Science.gov

Sample records for computational biology research

  1. Computational systems biology for aging research.

    PubMed

    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.

  2. Structural biology computing: Lessons for the biomedical research sciences.

    PubMed

    Morin, Andrew; Sliz, Piotr

    2013-11-01

    The field of structural biology, whose aim is to elucidate the molecular and atomic structures of biological macromolecules, has long been at the forefront of biomedical sciences in adopting and developing computational research methods. Operating at the intersection between biophysics, biochemistry, and molecular biology, structural biology's growth into a foundational framework on which many concepts and findings of molecular biology are interpreted1 has depended largely on parallel advancements in computational tools and techniques. Without these computing advances, modern structural biology would likely have remained an exclusive pursuit practiced by few, and not become the widely practiced, foundational field it is today. As other areas of biomedical research increasingly embrace research computing techniques, the successes, failures and lessons of structural biology computing can serve as a useful guide to progress in other biomedically related research fields.

  3. Computer Literacy for Life Sciences: Helping the Digital-Era Biology Undergraduates Face Today's Research

    ERIC Educational Resources Information Center

    Smolinski, Tomasz G.

    2010-01-01

    Computer literacy plays a critical role in today's life sciences research. Without the ability to use computers to efficiently manipulate and analyze large amounts of data resulting from biological experiments and simulations, many of the pressing questions in the life sciences could not be answered. Today's undergraduates, despite the ubiquity of…

  4. ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus.

    PubMed

    Karp, Peter D; Berger, Bonnie; Kovats, Diane; Lengauer, Thomas; Linial, Michal; Sabeti, Pardis; Hide, Winston; Rost, Burkhard

    2015-01-01

    Speed is of the essence in combating Ebola; thus, computational approaches should form a significant component of Ebola research. As for the development of any modern drug, computational biology is uniquely positioned to contribute through comparative analysis of the genome sequences of Ebola strains as well as 3-D protein modeling. Other computational approaches to Ebola may include large-scale docking studies of Ebola proteins with human proteins and with small-molecule libraries, computational modeling of the spread of the virus, computational mining of the Ebola literature, and creation of a curated Ebola database. Taken together, such computational efforts could significantly accelerate traditional scientific approaches. In recognition of the need for important and immediate solutions from the field of computational biology against Ebola, the International Society for Computational Biology (ISCB) announces a prize for an important computational advance in fighting the Ebola virus. ISCB will confer the ISCB Fight against Ebola Award, along with a prize of US$2,000, at its July 2016 annual meeting (ISCB Intelligent Systems for Molecular Biology (ISMB) 2016, Orlando, Florida).

  5. Computational systems chemical biology.

    PubMed

    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. Computational Systems Biology

    SciTech Connect

    McDermott, Jason E.; Samudrala, Ram; Bumgarner, Roger E.; Montogomery, Kristina; Ireton, Renee

    2009-05-01

    Computational systems biology is the term that we use to describe computational methods to identify, infer, model, and store relationships between the molecules, pathways, and cells (“systems”) involved in a living organism. Based on this definition, the field of computational systems biology has been in existence for some time. However, the recent confluence of high throughput methodology for biological data gathering, genome-scale sequencing and computational processing power has driven a reinvention and expansion of this field. The expansions include not only modeling of small metabolic{Ishii, 2004 #1129; Ekins, 2006 #1601; Lafaye, 2005 #1744} and signaling systems{Stevenson-Paulik, 2006 #1742; Lafaye, 2005 #1744} but also modeling of the relationships between biological components in very large systems, incluyding whole cells and organisms {Ideker, 2001 #1124; Pe'er, 2001 #1172; Pilpel, 2001 #393; Ideker, 2002 #327; Kelley, 2003 #1117; Shannon, 2003 #1116; Ideker, 2004 #1111}{Schadt, 2003 #475; Schadt, 2006 #1661}{McDermott, 2002 #878; McDermott, 2005 #1271}. Generally these models provide a general overview of one or more aspects of these systems and leave the determination of details to experimentalists focused on smaller subsystems. The promise of such approaches is that they will elucidate patterns, relationships and general features that are not evident from examining specific components or subsystems. These predictions are either interesting in and of themselves (for example, the identification of an evolutionary pattern), or are interesting and valuable to researchers working on a particular problem (for example highlight a previously unknown functional pathway). Two events have occurred to bring about the field computational systems biology to the forefront. One is the advent of high throughput methods that have generated large amounts of information about particular systems in the form of genetic studies, gene expression analyses (both protein and

  7. Large Scale Computing and Storage Requirements for Biological and Environmental Research

    SciTech Connect

    DOE Office of Science, Biological and Environmental Research Program Office ,

    2009-09-30

    In May 2009, NERSC, DOE's Office of Advanced Scientific Computing Research (ASCR), and DOE's Office of Biological and Environmental Research (BER) held a workshop to characterize HPC requirements for BER-funded research over the subsequent three to five years. The workshop revealed several key points, in addition to achieving its goal of collecting and characterizing computing requirements. Chief among them: scientific progress in BER-funded research is limited by current allocations of computational resources. Additionally, growth in mission-critical computing -- combined with new requirements for collaborative data manipulation and analysis -- will demand ever increasing computing, storage, network, visualization, reliability and service richness from NERSC. This report expands upon these key points and adds others. It also presents a number of"case studies" as significant representative samples of the needs of science teams within BER. Workshop participants were asked to codify their requirements in this"case study" format, summarizing their science goals, methods of solution, current and 3-5 year computing requirements, and special software and support needs. Participants were also asked to describe their strategy for computing in the highly parallel,"multi-core" environment that is expected to dominate HPC architectures over the next few years.

  8. Computational biology for ageing.

    PubMed

    Wieser, Daniela; Papatheodorou, Irene; Ziehm, Matthias; Thornton, Janet M

    2011-01-12

    High-throughput genomic and proteomic technologies have generated a wealth of publicly available data on ageing. Easy access to these data, and their computational analysis, is of great importance in order to pinpoint the causes and effects of ageing. Here, we provide a description of the existing databases and computational tools on ageing that are available for researchers. We also describe the computational approaches to data interpretation in the field of ageing including gene expression, comparative and pathway analyses, and highlight the challenges for future developments. We review recent biological insights gained from applying bioinformatics methods to analyse and interpret ageing data in different organisms, tissues and conditions.

  9. Computational biology for ageing

    PubMed Central

    Wieser, Daniela; Papatheodorou, Irene; Ziehm, Matthias; Thornton, Janet M.

    2011-01-01

    High-throughput genomic and proteomic technologies have generated a wealth of publicly available data on ageing. Easy access to these data, and their computational analysis, is of great importance in order to pinpoint the causes and effects of ageing. Here, we provide a description of the existing databases and computational tools on ageing that are available for researchers. We also describe the computational approaches to data interpretation in the field of ageing including gene expression, comparative and pathway analyses, and highlight the challenges for future developments. We review recent biological insights gained from applying bioinformatics methods to analyse and interpret ageing data in different organisms, tissues and conditions. PMID:21115530

  10. Interdisciplinary research and education at the biology-engineering-computer science interface: a perspective.

    PubMed

    Tadmor, Brigitta; Tidor, Bruce

    2005-09-01

    Progress in the life sciences, including genome sequencing and high-throughput experimentation, offers an opportunity for understanding biology and medicine from a systems perspective. This 'new view', which complements the more traditional component-based approach, involves the integration of biological research with approaches from engineering disciplines and computer science. The result is more than a new set of technologies. Rather, it promises a fundamental reconceptualization of the life sciences based on the development of quantitative and predictive models to describe crucial processes. To achieve this change, learning communities are being formed at the interface of the life sciences, engineering and computer science. Through these communities, research and education will be integrated across disciplines and the challenges associated with multidisciplinary team-based science will be addressed.

  11. Computer literacy for life sciences: helping the digital-era biology undergraduates face today's research.

    PubMed

    Smolinski, Tomasz G

    2010-01-01

    Computer literacy plays a critical role in today's life sciences research. Without the ability to use computers to efficiently manipulate and analyze large amounts of data resulting from biological experiments and simulations, many of the pressing questions in the life sciences could not be answered. Today's undergraduates, despite the ubiquity of computers in their lives, seem to be largely unfamiliar with how computers are being used to pursue and answer such questions. This article describes an innovative undergraduate-level course, titled Computer Literacy for Life Sciences, that aims to teach students the basics of a computerized scientific research pursuit. The purpose of the course is for students to develop a hands-on working experience in using standard computer software tools as well as computer techniques and methodologies used in life sciences research. This paper provides a detailed description of the didactical tools and assessment methods used in and outside of the classroom as well as a discussion of the lessons learned during the first installment of the course taught at Emory University in fall semester 2009.

  12. Calibrated peer review for computer-assisted learning of biological research competencies.

    PubMed

    Clase, Kari L; Gundlach, Ellen; Pelaez, Nancy J

    2010-09-01

    Recently, both science and technology faculty have been recognizing biological research competencies that are valued but rarely assessed. Some of these valued learning outcomes include scientific methods and thinking, critical assessment of primary papers, quantitative reasoning, communication, and putting biological research into a historical and broader social context. This article presents examples of Calibrated Peer Review (CPR) assignments that illustrate a computer-assisted method to help students achieve biological research competencies. A new release of CPR is appropriate for engaging students online in reading and writing about investigations. A participant perception inventory was designed for use as a repeated measure to discriminate among beginning, middle, and ending student perceptions. Examples are provided to demonstrate how to assess student perceptions of what they gain from instruction related to science research competencies. Results suggest that students in a large enrollment class consider CPR to be useful for helping them learn about quantitative and categorical research variables; the use of the experimental method to test ideas; the use of controls; analysis, interpretation, and presentation of data; and how to critically read primary papers.

  13. Calibrated Peer Review for Computer-Assisted Learning of Biological Research Competencies

    ERIC Educational Resources Information Center

    Clase, Kari L.; Gundlach, Ellen; Pelaez, Nancy J.

    2010-01-01

    Recently, both science and technology faculty have been recognizing biological research competencies that are valued but rarely assessed. Some of these valued learning outcomes include scientific methods and thinking, critical assessment of primary papers, quantitative reasoning, communication, and putting biological research into a historical and…

  14. Systems biology in psychiatric research: from complex data sets over wiring diagrams to computer simulations.

    PubMed

    Tretter, Felix; Gebicke-Haerter, Peter J

    2012-01-01

    The classification of psychiatric disorders has always been a problem in clinical settings. The present debate about the major systems in clinical practice, DSM-IV and ICD-10, has resulted in attempts to improve and replace those schemes by some that include more endophenotypic and molecular features. However, these disorders not only require more precise diagnostic tools, but also have to be viewed more extensively in their dynamic behaviors, which require more precise data sets related to their origins and developments. This enormous challenge in brain research has to be approached on different levels of the biological system by new methods, including improvements in electroencephalography, brain imaging, and molecular biology. All these methods entail accumulations of large data sets that become more and more difficult to interpret. In particular, on the molecular level, there is an apparent need to use highly sophisticated computer programs to tackle these problems. Evidently, only interdisciplinary work among mathematicians, physicists, biologists, and clinicians can further improve our understanding of complex diseases of the brain.

  15. Management and Analysis of Biological and Clinical Data: How Computer Science May Support Biomedical and Clinical Research

    NASA Astrophysics Data System (ADS)

    Veltri, Pierangelo

    The use of computer based solutions for data management in biology and clinical science has contributed to improve life-quality and also to gather research results in shorter time. Indeed, new algorithms and high performance computation have been using in proteomics and genomics studies for curing chronic diseases (e.g., drug designing) as well as supporting clinicians both in diagnosis (e.g., images-based diagnosis) and patient curing (e.g., computer based information analysis on information gathered from patient). In this paper we survey on examples of computer based techniques applied in both biology and clinical contexts. The reported applications are also results of experiences in real case applications at University Medical School of Catanzaro and also part of experiences of the National project Staywell SH 2.0 involving many research centers and companies aiming to study and improve citizen wellness.

  16. Aging and computational systems biology.

    PubMed

    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.

  17. An overview of computational life science databases & exchange formats of relevance to chemical biology research.

    PubMed

    Smalter Hall, Aaron; Shan, Yunfeng; Lushington, Gerald; Visvanathan, Mahesh

    2013-03-01

    Databases and exchange formats describing biological entities such as chemicals and proteins, along with their relationships, are a critical component of research in life sciences disciplines, including chemical biology wherein small information about small molecule properties converges with cellular and molecular biology. Databases for storing biological entities are growing not only in size, but also in type, with many similarities between them and often subtle differences. The data formats available to describe and exchange these entities are numerous as well. In general, each format is optimized for a particular purpose or database, and hence some understanding of these formats is required when choosing one for research purposes. This paper reviews a selection of different databases and data formats with the goal of summarizing their purposes, features, and limitations. Databases are reviewed under the categories of 1) protein interactions, 2) metabolic pathways, 3) chemical interactions, and 4) drug discovery. Representation formats will be discussed according to those describing chemical structures, and those describing genomic/proteomic entities.

  18. AN OVERVIEW OF COMPUTATIONAL LIFE SCIENCE DATABASES & EXCHANGE FORMATS OF RELEVANCE TO CHEMICAL BIOLOGY RESEARCH

    PubMed Central

    Hall, Aaron Smalter; Shan, Yunfeng; Lushington, Gerald; Visvanathan, Mahesh

    2016-01-01

    Databases and exchange formats describing biological entities such as chemicals and proteins, along with their relationships, are a critical component of research in life sciences disciplines, including chemical biology wherein small information about small molecule properties converges with cellular and molecular biology. Databases for storing biological entities are growing not only in size, but also in type, with many similarities between them and often subtle differences. The data formats available to describe and exchange these entities are numerous as well. In general, each format is optimized for a particular purpose or database, and hence some understanding of these formats is required when choosing one for research purposes. This paper reviews a selection of different databases and data formats with the goal of summarizing their purposes, features, and limitations. Databases are reviewed under the categories of 1) protein interactions, 2) metabolic pathways, 3) chemical interactions, and 4) drug discovery. Representation formats will be discussed according to those describing chemical structures, and those describing genomic/proteomic entities. PMID:22934944

  19. An Integrative Computational Framework for Hypotheses-Driven Systems Biology Research in Proteomics and Genomics

    SciTech Connect

    Cannon, William R.; Webb-Robertson, Bobbie-Jo M.; Willse, Alan R.; Singhal, Mudita; McCue, Lee Ann; McDermott, Jason E.; Taylor, Ronald C.; Waters, Katrina M.; Oehmen, Christopher S.

    2009-04-01

    Systems biology research is sometimes categorized as either discovery science or hypothesis-driven science. However, we believe that hypotheses are always used regardless, and that explicit recognition that hypothesis testing underlies all high-throughput data analysis leads to better experimental designs, data analysis and interpretation of the data. We outline the current use of hypothesis testing for proteomics data analysis in systems biology research for several projects at the Pacific Northwest National Laboratory, and provide examples of where scientific principles can be used to formulate the hypotheses used to analyze the data. We additionally discuss the data infrastructure is required to (1) track the data from different projects and diverse assays, (2) pull the data together in a congruent manner, (3) analyze the data with respect to cellular networks, and (4) visualize the resulting networks and contrast those with information from bioinformatics databases.

  20. InteractoMIX: a suite of computational tools to exploit interactomes in biological and clinical research.

    PubMed

    Poglayen, Daniel; Marín-López, Manuel Alejandro; Bonet, Jaume; Fornes, Oriol; Garcia-Garcia, Javier; Planas-Iglesias, Joan; Segura, Joan; Oliva, Baldo; Fernandez-Fuentes, Narcis

    2016-06-15

    Virtually all the biological processes that occur inside or outside cells are mediated by protein-protein interactions (PPIs). Hence, the charting and description of the PPI network, initially in organisms, the interactome, but more recently in specific tissues, is essential to fully understand cellular processes both in health and disease. The study of PPIs is also at the heart of renewed efforts in the medical and biotechnological arena in the quest of new therapeutic targets and drugs. Here, we present a mini review of 11 computational tools and resources tools developed by us to address different aspects of PPIs: from interactome level to their atomic 3D structural details. We provided details on each specific resource, aims and purpose and compare with equivalent tools in the literature. All the tools are presented in a centralized, one-stop, web site: InteractoMIX (http://interactomix.com). PMID:27284060

  1. Computational Biology, Advanced Scientific Computing, and Emerging Computational Architectures

    SciTech Connect

    2007-06-27

    This CRADA was established at the start of FY02 with $200 K from IBM and matching funds from DOE to support post-doctoral fellows in collaborative research between International Business Machines and Oak Ridge National Laboratory to explore effective use of emerging petascale computational architectures for the solution of computational biology problems. 'No cost' extensions of the CRADA were negotiated with IBM for FY03 and FY04.

  2. Synthetic biology: insights into biological computation.

    PubMed

    Manzoni, Romilde; Urrios, Arturo; Velazquez-Garcia, Silvia; de Nadal, Eulàlia; Posas, Francesc

    2016-04-18

    Organisms have evolved a broad array of complex signaling mechanisms that allow them to survive in a wide range of environmental conditions. They are able to sense external inputs and produce an output response by computing the information. Synthetic biology attempts to rationally engineer biological systems in order to perform desired functions. Our increasing understanding of biological systems guides this rational design, while the huge background in electronics for building circuits defines the methodology. In this context, biocomputation is the branch of synthetic biology aimed at implementing artificial computational devices using engineered biological motifs as building blocks. Biocomputational devices are defined as biological systems that are able to integrate inputs and return outputs following pre-determined rules. Over the last decade the number of available synthetic engineered devices has increased exponentially; simple and complex circuits have been built in bacteria, yeast and mammalian cells. These devices can manage and store information, take decisions based on past and present inputs, and even convert a transient signal into a sustained response. The field is experiencing a fast growth and every day it is easier to implement more complex biological functions. This is mainly due to advances in in vitro DNA synthesis, new genome editing tools, novel molecular cloning techniques, continuously growing part libraries as well as other technological advances. This allows that digital computation can now be engineered and implemented in biological systems. Simple logic gates can be implemented and connected to perform novel desired functions or to better understand and redesign biological processes. Synthetic biological digital circuits could lead to new therapeutic approaches, as well as new and efficient ways to produce complex molecules such as antibiotics, bioplastics or biofuels. Biological computation not only provides possible biomedical and

  3. Synthetic biology: insights into biological computation.

    PubMed

    Manzoni, Romilde; Urrios, Arturo; Velazquez-Garcia, Silvia; de Nadal, Eulàlia; Posas, Francesc

    2016-04-18

    Organisms have evolved a broad array of complex signaling mechanisms that allow them to survive in a wide range of environmental conditions. They are able to sense external inputs and produce an output response by computing the information. Synthetic biology attempts to rationally engineer biological systems in order to perform desired functions. Our increasing understanding of biological systems guides this rational design, while the huge background in electronics for building circuits defines the methodology. In this context, biocomputation is the branch of synthetic biology aimed at implementing artificial computational devices using engineered biological motifs as building blocks. Biocomputational devices are defined as biological systems that are able to integrate inputs and return outputs following pre-determined rules. Over the last decade the number of available synthetic engineered devices has increased exponentially; simple and complex circuits have been built in bacteria, yeast and mammalian cells. These devices can manage and store information, take decisions based on past and present inputs, and even convert a transient signal into a sustained response. The field is experiencing a fast growth and every day it is easier to implement more complex biological functions. This is mainly due to advances in in vitro DNA synthesis, new genome editing tools, novel molecular cloning techniques, continuously growing part libraries as well as other technological advances. This allows that digital computation can now be engineered and implemented in biological systems. Simple logic gates can be implemented and connected to perform novel desired functions or to better understand and redesign biological processes. Synthetic biological digital circuits could lead to new therapeutic approaches, as well as new and efficient ways to produce complex molecules such as antibiotics, bioplastics or biofuels. Biological computation not only provides possible biomedical and

  4. Computational Biology: A Strategic Initiative LDRD

    SciTech Connect

    Barksy, D; Colvin, M

    2002-02-07

    The goal of this Strategic Initiative LDRD project was to establish at LLNL a new core capability in computational biology, combining laboratory strengths in high performance computing, molecular biology, and computational chemistry and physics. As described in this report, this project has been very successful in achieving this goal. This success is demonstrated by the large number of referred publications, invited talks, and follow-on research grants that have resulted from this project. Additionally, this project has helped build connections to internal and external collaborators and funding agencies that will be critical to the long-term vitality of LLNL programs in computational biology. Most importantly, this project has helped establish on-going research groups in the Biology and Biotechnology Research Program, the Physics and Applied Technology Directorate, and the Computation Directorate. These groups include three laboratory staff members originally hired as post-doctoral researchers for this strategic initiative.

  5. Computational biology for cardiovascular biomarker discovery.

    PubMed

    Azuaje, Francisco; Devaux, Yvan; Wagner, Daniel

    2009-07-01

    Computational biology is essential in the process of translating biological knowledge into clinical practice, as well as in the understanding of biological phenomena based on the resources and technologies originating from the clinical environment. One such key contribution of computational biology is the discovery of biomarkers for predicting clinical outcomes using 'omic' information. This process involves the predictive modelling and integration of different types of data and knowledge for screening, diagnostic or prognostic purposes. Moreover, this requires the design and combination of different methodologies based on statistical analysis and machine learning. This article introduces key computational approaches and applications to biomarker discovery based on different types of 'omic' data. Although we emphasize applications in cardiovascular research, the computational requirements and advances discussed here are also relevant to other domains. We will start by introducing some of the contributions of computational biology to translational research, followed by an overview of methods and technologies used for the identification of biomarkers with predictive or classification value. The main types of 'omic' approaches to biomarker discovery will be presented with specific examples from cardiovascular research. This will include a review of computational methodologies for single-source and integrative data applications. Major computational methods for model evaluation will be described together with recommendations for reporting models and results. We will present recent advances in cardiovascular biomarker discovery based on the combination of gene expression and functional network analyses. The review will conclude with a discussion of key challenges for computational biology, including perspectives from the biosciences and clinical areas.

  6. Biology and medical research at the exascale.

    SciTech Connect

    Wolf, L.; Pieper, G. W.

    2010-01-01

    Advances in computational hardware and algorithms that have transformed areas of physics and engineering have recently brought similar benefits to biology and biomedical research. Biological sciences are undergoing a revolution. High-performance computing has accelerated the transition from hypothesis-driven to design-driven research at all scales, and computational simulation of biological systems is now driving the direction of biological experimentation and the generation of insights.

  7. Computational Biology and High Performance Computing 2000

    SciTech Connect

    Simon, Horst D.; Zorn, Manfred D.; Spengler, Sylvia J.; Shoichet, Brian K.; Stewart, Craig; Dubchak, Inna L.; Arkin, Adam P.

    2000-10-19

    The pace of extraordinary advances in molecular biology has accelerated in the past decade due in large part to discoveries coming from genome projects on human and model organisms. The advances in the genome project so far, happening well ahead of schedule and under budget, have exceeded any dreams by its protagonists, let alone formal expectations. Biologists expect the next phase of the genome project to be even more startling in terms of dramatic breakthroughs in our understanding of human biology, the biology of health and of disease. Only today can biologists begin to envision the necessary experimental, computational and theoretical steps necessary to exploit genome sequence information for its medical impact, its contribution to biotechnology and economic competitiveness, and its ultimate contribution to environmental quality. High performance computing has become one of the critical enabling technologies, which will help to translate this vision of future advances in biology into reality. Biologists are increasingly becoming aware of the potential of high performance computing. The goal of this tutorial is to introduce the exciting new developments in computational biology and genomics to the high performance computing community.

  8. Space biology research development

    NASA Technical Reports Server (NTRS)

    Bonting, Sjoerd L.

    1993-01-01

    The purpose of the Search for Extraterrestrial Intelligence (SETI) Institute is to conduct and promote research related activities regarding the search for extraterrestrial life, particularly intelligent life. Such research encompasses the broad discipline of 'Life in the Universe', including all scientific and technological aspects of astronomy and the planetary sciences, chemical evolution, the origin of life, biological evolution, and cultural evolution. The primary purpose was to provide funding for the Principal Investigator to collaborate with the personnel of the SETI Institute and the NASA-Ames Research center in order to plan and develop space biology research on and in connection with Space Station Freedom; to promote cooperation with the international partners in the space station; to conduct a study on the use of biosensors in space biology research and life support system operation; and to promote space biology research through the initiation of an annual publication 'Advances in Space Biology and Medicine'.

  9. India's Computational Biology Growth and Challenges.

    PubMed

    Chakraborty, Chiranjib; Bandyopadhyay, Sanghamitra; Agoramoorthy, Govindasamy

    2016-09-01

    India's computational science is growing swiftly due to the outburst of internet and information technology services. The bioinformatics sector of India has been transforming rapidly by creating a competitive position in global bioinformatics market. Bioinformatics is widely used across India to address a wide range of biological issues. Recently, computational researchers and biologists are collaborating in projects such as database development, sequence analysis, genomic prospects and algorithm generations. In this paper, we have presented the Indian computational biology scenario highlighting bioinformatics-related educational activities, manpower development, internet boom, service industry, research activities, conferences and trainings undertaken by the corporate and government sectors. Nonetheless, this new field of science faces lots of challenges.

  10. MODELING HOST-PATHOGEN INTERACTIONS: COMPUTATIONAL BIOLOGY AND BIOINFORMATICS FOR INFECTIOUS DISEASE RESEARCH (Session introduction)

    SciTech Connect

    McDermott, Jason E.; Braun, Pascal; Bonneau, Richard A.; Hyduke, Daniel R.

    2011-12-01

    Pathogenic infections are a major cause of both human disease and loss of crop yields and animal stocks and thus cause immense damage to the worldwide economy. The significance of infectious diseases is expected to increase in an ever more connected warming world, in which new viral, bacterial and fungal pathogens can find novel hosts and ecologic niches. At the same time, the complex and sophisticated mechanisms by which diverse pathogenic agents evade defense mechanisms and subvert their hosts networks to suit their lifestyle needs is still very incompletely understood especially from a systems perspective [1]. Thus, understanding host-pathogen interactions is both an important and a scientifically fascinating topic. Recently, technology has offered the opportunity to investigate host-pathogen interactions on a level of detail and scope that offers immense computational and analytical possibilities. Genome sequencing was pioneered on some of these pathogens, and the number of strains and variants of pathogens sequenced to date vastly outnumbers the number of host genomes available. At the same time, for both plant and human hosts more and more data on population level genomic variation becomes available and offers a rich field for analysis into the genetic interactions between host and pathogen.

  11. Computational Skills for Biology Students

    ERIC Educational Resources Information Center

    Gross, Louis J.

    2008-01-01

    This interview with Distinguished Science Award recipient Louis J. Gross highlights essential computational skills for modern biology, including: (1) teaching concepts listed in the Math & Bio 2010 report; (2) illustrating to students that jobs today require quantitative skills; and (3) resources and materials that focus on computational skills.

  12. Limits of computational biology.

    PubMed

    Bray, Dennis

    2015-01-01

    Are we close to a complete inventory of living processes so that we might expect in the near future to reproduce every essential aspect necessary for life? Or are there mechanisms and processes in cells and organisms that are presently inaccessible to us? Here I argue that a close examination of a particularly well-understood system--that of Escherichia coli chemotaxis--shows we are still a long way from a complete description. There is a level of molecular uncertainty, particularly that responsible for fine-tuning and adaptation to myriad external conditions, which we presently cannot resolve or reproduce on a computer. Moreover, the same uncertainty exists for any process in any organism and is especially pronounced and important in higher animals such as humans. Embryonic development, tissue homeostasis, immune recognition, memory formation, and survival in the real world, all depend on vast numbers of subtle variations in cell chemistry most of which are presently unknown or only poorly characterized. Overcoming these limitations will require us to not only accumulate large quantities of highly detailed data but also develop new computational methods able to recapitulate the massively parallel processing of living cells.

  13. Limits of computational biology

    PubMed Central

    Bray, Dennis

    2015-01-01

    Abstract Are we close to a complete inventory of living processes so that we might expect in the near future to reproduce every essential aspect necessary for life? Or are there mechanisms and processes in cells and organisms that are presently inaccessible to us? Here I argue that a close examination of a particularly well-understood system— that of Escherichia coli chemotaxis— shows we are still a long way from a complete description. There is a level of molecular uncertainty, particularly that responsible for fine-tuning and adaptation to myriad external conditions, which we presently cannot resolve or reproduce on a computer. Moreover, the same uncertainty exists for any process in any organism and is especially pronounced and important in higher animals such as humans. Embryonic development, tissue homeostasis, immune recognition, memory formation, and survival in the real world, all depend on vast numbers of subtle variations in cell chemistry most of which are presently unknown or only poorly characterized. Overcoming these limitations will require us to not only accumulate large quantities of highly detailed data but also develop new computational methods able to recapitulate the massively parallel processing of living cells. PMID:25318467

  14. Encouraging Student Biological Research.

    ERIC Educational Resources Information Center

    Frame, Kathy, Ed.; Hays, Rachel, Ed.; Mack, Alison, Ed.

    This publication encourages student involvement in biological research through student research with the cooperation of teachers and scientists. The contents of the book are divided into two sections. The first section introduces students to research investigations and includes: (1) "How the Investigations Are Set Up and the Rationale Behind Their…

  15. Computational representation of biological systems

    SciTech Connect

    Frazier, Zach; McDermott, Jason E.; Guerquin, Michal; Samudrala, Ram

    2009-04-20

    Integration of large and diverse biological data sets is a daunting problem facing systems biology researchers. Exploring the complex issues of data validation, integration, and representation, we present a systematic approach for the management and analysis of large biological data sets based on data warehouses. Our system has been implemented in the Bioverse, a framework combining diverse protein information from a variety of knowledge areas such as molecular interactions, pathway localization, protein structure, and protein function.

  16. BIONET: national computer resource for molecular biology.

    PubMed Central

    Smith, D H; Brutlag, D; Friedland, P; Kedes, L H

    1986-01-01

    This paper describes briefly the BIONET National Computer Resource for Molecular Biology. This presentation is intended as information for scientists in molecular biology and related disciplines who require access to computational methods for sequence analysis. We describe the goals, and the service and research opportunities offered to the community by BIONET, the relationship of BIONET to other national and regional resources, our recent efforts toward distribution of the resource to BIONET Satellites, and procedures for investigators to gain access to the Resource. PMID:3945548

  17. Computational optimization and biological evolution.

    PubMed

    Goryanin, Igor

    2010-10-01

    Modelling and optimization principles become a key concept in many biological areas, especially in biochemistry. Definitions of objective function, fitness and co-evolution, although they differ between biology and mathematics, are similar in a general sense. Although successful in fitting models to experimental data, and some biochemical predictions, optimization and evolutionary computations should be developed further to make more accurate real-life predictions, and deal not only with one organism in isolation, but also with communities of symbiotic and competing organisms. One of the future goals will be to explain and predict evolution not only for organisms in shake flasks or fermenters, but for real competitive multispecies environments.

  18. 2K09 and thereafter : the coming era of integrative bioinformatics, systems biology and intelligent computing for functional genomics and personalized medicine research.

    PubMed

    Yang, Jack Y; Niemierko, Andrzej; Bajcsy, Ruzena; Xu, Dong; Athey, Brian D; Zhang, Aidong; Ersoy, Okan K; Li, Guo-Zheng; Borodovsky, Mark; Zhang, Joe C; Arabnia, Hamid R; Deng, Youping; Dunker, A Keith; Liu, Yunlong; Ghafoor, Arif

    2010-12-01

    Significant interest exists in establishing synergistic research in bioinformatics, systems biology and intelligent computing. Supported by the United States National Science Foundation (NSF), International Society of Intelligent Biological Medicine (http://www.ISIBM.org), International Journal of Computational Biology and Drug Design (IJCBDD) and International Journal of Functional Informatics and Personalized Medicine, the ISIBM International Joint Conferences on Bioinformatics, Systems Biology and Intelligent Computing (ISIBM IJCBS 2009) attracted more than 300 papers and 400 researchers and medical doctors world-wide. It was the only inter/multidisciplinary conference aimed to promote synergistic research and education in bioinformatics, systems biology and intelligent computing. The conference committee was very grateful for the valuable advice and suggestions from honorary chairs, steering committee members and scientific leaders including Dr. Michael S. Waterman (USC, Member of United States National Academy of Sciences), Dr. Chih-Ming Ho (UCLA, Member of United States National Academy of Engineering and Academician of Academia Sinica), Dr. Wing H. Wong (Stanford, Member of United States National Academy of Sciences), Dr. Ruzena Bajcsy (UC Berkeley, Member of United States National Academy of Engineering and Member of United States Institute of Medicine of the National Academies), Dr. Mary Qu Yang (United States National Institutes of Health and Oak Ridge, DOE), Dr. Andrzej Niemierko (Harvard), Dr. A. Keith Dunker (Indiana), Dr. Brian D. Athey (Michigan), Dr. Weida Tong (FDA, United States Department of Health and Human Services), Dr. Cathy H. Wu (Georgetown), Dr. Dong Xu (Missouri), Drs. Arif Ghafoor and Okan K Ersoy (Purdue), Dr. Mark Borodovsky (Georgia Tech, President of ISIBM), Dr. Hamid R. Arabnia (UGA, Vice-President of ISIBM), and other scientific leaders. The committee presented the 2009 ISIBM Outstanding Achievement Awards to Dr. Joydeep Ghosh (UT

  19. 2K09 and thereafter : the coming era of integrative bioinformatics, systems biology and intelligent computing for functional genomics and personalized medicine research

    PubMed Central

    2010-01-01

    Significant interest exists in establishing synergistic research in bioinformatics, systems biology and intelligent computing. Supported by the United States National Science Foundation (NSF), International Society of Intelligent Biological Medicine (http://www.ISIBM.org), International Journal of Computational Biology and Drug Design (IJCBDD) and International Journal of Functional Informatics and Personalized Medicine, the ISIBM International Joint Conferences on Bioinformatics, Systems Biology and Intelligent Computing (ISIBM IJCBS 2009) attracted more than 300 papers and 400 researchers and medical doctors world-wide. It was the only inter/multidisciplinary conference aimed to promote synergistic research and education in bioinformatics, systems biology and intelligent computing. The conference committee was very grateful for the valuable advice and suggestions from honorary chairs, steering committee members and scientific leaders including Dr. Michael S. Waterman (USC, Member of United States National Academy of Sciences), Dr. Chih-Ming Ho (UCLA, Member of United States National Academy of Engineering and Academician of Academia Sinica), Dr. Wing H. Wong (Stanford, Member of United States National Academy of Sciences), Dr. Ruzena Bajcsy (UC Berkeley, Member of United States National Academy of Engineering and Member of United States Institute of Medicine of the National Academies), Dr. Mary Qu Yang (United States National Institutes of Health and Oak Ridge, DOE), Dr. Andrzej Niemierko (Harvard), Dr. A. Keith Dunker (Indiana), Dr. Brian D. Athey (Michigan), Dr. Weida Tong (FDA, United States Department of Health and Human Services), Dr. Cathy H. Wu (Georgetown), Dr. Dong Xu (Missouri), Drs. Arif Ghafoor and Okan K Ersoy (Purdue), Dr. Mark Borodovsky (Georgia Tech, President of ISIBM), Dr. Hamid R. Arabnia (UGA, Vice-President of ISIBM), and other scientific leaders. The committee presented the 2009 ISIBM Outstanding Achievement Awards to Dr. Joydeep Ghosh (UT

  20. Biomaterial science meets computational biology.

    PubMed

    Hutmacher, Dietmar W; Little, J Paige; Pettet, Graeme J; Loessner, Daniela

    2015-05-01

    There is a pressing need for a predictive tool capable of revealing a holistic understanding of fundamental elements in the normal and pathological cell physiology of organoids in order to decipher the mechanoresponse of cells. Therefore, the integration of a systems bioengineering approach into a validated mathematical model is necessary to develop a new simulation tool. This tool can only be innovative by combining biomaterials science with computational biology. Systems-level and multi-scale experimental data are incorporated into a single framework, thus representing both single cells and collective cell behaviour. Such a computational platform needs to be validated in order to discover key mechano-biological factors associated with cell-cell and cell-niche interactions.

  1. Applicability of computational systems biology in toxicology.

    PubMed

    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.

  2. From computational quantum chemistry to computational biology: experiments and computations are (full) partners.

    PubMed

    Ma, Buyong; Nussinov, Ruth

    2004-12-01

    Computations are being integrated into biological research at an increasingly fast pace. This has not only changed the way in which biological information is managed; it has also changed the way in which experiments are planned in order to obtain information from nature. Can experiments and computations be full partners? Computational chemistry has expanded over the years, proceeding from computations of a hydrogen molecule toward the challenging goal of systems biology, which attempts to handle the entire living cell. Applying theories from ab initio quantum mechanics to simplified models, the virtual worlds explored by computations provide replicas of real-world phenomena. At the same time, the virtual worlds can affect our perception of the real world. Computational biology targets a world of complex organization, for which a unified theory is unlikely to exist. A computational biology model, even if it has a clear physical or chemical basis, may not reduce to physics and chemistry. At the molecular level, computational biology and experimental biology have already been partners, mutually benefiting from each other. For the perception to become reality, computation and experiment should be united as full partners in biological research.

  3. PERSPECTIVE: From computational quantum chemistry to computational biology: experiments and computations are (full) partners

    NASA Astrophysics Data System (ADS)

    Ma, Buyong; Nussinov, Ruth

    2004-12-01

    Computations are being integrated into biological research at an increasingly fast pace. This has not only changed the way in which biological information is managed; it has also changed the way in which experiments are planned in order to obtain information from nature. Can experiments and computations be full partners? Computational chemistry has expanded over the years, proceeding from computations of a hydrogen molecule toward the challenging goal of systems biology, which attempts to handle the entire living cell. Applying theories from ab initio quantum mechanics to simplified models, the virtual worlds explored by computations provide replicas of real-world phenomena. At the same time, the virtual worlds can affect our perception of the real world. Computational biology targets a world of complex organization, for which a unified theory is unlikely to exist. A computational biology model, even if it has a clear physical or chemical basis, may not reduce to physics and chemistry. At the molecular level, computational biology and experimental biology have already been partners, mutually benefiting from each other. For the perception to become reality, computation and experiment should be united as full partners in biological research.

  4. India's Computational Biology Growth and Challenges.

    PubMed

    Chakraborty, Chiranjib; Bandyopadhyay, Sanghamitra; Agoramoorthy, Govindasamy

    2016-09-01

    India's computational science is growing swiftly due to the outburst of internet and information technology services. The bioinformatics sector of India has been transforming rapidly by creating a competitive position in global bioinformatics market. Bioinformatics is widely used across India to address a wide range of biological issues. Recently, computational researchers and biologists are collaborating in projects such as database development, sequence analysis, genomic prospects and algorithm generations. In this paper, we have presented the Indian computational biology scenario highlighting bioinformatics-related educational activities, manpower development, internet boom, service industry, research activities, conferences and trainings undertaken by the corporate and government sectors. Nonetheless, this new field of science faces lots of challenges. PMID:27465042

  5. Computational biology and bioinformatics in Nigeria.

    PubMed

    Fatumo, Segun A; Adoga, Moses P; Ojo, Opeolu O; Oluwagbemi, Olugbenga; Adeoye, Tolulope; Ewejobi, Itunuoluwa; Adebiyi, Marion; Adebiyi, Ezekiel; Bewaji, Clement; Nashiru, Oyekanmi

    2014-04-01

    Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries.

  6. Computational Biology and Bioinformatics in Nigeria

    PubMed Central

    Fatumo, Segun A.; Adoga, Moses P.; Ojo, Opeolu O.; Oluwagbemi, Olugbenga; Adeoye, Tolulope; Ewejobi, Itunuoluwa; Adebiyi, Marion; Adebiyi, Ezekiel; Bewaji, Clement; Nashiru, Oyekanmi

    2014-01-01

    Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries. PMID:24763310

  7. Deep learning for computational biology.

    PubMed

    Angermueller, Christof; Pärnamaa, Tanel; Parts, Leopold; Stegle, Oliver

    2016-01-01

    Technological advances in genomics and imaging have led to an explosion of molecular and cellular profiling data from large numbers of samples. This rapid increase in biological data dimension and acquisition rate is challenging conventional analysis strategies. Modern machine learning methods, such as deep learning, promise to leverage very large data sets for finding hidden structure within them, and for making accurate predictions. In this review, we discuss applications of this new breed of analysis approaches in regulatory genomics and cellular imaging. We provide background of what deep learning is, and the settings in which it can be successfully applied to derive biological insights. In addition to presenting specific applications and providing tips for practical use, we also highlight possible pitfalls and limitations to guide computational biologists when and how to make the most use of this new technology. PMID:27474269

  8. Deep learning for computational biology.

    PubMed

    Angermueller, Christof; Pärnamaa, Tanel; Parts, Leopold; Stegle, Oliver

    2016-07-29

    Technological advances in genomics and imaging have led to an explosion of molecular and cellular profiling data from large numbers of samples. This rapid increase in biological data dimension and acquisition rate is challenging conventional analysis strategies. Modern machine learning methods, such as deep learning, promise to leverage very large data sets for finding hidden structure within them, and for making accurate predictions. In this review, we discuss applications of this new breed of analysis approaches in regulatory genomics and cellular imaging. We provide background of what deep learning is, and the settings in which it can be successfully applied to derive biological insights. In addition to presenting specific applications and providing tips for practical use, we also highlight possible pitfalls and limitations to guide computational biologists when and how to make the most use of this new technology.

  9. Computational Biology of Olfactory Receptors

    PubMed Central

    Crasto, Chiquito J.

    2011-01-01

    Olfactory receptors, in addition to being involved in first step of the physiological processes that leads to olfaction, occupy an important place in mammalian genomes. ORs constitute super families in these genomes. Elucidating ol-factory receptor function at a molecular level can be aided by a computationally derived structure and an understanding of its interactions with odor molecules. Experimental functional analyses of olfactory receptors in conjunction with computational studies serve to validate findings and generate hypotheses. We present here a review of the research efforts in: creating computational models of olfactory receptors, identifying binding strategies for these receptors with odorant molecules, performing medium to long range simulation studies of odor ligands in the receptor binding region, and identifying amino acid positions within the receptor that are responsible for ligand-binding and olfactory receptor activation. Written as a primer and a teaching tool, this review will help researchers extend the methodologies described herein to other GPCRs. PMID:21984880

  10. Computational biology of RNA interactions.

    PubMed

    Dieterich, Christoph; Stadler, Peter F

    2013-01-01

    The biodiversity of the RNA world has been underestimated for decades. RNA molecules are key building blocks, sensors, and regulators of modern cells. The biological function of RNA molecules cannot be separated from their ability to bind to and interact with a wide space of chemical species, including small molecules, nucleic acids, and proteins. Computational chemists, physicists, and biologists have developed a rich tool set for modeling and predicting RNA interactions. These interactions are to some extent determined by the binding conformation of the RNA molecule. RNA binding conformations are approximated with often acceptable accuracy by sequence and secondary structure motifs. Secondary structure ensembles of a given RNA molecule can be efficiently computed in many relevant situations by employing a standard energy model for base pair interactions and dynamic programming techniques. The case of bi-molecular RNA-RNA interactions can be seen as an extension of this approach. However, unbiased transcriptome-wide scans for local RNA-RNA interactions are computationally challenging yet become efficient if the binding motif/mode is known and other external information can be used to confine the search space. Computational methods are less developed for proteins and small molecules, which bind to RNA with very high specificity. Binding descriptors of proteins are usually determined by in vitro high-throughput assays (e.g., microarrays or sequencing). Intriguingly, recent experimental advances, which are mostly based on light-induced cross-linking of binding partners, render in vivo binding patterns accessible yet require new computational methods for careful data interpretation. The grand challenge is to model the in vivo situation where a complex interplay of RNA binders competes for the same target RNA molecule. Evidently, bioinformaticians are just catching up with the impressive pace of these developments.

  11. Biological Basis For Computer Vision: Some Perspectives

    NASA Astrophysics Data System (ADS)

    Gupta, Madan M.

    1990-03-01

    Using biology as a basis for the development of sensors, devices and computer vision systems is a challenge to systems and vision scientists. It is also a field of promising research for engineering applications. Biological sensory systems, such as vision, touch and hearing, sense different physical phenomena from our environment, yet they possess some common mathematical functions. These mathematical functions are cast into the neural layers which are distributed throughout our sensory regions, sensory information transmission channels and in the cortex, the centre of perception. In this paper, we are concerned with the study of the biological vision system and the emulation of some of its mathematical functions, both retinal and visual cortex, for the development of a robust computer vision system. This field of research is not only intriguing, but offers a great challenge to systems scientists in the development of functional algorithms. These functional algorithms can be generalized for further studies in such fields as signal processing, control systems and image processing. Our studies are heavily dependent on the the use of fuzzy - neural layers and generalized receptive fields. Building blocks of such neural layers and receptive fields may lead to the design of better sensors and better computer vision systems. It is hoped that these studies will lead to the development of better artificial vision systems with various applications to vision prosthesis for the blind, robotic vision, medical imaging, medical sensors, industrial automation, remote sensing, space stations and ocean exploration.

  12. Designing integrated computational biology pipelines visually.

    PubMed

    Jamil, Hasan M

    2013-01-01

    The long-term cost of developing and maintaining a computational pipeline that depends upon data integration and sophisticated workflow logic is too high to even contemplate "what if" or ad hoc type queries. In this paper, we introduce a novel application building interface for computational biology research, called VizBuilder, by leveraging a recent query language called BioFlow for life sciences databases. Using VizBuilder, it is now possible to develop ad hoc complex computational biology applications at throw away costs. The underlying query language supports data integration and workflow construction almost transparently and fully automatically, using a best effort approach. Users express their application by drawing it with VizBuilder icons and connecting them in a meaningful way. Completed applications are compiled and translated as BioFlow queries for execution by the data management system LifeDB, for which VizBuilder serves as a front end. We discuss VizBuilder features and functionalities in the context of a real life application after we briefly introduce BioFlow. The architecture and design principles of VizBuilder are also discussed. Finally, we outline future extensions of VizBuilder. To our knowledge, VizBuilder is a unique system that allows visually designing computational biology pipelines involving distributed and heterogeneous resources in an ad hoc manner.

  13. Data-intensive computing laying foundation for biological breakthroughs

    SciTech Connect

    Hachigian, David J.

    2007-06-18

    Finding a different way is the goal of the Data-Intensive Computing for Complex Biological Systems (Biopilot) project—a joint research effort between the Pacific Northwest National Laboratory (PNNL) and Oak Ridge National Laboratory funded by the U.S. Department of Energy’s Office of Advanced Scientific Computing Research. The two national laboratories, both of whom are world leaders in computing and computational sciences, are teaming to support areas of biological research in urgent need of data-intensive computing capabilities.

  14. The case for biological quantum computer elements

    NASA Astrophysics Data System (ADS)

    Baer, Wolfgang; Pizzi, Rita

    2009-05-01

    An extension to vonNeumann's analysis of quantum theory suggests self-measurement is a fundamental process of Nature. By mapping the quantum computer to the brain architecture we will argue that the cognitive experience results from a measurement of a quantum memory maintained by biological entities. The insight provided by this mapping suggests quantum effects are not restricted to small atomic and nuclear phenomena but are an integral part of our own cognitive experience and further that the architecture of a quantum computer system parallels that of a conscious brain. We will then review the suggestions for biological quantum elements in basic neural structures and address the de-coherence objection by arguing for a self- measurement event model of Nature. We will argue that to first order approximation the universe is composed of isolated self-measurement events which guaranties coherence. Controlled de-coherence is treated as the input/output interactions between quantum elements of a quantum computer and the quantum memory maintained by biological entities cognizant of the quantum calculation results. Lastly we will present stem-cell based neuron experiments conducted by one of us with the aim of demonstrating the occurrence of quantum effects in living neural networks and discuss future research projects intended to reach this objective.

