centers (NEC) in the U.S. is presented concerning the U.S. electric power system today; electricity demand history and forecasts; history and forecasts of the electric utility industry; regional notes; the status, history, and forecasts of the nuclear role; power plant siting problems and practices; nuclear facilities siting problems and practices; origin and evolution of the nuclear energy center concept; conceptualized description of nuclear energy centers; potential role of nuclear energy centers; assumptions, criteria, and bases; typical evolution of a nuclear energy center; and the nuclear fuel cycle

  12. Review and application of group theory to molecular systems biology

    Directory of Open Access Journals (Sweden)

    Rietman Edward A

    2011-06-01

    Full Text Available Abstract In this paper we provide a review of selected mathematical ideas that can help us better understand the boundary between living and non-living systems. We focus on group theory and abstract algebra applied to molecular systems biology. Throughout this paper we briefly describe possible open problems. In connection with the genetic code we propose that it may be possible to use perturbation theory to explore the adjacent possibilities in the 64-dimensional space-time manifold of the evolving genome. With regards to algebraic graph theory, there are several minor open problems we discuss. In relation to network dynamics and groupoid formalism we suggest that the network graph might not be the main focus for understanding the phenotype but rather the phase space of the network dynamics. We show a simple case of a C6 network and its phase space network. We envision that the molecular network of a cell is actually a complex network of hypercycles and feedback circuits that could be better represented in a higher-dimensional space. We conjecture that targeting nodes in the molecular network that have key roles in the phase space, as revealed by analysis of the automorphism decomposition, might be a better way to drug discovery and treatment of cancer.

  13. Review and application of group theory to molecular systems biology.

    Science.gov (United States)

    Rietman, Edward A; Karp, Robert L; Tuszynski, Jack A

    2011-01-01

    In this paper we provide a review of selected mathematical ideas that can help us better understand the boundary between living and non-living systems. We focus on group theory and abstract algebra applied to molecular systems biology. Throughout this paper we briefly describe possible open problems. In connection with the genetic code we propose that it may be possible to use perturbation theory to explore the adjacent possibilities in the 64-dimensional space-time manifold of the evolving genome. With regards to algebraic graph theory, there are several minor open problems we discuss. In relation to network dynamics and groupoid formalism we suggest that the network graph might not be the main focus for understanding the phenotype but rather the phase space of the network dynamics. We show a simple case of a C6 network and its phase space network. We envision that the molecular network of a cell is actually a complex network of hypercycles and feedback circuits that could be better represented in a higher-dimensional space. We conjecture that targeting nodes in the molecular network that have key roles in the phase space, as revealed by analysis of the automorphism decomposition, might be a better way to drug discovery and treatment of cancer. PMID:21696623

  14. Solar activity, magnetic storms and their effects on biological systems

    International Nuclear Information System (INIS)

    Full text: In the present time much attention is spent on the electromagnetic waves, solar radiation and magnetic storms on biological systems, including on person. However, there are few publications describing the mechanism of these influences on human. First of all it is necessary to point out that electromagnetic waves, the flow of particles in space and magnetic storms, acting on person human-all is connected with biophysical processes. So approach to influence of these factors on organism follows the processes of influence of these waves on bio system. Magnetic storms are phenomena continuously connected with solar activity. Investigation of cosmic space has intensified the practical importance of the problem of interaction with natural factors of external ambience. Much attention deserves the cosmic radiation, geomagnetic field, elements of climate and weathers. However the mechanism of bio tropic action of these factors is not enough studied. Beginning XXI century was already signified the successes in investigation of Mars. The Space shuttles 'Spirit' and 'Opportunity' successfully have carried out some work on examining and finding of water on Mars. A flight of person to Mars is being considered. One of the important mechanisms of influence on human organism is, in our opinion, the rising of the resonance at coincidence of frequencies and their more important factor is a phenomena of electromagnetic induction and forming the radicals in the organism

  15. NASA Langley Research Center Systems Analysis & Concepts Directorate Participation in the Exploration Systems Architecture Study

    Science.gov (United States)

    Keyes, Jennifer; Troutman, Patrick A.; Saucillo, Rudolph; Cirillo, William M.; Cavanaugh, Steve; Stromgren, Chel