  15. Research in computer science

    NASA Technical Reports Server (NTRS)

    Ortega, J. M.

    1986-01-01

    Various graduate research activities in the field of computer science are reported. Among the topics discussed are: (1) failure probabilities in multi-version software; (2) Gaussian Elimination on parallel computers; (3) three dimensional Poisson solvers on parallel/vector computers; (4) automated task decomposition for multiple robot arms; (5) multi-color incomplete cholesky conjugate gradient methods on the Cyber 205; and (6) parallel implementation of iterative methods for solving linear equations.

  16. A first attempt to bring computational biology into advanced high school biology classrooms.

    PubMed

    Gallagher, Suzanne Renick; Coon, William; Donley, Kristin; Scott, Abby; Goldberg, Debra S

    2011-10-01

    Computer science has become ubiquitous in many areas of biological research, yet most high school and even college students are unaware of this. As a result, many college biology majors graduate without adequate computational skills for contemporary fields of biology. The absence of a computational element in secondary school biology classrooms is of growing concern to the computational biology community and biology teachers who would like to acquaint their students with updated approaches in the discipline. We present a first attempt to correct this absence by introducing a computational biology element to teach genetic evolution into advanced biology classes in two local high schools. Our primary goal was to show students how computation is used in biology and why a basic understanding of computation is necessary for research in many fields of biology. This curriculum is intended to be taught by a computational biologist who has worked with a high school advanced biology teacher to adapt the unit for his/her classroom, but a motivated high school teacher comfortable with mathematics and computing may be able to teach this alone. In this paper, we present our curriculum, which takes into consideration the constraints of the required curriculum, and discuss our experiences teaching it. We describe the successes and challenges we encountered while bringing this unit to high school students, discuss how we addressed these challenges, and make suggestions for future versions of this curriculum.We believe that our curriculum can be a valuable seed for further development of computational activities aimed at high school biology students. Further, our experiences may be of value to others teaching computational biology at this level. Our curriculum can be obtained at http://ecsite.cs.colorado.edu/?page_id=149#biology or by contacting the authors.

  17. Computer Analogies: Teaching Molecular Biology and Ecology.

    ERIC Educational Resources Information Center

    Rice, Stanley; McArthur, John

    2002-01-01

    Suggests that computer science analogies can aid the understanding of gene expression, including the storage of genetic information on chromosomes. Presents a matrix of biology and computer science concepts. (DDR)

  18. Computational cell biology at the home of the helix.

    PubMed

    Ward, Jonathan J; Nédélec, Francois J

    2010-06-01

    The Computational Cell Biology Conference, held jointly by the Cold Spring Harbor Laboratory and the Wellcome Trust, was convened in the grand surroundings of Hinxton Hall near Cambridge, UK. The high quality of the research presented at the meeting confirmed that the field of computational cell biology is maturing rapidly, which mirrors the progression of cell biology from being mostly descriptive to a more quantitative discipline.

  19. LINC: biology's revolutionary little computer.

    PubMed

    November, Joe

    2004-09-01

    The 1963 LINC (Laboratory INstrument Computer) stands at the center of two stories: the computerization of the biologist's laboratory and the advent of small-scale computing. The brainchild of Wesley Clark, 'the most brilliant computer designer of his generation', LINC was developed specifically to address the failure of biologists to adopt computer technology. To meet their unique needs, Clark built a machine the radical design of which defied and subverted the then dominant conventions of computer architecture.

  20. LINC: biology's revolutionary little computer.

    PubMed

    November, Joe

    2004-09-01

    The 1963 LINC (Laboratory INstrument Computer) stands at the center of two stories: the computerization of the biologist's laboratory and the advent of small-scale computing. The brainchild of Wesley Clark, 'the most brilliant computer designer of his generation', LINC was developed specifically to address the failure of biologists to adopt computer technology. To meet their unique needs, Clark built a machine the radical design of which defied and subverted the then dominant conventions of computer architecture. PMID:15350765

  1. Excellence in Computational Biology and Informatics — EDRN Public Portal

    Cancer.gov

    9th Early Detection Research Network (EDRN) Scientific Workshop. Excellence in Computational Biology and Informatics: Sponsored by the EDRN Data Sharing Subcommittee Moderator: Daniel Crichton, M.S., NASA Jet Propulsion Laboratory

  2. UC Merced Center for Computational Biology Final Report

    SciTech Connect

    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

  3. Research in computer science

    NASA Technical Reports Server (NTRS)

    Ortega, J. M.

    1985-01-01

    Synopses are given for NASA supported work in computer science at the University of Virginia. Some areas of research include: error seeding as a testing method; knowledge representation for engineering design; analysis of faults in a multi-version software experiment; implementation of a parallel programming environment; two computer graphics systems for visualization of pressure distribution and convective density particles; task decomposition for multiple robot arms; vectorized incomplete conjugate gradient; and iterative methods for solving linear equations on the Flex/32.

  4. Research in Computational Astrobiology

    NASA Technical Reports Server (NTRS)

    Chaban, Galina; Colombano, Silvano; Scargle, Jeff; New, Michael H.; Pohorille, Andrew; Wilson, Michael A.

    2003-01-01

    We report on several projects in the field of computational astrobiology, which is devoted to advancing our understanding of the origin, evolution and distribution of life in the Universe using theoretical and computational tools. Research projects included modifying existing computer simulation codes to use efficient, multiple time step algorithms, statistical methods for analysis of astrophysical data via optimal partitioning methods, electronic structure calculations on water-nuclei acid complexes, incorporation of structural information into genomic sequence analysis methods and calculations of shock-induced formation of polycylic aromatic hydrocarbon compounds.

  5. Bringing Advanced Computational Techniques to Energy Research

    SciTech Connect

    Mitchell, Julie C

    2012-11-17

    Please find attached our final technical report for the BACTER Institute award. BACTER was created as a graduate and postdoctoral training program for the advancement of computational biology applied to questions of relevance to bioenergy research.

  6. Data-intensive computing laying foundation for biological breakthroughs

    SciTech Connect

    Straatsma, TP

    2007-06-18

    Biological breakthroughs critical to solving society’s most challenging problems require new and innovative tools and a “different way” to analyze the enormous amounts of data being generated. This article for the Breakthroughs magazine focuses on the Data-Intensive Computing for Complex Biological Systems (Biopilot) project—a joint research effort between the Pacific Northwest National Laboratory (PNNL) and Oak Ridge National Laboratory funded by the U.S. Department of Energy’s Office of Advanced Scientific Computing Research. The two national laboratories, both of whom are world leaders in computing and computational sciences, are teaming to support areas of biological research in urgent need of data-intensive computing capabilities.

  7. Research in Computational Astrobiology

    NASA Technical Reports Server (NTRS)

    Chaban, Galina; Jaffe, Richard; Liang, Shoudan; New, Michael H.; Pohorille, Andrew; Wilson, Michael A.

    2002-01-01

    We present results from several projects in the new field of computational astrobiology, which is devoted to advancing our understanding of the origin, evolution and distribution of life in the Universe using theoretical and computational tools. We have developed a procedure for calculating long-range effects in molecular dynamics using a plane wave expansion of the electrostatic potential. This method is expected to be highly efficient for simulating biological systems on massively parallel supercomputers. We have perform genomics analysis on a family of actin binding proteins. We have performed quantum mechanical calculations on carbon nanotubes and nucleic acids, which simulations will allow us to investigate possible sources of organic material on the early earth. Finally, we have developed a model of protobiological chemistry using neural networks.

  8. Analog Computer Laboratory with Biological Examples.

    ERIC Educational Resources Information Center

    Strebel, Donald E.

    1979-01-01

    The use of biological examples in teaching applications of the analog computer is discussed and several examples from mathematical ecology, enzyme kinetics, and tracer dynamics are described. (Author/GA)

  9. Toward computational cumulative biology by combining models of biological datasets.

    PubMed

    Faisal, Ali; Peltonen, Jaakko; Georgii, Elisabeth; Rung, Johan; Kaski, Samuel

    2014-01-01

    A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine designed for relating a researcher's experimental dataset to earlier work in the field. The search is (i) data-driven to enable new findings, going beyond the state of the art of keyword searches in annotations, (ii) modeling-driven, to include both biological knowledge and insights learned from data, and (iii) scalable, as it is accomplished without building one unified grand model of all data. Assuming each dataset has been modeled beforehand, by the researchers or automatically by database managers, we apply a rapidly computable and optimizable combination model to decompose a new dataset into contributions from earlier relevant models. By using the data-driven decomposition, we identify a network of interrelated datasets from a large annotated human gene expression atlas. While tissue type and disease were major driving forces for determining relevant datasets, the found relationships were richer, and the model-based search was more accurate than the keyword search; moreover, it recovered biologically meaningful relationships that are not straightforwardly visible from annotations-for instance, between cells in different developmental stages such as thymocytes and T-cells. Data-driven links and citations matched to a large extent; the data-driven links even uncovered corrections to the publication data, as two of the most linked datasets were not highly cited and turned out to have wrong publication entries in the database.

  10. Toward Computational Cumulative Biology by Combining Models of Biological Datasets

    PubMed Central

    Faisal, Ali; Peltonen, Jaakko; Georgii, Elisabeth; Rung, Johan; Kaski, Samuel

    2014-01-01

    A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine designed for relating a researcher's experimental dataset to earlier work in the field. The search is (i) data-driven to enable new findings, going beyond the state of the art of keyword searches in annotations, (ii) modeling-driven, to include both biological knowledge and insights learned from data, and (iii) scalable, as it is accomplished without building one unified grand model of all data. Assuming each dataset has been modeled beforehand, by the researchers or automatically by database managers, we apply a rapidly computable and optimizable combination model to decompose a new dataset into contributions from earlier relevant models. By using the data-driven decomposition, we identify a network of interrelated datasets from a large annotated human gene expression atlas. While tissue type and disease were major driving forces for determining relevant datasets, the found relationships were richer, and the model-based search was more accurate than the keyword search; moreover, it recovered biologically meaningful relationships that are not straightforwardly visible from annotations—for instance, between cells in different developmental stages such as thymocytes and T-cells. Data-driven links and citations matched to a large extent; the data-driven links even uncovered corrections to the publication data, as two of the most linked datasets were not highly cited and turned out to have wrong publication entries in the database. PMID:25427176

  11. Computation of generating functions for biological molecules

    SciTech Connect

    Howell, J.A.; Smith, T.F.; Waterman, M.S.

    1980-08-01

    The object of this paper is to give algorithms and techniques for computing generating functions of certain RNA configurations. Combinatorics and symbolic computation are utilized to calculate the generating functions for small RNA molecules. From these generating functions, it is possible to obtain information about the bonding and structure of the molecules. Specific examples of interest to biology are given and discussed.

  12. Computational investigations of HNO in biology

    PubMed Central

    Zhang, Yong

    2013-01-01

    HNO (nitroxyl) has been found to have many physiological effects in numerous biological processes. Computational investigations have been employed to help understand the structural properties of HNO complexes and HNO reactivities in some interesting biologically relevant systems. The following computational aspects were reviewed in this work: 1) structural and energetic properties of HNO isomers; 2) interactions between HNO and non-metal molecules; 3) structural and spectroscopic properties of HNO metal complexes; 4) HNO reactions with biologically important non-metal systems; 5) involvement of HNO in reactions of metal complexes and metalloproteins. Results indicate that computational investigations are very helpful to elucidate interesting experimental phenomena and provide new insights into unique structural, spectroscopic, and mechanistic properties of HNO involvement in biology. PMID:23103077

  13. Integrating interactive computational modeling in biology curricula.

    PubMed

    Helikar, Tomáš; Cutucache, Christine E; Dahlquist, Lauren M; Herek, Tyler A; Larson, Joshua J; Rogers, Jim A

    2015-03-01

    While the use of computer tools to simulate complex processes such as computer circuits is normal practice in fields like engineering, the majority of life sciences/biological sciences courses continue to rely on the traditional textbook and memorization approach. To address this issue, we explored the use of the Cell Collective platform as a novel, interactive, and evolving pedagogical tool to foster student engagement, creativity, and higher-level thinking. Cell Collective is a Web-based platform used to create and simulate dynamical models of various biological processes. Students can create models of cells, diseases, or pathways themselves or explore existing models. This technology was implemented in both undergraduate and graduate courses as a pilot study to determine the feasibility of such software at the university level. First, a new (In Silico Biology) class was developed to enable students to learn biology by "building and breaking it" via computer models and their simulations. This class and technology also provide a non-intimidating way to incorporate mathematical and computational concepts into a class with students who have a limited mathematical background. Second, we used the technology to mediate the use of simulations and modeling modules as a learning tool for traditional biological concepts, such as T cell differentiation or cell cycle regulation, in existing biology courses. Results of this pilot application suggest that there is promise in the use of computational modeling and software tools such as Cell Collective to provide new teaching methods in biology and contribute to the implementation of the "Vision and Change" call to action in undergraduate biology education by providing a hands-on approach to biology.

  14. Integrating interactive computational modeling in biology curricula.

    PubMed

    Helikar, Tomáš; Cutucache, Christine E; Dahlquist, Lauren M; Herek, Tyler A; Larson, Joshua J; Rogers, Jim A

    2015-03-01

    While the use of computer tools to simulate complex processes such as computer circuits is normal practice in fields like engineering, the majority of life sciences/biological sciences courses continue to rely on the traditional textbook and memorization approach. To address this issue, we explored the use of the Cell Collective platform as a novel, interactive, and evolving pedagogical tool to foster student engagement, creativity, and higher-level thinking. Cell Collective is a Web-based platform used to create and simulate dynamical models of various biological processes. Students can create models of cells, diseases, or pathways themselves or explore existing models. This technology was implemented in both undergraduate and graduate courses as a pilot study to determine the feasibility of such software at the university level. First, a new (In Silico Biology) class was developed to enable students to learn biology by "building and breaking it" via computer models and their simulations. This class and technology also provide a non-intimidating way to incorporate mathematical and computational concepts into a class with students who have a limited mathematical background. Second, we used the technology to mediate the use of simulations and modeling modules as a learning tool for traditional biological concepts, such as T cell differentiation or cell cycle regulation, in existing biology courses. Results of this pilot application suggest that there is promise in the use of computational modeling and software tools such as Cell Collective to provide new teaching methods in biology and contribute to the implementation of the "Vision and Change" call to action in undergraduate biology education by providing a hands-on approach to biology. PMID:25790483

  15. Metacognition: computation, biology and function.

    PubMed

    Fleming, Stephen M; Dolan, Raymond J; Frith, Christopher D

    2012-05-19

    Many complex systems maintain a self-referential check and balance. In animals, such reflective monitoring and control processes have been grouped under the rubric of metacognition. In this introductory article to a Theme Issue on metacognition, we review recent and rapidly progressing developments from neuroscience, cognitive psychology, computer science and philosophy of mind. While each of these areas is represented in detail by individual contributions to the volume, we take this opportunity to draw links between disciplines, and highlight areas where further integration is needed. Specifically, we cover the definition, measurement, neurobiology and possible functions of metacognition, and assess the relationship between metacognition and consciousness. We propose a framework in which level of representation, order of behaviour and access consciousness are orthogonal dimensions of the conceptual landscape. PMID:22492746

  16. Metacognition: computation, biology and function

    PubMed Central

    Fleming, Stephen M.; Dolan, Raymond J.; Frith, Christopher D.

    2012-01-01

    Many complex systems maintain a self-referential check and balance. In animals, such reflective monitoring and control processes have been grouped under the rubric of metacognition. In this introductory article to a Theme Issue on metacognition, we review recent and rapidly progressing developments from neuroscience, cognitive psychology, computer science and philosophy of mind. While each of these areas is represented in detail by individual contributions to the volume, we take this opportunity to draw links between disciplines, and highlight areas where further integration is needed. Specifically, we cover the definition, measurement, neurobiology and possible functions of metacognition, and assess the relationship between metacognition and consciousness. We propose a framework in which level of representation, order of behaviour and access consciousness are orthogonal dimensions of the conceptual landscape. PMID:22492746

  17. Filling the gap between biology and computer science.

    PubMed

    Aguilar-Ruiz, Jesús S; Moore, Jason H; Ritchie, Marylyn D

    2008-07-17

    This editorial introduces BioData Mining, a new journal which publishes research articles related to advances in computational methods and techniques for the extraction of useful knowledge from heterogeneous biological data. We outline the aims and scope of the journal, introduce the publishing model and describe the open peer review policy, which fosters interaction within the research community.

  18. Filling the gap between biology and computer science

    PubMed Central

    Aguilar-Ruiz, Jesús S; Moore, Jason H; Ritchie, Marylyn D

    2008-01-01

    This editorial introduces BioData Mining, a new journal which publishes research articles related to advances in computational methods and techniques for the extraction of useful knowledge from heterogeneous biological data. We outline the aims and scope of the journal, introduce the publishing model and describe the open peer review policy, which fosters interaction within the research community. PMID:18822148

  19. Computational Biology in microRNA.

    PubMed

    Li, Yue; Zhang, Zhaolei

    2015-01-01

    MicroRNA (miRNA) is a class of small endogenous noncoding RNA species, which regulate gene expression post-transcriptionally by forming imperfect base-pair at the 3' untranslated regions of the messenger RNAs. Since the 1993 discovery of the first miRNA let-7 in worms, a vast number of studies have been dedicated to functionally characterizing miRNAs with a special emphasis on their roles in cancer. A single miRNA can potentially target ∼ 400 distinct genes, and there are over a 1000 distinct endogenous miRNAs in the human genome. Thus, miRNAs are likely involved in virtually all biological processes and pathways including carcinogenesis. However, functionally characterizing miRNAs hinges on the accurate identification of their mRNA targets, which has been a challenging problem due to imperfect base-pairing and condition-specific miRNA regulatory dynamics. In this review, we will survey the current state-of-the-art computational methods to predict miRNA targets, which are divided into three main categories: (1) sequence-based methods that primarily utilizes the canonical seed-match model, evolutionary conservation, and binding energy; (2) expression-based target prediction methods using the increasingly available miRNA and mRNA expression data measured for the same sample; and (3) network-based method that aims identify miRNA regulatory modules, which reflect their synergism in conferring a global impact to the biological system of interest. We hope that the review will serve as a good reference to the new comers to the ever-growing miRNA research field as well as veterans, who would appreciate the detailed review on the technicalities, strength, and limitations of each representative computational method.

  20. Biological Databases for Human Research

    PubMed Central

    Zou, Dong; Ma, Lina; Yu, Jun; Zhang, Zhang

    2015-01-01

    The completion of the Human Genome Project lays a foundation for systematically studying the human genome from evolutionary history to precision medicine against diseases. With the explosive growth of biological data, there is an increasing number of biological databases that have been developed in aid of human-related research. Here we present a collection of human-related biological databases and provide a mini-review by classifying them into different categories according to their data types. As human-related databases continue to grow not only in count but also in volume, challenges are ahead in big data storage, processing, exchange and curation. PMID:25712261

  1. Biological databases for human research.

    PubMed

    Zou, Dong; Ma, Lina; Yu, Jun; Zhang, Zhang

    2015-02-01

    The completion of the Human Genome Project lays a foundation for systematically studying the human genome from evolutionary history to precision medicine against diseases. With the explosive growth of biological data, there is an increasing number of biological databases that have been developed in aid of human-related research. Here we present a collection of human-related biological databases and provide a mini-review by classifying them into different categories according to their data types. As human-related databases continue to grow not only in count but also in volume, challenges are ahead in big data storage, processing, exchange and curation. PMID:25712261

  2. Biological pathways as communicating computer systems.

    PubMed

    Kwiatkowska, Marta Z; Heath, John K

    2009-08-15

    Time and cost are the enemies of cell biology. The number of experiments required to rigorously dissect and comprehend a pathway of even modest complexity is daunting. Methods are needed to formulate biological pathways in a machine-analysable fashion, which would automate the process of considering all possible experiments in a complex pathway and identify those that command attention. In this Essay, we describe a method that is based on the exploitation of computational tools that were originally developed to analyse reactive communicating computer systems such as mobile phones and web browsers. In this approach, the biological process is articulated as an executable computer program that can be interrogated using methods that were developed to analyse complex software systems. Using case studies of the FGF, MAPK and Delta/Notch pathways, we show that the application of this technology can yield interesting insights into the behaviour of signalling pathways, which have subsequently been corroborated by experimental data. PMID:19657015

  3. The "Biologically-Inspired Computing" Column

    NASA Technical Reports Server (NTRS)

    Hinchey, Mike

    2007-01-01

    Self-managing systems, whether viewed from the perspective of Autonomic Computing, or from that of another initiative, offers a holistic vision for the development and evolution of biologically-inspired computer-based systems. It aims to bring new levels of automation and dependability to systems, while simultaneously hiding their complexity and reducing costs. A case can certainly be made that all computer-based systems should exhibit autonomic properties [6], and we envisage greater interest in, and uptake of, autonomic principles in future system development.

  4. A Computer Applications Course for Biology Students.

    ERIC Educational Resources Information Center

    Ralph, Charles L.

    1989-01-01

    Describes a computer applications course developed for undergraduate biology students (primarily sophomores) to teach word processing, database and spreadsheet programs, graphing programs, telecommunications, and file transfer procedures. AppleWorks software is discussed, course content is explained, and the microcomputer laboratory is described.…

  5. Micro-Computers in Biology Inquiry.

    ERIC Educational Resources Information Center

    Barnato, Carolyn; Barrett, Kathy

    1981-01-01

    Describes the modification of computer programs (BISON and POLLUT) to accommodate species and areas indigenous to the Pacific Coast area. Suggests that these programs, suitable for PET microcomputers, may foster a long-term, ongoing, inquiry-directed approach in biology. (DS)

  6. Aluminium in Biological Environments: A Computational Approach

    PubMed Central

    Mujika, Jon I; Rezabal, Elixabete; Mercero, Jose M; Ruipérez, Fernando; Costa, Dominique; Ugalde, Jesus M; Lopez, Xabier

    2014-01-01

    The increased availability of aluminium in biological environments, due to human intervention in the last century, raises concerns on the effects that this so far “excluded from biology” metal might have on living organisms. Consequently, the bioinorganic chemistry of aluminium has emerged as a very active field of research. This review will focus on our contributions to this field, based on computational studies that can yield an understanding of the aluminum biochemistry at a molecular level. Aluminium can interact and be stabilized in biological environments by complexing with both low molecular mass chelants and high molecular mass peptides. The speciation of the metal is, nonetheless, dictated by the hydrolytic species dominant in each case and which vary according to the pH condition of the medium. In blood, citrate and serum transferrin are identified as the main low molecular mass and high molecular mass molecules interacting with aluminium. The complexation of aluminium to citrate and the subsequent changes exerted on the deprotonation pathways of its tritable groups will be discussed along with the mechanisms for the intake and release of aluminium in serum transferrin at two pH conditions, physiological neutral and endosomatic acidic. Aluminium can substitute other metals, in particular magnesium, in protein buried sites and trigger conformational disorder and alteration of the protonation states of the protein's sidechains. A detailed account of the interaction of aluminium with proteic sidechains will be given. Finally, it will be described how alumnium can exert oxidative stress by stabilizing superoxide radicals either as mononuclear aluminium or clustered in boehmite. The possibility of promotion of Fenton reaction, and production of hydroxyl radicals will also be discussed. PMID:24757505

  7. Perspectives on an education in computational biology and medicine.

    PubMed

    Rubinstein, Jill C

    2012-09-01

    The mainstream application of massively parallel, high-throughput assays in biomedical research has created a demand for scientists educated in Computational Biology and Bioinformatics (CBB). In response, formalized graduate programs have rapidly evolved over the past decade. Concurrently, there is increasing need for clinicians trained to oversee the responsible translation of CBB research into clinical tools. Physician-scientists with dedicated CBB training can facilitate such translation, positioning themselves at the intersection between computational biomedical research and medicine. This perspective explores key elements of the educational path to such a position, specifically addressing: 1) evolving perceptions of the role of the computational biologist and the impact on training and career opportunities; 2) challenges in and strategies for obtaining the core skill set required of a biomedical researcher in a computational world; and 3) how the combination of CBB with medical training provides a logical foundation for a career in academic medicine and/or biomedical research.

  8. Perspectives on an Education in Computational Biology and Medicine

    PubMed Central

    Rubinstein, Jill C.

    2012-01-01

    The mainstream application of massively parallel, high-throughput assays in biomedical research has created a demand for scientists educated in Computational Biology and Bioinformatics (CBB). In response, formalized graduate programs have rapidly evolved over the past decade. Concurrently, there is increasing need for clinicians trained to oversee the responsible translation of CBB research into clinical tools. Physician-scientists with dedicated CBB training can facilitate such translation, positioning themselves at the intersection between computational biomedical research and medicine. This perspective explores key elements of the educational path to such a position, specifically addressing: 1) evolving perceptions of the role of the computational biologist and the impact on training and career opportunities; 2) challenges in and strategies for obtaining the core skill set required of a biomedical researcher in a computational world; and 3) how the combination of CBB with medical training provides a logical foundation for a career in academic medicine and/or biomedical research. PMID:23012581

  9. Understanding biological computation: reliable learning and recognition.

    PubMed Central

    Hogg, T; Huberman, B A

    1984-01-01

    We experimentally examine the consequences of the hypothesis that the brain operates reliably, even though individual components may intermittently fail, by computing with dynamical attractors. Specifically, such a mechanism exploits dynamic collective behavior of a system with attractive fixed points in its phase space. In contrast to the usual methods of reliable computation involving a large number of redundant elements, this technique of self-repair only requires collective computation with a few units, and it is amenable to quantitative investigation. Experiments on parallel computing arrays show that this mechanism leads naturally to rapid self-repair, adaptation to the environment, recognition and discrimination of fuzzy inputs, and conditional learning, properties that are commonly associated with biological computation. PMID:6593731

  10. Space Station Biological Research Project.

    PubMed

    Johnson, C C; Wade, C E; Givens, J J

    1997-06-01

    To meet NASA's objective of using the unique aspects of the space environment to expand fundamental knowledge in the biological sciences, the Space Station Biological Research Project at Ames Research Center is developing, or providing oversight, for two major suites of hardware which will be installed on the International Space Station (ISS). The first, the Gravitational Biology Facility, consists of Habitats to support plants, rodents, cells, aquatic specimens, avian and reptilian eggs, and insects and the Habitat Holding Rack in which to house them at microgravity; the second, the Centrifuge Facility, consists of a 2.5 m diameter centrifuge that will provide acceleration levels between 0.01 g and 2.0 g and a Life Sciences Glovebox. These two facilities will support the conduct of experiments to: 1) investigate the effect of microgravity on living systems; 2) what level of gravity is required to maintain normal form and function, and 3) study the use of artificial gravity as a countermeasure to the deleterious effects of microgravity observed in the crew. Upon completion, the ISS will have three complementary laboratory modules provided by NASA, the European Space Agency and the Japanese space agency, NASDA. Use of all facilities in each of the modules will be available to investigators from participating space agencies. With the advent of the ISS, space-based gravitational biology research will transition from 10-16 day short-duration Space Shuttle flights to 90-day-or-longer ISS increments.

  11. Space Station Biological Research Project

    NASA Technical Reports Server (NTRS)

    Johnson, C. C.; Wade, C. E.; Givens, J. J.

    1997-01-01

    To meet NASA's objective of using the unique aspects of the space environment to expand fundamental knowledge in the biological sciences, the Space Station Biological Research Project at Ames Research Center is developing, or providing oversight, for two major suites of hardware which will be installed on the International Space Station (ISS). The first, the Gravitational Biology Facility, consists of Habitats to support plants, rodents, cells, aquatic specimens, avian and reptilian eggs, and insects and the Habitat Holding Rack in which to house them at microgravity; the second, the Centrifuge Facility, consists of a 2.5 m diameter centrifuge that will provide acceleration levels between 0.01 g and 2.0 g and a Life Sciences Glovebox. These two facilities will support the conduct of experiments to: 1) investigate the effect of microgravity on living systems; 2) what level of gravity is required to maintain normal form and function, and 3) study the use of artificial gravity as a countermeasure to the deleterious effects of microgravity observed in the crew. Upon completion, the ISS will have three complementary laboratory modules provided by NASA, the European Space Agency and the Japanese space agency, NASDA. Use of all facilities in each of the modules will be available to investigators from participating space agencies. With the advent of the ISS, space-based gravitational biology research will transition from 10-16 day short-duration Space Shuttle flights to 90-day-or-longer ISS increments.

  12. [Biological research and security institutes].

    PubMed

    Darsie, G; Falczuk, A J; Bergmann, I E

    2006-04-01

    The threat of using biological material for ago-bioterrorist ends has risen in recent years, which means that research and diagnostic laboratories, biological agent banks and other institutions authorised to carry out scientific activities have had to implement biosafety and biosecurity measures to counter the threat, while carrying out activities to help prevent and monitor the accidental or intentional introduction of exotic animal diseases. This article briefly sets outthe basic components of biosafety and biosecurity, as well as recommendations on organisational strategies to consider in laboratories that support agro-bioterrorist surveillance and prevention programs.

  13. Multiscale Computational Models of Complex Biological Systems

    PubMed Central

    Walpole, Joseph; Papin, Jason A.; Peirce, Shayn M.

    2014-01-01

    Integration of data across spatial, temporal, and functional scales is a primary focus of biomedical engineering efforts. The advent of powerful computing platforms, coupled with quantitative data from high-throughput experimental platforms, has allowed multiscale modeling to expand as a means to more comprehensively investigate biological phenomena in experimentally relevant ways. This review aims to highlight recently published multiscale models of biological systems while using their successes to propose the best practices for future model development. We demonstrate that coupling continuous and discrete systems best captures biological information across spatial scales by selecting modeling techniques that are suited to the task. Further, we suggest how to best leverage these multiscale models to gain insight into biological systems using quantitative, biomedical engineering methods to analyze data in non-intuitive ways. These topics are discussed with a focus on the future of the field, the current challenges encountered, and opportunities yet to be realized. PMID:23642247

  14. A formal language for computational systems biology.

    PubMed

    Errampalli, Daniel D; Priami, Corrado; Quaglia, Paola

    2004-01-01

    The post-genomic era has opened new insights into the complex biochemical reaction systems present in the cell and has generated huge amount of information. The biological systems are highly complex and can overwhelm the numerically computable models. Therefore, models employing symbolical techniques might provide a faster insight. This paper presents some preliminary results and recent trends in the above direction. Specifically, it presents an overview of the main features of some formalisms and techniques from the field of specification languages for concurrency and mobility, which have been proposed to model and simulate the dynamics of the interaction of complex biological systems. The ultimate goal of these symbolic approaches is the modeling, analysis, simulation, and hopefully prediction of the behavior of biological systems (vs. biological components).

  15. Novel opportunities for computational biology and sociology in drug discovery

    PubMed Central

    Yao, Lixia

    2009-01-01

    Drug discovery today is impossible without sophisticated modeling and computation. In this review we touch on previous advances in computational biology and by tracing the steps involved in pharmaceutical development, we explore a range of novel, high value opportunities for computational innovation in modeling the biological process of disease and the social process of drug discovery. These opportunities include text mining for new drug leads, modeling molecular pathways and predicting the efficacy of drug cocktails, analyzing genetic overlap between diseases and predicting alternative drug use. Computation can also be used to model research teams and innovative regions and to estimate the value of academy-industry ties for scientific and human benefit. Attention to these opportunities could promise punctuated advance, and will complement the well-established computational work on which drug discovery currently relies. PMID:19674801

  16. Novel opportunities for computational biology and sociology in drug discovery☆

    PubMed Central

    Yao, Lixia; Evans, James A.; Rzhetsky, Andrey

    2013-01-01

    Current drug discovery is impossible without sophisticated modeling and computation. In this review we outline previous advances in computational biology and, by tracing the steps involved in pharmaceutical development, explore a range of novel, high-value opportunities for computational innovation in modeling the biological process of disease and the social process of drug discovery. These opportunities include text mining for new drug leads, modeling molecular pathways and predicting the efficacy of drug cocktails, analyzing genetic overlap between diseases and predicting alternative drug use. Computation can also be used to model research teams and innovative regions and to estimate the value of academy–industry links for scientific and human benefit. Attention to these opportunities could promise punctuated advance and will complement the well-established computational work on which drug discovery currently relies. PMID:20349528

  17. Cancer research meets evolutionary biology

    PubMed Central

    Pepper, John W; Scott Findlay, C; Kassen, Rees; Spencer, Sabrina L; Maley, Carlo C

    2009-01-01

    There is increasing evidence that Darwin's theory of evolution by natural selection provides insights into the etiology and treatment of cancer. On a microscopic scale, neoplastic cells meet the conditions for evolution by Darwinian selection: cell reproduction with heritable variability that affects cell survival and replication. This suggests that, like other areas of biological and biomedical research, Darwinian theory can provide a general framework for understanding many aspects of cancer, including problems of great clinical importance. With the availability of raw molecular data increasing rapidly, this theory may provide guidance in translating data into understanding and progress. Several conceptual and analytical tools from evolutionary biology can be applied to cancer biology. Two clinical problems may benefit most from the application of Darwinian theory: neoplastic progression and acquired therapeutic resistance. The Darwinian theory of cancer has especially profound implications for drug development, both in terms of explaining past difficulties, and pointing the way toward new approaches. Because cancer involves complex evolutionary processes, research should incorporate both tractable (simplified) experimental systems, and also longitudinal observational studies of the evolutionary dynamics of cancer in laboratory animals and in human patients. Cancer biology will require new tools to control the evolution of neoplastic cells. PMID:25567847

  18. Research and the Personal Computer.

    ERIC Educational Resources Information Center

    Blackburn, D. A.

    1989-01-01

    Discussed is the history and elements of the personal computer. Its uses as a laboratory assistant and generic toolkit for mathematical analysis and modeling are included. The future of the personal computer in research is addressed. (KR)

  19. The fusion of biology, computer science, and engineering: towards efficient and successful synthetic biology.

    PubMed

    Linshiz, Gregory; Goldberg, Alex; Konry, Tania; Hillson, Nathan J

    2012-01-01

    Synthetic biology is a nascent field that emerged in earnest only around the turn of the millennium. It aims to engineer new biological systems and impart new biological functionality, often through genetic modifications. The design and construction of new biological systems is a complex, multistep process, requiring multidisciplinary collaborative efforts from "fusion" scientists who have formal training in computer science or engineering, as well as hands-on biological expertise. The public has high expectations for synthetic biology and eagerly anticipates the development of solutions to the major challenges facing humanity. This article discusses laboratory practices and the conduct of research in synthetic biology. It argues that the fusion science approach, which integrates biology with computer science and engineering best practices, including standardization, process optimization, computer-aided design and laboratory automation, miniaturization, and systematic management, will increase the predictability and reproducibility of experiments and lead to breakthroughs in the construction of new biological systems. The article also discusses several successful fusion projects, including the development of software tools for DNA construction design automation, recursive DNA construction, and the development of integrated microfluidics systems.

  20. Standards and Ontologies in Computational Systems Biology

    PubMed Central

    Sauro, Herbert M.; Bergmann, Frank

    2009-01-01

    With the growing importance of computational models in systems biology there has been much interest in recent years to develop standard model interchange languages that permit biologists to easily exchange models between different software tools. In this chapter two chief model exchange standards, SBML and CellML are described. In addition, other related features including visual layout initiatives, ontologies and best practices for model annotation are discussed. Software tools such as developer libraries and basic editing tools are also introduced together with a discussion on the future of modeling languages and visualization tools in systems biology. PMID:18793134

  1. A new online computational biology curriculum.

    PubMed

    Searls, David B

    2014-06-01

    A recent proliferation of Massive Open Online Courses (MOOCs) and other web-based educational resources has greatly increased the potential for effective self-study in many fields. This article introduces a catalog of several hundred free video courses of potential interest to those wishing to expand their knowledge of bioinformatics and computational biology. The courses are organized into eleven subject areas modeled on university departments and are accompanied by commentary and career advice.

  2. Computational Biology: Modeling Chronic Renal Allograft Injury.

    PubMed

    Stegall, Mark D; Borrows, Richard

    2015-01-01

    New approaches are needed to develop more effective interventions to prevent long-term rejection of organ allografts. Computational biology provides a powerful tool to assess the large amount of complex data that is generated in longitudinal studies in this area. This manuscript outlines how our two groups are using mathematical modeling to analyze predictors of graft loss using both clinical and experimental data and how we plan to expand this approach to investigate specific mechanisms of chronic renal allograft injury.

  3. A New Online Computational Biology Curriculum

    PubMed Central

    Searls, David B.

    2014-01-01

    A recent proliferation of Massive Open Online Courses (MOOCs) and other web-based educational resources has greatly increased the potential for effective self-study in many fields. This article introduces a catalog of several hundred free video courses of potential interest to those wishing to expand their knowledge of bioinformatics and computational biology. The courses are organized into eleven subject areas modeled on university departments and are accompanied by commentary and career advice. PMID:24921255

  4. Computational systems biology in cancer brain metastasis.

    PubMed

    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.

  5. NASA's computer science research program

    NASA Technical Reports Server (NTRS)

    Larsen, R. L.

    1983-01-01

    Following a major assessment of NASA's computing technology needs, a new program of computer science research has been initiated by the Agency. The program includes work in concurrent processing, management of large scale scientific databases, software engineering, reliable computing, and artificial intelligence. The program is driven by applications requirements in computational fluid dynamics, image processing, sensor data management, real-time mission control and autonomous systems. It consists of university research, in-house NASA research, and NASA's Research Institute for Advanced Computer Science (RIACS) and Institute for Computer Applications in Science and Engineering (ICASE). The overall goal is to provide the technical foundation within NASA to exploit advancing computing technology in aerospace applications.

  6. Bioconductor: open software development for computational biology and bioinformatics

    PubMed Central

    Gentleman, Robert C; Carey, Vincent J; Bates, Douglas M; Bolstad, Ben; Dettling, Marcel; Dudoit, Sandrine; Ellis, Byron; Gautier, Laurent; Ge, Yongchao; Gentry, Jeff; Hornik, Kurt; Hothorn, Torsten; Huber, Wolfgang; Iacus, Stefano; Irizarry, Rafael; Leisch, Friedrich; Li, Cheng; Maechler, Martin; Rossini, Anthony J; Sawitzki, Gunther; Smith, Colin; Smyth, Gordon; Tierney, Luke; Yang, Jean YH; Zhang, Jianhua

    2004-01-01

    The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples. PMID:15461798

  7. Catalyzing Inquiry at the Interface of Computing and Biology

    SciTech Connect

    John Wooley; Herbert S. Lin

    2005-10-30

    This study is the first comprehensive NRC study that suggests a high-level intellectual structure for Federal agencies for supporting work at the biology/computing interface. The report seeks to establish the intellectual legitimacy of a fundamentally cross-disciplinary collaboration between biologists and computer scientists. That is, while some universities are increasingly favorable to research at the intersection, life science researchers at other universities are strongly impeded in their efforts to collaborate. This report addresses these impediments and describes proven strategies for overcoming them. An important feature of the report is the use of well-documented examples that describe clearly to individuals not trained in computer science the value and usage of computing across the biological sciences, from genes and proteins to networks and pathways, from organelles to cells, and from individual organisms to populations and ecosystems. It is hoped that these examples will be useful to students in the life sciences to motivate (continued) study in computer science that will enable them to be more facile users of computing in their future biological studies.

  8. Computational Biology Support: RECOMB Conference Series (Conference Support)

    SciTech Connect

    Michael Waterman

    2006-06-15

    This funding was support for student and postdoctoral attendance at the Annual Recomb Conference from 2001 to 2005. The RECOMB Conference series was founded in 1997 to provide a scientific forum for theoretical advances in computational biology and their applications in molecular biology and medicine. The conference series aims at attracting research contributions in all areas of computational molecular biology. Typical, but not exclusive, the topics of interest are: Genomics, Molecular sequence analysis, Recognition of genes and regulatory elements, Molecular evolution, Protein structure, Structural genomics, Gene Expression, Gene Networks, Drug Design, Combinatorial libraries, Computational proteomics, and Structural and functional genomics. The origins of the conference came from the mathematical and computational side of the field, and there remains to be a certain focus on computational advances. However, the effective use of computational techniques to biological innovation is also an important aspect of the conference. The conference had a growing number of attendees, topping 300 in recent years and often exceeding 500. The conference program includes between 30 and 40 contributed papers, that are selected by a international program committee with around 30 experts during a rigorous review process rivaling the editorial procedure for top-rate scientific journals. In previous years papers selection has been made from up to 130--200 submissions from well over a dozen countries. 10-page extended abstracts of the contributed papers are collected in a volume published by ACM Press and Springer, and are available at the conference. Full versions of a selection of the papers are published annually in a special issue of the Journal of Computational Biology devoted to the RECOMB Conference. A further point in the program is a lively poster session. From 120-300 posters have been presented each year at RECOMB 2000. One of the highlights of each RECOMB conference is a

  9. Computational Tools to Assess Turbine Biological Performance

    SciTech Connect

    Richmond, Marshall C.; Serkowski, John A.; Rakowski, Cynthia L.; Strickler, Brad; Weisbeck, Molly; Dotson, Curtis L.

    2014-07-24

    Public Utility District No. 2 of Grant County (GCPUD) operates the Priest Rapids Dam (PRD), a hydroelectric facility on the Columbia River in Washington State. The dam contains 10 Kaplan-type turbine units that are now more than 50 years old. Plans are underway to refit these aging turbines with new runners. The Columbia River at PRD is a migratory pathway for several species of juvenile and adult salmonids, so passage of fish through the dam is a major consideration when upgrading the turbines. In this paper, a method for turbine biological performance assessment (BioPA) is demonstrated. Using this method, a suite of biological performance indicators is computed based on simulated data from a CFD model of a proposed turbine design. Each performance indicator is a measure of the probability of exposure to a certain dose of an injury mechanism. Using known relationships between the dose of an injury mechanism and frequency of injury (dose–response) from laboratory or field studies, the likelihood of fish injury for a turbine design can be computed from the performance indicator. By comparing the values of the indicators from proposed designs, the engineer can identify the more-promising alternatives. We present an application of the BioPA method for baseline risk assessment calculations for the existing Kaplan turbines at PRD that will be used as the minimum biological performance that a proposed new design must achieve.

  10. Research in computer science

    NASA Technical Reports Server (NTRS)

    Ortega, J. M.

    1984-01-01

    The research efforts of University of Virginia students under a NASA sponsored program are summarized and the status of the program is reported. The research includes: testing method evaluations for N version programming; a representation scheme for modeling three dimensional objects; fault tolerant protocols for real time local area networks; performance investigation of Cyber network; XFEM implementation; and vectorizing incomplete Cholesky conjugate gradients.

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

    PubMed Central

    2013-01-01

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

  12. Computational chemistry research

    NASA Technical Reports Server (NTRS)

    Levin, Eugene

    1987-01-01

    Task 41 is composed of two parts: (1) analysis and design studies related to the Numerical Aerodynamic Simulation (NAS) Extended Operating Configuration (EOC) and (2) computational chemistry. During the first half of 1987, Dr. Levin served as a member of an advanced system planning team to establish the requirements, goals, and principal technical characteristics of the NAS EOC. A paper entitled 'Scaling of Data Communications for an Advanced Supercomputer Network' is included. The high temperature transport properties (such as viscosity, thermal conductivity, etc.) of the major constituents of air (oxygen and nitrogen) were correctly determined. The results of prior ab initio computer solutions of the Schroedinger equation were combined with the best available experimental data to obtain complete interaction potentials for both neutral and ion-atom collision partners. These potentials were then used in a computer program to evaluate the collision cross-sections from which the transport properties could be determined. A paper entitled 'High Temperature Transport Properties of Air' is included.

  13. Towards molecular computers that operate in a biological environment

    NASA Astrophysics Data System (ADS)

    Kahan, Maya; Gil, Binyamin; Adar, Rivka; Shapiro, Ehud

    2008-07-01

    important consequences when performed in a proper context. We envision that molecular computers that operate in a biological environment can be the basis of “smart drugs”, which are potent drugs that activate only if certain environmental conditions hold. These conditions could include abnormalities in the molecular composition of the biological environment that are indicative of a particular disease. Here we review the research direction that set this vision and attempts to realize it.

  14. Developing an online programme in computational biology.

    PubMed

    Vincent, Heather M; Page, Christopher

    2013-11-01

    Much has been written about the need for continuing education and training to enable life scientists and computer scientists to manage and exploit the different types of biological data now becoming available. Here we describe the development of an online programme that combines short training courses, so that those who require an educational programme can progress to complete a formal qualification. Although this flexible approach fits the needs of course participants, it does not fit easily within the organizational structures of a campus-based university.

  15. Multiobjective optimization in bioinformatics and computational biology.

    PubMed

    Handl, Julia; Kell, Douglas B; Knowles, Joshua

    2007-01-01

    This paper reviews the application of multiobjective optimization in the fields of bioinformatics and computational biology. A survey of existing work, organized by application area, forms the main body of the review, following an introduction to the key concepts in multiobjective optimization. An original contribution of the review is the identification of five distinct "contexts," giving rise to multiple objectives: These are used to explain the reasons behind the use of multiobjective optimization in each application area and also to point the way to potential future uses of the technique.

  16. Research in computer science

    NASA Technical Reports Server (NTRS)

    Ortega, J. M.

    1984-01-01

    Several short summaries of the work performed during this reporting period are presented. Topics discussed in this document include: (1) resilient seeded errors via simple techniques; (2) knowledge representation for engineering design; (3) analysis of faults in a multiversion software experiment; (4) implementation of parallel programming environment; (5) symbolic execution of concurrent programs; (6) two computer graphics systems for visualization of pressure distribution and convective density particles; (7) design of a source code management system; (8) vectorizing incomplete conjugate gradient on the Cyber 203/205; (9) extensions of domain testing theory and; (10) performance analyzer for the pisces system.

  17. Computational Materials Research

    NASA Technical Reports Server (NTRS)

    Hinkley, Jeffrey A. (Editor); Gates, Thomas S. (Editor)

    1996-01-01

    Computational Materials aims to model and predict thermodynamic, mechanical, and transport properties of polymer matrix composites. This workshop, the second coordinated by NASA Langley, reports progress in measurements and modeling at a number of length scales: atomic, molecular, nano, and continuum. Assembled here are presentations on quantum calculations for force field development, molecular mechanics of interfaces, molecular weight effects on mechanical properties, molecular dynamics applied to poling of polymers for electrets, Monte Carlo simulation of aromatic thermoplastics, thermal pressure coefficients of liquids, ultrasonic elastic constants, group additivity predictions, bulk constitutive models, and viscoplasticity characterization.

  18. Nanomaterials in biological environment: a review of computer modelling studies.

    PubMed

    Makarucha, A J; Todorova, N; Yarovsky, I

    2011-02-01

    Nanotechnology is set to impact a vast range of fields, including computer science, materials technology, engineering/manufacturing and medicine. As nanotechnology grows so does exposure to nanostructured materials, thus investigation of the effects of nanomaterials on biological systems is paramount. Computational techniques can allow investigation of these systems at the nanoscale, providing insight into otherwise unexaminable properties, related to both the intentional and unintentional effects of nanomaterials. Herein, we review the current literature involving computational modelling of nanoparticles and biological systems. This literature has highlighted the common modes in which nanostructured materials interact with biological molecules such as membranes, peptides/proteins and DNA. Hydrophobic interactions are the most favoured, with π-stacking of the aromatic side-chains common when binding to a carbonaceous nanoparticle or surface. van der Waals forces are found to dominate in the insertion process of DNA molecules into carbon nanotubes. Generally, nanoparticles have been observed to disrupt the tertiary structure of proteins due to the curvature and atomic arrangement of the particle surface. Many hydrophobic nanoparticles are found to be able to transverse a lipid membrane, with some nanoparticles even causing mechanical damage to the membrane, thus potentially leading to cytotoxic effects. Current computational techniques have revealed how some nanoparticles interact with biological systems. However, further research is required to determine both useful applications and possible cytotoxic effects that nanoparticles may have on DNA, protein and membrane structure and function within biosystems.

  19. Space Station Biological Research Project

    NASA Technical Reports Server (NTRS)

    Johnson, Catherine C.; Hargens, Alan R.; Wade, Charles E.

    1995-01-01

    NASA Ames Research Center is responsible for the development of the Space Station Biological Research Project (SSBRP) which will support non-human life sciences research on the International Space Station Alpha (ISSA). The SSBRP is designed to support both basic research to understand the effect of altered gravity fields on biological systems and applied research to investigate the effects of space flight on biological systems. The SSBRP will provide the necessary habitats to support avian and reptile eggs, cells and tissues, plants and rodents. In addition a habitat to support aquatic specimens will be provided by our international partners. Habitats will be mounted in ISSA compatible racks at u-g and will also be mounted on a 2.5 m diameter centrifuge except for the egg incubator which has an internal centrifuge. The 2.5 m centrifuge will provide artificial gravity levels over the range of 0.01 G to 2 G. The current schedule is to launch the first rack in 1999, the Life Sciences glovebox and a second rack early in 2001, a 4 habitat 2.5 in centrifuge later the same year in its own module, and to upgrade the centrifuge to 8 habitats in 2004. The rodent habitats will be derived from the Advanced Animal Habitat currently under development for the Shuttle program and will be capable of housing either rats or mice individually or in groups (6 rats/group and at least 12 mice/group). The egg incubator will be an upgraded Avian Development Facility also developed for the Shuttle program through a Small Business and Innovative Research grant. The Space Tissue Loss cell culture apparatus, developed by Walter Reed Army Institute of Research, is being considered for the cell and tissue culture habitat. The Life Sciences Glovebox is crucial to all life sciences experiments for specimen manipulation and performance of science procedures. It will provide two levels of containment between the work volume and the crew through the use of seals and negative pressure. The glovebox

  20. A complex systems approach to computational molecular biology

    SciTech Connect

    Lapedes, A. |

    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.

  1. Computer Science Research at Langley

    NASA Technical Reports Server (NTRS)

    Voigt, S. J. (Editor)

    1982-01-01

    A workshop was held at Langley Research Center, November 2-5, 1981, to highlight ongoing computer science research at Langley and to identify additional areas of research based upon the computer user requirements. A panel discussion was held in each of nine application areas, and these are summarized in the proceedings. Slides presented by the invited speakers are also included. A survey of scientific, business, data reduction, and microprocessor computer users helped identify areas of focus for the workshop. Several areas of computer science which are of most concern to the Langley computer users were identified during the workshop discussions. These include graphics, distributed processing, programmer support systems and tools, database management, and numerical methods.

  2. The Biological Flight Research Facility

    NASA Technical Reports Server (NTRS)

    Johnson, Catherine C.

    1991-01-01

    NASA Ames Research Center is building a research facility, the Biological Flight Research Facility (BFRF), to meet the needs of life scientists to study the long-term effects of variable gravity on living systems. The facility will be housed on Space Station Freedom and is anticipated to operate for the lifetime of the station, approximately 30 years. It will allow plant and animal biologists to study the role of gravity, or its absence, at varying gravity intensities for varying periods of time and with various organisms. The principal difference between current Spacelab missions and those on Space Station Freedom, other than length of mission, will be the capability to perform on-orbit science procedures and the capability to simulate earth gravity. Initially, the facility will house plants and rodents in habitats which can be maintained at microgravity or can be placed on a 2.5-m diam centrifuge. However, the facility is also being designed to accommodate future habitats for small primates, avian, and aquatic specimens. The centrifuge will provide 1 g for controls and will also be able to provide gravity from 0.01 to 2.0 g for threshold gravity studies as well as hypergravity studies. The BFRF will provide the means to conduct basic experiments to gain an understanding of the effects of microgravity on the structure and function of plants and animals, as well as investigate the role of gravity as a potential countermeasure for the physiological changes observed in microgravity.

  3. Global Biology Research Program: Program plan

    NASA Technical Reports Server (NTRS)

    1983-01-01

    Biological processes which play a dominant role in these cycles which transform and transfer much of this material throughout the biosphere are examined. A greater understanding of planetary biological processes as revealed by the interaction of the biota and the environment. The rationale, scope, research strategy, and research priorities of the global biology is presented.

  4. The Biological Flight Research Facility

    NASA Technical Reports Server (NTRS)

    Johnson, Catherine C.

    1993-01-01

    NASA Ames Research Center (ARC) is building a research facility, the Biological Flight Research Facility (BFRF), to meet the needs of life scientists to study the long-term effects of variable gravity on living systems. The facility will be housed on Space Station Freedom and is anticipated to operate for the lifetime of the station, approximately thirty years. It will allow plant and animal biologists to study the role of gravity, or its absence, at varying gravity intensities for varying periods of time and with various organisms. The principal difference between current Spacelab missions and those on Space Station Freedom, other than length of mission, will be the capability to perform on-orbit science procedures and the capability to simulate earth gravity. Initially the facility will house plants and rodents in habitats which can be maintained at microgravity or can be placed on a 2.5 meter diameter centrifuge. However, the facility is also being designed to accommodate future habitats for small primates, avian, and aquatic specimens. The centrifuge will provide 1 g for controls and will also be able to provide gravity from 0.01 to 2.0 g for threshold gravity studies as well as hypergravity studies. Included in the facility are a service unit for providing clean chambers for the specimens and a glovebox for manipulating the plant and animal specimens and for performing experimental protocols. The BFRF will provide the means to conduct basic experiments to gain an understanding of the effects of microgravity on the structure and function of plants and animals, as well as investigate the role of gravity as a potential countermeasure for the physiological changes observed in microgravity.

  5. Personal Computers in Clinical Research

    PubMed Central

    McAlister, Neil; Andrews, David

    1984-01-01

    Personal computers have proved useful in several identifiable areas of clinical research support. However, they have limitations. Popular microcomputer systems typically fail to meet all of the traditional data processing requirements of serious clinical investigators — usually because of software restrictions. Objective evaluation of the strengths and weaknesses of these small systems, and particularly of their software, ensures effective use of research budgets and personnel. An analysis of clinical research needs that personal computers serve well, and of those that they serve poorly, is therefore presented.

  6. Structural Biology and Molecular Applications Research

    Cancer.gov

    Part of NCI's Division of Cancer Biology's research portfolio, research and development in this area focuses on enabling technologies, models, and methodologies to support basic and applied cancer research.

  7. Computational Laser Spectroscopy in a Biological Tissue

    PubMed Central

    Gantri, M.; Trabelsi, H.; Sediki, E.; Ben Salah, R.

    2010-01-01

    We present a numerical spectroscopic study of visible and infrared laser radiation in a biological tissue. We derive a solution of a general two-dimensional time dependent radiative transfer equation in a tissue-like medium. The used model is suitable for many situations especially when the external source is time-dependent or continuous. We use a control volume-discrete ordinate method associated with an implicit three-level second-order time differencing scheme. We consider a very thin rectangular biological-tissue-like medium submitted to a visible or a near infrared light sources. The RTE is solved for a set of different wavelength source. All sources are assumed to be monochromatic and collimated. The energetic fluence rate is computed at a set of detector points on the boundaries. According to the source type, we investigate either the steady-state or transient response of the medium. The used model is validated in the case of a heterogeneous tissue-like medium using referencing experimental results from the literature. Also, the developed model is used to study changes on transmitted light in a rat-liver tissue-like medium. Optical properties depend on the source wavelength and they are taken from the literature. In particular, light-transmission in the medium is studied for continuous wave and for short pulse. PMID:20396377

  8. Computer applications in recombinant DNA research.

    PubMed

    Modelevsky, J L

    1983-01-01

    I have tried to describe why the computer is an essential tool for the recombinant DNA scientist. As our data bases grow, we will require information storage and communication systems unlike the paper based record systems with which we currently work. Molecular biological data is being generated so rapidly that I believe electronic data exchange will soon be the only way we will be able to keep each other up to date. We have seen some specific computer applications which provide assistance to the researcher at the bench. Sequence manipulation, analysis, and display are too difficult for the unaided molecular biologist to accomplish readily. The computer, being able to provide intelligence at speeds unmatchable by humans, will continue to be used as a tool in recombinant DNA research and will rapidly grow to be an essential tool for all scientists.

  9. Perspectives: Appropriate Research in Biology Education.

    ERIC Educational Resources Information Center

    Stewart, James

    1980-01-01

    Discusses an approach to science education research that focuses on the content of science, such as describing the preconceptions of biology students or common misconceptions following instruction. (CS)

  10. Biology Education Research: Lessons and Future Directions

    ERIC Educational Resources Information Center

    Singer, Susan R.; Nielsen, Natalie R.; Schweingruber, Heidi A.

    2013-01-01

    Biologists have long been concerned about the quality of undergraduate biology education. Over time, however, biology faculty members have begun to study increasingly sophisticated questions about teaching and learning in the discipline. These scholars, often called biology education researchers, are part of a growing field of inquiry called…

  11. Biological and Environmental Research Network Requirements

    SciTech Connect

    Balaji, V.; Boden, Tom; Cowley, Dave; Dart, Eli; Dattoria, Vince; Desai, Narayan; Egan, Rob; Foster, Ian; Goldstone, Robin; Gregurick, Susan; Houghton, John; Izaurralde, Cesar; Johnston, Bill; Joseph, Renu; Kleese-van Dam, Kerstin; Lipton, Mary; Monga, Inder; Pritchard, Matt; Rotman, Lauren; Strand, Gary; Stuart, Cory; Tatusova, Tatiana; Tierney, Brian; Thomas, Brian; Williams, Dean N.; Zurawski, Jason

    2013-09-01

    The Energy Sciences Network (ESnet) is the primary provider of network connectivity for the U.S. Department of Energy (DOE) Office of Science (SC), the single largest supporter of basic research in the physical sciences in the United States. In support of SC programs, ESnet regularly updates and refreshes its understanding of the networking requirements of the instruments, facilities, scientists, and science programs that it serves. This focus has helped ESnet be a highly successful enabler of scientific discovery for over 25 years. In November 2012, ESnet and the Office of Biological and Environmental Research (BER) of the DOE SC organized a review to characterize the networking requirements of the programs funded by the BER program office. Several key findings resulted from the review. Among them: 1) The scale of data sets available to science collaborations continues to increase exponentially. This has broad impact, both on the network and on the computational and storage systems connected to the network. 2) Many science collaborations require assistance to cope with the systems and network engineering challenges inherent in managing the rapid growth in data scale. 3) Several science domains operate distributed facilities that rely on high-performance networking for success. Key examples illustrated in this report include the Earth System Grid Federation (ESGF) and the Systems Biology Knowledgebase (KBase). This report expands on these points, and addresses others as well. The report contains a findings section as well as the text of the case studies discussed at the review.

  12. Biologically inspired path to quantum computer

    NASA Astrophysics Data System (ADS)

    Ogryzko, Vasily; Ozhigov, Yuri

    2014-12-01

    We describe an approach to quantum computer inspired by the information processing at the molecular level in living cells. It is based on the separation of a small ensemble of qubits inside the living system (e.g., a bacterial cell), such that coherent quantum states of this ensemble remain practically unchanged for a long time. We use the notion of a quantum kernel to describe such an ensemble. Quantum kernel is not strictly connected with certain particles; it permanently exchanges atoms and molecules with the environment, which makes quantum kernel a virtual notion. There are many reasons to expect that the state of quantum kernel of a living system can be treated as the stationary state of some Hamiltonian. While the quantum kernel is responsible for the stability of dynamics at the time scale of cellular life, at the longer inter-generation time scale it can change, varying smoothly in the course of biological evolution. To the first level of approximation, quantum kernel can be described in the framework of qubit modification of Jaynes-Cummings-Hubbard model, in which the relaxation corresponds to the exchange of matter between quantum kernel and the rest of the cell and is represented as Lindblad super-operators.

  13. From biological neural networks to thinking machines: Transitioning biological organizational principles to computer technology

    NASA Technical Reports Server (NTRS)

    Ross, Muriel D.

    1991-01-01

    The three-dimensional organization of the vestibular macula is under study by computer assisted reconstruction and simulation methods as a model for more complex neural systems. One goal of this research is to transition knowledge of biological neural network architecture and functioning to computer technology, to contribute to the development of thinking computers. Maculas are organized as weighted neural networks for parallel distributed processing of information. The network is characterized by non-linearity of its terminal/receptive fields. Wiring appears to develop through constrained randomness. A further property is the presence of two main circuits, highly channeled and distributed modifying, that are connected through feedforward-feedback collaterals and biasing subcircuit. Computer simulations demonstrate that differences in geometry of the feedback (afferent) collaterals affects the timing and the magnitude of voltage changes delivered to the spike initiation zone. Feedforward (efferent) collaterals act as voltage followers and likely inhibit neurons of the distributed modifying circuit. These results illustrate the importance of feedforward-feedback loops, of timing, and of inhibition in refining neural network output. They also suggest that it is the distributed modifying network that is most involved in adaptation, memory, and learning. Tests of macular adaptation, through hyper- and microgravitational studies, support this hypothesis since synapses in the distributed modifying circuit, but not the channeled circuit, are altered. Transitioning knowledge of biological systems to computer technology, however, remains problematical.

  14. Biological data sciences in genome research.

    PubMed

    Schatz, Michael C

    2015-10-01

    The last 20 years have been a remarkable era for biology and medicine. One of the most significant achievements has been the sequencing of the first human genomes, which has laid the foundation for profound insights into human genetics, the intricacies of regulation and development, and the forces of evolution. Incredibly, as we look into the future over the next 20 years, we see the very real potential for sequencing more than 1 billion genomes, bringing even deeper insight into human genetics as well as the genetics of millions of other species on the planet. Realizing this great potential for medicine and biology, though, will only be achieved through the integration and development of highly scalable computational and quantitative approaches that can keep pace with the rapid improvements to biotechnology. In this perspective, I aim to chart out these future technologies, anticipate the major themes of research, and call out the challenges ahead. One of the largest shifts will be in the training used to prepare the class of 2035 for their highly interdisciplinary world.

  15. Biological data sciences in genome research.

    PubMed

    Schatz, Michael C

    2015-10-01

    The last 20 years have been a remarkable era for biology and medicine. One of the most significant achievements has been the sequencing of the first human genomes, which has laid the foundation for profound insights into human genetics, the intricacies of regulation and development, and the forces of evolution. Incredibly, as we look into the future over the next 20 years, we see the very real potential for sequencing more than 1 billion genomes, bringing even deeper insight into human genetics as well as the genetics of millions of other species on the planet. Realizing this great potential for medicine and biology, though, will only be achieved through the integration and development of highly scalable computational and quantitative approaches that can keep pace with the rapid improvements to biotechnology. In this perspective, I aim to chart out these future technologies, anticipate the major themes of research, and call out the challenges ahead. One of the largest shifts will be in the training used to prepare the class of 2035 for their highly interdisciplinary world. PMID:26430150

  16. Biological data sciences in genome research

    PubMed Central

    Schatz, Michael C.

    2015-01-01

    The last 20 years have been a remarkable era for biology and medicine. One of the most significant achievements has been the sequencing of the first human genomes, which has laid the foundation for profound insights into human genetics, the intricacies of regulation and development, and the forces of evolution. Incredibly, as we look into the future over the next 20 years, we see the very real potential for sequencing more than 1 billion genomes, bringing even deeper insight into human genetics as well as the genetics of millions of other species on the planet. Realizing this great potential for medicine and biology, though, will only be achieved through the integration and development of highly scalable computational and quantitative approaches that can keep pace with the rapid improvements to biotechnology. In this perspective, I aim to chart out these future technologies, anticipate the major themes of research, and call out the challenges ahead. One of the largest shifts will be in the training used to prepare the class of 2035 for their highly interdisciplinary world. PMID:26430150

  17. Computer-Based Semantic Network in Molecular Biology: A Demonstration.

    ERIC Educational Resources Information Center

    Callman, Joshua L.; And Others

    This paper analyzes the hardware and software features that would be desirable in a computer-based semantic network system for representing biology knowledge. It then describes in detail a prototype network of molecular biology knowledge that has been developed using Filevision software and a Macintosh computer. The prototype contains about 100…

  18. Initiatives in biological research in Indian psychiatry

    PubMed Central

    Shrivatava, Amresh

    2010-01-01

    Biological psychiatry is an exploratory science for mental health. These biological changes provide some explicit insight into the complex area of ‘brain-mind and behavior’. One major achievement of research in biological field is the finding to explain how biological factors cause changes in behavior. In India, we have a clear history of initiatives in research from a biological perspective, which goes back to 1958. In the last 61 years, this field has seen significant evolution, precision and effective utilization of contemporary technological advances. It is a matter of great pride to see that in spite of difficult times in terms of challenges of practice and services, administration, resource, funding and manpower the zest for research was very forthcoming. There was neither dedicated time nor any funding for conducting research. It came from the intellectual insight of our fore fathers in the field of mental health to gradually grow to the state of strategic education in research, training in research, international research collaborations and setting up of internationally accredited centers. During difficult economic conditions in the past, the hypothesis tested and conclusions derived have not been so important. It is more important how it was done, how it was made possible and how robust traditions were established. Almost an entire spectrum of biological research has been touched upon by Indian researchers. Some of these are electroconvulsive therapy, biological markers, neurocognition, neuroimaging, neuroendocrine, neurochemistry, electrophysiology and genetics. A lot has been published given the limited space in the Indian Journal of Psychiatry and other medical journals published in India. A large body of biological research conducted on Indian patients has also been published in International literature (which I prefer to call non-Indian journals). Newer research questions in biological psychiatry, keeping with trend of international standards are

  19. Initiatives in biological research in Indian psychiatry.

    PubMed

    Shrivatava, Amresh

    2010-01-01

    Biological psychiatry is an exploratory science for mental health. These biological changes provide some explicit insight into the complex area of 'brain-mind and behavior'. One major achievement of research in biological field is the finding to explain how biological factors cause changes in behavior. In India, we have a clear history of initiatives in research from a biological perspective, which goes back to 1958. In the last 61 years, this field has seen significant evolution, precision and effective utilization of contemporary technological advances. It is a matter of great pride to see that in spite of difficult times in terms of challenges of practice and services, administration, resource, funding and manpower the zest for research was very forthcoming. There was neither dedicated time nor any funding for conducting research. It came from the intellectual insight of our fore fathers in the field of mental health to gradually grow to the state of strategic education in research, training in research, international research collaborations and setting up of internationally accredited centers. During difficult economic conditions in the past, the hypothesis tested and conclusions derived have not been so important. It is more important how it was done, how it was made possible and how robust traditions were established. Almost an entire spectrum of biological research has been touched upon by Indian researchers. Some of these are electroconvulsive therapy, biological markers, neurocognition, neuroimaging, neuroendocrine, neurochemistry, electrophysiology and genetics. A lot has been published given the limited space in the Indian Journal of Psychiatry and other medical journals published in India. A large body of biological research conducted on Indian patients has also been published in International literature (which I prefer to call non-Indian journals). Newer research questions in biological psychiatry, keeping with trend of international standards are

  20. Systems biology approaches in aging research.

    PubMed

    Chauhan, Anuradha; Liebal, Ulf W; Vera, Julio; Baltrusch, Simone; Junghanß, Christian; Tiedge, Markus; Fuellen, Georg; Wolkenhauer, Olaf; Köhling, Rüdiger

    2015-01-01

    Aging is a systemic process which progressively manifests itself at multiple levels of structural and functional organization from molecular reactions and cell-cell interactions in tissues to the physiology of an entire organ. There is ever increasing data on biomedical relevant network interactions for the aging process at different scales of time and space. To connect the aging process at different structural, temporal and spatial scales, extensive systems biological approaches need to be deployed. Systems biological approaches can not only systematically handle the large-scale datasets (like high-throughput data) and the complexity of interactions (feedback loops, cross talk), but also can delve into nonlinear behaviors exhibited by several biological processes which are beyond intuitive reasoning. Several public-funded agencies have identified the synergistic role of systems biology in aging research. Using one of the notable public-funded programs (GERONTOSYS), we discuss how systems biological approaches are helping the scientists to find new frontiers in aging research. We elaborate on some systems biological approaches deployed in one of the projects of the consortium (ROSage). The systems biology field in aging research is at its infancy. It is open to adapt existing systems biological methodologies from other research fields and devise new aging-specific systems biological methodologies.

  1. Progressive inquiry in a computer-supported biology class

    NASA Astrophysics Data System (ADS)

    Hakkarainen, Kai

    2003-12-01

    The problem addressed in the study was whether 10- and 11-year-old children, collaborating within a computer-supported classroom, could engage in progressive inquiry that exhibits an essential principal feature of mature scientific inquiry: namely, engagement in increasingly deep levels of explanation. Technical infrastructure for the study was provided by the Computer-Supported Intentional Learning Environment (CSILE). The study was carried out by qualitatively analyzing written notes logged by 28 Grade 5/6 students to CSILE's database. Results of the study indicated that with teacher guidance, students were able to produce meaningful intuitive explanations about biological phenomena, guide this process by pursuing their own research questions, and engage in constructive peer interaction that helped them go beyond their intuitive explanations and toward theoretical scientific explanations. Expert evaluations by three widely recognized philosophers of science confirmed the progressive nature of students' inquiry.

  2. Computational Systems Biology in Cancer: Modeling Methods and Applications

    PubMed Central

    Materi, Wayne; Wishart, David S.

    2007-01-01

    In recent years it has become clear that carcinogenesis is a complex process, both at the molecular and cellular levels. Understanding the origins, growth and spread of cancer, therefore requires an integrated or system-wide approach. Computational systems biology is an emerging sub-discipline in systems biology that utilizes the wealth of data from genomic, proteomic and metabolomic studies to build computer simulations of intra and intercellular processes. Several useful descriptive and predictive models of the origin, growth and spread of cancers have been developed in an effort to better understand the disease and potential therapeutic approaches. In this review we describe and assess the practical and theoretical underpinnings of commonly-used modeling approaches, including ordinary and partial differential equations, petri nets, cellular automata, agent based models and hybrid systems. A number of computer-based formalisms have been implemented to improve the accessibility of the various approaches to researchers whose primary interest lies outside of model development. We discuss several of these and describe how they have led to novel insights into tumor genesis, growth, apoptosis, vascularization and therapy. PMID:19936081

  3. ADVANCED COMPUTATIONAL METHODS IN DOSE MODELING: APPLICATION OF COMPUTATIONAL BIOPHYSICAL TRANSPORT, COMPUTATIONAL CHEMISTRY, AND COMPUTATIONAL BIOLOGY

    EPA Science Inventory

    Computational toxicology (CompTox) leverages the significant gains in computing power and computational techniques (e.g., numerical approaches, structure-activity relationships, bioinformatics) realized over the last few years, thereby reducing costs and increasing efficiency i...

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

    PubMed Central

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

    2014-01-01

    Motivation: Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming. Results: We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies. Availability and implementation: Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information. Contact: seunghwa.kang@pnnl.gov PMID:25064572

  5. The biological microprocessor, or how to build a computer with biological parts.

    PubMed

    Moe-Behrens, Gerd Hg

    2013-01-01

    Systemics, a revolutionary paradigm shift in scientific thinking, with applications in systems biology, and synthetic biology, have led to the idea of using silicon computers and their engineering principles as a blueprint for the engineering of a similar machine made from biological parts. Here we describe these building blocks and how they can be assembled to a general purpose computer system, a biological microprocessor. Such a system consists of biological parts building an input / output device, an arithmetic logic unit, a control unit, memory, and wires (busses) to interconnect these components. A biocomputer can be used to monitor and control a biological system.

  6. The biological microprocessor, or how to build a computer with biological parts

    PubMed Central

    Moe-Behrens, Gerd HG

    2013-01-01

    Systemics, a revolutionary paradigm shift in scientific thinking, with applications in systems biology, and synthetic biology, have led to the idea of using silicon computers and their engineering principles as a blueprint for the engineering of a similar machine made from biological parts. Here we describe these building blocks and how they can be assembled to a general purpose computer system, a biological microprocessor. Such a system consists of biological parts building an input / output device, an arithmetic logic unit, a control unit, memory, and wires (busses) to interconnect these components. A biocomputer can be used to monitor and control a biological system. PMID:24688733

  7. Molecular biology for the computer scientist

    SciTech Connect

    Subramaniam, S.

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. This tutorial focuses on the following: the cell and the structural and energetic basis of life molecules; membrane structure; bioenergetics; eukaryotes and functional specialization; examples of molecular systems; evolution and diversity; and modern techniques in molecular biology.

  8. Center for Computing Research Summer Research Proceedings 2015.

    SciTech Connect

    Bradley, Andrew Michael; Parks, Michael L.

    2015-12-18

    The Center for Computing Research (CCR) at Sandia National Laboratories organizes a summer student program each summer, in coordination with the Computer Science Research Institute (CSRI) and Cyber Engineering Research Institute (CERI).

  9. Computational Approaches to Vestibular Research

    NASA Technical Reports Server (NTRS)

    Ross, Muriel D.; Wade, Charles E. (Technical Monitor)

    1994-01-01

    The Biocomputation Center at NASA Ames Research Center is dedicated to a union between computational, experimental and theoretical approaches to the study of neuroscience and of life sciences in general. The current emphasis is on computer reconstruction and visualization of vestibular macular architecture in three-dimensions (3-D), and on mathematical modeling and computer simulation of neural activity in the functioning system. Our methods are being used to interpret the influence of spaceflight on mammalian vestibular maculas in a model system, that of the adult Sprague-Dawley rat. More than twenty 3-D reconstructions of type I and type II hair cells and their afferents have been completed by digitization of contours traced from serial sections photographed in a transmission electron microscope. This labor-intensive method has now been replace d by a semiautomated method developed in the Biocomputation Center in which conventional photography is eliminated. All viewing, storage and manipulation of original data is done using Silicon Graphics workstations. Recent improvements to the software include a new mesh generation method for connecting contours. This method will permit the investigator to describe any surface, regardless of complexity, including highly branched structures such as are routinely found in neurons. This same mesh can be used for 3-D, finite volume simulation of synapse activation and voltage spread on neuronal surfaces visualized via the reconstruction process. These simulations help the investigator interpret the relationship between neuroarchitecture and physiology, and are of assistance in determining which experiments will best test theoretical interpretations. Data are also used to develop abstract, 3-D models that dynamically display neuronal activity ongoing in the system. Finally, the same data can be used to visualize the neural tissue in a virtual environment. Our exhibit will depict capabilities of our computational approaches and

  10. Modelling, abstraction, and computation in systems biology: A view from computer science.

    PubMed

    Melham, Tom

    2013-04-01

    Systems biology is centrally engaged with computational modelling across multiple scales and at many levels of abstraction. Formal modelling, precise and formalised abstraction relationships, and computation also lie at the heart of computer science--and over the past decade a growing number of computer scientists have been bringing their discipline's core intellectual and computational tools to bear on biology in fascinating new ways. This paper explores some of the apparent points of contact between the two fields, in the context of a multi-disciplinary discussion on conceptual foundations of systems biology.

  11. Biology Education Research Trends in Turkey

    ERIC Educational Resources Information Center

    Gul, Seyda; Sozbilir, Mustafa

    2015-01-01

    This paper reports on a content analysis of 633 biology education research [BER] papers published by Turkish science educators in national and international journals. The findings indicate that more research has been undertaken in environment and ecology, the cell and animal form and functions. In addition learning, teaching and attitudes were in…

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

    PubMed Central

    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. PMID:26795950

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

    PubMed

    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.

  14. Arrhythmogenesis Research: A Perspective from Computational Electrophysiology Viewpoint

    PubMed Central

    Trayanova, Natalia; Plank, Gernot

    2012-01-01

    The mechanisms by which arrhythmias are generated in the heart remains a field of intensive research. Recent advances in computational biology and electrophysiology have enabled researchers to use an alternative tool in the study of arrhythmia mechanisms, the multi-scale modeling and simulation of cardiac arrhythmogenesis at the organ level. This article reviews the recent advances and achievements using this approach. PMID:18001976

  15. Modeling Mendel's Laws on Inheritance in Computational Biology and Medical Sciences

    ERIC Educational Resources Information Center

    Singh, Gurmukh; Siddiqui, Khalid; Singh, Mankiran; Singh, Satpal

    2011-01-01

    The current research article is based on a simple and practical way of employing the computational power of widely available, versatile software MS Excel 2007 to perform interactive computer simulations for undergraduate/graduate students in biology, biochemistry, biophysics, microbiology, medicine in college and university classroom setting. To…

  16. A Descriptive Analysis of Computer-Assisted Teaching and Learning in Molecular Biological Education

    ERIC Educational Resources Information Center

    Li, Guangxing; Yin, Jiechao; Ren, Yudong; Wang, Binjie; Ren, Xiaofeng

    2006-01-01

    The role and importance of computer-assisted teaching and learning in molecular biological-related education and research has been emphasized and pinpointed. In this study, some benefit viewpoints and discussion are provided for applying the computer-assisted teaching and learning more efficiently in the process of knowledge acquisition and…

  17. 2003 Biology and Biotechnology Research Program Overview and Highlights

    SciTech Connect

    Prange, C

    2003-03-01

    LLNL conducts multidisciplinary bioscience to fill national needs. Our primary roles are to: develop knowledge and tools which enhance national security, including biological, chemical and nuclear capabilities, and energy and environmental security; develop understanding of genetic and biochemical processes to enhance disease prevention, detection and treatment; develop unique biochemical measurement and computational modeling capabilities which enable understanding of biological processes; and develop technology and tools which enhance healthcare. We execute our roles through integrated multidisciplinary programs that apply our competencies in: microbial and mammalian genomics--the characterization of DNA, the genes it encodes, their regulation and function and their role in living systems; protein function and biochemistry - the structure, function, and interaction of proteins and other molecules involved in the integrated biochemical function of the processes of life; computational modeling and understanding of biochemical systems--the application of high-speed computing technology to simulate and visualize complex, integrated biological processes; bioinformatics--databasing, networking, and analysis of biological data; and bioinstrumentation--the application of physical and engineering technologies to novel biological and biochemical measurements, laboratory automation, medical device development, and healthcare technologies. We leverage the Laboratory's exceptional capabilities in the physical, computational, chemical, environmental and engineering sciences. We partner with industry and universities to utilize their state-of-the art technology and science and to make our capabilities and discoveries available to the broader research community.

  18. 76 FR 78908 - Biological and Environmental Research Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-20

    ... Biological and Environmental Research Advisory Committee AGENCY: Office of Science, Department of Energy. ACTION: Notice of renewal of the Biological and Environmental Research Advisory Committee. SUMMARY... Biological and Environmental Research Advisory Committee will be renewed for a two- year period...

  19. 76 FR 31319 - Biological and Environmental Research Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-31

    ... Biological and Environmental Research Advisory Committee AGENCY: Office of Science, Department of Energy... the Biological and Environmental Research Advisory Committee (BERAC). The Federal Advisory Committee..., Office of Biological and Environmental Research, SC-23/Germantown Building, 1000 Independence Avenue,...

  20. Computer Modelling of Biological Molecules: Free Resources on the Internet.

    ERIC Educational Resources Information Center

    Millar, Neil

    1996-01-01

    Describes a three-dimensional computer modeling system for biological molecules which is suitable for sixth-form teaching. Consists of the modeling program "RasMol" together with structure files of proteins, DNA, and small biological molecules. Describes how the whole system can be downloaded from various sites on the Internet. (Author/JRH)

  1. Research on computer systems benchmarking

    NASA Technical Reports Server (NTRS)

    Smith, Alan Jay (Principal Investigator)

    1996-01-01

    This grant addresses the topic of research on computer systems benchmarking and is more generally concerned with performance issues in computer systems. This report reviews work in those areas during the period of NASA support under this grant. The bulk of the work performed concerned benchmarking and analysis of CPUs, compilers, caches, and benchmark programs. The first part of this work concerned the issue of benchmark performance prediction. A new approach to benchmarking and machine characterization was reported, using a machine characterizer that measures the performance of a given system in terms of a Fortran abstract machine. Another report focused on analyzing compiler performance. The performance impact of optimization in the context of our methodology for CPU performance characterization was based on the abstract machine model. Benchmark programs are analyzed in another paper. A machine-independent model of program execution was developed to characterize both machine performance and program execution. By merging these machine and program characterizations, execution time can be estimated for arbitrary machine/program combinations. The work was continued into the domain of parallel and vector machines, including the issue of caches in vector processors and multiprocessors. All of the afore-mentioned accomplishments are more specifically summarized in this report, as well as those smaller in magnitude supported by this grant.

  2. The computational linguistics of biological sequences

    SciTech Connect

    Searls, D.

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. Protein sequences are analogous in many respects, particularly their folding behavior. Proteins have a much richer variety of interactions, but in theory the same linguistic principles could come to bear in describing dependencies between distant residues that arise by virtue of three-dimensional structure. This tutorial will concentrate on nucleic acid sequences.

  3. Reinforcement learning: Computational theory and biological mechanisms.

    PubMed

    Doya, Kenji

    2007-05-01

    Reinforcement learning is a computational framework for an active agent to learn behaviors on the basis of a scalar reward signal. The agent can be an animal, a human, or an artificial system such as a robot or a computer program. The reward can be food, water, money, or whatever measure of the performance of the agent. The theory of reinforcement learning, which was developed in an artificial intelligence community with intuitions from animal learning theory, is now giving a coherent account on the function of the basal ganglia. It now serves as the "common language" in which biologists, engineers, and social scientists can exchange their problems and findings. This article reviews the basic theoretical framework of reinforcement learning and discusses its recent and future contributions toward the understanding of animal behaviors and human decision making.

  4. Reinforcement learning: Computational theory and biological mechanisms

    PubMed Central

    Doya, Kenji

    2007-01-01

    Reinforcement learning is a computational framework for an active agent to learn behaviors on the basis of a scalar reward signal. The agent can be an animal, a human, or an artificial system such as a robot or a computer program. The reward can be food, water, money, or whatever measure of the performance of the agent. The theory of reinforcement learning, which was developed in an artificial intelligence community with intuitions from animal learning theory, is now giving a coherent account on the function of the basal ganglia. It now serves as the “common language” in which biologists, engineers, and social scientists can exchange their problems and findings. This article reviews the basic theoretical framework of reinforcement learning and discusses its recent and future contributions toward the understanding of animal behaviors and human decision making. PMID:19404458

  5. Computer display and manipulation of biological molecules

    NASA Technical Reports Server (NTRS)

    Coeckelenbergh, Y.; Macelroy, R. D.; Hart, J.; Rein, R.

    1978-01-01

    This paper describes a computer model that was designed to investigate the conformation of molecules, macromolecules and subsequent complexes. Utilizing an advanced 3-D dynamic computer display system, the model is sufficiently versatile to accommodate a large variety of molecular input and to generate data for multiple purposes such as visual representation of conformational changes, and calculation of conformation and interaction energy. Molecules can be built on the basis of several levels of information. These include the specification of atomic coordinates and connectivities and the grouping of building blocks and duplicated substructures using symmetry rules found in crystals and polymers such as proteins and nucleic acids. Called AIMS (Ames Interactive Molecular modeling System), the model is now being used to study pre-biotic molecular evolution toward life.

  6. Report on the research conducted under the funding of the Sloan foundation postdoctoral fellowship in Computational Molecular Biology [Systematic study of protein-protein complexes] Final report

    SciTech Connect

    Sheinerman, Felix

    2001-06-01

    A central question in molecular biology is what structural features are common at protein-protein interfaces and what energetic factors define the affinity and specificity of protein-protein association. Analysis of structural and mutational data on protein-protein interfaces revealed that protein-protein interfaces of different functional classes contain many more energetically important charged and polar residues than was previously thought. Since, in the context of protein folding studies, polar interactions are believed to destabilize the folded proteins, this observation raised the question as to the forces that determine the stability of protein complexes. To investigate this issue in detail, the authors developed a number of partitioning schemes that allowed them to investigate the role of selected residues, ion pairs, and networks of polar interactions in protein-protein association. The methods developed were applied to the analysis of four different protein-protein interfaces: the ribonuclease barnase and its inhibitor barstar, the human growth hormone and its receptor, subtype N9 influenze virus neuraminidase and NC41 antibody, and the Ras Binding Domain of kinase cRaf and a Ras homologue Rap1A. The calculations revealed a surprising variability in how polar interactions affect the stability of different complexes. The finding that positions of charged and polar residues on protein-protein interfaces are optimized with respect to electrostatic interactions suggests that this property can be employed for the discrimination between native conformations and trial complexes generated by a docking algorithm. Analysis indicated the presence of SH2 domains in Janus family of non-receptor protein tyrosine kinases.

  7. Using a Computer Animation to Teach High School Molecular Biology

    ERIC Educational Resources Information Center

    Rotbain, Yosi; Marbach-Ad, Gili; Stavy, Ruth

    2008-01-01

    We present an active way to use a computer animation in secondary molecular genetics class. For this purpose we developed an activity booklet that helps students to work interactively with a computer animation which deals with abstract concepts and processes in molecular biology. The achievements of the experimental group were compared with those…

  8. The Center for Computational Biology: resources, achievements, and challenges.

    PubMed

    Toga, Arthur W; Dinov, Ivo D; Thompson, Paul M; Woods, Roger P; Van Horn, John D; Shattuck, David W; Parker, D Stott

    2012-01-01

    The Center for Computational Biology (CCB) is a multidisciplinary program where biomedical scientists, engineers, and clinicians work jointly to combine modern mathematical and computational techniques, to perform phenotypic and genotypic studies of biological structure, function, and physiology in health and disease. CCB has developed a computational framework built around the Manifold Atlas, an integrated biomedical computing environment that enables statistical inference on biological manifolds. These manifolds model biological structures, features, shapes, and flows, and support sophisticated morphometric and statistical analyses. The Manifold Atlas includes tools, workflows, and services for multimodal population-based modeling and analysis of biological manifolds. The broad spectrum of biomedical topics explored by CCB investigators include the study of normal and pathological brain development, maturation and aging, discovery of associations between neuroimaging and genetic biomarkers, and the modeling, analysis, and visualization of biological shape, form, and size. CCB supports a wide range of short-term and long-term collaborations with outside investigators, which drive the center's computational developments and focus the validation and dissemination of CCB resources to new areas and scientific domains.

  9. Computational Biology for Drug Discovery and Characterization

    SciTech Connect

    Lightstone, F C; Bennion, B J

    2009-02-24

    We proposed to determine the underpinnings of a high-throughput computational infrastructure that would support future efforts in therapeutics against biothreat pathogens. Existing modeling capabilities focus on pathogen detection, but extending such capabilities to high-throughput molecular docking would lead to a proactive method to guide the development of therapeutics. This project will focus on determining the feasibility of extending current databases to accommodate molecular docking. We will also examine the feasibility of massive parallelization of docking algorithms and the utility of docking libraries. Transferring this new technique to a high-performance computing (HPC) platform at LLNL would result in a unique capability not available elsewhere in government or industry. We have accomplished the proposed work defined in this LDRD FS study. (1) We successfully defined the feasibility of using three different small-molecule databases for high-throughput docking, the NCI diversity set, ZINC and the ACD. (2) We analyzed the accuracy and parallelization capabilities of six separate docking programs: DOCK, AutoDock, FlexX, Glide, and eHiTS. Each program is completely amenable to parallel execution. The fastest code was eHiTS, and Glide was the most accurate. (3) Customizing large libraries was cumbersome without the proper software, making the databases a bit difficult to tailor. The ZINC database has some prefiltered versions. (4) Scripts were created for quality and job control functions. Further development is needed for analysis and visualization needs. The successful conclusion of this project enables LLNL to have a high-throughput computational docking capability where we have evaluated the codes to specific docking problems and utilized LLNL's HPC for significant gains in performance. We have established a CRADA with an industrial partner (funded by the National Institutes of Health) that will fully utilize this technology for biodefense therapeutic

  10. DNA computing, computation complexity and problem of biological evolution rate.

    PubMed

    Melkikh, Alexey V

    2008-12-01

    An analogy between the evolution of organisms and some complex computational problems (cryptosystem cracking, determination of the shortest path in a graph) is considered. It is shown that in the absence of a priori information about possible species of organisms such a problem is complex (is rated in the class NP) and cannot be solved in a polynomial number of steps. This conclusion suggests the need for re-examination of evolution mechanisms. Ideas of a deterministic approach to the evolution are discussed.

  11. Using computer algebra and SMT solvers in algebraic biology

    NASA Astrophysics Data System (ADS)

    Pineda Osorio, Mateo

    2014-05-01

    Biologic processes are represented as Boolean networks, in a discrete time. The dynamics within these networks are approached with the help of SMT Solvers and the use of computer algebra. Software such as Maple and Z3 was used in this case. The number of stationary states for each network was calculated. The network studied here corresponds to the immune system under the effects of drastic mood changes. Mood is considered as a Boolean variable that affects the entire dynamics of the immune system, changing the Boolean satisfiability and the number of stationary states of the immune network. Results obtained show Z3's great potential as a SMT Solver. Some of these results were verified in Maple, even though it showed not to be as suitable for the problem approach. The solving code was constructed using Z3-Python and Z3-SMT-LiB. Results obtained are important in biology systems and are expected to help in the design of immune therapies. As a future line of research, more complex Boolean network representations of the immune system as well as the whole psychological apparatus are suggested.

  12. DOE EPSCoR Initiative in Structural and computational Biology/Bioinformatics

    SciTech Connect

    Wallace, Susan S.

    2008-02-21

    The overall goal of the DOE EPSCoR Initiative in Structural and Computational Biology was to enhance the competiveness of Vermont research in these scientific areas. To develop self-sustaining infrastructure, we increased the critical mass of faculty, developed shared resources that made junior researchers more competitive for federal research grants, implemented programs to train graduate and undergraduate students who participated in these research areas and provided seed money for research projects. During the time period funded by this DOE initiative: (1) four new faculty were recruited to the University of Vermont using DOE resources, three in Computational Biology and one in Structural Biology; (2) technical support was provided for the Computational and Structural Biology facilities; (3) twenty-two graduate students were directly funded by fellowships; (4) fifteen undergraduate students were supported during the summer; and (5) twenty-eight pilot projects were supported. Taken together these dollars resulted in a plethora of published papers, many in high profile journals in the fields and directly impacted competitive extramural funding based on structural or computational biology resulting in 49 million dollars awarded in grants (Appendix I), a 600% return on investment by DOE, the State and University.

  13. Biologically Inspired Micro-Flight Research

    NASA Technical Reports Server (NTRS)

    Raney, David L.; Waszak, Martin R.

    2003-01-01

    Natural fliers demonstrate a diverse array of flight capabilities, many of which are poorly understood. NASA has established a research project to explore and exploit flight technologies inspired by biological systems. One part of this project focuses on dynamic modeling and control of micro aerial vehicles that incorporate flexible wing structures inspired by natural fliers such as insects, hummingbirds and bats. With a vast number of potential civil and military applications, micro aerial vehicles represent an emerging sector of the aerospace market. This paper describes an ongoing research activity in which mechanization and control concepts for biologically inspired micro aerial vehicles are being explored. Research activities focusing on a flexible fixed- wing micro aerial vehicle design and a flapping-based micro aerial vehicle concept are presented.

  14. Computational Approaches for Translational Clinical Research in Disease Progression

    PubMed Central

    McGuire, Mary F.; Iyengar, M. Sriram; Mercer, David W.

    2011-01-01

    Today, there is an ever-increasing amount of biological and clinical data available that could be used to enhance a systems-based understanding of disease progression through innovative computational analysis. In this paper we review a selection of published research regarding computational methodologies, primarily from systems biology, that support translational research from the molecular level to the bedside, with a focus on applications in trauma and critical care. Trauma is the leading cause of mortality in Americans under 45 years of age, and its rapid progression offers both opportunities and challenges for computational analysis of trends in molecular patterns associated with outcomes and therapeutic interventions. This review presents methods and domain-specific examples that may inspire the development of new algorithms and computational methods that utilize both molecular and clinical data for diagnosis, prognosis and therapy in disease progression. PMID:21712727

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

    PubMed

    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.

  16. Computational intelligence techniques for biological data mining: An overview

    NASA Astrophysics Data System (ADS)

    Faye, Ibrahima; Iqbal, Muhammad Javed; Said, Abas Md; Samir, Brahim Belhaouari

    2014-10-01

    Computational techniques have been successfully utilized for a highly accurate analysis and modeling of multifaceted and raw biological data gathered from various genome sequencing projects. These techniques are proving much more effective to overcome the limitations of the traditional in-vitro experiments on the constantly increasing sequence data. However, most critical problems that caught the attention of the researchers may include, but not limited to these: accurate structure and function prediction of unknown proteins, protein subcellular localization prediction, finding protein-protein interactions, protein fold recognition, analysis of microarray gene expression data, etc. To solve these problems, various classification and clustering techniques using machine learning have been extensively used in the published literature. These techniques include neural network algorithms, genetic algorithms, fuzzy ARTMAP, K-Means, K-NN, SVM, Rough set classifiers, decision tree and HMM based algorithms. Major difficulties in applying the above algorithms include the limitations found in the previous feature encoding and selection methods while extracting the best features, increasing classification accuracy and decreasing the running time overheads of the learning algorithms. The application of this research would be potentially useful in the drug design and in the diagnosis of some diseases. This paper presents a concise overview of the well-known protein classification techniques.

  17. Computation and graphics in mathematical research

    SciTech Connect

    Hoffman, D.A.; Spruck, J.

    1993-06-01

    Current research is described on: grain boundaries and dislocations in compound polymers, boundary value problems for hypersurfaces constant Gaussian curvature, and discrete computational geometry. 19 refs, 4 figs.

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

    PubMed

    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.

  19. Advances in nicotine research in Addiction Biology.

    PubMed

    Bernardi, Rick E

    2015-09-01

    The aim of Addiction Biology is to advance our understanding of the action of drugs of abuse and addictive processes via the publication of high-impact clinical and pre-clinical findings resulting from behavioral, molecular, genetic, biochemical, neurobiological and pharmacological research. As of 2013, Addiction Biology is ranked number 1 in the category of Substance Abuse journals (SCI). Occasionally, Addiction Biology likes to highlight via review important findings focused on a particular topic and recently published in the journal. The current review summarizes a number of key publications from Addiction Biology that have contributed to the current knowledge of nicotine research, comprising a wide spectrum of approaches, both clinical and pre-clinical, at the cellular, molecular, systems and behavioral levels. A number of findings from human studies have identified, using imaging techniques, alterations in common brain circuits, as well as morphological and network activity changes, associated with tobacco use. Furthermore, both clinical and pre-clinical studies have characterized a number of mechanistic targets critical to understanding the effects of nicotine and tobacco addiction. Together, these findings will undoubtedly drive future studies examining the dramatic impact of tobacco use and the development of treatments to counter nicotine dependence. PMID:25997723

  20. Advances in nicotine research in Addiction Biology.

    PubMed

    Bernardi, Rick E

    2015-09-01

    The aim of Addiction Biology is to advance our understanding of the action of drugs of abuse and addictive processes via the publication of high-impact clinical and pre-clinical findings resulting from behavioral, molecular, genetic, biochemical, neurobiological and pharmacological research. As of 2013, Addiction Biology is ranked number 1 in the category of Substance Abuse journals (SCI). Occasionally, Addiction Biology likes to highlight via review important findings focused on a particular topic and recently published in the journal. The current review summarizes a number of key publications from Addiction Biology that have contributed to the current knowledge of nicotine research, comprising a wide spectrum of approaches, both clinical and pre-clinical, at the cellular, molecular, systems and behavioral levels. A number of findings from human studies have identified, using imaging techniques, alterations in common brain circuits, as well as morphological and network activity changes, associated with tobacco use. Furthermore, both clinical and pre-clinical studies have characterized a number of mechanistic targets critical to understanding the effects of nicotine and tobacco addiction. Together, these findings will undoubtedly drive future studies examining the dramatic impact of tobacco use and the development of treatments to counter nicotine dependence.