    2006-01-01

    The NASA Langley Research Center (LaRC) Systems Analysis & Concepts Directorate (SACD) began studying human exploration missions beyond low Earth orbit (LEO) in the year 1999. This included participation in NASA s Decadal Planning Team (DPT), the NASA Exploration Team (NExT), Space Architect studies and Revolutionary Aerospace Systems Concepts (RASC) architecture studies that were used in formulating the new Vision for Space Exploration. In May of 2005, NASA initiated the Exploration Systems Architecture Study (ESAS). The primary outputs of the ESAS activity were concepts and functional requirements for the Crewed Exploration Vehicle (CEV), its supporting launch vehicle infrastructure and identification of supporting technology requirements and investments. An exploration systems analysis capability has evolved to support these functions in the past and continues to evolve to support anticipated future needs. SACD had significant roles in supporting the ESAS study team. SACD personnel performed the liaison function between the ESAS team and the Shuttle/Station Configuration Options Team (S/SCOT), an agency-wide team charged with using the Space Shuttle to complete the International Space Station (ISS) by the end of Fiscal Year (FY) 2010. The most significant of the identified issues involved the ability of the Space Shuttle system to achieve the desired number of flights in the proposed time frame. SACD with support from the Kennedy Space Center performed analysis showing that, without significant investments in improving the shuttle processing flow, that there was almost no possibility of completing the 28-flight sequence by the end of 2010. SACD performed numerous Lunar Surface Access Module (LSAM) trades to define top level element requirements and establish architecture propellant needs. Configuration trades were conducted to determine the impact of varying degrees of segmentation of the living capabilities of the combined descent stage, ascent stage, and other

  16. Prediction-based manufacturing center self-adaptive demand side energy optimization in cyber physical systems

    Science.gov (United States)

    Sun, Xinyao; Wang, Xue; Wu, Jiangwei; Liu, Youda

    2014-05-01

    Cyber physical systems(CPS) recently emerge as a new technology which can provide promising approaches to demand side management(DSM), an important capability in industrial power systems. Meanwhile, the manufacturing center is a typical industrial power subsystem with dozens of high energy consumption devices which have complex physical dynamics. DSM, integrated with CPS, is an effective methodology for solving energy optimization problems in manufacturing center. This paper presents a prediction-based manufacturing center self-adaptive energy optimization method for demand side management in cyber physical systems. To gain prior knowledge of DSM operating results, a sparse Bayesian learning based componential forecasting method is introduced to predict 24-hour electric load levels for specific industrial areas in China. From this data, a pricing strategy is designed based on short-term load forecasting results. To minimize total energy costs while guaranteeing manufacturing center service quality, an adaptive demand side energy optimization algorithm is presented. The proposed scheme is tested in a machining center energy optimization experiment. An AMI sensing system is then used to measure the demand side energy consumption of the manufacturing center. Based on the data collected from the sensing system, the load prediction-based energy optimization scheme is implemented. By employing both the PSO and the CPSO method, the problem of DSM in the manufacturing center is solved. The results of the experiment show the self-adaptive CPSO energy optimization method enhances optimization by 5% compared with the traditional PSO optimization method.

  17. Health Center Program Data-Uniform Data System

    Data.gov (United States)

    U.S. Department of Health & Human Services — HRSA's Bureau of Primary Health Care's Uniform Data System (UDS) tracks a variety of information, including patient demographics, services provided, clinical...

  18. Toward a learner-centered system for adult learning

    OpenAIRE

    Hermans, Henry; KALZ Marco; Koper, Rob

    2014-01-01

    This paper presents an e-learning system that integrates the use of concepts of virtual learning environments, personal learning environments, and social network sites. The system is based on a learning model which comprises and integrates three learning contexts for the adult learner: the formal, instructional context, the personal context for learning management, and the social peer context. The paper outlines how the Open University of the Netherlands (OUN)implemented this model in the Ope...

  19. Biological Sample Monitoring Database (BSMDBS)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Biological Sample Monitoring Database System (BSMDBS) was developed for the Northeast Fisheries Regional Office and Science Center (NER/NEFSC) to record and...

  20. Eukaryotic Systems Broaden the Scope of Synthetic Biology

    OpenAIRE

    Haynes, Karmella A.; Silver, Pamela A.

    2009-01-01

    Synthetic biology aims to engineer novel cellular functions by assembling well-characterized molecular parts (i.e., nucleic acids and proteins) into biological “devices” that exhibit predictable behavior. Recently, efforts in eukaryotic synthetic biology have sprung from foundational work in bacteria. Designing synthetic circuits to operate reliably in the context of differentiating and morphologically complex cells presents unique challenges and opportunities for progress in the field. This ...