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

    PubMed

    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.

  2. Onchocerciasis control: biological research is still needed.

    PubMed

    Boussinesq, M

    2008-09-01

    Achievements obtained by the onchocerciasis control programmes should not lead to a relaxation in the biological research on Onchocerco volvulus. Issues such as the Loa loa-related post-ivermectin serious adverse events, the uncertainties as to whether onchocerciasis can be eliminated by ivermectin treatments, and the possible emergence of ivermectin-resistant O. volvulus populations should be addressed proactively. Doxycycline, moxidectin and emodepside appear to be promising as alternative drugs against onchocerciasis but support to researches in immunology and genomics should also be increased to develop new control tools, including both vaccines and macrofilaricidal drugs. PMID:18814732

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

    PubMed

    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.

  4. Biology Students Building Computer Simulations Using StarLogo TNG

    ERIC Educational Resources Information Center

    Smith, V. Anne; Duncan, Ishbel

    2011-01-01

    Confidence is an important issue for biology students in handling computational concepts. This paper describes a practical in which honours-level bioscience students simulate complex animal behaviour using StarLogo TNG, a freely-available graphical programming environment. The practical consists of two sessions, the first of which guides students…

  5. Integrating Computer Interfaced Videodisc Systems in Introductory College Biology.

    ERIC Educational Resources Information Center

    Ebert-Zawasky, Kathleen; Abegg, Gerald L.

    This study was designed as a systematic investigation of the feasibility and effectiveness of student authored videodisc presentations in a non-major introductory level college biology course. Students (n=66) used a quick-learn authoring system, the Macintosh computer, and videodisc player with color monitor. Results included: (1) students managed…

  6. Biological effectiveness of neutrons: Research needs

    SciTech Connect

    Casarett, G.W.; Braby, L.A.; Broerse, J.J.; Elkind, M.M.; Goodhead, D.T.; Oleinick, N.L.

    1994-02-01

    The goal of this report was to provide a conceptual plan for a research program that would provide a basis for determining more precisely the biological effectiveness of neutron radiation with emphasis on endpoints relevant to the protection of human health. This report presents the findings of the experts for seven particular categories of scientific information on neutron biological effectiveness. Chapter 2 examines the radiobiological mechanisms underlying the assumptions used to estimate human risk from neutrons and other radiations. Chapter 3 discusses the qualitative and quantitative models used to organize and evaluate experimental observations and to provide extrapolations where direct observations cannot be made. Chapter 4 discusses the physical principles governing the interaction of radiation with biological systems and the importance of accurate dosimetry in evaluating radiation risk and reducing the uncertainty in the biological data. Chapter 5 deals with the chemical and molecular changes underlying cellular responses and the LET dependence of these changes. Chapter 6, in turn, discusses those cellular and genetic changes which lead to mutation or neoplastic transformation. Chapters 7 and 8 examine deterministic and stochastic effects, respectively, and the data required for the prediction of such effects at different organizational levels and for the extrapolation from experimental results in animals to risks for man. Gaps and uncertainties in this data are examined relative to data required for establishing radiation protection standards for neutrons and procedures for the effective and safe use of neutron and other high-LET radiation therapy.

  7. Graphics supercomputer for computational fluid dynamics research

    NASA Astrophysics Data System (ADS)

    Liaw, Goang S.

    1994-11-01

    The objective of this project is to purchase a state-of-the-art graphics supercomputer to improve the Computational Fluid Dynamics (CFD) research capability at Alabama A & M University (AAMU) and to support the Air Force research projects. A cutting-edge graphics supercomputer system, Onyx VTX, from Silicon Graphics Computer Systems (SGI), was purchased and installed. Other equipment including a desktop personal computer, PC-486 DX2 with a built-in 10-BaseT Ethernet card, a 10-BaseT hub, an Apple Laser Printer Select 360, and a notebook computer from Zenith were also purchased. A reading room has been converted to a research computer lab by adding some furniture and an air conditioning unit in order to provide an appropriate working environments for researchers and the purchase equipment. All the purchased equipment were successfully installed and are fully functional. Several research projects, including two existing Air Force projects, are being performed using these facilities.

  8. Chaste: using agile programming techniques to develop computational biology software.

    PubMed

    Pitt-Francis, Joe; Bernabeu, Miguel O; Cooper, Jonathan; Garny, Alan; Momtahan, Lee; Osborne, James; Pathmanathan, Pras; Rodriguez, Blanca; Whiteley, Jonathan P; Gavaghan, David J

    2008-09-13

    Cardiac modelling is the area of physiome modelling where the available simulation software is perhaps most mature, and it therefore provides an excellent starting point for considering the software requirements for the wider physiome community. In this paper, we will begin by introducing some of the most advanced existing software packages for simulating cardiac electrical activity. We consider the software development methods used in producing codes of this type, and discuss their use of numerical algorithms, relative computational efficiency, usability, robustness and extensibility. We then go on to describe a class of software development methodologies known as test-driven agile methods and argue that such methods are more suitable for scientific software development than the traditional academic approaches. A case study is a project of our own, Cancer, Heart and Soft Tissue Environment, which is a library of computational biology software that began as an experiment in the use of agile programming methods. We present our experiences with a review of our progress thus far, focusing on the advantages and disadvantages of this new approach compared with the development methods used in some existing packages. We conclude by considering whether the likely wider needs of the cardiac modelling community are currently being met and suggest that, in order to respond effectively to changing requirements, it is essential that these codes should be more malleable. Such codes will allow for reliable extensions to include both detailed mathematical models--of the heart and other organs--and more efficient numerical techniques that are currently being developed by many research groups worldwide. PMID:18565813

  9. Chaste: using agile programming techniques to develop computational biology software.

    PubMed

    Pitt-Francis, Joe; Bernabeu, Miguel O; Cooper, Jonathan; Garny, Alan; Momtahan, Lee; Osborne, James; Pathmanathan, Pras; Rodriguez, Blanca; Whiteley, Jonathan P; Gavaghan, David J

    2008-09-13

    Cardiac modelling is the area of physiome modelling where the available simulation software is perhaps most mature, and it therefore provides an excellent starting point for considering the software requirements for the wider physiome community. In this paper, we will begin by introducing some of the most advanced existing software packages for simulating cardiac electrical activity. We consider the software development methods used in producing codes of this type, and discuss their use of numerical algorithms, relative computational efficiency, usability, robustness and extensibility. We then go on to describe a class of software development methodologies known as test-driven agile methods and argue that such methods are more suitable for scientific software development than the traditional academic approaches. A case study is a project of our own, Cancer, Heart and Soft Tissue Environment, which is a library of computational biology software that began as an experiment in the use of agile programming methods. We present our experiences with a review of our progress thus far, focusing on the advantages and disadvantages of this new approach compared with the development methods used in some existing packages. We conclude by considering whether the likely wider needs of the cardiac modelling community are currently being met and suggest that, in order to respond effectively to changing requirements, it is essential that these codes should be more malleable. Such codes will allow for reliable extensions to include both detailed mathematical models--of the heart and other organs--and more efficient numerical techniques that are currently being developed by many research groups worldwide.

  10. Computational Biology Methods for Characterization of Pluripotent Cells.

    PubMed

    Araúzo-Bravo, Marcos J

    2016-01-01

    Pluripotent cells are a powerful tool for regenerative medicine and drug discovery. Several techniques have been developed to induce pluripotency, or to extract pluripotent cells from different tissues and biological fluids. However, the characterization of pluripotency requires tedious, expensive, time-consuming, and not always reliable wet-lab experiments; thus, an easy, standard quality-control protocol of pluripotency assessment remains to be established. Here to help comes the use of high-throughput techniques, and in particular, the employment of gene expression microarrays, which has become a complementary technique for cellular characterization. Research has shown that the transcriptomics comparison with an Embryonic Stem Cell (ESC) of reference is a good approach to assess the pluripotency. Under the premise that the best protocol is a computer software source code, here I propose and explain line by line a software protocol coded in R-Bioconductor for pluripotency assessment based on the comparison of transcriptomics data of pluripotent cells with an ESC of reference. I provide advice for experimental design, warning about possible pitfalls, and guides for results interpretation.

  11. Japan sets up program for biological research

    SciTech Connect

    Lepkowski, W.

    1988-05-16

    Japanese officials have put final touches on plans for a global biological research program, called the Human Frontier Science Program, that they hope will launch their country into a new era of international science. Japan will establish a nongovernmental secretariat for the program and will manage it through an international governing council. Almost all the funding in the countries involved- Japan, the U.S., Canada, and the European Community countries- will be provided by Japan, at least at first. In its present design, the program consists of two thrusts- one in the neurosciences with emphasis on brain function, the other on the chemistry and molecular biology of gene expression. The program in the first year would consist of 30 to 50 direct research grants to researchers working in teams, 100 to 200 postdoctoral fellowships, and 10 to 20 workshops. Young researchers would be favored for funding. The average annual grant size would total $500,000, and postdoctoral awards would average $50,000.

  12. Trademark Research with the Computer.

    ERIC Educational Resources Information Center

    Jordan, Anne S.

    1985-01-01

    Discusses computer use in practice of trademark law by following adoption, filing, and prior use of the trademark "Aspen" (for a fruit juice drink). Databases searched to track previous use of mark, trace possible conflicts, and assist in their resolution are mentioned. Database chart and list of vendors is included. (EJS)

  13. Reproducible Research in Computational Science

    PubMed Central

    Peng, Roger D.

    2012-01-01

    Computational science has led to exciting new developments, but the nature of the work has exposed limitations in our ability to evaluate published findings. Reproducibility has the potential to serve as a minimum standard for judging scientific claims when full independent replication of a study is not possible. PMID:22144613

  14. Reproducible research in computational science.

    PubMed

    Peng, Roger D

    2011-12-01

    Computational science has led to exciting new developments, but the nature of the work has exposed limitations in our ability to evaluate published findings. Reproducibility has the potential to serve as a minimum standard for judging scientific claims when full independent replication of a study is not possible.

  15. Gordon Research Conference on Mammary Gland Biology

    SciTech Connect

    Not Available

    1989-01-01

    The 1989 conference was the tenth in the series of biennial Gordon Research Conferences on Mammary Gland Biology. Traditionally this conference brings together scientists from diverse backgrounds and experience but with a common interest in the biology of the mammary gland. Investigators from agricultural and medical schools, biochemists, cell and molecular biologists, endocrinologists, immunologists, and representatives from the emerging biotechnology industries met to discuss current concepts and results on the function and regulation of the normal and neoplastic mammary gland in a variety of species. Of the participants, approximately three-fourths were engaged in studying the normal mammary gland function, whereas the other quarter were engaged in studying the neoplastic gland. The interactions between scientists, clinicians, veterinarians examining both normal and neoplastic cell function serves to foster the multi-disciplinary goals of the conference and has stimulated many cooperative projects among participants in previous years.

  16. 10 years for the Journal of Bioinformatics and Computational Biology (2003-2013) -- a retrospective.

    PubMed

    Eisenhaber, Frank; Sherman, Westley Arthur

    2014-06-01

    The Journal of Bioinformatics and Computational Biology (JBCB) started publishing scientific articles in 2003. It has established itself as home for solid research articles in the field (~ 60 per year) that are surprisingly well cited. JBCB has an important function as alternative publishing channel in addition to other, bigger journals.

  17. Effects of Computer Assisted Instruction (CAI) on Secondary School Students' Performance in Biology

    ERIC Educational Resources Information Center

    Yusuf, Mudasiru Olalere; Afolabi, Adedeji Olufemi

    2010-01-01

    This study investigated the effects of computer assisted instruction (CAI) on secondary school students' performance in biology. Also, the influence of gender on the performance of students exposed to CAI in individualised or cooperative learning settings package was examined. The research was a quasi experimental involving a 3 x 2 factorial…

  18. PARTNERING WITH DOE TO APPLY ADVANCED BIOLOGICAL, ENVIRONMENTAL, AND COMPUTATIONAL SCIENCE TO ENVIRONMENTAL ISSUES

    EPA Science Inventory

    On February 18, 2004, the U.S. Environmental Protection Agency and Department of Energy signed a Memorandum of Understanding to expand the research collaboration of both agencies to advance biological, environmental, and computational sciences for protecting human health and the ...

  19. Delivering The Benefits of Chemical-Biological Integration in Computational Toxicology at the EPA (ACS Fall meeting)

    EPA Science Inventory

    Abstract: Researchers at the EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The intent...

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

    SciTech Connect

    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.

  1. Radioisotopic methods for biological and medical research

    SciTech Connect

    Knoche, H.W.

    1991-01-01

    This book provides a theoretical basis for the effective and safe use of radioactive materials in research. Particular attention is given to the four major topic areas specified in NRC's license application forms: (1) principles and practices of radiation protection; (2) radioactivity measurement, standardization and monitoring techniques, and instruments; (3) mathematics and calculations basic to the use and measurement of radioactivity; (4) biological effects of radiation. Overview and background information, including a section reviewing nuclear physics, is used where needed throughout the text, and problem sets are included in many of the chapters. Appendices for physical constants and conversion factors and for answers to problems are added.

  2. An interdepartmental Ph.D. program in computational biology and bioinformatics: the Yale perspective.

    PubMed

    Gerstein, Mark; Greenbaum, Dov; Cheung, Kei; Miller, Perry L

    2007-02-01

    Computational biology and bioinformatics (CBB), the terms often used interchangeably, represent a rapidly evolving biological discipline. With the clear potential for discovery and innovation, and the need to deal with the deluge of biological data, many academic institutions are committing significant resources to develop CBB research and training programs. Yale formally established an interdepartmental Ph.D. program in CBB in May 2003. This paper describes Yale's program, discussing the scope of the field, the program's goals and curriculum, as well as a number of issues that arose in implementing the program. (Further updated information is available from the program's website, www.cbb.yale.edu.)

  3. Race in Biological and Biomedical Research

    PubMed Central

    Cooper, Richard S.

    2013-01-01

    The concept of race has had a significant influence on research in human biology since the early 19th century. But race was given its meaning and social impact in the political sphere and subsequently intervened in science as a foreign concept, not grounded in the dominant empiricism of modern biology. The uses of race in science were therefore often disruptive and controversial; at times, science had to be retrofitted to accommodate race, and science in turn was often used to explain and justify race. This relationship was unstable in large part because race was about a phenomenon that could not be observed directly, being based on claims about the structure and function of genomic DNA. Over time, this relationship has been characterized by distinct phases, evolving from the inference of genetic effects based on the observed phenotype to the measurement of base-pair variation in DNA. Despite this fundamental advance in methodology, liabilities imposed by the dual political-empirical origins of race persist. On the one hand, an optimistic prediction can be made that just as geology made it possible to overturn the myth of the recent creation of the earth and evolution told us where the living world came from, molecular genetics will end the use of race in biology. At the same time, because race is fundamentally a political and not a scientific idea, it is possible that only a political intervention will relieve us of the burden of race. PMID:24186487

  4. A comprehensive approach to decipher biological computation to achieve next generation high-performance exascale computing.

    SciTech Connect

    James, Conrad D.; Schiess, Adrian B.; Howell, Jamie; Baca, Michael J.; Partridge, L. Donald; Finnegan, Patrick Sean; Wolfley, Steven L.; Dagel, Daryl James; Spahn, Olga Blum; Harper, Jason C.; Pohl, Kenneth Roy; Mickel, Patrick R.; Lohn, Andrew; Marinella, Matthew

    2013-10-01

    The human brain (volume=1200cm3) consumes 20W and is capable of performing > 10^16 operations/s. Current supercomputer technology has reached 1015 operations/s, yet it requires 1500m^3 and 3MW, giving the brain a 10^12 advantage in operations/s/W/cm^3. Thus, to reach exascale computation, two achievements are required: 1) improved understanding of computation in biological tissue, and 2) a paradigm shift towards neuromorphic computing where hardware circuits mimic properties of neural tissue. To address 1), we will interrogate corticostriatal networks in mouse brain tissue slices, specifically with regard to their frequency filtering capabilities as a function of input stimulus. To address 2), we will instantiate biological computing characteristics such as multi-bit storage into hardware devices with future computational and memory applications. Resistive memory devices will be modeled, designed, and fabricated in the MESA facility in consultation with our internal and external collaborators.

  5. 78 FR 77111 - Biological and Environmental Research Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-20

    ... Biological and Environmental Research Advisory Committee AGENCY: Office of Science, Department of Energy...), and following consultation with the Committee Management Secretariat, General Services Administration, notice is hereby given that the Biological and Environmental Research Advisory Committee will be...

  6. Computational design of digital and memory biological devices

    PubMed Central

    Rodrigo, Guillermo

    2008-01-01

    The use of combinatorial optimization techniques with computational design allows the development of automated methods to design biological systems. Automatic design integrates design principles in an unsupervised algorithm to sample a larger region of the biological network space, at the topology and parameter levels. The design of novel synthetic transcriptional networks with targeted behaviors will be key to understand the design principles underlying biological networks. In this work, we evolve transcriptional networks towards a targeted dynamics, by using a library of promoters and coding sequences, to design a complex biological memory device. The designed sequential transcription network implements a JK-Latch, which is fully predictable and richer than other memory devices. Furthermore, we present designs of transcriptional devices behaving as logic gates, and we show how to create digital behavior from analog promoters. Our procedure allows us to propose a scenario for the evolution of multi-functional genetic networks. In addition, we discuss the decomposability of regulatory networks in terms of genetic modules to develop a given cellular function. Summary. We show how to use an automated procedure to design logic and sequential transcription circuits. This methodology will allow advancing the rational design of biological devices to more complex systems, and we propose the first design of a biological JK-latch memory device. Electronic supplementary material The online version of this article (doi:10.1007/s11693-008-9017-0) contains supplementary material, which is available to authorized users. PMID:19003443

  7. Computational Neuroscience: Modeling the Systems Biology of Synaptic Plasticity

    PubMed Central

    Kotaleski, Jeanette Hellgren; Blackwell, Kim T.

    2016-01-01

    Preface Synaptic plasticity is a mechanism proposed to underlie learning and memory. The complexity of the interactions between ion channels, enzymes, and genes involved in synaptic plasticity impedes a deep understanding of this phenomenon. Computer modeling is an approach to investigate the information processing that is performed by signaling pathways underlying synaptic plasticity. In the past few years, new software developments that blend computational neuroscience techniques with systems biology techniques have allowed large-scale, quantitative modeling of synaptic plasticity in neurons. We highlight significant advancements produced by these modeling efforts and introduce promising approaches that utilize advancements in live cell imaging. PMID:20300102

  8. Systems Biology in Immunology – A Computational Modeling Perspective

    PubMed Central

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

    2011-01-01

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

  9. Computational approaches in modeling spectra of biological chromophores

    NASA Astrophysics Data System (ADS)

    Nemukhin, Alexander V.; Grigorenko, Bella L.; Bochenkova, Anastasia V.; Bravaya, Ksenia B.; Savitsky, Alexander P.

    2008-02-01

    Computational approaches to describe optical spectra of biological chromophores in proteins, in solutions and in the gas phase are discussed. Recently, accurate measurements of spectral properties for the series of chromophores in different media allowed the authors to estimate the positions of the bands with a high accuracy and to challenge theoreticians by stating that the measured S 0-S I transition wavelengths may be used as new benchmark values for the theory. The novel computational approaches based on the multiconfigurational quasidegenerate perturbation theory present the practical means how to adapt the high level methodology for calculations of accurate excitation energies in large biological chromophores. The theory is illustrated for a series of model compounds for which experimental data are available: the retinal molecule in the protonated Shiff-base form, the chromophores from the Green Fluorescent Protein family including the kindling protein asFP595, and the chromophore from the BLUF domain containing photoreceptor proteins.

  10. 2010 Plant Molecular Biology Gordon Research Conference

    SciTech Connect

    Michael Sussman

    2010-07-23

    The Plant Molecular Biology Conference has traditionally covered a breadth of exciting topics and the 2010 conference will continue in that tradition. Emerging concerns about food security have inspired a program with three main themes: (1) genomics, natural variation and breeding to understand adaptation and crop improvement, (2) hormonal cross talk, and (3) plant/microbe interactions. There are also sessions on epigenetics and proteomics/metabolomics. Thus this conference will bring together a range of disciplines, will foster the exchange of ideas and enable participants to learn of the latest developments and ideas in diverse areas of plant biology. The conference provides an excellent opportunity for individuals to discuss their research because additional speakers in each session will be selected from submitted abstracts. There will also be a poster session each day for a two-hour period prior to dinner. In particular, this conference plays a key role in enabling students and postdocs (the next generation of research leaders) to mingle with pioneers in multiple areas of plant science.

  11. Exploiting graphics processing units for computational biology and bioinformatics.

    PubMed

    Payne, Joshua L; Sinnott-Armstrong, Nicholas A; Moore, Jason H

    2010-09-01

    Advances in the video gaming industry have led to the production of low-cost, high-performance graphics processing units (GPUs) that possess more memory bandwidth and computational capability than central processing units (CPUs), the standard workhorses of scientific computing. With the recent release of generalpurpose GPUs and NVIDIA's GPU programming language, CUDA, graphics engines are being adopted widely in scientific computing applications, particularly in the fields of computational biology and bioinformatics. The goal of this article is to concisely present an introduction to GPU hardware and programming, aimed at the computational biologist or bioinformaticist. To this end, we discuss the primary differences between GPU and CPU architecture, introduce the basics of the CUDA programming language, and discuss important CUDA programming practices, such as the proper use of coalesced reads, data types, and memory hierarchies. We highlight each of these topics in the context of computing the all-pairs distance between instances in a dataset, a common procedure in numerous disciplines of scientific computing. We conclude with a runtime analysis of the GPU and CPU implementations of the all-pairs distance calculation. We show our final GPU implementation to outperform the CPU implementation by a factor of 1700.

  12. Topological properties of robust biological and computational networks

    PubMed Central

    Navlakha, Saket; He, Xin; Faloutsos, Christos; Bar-Joseph, Ziv

    2014-01-01

    Network robustness is an important principle in biology and engineering. Previous studies of global networks have identified both redundancy and sparseness as topological properties used by robust networks. By focusing on molecular subnetworks, or modules, we show that module topology is tightly linked to the level of environmental variability (noise) the module expects to encounter. Modules internal to the cell that are less exposed to environmental noise are more connected and less robust than external modules. A similar design principle is used by several other biological networks. We propose a simple change to the evolutionary gene duplication model which gives rise to the rich range of module topologies observed within real networks. We apply these observations to evaluate and design communication networks that are specifically optimized for noisy or malicious environments. Combined, joint analysis of biological and computational networks leads to novel algorithms and insights benefiting both fields. PMID:24789562

  13. Argonne's Magellan Cloud Computing Research Project

    SciTech Connect

    Beckman, Pete

    2009-01-01

    Pete Beckman, head of Argonne's Leadership Computing Facility (ALCF), discusses the Department of Energy's new $32-million Magellan project, which designed to test how cloud computing can be used for scientific research. More information: http://www.anl.gov/Media_Center/News/2009/news091014a.html

  14. Argonne's Magellan Cloud Computing Research Project

    ScienceCinema

    Beckman, Pete

    2016-07-12

    Pete Beckman, head of Argonne's Leadership Computing Facility (ALCF), discusses the Department of Energy's new $32-million Magellan project, which designed to test how cloud computing can be used for scientific research. More information: http://www.anl.gov/Media_Center/News/2009/news091014a.html

  15. Computational immuno-biology for organ transplantation and regenerative medicine.

    PubMed

    Vásquez-Montoya, Gustavo A; Danobeitia, Juan S; Fernández, Luis A; Hernández-Ortiz, Juan P

    2016-10-01

    Organ transplantation and regenerative medicine are adopted platforms that provide replacement tissues and organs from natural or engineered sources. Acceptance, tolerance and rejection depend greatly on the proper control of the immune response against graft antigens, motivating the development of immunological and genetical therapies that prevent organ failure. They rely on a complete, or partial, understanding of the immune system. Ultimately, they are innovative technologies that ensure permanent graft tolerance and indefinite graft survival through the modulation of the immune system. Computational immunology has arisen as a tool towards a mechanistic understanding of the biological and physicochemical processes surrounding an immune response. It comprehends theoretical and computational frameworks that simulate immuno-biological systems. The challenge is centered on the multi-scale character of the immune system that spans from atomistic scales, during peptide-epitope and protein interactions, to macroscopic scales, for lymph transport and organ-organ reactions. In this paper, we discuss, from an engineering perspective, the biological processes that are involved during the immune response of organ transplantation. Previous computational efforts, including their characteristics and visible limitations, are described. Finally, future perspectives and challenges are listed to motivate further developments.

  16. 78 FR 6087 - Biological and Environmental Research Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-29

    ... Update from the Office of Science Report from the Office of Biological and Environmental Research News... Biological and Environmental Research Advisory Committee AGENCY: Office of Science, Department of Energy.... Department of Energy, Office of Science, Office of Biological and Environmental Research,...

  17. Beyond moore computing research challenge workshop report.

    SciTech Connect

    Huey, Mark C.; Aidun, John Bahram

    2013-10-01

    We summarize the presentations and break out session discussions from the in-house workshop that was held on 11 July 2013 to acquaint a wider group of Sandians with the Beyond Moore Computing research challenge.

  18. Division of Biological and Medical Research annual research summary, 1983

    SciTech Connect

    Barr, S.H.

    1984-08-01

    This research summary contains brief descriptions of research in the following areas: (1) mechanisms of hepatocarcinogenesis; (2) role of metals in cocarcinogenesis and the use of liposomes for metal mobilization; (3) control of mutagenesis and cell differentiation in cultured cells by tumor promoters; (4) radiation effects in mammalian cells; (5) radiation carcinogenesis and radioprotectors; (6) life shortening, tumor induction, and tissue dose for fission-neutron and gamma-ray irradiations; (7) mammalian genetics and biostatistics; (8) radiation toxicity studies; (9) hematopoiesis in chronic toxicity; (10) molecular biology studies; (11) chemical toxicology; (12) carcinogen identification and metabolism; (13) metal metabolism and toxicity; and (14) neurobehavioral chronobiology. (ACR)

  19. Space Station Biological Research Project Habitat: Incubator

    NASA Technical Reports Server (NTRS)

    Nakamura, G. J.; Kirven-Brooks, M.; Scheller, N. M.

    2001-01-01

    Developed as part of the suite of Space Station Biological Research Project (SSBRP) hardware to support research aboard the International Space Station (ISS), the Incubator is a temperature-controlled chamber, for conducting life science research with small animal, plant and microbial specimens. The Incubator is designed for use only on the ISS and is transported to/from the ISS, unpowered and without specimens, in the Multi-Purpose Logistics Module (MPLM) of the Shuttle. The Incubator interfaces with the three SSBRP Host Systems; the Habitat Holding Racks (HHR), the Life Sciences Glovebox (LSG) and the 2.5 m Centrifuge Rotor (CR), providing investigators with the ability to conduct research in microgravity and at variable gravity levels of up to 2-g. The temperature within the Specimen Chamber can be controlled between 4 and 45 C. Cabin air is recirculated within the Specimen Chamber and can be exchanged with the ISS cabin at a rate of approximately equal 50 cc/min. The humidity of the Specimen Chamber is monitored. The Specimen Chamber has a usable volume of approximately equal 19 liters and contains two (2) connectors at 28v dc, (60W) for science equipment; 5 dedicated thermometers for science; ports to support analog and digital signals from experiment unique sensors or other equipment; an Ethernet port; and a video port. It is currently manifested for UF-3 and will be launched integrated within the first SSBRP Habitat Holding Rack.

  20. Optical computing at NASA Ames Research Center

    NASA Technical Reports Server (NTRS)

    Reid, Max B.; Bualat, Maria G.; Downie, John D.; Galant, David; Gary, Charles K.; Hine, Butler P.; Ma, Paul W.; Pryor, Anna H.; Spirkovska, Lilly

    1991-01-01

    Optical computing research at NASA Ames Research Center seeks to utilize the capability of analog optical processing, involving free-space propagation between components, to produce natural implementations of algorithms requiring large degrees of parallel computation. Potential applications being investigated include robotic vision, planetary lander guidance, aircraft engine exhaust analysis, analysis of remote sensing satellite multispectral images, control of space structures, and autonomous aircraft inspection.

  1. Research Institute for Advanced Computer Science

    NASA Technical Reports Server (NTRS)

    Gross, Anthony R. (Technical Monitor); Leiner, Barry M.

    2000-01-01

    The Research Institute for Advanced Computer Science (RIACS) carries out basic research and technology development in computer science, in support of the National Aeronautics and Space Administration's missions. RIACS is located at the NASA Ames Research Center. It currently operates under a multiple year grant/cooperative agreement that began on October 1, 1997 and is up for renewal in the year 2002. Ames has been designated NASA's Center of Excellence in Information Technology. In this capacity, Ames is charged with the responsibility to build an Information Technology Research Program that is preeminent within NASA. RIACS serves as a bridge between NASA Ames and the academic community, and RIACS scientists and visitors work in close collaboration with NASA scientists. RIACS has the additional goal of broadening the base of researchers in these areas of importance to the nation's space and aeronautics enterprises. RIACS research focuses on the three cornerstones of information technology research necessary to meet the future challenges of NASA missions: (1) Automated Reasoning for Autonomous Systems. Techniques are being developed enabling spacecraft that will be self-guiding and self-correcting to the extent that they will require little or no human intervention. Such craft will be equipped to independently solve problems as they arise, and fulfill their missions with minimum direction from Earth; (2) Human-Centered Computing. Many NASA missions require synergy between humans and computers, with sophisticated computational aids amplifying human cognitive and perceptual abilities; (3) High Performance Computing and Networking. Advances in the performance of computing and networking continue to have major impact on a variety of NASA endeavors, ranging from modeling and simulation to data analysis of large datasets to collaborative engineering, planning and execution. In addition, RIACS collaborates with NASA scientists to apply information technology research to a

  2. Mathematical and Computational Challenges in Population Biology and Ecosystems Science

    NASA Technical Reports Server (NTRS)

    Levin, Simon A.; Grenfell, Bryan; Hastings, Alan; Perelson, Alan S.

    1997-01-01

    Mathematical and computational approaches provide powerful tools in the study of problems in population biology and ecosystems science. The subject has a rich history intertwined with the development of statistics and dynamical systems theory, but recent analytical advances, coupled with the enhanced potential of high-speed computation, have opened up new vistas and presented new challenges. Key challenges involve ways to deal with the collective dynamics of heterogeneous ensembles of individuals, and to scale from small spatial regions to large ones. The central issues-understanding how detail at one scale makes its signature felt at other scales, and how to relate phenomena across scales-cut across scientific disciplines and go to the heart of algorithmic development of approaches to high-speed computation. Examples are given from ecology, genetics, epidemiology, and immunology.

  3. Molecular biology approaches in bioadhesion research

    PubMed Central

    Rodrigues, Marcelo; Lengerer, Birgit; Ostermann, Thomas

    2014-01-01

    Summary The use of molecular biology tools in the field of bioadhesion is still in its infancy. For new research groups who are considering taking a molecular approach, the techniques presented here are essential to unravelling the sequence of a gene, its expression and its biological function. Here we provide an outline for addressing adhesion-related genes in diverse organisms. We show how to gradually narrow down the number of candidate transcripts that are involved in adhesion by (1) generating a transcriptome and a differentially expressed cDNA list enriched for adhesion-related transcripts, (2) setting up a BLAST search facility, (3) perform an in situ hybridization screen, and (4) functional analyses of selected genes by using RNA interference knock-down. Furthermore, latest developments in genome-editing are presented as new tools to study gene function. By using this iterative multi-technologies approach, the identification, isolation, expression and function of adhesion-related genes can be studied in most organisms. These tools will improve our understanding of the diversity of molecules used for adhesion in different organisms and these findings will help to develop innovative bio-inspired adhesives. PMID:25161834

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

    SciTech Connect

    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.

  5. A Systems Biology Approach to Infectious Disease Research: Innovating the Pathogen-Host Research Paradigm

    SciTech Connect

    Aderem, Alan; Adkins, Joshua N.; Ansong, Charles; Galagan, James; Kaiser, Shari; Korth, Marcus J.; Law, G. L.; McDermott, Jason E.; Proll, Sean; Rosenberger, Carrie; Schoolnik, Gary; Katze, Michael G.

    2011-02-01

    The 20th century was marked by extraordinary advances in our understanding of microbes and infectious disease, but pandemics remain, food and water borne illnesses are frequent, multi-drug resistant microbes are on the rise, and the needed drugs and vaccines have not been developed. The scientific approaches of the past—including the intense focus on individual genes and proteins typical of molecular biology—have not been sufficient to address these challenges. The first decade of the 21st century has seen remarkable innovations in technology and computational methods. These new tools provide nearly comprehensive views of complex biological systems and can provide a correspondingly deeper understanding of pathogen-host interactions. To take full advantage of these innovations, the National Institute of Allergy and Infectious Diseases recently initiated the Systems Biology Program for Infectious Disease Research. As participants of the Systems Biology Program we think that the time is at hand to redefine the pathogen-host research paradigm.

  6. Computational problems in magnetic fusion research

    SciTech Connect

    Killeen, J.

    1981-08-31

    Numerical calculations have had an important role in fusion research since its beginning, but the application of computers to plasma physics has advanced rapidly in the last few years. One reason for this is the increasing sophistication of the mathematical models of plasma behavior, and another is the increased speed and memory of the computers which made it reasonable to consider numerical simulation of fusion devices. The behavior of a plasma is simulated by a variety of numerical models. Some models used for short times give detailed knowledge of the plasma on a microscopic scale, while other models used for much longer times compute macroscopic properties of the plasma dynamics. The computer models used in fusion research are surveyed. One of the most active areas of research is in time-dependent, three-dimensional, resistive magnetohydrodynamic models. These codes are reviewed briefly.

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

    PubMed Central

    Sevimoglu, Tuba

    2015-01-01

    Abstract 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. PMID:26480058

  8. Space plant biology research in Lithuania.

    PubMed

    Ričkienė, Aurika

    2012-09-01

    In 1957, the Soviet Union launched the first artificial Earth satellite, initiating its space exploration programs. Throughout the rest of the twentieth century, the development of these space programs received special attention from Soviet Union authorities. Scientists from the former Soviet Republics, including Lithuania, participated in these programs. From 1971 to 1990, Lithuanians designed more than 20 experiments on higher plant species during space flight. Some of these experiments had never before been attempted and, therefore, made scientific history. However, the formation and development of space plant biology research in Lithuania or its origins, context of formation, and placement in a worldwide context have not been explored from a historical standpoint. By investigating these topics, this paper seeks to construct an image of the development of a very specific field of science in a small former Soviet republic.

  9. Space plant biology research in Lithuania.

    PubMed

    Ričkienė, Aurika

    2012-09-01

    In 1957, the Soviet Union launched the first artificial Earth satellite, initiating its space exploration programs. Throughout the rest of the twentieth century, the development of these space programs received special attention from Soviet Union authorities. Scientists from the former Soviet Republics, including Lithuania, participated in these programs. From 1971 to 1990, Lithuanians designed more than 20 experiments on higher plant species during space flight. Some of these experiments had never before been attempted and, therefore, made scientific history. However, the formation and development of space plant biology research in Lithuania or its origins, context of formation, and placement in a worldwide context have not been explored from a historical standpoint. By investigating these topics, this paper seeks to construct an image of the development of a very specific field of science in a small former Soviet republic. PMID:22613222

  10. Has Modern Biology Entered the Mouth? The Clinical Impact of Biological Research.

    ERIC Educational Resources Information Center

    Baum, Bruce J.

    1991-01-01

    Three areas of biological research that are beginning to have an impact on clinical medicine are examined, including molecular biology, cell biology, and biotechnology. It is concluded that oral biologists and educators must work cooperatively to bring rapid biological and biomedical advances into dental training in a meaningful way. (MSE)

  11. Research in mathematical theory of computation. [computer programming applications

    NASA Technical Reports Server (NTRS)

    Mccarthy, J.

    1973-01-01

    Research progress in the following areas is reviewed: (1) new version of computer program LCF (logic for computable functions) including a facility to search for proofs automatically; (2) the description of the language PASCAL in terms of both LCF and in first order logic; (3) discussion of LISP semantics in LCF and attempt to prove the correctness of the London compilers in a formal way; (4) design of both special purpose and domain independent proving procedures specifically program correctness in mind; (5) design of languages for describing such proof procedures; and (6) the embedding of ideas in the first order checker.

  12. Computational Fluid Dynamics Framework for Turbine Biological Performance Assessment

    SciTech Connect

    Richmond, Marshall C.; Serkowski, John A.; Carlson, Thomas J.; Ebner, Laurie L.; Sick, Mirjam; Cada, G. F.

    2011-05-04

    In this paper, a method for turbine biological performance assessment is introduced to bridge the gap between field and laboratory studies on fish injury and turbine design. Using this method, a suite of biological performance indicators is computed based on simulated data from a computational fluid dynamics (CFD) model of a proposed turbine design. Each performance indicator is a measure of the probability of exposure to a certain dose of an injury mechanism. If the relationship between the dose of an injury mechanism and frequency of injury (dose-response) is known from laboratory or field studies, the likelihood of fish injury for a turbine design can be computed from the performance indicator. By comparing the values of the indicators from various turbine designs, the engineer can identify the more-promising designs. Discussion here is focused on Kaplan-type turbines, although the method could be extended to other designs. Following the description of the general methodology, we will present sample risk assessment calculations based on CFD data from a model of the John Day Dam on the Columbia River in the USA.

  13. MORT: a powerful foundational library for computational biology and CADD

    PubMed Central

    2014-01-01

    Background A foundational library called MORT (Molecular Objects and Relevant Templates) for the development of new software packages and tools employed in computational biology and computer-aided drug design (CADD) is described here. Results MORT contains several advantages compared with the other libraries. Firstly, MORT written in C++ natively supports the paradigm of object-oriented design, and thus it can be understood and extended easily. Secondly, MORT employs the relational model to represent a molecule, and it is more convenient and flexible than the traditional hierarchical model employed by many other libraries. Thirdly, a lot of functions have been included in this library, and a molecule can be manipulated easily at different levels. For example, it can parse a variety of popular molecular formats (MOL/SDF, MOL2, PDB/ENT, SMILES/SMARTS, etc.), create the topology and coordinate files for the simulations supported by AMBER, calculate the energy of a specific molecule based on the AMBER force fields, etc. Conclusions We believe that MORT can be used as a foundational library for programmers to develop new programs and applications for computational biology and CADD. Source code of MORT is available at http://cadd.suda.edu.cn/MORT/index.htm.

  14. iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources

    PubMed Central

    Dinov, Ivo D.; Rubin, Daniel; Lorensen, William; Dugan, Jonathan; Ma, Jeff; Murphy, Shawn; Kirschner, Beth; Bug, William; Sherman, Michael; Floratos, Aris; Kennedy, David; Jagadish, H. V.; Schmidt, Jeanette; Athey, Brian; Califano, Andrea; Musen, Mark; Altman, Russ; Kikinis, Ron; Kohane, Isaac; Delp, Scott; Parker, D. Stott; Toga, Arthur W.

    2008-01-01

    The advancement of the computational biology field hinges on progress in three fundamental directions – the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources–data, software tools and web-services. The iTools design, implementation and resource meta - data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long-term resource

  15. iTools: a framework for classification, categorization and integration of computational biology resources.

    PubMed

    Dinov, Ivo D; Rubin, Daniel; Lorensen, William; Dugan, Jonathan; Ma, Jeff; Murphy, Shawn; Kirschner, Beth; Bug, William; Sherman, Michael; Floratos, Aris; Kennedy, David; Jagadish, H V; Schmidt, Jeanette; Athey, Brian; Califano, Andrea; Musen, Mark; Altman, Russ; Kikinis, Ron; Kohane, Isaac; Delp, Scott; Parker, D Stott; Toga, Arthur W

    2008-05-28

    The advancement of the computational biology field hinges on progress in three fundamental directions--the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources--data, software tools and web-services. The iTools design, implementation and resource meta-data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long-term resource management

  16. 75 FR 6651 - Biological and Environmental Research Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-10

    ... the Office of Biological and Environmental Research News From the Biological Systems Science and... Biological and Environmental Research Advisory Committee AGENCY: Department of Energy; Office of Science.... David Thomassen, Designated Federal Officer, BERAC, U.S. Department of Energy, Office of Science,...

  17. pClone: Synthetic Biology Tool Makes Promoter Research Accessible to Beginning Biology Students

    ERIC Educational Resources Information Center

    Campbell, A. Malcolm; Eckdahl, Todd; Cronk, Brian; Andresen, Corinne; Frederick, Paul; Huckuntod, Samantha; Shinneman, Claire; Wacker, Annie; Yuan, Jason

    2014-01-01

    The "Vision and Change" report recommended genuine research experiences for undergraduate biology students. Authentic research improves science education, increases the number of scientifically literate citizens, and encourages students to pursue research. Synthetic biology is well suited for undergraduate research and is a growing area…

  18. Computational biology in the cloud: methods and new insights from computing at scale.

    PubMed

    Kasson, Peter M

    2013-01-01

    The past few years have seen both explosions in the size of biological data sets and the proliferation of new, highly flexible on-demand computing capabilities. The sheer amount of information available from genomic and metagenomic sequencing, high-throughput proteomics, experimental and simulation datasets on molecular structure and dynamics affords an opportunity for greatly expanded insight, but it creates new challenges of scale for computation, storage, and interpretation of petascale data. Cloud computing resources have the potential to help solve these problems by offering a utility model of computing and storage: near-unlimited capacity, the ability to burst usage, and cheap and flexible payment models. Effective use of cloud computing on large biological datasets requires dealing with non-trivial problems of scale and robustness, since performance-limiting factors can change substantially when a dataset grows by a factor of 10,000 or more. New computing paradigms are thus often needed. The use of cloud platforms also creates new opportunities to share data, reduce duplication, and to provide easy reproducibility by making the datasets and computational methods easily available.

  19. Next generation distributed computing for cancer research.

    PubMed

    Agarwal, Pankaj; Owzar, Kouros

    2014-01-01

    Advances in next generation sequencing (NGS) and mass spectrometry (MS) technologies have provided many new opportunities and angles for extending the scope of translational cancer research while creating tremendous challenges in data management and analysis. The resulting informatics challenge is invariably not amenable to the use of traditional computing models. Recent advances in scalable computing and associated infrastructure, particularly distributed computing for Big Data, can provide solutions for addressing these challenges. In this review, the next generation of distributed computing technologies that can address these informatics problems is described from the perspective of three key components of a computational platform, namely computing, data storage and management, and networking. A broad overview of scalable computing is provided to set the context for a detailed description of Hadoop, a technology that is being rapidly adopted for large-scale distributed computing. A proof-of-concept Hadoop cluster, set up for performance benchmarking of NGS read alignment, is described as an example of how to work with Hadoop. Finally, Hadoop is compared with a number of other current technologies for distributed computing.

  20. Next generation distributed computing for cancer research.

    PubMed

    Agarwal, Pankaj; Owzar, Kouros

    2014-01-01

    Advances in next generation sequencing (NGS) and mass spectrometry (MS) technologies have provided many new opportunities and angles for extending the scope of translational cancer research while creating tremendous challenges in data management and analysis. The resulting informatics challenge is invariably not amenable to the use of traditional computing models. Recent advances in scalable computing and associated infrastructure, particularly distributed computing for Big Data, can provide solutions for addressing these challenges. In this review, the next generation of distributed computing technologies that can address these informatics problems is described from the perspective of three key components of a computational platform, namely computing, data storage and management, and networking. A broad overview of scalable computing is provided to set the context for a detailed description of Hadoop, a technology that is being rapidly adopted for large-scale distributed computing. A proof-of-concept Hadoop cluster, set up for performance benchmarking of NGS read alignment, is described as an example of how to work with Hadoop. Finally, Hadoop is compared with a number of other current technologies for distributed computing. PMID:25983539

  1. Next Generation Distributed Computing for Cancer Research

    PubMed Central

    Agarwal, Pankaj; Owzar, Kouros

    2014-01-01

    Advances in next generation sequencing (NGS) and mass spectrometry (MS) technologies have provided many new opportunities and angles for extending the scope of translational cancer research while creating tremendous challenges in data management and analysis. The resulting informatics challenge is invariably not amenable to the use of traditional computing models. Recent advances in scalable computing and associated infrastructure, particularly distributed computing for Big Data, can provide solutions for addressing these challenges. In this review, the next generation of distributed computing technologies that can address these informatics problems is described from the perspective of three key components of a computational platform, namely computing, data storage and management, and networking. A broad overview of scalable computing is provided to set the context for a detailed description of Hadoop, a technology that is being rapidly adopted for large-scale distributed computing. A proof-of-concept Hadoop cluster, set up for performance benchmarking of NGS read alignment, is described as an example of how to work with Hadoop. Finally, Hadoop is compared with a number of other current technologies for distributed computing. PMID:25983539

  2. Publication Bias in Methodological Computational Research

    PubMed Central

    Boulesteix, Anne-Laure; Stierle, Veronika; Hapfelmeier, Alexander

    2015-01-01

    The problem of publication bias has long been discussed in research fields such as medicine. There is a consensus that publication bias is a reality and that solutions should be found to reduce it. In methodological computational research, including cancer informatics, publication bias may also be at work. The publication of negative research findings is certainly also a relevant issue, but has attracted very little attention to date. The present paper aims at providing a new formal framework to describe the notion of publication bias in the context of methodological computational research, facilitate and stimulate discussions on this topic, and increase awareness in the scientific community. We report an exemplary pilot study that aims at gaining experiences with the collection and analysis of information on unpublished research efforts with respect to publication bias, and we outline the encountered problems. Based on these experiences, we try to formalize the notion of publication bias. PMID:26508827

  3. Study on global cloud computing research trend

    NASA Astrophysics Data System (ADS)

    Ma, Feicheng; Zhan, Nan

    2014-01-01

    Since "cloud computing" was put forward by Google , it quickly became the most popular concept in IT industry and widely permeated into various areas promoted by IBM, Microsoft and other IT industry giants. In this paper the methods of bibliometric analysis were used to investigate the global cloud computing research trend based on Web of Science (WoS) database and the Engineering Index (EI) Compendex database. In this study, the publication, countries, institutes, keywords of the papers was deeply studied in methods of quantitative analysis, figures and tables are used to describe the production and the development trends of cloud computing.

  4. Biology of an Enzyme: A Research-Like Experience for Introductory Biology Students.

    ERIC Educational Resources Information Center

    Towle, David W.

    1992-01-01

    Presents a series of laboratory exercises designed to introduce students to a realistic experience in biological research that is feasible with large numbers of beginning biology majors. The exercises center on the study of alkaline phosphatase. (DDR)

  5. Computations and algorithms in physical and biological problems

    NASA Astrophysics Data System (ADS)

    Qin, Yu

    This dissertation presents the applications of state-of-the-art computation techniques and data analysis algorithms in three physical and biological problems: assembling DNA pieces, optimizing self-assembly yield, and identifying correlations from large multivariate datasets. In the first topic, in-depth analysis of using Sequencing by Hybridization (SBH) to reconstruct target DNA sequences shows that a modified reconstruction algorithm can overcome the theoretical boundary without the need for different types of biochemical assays and is robust to error. In the second topic, consistent with theoretical predictions, simulations using Graphics Processing Unit (GPU) demonstrate how controlling the short-ranged interactions between particles and controlling the concentrations optimize the self-assembly yield of a desired structure, and nonequilibrium behavior when optimizing concentrations is also unveiled by leveraging the computation capacity of GPUs. In the last topic, a methodology to incorporate existing categorization information into the search process to efficiently reconstruct the optimal true correlation matrix for multivariate datasets is introduced. Simulations on both synthetic and real financial datasets show that the algorithm is able to detect signals below the Random Matrix Theory (RMT) threshold. These three problems are representatives of using massive computation techniques and data analysis algorithms to tackle optimization problems, and outperform theoretical boundary when incorporating prior information into the computation.

  6. TORCH Computational Reference Kernels - A Testbed for Computer Science Research

    SciTech Connect

    Kaiser, Alex; Williams, Samuel Webb; Madduri, Kamesh; Ibrahim, Khaled; Bailey, David H.; Demmel, James W.; Strohmaier, Erich

    2010-12-02

    For decades, computer scientists have sought guidance on how to evolve architectures, languages, and programming models in order to improve application performance, efficiency, and productivity. Unfortunately, without overarching advice about future directions in these areas, individual guidance is inferred from the existing software/hardware ecosystem, and each discipline often conducts their research independently assuming all other technologies remain fixed. In today's rapidly evolving world of on-chip parallelism, isolated and iterative improvements to performance may miss superior solutions in the same way gradient descent optimization techniques may get stuck in local minima. To combat this, we present TORCH: A Testbed for Optimization ResearCH. These computational reference kernels define the core problems of interest in scientific computing without mandating a specific language, algorithm, programming model, or implementation. To compliment the kernel (problem) definitions, we provide a set of algorithmically-expressed verification tests that can be used to verify a hardware/software co-designed solution produces an acceptable answer. Finally, to provide some illumination as to how researchers have implemented solutions to these problems in the past, we provide a set of reference implementations in C and MATLAB.

  7. Removing the center from computing: biology's new mode of digital knowledge production.

    PubMed

    November, Joseph

    2011-06-01

    This article shows how the USA's National Institutes of Health (NIH) helped to bring about a major shift in the way computers are used to produce knowledge and in the design of computers themselves as a consequence of its early 1960s efforts to introduce information technology to biologists. Starting in 1960 the NIH sought to reform the life sciences by encouraging researchers to make use of digital electronic computers, but despite generous federal support biologists generally did not embrace the new technology. Initially the blame fell on biologists' lack of appropriate (i.e. digital) data for computers to process. However, when the NIH consulted MIT computer architect Wesley Clark about this problem, he argued that the computer's quality as a device that was centralized posed an even greater challenge to potential biologist users than did the computer's need for digital data. Clark convinced the NIH that if the agency hoped to effectively computerize biology, it would need to satisfy biologists' experimental and institutional needs by providing them the means to use a computer without going to a computing center. With NIH support, Clark developed the 1963 Laboratory Instrument Computer (LINC), a small, real-time interactive computer intended to be used inside the laboratory and controlled entirely by its biologist users. Once built, the LINC provided a viable alternative to the 1960s norm of large computers housed in computing centers. As such, the LINC not only became popular among biologists, but also served in later decades as an important precursor of today's computing norm in the sciences and far beyond, the personal computer.

  8. Plant biology research and training for the 21st century

    SciTech Connect

    Kelly, K.

    1992-01-01

    The committee was assembled in response to a request from the National Science Foundation (NSF), the US Department of Agriculture (USDA), and the US Department of Energy (DoE). The leadership of these agencies asked the National Academy of Sciences through the National Research Council (NRC) to assess the status of plant-science research in the United States in light of the opportunities arising from advances inother areas of biology. NRC was asked to suggest ways of accelerating the application of these new biologic concepts and tools to research in plant science with the aim of enhancing the acquisition of new knowledge about plants. The charge to the committee was to examine the following: Organizations, departments, and institutions conducting plant biology research; human resources involved in plant biology research; graduate training programs in plant biology; federal, state, and private sources of support for plant-biology research; the role of industry in conducting and supporting plant-biology research; the international status of US plant-biology research; and the relationship of plant biology to leading-edge research in biology.

  9. Plant biology research and training for the 21st century

    SciTech Connect

    Kelly, K.

    1992-12-31

    The committee was assembled in response to a request from the National Science Foundation (NSF), the US Department of Agriculture (USDA), and the US Department of Energy (DoE). The leadership of these agencies asked the National Academy of Sciences through the National Research Council (NRC) to assess the status of plant-science research in the United States in light of the opportunities arising from advances inother areas of biology. NRC was asked to suggest ways of accelerating the application of these new biologic concepts and tools to research in plant science with the aim of enhancing the acquisition of new knowledge about plants. The charge to the committee was to examine the following: Organizations, departments, and institutions conducting plant biology research; human resources involved in plant biology research; graduate training programs in plant biology; federal, state, and private sources of support for plant-biology research; the role of industry in conducting and supporting plant-biology research; the international status of US plant-biology research; and the relationship of plant biology to leading-edge research in biology.

  10. Proceedings of the Second Annual Conference of the MidSouth Computational Biology and Bioinformatics Society

    PubMed Central

    Wren, Jonathan D; Slikker, William

    2005-01-01

    The MCBIOS 2004 conference brought together regional researchers and students in biology, computer science and bioinformatics on October 7th-9th 2004 to present their latest work. This editorial describes the conference itself and introduces the twelve peer-reviewed manuscripts accepted for publication in the Proceedings of the MCBIOS 2004 Conference. These manuscripts included new methods for analysis of high-throughput gene expression experiments, EST clustering, analysis of mass spectrometry data and genomic analysis PMID:16026594

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

    PubMed Central

    Lee, Soojin

    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 analysis and inference, and modeling and systems prediction. Results: The existing databases are mostly associated with medicinal herbs and their activities, but new databases reflecting clinical situations and platforms to extract, visualize and analyze data easily need to be constructed. Network pharmacology is a key element of systems biology, so addressing the multi-component, multi-target aspect of pharmacology is important. Studies of network pharmacology highlight the drug target network and network target. Mathematical modeling and simulation are just in their infancy, but mathematical modeling of dynamic biological processes is a central aspect of systems biology. Computational simulations allow structured systems and their functional properties to be understood and the effects of herbal medicines in clinical situations to be predicted. Conclusion: Systems biology based on a holistic approach is a pivotal research methodology for understanding the mechanisms of traditional medicine. If systems biology is to be incorporated into traditional medicine, computational technologies and holistic insights need to be integrated. PMID:26388998

  12. 75 FR 53685 - Biological and Environmental Research Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-01

    ... Biological and Environmental Research Advisory Committee AGENCY: Department of Energy, Office of Science... Environmental Research Advisory Committee (BERAC). The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat... of Biological and Environmental Research, SC-23/Germantown Building, 1000 Independence Avenue,...

  13. 76 FR 57028 - Biological and Environmental Research Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-15

    ... Biological and Environmental Research Advisory Committee AGENCY: Department of Energy; Office of Science... Environmental Research Advisory Committee (BERAC). The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat....S. Department of Energy, Office of Science, Office of Biological and Environmental Research,...

  14. [Progress in research on the biological reason of male homosexuality].

    PubMed

    Yu, Wei; Feng, Tie-jian

    2012-04-01

    Male homosexuality is a complex phenomenon which is universal and with unknown causes. Researchers believe that both biological and environmental factors have played a role in its pathogenesis. Researches focusing on genetics, neurobiology, development and endocrinology have made certain progress. In this paper, we have reviewed the biological causes of male homosexuality, which may provide clues for further research in this field.

  15. 78 FR 63170 - Biological and Environmental Research Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-23

    ... Biological and Environmental Research Advisory Committee AGENCY: Office of Science, Department of Energy... Environmental Research Advisory Committee (BERAC). The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat... Energy, Office of Science, Office of Biological and Environmental Research, SC-23/Germantown...

  16. Accelerating cancer systems biology research through Semantic Web technology.

    PubMed

    Wang, Zhihui; Sagotsky, Jonathan; Taylor, Thomas; Shironoshita, Patrick; Deisboeck, Thomas S

    2013-01-01

    Cancer systems biology is an interdisciplinary, rapidly expanding research field in which collaborations are a critical means to advance the field. Yet the prevalent database technologies often isolate data rather than making it easily accessible. The Semantic Web has the potential to help facilitate web-based collaborative cancer research by presenting data in a manner that is self-descriptive, human and machine readable, and easily sharable. We have created a semantically linked online Digital Model Repository (DMR) for storing, managing, executing, annotating, and sharing computational cancer models. Within the DMR, distributed, multidisciplinary, and inter-organizational teams can collaborate on projects, without forfeiting intellectual property. This is achieved by the introduction of a new stakeholder to the collaboration workflow, the institutional licensing officer, part of the Technology Transfer Office. Furthermore, the DMR has achieved silver level compatibility with the National Cancer Institute's caBIG, so users can interact with the DMR not only through a web browser but also through a semantically annotated and secure web service. We also discuss the technology behind the DMR leveraging the Semantic Web, ontologies, and grid computing to provide secure inter-institutional collaboration on cancer modeling projects, online grid-based execution of shared models, and the collaboration workflow protecting researchers' intellectual property.

  17. Biology Teacher and Expert Opinions about Computer Assisted Biology Instruction Materials: A Software Entitled Nucleic Acids and Protein Synthesis

    ERIC Educational Resources Information Center

    Hasenekoglu, Ismet; Timucin, Melih

    2007-01-01

    The aim of this study is to collect and evaluate opinions of CAI experts and biology teachers about a high school level Computer Assisted Biology Instruction Material presenting computer-made modelling and simulations. It is a case study. A material covering "Nucleic Acids and Protein Synthesis" topic was developed as the "case". The goal of the…

  18. Handheld Computers in Education. Research Brief

    ERIC Educational Resources Information Center

    Education Partnerships, Inc., 2003

    2003-01-01

    For over the last 20 years, educators have been trying to find the best practice in using technology for student learning. Some of the most widely used applications with computers have been student learning of programming, word processing, Web research, spreadsheets, games, and Web design. The difficulty with integrating many of these activities…

  19. Computer Modeling and Research in the Classroom

    ERIC Educational Resources Information Center

    Ramos, Maria Joao; Fernandes, Pedro Alexandrino

    2005-01-01

    We report on a computational chemistry course for undergraduate students that successfully incorporated a research project on the design of new contrast agents for magnetic resonance imaging and shift reagents for in vivo NMR. Course outcomes were positive: students were quite motivated during the whole year--they learned what was required of…

  20. Cloud Computing Technologies Facilitate Earth Research

    NASA Technical Reports Server (NTRS)

    2015-01-01

    Under a Space Act Agreement, NASA partnered with Seattle-based Amazon Web Services to make the agency's climate and Earth science satellite data publicly available on the company's servers. Users can access the data for free, but they can also pay to use Amazon's computing services to analyze and visualize information using the same software available to NASA researchers.

  1. Algorithms in nature: the convergence of systems biology and computational thinking.

    PubMed

    Navlakha, Saket; Bar-Joseph, Ziv

    2011-11-08

    Computer science and biology have enjoyed a long and fruitful relationship for decades. Biologists rely on computational methods to analyze and integrate large data sets, while several computational methods were inspired by the high-level design principles of biological systems. Recently, these two directions have been converging. In this review, we argue that thinking computationally about biological processes may lead to more accurate models, which in turn can be used to improve the design of algorithms. We discuss the similar mechanisms and requirements shared by computational and biological processes and then present several recent studies that apply this joint analysis strategy to problems related to coordination, network analysis, and tracking and vision. We also discuss additional biological processes that can be studied in a similar manner and link them to potential computational problems. With the rapid accumulation of data detailing the inner workings of biological systems, we expect this direction of coupling biological and computational studies to greatly expand in the future.

  2. Research computing in a distributed cloud environment

    NASA Astrophysics Data System (ADS)

    Fransham, K.; Agarwal, A.; Armstrong, P.; Bishop, A.; Charbonneau, A.; Desmarais, R.; Hill, N.; Gable, I.; Gaudet, S.; Goliath, S.; Impey, R.; Leavett-Brown, C.; Ouellete, J.; Paterson, M.; Pritchet, C.; Penfold-Brown, D.; Podaima, W.; Schade, D.; Sobie, R. J.

    2010-11-01

    The recent increase in availability of Infrastructure-as-a-Service (IaaS) computing clouds provides a new way for researchers to run complex scientific applications. However, using cloud resources for a large number of research jobs requires significant effort and expertise. Furthermore, running jobs on many different clouds presents even more difficulty. In order to make it easy for researchers to deploy scientific applications across many cloud resources, we have developed a virtual machine resource manager (Cloud Scheduler) for distributed compute clouds. In response to a user's job submission to a batch system, the Cloud Scheduler manages the distribution and deployment of user-customized virtual machines across multiple clouds. We describe the motivation for and implementation of a distributed cloud using the Cloud Scheduler that is spread across both commercial and dedicated private sites, and present some early results of scientific data analysis using the system.

  3. Systems biology driven software design for the research enterprise

    PubMed Central

    Boyle, John; Cavnor, Christopher; Killcoyne, Sarah; Shmulevich, Ilya

    2008-01-01

    Background In systems biology, and many other areas of research, there is a need for the interoperability of tools and data sources that were not originally designed to be integrated. Due to the interdisciplinary nature of systems biology, and its association with high throughput experimental platforms, there is an additional need to continually integrate new technologies. As scientists work in isolated groups, integration with other groups is rarely a consideration when building the required software tools. Results We illustrate an approach, through the discussion of a purpose built software architecture, which allows disparate groups to reuse tools and access data sources in a common manner. The architecture allows for: the rapid development of distributed applications; interoperability, so it can be used by a wide variety of developers and computational biologists; development using standard tools, so that it is easy to maintain and does not require a large development effort; extensibility, so that new technologies and data types can be incorporated; and non intrusive development, insofar as researchers need not to adhere to a pre-existing object model. Conclusion By using a relatively simple integration strategy, based upon a common identity system and dynamically discovered interoperable services, a light-weight software architecture can become the focal point through which scientists can both get access to and analyse the plethora of experimentally derived data. PMID:18578887

  4. Computational Approaches for Predicting Biomedical Research Collaborations

    PubMed Central

    Zhang, Qing; Yu, Hong

    2014-01-01

    Biomedical research is increasingly collaborative, and successful collaborations often produce high impact work. Computational approaches can be developed for automatically predicting biomedical research collaborations. Previous works of collaboration prediction mainly explored the topological structures of research collaboration networks, leaving out rich semantic information from the publications themselves. In this paper, we propose supervised machine learning approaches to predict research collaborations in the biomedical field. We explored both the semantic features extracted from author research interest profile and the author network topological features. We found that the most informative semantic features for author collaborations are related to research interest, including similarity of out-citing citations, similarity of abstracts. Of the four supervised machine learning models (naïve Bayes, naïve Bayes multinomial, SVMs, and logistic regression), the best performing model is logistic regression with an ROC ranging from 0.766 to 0.980 on different datasets. To our knowledge we are the first to study in depth how research interest and productivities can be used for collaboration prediction. Our approach is computationally efficient, scalable and yet simple to implement. The datasets of this study are available at https://github.com/qingzhanggithub/medline-collaboration-datasets. PMID:25375164

  5. GUI to Facilitate Research on Biological Damage from Radiation

    NASA Technical Reports Server (NTRS)

    Cucinotta, Frances A.; Ponomarev, Artem Lvovich

    2010-01-01

    A graphical-user-interface (GUI) computer program has been developed to facilitate research on the damage caused by highly energetic particles and photons impinging on living organisms. The program brings together, into one computational workspace, computer codes that have been developed over the years, plus codes that will be developed during the foreseeable future, to address diverse aspects of radiation damage. These include codes that implement radiation-track models, codes for biophysical models of breakage of deoxyribonucleic acid (DNA) by radiation, pattern-recognition programs for extracting quantitative information from biological assays, and image-processing programs that aid visualization of DNA breaks. The radiation-track models are based on transport models of interactions of radiation with matter and solution of the Boltzmann transport equation by use of both theoretical and numerical models. The biophysical models of breakage of DNA by radiation include biopolymer coarse-grained and atomistic models of DNA, stochastic- process models of deposition of energy, and Markov-based probabilistic models of placement of double-strand breaks in DNA. The program is designed for use in the NT, 95, 98, 2000, ME, and XP variants of the Windows operating system.

  6. The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt

    PubMed Central

    Mulder, Nicola J.; Christoffels, Alan; de Oliveira, Tulio; Gamieldien, Junaid; Hazelhurst, Scott; Joubert, Fourie; Kumuthini, Judit; Pillay, Ché S.; Snoep, Jacky L.; Tastan Bishop, Özlem; Tiffin, Nicki

    2016-01-01

    Bioinformatics is now a critical skill in many research and commercial environments as biological data are increasing in both size and complexity. South African researchers recognized this need in the mid-1990s and responded by working with the government as well as international bodies to develop initiatives to build bioinformatics capacity in the country. Significant injections of support from these bodies provided a springboard for the establishment of computational biology units at multiple universities throughout the country, which took on teaching, basic research and support roles. Several challenges were encountered, for example with unreliability of funding, lack of skills, and lack of infrastructure. However, the bioinformatics community worked together to overcome these, and South Africa is now arguably the leading country in bioinformatics on the African continent. Here we discuss how the discipline developed in the country, highlighting the challenges, successes, and lessons learnt. PMID:26845152

  7. The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt.

    PubMed

    Mulder, Nicola J; Christoffels, Alan; de Oliveira, Tulio; Gamieldien, Junaid; Hazelhurst, Scott; Joubert, Fourie; Kumuthini, Judit; Pillay, Ché S; Snoep, Jacky L; Tastan Bishop, Özlem; Tiffin, Nicki

    2016-02-01

    Bioinformatics is now a critical skill in many research and commercial environments as biological data are increasing in both size and complexity. South African researchers recognized this need in the mid-1990s and responded by working with the government as well as international bodies to develop initiatives to build bioinformatics capacity in the country. Significant injections of support from these bodies provided a springboard for the establishment of computational biology units at multiple universities throughout the country, which took on teaching, basic research and support roles. Several challenges were encountered, for example with unreliability of funding, lack of skills, and lack of infrastructure. However, the bioinformatics community worked together to overcome these, and South Africa is now arguably the leading country in bioinformatics on the African continent. Here we discuss how the discipline developed in the country, highlighting the challenges, successes, and lessons learnt.

  8. Synthetic biology: An emerging research field in China

    PubMed Central

    Pei, Lei; Schmidt, Markus; Wei, Wei

    2011-01-01

    Synthetic biology is considered as an emerging research field that will bring new opportunities to biotechnology. There is an expectation that synthetic biology will not only enhance knowledge in basic science, but will also have great potential for practical applications. Synthetic biology is still in an early developmental stage in China. We provide here a review of current Chinese research activities in synthetic biology and its different subfields, such as research on genetic circuits, minimal genomes, chemical synthetic biology, protocells and DNA synthesis, using literature reviews and personal communications with Chinese researchers. To meet the increasing demand for a sustainable development, research on genetic circuits to harness biomass is the most pursed research within Chinese researchers. The environmental concerns are driven force of research on the genetic circuits for bioremediation. The research on minimal genomes is carried on identifying the smallest number of genomes needed for engineering minimal cell factories and research on chemical synthetic biology is focused on artificial proteins and expanded genetic code. The research on protocells is more in combination with the research on molecular-scale motors. The research on DNA synthesis and its commercialisation are also reviewed. As for the perspective on potential future Chinese R&D activities, it will be discussed based on the research capacity and governmental policy. PMID:21729747

  9. Research on computer virus database management system

    NASA Astrophysics Data System (ADS)

    Qi, Guoquan

    2011-12-01

    The growing proliferation of computer viruses becomes the lethal threat and research focus of the security of network information. While new virus is emerging, the number of viruses is growing, virus classification increasing complex. Virus naming because of agencies' capture time differences can not be unified. Although each agency has its own virus database, the communication between each other lacks, or virus information is incomplete, or a small number of sample information. This paper introduces the current construction status of the virus database at home and abroad, analyzes how to standardize and complete description of virus characteristics, and then gives the information integrity, storage security and manageable computer virus database design scheme.

  10. Biological insertion of computationally designed short transmembrane segments.

    PubMed

    Baeza-Delgado, Carlos; von Heijne, Gunnar; Marti-Renom, Marc A; Mingarro, Ismael

    2016-01-01

    The great majority of helical membrane proteins are inserted co-translationally into the ER membrane through a continuous ribosome-translocon channel. The efficiency of membrane insertion depends on transmembrane (TM) helix amino acid composition, the helix length and the position of the amino acids within the helix. In this work, we conducted a computational analysis of the composition and location of amino acids in transmembrane helices found in membrane proteins of known structure to obtain an extensive set of designed polypeptide segments with naturally occurring amino acid distributions. Then, using an in vitro translation system in the presence of biological membranes, we experimentally validated our predictions by analyzing its membrane integration capacity. Coupled with known strategies to control membrane protein topology, these findings may pave the way to de novo membrane protein design. PMID:26987712

  11. Biological insertion of computationally designed short transmembrane segments

    PubMed Central

    Baeza-Delgado, Carlos; von Heijne, Gunnar; Marti-Renom, Marc A.; Mingarro, Ismael

    2016-01-01

    The great majority of helical membrane proteins are inserted co-translationally into the ER membrane through a continuous ribosome-translocon channel. The efficiency of membrane insertion depends on transmembrane (TM) helix amino acid composition, the helix length and the position of the amino acids within the helix. In this work, we conducted a computational analysis of the composition and location of amino acids in transmembrane helices found in membrane proteins of known structure to obtain an extensive set of designed polypeptide segments with naturally occurring amino acid distributions. Then, using an in vitro translation system in the presence of biological membranes, we experimentally validated our predictions by analyzing its membrane integration capacity. Coupled with known strategies to control membrane protein topology, these findings may pave the way to de novo membrane protein design. PMID:26987712

  12. Computational modeling structure and spectra of biological chromophores

    NASA Astrophysics Data System (ADS)

    Collins, Jack R.; Topol, Igor A.; Nemukhin, Alexander V.; Savitsky, Alexander P.

    2009-02-01

    Modern computational approaches based on quantum mechanical methods to characterize structures and optical spectra of biological chromophores in the gas phase, in solutions and proteins are discussed. Primary attention is paid to the chromophores from the family of the green fluorescent protein (GFP) widely used as a biomarker in living cells. Beyond GFP, photophysical properties of the monomeric teal fluorescent protein (mTFPI) and the kindling fluorescent protein asFP595 are simulated. We apply modern quantum chemical approaches for high level calculations of the structures of the chromophore binding pockets and to estimate spectral bands corresponding to the S0-S1 optical transitions. A special attention is paid to evaluate effects of point mutations in the vicinity of the chromophore group. Theoretical data provide important information on the chromophore properties aiming to interpret the results of experimental studies of fluorescent proteins.

  13. Overview of ICLASS research: Reliable and parallel computing

    NASA Technical Reports Server (NTRS)

    Iyer, Ravi K.

    1987-01-01

    An overview of Illinois Computer Laboratory for Aerospace Systems and Software (ICLASS) Research: Reliable and Parallel Computing is presented. Topics covered include: reliable and fault tolerant computing; fault tolerant multiprocessor architectures; fault tolerant matrix computation; and parallel processing.

  14. Accelerating Cancer Systems Biology Research through Semantic Web Technology

    PubMed Central

    Wang, Zhihui; Sagotsky, Jonathan; Taylor, Thomas; Shironoshita, Patrick; Deisboeck, Thomas S.

    2012-01-01

    Cancer systems biology is an interdisciplinary, rapidly expanding research field in which collaborations are a critical means to advance the field. Yet the prevalent database technologies often isolate data rather than making it easily accessible. The Semantic Web has the potential to help facilitate web-based collaborative cancer research by presenting data in a manner that is self-descriptive, human and machine readable, and easily sharable. We have created a semantically linked online Digital Model Repository (DMR) for storing, managing, executing, annotating, and sharing computational cancer models. Within the DMR, distributed, multidisciplinary, and inter-organizational teams can collaborate on projects, without forfeiting intellectual property. This is achieved by the introduction of a new stakeholder to the collaboration workflow, the institutional licensing officer, part of the Technology Transfer Office. Furthermore, the DMR has achieved silver level compatibility with the National Cancer Institute’s caBIG®, so users can not only interact with the DMR through a web browser but also through a semantically annotated and secure web service. We also discuss the technology behind the DMR leveraging the Semantic Web, ontologies, and grid computing to provide secure inter-institutional collaboration on cancer modeling projects, online grid-based execution of shared models, and the collaboration workflow protecting researchers’ intellectual property. PMID:23188758

  15. Complex network problems in physics, computer science and biology

    NASA Astrophysics Data System (ADS)

    Cojocaru, Radu Ionut

    There is a close relation between physics and mathematics and the exchange of ideas between these two sciences are well established. However until few years ago there was no such a close relation between physics and computer science. Even more, only recently biologists started to use methods and tools from statistical physics in order to study the behavior of complex system. In this thesis we concentrate on applying and analyzing several methods borrowed from computer science to biology and also we use methods from statistical physics in solving hard problems from computer science. In recent years physicists have been interested in studying the behavior of complex networks. Physics is an experimental science in which theoretical predictions are compared to experiments. In this definition, the term prediction plays a very important role: although the system is complex, it is still possible to get predictions for its behavior, but these predictions are of a probabilistic nature. Spin glasses, lattice gases or the Potts model are a few examples of complex systems in physics. Spin glasses and many frustrated antiferromagnets map exactly to computer science problems in the NP-hard class defined in Chapter 1. In Chapter 1 we discuss a common result from artificial intelligence (AI) which shows that there are some problems which are NP-complete, with the implication that these problems are difficult to solve. We introduce a few well known hard problems from computer science (Satisfiability, Coloring, Vertex Cover together with Maximum Independent Set and Number Partitioning) and then discuss their mapping to problems from physics. In Chapter 2 we provide a short review of combinatorial optimization algorithms and their applications to ground state problems in disordered systems. We discuss the cavity method initially developed for studying the Sherrington-Kirkpatrick model of spin glasses. We extend this model to the study of a specific case of spin glass on the Bethe

  16. Meta-Research: Broadening the Scope of PLOS Biology.

    PubMed

    Kousta, Stavroula; Ferguson, Christine; Ganley, Emma

    2016-01-01

    In growing recognition of the importance of how scientific research is designed, performed, communicated, and evaluated, PLOS Biology announces a broadening of its scope to cover meta-research articles.

  17. A research program in empirical computer science

    NASA Technical Reports Server (NTRS)

    Knight, J. C.

    1991-01-01

    During the grant reporting period our primary activities have been to begin preparation for the establishment of a research program in experimental computer science. The focus of research in this program will be safety-critical systems. Many questions that arise in the effort to improve software dependability can only be addressed empirically. For example, there is no way to predict the performance of the various proposed approaches to building fault-tolerant software. Performance models, though valuable, are parameterized and cannot be used to make quantitative predictions without experimental determination of underlying distributions. In the past, experimentation has been able to shed some light on the practical benefits and limitations of software fault tolerance. It is common, also, for experimentation to reveal new questions or new aspects of problems that were previously unknown. A good example is the Consistent Comparison Problem that was revealed by experimentation and subsequently studied in depth. The result was a clear understanding of a previously unknown problem with software fault tolerance. The purpose of a research program in empirical computer science is to perform controlled experiments in the area of real-time, embedded control systems. The goal of the various experiments will be to determine better approaches to the construction of the software for computing systems that have to be relied upon. As such it will validate research concepts from other sources, provide new research results, and facilitate the transition of research results from concepts to practical procedures that can be applied with low risk to NASA flight projects. The target of experimentation will be the production software development activities undertaken by any organization prepared to contribute to the research program. Experimental goals, procedures, data analysis and result reporting will be performed for the most part by the University of Virginia.

  18. Creating a knowledge base of biological research papers

    SciTech Connect

    Hafner, C.D.; Baclawski, K.; Futrelle, R.P.; Fridman, N.

    1994-12-31

    Intelligent text-oriented tools for representing and searching the biological research literature are being developed, which combine object-oriented databases with artificial intelligence techniques to create a richly structured knowledge base of Materials and Methods sections of biological research papers. A knowledge model of experimental processes, biological and chemical substances, and analytical techniques is described, based on the representation techniques of taxonomic semantic nets and knowledge frames. Two approaches to populating the knowledge base with the contents of biological research papers are described: natural language processing and an interactive knowledge definition tool.

  19. Incorporating computational resources in a cancer research program

    PubMed Central

    Woods, Nicholas T.; Jhuraney, Ankita; Monteiro, Alvaro N.A.

    2015-01-01

    Recent technological advances have transformed cancer genetics research. These advances have served as the basis for the generation of a number of richly annotated datasets relevant to the cancer geneticist. In addition, many of these technologies are now within reach of smaller laboratories to answer specific biological questions. Thus, one of the most pressing issues facing an experimental cancer biology research program in genetics is incorporating data from multiple sources to annotate, visualize, and analyze the system under study. Fortunately, there are several computational resources to aid in this process. However, a significant effort is required to adapt a molecular biology-based research program to take advantage of these datasets. Here, we discuss the lessons learned in our laboratory and share several recommendations to make this transition effectively. This article is not meant to be a comprehensive evaluation of all the available resources, but rather highlight those that we have incorporated into our laboratory and how to choose the most appropriate ones for your research program. PMID:25324189

  20. 77 FR 55200 - Biological and Environmental Research Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-07

    ... Office of Biological and Environmental Research News from the Biological Systems Science and Climate and... BERAC ``Long Term Vision'' report Updates on the Bioenergy Research Centers and the Program for Climate Model Diagnosis and Intercomparison Workshop updates New Business Public Comment Public...

  1. [Analogies and analogy research in technical biology and bionics].

    PubMed

    Nachtigall, Werner

    2010-01-01

    The procedural approaches of Technical Biology and Bionics are characterized, and analogy research is identified as their common basis. The actual creative aspect in bionical research lies in recognizing and exploiting technically oriented analogies underlying a specific biological prototype to indicate a specific technical application.

  2. Energy and time determine scaling in biological and computer designs.

    PubMed

    Moses, Melanie; Bezerra, George; Edwards, Benjamin; Brown, James; Forrest, Stephanie

    2016-08-19

    Metabolic rate in animals and power consumption in computers are analogous quantities that scale similarly with size. We analyse vascular systems of mammals and on-chip networks of microprocessors, where natural selection and human engineering, respectively, have produced systems that minimize both energy dissipation and delivery times. Using a simple network model that simultaneously minimizes energy and time, our analysis explains empirically observed trends in the scaling of metabolic rate in mammals and power consumption and performance in microprocessors across several orders of magnitude in size. Just as the evolutionary transitions from unicellular to multicellular animals in biology are associated with shifts in metabolic scaling, our model suggests that the scaling of power and performance will change as computer designs transition to decentralized multi-core and distributed cyber-physical systems. More generally, a single energy-time minimization principle may govern the design of many complex systems that process energy, materials and information.This article is part of the themed issue 'The major synthetic evolutionary transitions'. PMID:27431524

  3. Stochastic Effects in Computational Biology of Space Radiation Cancer Risk

    NASA Technical Reports Server (NTRS)

    Cucinotta, Francis A.; Pluth, Janis; Harper, Jane; O'Neill, Peter

    2007-01-01

    Estimating risk from space radiation poses important questions on the radiobiology of protons and heavy ions. We are considering systems biology models to study radiation induced repair foci (RIRF) at low doses, in which less than one-track on average transverses the cell, and the subsequent DNA damage processing and signal transduction events. Computational approaches for describing protein regulatory networks coupled to DNA and oxidative damage sites include systems of differential equations, stochastic equations, and Monte-Carlo simulations. We review recent developments in the mathematical description of protein regulatory networks and possible approaches to radiation effects simulation. These include robustness, which states that regulatory networks maintain their functions against external and internal perturbations due to compensating properties of redundancy and molecular feedback controls, and modularity, which leads to general theorems for considering molecules that interact through a regulatory mechanism without exchange of matter leading to a block diagonal reduction of the connecting pathways. Identifying rate-limiting steps, robustness, and modularity in pathways perturbed by radiation damage are shown to be valid techniques for reducing large molecular systems to realistic computer simulations. Other techniques studied are the use of steady-state analysis, and the introduction of composite molecules or rate-constants to represent small collections of reactants. Applications of these techniques to describe spatial and temporal distributions of RIRF and cell populations following low dose irradiation are described.

  4. Computational biology: plus c'est la même chose, plus ça change.

    PubMed

    Huttenhower, Curtis

    2011-08-23

    A report on the joint 19th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB)/10th Annual European Conference on Computational Biology (ECCB) meetings and the 7th International Society for Computational Biology Student Council Symposium, Vienna, Austria, 15-19 July 2011.

  5. CFD Research, Parallel Computation and Aerodynamic Optimization

    NASA Technical Reports Server (NTRS)

    Ryan, James S.

    1995-01-01

    During the last five years, CFD has matured substantially. Pure CFD research remains to be done, but much of the focus has shifted to integration of CFD into the design process. The work under these cooperative agreements reflects this trend. The recent work, and work which is planned, is designed to enhance the competitiveness of the US aerospace industry. CFD and optimization approaches are being developed and tested, so that the industry can better choose which methods to adopt in their design processes. The range of computer architectures has been dramatically broadened, as the assumption that only huge vector supercomputers could be useful has faded. Today, researchers and industry can trade off time, cost, and availability, choosing vector supercomputers, scalable parallel architectures, networked workstations, or heterogenous combinations of these to complete required computations efficiently.

  6. Microfluidic tools for cell biological research

    PubMed Central

    Velve-Casquillas, Guilhem; Le Berre, Maël; Piel, Matthieu; Tran, Phong T.

    2010-01-01

    Summary Microfluidic technology is creating powerful tools for cell biologists to control the complete cellular microenvironment, leading to new questions and new discoveries. We review here the basic concepts and methodologies in designing microfluidic devices, and their diverse cell biological applications. PMID:21152269

  7. High performance computing applications in neurobiological research

    NASA Technical Reports Server (NTRS)

    Ross, Muriel D.; Cheng, Rei; Doshay, David G.; Linton, Samuel W.; Montgomery, Kevin; Parnas, Bruce R.

    1994-01-01

    The human nervous system is a massively parallel processor of information. The vast numbers of neurons, synapses and circuits is daunting to those seeking to understand the neural basis of consciousness and intellect. Pervading obstacles are lack of knowledge of the detailed, three-dimensional (3-D) organization of even a simple neural system and the paucity of large scale, biologically relevant computer simulations. We use high performance graphics workstations and supercomputers to study the 3-D organization of gravity sensors as a prototype architecture foreshadowing more complex systems. Scaled-down simulations run on a Silicon Graphics workstation and scale-up, three-dimensional versions run on the Cray Y-MP and CM5 supercomputers.

  8. Computational Unification: a Vision for Connecting Researchers

    NASA Astrophysics Data System (ADS)

    Troy, R. M.; Kingrey, O. J.

    2002-12-01

    Computational Unification of science, once only a vision, is becoming a reality. This technology is based upon a scientifically defensible, general solution for Earth Science data management and processing. The computational unification of science offers a real opportunity to foster inter and intra-discipline cooperation, and the end of 're-inventing the wheel'. As we move forward using computers as tools, it is past time to move from computationally isolating, "one-off" or discipline-specific solutions into a unified framework where research can be more easily shared, especially with researchers in other disciplines. The author will discuss how distributed meta-data, distributed processing and distributed data objects are structured to constitute a working interdisciplinary system, including how these resources lead to scientific defensibility through known lineage of all data products. Illustration of how scientific processes are encapsulated and executed illuminates how previously written processes and functions are integrated into the system efficiently and with minimal effort. Meta-data basics will illustrate how intricate relationships may easily be represented and used to good advantage. Retrieval techniques will be discussed including trade-offs of using meta-data versus embedded data, how the two may be integrated, and how simplifying assumptions may or may not help. This system is based upon the experience of the Sequoia 2000 and BigSur research projects at the University of California, Berkeley, whose goals were to find an alternative to the Hughes EOS-DIS system and is presently offered by Science Tools corporation, of which the author is a principal.

  9. Structural biology research at the National Synchroton Light Source

    SciTech Connect

    1996-05-01

    The world`s foremost facility for scientific research using x-rays and ultraviolet and infrared radiation is operated by the national synchrotron Light Source Department. This year alone, a total of 2200 guest researchers performed experiments at the world`s largest source of synchrotron light. Researchers are trying to define the three- dimensional structures of biological macromolecules to create a map of life, a guide for exploring the biological and chemical interactions of the vast variety of molecules found in living organisms. Studies in structural biology may lead to new insights into how biological systems are formed and nourished, how they survive and grow, how they are damaged and die. This document discusses some the the structural biological research done at the National Synchrotron Light Source.

  10. COMPUTATIONAL METHODS FOR STUDYING THE INTERACTION BETWEEN POLYCYCLIC AROMATIC HYDROCARBONS AND BIOLOGICAL MACROMOLECULES

    EPA Science Inventory

    Computational Methods for Studying the Interaction between Polycyclic Aromatic Hydrocarbons and Biological Macromolecules .

    The mechanisms for the processes that result in significant biological activity of PAHs depend on the interaction of these molecules or their metabol...

  11. Computational Nanotechnology at NASA Ames Research Center, 1996

    NASA Technical Reports Server (NTRS)

    Globus, Al; Bailey, David; Langhoff, Steve; Pohorille, Andrew; Levit, Creon; Chancellor, Marisa K. (Technical Monitor)

    1996-01-01

    Some forms of nanotechnology appear to have enormous potential to improve aerospace and computer systems; computational nanotechnology, the design and simulation of programmable molecular machines, is crucial to progress. NASA Ames Research Center has begun a computational nanotechnology program including in-house work, external research grants, and grants of supercomputer time. Four goals have been established: (1) Simulate a hypothetical programmable molecular machine replicating itself and building other products. (2) Develop molecular manufacturing CAD (computer aided design) software and use it to design molecular manufacturing systems and products of aerospace interest, including computer components. (3) Characterize nanotechnologically accessible materials of aerospace interest. Such materials may have excellent strength and thermal properties. (4) Collaborate with experimentalists. Current in-house activities include: (1) Development of NanoDesign, software to design and simulate a nanotechnology based on functionalized fullerenes. Early work focuses on gears. (2) A design for high density atomically precise memory. (3) Design of nanotechnology systems based on biology. (4) Characterization of diamonoid mechanosynthetic pathways. (5) Studies of the laplacian of the electronic charge density to understand molecular structure and reactivity. (6) Studies of entropic effects during self-assembly. Characterization of properties of matter for clusters up to sizes exhibiting bulk properties. In addition, the NAS (NASA Advanced Supercomputing) supercomputer division sponsored a workshop on computational molecular nanotechnology on March 4-5, 1996 held at NASA Ames Research Center. Finally, collaborations with Bill Goddard at CalTech, Ralph Merkle at Xerox Parc, Don Brenner at NCSU (North Carolina State University), Tom McKendree at Hughes, and Todd Wipke at UCSC are underway.

  12. How to integrate biological research into society and exclude errors in biomedical publications? Progress in theoretical and systems biology releases pressure on experimental research.

    PubMed

    Volkov, Vadim

    2014-01-01

    This brief opinion proposes measures to increase efficiency and exclude errors in biomedical research under the existing dynamic situation. Rapid changes in biology began with the description of the three dimensional structure of DNA 60 years ago; today biology has progressed by interacting with computer science and nanoscience together with the introduction of robotic stations for the acquisition of large-scale arrays of data. These changes have had an increasing influence on the entire research and scientific community. Future advance demands short-term measures to ensure error-proof and efficient development. They can include the fast publishing of negative results, publishing detailed methodical papers and excluding a strict connection between career progression and publication activity, especially for younger researchers. Further development of theoretical and systems biology together with the use of multiple experimental methods for biological experiments could also be helpful in the context of years and decades. With regards to the links between science and society, it is reasonable to compare both these systems, to find and describe specific features for biology and to integrate it into the existing stream of social life and financial fluxes. It will increase the level of scientific research and have mutual positive effects for both biology and society. Several examples are given for further discussion.

  13. How to integrate biological research into society and exclude errors in biomedical publications? Progress in theoretical and systems biology releases pressure on experimental research

    PubMed Central

    Volkov, Vadim

    2014-01-01

    This brief opinion proposes measures to increase efficiency and exclude errors in biomedical research under the existing dynamic situation. Rapid changes in biology began with the description of the three dimensional structure of DNA 60 years ago; today biology has progressed by interacting with computer science and nanoscience together with the introduction of robotic stations for the acquisition of large-scale arrays of data. These changes have had an increasing influence on the entire research and scientific community. Future advance demands short-term measures to ensure error-proof and efficient development. They can include the fast publishing of negative results, publishing detailed methodical papers and excluding a strict connection between career progression and publication activity, especially for younger researchers. Further development of theoretical and systems biology together with the use of multiple experimental methods for biological experiments could also be helpful in the context of years and decades. With regards to the links between science and society, it is reasonable to compare both these systems, to find and describe specific features for biology and to integrate it into the existing stream of social life and financial fluxes. It will increase the level of scientific research and have mutual positive effects for both biology and society. Several examples are given for further discussion. PMID:24748913

  14. How to integrate biological research into society and exclude errors in biomedical publications? Progress in theoretical and systems biology releases pressure on experimental research.

    PubMed

    Volkov, Vadim

    2014-01-01

    This brief opinion proposes measures to increase efficiency and exclude errors in biomedical research under the existing dynamic situation. Rapid changes in biology began with the description of the three dimensional structure of DNA 60 years ago; today biology has progressed by interacting with computer science and nanoscience together with the introduction of robotic stations for the acquisition of large-scale arrays of data. These changes have had an increasing influence on the entire research and scientific community. Future advance demands short-term measures to ensure error-proof and efficient development. They can include the fast publishing of negative results, publishing detailed methodical papers and excluding a strict connection between career progression and publication activity, especially for younger researchers. Further development of theoretical and systems biology together with the use of multiple experimental methods for biological experiments could also be helpful in the context of years and decades. With regards to the links between science and society, it is reasonable to compare both these systems, to find and describe specific features for biology and to integrate it into the existing stream of social life and financial fluxes. It will increase the level of scientific research and have mutual positive effects for both biology and society. Several examples are given for further discussion. PMID:24748913

  15. Network-based drug discovery by integrating systems biology and computational technologies.

    PubMed

    Leung, Elaine L; Cao, Zhi-Wei; Jiang, Zhi-Hong; Zhou, Hua; Liu, Liang

    2013-07-01

    Network-based intervention has been a trend of curing systemic diseases, but it relies on regimen optimization and valid multi-target actions of the drugs. The complex multi-component nature of medicinal herbs may serve as valuable resources for network-based multi-target drug discovery due to its potential treatment effects by synergy. Recently, robustness of multiple systems biology platforms shows powerful to uncover molecular mechanisms and connections between the drugs and their targeting dynamic network. However, optimization methods of drug combination are insufficient, owning to lacking of tighter integration across multiple '-omics' databases. The newly developed algorithm- or network-based computational models can tightly integrate '-omics' databases and optimize combinational regimens of drug development, which encourage using medicinal herbs to develop into new wave of network-based multi-target drugs. However, challenges on further integration across the databases of medicinal herbs with multiple system biology platforms for multi-target drug optimization remain to the uncertain reliability of individual data sets, width and depth and degree of standardization of herbal medicine. Standardization of the methodology and terminology of multiple system biology and herbal database would facilitate the integration. Enhance public accessible databases and the number of research using system biology platform on herbal medicine would be helpful. Further integration across various '-omics' platforms and computational tools would accelerate development of network-based drug discovery and network medicine.

  16. Network-based drug discovery by integrating systems biology and computational technologies

    PubMed Central

    Leung, Elaine L.; Cao, Zhi-Wei; Jiang, Zhi-Hong; Zhou, Hua

    2013-01-01

    Network-based intervention has been a trend of curing systemic diseases, but it relies on regimen optimization and valid multi-target actions of the drugs. The complex multi-component nature of medicinal herbs may serve as valuable resources for network-based multi-target drug discovery due to its potential treatment effects by synergy. Recently, robustness of multiple systems biology platforms shows powerful to uncover molecular mechanisms and connections between the drugs and their targeting dynamic network. However, optimization methods of drug combination are insufficient, owning to lacking of tighter integration across multiple ‘-omics’ databases. The newly developed algorithm- or network-based computational models can tightly integrate ‘-omics’ databases and optimize combinational regimens of drug development, which encourage using medicinal herbs to develop into new wave of network-based multi-target drugs. However, challenges on further integration across the databases of medicinal herbs with multiple system biology platforms for multi-target drug optimization remain to the uncertain reliability of individual data sets, width and depth and degree of standardization of herbal medicine. Standardization of the methodology and terminology of multiple system biology and herbal database would facilitate the integration. Enhance public accessible databases and the number of research using system biology platform on herbal medicine would be helpful. Further integration across various ‘-omics’ platforms and computational tools would accelerate development of network-based drug discovery and network medicine. PMID:22877768

  17. Understanding sequence similarity and framework analysis between centromere proteins using computational biology.

    PubMed

    Doss, C George Priya; Chakrabarty, Chiranjib; Debajyoti, C; Debottam, S

    2014-11-01

    Certain mysteries pointing toward their recruitment pathways, cell cycle regulation mechanisms, spindle checkpoint assembly, and chromosome segregation process are considered the centre of attraction in cancer research. In modern times, with the established databases, ranges of computational platforms have provided a platform to examine almost all the physiological and biochemical evidences in disease-associated phenotypes. Using existing computational methods, we have utilized the amino acid residues to understand the similarity within the evolutionary variance of different associated centromere proteins. This study related to sequence similarity, protein-protein networking, co-expression analysis, and evolutionary trajectory of centromere proteins will speed up the understanding about centromere biology and will create a road map for upcoming researchers who are initiating their work of clinical sequencing using centromere proteins.

  18. Reduction of dynamical biochemical reactions networks in computational biology

    PubMed Central

    Radulescu, O.; Gorban, A. N.; Zinovyev, A.; Noel, V.

    2012-01-01

    Biochemical networks are used in computational biology, to model mechanistic details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as combinatorial explosion are strong obstacles against analyzing the dynamics of large models of this type. Multiscaleness, an important property of these networks, can be used to get past some of these obstacles. Networks with many well separated time scales, can be reduced to simpler models, in a way that depends only on the orders of magnitude and not on the exact values of the kinetic parameters. The main idea used for such robust simplifications of networks is the concept of dominance among model elements, allowing hierarchical organization of these elements according to their effects on the network dynamics. This concept finds a natural formulation in tropical geometry. We revisit, in the light of these new ideas, the main approaches to model reduction of reaction networks, such as quasi-steady state (QSS) and quasi-equilibrium approximations (QE), and provide practical recipes for model reduction of linear and non-linear networks. We also discuss the application of model reduction to the problem of parameter identification, via backward pruning machine learning techniques. PMID:22833754

  19. Can computational biology improve the phylogenetic analysis of insulin?

    PubMed

    Chakraborty, Chiranjib; Roy, Sanjiban S; Hsu, Minna J; Agoramoorthy, Govindasamy

    2012-11-01

    Using computational biology, we have depicted the insulin phylogenetics. We have also analyzed the sequence alignment and sequence logos formation for both the insulin chain A and B for three groups namely, the mammalian group, vertebrates group and fish group. We have also analyzed cladograms of insulin for the mammalian group. In accordance with that path lengths, matrix for distance analysis, matching representation of nodes of the cladogram and dissimilarity between two nodes have been performed for both of the A and B chains of the mammalian group. Our results show that 12 amino acid residues (GlyA1, IleA2, ValA3, TyrA19, CysA20, AsnA21, LeuB6, GlyB8, LeuB11, ValB12, GlyB23 and PheB24) are highly conserved for all groups and among them some (GlyA1, IleA2, ValA3);(TyrA19, CysA20, AsnA21) are continuous. This study shows a rapid method to calculate the amino acid sequences in terms of evolutionary conservation rates as well as molecular phylogenetics. PMID:22265574

  20. Parallel computing in genomic research: advances and applications.

    PubMed

    Ocaña, Kary; de Oliveira, Daniel

    2015-01-01

    Today's genomic experiments have to process the so-called "biological big data" that is now reaching the size of Terabytes and Petabytes. To process this huge amount of data, scientists may require weeks or months if they use their own workstations. Parallelism techniques and high-performance computing (HPC) environments can be applied for reducing the total processing time and to ease the management, treatment, and analyses of this data. However, running bioinformatics experiments in HPC environments such as clouds, grids, clusters, and graphics processing unit requires the expertise from scientists to integrate computational, biological, and mathematical techniques and technologies. Several solutions have already been proposed to allow scientists for processing their genomic experiments using HPC capabilities and parallelism techniques. This article brings a systematic review of literature that surveys the most recently published research involving genomics and parallel computing. Our objective is to gather the main characteristics, benefits, and challenges that can be considered by scientists when running their genomic experiments to benefit from parallelism techniques and HPC capabilities.

  1. Parallel computing in genomic research: advances and applications.

    PubMed

    Ocaña, Kary; de Oliveira, Daniel

    2015-01-01

    Today's genomic experiments have to process the so-called "biological big data" that is now reaching the size of Terabytes and Petabytes. To process this huge amount of data, scientists may require weeks or months if they use their own workstations. Parallelism techniques and high-performance computing (HPC) environments can be applied for reducing the total processing time and to ease the management, treatment, and analyses of this data. However, running bioinformatics experiments in HPC environments such as clouds, grids, clusters, and graphics processing unit requires the expertise from scientists to integrate computational, biological, and mathematical techniques and technologies. Several solutions have already been proposed to allow scientists for processing their genomic experiments using HPC capabilities and parallelism techniques. This article brings a systematic review of literature that surveys the most recently published research involving genomics and parallel computing. Our objective is to gather the main characteristics, benefits, and challenges that can be considered by scientists when running their genomic experiments to benefit from parallelism techniques and HPC capabilities. PMID:26604801

  2. Parallel computing in genomic research: advances and applications

    PubMed Central

    Ocaña, Kary; de Oliveira, Daniel

    2015-01-01

    Today’s genomic experiments have to process the so-called “biological big data” that is now reaching the size of Terabytes and Petabytes. To process this huge amount of data, scientists may require weeks or months if they use their own workstations. Parallelism techniques and high-performance computing (HPC) environments can be applied for reducing the total processing time and to ease the management, treatment, and analyses of this data. However, running bioinformatics experiments in HPC environments such as clouds, grids, clusters, and graphics processing unit requires the expertise from scientists to integrate computational, biological, and mathematical techniques and technologies. Several solutions have already been proposed to allow scientists for processing their genomic experiments using HPC capabilities and parallelism techniques. This article brings a systematic review of literature that surveys the most recently published research involving genomics and parallel computing. Our objective is to gather the main characteristics, benefits, and challenges that can be considered by scientists when running their genomic experiments to benefit from parallelism techniques and HPC capabilities. PMID:26604801

  3. Plant seeds in biological research in space

    NASA Technical Reports Server (NTRS)

    Miller, A. T.

    1982-01-01

    Data of 15 years of space flight and laboratory tests of plant seeds of 20 species, mainly on the combined and separate effects of launch vibration, ionizing radiation and weightlessness, are surveyed. It is concluded that plants do not show a pronounced response to space flight factors. Conditions of return to Earth, the number of heavy cosmic ray particles striking biological targets and effects of change in magnetic an electromagnetic fields have been little studied, and that more study of growing plants in space is needed.

  4. Toward a computational framework for cognitive biology: unifying approaches from cognitive neuroscience and comparative cognition.

    PubMed

    Fitch, W Tecumseh

    2014-09-01

    Progress in understanding cognition requires a quantitative, theoretical framework, grounded in the other natural sciences and able to bridge between implementational, algorithmic and computational levels of explanation. I review recent results in neuroscience and cognitive biology that, when combined, provide key components of such an improved conceptual framework for contemporary cognitive science. Starting at the neuronal level, I first discuss the contemporary realization that single neurons are powerful tree-shaped computers, which implies a reorientation of computational models of learning and plasticity to a lower, cellular, level. I then turn to predictive systems theory (predictive coding and prediction-based learning) which provides a powerful formal framework for understanding brain function at a more global level. Although most formal models concerning predictive coding are framed in associationist terms, I argue that modern data necessitate a reinterpretation of such models in cognitive terms: as model-based predictive systems. Finally, I review the role of the theory of computation and formal language theory in the recent explosion of comparative biological research attempting to isolate and explore how different species differ in their cognitive capacities. Experiments to date strongly suggest that there is an important difference between humans and most other species, best characterized cognitively as a propensity by our species to infer tree structures from sequential data. Computationally, this capacity entails generative capacities above the regular (finite-state) level; implementationally, it requires some neural equivalent of a push-down stack. I dub this unusual human propensity "dendrophilia", and make a number of concrete suggestions about how such a system may be implemented in the human brain, about how and why it evolved, and what this implies for models of language acquisition. I conclude that, although much remains to be done, a

  5. Toward a computational framework for cognitive biology: unifying approaches from cognitive neuroscience and comparative cognition.

    PubMed

    Fitch, W Tecumseh

    2014-09-01

    Progress in understanding cognition requires a quantitative, theoretical framework, grounded in the other natural sciences and able to bridge between implementational, algorithmic and computational levels of explanation. I review recent results in neuroscience and cognitive biology that, when combined, provide key components of such an improved conceptual framework for contemporary cognitive science. Starting at the neuronal level, I first discuss the contemporary realization that single neurons are powerful tree-shaped computers, which implies a reorientation of computational models of learning and plasticity to a lower, cellular, level. I then turn to predictive systems theory (predictive coding and prediction-based learning) which provides a powerful formal framework for understanding brain function at a more global level. Although most formal models concerning predictive coding are framed in associationist terms, I argue that modern data necessitate a reinterpretation of such models in cognitive terms: as model-based predictive systems. Finally, I review the role of the theory of computation and formal language theory in the recent explosion of comparative biological research attempting to isolate and explore how different species differ in their cognitive capacities. Experiments to date strongly suggest that there is an important difference between humans and most other species, best characterized cognitively as a propensity by our species to infer tree structures from sequential data. Computationally, this capacity entails generative capacities above the regular (finite-state) level; implementationally, it requires some neural equivalent of a push-down stack. I dub this unusual human propensity "dendrophilia", and make a number of concrete suggestions about how such a system may be implemented in the human brain, about how and why it evolved, and what this implies for models of language acquisition. I conclude that, although much remains to be done, a

  6. Toward a computational framework for cognitive biology: Unifying approaches from cognitive neuroscience and comparative cognition

    NASA Astrophysics Data System (ADS)

    Fitch, W. Tecumseh

    2014-09-01

    Progress in understanding cognition requires a quantitative, theoretical framework, grounded in the other natural sciences and able to bridge between implementational, algorithmic and computational levels of explanation. I review recent results in neuroscience and cognitive biology that, when combined, provide key components of such an improved conceptual framework for contemporary cognitive science. Starting at the neuronal level, I first discuss the contemporary realization that single neurons are powerful tree-shaped computers, which implies a reorientation of computational models of learning and plasticity to a lower, cellular, level. I then turn to predictive systems theory (predictive coding and prediction-based learning) which provides a powerful formal framework for understanding brain function at a more global level. Although most formal models concerning predictive coding are framed in associationist terms, I argue that modern data necessitate a reinterpretation of such models in cognitive terms: as model-based predictive systems. Finally, I review the role of the theory of computation and formal language theory in the recent explosion of comparative biological research attempting to isolate and explore how different species differ in their cognitive capacities. Experiments to date strongly suggest that there is an important difference between humans and most other species, best characterized cognitively as a propensity by our species to infer tree structures from sequential data. Computationally, this capacity entails generative capacities above the regular (finite-state) level; implementationally, it requires some neural equivalent of a push-down stack. I dub this unusual human propensity "dendrophilia", and make a number of concrete suggestions about how such a system may be implemented in the human brain, about how and why it evolved, and what this implies for models of language acquisition. I conclude that, although much remains to be done, a

  7. Self Organizing Systems and the Research Implications for Biological Systems

    NASA Astrophysics Data System (ADS)

    Denkins-Taffe, Lauren R.; Alfred, Marcus; Lindesay, James

    2008-03-01

    The knowledge gained from the human genome project, has provided an added opportunity to study the dynamical relationships within biological systems and can lead to an increased knowledge of diseases and subsequent drug discovery. Through computation, methods in which to rebuild these systems are being studied. These methods, which have first been applied to simpler systems: predator-prey, and self sustaining ecosystems can be applied to the study of microscopic biological systems.

  8. Teacher Perceptions of the Integration of Laptop Computers in Their High School Biology Classrooms

    NASA Astrophysics Data System (ADS)

    Gundy, Morag S.

    2011-12-01

    Studies indicate that teachers, and in particular science teachers in the senior high school grades, do not integrate laptop computers into their instruction to the extent anticipated by researchers. This technology has not spread easily to other teachers even with improved access to hardware and software, increased support, and a paradigm shift from teacher-centred to student-centred education. Although a number of studies have focused on the issues and problems related to the integration of laptops in classroom instruction, these studies, largely quantitative in nature, have tended to bypass the role teachers play in integrating laptop computers into their instruction. This thesis documents and describes the role of Ontario high school science teachers in the integration of laptop computers in the classroom. Ten teachers who have successfully integrated laptop computers into their biology courses participated in this descriptive study. Their perceptions of implementing laptops into their biology courses, key factors about the implementation process, and how the implementation was accomplished are examined. The study also identifies the conditions which they feel would allow this innovation to be implemented by other teachers. Key findings of the study indicate that teachers must initiate, implement and sustain an emergent and still evolving innovation; teacher perceptions change and continue to change with increased experience using laptops in the science classroom; changes in teaching approaches are significant as a result of the introduction of laptop technology; and, the teachers considered the acquisition and use of new teaching materials to be an important aspect of integrating laptop computers into instruction. Ongoing challenges for appropriate professional development, sharing of knowledge, skills and teaching materials are identified. The study provides a body of practical knowledge for biology teachers who are considering the integration of laptops into

  9. Connecting Biology and Organic Chemistry Introductory Laboratory Courses through a Collaborative Research Project

    ERIC Educational Resources Information Center

    Boltax, Ariana L.; Armanious, Stephanie; Kosinski-Collins, Melissa S.; Pontrello, Jason K.

    2015-01-01

    Modern research often requires collaboration of experts in fields, such as math, chemistry, biology, physics, and computer science to develop unique solutions to common problems. Traditional introductory undergraduate laboratory curricula in the sciences often do not emphasize connections possible between the various disciplines. We designed an…

  10. 76 FR 8357 - Biological and Environmental Research Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-14

    ... News from the Biological Systems Science and Climate and Environmental Sciences Divisions Discussions... Biological and Environmental Research Advisory Committee AGENCY: Department of Energy; Office of Science...) 903-9817; fax (301) 903-5051 or e-mail: david.thomassen@science.doe.gov . The most current...

  11. [New concepts in molecular biology applied to traslational research].

    PubMed

    Mengual, Lourdes

    2013-06-01

    This chapter intends to introduce the new concepts that have been established in molecular biology over the last years and are being applied in translational research. The chapter is divided in four big blocks, which treat the molecular biology concepts and techniques in relation to DNA, RNA, proteins and metabolites, respectively. Moreover, we give examples of translational application of these new methodologies described.

  12. Advanced Scientific Computing Research Network Requirements

    SciTech Connect

    Bacon, Charles; Bell, Greg; Canon, Shane; Dart, Eli; Dattoria, Vince; Goodwin, Dave; Lee, Jason; Hicks, Susan; Holohan, Ed; Klasky, Scott; Lauzon, Carolyn; Rogers, Jim; Shipman, Galen; Skinner, David; Tierney, Brian

    2013-03-08

    The Energy Sciences Network (ESnet) is the primary provider of network connectivity for the U.S. Department of Energy (DOE) Office of Science (SC), the single largest supporter of basic research in the physical sciences in the United States. In support of SC programs, ESnet regularly updates and refreshes its understanding of the networking requirements of the instruments, facilities, scientists, and science programs that it serves. This focus has helped ESnet to be a highly successful enabler of scientific discovery for over 25 years. In October 2012, ESnet and the Office of Advanced Scientific Computing Research (ASCR) of the DOE SC organized a review to characterize the networking requirements of the programs funded by the ASCR program office. The requirements identified at the review are summarized in the Findings section, and are described in more detail in the body of the report.

  13. How computational models can help unlock biological systems.

    PubMed

    Brodland, G Wayne

    2015-12-01

    With computation models playing an ever increasing role in the advancement of science, it is important that researchers understand what it means to model something; recognize the implications of the conceptual, mathematical and algorithmic steps of model construction; and comprehend what models can and cannot do. Here, we use examples to show that models can serve a wide variety of roles, including hypothesis testing, generating new insights, deepening understanding, suggesting and interpreting experiments, tracing chains of causation, doing sensitivity analyses, integrating knowledge, and inspiring new approaches. We show that models can bring together information of different kinds and do so across a range of length scales, as they do in multi-scale, multi-faceted embryogenesis models, some of which connect gene expression, the cytoskeleton, cell properties, tissue mechanics, morphogenetic movements and phenotypes. Models cannot replace experiments nor can they prove that particular mechanisms are at work in a given situation. But they can demonstrate whether or not a proposed mechanism is sufficient to produce an observed phenomenon. Although the examples in this article are taken primarily from the field of embryo mechanics, most of the arguments and discussion are applicable to any form of computational modelling.

  14. Proceedings of the 2013 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.

    PubMed

    Wren, Jonathan D; Dozmorov, Mikhail G; Burian, Dennis; Kaundal, Rakesh; Perkins, Andy; Perkins, Ed; Kupfer, Doris M; Springer, Gordon K

    2013-01-01

    The tenth annual conference of the MidSouth Computational Biology and Bioinformatics Society (MCBIOS 2013), "The 10th Anniversary in a Decade of Change: Discovery in a Sea of Data", took place at the Stoney Creek Inn & Conference Center in Columbia, Missouri on April 5-6, 2013. This year's Conference Chairs were Gordon Springer and Chi-Ren Shyu from the University of Missouri and Edward Perkins from the US Army Corps of Engineers Engineering Research and Development Center, who is also the current MCBIOS President (2012-3). There were 151 registrants and a total of 111 abstracts (51 oral presentations and 60 poster session abstracts).

  15. Amphipols: Polymeric surfactants for membrane biology research.

    SciTech Connect

    Popot, J.-L.; Berry, E.A.; Charvolin, D.; Creuzenet, C.; Ebel, C.; Engelman, D.M.; Flotenmeyer, M.; Giusti, F.; Gohon, Y.; Hong, Q.; Lakey, J.H.; Leonard, K.; Shuman, H.A.; Timmins, P.; Warschawski, D.E.; Zito, F.; Zoonens, M.; Pucci, B.; Tribet, C.

    2003-06-20

    Membrane proteins classically are handled in aqueous solutions as complexes with detergents. The dissociating character of detergents, combined with the need to maintain an excess of them, frequently results in more or less rapid inactivation of the protein under study. Over the past few years, we have endeavored to develop a novel family of surfactants, dubbed amphipols (APs). APs are amphiphilic polymers that bind to the transmembrane surface of the protein in a noncovalent but, in the absence of a competing surfactant, quasi-irreversible manner. Membrane proteins complexed by APs are in their native state, stable, and they remain water soluble in the absence of detergent or free APs. An update is presented of the current knowledge about these compounds and their demonstrated or putative uses in membrane biology.

  16. Biological Research in Canisters (BRIC) - Light Emitting Diode (LED)

    NASA Technical Reports Server (NTRS)

    Levine, Howard G.; Caron, Allison

    2016-01-01

    The Biological Research in Canisters - LED (BRIC-LED) is a biological research system that is being designed to complement the capabilities of the existing BRIC-Petri Dish Fixation Unit (PDFU) for the Space Life and Physical Sciences (SLPS) Program. A diverse range of organisms can be supported, including plant seedlings, callus cultures, Caenorhabditis elegans, microbes, and others. In the event of a launch scrub, the entire assembly can be replaced with an identical back-up unit containing freshly loaded specimens.

  17. Quantum computation in brain microtubules: Decoherence and biological feasibility

    NASA Astrophysics Data System (ADS)

    Hagan, S.; Hameroff, S. R.; Tuszyński, J. A.

    2002-06-01

    The Penrose-Hameroff orchestrated objective reduction (orch. OR) model assigns a cognitive role to quantum computations in microtubules within the neurons of the brain. Despite an apparently ``warm, wet, and noisy'' intracellular milieu, the proposal suggests that microtubules avoid environmental decoherence long enough to reach threshold for ``self-collapse'' (objective reduction) by a quantum gravity mechanism put forth by Penrose. The model has been criticized as regards the issue of environmental decoherence, and a recent report by Tegmark finds that microtubules can maintain quantum coherence for only 10-13 s, far too short to be neurophysiologically relevant. Here, we critically examine the decoherence mechanisms likely to dominate in a biological setting and find that (1) Tegmark's commentary is not aimed at an existing model in the literature but rather at a hybrid that replaces the superposed protein conformations of the orch. OR theory with a soliton in superposition along the microtubule; (2) recalculation after correcting for differences between the model on which Tegmark bases his calculations and the orch. OR model (superposition separation, charge vs dipole, dielectric constant) lengthens the decoherence time to 10-5-10-4 s (3) decoherence times on this order invalidate the assumptions of the derivation and determine the approximation regime considered by Tegmark to be inappropriate to the orch. OR superposition; (4) Tegmark's formulation yields decoherence times that increase with temperature contrary to well-established physical intuitions and the observed behavior of quantum coherent states; (5) incoherent metabolic energy supplied to the collective dynamics ordering water in the vicinity of microtubules at a rate exceeding that of decoherence can counter decoherence effects (in the same way that lasers avoid decoherence at room temperature); (6) microtubules are surrounded by a Debye layer of counterions, which can screen thermal fluctuations

  18. Interactomes to Biological Phase Space: a call to begin thinking at a new level in computational biology.

    SciTech Connect

    Davidson, George S.; Brown, William Michael

    2007-09-01

    Techniques for high throughput determinations of interactomes, together with high resolution protein collocalizations maps within organelles and through membranes will soon create a vast resource. With these data, biological descriptions, akin to the high dimensional phase spaces familiar to physicists, will become possible. These descriptions will capture sufficient information to make possible realistic, system-level models of cells. The descriptions and the computational models they enable will require powerful computing techniques. This report is offered as a call to the computational biology community to begin thinking at this scale and as a challenge to develop the required algorithms and codes to make use of the new data.3

  19. Programs for Use in Teaching Research Methods for Small Computers

    ERIC Educational Resources Information Center

    Halley, Fred S.

    1975-01-01

    Description of Sociology Library (SOLIB), presented as a package of computer programs designed for smaller computers used in research methods courses and by students performing independent research. (Author/ND)

  20. Theoretical and computational models of biological ion channels

    NASA Astrophysics Data System (ADS)

    Roux, Benoit

    2004-03-01

    A theoretical framework for describing ion conduction through biological molecular pores is established and explored. The framework is based on a statistical mechanical formulation of the transmembrane potential (1) and of the equilibrium multi-ion potential of mean forces through selective ion channels (2). On the basis of these developments, it is possible to define computational schemes to address questions about the non-equilibrium flow of ions through ion channels. In the case of narrow channels (gramicidin or KcsA), it is possible to characterize the ion conduction in terms of the potential of mean force of the ions along the channel axis (i.e., integrating out the off-axis motions). This has been used for gramicidin (3) and for KcsA (4,5). In the case of wide pores (i.e., OmpF porin), this is no longer a good idea, but it is possible to use a continuum solvent approximations. In this case, a grand canonical monte carlo brownian dynamics algorithm was constructed for simulating the non-equilibrium flow of ions through wide pores. The results were compared with those from the Poisson-Nernst-Planck mean-field electrodiffusion theory (6-8). References; 1. B. Roux, Biophys. J. 73:2980-2989 (1997); 2. B. Roux, Biophys. J. 77, 139-153 (1999); 3. Allen, Andersen and Roux, PNAS (2004, in press); 4. Berneche and Roux. Nature, 414:73-77 (2001); 5. Berneche and Roux. PNAS, 100:8644-8648 (2003); 6. W. Im and S. Seefeld and B. Roux, Biophys. J. 79:788-801 (2000); 7. W. Im and B. Roux, J. Chem. Phys. 115:4850-4861 (2001); 8. W. Im and B. Roux, J. Mol. Biol. 322:851-869 (2002).

  1. Synthesis on biological soil crust research

    USGS Publications Warehouse

    Weber, Bettina; Belnap, Jayne; Buedel, Burkhard

    2016-01-01

    In this closing chapter, we summarize the advances in biocrust research made during the last 1.5 decades. In the first part of the chapter, we discuss how in some research fields, such as the microbial diversity of fungi, bacteria, and microfauna; the interaction between biocrusts and vascular plants; and in the rehabilitation of biocrusts; particularly large achievements have been made. In other fields, previously established knowledge of overall patterns has been corroborated and refined by additional studies, e.g., in the fields of soil stabilization and disturbance effects. In the second part of the chapter, we outline the research gaps and challenges foreseen by us. We identify multiple knowledge gaps, including many understudied geographic regions, the largely missing link between genetic and morphological species identification data, and the answers to some mechanistic questions, such as the overall role of biocrusts in hydrology and nutrient cycles. With some ideas on promising new research questions and approaches we close this chapter and the overall book.

  2. Biological Extreme Events: A Research Framework

    NASA Astrophysics Data System (ADS)

    Gutschick, Vincent P.; BassiriRad, Hormoz

    2010-03-01

    Efforts designed to understand and predict adaptation responses of organisms and populations to global climate change must make a clear distinction between responses to changes in average conditions (e.g., doubling of atmospheric carbon dioxide concentration accompanied by an average increase of 1°-3°C in global air temperature by the end of this century) and responses resulting from increased incidence of extreme events [Loehle and LeBlanc, 1996; Easterling et al., 2000; Garrett et al., 2006]. Such distinction is critical because, unlike changes in average conditions, extremes (e.g., megadroughts, fire, flooding, hurricanes, heat waves, and pest outbreaks) are typically short in duration but challenge organisms and populations considerably further beyond their ability to acclimate than those expected from average trends in climate changes. There is growing evidence that climatic extremes have been rising in frequency or magnitude during the last part of the twentieth century and will continue to increase during the remainder of this century [Easterling et al., 2000; Meehl et al., 2000; Parmesan and Yohe, 2003; Barnett et al., 2006]. More important, the frequency of extremes is likely to increase even if the climatic means do not change substantially [Intergovernmental Panel on Climate Change (IPCC), 2001, chapter 10]. Therefore, it makes sense to pay special attention to extremes as major agents of biological adaption (genetic change) when considering global climate change.

  3. Highlights from the Third International Society for Computational Biology (ISCB) European Student Council Symposium 2014.

    PubMed

    Francescatto, Margherita; Hermans, Susanne M A; Babaei, Sepideh; Vicedo, Esmeralda; Borrel, Alexandre; Meysman, Pieter

    2015-01-01

    In this meeting report, we give an overview of the talks, presentations and posters presented at the third European Symposium of the International Society for Computational Biology (ISCB) Student Council. The event was organized as a satellite meeting of the 13th European Conference for Computational Biology (ECCB) and took place in Strasbourg, France on September 6th, 2014.

  4. A proposal for augmenting biological model construction with a semi-intelligent computational modeling assistant

    PubMed Central

    Christley, Scott; An, Gary

    2013-01-01

    The translational challenge in biomedical research lies in the effective and efficient transfer of mechanistic knowledge from one biological context to another. Implicit in this process is the establishment of causality from correlation in the form of mechanistic hypotheses. Effectively addressing the translational challenge requires the use of automated methods, including the ability to computationally capture the dynamic aspect of putative hypotheses such that they can be evaluated in a high throughput fashion. Ontologies provide structure and organization to biomedical knowledge; converting these representations into executable models/simulations is the next necessary step. Researchers need the ability to map their conceptual models into a model specification that can be transformed into an executable simulation program. We suggest this mapping process, which approximates certain steps in the development of a computational model, can be expressed as a set of logical rules, and a semi-intelligent computational agent, the Computational Modeling Assistant (CMA), can perform reasoning to develop a plan to achieve the construction of an executable model. Presented herein is a description and implementation for a model construction reasoning process between biomedical and simulation ontologies that is performed by the CMA to produce the specification of an executable model that can be used for dynamic knowledge representation. PMID:23990750

  5. Characterization of an orthovoltage biological irradiator used for radiobiological research.

    PubMed

    Azimi, Rezvan; Alaei, Parham; Spezi, Emiliano; Hui, Susanta K

    2015-05-01

    Orthovoltage irradiators are routinely used to irradiate specimens and small animals in biological research. There are several reports on the characteristics of these units for small field irradiations. However, there is limited knowledge about use of these units for large fields, which are essential for emerging large-field irregular shape irradiations, namely total marrow irradiation used as a conditioning regimen for hematological malignancies. This work describes characterization of a self-contained Orthovoltage biological irradiator for large fields using measurements and Monte Carlo simulations that could be used to compute the dose for in vivo or in vitro studies for large-field irradiation using this or a similar unit. Percentage depth dose, profiles, scatter factors, and half-value layers were measured and analyzed. A Monte Carlo model of the unit was created and used to generate depth dose and profiles, as well as scatter factors. An ion chamber array was also used for profile measurements of flatness and symmetry. The output was determined according to AAPM Task Group 61 guidelines. The depth dose measurements compare well with published data for similar beams. The Monte Carlo-generated depth dose and profiles match our measured doses to within 2%. Scatter factor measurements indicate gradual variation of these factors with field size. Dose rate measured by placing the ion chamber atop the unit's steel plate or solid water indicate enhanced readings of 5 to 28% compared with those measured in air. The stability of output over a 5-year period is within 2% of the 5-year average. PMID:25694476

  6. FOREWORD: Third Nordic Symposium on Computer Simulation in Physics, Chemistry, Biology and Mathematics

    NASA Astrophysics Data System (ADS)

    Kaski, K.; Salomaa, M.

    1990-01-01

    These are Proceedings of the Third Nordic Symposium on Computer Simulation in Physics, Chemistry, Biology, and Mathematics, held August 25-26, 1989, at Lahti (Finland). The Symposium belongs to an annual series of Meetings, the first one of which was arranged in 1987 at Lund (Sweden) and the second one in 1988 at Kolle-Kolle near Copenhagen (Denmark). Although these Symposia have thus far been essentially Nordic events, their international character has increased significantly; the trend is vividly reflected through contributions in the present Topical Issue. The interdisciplinary nature of Computational Science is central to the activity; this fundamental aspect is also responsible, in an essential way, for its rapidly increasing impact. Crucially important to a wide spectrum of superficially disparate fields is the common need for extensive - and often quite demanding - computational modelling. For such theoretical models, no closed-form (analytical) solutions are available or they would be extremely difficult to find; hence one must rather resort to the Art of performing computational investigations. Among the unifying features in the computational research are the methods of simulation employed; methods which frequently are quite closely related with each other even for faculties of science that are quite unrelated. Computer simulation in Natural Sciences is presently apprehended as a discipline on its own right, occupying a broad region somewhere between the experimental and theoretical methods, but also partially overlapping with and complementing them. - Whichever its proper definition may be, the computational approach serves as a novel and an extremely versatile tool with which one can equally well perform "pure" experimental modelling and conduct "computational theory". Computational studies that have earlier been made possible only through supercomputers have opened unexpected, as well as exciting, novel frontiers equally in mathematics (e.g., fractals

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

    ERIC Educational Resources Information Center

    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…

  8. CFD research, parallel computation and aerodynamic optimization

    NASA Technical Reports Server (NTRS)

    Ryan, James S.

    1995-01-01

    Over five years of research in Computational Fluid Dynamics and its applications are covered in this report. Using CFD as an established tool, aerodynamic optimization on parallel architectures is explored. The objective of this work is to provide better tools to vehicle designers. Submarine design requires accurate force and moment calculations in flow with thick boundary layers and large separated vortices. Low noise production is critical, so flow into the propulsor region must be predicted accurately. The High Speed Civil Transport (HSCT) has been the subject of recent work. This vehicle is to be a passenger vehicle with the capability of cutting overseas flight times by more than half. A successful design must surpass the performance of comparable planes. Fuel economy, other operational costs, environmental impact, and range must all be improved substantially. For all these reasons, improved design tools are required, and these tools must eventually integrate optimization, external aerodynamics, propulsion, structures, heat transfer and other disciplines.

  9. Computational fire modeling for aircraft fire research

    SciTech Connect

    Nicolette, V.F.

    1996-11-01

    This report summarizes work performed by Sandia National Laboratories for the Federal Aviation Administration. The technical issues involved in fire modeling for aircraft fire research are identified, as well as computational fire tools for addressing those issues, and the research which is needed to advance those tools in order to address long-range needs. Fire field models are briefly reviewed, and the VULCAN model is selected for further evaluation. Calculations are performed with VULCAN to demonstrate its applicability to aircraft fire problems, and also to gain insight into the complex problem of fires involving aircraft. Simulations are conducted to investigate the influence of fire on an aircraft in a cross-wind. The interaction of the fuselage, wind, fire, and ground plane is investigated. Calculations are also performed utilizing a large eddy simulation (LES) capability to describe the large- scale turbulence instead of the more common k-{epsilon} turbulence model. Additional simulations are performed to investigate the static pressure and velocity distributions around a fuselage in a cross-wind, with and without fire. The results of these simulations provide qualitative insight into the complex interaction of a fuselage, fire, wind, and ground plane. Reasonable quantitative agreement is obtained in the few cases for which data or other modeling results exist Finally, VULCAN is used to quantify the impact of simplifying assumptions inherent in a risk assessment compatible fire model developed for open pool fire environments. The assumptions are seen to be of minor importance for the particular problem analyzed. This work demonstrates the utility of using a fire field model for assessing the limitations of simplified fire models. In conclusion, the application of computational fire modeling tools herein provides both qualitative and quantitative insights into the complex problem of aircraft in fires.

  10. Bioconductor: an open source framework for bioinformatics and computational biology.

    PubMed

    Reimers, Mark; Carey, Vincent J

    2006-01-01

    This chapter describes the Bioconductor project and details of its open source facilities for analysis of microarray and other high-throughput biological experiments. Particular attention is paid to concepts of container and workflow design, connections of biological metadata to statistical analysis products, support for statistical quality assessment, and calibration of inference uncertainty measures when tens of thousands of simultaneous statistical tests are performed.

  11. The NASA computer science research program plan

    NASA Technical Reports Server (NTRS)

    1983-01-01

    A taxonomy of computer science is included, one state of the art of each of the major computer science categories is summarized. A functional breakdown of NASA programs under Aeronautics R and D, space R and T, and institutional support is also included. These areas were assessed against the computer science categories. Concurrent processing, highly reliable computing, and information management are identified.

  12. Research Trends in Computational Linguistics. Conference Report.

    ERIC Educational Resources Information Center

    Center for Applied Linguistics, Washington, DC.

    This document contains the reports summarizing the main discussion held during the March 1972 Computational Linguistics Conference. The first report, "Computational Linguistics and Linguistics," helps to establish definitions and an understanding of the scope of computational linguistics. "Integrated Computer Systems for Language" and…

  13. Bridging Emotion Research: From Biology to Social Structure

    ERIC Educational Resources Information Center

    Rogers, Kimberly B.; Kavanagh, Liam

    2010-01-01

    Emotion research demonstrates that problems of theoretical interest or practical significance are not divided neatly along disciplinary boundaries. Researchers acknowledge both organic and social underpinnings of emotion, but the intersections between biological and structural processes can be difficult to negotiate. In this article, the authors…

  14. The dilemma of dual use biological research: Polish perspective.

    PubMed

    Czarkowski, Marek

    2010-03-01

    Biological research with legitimate scientific purpose that may be misused to pose a biological threat to public health and/or national security is termed dual use. In Poland there are adequate conditions for conducting experiments that could be qualified as dual use research, and therefore, a risk of attack on Poland or other countries exists. Optimal solutions for limiting such threats are required, and the national system of biosecurity should enable early, reliable, and complete identification of this type of research. Scientists should have a fundamental role in this process, their duty being to immediately, upon identification, report research with dual use potential. An important entity in the identification system of dual use research should also be the Central Register of Biological and Biomedical Research, which gathers information about all biological and biomedical research being conducted in a given country. Publishers, editors, and review committees of journals and other scientific publications should be involved in evaluating results of clinical trials. The National Council of Biosecurity should be the governmental institution responsible for developing a system of dual use research threat prevention. Its role would be to develop codes of conduct, form counsel of expertise, and monitor the problem at national level, while the Dual Use Research Committee would be responsible for individual cases. In Poland, current actions aiming to provide biological safety were based on developing and passing an act about genetically modified organisms (GMO's) and creating a GMO Committee. Considering experiences of other nations, one should view these actions as fragmentary, and thus insufficient protection against dual use research threats. PMID:18546061

  15. The dilemma of dual use biological research: Polish perspective.

    PubMed

    Czarkowski, Marek

    2010-03-01

    Biological research with legitimate scientific purpose that may be misused to pose a biological threat to public health and/or national security is termed dual use. In Poland there are adequate conditions for conducting experiments that could be qualified as dual use research, and therefore, a risk of attack on Poland or other countries exists. Optimal solutions for limiting such threats are required, and the national system of biosecurity should enable early, reliable, and complete identification of this type of research. Scientists should have a fundamental role in this process, their duty being to immediately, upon identification, report research with dual use potential. An important entity in the identification system of dual use research should also be the Central Register of Biological and Biomedical Research, which gathers information about all biological and biomedical research being conducted in a given country. Publishers, editors, and review committees of journals and other scientific publications should be involved in evaluating results of clinical trials. The National Council of Biosecurity should be the governmental institution responsible for developing a system of dual use research threat prevention. Its role would be to develop codes of conduct, form counsel of expertise, and monitor the problem at national level, while the Dual Use Research Committee would be responsible for individual cases. In Poland, current actions aiming to provide biological safety were based on developing and passing an act about genetically modified organisms (GMO's) and creating a GMO Committee. Considering experiences of other nations, one should view these actions as fragmentary, and thus insufficient protection against dual use research threats.

  16. Computer System Requirements for CAI/CMI Research.

    ERIC Educational Resources Information Center

    Fitzhugh, Robert J.

    This paper oriented for new researchers entering the field of CAI research discusses the research experience in this area, outlines some of the important computer requirements of CAI research, and proposes a conservative computer development strategy to meet those requirements. The development of PLATO and TICCIT are described as examples of the…

  17. Biological and Physical Space Research Laboratory 2002 Science Review

    NASA Technical Reports Server (NTRS)

    Curreri, P. A. (Editor); Robinson, M. B. (Editor); Murphy, K. L. (Editor)

    2003-01-01

    With the International Space Station Program approaching core complete, our NASA Headquarters sponsor, the new Code U Enterprise, Biological and Physical Research, is shifting its research emphasis from purely fundamental microgravity and biological sciences to strategic research aimed at enabling human missions beyond Earth orbit. Although we anticipate supporting microgravity research on the ISS for some time to come, our laboratory has been vigorously engaged in developing these new strategic research areas.This Technical Memorandum documents the internal science research at our laboratory as presented in a review to Dr. Ann Whitaker, MSFC Science Director, in July 2002. These presentations have been revised and updated as appropriate for this report. It provides a snapshot of the internal science capability of our laboratory as an aid to other NASA organizations and the external scientific community.

  18. Trends in Computing for Climate Research

    NASA Astrophysics Data System (ADS)

    Lawrence, B.

    2014-12-01

    The grand challenges of climate science will stress our informatics infrastructure severely in the next decade. Our drive for ever greater simulation resolution/complexity/length/repetition, coupled with new remote and in-situ sensing platforms present us with problems in computation, data handling, and information management, to name but three. These problems are compounded by the background trends: Moore's Law is no longer doing us any favours: computing is getting harder to exploit as we have to bite the parallelism bullet, and Kryder's Law (if it ever existed) isn't going to help us store the data volumes we can see ahead. The variety of data, the rate it arrives, and the complexity of the tools we need and use, all strain our ability to cope. The solutions, as ever, will revolve around more and better software, but "more" and "better" will require some attention. In this talk we discuss how these issues have played out in the context of CMIP5, and might be expected to play out in CMIP6 and successors. Although the CMIPs will provide the thread, we will digress into modelling per se, regional climate modelling (CORDEX), observations from space (Obs4MIPs and friends), climate services (as they might play out in Europe), and the dependency of progress on how we manage people in our institutions. It will be seen that most of the issues we discuss apply to the wider environmental sciences, if not science in general. They all have implications for the need for both sustained infrastructure and ongoing research into environmental informatics.

  19. Research on Key Technologies of Cloud Computing

    NASA Astrophysics Data System (ADS)

    Zhang, Shufen; Yan, Hongcan; Chen, Xuebin

    With the development of multi-core processors, virtualization, distributed storage, broadband Internet and automatic management, a new type of computing mode named cloud computing is produced. It distributes computation task on the resource pool which consists of massive computers, so the application systems can obtain the computing power, the storage space and software service according to its demand. It can concentrate all the computing resources and manage them automatically by the software without intervene. This makes application offers not to annoy for tedious details and more absorbed in his business. It will be advantageous to innovation and reduce cost. It's the ultimate goal of cloud computing to provide calculation, services and applications as a public facility for the public, So that people can use the computer resources just like using water, electricity, gas and telephone. Currently, the understanding of cloud computing is developing and changing constantly, cloud computing still has no unanimous definition. This paper describes three main service forms of cloud computing: SAAS, PAAS, IAAS, compared the definition of cloud computing which is given by Google, Amazon, IBM and other companies, summarized the basic characteristics of cloud computing, and emphasized on the key technologies such as data storage, data management, virtualization and programming model.

  20. X-38 research aircraft deorbit - computer animation

    NASA Technical Reports Server (NTRS)

    1997-01-01

    In the mid-1990's researchers at the NASA Dryden Flight Research Center, Edwards, California, and Johnson Space Center in Houston, Texas, began working actively with the sub-scale X-38 prototype crew return vehicle (CRV). This was an unpiloted lifting body designed at 80 percent of the size of a projected emergency crew return vehicle for the International Space Station. The X-38 and the actual CRV are patterned after a lifting-body shape first employed in the Air Force X-23 (SV-5) program in the mid-1960's and the Air Force-NASA X-24A lifting-body project in the early to mid-1970's. Built by Scaled Composites, Inc., in Mojave, California, and outfitted with avionics, computer systems, and other hardware at Johnson Space Center, two X-38 aircraft were involved in flight research at Dryden beginning in July of 1997. Before that, however, Dryden conducted some 13 flights at a drop zone near California City, California. These tests were done with a 1/6-scale model of the X-38 to test the parafoil concept that would be employed on the X-38 and the actual CRV. The basic concept is that the actual CRV will use an inertial navigation system together with the Global Positioning System of satellites to guide it from the International Space Station into the earth's atmosphere. A deorbit engine module will redirect the vehicle from orbit into the atmosphere where a series of parachutes and a parafoil will deploy in sequence to bring the vehicle to a landing, possibly in a field next to a hospital. Flight research at NASA Dryden for the X-38 began with an unpiloted captive carry flight in which the vehicle remained attached to its future launch vehicle, the Dryden B-52 008. There were four captive flights in 1997 and three in 1998, plus the first drop test on March 12, 1998, using the parachutes and parafoil. Further captive and drop tests occurred in 1999. Although the X-38 landed safely on the lakebed at Edwards after the March 1998 drop test, there had been some problems

  1. X-38 research aircraft landing - computer animation

    NASA Technical Reports Server (NTRS)

    1997-01-01

    In the mid-1990's researchers at the NASA Dryden Flight Research Center, Edwards, California, and Johnson Space Center in Houston, Texas, began working actively with the sub-scale X-38 prototype crew return vehicle (CRV). This was an unpiloted lifting body designed at 80 percent of the size of a projected emergency crew return vehicle for the International Space Station. The X-38 and the actual CRV are patterned after a lifting-body shape first employed in the Air Force X-23 (SV-5) program in the mid-1960's and the Air Force-NASA X-24A lifting-body project in the early to mid-1970's. Built by Scaled Composites, Inc., in Mojave, California, and outfitted with avionics, computer systems, and other hardware at Johnson Space Center, two X-38 aircraft were involved in flight research at Dryden beginning in July of 1997. Before that, however, Dryden conducted some 13 flights at a drop zone near California City, California. These tests were done with a 1/6-scale model of the X-38 aircraft to test the parafoil concept that would be employed on the X-38 aircraft and the actual CRV. The basic concept is that the actual CRV will use an inertial navigation system together with the Global Positioning System of satellites to guide it from the International Space Station into the earth's atmosphere. A deorbit engine module will redirect the vehicle from orbit into the atmosphere where a series of parachutes and a parafoil will deploy in sequence to bring the vehicle to a landing, possibly in a field next to a hospital. Flight research at NASA Dryden for the X-38 began with an unpiloted captive carry flight in which the vehicle remained attached to its future launch vehicle, the Dryden B-52 008. There were four captive flights in 1997 and three in 1998, plus the first drop test on March 12, 1998, using the parachutes and parafoil. Further captive and drop tests occurred in 1999. Although the X-38 landed safely on the lakebed at Edwards after the March 1998 drop test, there had

  2. Chemical master equation closure for computer-aided synthetic biology.

    PubMed

    Smadbeck, Patrick; Kaznessis, Yiannis N

    2015-01-01

    With inexpensive DNA synthesis technologies, we can now construct biological systems by quickly piecing together DNA sequences. Synthetic biology is the promising discipline that focuses on the construction of these new biological systems. Synthetic biology is an engineering discipline, and as such, it can benefit from mathematical modeling. This chapter focuses on mathematical models of biological systems. These models take the form of chemical reaction networks. The importance of stochasticity is discussed and methods to simulate stochastic reaction networks are reviewed. A closure scheme solution is also presented for the master equation of chemical reaction networks. The master equation is a complete model of randomly evolving molecular populations. Because of its ambitious character, the master equation remained unsolved for all but the simplest of molecular interaction networks for over 70 years. With the first complete solution of chemical master equations, a wide range of experimental observations of biomolecular interactions may be mathematically conceptualized. We anticipate that models based on the closure scheme described herein may assist in rationally designing synthetic biological systems.

  3. Chemical Master Equation Closure for Computer-Aided Synthetic Biology

    PubMed Central

    Smadbeck, Patrick; Kaznessis, Yiannis N.

    2016-01-01

    SUMMARY With inexpensive DNA synthesis technologies, we can now construct biological systems by quickly piecing together DNA sequences. Synthetic biology is the promising discipline that focuses on the construction of these new biological systems. Synthetic biology is an engineering discipline, and as such, it can benefit from mathematical modeling. This chapter focuses on mathematical models of biological systems. These models take the form of chemical reaction networks. The importance of stochasticity is discussed and methods to simulate stochastic reaction networks are reviewed. A closure scheme solution is also presented for the master equation of chemical reaction networks. The master equation is a complete model of randomly evolving molecular populations. Because of its ambitious character, the master equation remained unsolved for all but the simplest of molecular interaction networks for over seventy years. With the first complete solution of chemical master equations, a wide range of experimental observations of biomolecular interactions may be mathematically conceptualized. We anticipate that models based on the closure scheme described herein may assist in rationally designing synthetic biological systems. PMID:25487098

  4. Algorithms in nature: the convergence of systems biology and computational thinking

    PubMed Central

    Navlakha, Saket; Bar-Joseph, Ziv

    2011-01-01

    Computer science and biology have enjoyed a long and fruitful relationship for decades. Biologists rely on computational methods to analyze and integrate large data sets, while several computational methods were inspired by the high-level design principles of biological systems. Recently, these two directions have been converging. In this review, we argue that thinking computationally about biological processes may lead to more accurate models, which in turn can be used to improve the design of algorithms. We discuss the similar mechanisms and requirements shared by computational and biological processes and then present several recent studies that apply this joint analysis strategy to problems related to coordination, network analysis, and tracking and vision. We also discuss additional biological processes that can be studied in a similar manner and link them to potential computational problems. With the rapid accumulation of data detailing the inner workings of biological systems, we expect this direction of coupling biological and computational studies to greatly expand in the future. PMID:22068329

  5. Accomplishment Summary 1968-1969. Biological Computer Laboratory.

    ERIC Educational Resources Information Center

    Von Foerster, Heinz; And Others

    This report summarizes theoretical, applied, and experimental studies in the areas of computational principles in complex intelligent systems, cybernetics, multivalued logic, and the mechanization of cognitive processes. This work is summarized under the following topic headings: properties of complex dynamic systems; computers and the language…

  6. NASA Space Biology Plant Research for 2010-2020

    NASA Technical Reports Server (NTRS)

    Levine, H. G.; Tomko, D. L.; Porterfield, D. M.

    2012-01-01

    The U.S. National Research Council (NRC) recently published "Recapturing a Future for Space Exploration: Life and Physical Sciences Research for a New Era" (http://www.nap.edu/catalog.php?record id=13048), and NASA completed a Space Biology Science Plan to develop a strategy for implementing its recommendations ( http://www.nasa.gov/exploration/library/esmd documents.html). The most important recommendations of the NRC report on plant biology in space were that NASA should: (1) investigate the roles of microbial-plant systems in long-term bioregenerative life support systems, and (2) establish a robust spaceflight program of research analyzing plant growth and physiological responses to the multiple stimuli encountered in spaceflight environments. These efforts should take advantage of recently emerged analytical technologies (genomics, transcriptomics, proteomics, metabolomics) and apply modern cellular and molecular approaches in the development of a vigorous flight-based and ground-based research program. This talk will describe NASA's strategy and plans for implementing these NRC Plant Space Biology recommendations. New research capabilities for Plant Biology, optimized by providing state-of-the-art automated technology and analytical techniques to maximize scientific return, will be described. Flight experiments will use the most appropriate platform to achieve science results (e.g., ISS, free flyers, sub-orbital flights) and NASA will work closely with its international partners and other U.S. agencies to achieve its objectives. One of NASA's highest priorities in Space Biology is the development research capabilities for use on the International Space Station and other flight platforms for studying multiple generations of large plants. NASA will issue recurring NASA Research Announcements (NRAs) that include a rapid turn-around model to more fully engage the biology community in designing experiments to respond to the NRC recommendations. In doing so, NASA

  7. An open investigation of the reproducibility of cancer biology research.

    PubMed

    Errington, Timothy M; Iorns, Elizabeth; Gunn, William; Tan, Fraser Elisabeth; Lomax, Joelle; Nosek, Brian A

    2014-12-10

    It is widely believed that research that builds upon previously published findings has reproduced the original work. However, it is rare for researchers to perform or publish direct replications of existing results. The Reproducibility Project: Cancer Biology is an open investigation of reproducibility in preclinical cancer biology research. We have identified 50 high impact cancer biology articles published in the period 2010-2012, and plan to replicate a subset of experimental results from each article. A Registered Report detailing the proposed experimental designs and protocols for each subset of experiments will be peer reviewed and published prior to data collection. The results of these experiments will then be published in a Replication Study. The resulting open methodology and dataset will provide evidence about the reproducibility of high-impact results, and an opportunity to identify predictors of reproducibility.

  8. Division of Computer Research Summary of Awards. Fiscal Year 1984.

    ERIC Educational Resources Information Center

    National Science Foundation, Washington, DC. Directorate for Mathematical and Physical Sciences.

    Provided in this report are summaries of grants awarded by the National Science Foundation Division of Computer Research in fiscal year 1984. Similar areas of research are grouped (for the purposes of this report only) into these major categories: (1) computational mathematics; (2) computer systems design; (3) intelligent systems; (4) software…

  9. Computers in aeronautics and space research at the Lewis Research Center

    NASA Technical Reports Server (NTRS)

    1991-01-01

    This brochure presents a general discussion of the role of computers in aerospace research at NASA's Lewis Research Center (LeRC). Four particular areas of computer applications are addressed: computer modeling and simulation, computer assisted engineering, data acquisition and analysis, and computer controlled testing.

  10. Fundamental Biological Research on the International Space Station

    NASA Technical Reports Server (NTRS)

    Souza, K. A.; Yost, Bruce; Fletcher, L.; Dalton, Bonnie P. (Technical Monitor)

    2000-01-01

    The fundamental Biology Program of NASA's Life Sciences Division is chartered with enabling and sponsoring research on the International Space Station (ISS) in order to understand the effects of the space flight environment, particularly microgravity, on living systems. To accomplish this goal, NASA Ames Research Center (ARC) has been tasked with managing the development of a number of biological habitats, along with their support systems infrastructure. This integrated suite of habitats and support systems is being designed to support research requirements identified by the scientific community. As such, it will support investigations using cells and tissues, avian eggs, insects, plants, aquatic organisms and rodents. Studies following organisms through complete life cycles and over multiple generations will eventually be possible. As an adjunct to the development of these basic habitats, specific analytical and monitoring technologies are being targeted for maturation to complete the research cycle by transferring existing or emerging analytical techniques, sensors, and processes from the laboratory bench to the ISS research platform.

  11. Computational approaches to stochastic systems in physics and biology

    NASA Astrophysics Data System (ADS)

    Jeraldo Maldonado, Patricio Rodrigo

    calculation of the corresponding scaling laws. In Part II, I investigate the evolutionary dynamics of communities of microbes living in the gastrointestinal tracts of vertebrates, and ask to what degree their evolution is niche-driven, where organisms fitter to their environment become dominant, or if it is neutral, where the organisms evolve stochastically and are otherwise functionally equivalent within their communities. To that end, a series of computational tools were developed to pre-process, curate and reduce the data sets. In Chapter 4, I analyze the raw data for this research, namely short reads of 16S ribosomal RNA, and quantify how much of phylogenetic information is lost by using these short reads instead of full-length reads, and show that for lengths spanning 300 to 400 base pairs, we can recover some meaningful phylogenetic information. In Chapter 5, I introduce a pipeline for pre-processing, alignment and curation of libraries of short reads of rRNA. We show that this pipeline significantly reduces the artifacts usually associated with these sequences, resulting in better clustering of the sequences, and better phylogenetic trees representing their organismal relationships. In Chapter 6 I use the data processed with the above tools to analyze communities of microbes living in gastrointestinal tracts of vertebrates, and we ask to what extent the evolutionary dynamics of these communities is dominated by niche-based evolution, or if the communities behave neutrally, where evolution is random and all organisms are functionally equivalent. We conclude that there is evidence for strong niche-based dynamics, though we cannot fully discard some degree of neutral evolution. Finally, in Chapter 7 I propose a method to quantify the balance present in phylogenetic trees to compare a large-scale molecular phylogeny to full organismal taxonomies. I show that there is considerable structure in all of them, but direct comparison of both types of trees is difficult at the

  12. FOREWORD: Third Nordic Symposium on Computer Simulation in Physics, Chemistry, Biology and Mathematics

    NASA Astrophysics Data System (ADS)

    Kaski, K.; Salomaa, M.

    1990-01-01

    These are Proceedings of the Third Nordic Symposium on Computer Simulation in Physics, Chemistry, Biology, and Mathematics, held August 25-26, 1989, at Lahti (Finland). The Symposium belongs to an annual series of Meetings, the first one of which was arranged in 1987 at Lund (Sweden) and the second one in 1988 at Kolle-Kolle near Copenhagen (Denmark). Although these Symposia have thus far been essentially Nordic events, their international character has increased significantly; the trend is vividly reflected through contributions in the present Topical Issue. The interdisciplinary nature of Computational Science is central to the activity; this fundamental aspect is also responsible, in an essential way, for its rapidly increasing impact. Crucially important to a wide spectrum of superficially disparate fields is the common need for extensive - and often quite demanding - computational modelling. For such theoretical models, no closed-form (analytical) solutions are available or they would be extremely difficult to find; hence one must rather resort to the Art of performing computational investigations. Among the unifying features in the computational research are the methods of simulation employed; methods which frequently are quite closely related with each other even for faculties of science that are quite unrelated. Computer simulation in Natural Sciences is presently apprehended as a discipline on its own right, occupying a broad region somewhere between the experimental and theoretical methods, but also partially overlapping with and complementing them. - Whichever its proper definition may be, the computational approach serves as a novel and an extremely versatile tool with which one can equally well perform "pure" experimental modelling and conduct "computational theory". Computational studies that have earlier been made possible only through supercomputers have opened unexpected, as well as exciting, novel frontiers equally in mathematics (e.g., fractals

  13. Research in Applied Mathematics, Fluid Mechanics and Computer Science

    NASA Technical Reports Server (NTRS)

    1999-01-01

    This report summarizes research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, fluid mechanics, and computer science during the period October 1, 1998 through March 31, 1999.

  14. [Research activities in applied mathematics, fluid mechanics, and computer science

    NASA Technical Reports Server (NTRS)

    1995-01-01

    This report summarizes research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, fluid mechanics, and computer science during the period April 1, 1995 through September 30, 1995.

  15. The Human Genome Project: Biology, Computers, and Privacy.

    ERIC Educational Resources Information Center

    Cutter, Mary Ann G.; Drexler, Edward; Gottesman, Kay S.; Goulding, Philip G.; McCullough, Laurence B.; McInerney, Joseph D.; Micikas, Lynda B.; Mural, Richard J.; Murray, Jeffrey C.; Zola, John

    This module, for high school teachers, is the second of two modules about the Human Genome Project (HGP) produced by the Biological Sciences Curriculum Study (BSCS). The first section of this module provides background information for teachers about the structure and objectives of the HGP, aspects of the science and technology that underlie the…

  16. Advances and computational tools towards predictable design in biological engineering.

    PubMed

    Pasotti, Lorenzo; Zucca, Susanna

    2014-01-01

    The design process of complex systems in all the fields of engineering requires a set of quantitatively characterized components and a method to predict the output of systems composed by such elements. This strategy relies on the modularity of the used components or the prediction of their context-dependent behaviour, when parts functioning depends on the specific context. Mathematical models usually support the whole process by guiding the selection of parts and by predicting the output of interconnected systems. Such bottom-up design process cannot be trivially adopted for biological systems engineering, since parts function is hard to predict when components are reused in different contexts. This issue and the intrinsic complexity of living systems limit the capability of synthetic biologists to predict the quantitative behaviour of biological systems. The high potential of synthetic biology strongly depends on the capability of mastering this issue. This review discusses the predictability issues of basic biological parts (promoters, ribosome binding sites, coding sequences, transcriptional terminators, and plasmids) when used to engineer simple and complex gene expression systems in Escherichia coli. A comparison between bottom-up and trial-and-error approaches is performed for all the discussed elements and mathematical models supporting the prediction of parts behaviour are illustrated.

  17. Computational mechanics and physics at NASA Langley Research Center

    NASA Technical Reports Server (NTRS)

    South, Jerry C., Jr.

    1987-01-01

    An overview is given of computational mechanics and physics at NASA Langley Research Center. Computational analysis is a major component and tool in many of Langley's diverse research disciplines, as well as in the interdisciplinary research. Examples are given for algorithm development and advanced applications in aerodynamics, transition to turbulence and turbulence simulation, hypersonics, structures, and interdisciplinary optimization.

  18. Connecting biology and organic chemistry introductory laboratory courses through a collaborative research project.

    PubMed

    Boltax, Ariana L; Armanious, Stephanie; Kosinski-Collins, Melissa S; Pontrello, Jason K

    2015-01-01

    Modern research often requires collaboration of experts in fields, such as math, chemistry, biology, physics, and computer science to develop unique solutions to common problems. Traditional introductory undergraduate laboratory curricula in the sciences often do not emphasize connections possible between the various disciplines. We designed an interdisciplinary, medically relevant, project intended to help students see connections between chemistry and biology. Second term organic chemistry laboratory students designed and synthesized potential polymer inhibitors or inducers of polyglutamine protein aggregation. The use of novel target compounds added the uncertainty of scientific research to the project. Biology laboratory students then tested the novel potential pharmaceuticals in Huntington's disease model assays, using in vitro polyglutamine peptide aggregation and in vivo lethality studies in Drosophila. Students read articles from the primary literature describing the system from both chemical and biological perspectives. Assessment revealed that students emerged from both courses with a deeper understanding of the interdisciplinary nature of biology and chemistry and a heightened interest in basic research. The design of this collaborative project for introductory biology and organic chemistry labs demonstrated how the local interests and expertise at a university can be drawn from to create an effective way to integrate these introductory courses. Rather than simply presenting a series of experiments to be replicated, we hope that our efforts will inspire other scientists to think about how some aspect of authentic work can be brought into their own courses, and we also welcome additional collaborations to extend the scope of the scientific exploration.

  19. An overview of computer viruses in a research environment

    NASA Technical Reports Server (NTRS)

    Bishop, Matt

    1991-01-01

    The threat of attack by computer viruses is in reality a very small part of a much more general threat, specifically threats aimed at subverting computer security. Here, computer viruses are examined as a malicious logic in a research and development environment. A relation is drawn between the viruses and various models of security and integrity. Current research techniques aimed at controlling the threats posed to computer systems by threatening viruses in particular and malicious logic in general are examined. Finally, a brief examination of the vulnerabilities of research and development systems that malicious logic and computer viruses may exploit is undertaken.

  20. In focus: molecular and cell biology research in China.

    PubMed

    Yao, Xuebiao; Li, Dangsheng; Pei, Gang

    2013-09-01

    An interactive, intellectual environment with good funding opportunities is essential for the development and success of basic research. The fast-growing economy and investment in science, together with a visionary plan, have attracted foreign scholars to work in China, motivated world-class Chinese scientists to return and strengthened the country's international collaborations. As a result, molecular and cell biology research in China has evolved rapidly over the past decade.

  1. Biologically Enhanced Carbon Sequestration: Research Needs and Opportunities

    SciTech Connect

    Oldenburg, Curtis; Oldenburg, Curtis M.; Torn, Margaret S.

    2008-03-21

    Fossil fuel combustion, deforestation, and biomass burning are the dominant contributors to increasing atmospheric carbon dioxide (CO{sub 2}) concentrations and global warming. Many approaches to mitigating CO{sub 2} emissions are being pursued, and among the most promising are terrestrial and geologic carbon sequestration. Recent advances in ecology and microbial biology offer promising new possibilities for enhancing terrestrial and geologic carbon sequestration. A workshop was held October 29, 2007, at Lawrence Berkeley National Laboratory (LBNL) on Biologically Enhanced Carbon Sequestration (BECS). The workshop participants (approximately 30 scientists from California, Illinois, Oregon, Montana, and New Mexico) developed a prioritized list of research needed to make progress in the development of biological enhancements to improve terrestrial and geologic carbon sequestration. The workshop participants also identified a number of areas of supporting science that are critical to making progress in the fundamental research areas. The purpose of this position paper is to summarize and elaborate upon the findings of the workshop. The paper considers terrestrial and geologic carbon sequestration separately. First, we present a summary in outline form of the research roadmaps for terrestrial and geologic BECS. This outline is elaborated upon in the narrative sections that follow. The narrative sections start with the focused research priorities in each area followed by critical supporting science for biological enhancements as prioritized during the workshop. Finally, Table 1 summarizes the potential significance or 'materiality' of advances in these areas for reducing net greenhouse gas emissions.

  2. Glimpses of Biological Research and Education in Cuba.

    ERIC Educational Resources Information Center

    Margulis, Lynn; Kunz, Thomas H.

    1984-01-01

    Discusses Cuban medical facilities, biological research (focusing on sugarcane tissue culture, interferon, hybrid cattle, tropical fruits, and yeast biosynthetic pathways), science education programs at all levels, and institutions of higher education. Also examines such concerns as the Cuban literacy rate and efforts to improve the environment.…

  3. The Research Proposal in Biomechanical and Biological Engineering Courses

    ERIC Educational Resources Information Center

    Harrison, Roger G.; Nollert, Matthias U.; Schmidtke, David W.; Sikavitsas, Vassilios I.

    2006-01-01

    Students in four biochemical and biological engineering courses for upper-­level undergraduates and graduate students were required to write a research proposal. Breaking the requirements down into segments (such as a summary with specific aims, rough draft, and final draft) due on different dates helped make the assignment more manageable for the…

  4. Biomedical Research Experiences for Biology Majors at a Small College

    ERIC Educational Resources Information Center

    Stover, Shawn K.; Mabry, Michelle L.

    2010-01-01

    A program-level assessment of the biology curriculum at a small liberal arts college validates a previous study demonstrating success in achieving learning outcomes related to content knowledge and communication skills. Furthermore, research opportunities have been provided to complement pedagogical strategies and give students a more complete…

  5. Computational structural mechanics methods research using an evolving framework

    NASA Technical Reports Server (NTRS)

    Knight, N. F., Jr.; Lotts, C. G.; Gillian, R. E.

    1990-01-01

    Advanced structural analysis and computational methods that exploit high-performance computers are being developed in a computational structural mechanics research activity sponsored by the NASA Langley Research Center. These new methods are developed in an evolving framework and applied to representative complex structural analysis problems from the aerospace industry. An overview of the methods development environment is presented, and methods research areas are described. Selected application studies are also summarized.

  6. Virtual Cell: computational tools for modeling in cell biology

    PubMed Central

    Resasco, Diana C.; Gao, Fei; Morgan, Frank; Novak, Igor L.; Schaff, James C.; Slepchenko, Boris M.

    2011-01-01

    The Virtual Cell (VCell) is a general computational framework for modeling physico-chemical and electrophysiological processes in living cells. Developed by the National Resource for Cell Analysis and Modeling at the University of Connecticut Health Center, it provides automated tools for simulating a wide range of cellular phenomena in space and time, both deterministically and stochastically. These computational tools allow one to couple electrophysiology and reaction kinetics with transport mechanisms, such as diffusion and directed transport, and map them onto spatial domains of various shapes, including irregular three-dimensional geometries derived from experimental images. In this article, we review new robust computational tools recently deployed in VCell for treating spatially resolved models. PMID:22139996

  7. Applications of computer modeling to fusion research

    SciTech Connect

    Dawson, J.M.

    1989-01-01

    Progress achieved during this report period is presented on the following topics: Development and application of gyrokinetic particle codes to tokamak transport, development of techniques to take advantage of parallel computers; model dynamo and bootstrap current drive; and in general maintain our broad-based program in basic plasma physics and computer modeling.

  8. Space Station Biological Research Project: Reference Experiment Book

    NASA Technical Reports Server (NTRS)

    Johnson, Catherine (Editor); Wade, Charles (Editor)

    1996-01-01

    The Space Station Biological Research Project (SSBRP), which is the combined efforts of the Centrifuge Facility (CF) and the Gravitational Biology Facility (GBF), is responsible for the development of life sciences hardware to be used on the International Space Station to support cell, developmental, and plant biology research. The SSBRP Reference Experiment Book was developed to use as a tool for guiding this development effort. The reference experiments characterize the research interests of the international scientific community and serve to identify the hardware capabilities and support equipment needed to support such research. The reference experiments also serve as a tool for understanding the operational aspects of conducting research on board the Space Station. This material was generated by the science community by way of their responses to reference experiment solicitation packages sent to them by SSBRP scientists. The solicitation process was executed in two phases. The first phase was completed in February of 1992 and the second phase completed in November of 1995. Representing these phases, the document is subdivided into a Section 1 and a Section 2. The reference experiments contained in this document are only representative microgravity experiments. They are not intended to define actual flight experiments. Ground and flight experiments will be selected through the formal NASA Research Announcement (NRA) and Announcement of Opportunity (AO) experiment solicitation, review, and selection process.

  9. Workshop in computational molecular biology, April 15, 1991--April 14, 1994

    SciTech Connect

    Tavare, S.

    1995-04-12

    Funds from this award were used to the Workshop in Computational Molecular Biology, `91 Symposium entitled Interface: Computing Science and Statistics, Seattle, Washington, April 21, 1991; the Workshop in Statistical Issues in Molecular Biology held at Stanford, California, August 8, 1993; and the Session on Population Genetics a part of the 56th Annual Meeting, Institute of Mathematical Statistics, San Francisco, California, August 9, 1993.

  10. Biological and computational evaluation of resveratrol inhibitors against Alzheimer's disease.

    PubMed

    Koukoulitsa, Catherine; Villalonga-Barber, Caroline; Csonka, Robert; Alexi, Xanthippi; Leonis, Georgios; Dellis, Dimitris; Hamelink, Elizabeth; Belda, Oscar; Steele, Barry R; Micha-Screttas, Maria; Alexis, Michael N; Papadopoulos, Manthos G; Mavromoustakos, Thomas

    2016-01-01

    It has been reported that beta amyloid induces production of radical oxygen species and oxidative stress in neuronal cells, which in turn upregulates β-secretase (BACE-1) expression and beta amyloid levels, thereby propagating oxidative stress and increasing neuronal injury. A series of resveratrol derivatives, known to be inhibitors of oxidative stress-induced neuronal cell death (oxytosis) were biologically evaluated against BACE-1 using homogeneous time-resolved fluorescence (TRF) assay. Correlation between oxytosis inhibitory and BACE-1 inhibitory activity of resveratrol derivatives was statistically significant, supporting the notion that BACE-1 may act as pivotal mediator of neuronal cell oxytosis. Four of the biologically evaluated resveratrol analogs demonstrated considerably higher activity than resveratrol in either assay. The discovery of some "hits" led us to initiate detailed docking studies associated with Molecular Dynamics in order to provide a plausible explanation for the experimental results and understand their molecular basis of action.

  11. BIO2010 and beyond: What undergraduate physics does the next generation of molecular biology researchers need?

    NASA Astrophysics Data System (ADS)

    Howard, Jonathon

    2004-03-01

    What fundamental skills in mathematics, chemistry, physics, computer science and engineering are required at the undergraduate level to prepare the next generation of biology majors who will become research scientists? To address this question, Bruce Alberts, President of the National Academy of Sciences, established BIO2010, a committee of the National Research Council (USA), chaired by Lubert Stryer. The report of the committee was published in 2003 as BIO2010: Transforming Undergraduate Education for Future Research Biologists (National Academies Press, Washington DC, www.national-academies.com). I will summarize the recommendations of the Physics and Engineering Panel that was chaired by John Hopfield and give my own views of what physics is essential for researchers in cell and molecular biology.

  12. Design-driven, multi-use research agendas to enable applied synthetic biology for global health.

    PubMed

    Carothers, James M

    2013-09-01

    Many of the synthetic biological devices, pathways and systems that can be engineered are multi-use, in the sense that they could be used both for commercially-important applications and to help meet global health needs. The on-going development of models and simulation tools for assembling component parts into functionally-complex devices and systems will enable successful engineering with much less trial-and-error experimentation and laboratory infrastructure. As illustrations, I draw upon recent examples from my own work and the broader Keasling research group at the University of California Berkeley and the Joint BioEnergy Institute, of which I was formerly a part. By combining multi-use synthetic biology research agendas with advanced computer-aided design tool creation, it may be possible to more rapidly engineer safe and effective synthetic biology technologies that help address a wide range of global health problems.

  13. The Effects of 3D Computer Simulation on Biology Students' Achievement and Memory Retention

    ERIC Educational Resources Information Center

    Elangovan, Tavasuria; Ismail, Zurida

    2014-01-01

    A quasi experimental study was conducted for six weeks to determine the effectiveness of two different 3D computer simulation based teaching methods, that is, realistic simulation and non-realistic simulation on Form Four Biology students' achievement and memory retention in Perak, Malaysia. A sample of 136 Form Four Biology students in Perak,…

  14. An Introduction to Computer Assisted Analysis in the Biological Sciences.

    ERIC Educational Resources Information Center

    Banaugh, R. P.

    This set of notes is designed to introduce the student to the development and use of computer-based models, and to analyze quantitative phenomena in the life sciences. Only BASIC programming language is used. The ten chapter titles are: The Growth of a Single Species; The Association of Two Species; Parameter Determination; Automated Parameter…

  15. Scalable Computational Methods for the Analysis of High-Throughput Biological Data

    SciTech Connect

    Langston, Michael A

    2012-09-06

    This primary focus of this research project is elucidating genetic regulatory mechanisms that control an organism's responses to low-dose ionizing radiation. Although low doses (at most ten centigrays) are not lethal to humans, they elicit a highly complex physiological response, with the ultimate outcome in terms of risk to human health unknown. The tools of molecular biology and computational science will be harnessed to study coordinated changes in gene expression that orchestrate the mechanisms a cell uses to manage the radiation stimulus. High performance implementations of novel algorithms that exploit the principles of fixed-parameter tractability will be used to extract gene sets suggestive of co-regulation. Genomic mining will be performed to scrutinize, winnow and highlight the most promising gene sets for more detailed investigation. The overall goal is to increase our understanding of the health risks associated with exposures to low levels of radiation.

  16. Physical and Computational Modeling for Chemical and Biological Weapons Airflow Applications

    SciTech Connect

    McEligot, Donald Marinus; Mc Creery, Glenn Ernest; Pink, Robert John; Barringer, C.; Knight, K. J.

    2002-11-01

    There is a need for information on dispersion and infiltration of chemical and biological agents in complex building environments. A recent collaborative study conducted at the Idaho National Engineering and Environmental Laboratory (INEEL) and Bechtel Corporation Research and Development had the objective of assessing computational fluid dynamics (CFD) models for simulation of flow around complicated buildings through a comparison of experimental and numerical results. The test facility used in the experiments was INEEL’s unique large Matched-Index-of-Refraction (MIR) flow system. The CFD code used for modeling was Fluent, a widely available commercial flow simulation package. For the experiment, a building plan was selected to approximately represent an existing facility. It was found that predicted velocity profiles from above the building and in front of the building were in good agreement with the measurements.

  17. Methods of information geometry in computational system biology (consistency between chemical and biological evolution).

    PubMed

    Astakhov, Vadim

    2009-01-01

    Interest in simulation of large-scale metabolic networks, species development, and genesis of various diseases requires new simulation techniques to accommodate the high complexity of realistic biological networks. Information geometry and topological formalisms are proposed to analyze information processes. We analyze the complexity of large-scale biological networks as well as transition of the system functionality due to modification in the system architecture, system environment, and system components. The dynamic core model is developed. The term dynamic core is used to define a set of causally related network functions. Delocalization of dynamic core model provides a mathematical formalism to analyze migration of specific functions in biosystems which undergo structure transition induced by the environment. The term delocalization is used to describe these processes of migration. We constructed a holographic model with self-poetic dynamic cores which preserves functional properties under those transitions. Topological constraints such as Ricci flow and Pfaff dimension were found for statistical manifolds which represent biological networks. These constraints can provide insight on processes of degeneration and recovery which take place in large-scale networks. We would like to suggest that therapies which are able to effectively implement estimated constraints, will successfully adjust biological systems and recover altered functionality. Also, we mathematically formulate the hypothesis that there is a direct consistency between biological and chemical evolution. Any set of causal relations within a biological network has its dual reimplementation in the chemistry of the system environment.

  18. Recent advances, and unresolved issues, in the application of computational modelling to the prediction of the biological effects of nanomaterials.

    PubMed

    Winkler, David A

    2016-05-15

    Nanomaterials research is one of the fastest growing contemporary research areas. The unprecedented properties of these materials have meant that they are being incorporated into products very quickly. Regulatory agencies are concerned they cannot assess the potential hazards of these materials adequately, as data on the biological properties of nanomaterials are still relatively limited and expensive to acquire. Computational modelling methods have much to offer in helping understand the mechanisms by which toxicity may occur, and in predicting the likelihood of adverse biological impacts of materials not yet tested experimentally. This paper reviews the progress these methods, particularly those QSAR-based, have made in understanding and predicting potentially adverse biological effects of nanomaterials, and also the limitations and pitfalls of these methods.

  19. pClone: Synthetic Biology Tool Makes Promoter Research Accessible to Beginning Biology Students.

    PubMed

    Campbell, A Malcolm; Eckdahl, Todd; Cronk, Brian; Andresen, Corinne; Frederick, Paul; Huckuntod, Samantha; Shinneman, Claire; Wacker, Annie; Yuan, Jason

    2014-01-01

    The Vision and Change report recommended genuine research experiences for undergraduate biology students. Authentic research improves science education, increases the number of scientifically literate citizens, and encourages students to pursue research. Synthetic biology is well suited for undergraduate research and is a growing area of science. We developed a laboratory module called pClone that empowers students to use advances in molecular cloning methods to discover new promoters for use by synthetic biologists. Our educational goals are consistent with Vision and Change and emphasize core concepts and competencies. pClone is a family of three plasmids that students use to clone a new transcriptional promoter or mutate a canonical promoter and measure promoter activity in Escherichia coli. We also developed the Registry of Functional Promoters, an open-access database of student promoter research results. Using pre- and posttests, we measured significant learning gains among students using pClone in introductory biology and genetics classes. Student posttest scores were significantly better than scores of students who did not use pClone. pClone is an easy and affordable mechanism for large-enrollment labs to meet the high standards of Vision and Change.

  20. Stem Cells: A Renaissance in Human Biology Research.

    PubMed

    Wu, Jun; Izpisua Belmonte, Juan Carlos

    2016-06-16

    The understanding of human biology and how it relates to that of other species represents an ancient quest. Limited access to human material, particularly during early development, has restricted researchers to only scratching the surface of this inherently challenging subject. Recent technological innovations, such as single cell "omics" and human stem cell derivation, have now greatly accelerated our ability to gain insights into uniquely human biology. The opportunities afforded to delve molecularly into scarce material and to model human embryogenesis and pathophysiological processes are leading to new insights of human development and are changing our understanding of disease and choice of therapy options.

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

    NASA Technical Reports Server (NTRS)

    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.

  2. Stem Cells: A Renaissance in Human Biology Research.

    PubMed

    Wu, Jun; Izpisua Belmonte, Juan Carlos

    2016-06-16

    The understanding of human biology and how it relates to that of other species represents an ancient quest. Limited access to human material, particularly during early development, has restricted researchers to only scratching the surface of this inherently challenging subject. Recent technological innovations, such as single cell "omics" and human stem cell derivation, have now greatly accelerated our ability to gain insights into uniquely human biology. The opportunities afforded to delve molecularly into scarce material and to model human embryogenesis and pathophysiological processes are leading to new insights of human development and are changing our understanding of disease and choice of therapy options. PMID:27315475

  3. LifeSat - A satellite for space biological research

    NASA Technical Reports Server (NTRS)

    Halstead, Thora W.; Morey-Holton, Emily R.

    1990-01-01

    The LifeSat Program addresses the need for continuing access by biological scientists to space experimentation by accommodating a wide range of experiments involving animals and plants for durations up to 60 days in an unmanned satellite. The program will encourage interdisciplinary and international cooperation at both the agency and scientist levels, and will provide a recoverable, reusable facility for low-cost missions addressing key scientific issues that can only be answered by space experimentation. It will provide opportunities for research in gravitational biology and on the effects of cosmic radiation on life systems. The scientific aspects of LifeSat are addressed here.

  4. Current dichotomy between traditional molecular biological and omic research in cancer biology and pharmacology.

    PubMed

    Reinhold, William C

    2015-12-10

    There is currently a split within the cancer research community between traditional molecular biological hypothesis-driven and the more recent "omic" forms or research. While the molecular biological approach employs the tried and true single alteration-single response formulations of experimentation, the omic employs broad-based assay or sample collection approaches that generate large volumes of data. How to integrate the benefits of these two approaches in an efficient and productive fashion remains an outstanding issue. Ideally, one would merge the understandability, exactness, simplicity, and testability of the molecular biological approach, with the larger amounts of data, simultaneous consideration of multiple alterations, consideration of genes both of known interest along with the novel, cross-sample comparisons among cell lines and patient samples, and consideration of directed questions while simultaneously gaining exposure to the novel provided by the omic approach. While at the current time integration of the two disciplines remains problematic, attempts to do so are ongoing, and will be necessary for the understanding of the large cell line screens including the Developmental Therapeutics Program's NCI-60, the Broad Institute's Cancer Cell Line Encyclopedia, and the Wellcome Trust Sanger Institute's Cancer Genome Project, as well as the the Cancer Genome Atlas clinical samples project. Going forward there is significant benefit to be had from the integration of the molecular biological and the omic forms or research, with the desired goal being improved translational understanding and application.

  5. [Research toward a heterogeneous networked computing cluster

    SciTech Connect

    Duke, D.W.; Green, T.P.

    1998-08-11

    Over the last year the Systems Development Group, SDG, has been involved in a number of projects. The primary projects include extending the UNIX version of DQS, a DCE version of DQS, a Java based queuing system, a Computer Aided Learning and Instruction model and working with the Florida Department of Law Enforcement in the formation of the Florida Computer Crime Center. Additionally SDG has assisted a number of state and local agencies. A synopsis of these projects is contained in this report.

  6. Current Trends and New Challenges of Databases and Web Applications for Systems Driven Biological Research

    PubMed Central

    Sreenivasaiah, Pradeep Kumar; Kim, Do Han

    2010-01-01

    Dynamic and rapidly evolving nature of systems driven research imposes special requirements on the technology, approach, design and architecture of computational infrastructure including database and Web application. Several solutions have been proposed to meet the expectations and novel methods have been developed to address the persisting problems of data integration. It is important for researchers to understand different technologies and approaches. Having familiarized with the pros and cons of the existing technologies, researchers can exploit its capabilities to the maximum potential for integrating data. In this review we discuss the architecture, design and key technologies underlying some of the prominent databases and Web applications. We will mention their roles in integration of biological data and investigate some of the emerging design concepts and computational technologies that are likely to have a key role in the future of systems driven biomedical research. PMID:21423387

  7. Current trends and new challenges of databases and web applications for systems driven biological research.

    PubMed

    Sreenivasaiah, Pradeep Kumar; Kim, Do Han

    2010-01-01

    Dynamic and rapidly evolving nature of systems driven research imposes special requirements on the technology, approach, design and architecture of computational infrastructure including database and Web application. Several solutions have been proposed to meet the expectations and novel methods have been developed to address the persisting problems of data integration. It is important for researchers to understand different technologies and approaches. Having familiarized with the pros and cons of the existing technologies, researchers can exploit its capabilities to the maximum potential for integrating data. In this review we discuss the architecture, design and key technologies underlying some of the prominent databases and Web applications. We will mention their roles in integration of biological data and investigate some of the emerging design concepts and computational technologies that are likely to have a key role in the future of systems driven biomedical research.

  8. Human biological materials in research: ethical issues and the role of stewardship in minimizing research risks.

    PubMed

    Jeffers, B R

    2001-12-01

    Recent scientific and technologic advances generated from the human genome project have increased the ability of researchers to study human biological materials. This has enhanced the ease with which highly personal information such as genetic makeup can be revealed about individuals, families, and communities. In addition, a change in the societal value of human biological tissue from waste to commercial resource has occurred. A new model of stewardship is developed that can be used as a guide for protecting human research participants who are involved in studies that include collecting and handling human biological samples. Nursing implications to ensure protection of human research participants are discussed.

  9. The opportunities for space biology research on the Space Station

    NASA Technical Reports Server (NTRS)

    Ballard, Rodney W.; Souza, Kenneth A.

    1987-01-01

    The life sciences research facilities for the Space Station are being designed to accommodate both animal and plant specimens for long durations studies. This will enable research on how living systems adapt to microgravity, how gravity has shaped and affected life on earth, and further the understanding of basic biological phenomena. This would include multigeneration experiments on the effects of microgravity on the reproduction, development, growth, physiology, behavior, and aging of organisms. To achieve these research goals, a modular habitat system and on-board variable gravity centrifuges, capable of holding various animal, plant, cells and tissues, is proposed for the science laboratory.

  10. BIOPACK: the ground controlled late access biological research facility.

    PubMed

    van Loon, Jack J W A

    2004-03-01

    Future Space Shuttle flights shall be characterized by activities necessary to further build the International Space Station, ISS. During these missions limited resources are available to conduct biological experiments in space. The Shuttles' Middeck is a very suitable place to conduct science during the ISS assembly missions or dedicated science missions. The BIOPACK, which flew its first mission during the STS-107, provides a versatile Middeck Locker based research tool for gravitational biology studies. The core facility occupies the space of only two Middeck Lockers. Experiment temperatures are controlled for bacteria, plant, invertebrate and mammalian cultures. Gravity levels and profiles can be set ranging from 0 to 2.0 x g on three independent centrifuges. This provides the experimenter with a 1.0 x g on-board reference and intermediate hypogravity and hypergravity data points to investigate e.g. threshold levels in biological responses. Temperature sensitive items can be stored in the facilities' -10 degrees C and +4 degrees C stowage areas. During STS-107 the facility also included a small glovebox (GBX) and passive temperature controlled units (PTCU). The GBX provides the experimenter with two extra levels of containment for safe sample handling. This biological research facility is a late access (L-10 hrs) laboratory, which, when reaching orbit, could automatically be starting up reducing important experiment lag-time and valuable crew time. The system is completely telecommanded when needed. During flight system parameters like temperatures, centrifuge speeds, experiment commanding or sensor readouts can be monitored and changed when needed. Although ISS provides a wide range of research facilities there is still need for an STS-based late access facility such as the BIOPACK providing experimenters with a very versatile research cabinet for biological experiments under microgravity and in-flight control conditions.

  11. Gold nanoparticles in model biological membranes: A computational perspective.

    PubMed

    Rossi, Giulia; Monticelli, Luca

    2016-10-01

    The electronic, optical, catalytic, and magnetic properties of metal nanoparticles (NPs) make them extremely interesting for biomedical applications. In this rapidly moving field, monolayer-protected gold nanoparticles emerge both as a reference system and as promising candidates for drug and gene delivery, photothermal treatment, and imaging applications. Despite the technological relevance, there is still poor understanding of the molecular processes driving the interactions of metal nanoparticles with cells, and with cell membranes in particular. In this paper we review molecular-level computational studies of the interaction between monolayer-protected gold NPs and model lipid membranes. Our review comprises a brief description of the most relevant experimental results in this field and of the questions they raised, followed by a description of the computational achievements reported so far. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

  12. Dynamically repairing and replacing neural networks: using hybrid computational and biological tools.

    PubMed

    Sanchez, Justin; Lytton, William; Carmena, Jose; Principe, Jose; Fortes, Jose; Barbour, Randall; Francis, Joseph

    2012-01-01

    The debilitating effects of injury to the nervous system can have a profound effect on daily life activities of the injured person. In this article, we present a project overview in which we are utilizing computational and biological principles, along with simulation and experimentation, to create a realistic computational model of natural and injured sensorimotor control systems. Through the development of hybrid in silico/biological coadaptive symbiotic systems, the goal is to create new technologies that yield transformative neuroprosthetic rehabilitative solutions and a new test bed for the development of integrative medical devices for the repair and enhancement of biological systems. PMID:22344954

  13. Computer Skills Acquisition: A Review and Future Directions for Research.

    ERIC Educational Resources Information Center

    Gattiker, Urs E.

    A review of past research on training employees for computer-mediated work leads to the development of theory and propositions concerning the relationship between different variables, such as: (1) individual factors; (2) task and person-computer interface; (3) characteristics of training design for the acquisition of computer skills; and (4) the…

  14. Research Issues in Computer-Assisted Learning Environments.

    ERIC Educational Resources Information Center

    MacGregor, S. Kim

    This review of the research on concerns associated with the use of computers in school learning environments focuses primarily on issues related to the impact of computer technology on equity, especially the reasons for differential use of computers by boys and girls and the effects of economic disparities among schools and students; differences…

  15. Using parallel evolutionary development for a biologically-inspired computer vision system for mobile robots.

    PubMed

    Wright, Cameron H G; Barrett, Steven F; Pack, Daniel J

    2005-01-01

    We describe a new approach to attacking the problem of robust computer vision for mobile robots. The overall strategy is to mimic the biological evolution of animal vision systems. Our basic imaging sensor is based upon the eye of the common house fly, Musca domestica. The computational algorithms are a mix of traditional image processing, subspace techniques, and multilayer neural networks.

  16. Signal-to-Noise Ratio Measures Efficacy of Biological Computing Devices and Circuits

    PubMed Central

    Beal, Jacob

    2015-01-01

    Engineering biological cells to perform computations has a broad range of important potential applications, including precision medical therapies, biosynthesis process control, and environmental sensing. Implementing predictable and effective computation, however, has been extremely difficult to date, due to a combination of poor composability of available parts and of insufficient characterization of parts and their interactions with the complex environment in which they operate. In this paper, the author argues that this situation can be improved by quantitative signal-to-noise analysis of the relationship between computational abstractions and the variation and uncertainty endemic in biological organisms. This analysis takes the form of a ΔSNRdB function for each computational device, which can be computed from measurements of a device’s input/output curve and expression noise. These functions can then be combined to predict how well a circuit will implement an intended computation, as well as evaluating the general suitability of biological devices for engineering computational circuits. Applying signal-to-noise analysis to current repressor libraries shows that no library is currently sufficient for general circuit engineering, but also indicates key targets to remedy this situation and vastly improve the range of computations that can be used effectively in the implementation of biological applications. PMID:26177070

  17. Signal-to-Noise Ratio Measures Efficacy of Biological Computing Devices and Circuits.

    PubMed

    Beal, Jacob

    2015-01-01

    Engineering biological cells to perform computations has a broad range of important potential applications, including precision medical therapies, biosynthesis process control, and environmental sensing. Implementing predictable and effective computation, however, has been extremely difficult to date, due to a combination of poor composability of available parts and of insufficient characterization of parts and their interactions with the complex environment in which they operate. In this paper, the author argues that this situation can be improved by quantitative signal-to-noise analysis of the relationship between computational abstractions and the variation and uncertainty endemic in biological organisms. This analysis takes the form of a ΔSNRdB function for each computational device, which can be computed from measurements of a device's input/output curve and expression noise. These functions can then be combined to predict how well a circuit will implement an intended computation, as well as evaluating the general suitability of biological devices for engineering computational circuits. Applying signal-to-noise analysis to current repressor libraries shows that no library is currently sufficient for general circuit engineering, but also indicates key targets to remedy this situation and vastly improve the range of computations that can be used effectively in the implementation of biological applications. PMID:26177070

  18. A Computer-Aided Self-Testing System for Biological Psychology.

    ERIC Educational Resources Information Center

    Leiblum, M. D.; And Others

    1994-01-01

    Describes the production of a computer-aided, self-testing system for university students enrolled in a first-year course in biological psychology. Project aspects described include selection, acquisition and description of software; question banks and test structures; modes of use (computer or printed version); evaluation; and future plans. (11…

  19. Using Mathematics to Bridge the Gap between Biology and Computer Science

    ERIC Educational Resources Information Center

    Hammerman, Natalie; Tolvo, Anthony; Goldberg, Robert

    2004-01-01

    The rapid rate of expansion of the disciplines of biotechnology, genomics, and bioinformatics emphasizes the increased interdependency between computer science and biology, with mathematics serving as the bridge between these disciplines. This paper demonstrates this inter-relationship within the context of a computational model for a biological…

  20. Machine learning in cell biology - teaching computers to recognize phenotypes.

    PubMed

    Sommer, Christoph; Gerlich, Daniel W

    2013-12-15

    Recent advances in microscope automation provide new opportunities for high-throughput cell biology, such as image-based screening. High-complex image analysis tasks often make the implementation of static and predefined processing rules a cumbersome effort. Machine-learning methods, instead, seek to use intrinsic data structure, as well as the expert annotations of biologists to infer models that can be used to solve versatile data analysis tasks. Here, we explain how machine-learning methods work and what needs to be considered for their successful application in cell biology. We outline how microscopy images can be converted into a data representation suitable for machine learning, and then introduce various state-of-the-art machine-learning algorithms, highlighting recent applications in image-based screening. Our Commentary aims to provide the biologist with a guide to the application of machine learning to microscopy assays and we therefore include extensive discussion on how to optimize experimental workflow as well as the data analysis pipeline. PMID:24259662

  1. Machine learning in cell biology - teaching computers to recognize phenotypes.

    PubMed

    Sommer, Christoph; Gerlich, Daniel W

    2013-12-15

    Recent advances in microscope automation provide new opportunities for high-throughput cell biology, such as image-based screening. High-complex image analysis tasks often make the implementation of static and predefined processing rules a cumbersome effort. Machine-learning methods, instead, seek to use intrinsic data structure, as well as the expert annotations of biologists to infer models that can be used to solve versatile data analysis tasks. Here, we explain how machine-learning methods work and what needs to be considered for their successful application in cell biology. We outline how microscopy images can be converted into a data representation suitable for machine learning, and then introduce various state-of-the-art machine-learning algorithms, highlighting recent applications in image-based screening. Our Commentary aims to provide the biologist with a guide to the application of machine learning to microscopy assays and we therefore include extensive discussion on how to optimize experimental workflow as well as the data analysis pipeline.

  2. Research in applied mathematics, numerical analysis, and computer science

    NASA Technical Reports Server (NTRS)

    1984-01-01

    Research conducted at the Institute for Computer Applications in Science and Engineering (ICASE) in applied mathematics, numerical analysis, and computer science is summarized and abstracts of published reports are presented. The major categories of the ICASE research program are: (1) numerical methods, with particular emphasis on the development and analysis of basic numerical algorithms; (2) control and parameter identification; (3) computational problems in engineering and the physical sciences, particularly fluid dynamics, acoustics, and structural analysis; and (4) computer systems and software, especially vector and parallel computers.

  3. Computation and graphics in mathematical research

    SciTech Connect

    Hoffman, D.A.; Spruck, J.

    1992-08-13

    This report discusses: The description of the GANG Project and results for prior research; the center for geometry, analysis, numerics and graphics; description of GANG Laboratory; software development at GANG; and mathematical and scientific research activities.

  4. Cell stretching devices as research tools: engineering and biological considerations.

    PubMed

    Kamble, Harshad; Barton, Matthew J; Jun, Myeongjun; Park, Sungsu; Nguyen, Nam-Trung

    2016-08-16

    Cells within the human body are subjected to continuous, cyclic mechanical strain caused by various organ functions, movement, and growth. Cells are well known to have the ability to sense and respond to mechanical stimuli. This process is referred to as mechanotransduction. A better understanding of mechanotransduction is of great interest to clinicians and scientists alike to improve clinical diagnosis and understanding of medical pathology. However, the complexity involved in in vivo biological systems creates a need for better in vitro technologies, which can closely mimic the cells' microenvironment using induced mechanical strain. This technology gap motivates the development of cell stretching devices for better understanding of the cell response to mechanical stimuli. This review focuses on the engineering and biological considerations for the development of such cell stretching devices. The paper discusses different types of stretching concepts, major design consideration and biological aspects of cell stretching and provides a perspective for future development in this research area. PMID:27440436

  5. DOE research in utilization of high-performance computers

    SciTech Connect

    Buzbee, B.L.; Worlton, W.J.; Michael, G.; Rodrigue, G.

    1980-12-01

    Department of Energy (DOE) and other Government research laboratories depend on high-performance computer systems to accomplish their programatic goals. As the most powerful computer systems become available, they are acquired by these laboratories so that advances can be made in their disciplines. These advances are often the result of added sophistication to numerical models whose execution is made possible by high-performance computer systems. However, high-performance computer systems have become increasingly complex; consequently, it has become increasingly difficult to realize their potential performance. The result is a need for research on issues related to the utilization of these systems. This report gives a brief description of high-performance computers, and then addresses the use of and future needs for high-performance computers within DOE, the growing complexity of applications within DOE, and areas of high-performance computer systems warranting research. 1 figure.

  6. Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

    PubMed Central

    Waltemath, Dagmar; Bergmann, Frank T.; Chaouiya, Claudine; Czauderna, Tobias; Gleeson, Padraig; Goble, Carole; Golebiewski, Martin; Hucka, Michael; Juty, Nick; Krebs, Olga; Le Novère, Nicolas; Mi, Huaiyu; Moraru, Ion I.; Myers, Chris J.; Nickerson, David; Olivier, Brett G.; Rodriguez, Nicolas; Schreiber, Falk; Smith, Lucian; Zhang, Fengkai; Bonnet, Eric

    2014-01-01

    The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of community standards and formats in computational systems biology and related fields. This report summarizes the topics and activities of the fourth edition of the annual COMBINE meeting, held in Paris during September 16-20 2013, and attended by a total of 96 people. This edition pioneered a first day devoted to modeling approaches in biology, which attracted a broad audience of scientists thanks to a panel of renowned speakers. During subsequent days, discussions were held on many subjects including the introduction of new features in the various COMBINE standards, new software tools that use the standards, and outreach efforts. Significant emphasis went into work on extensions of the SBML format, and also into community-building. This year’s edition once again demonstrated that the COMBINE community is thriving, and still manages to help coordinate activities between different standards in computational systems biology.

  7. Invited review article: Advanced light microscopy for biological space research.

    PubMed

    De Vos, Winnok H; Beghuin, Didier; Schwarz, Christian J; Jones, David B; van Loon, Jack J W A; Bereiter-Hahn, Juergen; Stelzer, Ernst H K

    2014-10-01

    As commercial space flights have become feasible and long-term extraterrestrial missions are planned, it is imperative that the impact of space travel and the space environment on human physiology be thoroughly characterized. Scrutinizing the effects of potentially detrimental factors such as ionizing radiation and microgravity at the cellular and tissue level demands adequate visualization technology. Advanced light microscopy (ALM) is the leading tool for non-destructive structural and functional investigation of static as well as dynamic biological systems. In recent years, technological developments and advances in photochemistry and genetic engineering have boosted all aspects of resolution, readout and throughput, rendering ALM ideally suited for biological space research. While various microscopy-based studies have addressed cellular response to space-related environmental stressors, biological endpoints have typically been determined only after the mission, leaving an experimental gap that is prone to bias results. An on-board, real-time microscopical monitoring device can bridge this gap. Breadboards and even fully operational microscope setups have been conceived, but they need to be rendered more compact and versatile. Most importantly, they must allow addressing the impact of gravity, or the lack thereof, on physiologically relevant biological systems in space and in ground-based simulations. In order to delineate the essential functionalities for such a system, we have reviewed the pending questions in space science, the relevant biological model systems, and the state-of-the art in ALM. Based on a rigorous trade-off, in which we recognize the relevance of multi-cellular systems and the cellular microenvironment, we propose a compact, but flexible concept for space-related cell biological research that is based on light sheet microscopy. PMID:25362364

  8. Invited Review Article: Advanced light microscopy for biological space research

    SciTech Connect

    De Vos, Winnok H.; Beghuin, Didier; Schwarz, Christian J.; Jones, David B.; Loon, Jack J. W. A. van

    2014-10-15

    As commercial space flights have become feasible and long-term extraterrestrial missions are planned, it is imperative that the impact of space travel and the space environment on human physiology be thoroughly characterized. Scrutinizing the effects of potentially detrimental factors such as ionizing radiation and microgravity at the cellular and tissue level demands adequate visualization technology. Advanced light microscopy (ALM) is the leading tool for non-destructive structural and functional investigation of static as well as dynamic biological systems. In recent years, technological developments and advances in photochemistry and genetic engineering have boosted all aspects of resolution, readout and throughput, rendering ALM ideally suited for biological space research. While various microscopy-based studies have addressed cellular response to space-related environmental stressors, biological endpoints have typically been determined only after the mission, leaving an experimental gap that is prone to bias results. An on-board, real-time microscopical monitoring device can bridge this gap. Breadboards and even fully operational microscope setups have been conceived, but they need to be rendered more compact and versatile. Most importantly, they must allow addressing the impact of gravity, or the lack thereof, on physiologically relevant biological systems in space and in ground-based simulations. In order to delineate the essential functionalities for such a system, we have reviewed the pending questions in space science, the relevant biological model systems, and the state-of-the art in ALM. Based on a rigorous trade-off, in which we recognize the relevance of multi-cellular systems and the cellular microenvironment, we propose a compact, but flexible concept for space-related cell biological research that is based on light sheet microscopy.

  9. Invited review article: Advanced light microscopy for biological space research.

    PubMed

    De Vos, Winnok H; Beghuin, Didier; Schwarz, Christian J; Jones, David B; van Loon, Jack J W A; Bereiter-Hahn, Juergen; Stelzer, Ernst H K

    2014-10-01

    As commercial space flights have become feasible and long-term extraterrestrial missions are planned, it is imperative that the impact of space travel and the space environment on human physiology be thoroughly characterized. Scrutinizing the effects of potentially detrimental factors such as ionizing radiation and microgravity at the cellular and tissue level demands adequate visualization technology. Advanced light microscopy (ALM) is the leading tool for non-destructive structural and functional investigation of static as well as dynamic biological systems. In recent years, technological developments and advances in photochemistry and genetic engineering have boosted all aspects of resolution, readout and throughput, rendering ALM ideally suited for biological space research. While various microscopy-based studies have addressed cellular response to space-related environmental stressors, biological endpoints have typically been determined only after the mission, leaving an experimental gap that is prone to bias results. An on-board, real-time microscopical monitoring device can bridge this gap. Breadboards and even fully operational microscope setups have been conceived, but they need to be rendered more compact and versatile. Most importantly, they must allow addressing the impact of gravity, or the lack thereof, on physiologically relevant biological systems in space and in ground-based simulations. In order to delineate the essential functionalities for such a system, we have reviewed the pending questions in space science, the relevant biological model systems, and the state-of-the art in ALM. Based on a rigorous trade-off, in which we recognize the relevance of multi-cellular systems and the cellular microenvironment, we propose a compact, but flexible concept for space-related cell biological research that is based on light sheet microscopy.

  10. Invited Review Article: Advanced light microscopy for biological space research

    NASA Astrophysics Data System (ADS)

    De Vos, Winnok H.; Beghuin, Didier; Schwarz, Christian J.; Jones, David B.; van Loon, Jack J. W. A.; Bereiter-Hahn, Juergen; Stelzer, Ernst H. K.

    2014-10-01

    As commercial space flights have become feasible and long-term extraterrestrial missions are planned, it is imperative that the impact of space travel and the space environment on human physiology be thoroughly characterized. Scrutinizing the effects of potentially detrimental factors such as ionizing radiation and microgravity at the cellular and tissue level demands adequate visualization technology. Advanced light microscopy (ALM) is the leading tool for non-destructive structural and functional investigation of static as well as dynamic biological systems. In recent years, technological developments and advances in photochemistry and genetic engineering have boosted all aspects of resolution, readout and throughput, rendering ALM ideally suited for biological space research. While various microscopy-based studies have addressed cellular response to space-related environmental stressors, biological endpoints have typically been determined only after the mission, leaving an experimental gap that is prone to bias results. An on-board, real-time microscopical monitoring device can bridge this gap. Breadboards and even fully operational microscope setups have been conceived, but they need to be rendered more compact and versatile. Most importantly, they must allow addressing the impact of gravity, or the lack thereof, on physiologically relevant biological systems in space and in ground-based simulations. In order to delineate the essential functionalities for such a system, we have reviewed the pending questions in space science, the relevant biological model systems, and the state-of-the art in ALM. Based on a rigorous trade-off, in which we recognize the relevance of multi-cellular systems and the cellular microenvironment, we propose a compact, but flexible concept for space-related cell biological research that is based on light sheet microscopy.

  11. 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

    NASA Technical Reports Server (NTRS)

    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

  12. openBIS: a flexible framework for managing and analyzing complex data in biology research

    PubMed Central

    2011-01-01

    Background Modern data generation techniques used in distributed systems biology research projects often create datasets of enormous size and diversity. We argue that in order to overcome the challenge of managing those large quantitative datasets and maximise the biological information extracted from them, a sound information system is required. Ease of integration with data analysis pipelines and other computational tools is a key requirement for it. Results We have developed openBIS, an open source software framework for constructing user-friendly, scalable and powerful information systems for data and metadata acquired in biological experiments. openBIS enables users to collect, integrate, share, publish data and to connect to data processing pipelines. This framework can be extended and has been customized for different data types acquired by a range of technologies. Conclusions openBIS is currently being used by several SystemsX.ch and EU projects applying mass spectrometric measurements of metabolites and proteins, High Content Screening, or Next Generation Sequencing technologies. The attributes that make it interesting to a large research community involved in systems biology projects include versatility, simplicity in deployment, scalability to very large data, flexibility to handle any biological data type and extensibility to the needs of any research domain. PMID:22151573

  13. A versatile computer-controlled biological stimulus sequencer.

    PubMed

    Boyechko, G; Bose, D

    1984-08-01

    A computer-controlled stimulus sequencer has been developed. This device can be controlled by several commonly available, inexpensive 8-bit microcomputers in which the address, data, and control lines are externally accessible. Although the Apple implementation has been described, a similar interface has also been devised for the Radio Shack Color Computer. The hardware relies on the Rockwell Versatile Interface Adapter (VIA) chip (which has two 16-bit timers capable of functioning as frequency dividers, event counters, or one-shots) and a 12-bit digital-to-analog converter (DAC) chip. This hardware combination, along with software written in Basic and machine language (stored in an EPROM for turn-key operation), allows creation of a large number of unique trains that can be chained together in any sequence. This is aided by storing the train characteristics economically in the computer memory and chaining different train parameters in a link-list. Several train parameters can be incremented or decremented manually by a pair of keys. The amplitude of the train can be changed manually or under program control. Once created, the trains can be edited on the run or deleted from the sequence. The device also generates a trigger pulse that can be referenced to any pulse in a train and can be used to pretrigger an oscilloscope. The software has provision for detecting an external signal, and this information can be used to modify train parameters. The interface is interrupt driven and therefore does not require continuous use of the Basic interpreter.(ABSTRACT TRUNCATED AT 250 WORDS)

  14. Wired Students: Computer-Assisted Research and Education.

    ERIC Educational Resources Information Center

    Kawamoto, Kevin

    1994-01-01

    Discussion of library automation and changes in research methodology focuses on computer-assisted research curricula. Topics addressed include public access to government information; the information superhighway; commercialization of government documents that may restrict public access; computer literacy; and a proposed curriculum plan for a…

  15. Computational systems biology approaches to anti-angiogenic cancer therapeutics.

    PubMed

    Finley, Stacey D; Chu, Liang-Hui; Popel, Aleksander S

    2015-02-01

    Angiogenesis is an exquisitely regulated process that is required for physiological processes and is also important in numerous diseases. Tumors utilize angiogenesis to generate the vascular network needed to supply the cancer cells with nutrients and oxygen, and many cancer drugs aim to inhibit tumor angiogenesis. Anti-angiogenic therapy involves inhibiting multiple cell types, molecular targets, and intracellular signaling pathways. Computational tools are useful in guiding treatment strategies, predicting the response to treatment, and identifying new targets of interest. Here, we describe progress that has been made in applying mathematical modeling and bioinformatics approaches to study anti-angiogenic therapeutics in cancer.

  16. Computer architectures for computational physics work done by Computational Research and Technology Branch and Advanced Computational Concepts Group

    NASA Technical Reports Server (NTRS)

    1985-01-01

    Slides are reproduced that describe the importance of having high performance number crunching and graphics capability. They also indicate the types of research and development underway at Ames Research Center to ensure that, in the near term, Ames is a smart buyer and user, and in the long-term that Ames knows the best possible solutions for number crunching and graphics needs. The drivers for this research are real computational physics applications of interest to Ames and NASA. They are concerned with how to map the applications, and how to maximize the physics learned from the results of the calculations. The computer graphics activities are aimed at getting maximum information from the three-dimensional calculations by using the real time manipulation of three-dimensional data on the Silicon Graphics workstation. Work is underway on new algorithms that will permit the display of experimental results that are sparse and random, the same way that the dense and regular computed results are displayed.

  17. The Colorado Plateau: cultural, biological, and physical research

    USGS Publications Warehouse

    Cole, Kenneth L.; van Riper, Charles

    2004-01-01

    Stretching from the four corners of Arizona, New Mexico, Colorado, and Utah, the Colorado Plateau is a natural laboratory for a wide range of studies. This volume presents 23 original articles drawn from more than 100 research projects presented at the Sixth Biennial Conference of Research on the Colorado Plateau. This scientific gathering revolved around research, inventory, and monitoring of lands in the region. The book's contents cover management techniques for cultural, biological, and physical resources, representing collaborative efforts among federal, university, and private sector scientists and land managers. Chapters on cultural concerns cover benchmarks of modern southwestern anthropological knowledge, models of past human activity and impact of modern visitation at newly established national monuments, challenges in implementing the 1964 Wilderness Act, and opportunities for increased federal research on Native American lands. The section on biological resources comprises sixteen chapters, with coverage that ranges from mammalian biogeography to responses of elk at the urban-wildland interface. Additional biological studies include the effects of fire and grazing on vegetation; research on bald eagles at Grand Canyon and tracking wild turkeys using radio collars; and management of palentological resources. Two final chapters on physical resources consider a proposed rerouting of the Rio de Flag River in urban Flagstaff, Arizona, and an examination of past climate patterns over the Plateau, using stream flow records and tree ring data. In light of similarities in habitat and climate across the Colorado Plateau, techniques useful to particular management units have been found to be applicable in many locations. This volume highlights an abundance of research that will prove useful for all of those working in the region, as well as for others seeking comparative studies that integrate research into land management actions.

  18. Activation of PPARδ: from computer modelling to biological effects

    PubMed Central

    Kahremany, Shirin; Livne, Ariela; Gruzman, Arie; Senderowitz, Hanoch; Sasson, Shlomo

    2015-01-01

    PPARδ is a ligand-activated receptor that dimerizes with another nuclear receptor of the retinoic acid receptor family. The dimers interact with other co-activator proteins and form active complexes that bind to PPAR response elements and promote transcription of genes involved in lipid metabolism. It appears that various natural fatty acids and their metabolites serve as endogenous activators of PPARδ; however, there is no consensus in the literature on the nature of the prime activators of the receptor. In vitro and cell-based assays of PPARδ activation by fatty acids and their derivatives often produce conflicting results. The search for synthetic and selective PPARδ agonists, which may be pharmacologically useful, is intense. Current rational modelling used to obtain such compounds relies mostly on crystal structures of synthetic PPARδ ligands with the recombinant ligand binding domain (LBD) of the receptor. Here, we introduce an original computational prediction model for ligand binding to PPARδ LBD. The model was built based on EC50 data of 16 ligands with available crystal structures and validated by calculating binding probabilities of 82 different natural and synthetic compounds from the literature. These compounds were independently tested in cell-free and cell-based assays for their capacity to bind or activate PPARδ, leading to prediction accuracy of between 70% and 93% (depending on ligand type). This new computational tool could therefore be used in the search for natural and synthetic agonists of the receptor. PMID:25255770

  19. Chaste: An Open Source C++ Library for Computational Physiology and Biology

    PubMed Central

    Mirams, Gary R.; Arthurs, Christopher J.; Bernabeu, Miguel O.; Bordas, Rafel; Cooper, Jonathan; Corrias, Alberto; Davit, Yohan; Dunn, Sara-Jane; Fletcher, Alexander G.; Harvey, Daniel G.; Marsh, Megan E.; Osborne, James M.; Pathmanathan, Pras; Pitt-Francis, Joe; Southern, James; Zemzemi, Nejib; Gavaghan, David J.

    2013-01-01

    Chaste — Cancer, Heart And Soft Tissue Environment — is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high-performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to ‘re-invent the wheel’ with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials. PMID:23516352

  20. Facilities for Biological Research Aboard the International Space Station

    NASA Technical Reports Server (NTRS)

    Souza, Kenneth A.; Yost, Bruce D.; Berry, William E.; Johnson, Catherine C.

    1996-01-01

    A centrifuge designed as part of an integrated biological facility for installation onboard the International Space Station is presented. The requirements for the 2.5 m diameter centrifuge, which is designed for the support of biological experiments are discussed. The scientific objectives of the facility are to: provide a means of conducting fundamental studies in which gravitational acceleration is a controllable variable; provide a 1g control; determine the threshold acceleration for physiological response, and determine the value of centrifugation as a potential countermeasure for the biomedical problems associated with space flight. The implementation of the facility is reported on, and the following aspects of the facility are described: the host resources systems supply requirements such as power and data control; the habitat holding rack; the life sciences glove box; the centrifuge; the different habitats for cell culture, aquatic studies, plant research and insect research; the egg incubator, and the laboratory support equipment.

  1. Re-Centering the Research Computing Enterprise

    ERIC Educational Resources Information Center

    McRobbie, Michael A.

    2006-01-01

    The insatiable institutional demands for computing cycles, network bandwidth, and storage clearly demonstrate that IT is a mission-critical function in nearly all areas of higher education. Not too long ago, the important issue for the central data center was physical size and floor space. As IT leaders struggle to meet relentlessly increasing…

  2. Managing computer security: How can research help

    SciTech Connect

    Bailey, D.J.

    1990-01-01

    This paper points out significant problems in managing the security of large systems. Addressed to the research community, it suggests research questions whose solution would benefit the people charged with protecting actual systems, and, hence, would create real improvements in system security. The problems of managing connection-rich distributed systems are discussed, and a research direction leading to a solution for the problems of distributed systems is suggested.

  3. BRIC-60: Biological Research in Canisters (BRIC)-60

    NASA Technical Reports Server (NTRS)

    Richards, Stephanie E. (Compiler); Levine, Howard G.; Romero, Vergel

    2016-01-01

    The Biological Research in Canisters (BRIC) is an anodized-aluminum cylinder used to provide passive stowage for investigations evaluating the effects of space flight on small organisms. Specimens flown in the BRIC 60 mm petri dish (BRIC-60) hardware include Lycoperscion esculentum (tomato), Arabidopsis thaliana (thale cress), Glycine max (soybean) seedlings, Physarum polycephalum (slime mold) cells, Pothetria dispar (gypsy moth) eggs and Ceratodon purpureus (moss).

  4. Computational biology approach to uncover hepatitis C virus helicase operation.

    PubMed

    Flechsig, Holger

    2014-04-01

    Hepatitis C virus (HCV) helicase is a molecular motor that splits nucleic acid duplex structures during viral replication, therefore representing a promising target for antiviral treatment. Hence, a detailed understanding of the mechanism by which it operates would facilitate the development of efficient drug-assisted therapies aiming to inhibit helicase activity. Despite extensive investigations performed in the past, a thorough understanding of the activity of this important protein was lacking since the underlying internal conformational motions could not be resolved. Here we review investigations that have been previously performed by us for HCV helicase. Using methods of structure-based computational modelling it became possible to follow entire operation cycles of this motor protein in structurally resolved simulations and uncover the mechanism by which it moves along the nucleic acid and accomplishes strand separation. We also discuss observations from that study in the light of recent experimental studies that confirm our findings.

  5. Computational biology approach to uncover hepatitis C virus helicase operation

    PubMed Central

    Flechsig, Holger

    2014-01-01

    Hepatitis C virus (HCV) helicase is a molecular motor that splits nucleic acid duplex structures during viral replication, therefore representing a promising target for antiviral treatment. Hence, a detailed understanding of the mechanism by which it operates would facilitate the development of efficient drug-assisted therapies aiming to inhibit helicase activity. Despite extensive investigations performed in the past, a thorough understanding of the activity of this important protein was lacking since the underlying internal conformational motions could not be resolved. Here we review investigations that have been previously performed by us for HCV helicase. Using methods of structure-based computational modelling it became possible to follow entire operation cycles of this motor protein in structurally resolved simulations and uncover the mechanism by which it moves along the nucleic acid and accomplishes strand separation. We also discuss observations from that study in the light of recent experimental studies that confirm our findings. PMID:24707123

  6. Experimental Data from the Proteomics Research Center for Integrative Biology

    DOE Data Explorer

    Smith, Richard D.

    The possible roles and importance of proteomics are rapidly growing across essentially all areas of biological research. The precise and comprehensive measurement of levels of expressed proteins and their modified forms can provide new insights into the molecular nature of cell-signaling pathways and networks, the cell cycle, cellular differentiation, and other processes relevant to understanding human health and the progression of various disease states. The ability to characterize protein complexes complements this capability, allowing hypotheses to be tested and the biological system operation to be defined. The Proteomics Research Center for Integrative Biology is a national user facility established and funded by the National Institute of General Medical Sciences component of the National Institutes of Health. This Center has been established to serve the biomedical research community by developing and integrating new proteomic technologies for collaborative and service studies, disseminating the new technologies, and training scientists in their use. The Center is housed in DOE’s William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory.

  7. Space Station Freedom: a unique laboratory for gravitational biology research

    NASA Technical Reports Server (NTRS)

    Phillips, R. W.; Cowing, K. L.

    1993-01-01

    The advent of Space Station Freedom (SSF) will provide a permanent laboratory in space with unparalleled opportunities to perform biological research. As with any spacecraft there will also be limitations. It is our intent to describe this space laboratory and present a picture of how scientists will conduct research in this unique environment we call space. SSF is an international venture which will continue to serve as a model for other peaceful international efforts. It is hoped that as the human race moves out from this planet back to the moon and then on to Mars that SSF can serve as a successful example of how things can and should be done.

  8. Biological and chemical technologies research. FY 1995 annual summary report

    SciTech Connect

    1996-03-01

    The annual summary report presents the fiscal year (FY) 1995 research activities and accomplishments for the United States Department of Energy (DOE) Biological and Chemical Technologies Research (BCTR) Program. This BCTR program resides within the Office of Industrial Technologies (OIT) of the Office of Energy Efficiency and Renewable Energy (EE). The annual summary report for 1995 (ASR 95) contains the following: program description (including BCTR program mission statement, historical background, relevance, goals and objectives); program structure and organization, selected technical and programmatic highlights for 1995; detailed descriptions of individual projects; a listing of program output, including a bibliography of published work; patents; and awards arising from work supported by the BCTR.

  9. An ecological perspective on research with computers in science education

    NASA Astrophysics Data System (ADS)

    Brown, Mark

    1992-12-01

    This paper presents an “ecological perspective” on research with computers in science education. It is proposed that current and past research within the computer education field has been characterised by an over-emphasis on technical applications of the machinery, rather than a deeper consideration of the teaching and learning process. This tendency toward “technocentric thinking” has usually failed to take into account the important social and cognitive interactions within the computer learning environment. The view advanced here, is that an understanding of the effects of computers on students' learning can be achieved only through an analysis of the dynamic interactions between students and teachers as they work with computers in a particular environment. A theoretical framework for understanding this range of interactions is presented. Finally, an ecological model is proposed for conducting future research on the application of computers in science education.

  10. Division of Biological and Medical Research annual technical report, 1981

    SciTech Connect

    Rosenthal, M.W.

    1982-06-01

    This report summarizes research during 1981 in the Division of Biological and Medical Research, Argonne National Laboratory. Studies in Low Level Radiation include comparison of lifetime effects in mice of low level neutron and gamma irradiation, delineation of the responses of dogs to continuous low level gamma irradiation, elucidation of mechanisms of radiation damage and repair in mammalian cells, and study of the genetic effects of high LET radiations. Carcinogenesis research addresses mechanisms of tumor initiation and promotion in rat liver, chemical carcinogenesis in cultured mammalian cells, and molecular and genetic mechanisms of chemical and ultraviolet mutagenesis in bacteria. Research in Toxicology uses a variety of cellular, whole animal, and chronobiological end points, chemical separations, and statistical models to evaluate the hazards and mechanisms of actions of metals, coal gasification by products, and other energy-related pollutants. Human Protein Index studies develop two-dimensional electrophoresis systems for diagnosis and detection of cancer and other disease. Biophysics research includes fundamental structural and biophysical investigations of immunoglobulins and key biological molecules using NMR, crystallographic, and x-ray and neutron small-angle scattering techniques. The final sections cover support facilities, educational activities, seminars, staff talks, staff, and funding agencies.

  11. Open-Source Software in Computational Research: A Case Study

    DOE PAGES

    Syamlal, Madhava; O'Brien, Thomas J.; Benyahia, Sofiane; Gel, Aytekin; Pannala, Sreekanth

    2008-01-01

    A case study of open-source (OS) development of the computational research software MFIX, used for multiphase computational fluid dynamics simulations, is presented here. The verification and validation steps required for constructing modern computational software and the advantages of OS development in those steps are discussed. The infrastructure used for enabling the OS development of MFIX is described. The impact of OS development on computational research and education in gas-solids flow, as well as the dissemination of information to other areas such as geophysical and volcanology research, is demonstrated. This study shows that the advantages of OS development were realized inmore » the case of MFIX: verification by many users, which enhances software quality; the use of software as a means for accumulating and exchanging information; the facilitation of peer review of the results of computational research.« less

  12. Division of Biological and Medical Research research summary 1984-1985

    SciTech Connect

    Barr, S.H.

    1985-08-01

    The Division of Biological and Medical Research at Argonne National Laboratory conducts multidisciplinary research aimed at defining the biological and medical hazards to man from energy technologies and new energy options. These technically oriented studies have a strong base in fundamental research in a variety of scientific disciplines, including molecular and cellular biology, biophysics, genetics, radiobiology, pharmacology, biochemistry, chemistry, environmental toxicology, and epidemiology. This research summary is organized into six parts. The first five parts reflect the Divisional structure and contain the scientific program chapters, which summarize the activities of the individual groups during the calendar year 1984 and the first half of 1985. To provide better continuity and perspective, previous work is sometimes briefly described. Although the summaries are short, efforts have been made to indicate the range of research activities for each group.

  13. Multiscale computational models in physical systems biology of intracellular trafficking

    PubMed Central

    Tourdot, Richard W.; Bradley, Ryan P.; Ramakrishnan, Natesan

    2015-01-01

    In intracellular trafficking, a definitive understanding of the interplay between protein binding and membrane morphology remains incomplete. The authors describe a computational approach by integrating coarse-grained molecular dynamics (CGMD) simulations with continuum Monte Carlo (CM) simulations of the membrane to study protein–membrane interactions and the ensuing membrane curvature. They relate the curvature field strength discerned from the molecular level to its effect at the cellular length-scale. They perform thermodynamic integration on the CM model to describe the free energy landscape of vesiculation in clathrin-mediated endocytosis. The method presented here delineates membrane morphologies and maps out the free energy changes associated with membrane remodeling due to varying coat sizes, coat curvature strengths, membrane bending rigidities, and tensions; furthermore several constraints on mechanisms underlying clathrin-mediated endocytosis have also been identified, Their CGMD simulations have revealed the importance of PIP2 for stable binding of proteins essential for curvature induction in the bilayer and have provided a molecular basis for the positive curvature induction by the epsin N-terminal homology (EIMTH) domain. Calculation of the free energy landscape for vesicle budding has identified the critical size and curvature strength of a clathrin coat required for nucleation and stabilisation of a mature vesicle. PMID:25257021

  14. Impact of Interdisciplinary Undergraduate Research in mathematics and biology on the development of a new course integrating five STEM disciplines.

    PubMed

    Caudill, Lester; Hill, April; Hoke, Kathy; Lipan, Ovidiu

    2010-01-01

    Funded by innovative programs at the National Science Foundation and the Howard Hughes Medical Institute, University of Richmond faculty in biology, chemistry, mathematics, physics, and computer science teamed up to offer first- and second-year students the opportunity to contribute to vibrant, interdisciplinary research projects. The result was not only good science but also good science that motivated and informed course development. Here, we describe four recent undergraduate research projects involving students and faculty in biology, physics, mathematics, and computer science and how each contributed in significant ways to the conception and implementation of our new Integrated Quantitative Science course, a course for first-year students that integrates the material in the first course of the major in each of biology, chemistry, mathematics, computer science, and physics.

  15. National Energy Research Scientific Computing Center (NERSC): Advancing the frontiers of computational science and technology

    SciTech Connect

    Hules, J.

    1996-11-01

    National Energy Research Scientific Computing Center (NERSC) provides researchers with high-performance computing tools to tackle science`s biggest and most challenging problems. Founded in 1974 by DOE/ER, the Controlled Thermonuclear Research Computer Center was the first unclassified supercomputer center and was the model for those that followed. Over the years the center`s name was changed to the National Magnetic Fusion Energy Computer Center and then to NERSC; it was relocated to LBNL. NERSC, one of the largest unclassified scientific computing resources in the world, is the principal provider of general-purpose computing services to DOE/ER programs: Magnetic Fusion Energy, High Energy and Nuclear Physics, Basic Energy Sciences, Health and Environmental Research, and the Office of Computational and Technology Research. NERSC users are a diverse community located throughout US and in several foreign countries. This brochure describes: the NERSC advantage, its computational resources and services, future technologies, scientific resources, and computational science of scale (interdisciplinary research over a decade or longer; examples: combustion in engines, waste management chemistry, global climate change modeling).

  16. Computer science security research and human subjects: emerging considerations for research ethics boards.

    PubMed

    Buchanan, Elizabeth; Aycock, John; Dexter, Scott; Dittrich, David; Hvizdak, Erin

    2011-06-01

    This paper explores the growing concerns with computer science research, and in particular, computer security research and its relationship with the committees that review human subjects research. It offers cases that review boards are likely to confront, and provides a context for appropriate consideration of such research, as issues of bots, clouds, and worms enter the discourse of human subjects review.

  17. Computer-Assisted Microscopy in Science Teaching and Research.

    ERIC Educational Resources Information Center

    Radice, Gary P.

    1997-01-01

    Describes a technological approach to teaching the relationships between biological form and function. Computer-assisted image analysis was integrated into a microanatomy course. Students spend less time memorizing and more time observing, measuring, and interpreting, building technical and analytical skills. Appendices list hardware and software…

  18. [Activities of Research Institute for Advanced Computer Science

    NASA Technical Reports Server (NTRS)

    Gross, Anthony R. (Technical Monitor); Leiner, Barry M.

    2001-01-01

    The Research Institute for Advanced Computer Science (RIACS) carries out basic research and technology development in computer science, in support of the National Aeronautics and Space Administrations missions. RIACS is located at the NASA Ames Research Center, Moffett Field, California. RIACS research focuses on the three cornerstones of IT research necessary to meet the future challenges of NASA missions: 1. Automated Reasoning for Autonomous Systems Techniques are being developed enabling spacecraft that will be self-guiding and self-correcting to the extent that they will require little or no human intervention. Such craft will be equipped to independently solve problems as they arise, and fulfill their missions with minimum direction from Earth. 2. Human-Centered Computing Many NASA missions require synergy between humans and computers, with sophisticated computational aids amplifying human cognitive and perceptual abilities. 3. High Performance Computing and Networking Advances in the performance of computing and networking continue to have major impact on a variety of NASA endeavors, ranging from modeling and simulation to analysis of large scientific datasets to collaborative engineering, planning and execution. In addition, RIACS collaborates with NASA scientists to apply IT research to a variety of NASA application domains. RIACS also engages in other activities, such as workshops, seminars, visiting scientist programs and student summer programs, designed to encourage and facilitate collaboration between the university and NASA IT research communities.

  19. Division of Biological and Medical Research annual technical report 1982

    SciTech Connect

    Rosenthal, M.W.

    1983-05-01

    This report summarizes research during 1982 in the Division of Biological and Medical Research, Argonne National Laboratory. Studies in Carcinogenesis address mechanisms of chemical and radiation carcinogenesis including the processes of tumor initiation and promotion. The studies employ rat liver and mouse skin models as well as human rodent cell culture systems. The use of liposomes for metal mobilization is also explored. Low Level Radiation studies include delineation of the hematopoietic and other responses of dogs to continuous low level gamma irradiation, comparison of lifetime effects in mice of low level neutron and gamma irradiation, and study of the genetic effects of high LET radiation. Molecular Biology research develops two-dimensional electrophoresis systems for diagnosis and detection of cancer and other diseases. Fundamental structural and biophysical investigations of immunoglobulins and other key proteins are included, as are studies of cell growth, and of molecular and cellular effects of solar uv light. Research in Toxicology uses cellular, physiological, whole animal, and chronobiological end points and chemical separations to elucidate mechanisms and evaluate hazards of coal conversion by-products, actinides, and toxic metals. The final sections cover support facilities, educational activities, seminars, staff talks, staff, and funding agencies.

  20. Persistence and availability of Web services in computational biology.

    PubMed

    Schultheiss, Sebastian J; Münch, Marc-Christian; Andreeva, Gergana D; Rätsch, Gunnar

    2011-01-01

    We have conducted a study on the long-term availability of bioinformatics Web services: an observation of 927 Web services published in the annual Nucleic Acids Research Web Server Issues between 2003 and 2009. We found that 72% of Web sites are still available at the published addresses, only 9% of services are completely unavailable. Older addresses often redirect to new pages. We checked the functionality of all available services: for 33%, we could not test functionality because there was no example data or a related problem; 13% were truly no longer working as expected; we could positively confirm functionality only for 45% of all services. Additionally, we conducted a survey among 872 Web Server Issue corresponding authors; 274 replied. 78% of all respondents indicate their services have been developed solely by students and researchers without a permanent position. Consequently, these services are in danger of falling into disrepair after the original developers move to another institution, and indeed, for 24% of services, there is no plan for maintenance, according to the respondents. We introduce a Web service quality scoring system that correlates with the number of citations: services with a high score are cited 1.8 times more often than low-scoring services. We have identified key characteristics that are predictive of a service's survival, providing reviewers, editors, and Web service developers with the means to assess or improve Web services. A Web service conforming to these criteria receives more citations and provides more reliable service for its users. The most effective way of ensuring continued access to a service is a persistent Web address, offered either by the publishing journal, or created on the authors' own initiative, for example at http://bioweb.me. The community would benefit the most from a policy requiring any source code needed to reproduce results to be deposited in a public repository.

  1. Persistence and availability of Web services in computational biology.

    PubMed

    Schultheiss, Sebastian J; Münch, Marc-Christian; Andreeva, Gergana D; Rätsch, Gunnar

    2011-01-01

    We have conducted a study on the long-term availability of bioinformatics Web services: an observation of 927 Web services published in the annual Nucleic Acids Research Web Server Issues between 2003 and 2009. We found that 72% of Web sites are still available at the published addresses, only 9% of services are completely unavailable. Older addresses often redirect to new pages. We checked the functionality of all available services: for 33%, we could not test functionality because there was no example data or a related problem; 13% were truly no longer working as expected; we could positively confirm functionality only for 45% of all services. Additionally, we conducted a survey among 872 Web Server Issue corresponding authors; 274 replied. 78% of all respondents indicate their services have been developed solely by students and researchers without a permanent position. Consequently, these services are in danger of falling into disrepair after the original developers move to another institution, and indeed, for 24% of services, there is no plan for maintenance, according to the respondents. We introduce a Web service quality scoring system that correlates with the number of citations: services with a high score are cited 1.8 times more often than low-scoring services. We have identified key characteristics that are predictive of a service's survival, providing reviewers, editors, and Web service developers with the means to assess or improve Web services. A Web service conforming to these criteria receives more citations and provides more reliable service for its users. The most effective way of ensuring continued access to a service is a persistent Web address, offered either by the publishing journal, or created on the authors' own initiative, for example at http://bioweb.me. The community would benefit the most from a policy requiring any source code needed to reproduce results to be deposited in a public repository. PMID:21966383

  2. Recent Developments in the Application of Biologically Inspired Computation to Chemical Sensing

    NASA Astrophysics Data System (ADS)

    Marco, S.; Gutierrez-Gálvez, A.

    2009-05-01

    Biological olfaction outperforms chemical instrumentation in specificity, response time, detection limit, coding capacity, time stability, robustness, size, power consumption, and portability. This biological function provides outstanding performance due, to a large extent, to the unique architecture of the olfactory pathway, which combines a high degree of redundancy, an efficient combinatorial coding along with unmatched chemical information processing mechanisms. The last decade has witnessed important advances in the understanding of the computational primitives underlying the functioning of the olfactory system. In this work, the state of the art concerning biologically inspired computation for chemical sensing will be reviewed. Instead of reviewing the whole body of computational neuroscience of olfaction, we restrict this review to the application of models to the processing of real chemical sensor data.

  3. Biologically Weighted Quantities in Radiotherapy: an EMRP Joint Research Project

    NASA Astrophysics Data System (ADS)

    Rabus, Hans; Palmans, Hugo; Hilgers, Gerhard; Sharpe, Peter; Pinto, Massimo; Villagrasa, Carmen; Nettelbeck, Heidi; Moro, Davide; Pola, Andrea; Pszona, Stanislaw; Teles, Pedro

    2014-08-01

    Funded within the European Metrology Research Programme (EMRP) [1], the joint research project "Biologically weighted quantities in radiotherapy" (BioQuaRT) [2] aims to develop measurement and simulation techniques for determining the physical properties of ionising particle tracks on different length scales (about 2 nm to 10 μm), and to investigate the correlation of these track structure characteristics with the biological effects of radiation at the cellular level. Work package 1 develops micro-calorimeter prototypes for the direct measurement of lineal energy and will characterise their response for different ion beams by experiment and modelling. Work package 2 develops techniques to measure particle track structure on different length scales in the nanometre range as well as a measurement device integrating a silicon microdosimeter and a nanodosimeter. Work package 3 investigates the indirect effects of radiation based on probes for quantifying particular radical and reactive oxygen species (ROS). Work package 4 focuses on the biological aspects of radiation damage and will produce data on initial DNA damage and late effects for radiotherapy beams of different qualities. Work package 5 provides evaluated data sets of DNA cross-sections and develops a multi-scale model to address microscopic and nanometric track structure properties. The project consortium includes three linked researchers holding so-called Researcher Excellence Grants, who carry out ancillary investigations such as developing and benchmarking a new biophysical model for induction of early radiation damage and developing methods for the translation of quantities derived from particle track structure to clinical applications in ion beam therapy.

  4. An African Research Agenda for Computers in Education

    ERIC Educational Resources Information Center

    Cronje, Johannes

    2014-01-01

    This article presents an overview of research into computers and education undertaken at a the University of Pretoria since 1995. It seeks to explore the patterns that have emerged and to indicate potential directions for future research. In response to a call for research in the field to be taken seriously the article identifies the main themes…

  5. A Methodological Review of Computer Science Education Research

    ERIC Educational Resources Information Center

    Randolph, Justus; Julnes, George; Sutinen, Erkki; Lehman, Steve

    2008-01-01

    Methodological reviews have been used successfully to identify research trends and improve research practice in a variety of academic fields. Although there have been three methodological reviews of the emerging field of computer science education research, they lacked reliability or generalizability. Therefore, because of the capacity for a…

  6. Educational Technology Research Journals: Computers & Education, 2002-2011

    ERIC Educational Resources Information Center

    Rackham, David D.; Hyatt, Frederick R.; Macfarlane, David C.; Nisse, Tony; Woodfield, Wendy; West, Richard E.

    2013-01-01

    In this study, the authors examined the journal "Computers & Education" to discover research trends in the articles published during 2002-2011. Research articles were analyzed to determine trends in the research methods and types of articles published, as well as the key topics published, top authors, and some of the most-cited…

  7. Fiction as an Introduction to Computer Science Research

    ERIC Educational Resources Information Center

    Goldsmith, Judy; Mattei, Nicholas

    2014-01-01

    The undergraduate computer science curriculum is generally focused on skills and tools; most students are not exposed to much research in the field, and do not learn how to navigate the research literature. We describe how fiction reviews (and specifically science fiction) are used as a gateway to research reviews. Students learn a little about…

  8. Life lines: An art history of biological research around 1800.

    PubMed

    Bruhn, Matthias

    2011-12-01

    Around 1800, the scientific "illustrator" emerged as a new artistic profession in Europe. Artists were increasingly sought after in order to picture anatomical dissections and microscopic observations and to translate drawings into artworks for books and journals. By training and technical expertise, they introduced a particular kind of knowledge into scientific perception that also shaped the common image of nature. Illustrations of scientific publications, often undervalued as a biased interpretation of facts and subordinate to logic and description, thus convey an 'art history' of science in its own right, relevant both for the understanding of biological thought around 1800 as well as for the development of the arts and their historiography. The article is based on an analysis of botanical treatises produced for the Göttingen Society of Sciences in 1803, during an early phase of microscopic cell research, in order to determine the constitutive role of artistic knowledge and the media employed for the visualization and conceptualization of biological issues.

  9. Electrical and chemical sensors for biological cell research

    NASA Astrophysics Data System (ADS)

    Edell, D. J.; McNeil, V. M.; Curley, M. G.; Wolfe, J. H.

    Electrical and chemical microsensors for biological cell research allow for the continuous study of biological systems under normal physiological conditions. Two sensor technologies which take most advantage of microfabrication technology are discussed. One is being developed for monitoring the environment of cancer cells during radiotherapy, chemotherapy, and hyperthermia treatment. Of current interest is the measurement of temperature and interstitial free oxygen concentration distributions in cancer tissues prior to and during various treatments. The second technology discussed is being developed for monitoring the extracellular ionic currents from electrogenic cells in culture. The ability to build integrated circuits over large areas of a silicon wafer which can impedance transform the signals and multiplex a large array of contacts is being used.

  10. Integrating -Omics: Systems Biology as Explored Through C. elegans Research.

    PubMed

    Van Assche, Roel; Broeckx, Valérie; Boonen, Kurt; Maes, Evelyne; De Haes, Wouter; Schoofs, Liliane; Temmerman, Liesbet

    2015-10-23

    -Omics data have become indispensable to systems biology, which aims to describe the full complexity of functional cells, tissues, organs and organisms. Generating vast amounts of data via such methods, researchers have invested in ways of handling and interpreting these. From the large volumes of -omics data that have been gathered over the years, it is clear that the information derived from one -ome is usually far from complete. Now, individual techniques and methods for integration are maturing to the point that researchers can focus on network-based integration rather than simply interpreting single -ome studies. This review evaluates the application of integrated -omics approaches with a focus on Caenorhabditis elegans studies, intending to direct researchers in this field to useful databases and inspiring examples.

  11. A Computational Lens on Design Research

    ERIC Educational Resources Information Center

    Hoyles, Celia; Noss, Richard

    2015-01-01

    In this commentary, we briefly review the collective effort of design researchers to weave theory with empirical results, in order to gain a better understanding of the processes of learning. We seek to respond to this challenging agenda by centring on the evolution of one sub-field: namely that which involves investigations within a…

  12. Computing & Interpreting Effect Sizes in Educational Research

    ERIC Educational Resources Information Center

    Thompson, Bruce

    2009-01-01

    The present article provides a primer on using effect sizes in research. A small heuristic data set is used in order to make the discussion concrete. Additionally, various admonitions for best practice in reporting and interpreting effect sizes are presented. Among these is the admonition to not use Cohen's benchmarks for "small," "medium," and…

  13. Library Online! A Guide to Computer Research.

    ERIC Educational Resources Information Center

    Turrell, Linda

    The world of electronic technology is opening up vast new opportunities for learning, gathering, and sharing information. This guide is for teachers and students in grades 4-8 to learn how to use electronic tools to conduct research to find information at school or around the world. The guide includes introductory pages for each topic, student…

  14. Computers and Writing: The Research Says YES!

    ERIC Educational Resources Information Center

    Patterson, Nancy

    2006-01-01

    Word processing continues to be the focus in many classrooms, although more and more teachers now ask students to publish on the Web, engage in e-mail conversations regarding their reading and writing, create slide presentations that represent their learning, post to blog sites, etc. And while there is a growing body of research that supports…

  15. Quantifying reproducibility in computational biology: the case of the tuberculosis drugome.

    PubMed

    Garijo, Daniel; Kinnings, Sarah; Xie, Li; Xie, Lei; Zhang, Yinliang; Bourne, Philip E; Gil, Yolanda

    2013-01-01

    How easy is it to reproduce the results found in a typical computational biology paper? Either through experience or intuition the reader will already know that the answer is with difficulty or not at all. In this paper we attempt to quantify this difficulty by reproducing a previously published paper for different classes of users (ranging from users with little expertise to domain experts) and suggest ways in which the situation might be improved. Quantification is achieved by estimating the time required to reproduce each of the steps in the method described in the original paper and make them part of an explicit workflow that reproduces the original results. Reproducing the method took several months of effort, and required using new versions and new software that posed challenges to reconstructing and validating the results. The quantification leads to "reproducibility maps" that reveal that novice researchers would only be able to reproduce a few of the steps in the method, and that only expert researchers with advance knowledge of the domain would be able to reproduce the method in its entirety. The workflow itself is published as an online resource together with supporting software and data. The paper concludes with a brief discussion of the complexities of requiring reproducibility in terms of cost versus benefit, and a desiderata with our observations and guidelines for improving reproducibility. This has implications not only in reproducing the work of others from published papers, but reproducing work from one's own laboratory.

  16. Computer vision research with new imaging technology

    NASA Astrophysics Data System (ADS)

    Hou, Guangqi; Liu, Fei; Sun, Zhenan

    2015-12-01

    Light field imaging is capable of capturing dense multi-view 2D images in one snapshot, which record both intensity values and directions of rays simultaneously. As an emerging 3D device, the light field camera has been widely used in digital refocusing, depth estimation, stereoscopic display, etc. Traditional multi-view stereo (MVS) methods only perform well on strongly texture surfaces, but the depth map contains numerous holes and large ambiguities on textureless or low-textured regions. In this paper, we exploit the light field imaging technology on 3D face modeling in computer vision. Based on a 3D morphable model, we estimate the pose parameters from facial feature points. Then the depth map is estimated through the epipolar plane images (EPIs) method. At last, the high quality 3D face model is exactly recovered via the fusing strategy. We evaluate the effectiveness and robustness on face images captured by a light field camera with different poses.

  17. Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

    PubMed Central

    2011-01-01

    Background The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. Results In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. Conclusions With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from

  18. Explorations: A Research-Based Program Introducing Undergraduates to Diverse Biology Research Topics Taught by Grad Students and Postdocs

    ERIC Educational Resources Information Center

    Brownell, Sara E.; Khalfan, Waheeda; Bergmann, Dominique; Simoni, Robert

    2013-01-01

    Undergraduate biology majors are often overwhelmed by and underinformed about the diversity and complexity of biological research that is conducted on research-intensive campuses. We present a program that introduces undergraduates to the diversity and scope of biological research and also provides unique teaching opportunities for graduate…

  19. New facilities and instruments for developmental biology research in space.

    PubMed

    Brinckmann, Enno

    2003-01-01

    Three new ESA facilities will be available for biological experiments in Space, Biopack on the Space Shuttle and two instruments on the International Space Station (ISS): BIOLAB in the European "Columbus" Laboratory and the European Modular Cultivation System (EMCS) in the US Lab "Destiny". The experiments are housed in standard Experiment Containers, allowing either research in microgravity or acceleration studies with variable g-levels, if mounted on the centrifuges. While Biopack provides only thermal control, BIOLAB and EMCS supply each container with a dedicated atmosphere (controlled CO2, O2 concentration and relative humidity, trace gas removal): EMCS contains also fresh and wastewater reservoirs on its rotors. Power and data lines are available in all the described facilities. Highly automated systems, like BIOLAB's Handling Mechanism and Analysis Instruments, support the telescience concept and help reducing crew time in orbit. A BioGlovebox with its support instruments allows unique research possibilities in Space. The feasibility of experiment hardware inside the containers has been studied by ESA for several kinds of Experiment Support Equipment with potential use for research in Developmental Biology: design concepts for experiments with small eggs, cells and tissues, with small aquatic animals, with insects and with plants are described in this article.

  20. Research in thermal biology: Burning questions for coldwater stream fishes

    SciTech Connect

    McCullough, Dr. Dale; Bartholow, Dr. John; Jager, Yetta; al., et.

    2009-01-01

    With the increasing appreciation of global warming impacts on ecological systems in addition to the myriad of land management effects on water quality, the number of literature citations dealing with the effects of water temperature on freshwater fish has escalated in the past decade. Given the many biological scales at which water temperature effects have been studied and the growing need to integrate knowledge from multiple disciplines of thermal biology to fully protect beneficial uses, we held that a survey of the most promising recent developments and an expression of some of the remaining unanswered questions with significant management implications would best be approached collectively by a diverse research community. We have identified five specific topic areas of renewed research where new techniques and critical thought could benefit coldwater stream fishes (particularly salmonids): molecular, organism, population/species, community and ecosystem, and policy issues in water quality. Our hope is that information gained through examination of recent research fronts linking knowledge at various scales will prove useful in managing water quality at a basin level to protect fish populations and whole ecosystems. Standards of the past were based largely on incipient lethal and optimum growth rate temperatures for fish species, while future standards should consider all integrated thermal impacts to the organism and ecosystem.

  1. Xenopus laevis a success story of biological research in space

    NASA Astrophysics Data System (ADS)

    Horn, Eberhard R.

    2006-01-01

    The clawed toad Xenopus laevis is a common experimental animal used in many disciplines of life sciences, such as integrative, developmental and molecular biology or experimental medicine. Since 30 years, Xenopus is used in biological research in space. Important milestones were the years 1975, when Xenopus embryos flew for the first time on the Russian space station Salut-4 and 1994, when Xenopus eggs were successfully fertilized for the first time in space during the Japanese Spacelab mission STS-47 and developed in microgravity to vital tadpoles. Most Xenopus studies were related to embryogenesis and development. Observations during and after altered gravity revealed changes such as the thickening of the blastocoel roof, the dorsalization of the tail, and modifications of vestibular reflexes, fictive and freely swimming. Many changes were reversible even during microgravity exposure. Studies about the vestibuloocular reflex or synapse formation revealed an age-related sensitivity to altered gravity. Xenopus offers useful tools for studies about microgravity effects on living systems. Its oocyte is a suitable model to study ion channel function in space; the dorsalization model can be used to analyse growth factor sensibilities. Hardware for life support of adults, tadpoles and embryos (cf. SUPPLY unit in combination with miniaquaria) as well as for controlled experiments in space are prerequisites for an extension of research with Xenopus. The application aspect is based on the fact that fundamental research per se brings benefit to man.

  2. Research in thermal biology: Burning questions for coldwater stream fishes

    USGS Publications Warehouse

    McCullough, D.A.; Bartholow, J.M.; Jager, H.I.; Beschta, R.L.; Cheslak, E.F.; Deas, M.L.; Ebersole, J.L.; Foott, J.S.; Johnson, S.L.; Marine, K.R.; Mesa, M.G.; Petersen, J.H.; Souchon, Y.; Tiffan, K.F.; Wurtsbaugh, W.A.

    2009-01-01

    With the increasing appreciation of global warming impacts on ecological systems, in addition to the myriad of land management effects on water quality, the number of literature citations dealing with the effects of water temperature on freshwater fish has escalated in the past decade. Given the many biological scales at which water temperature effects have been studied, and the growing need to integrate knowledge from multiple disciplines of thermal biology to fully protect beneficial uses, we held that a survey of the most promising recent developments and an expression of some of the remaining unanswered questions with significant management implications would best be approached collectively by a diverse research community. We have identified five specific topic areas of renewed research where new techniques and critical thought could benefit coldwater stream fishes (particularly salmonids): molecular, organism, population/species, community and ecosystem, and policy issues in water quality. Our hope is that information gained through examination of recent research fronts linking knowledge at various scales will prove useful in managing water quality at a basin level to protect fish populations and whole ecosystems. Standards of the past were based largely on incipient lethal and optimum growth rate temperatures for fish species, while future standards should consider all integrated thermal impacts to the organism and ecosystem. ?? Taylor and Francis Group, LLC.

  3. Advancing vector biology research: a community survey for future directions, research applications and infrastructure requirements.

    PubMed

    Kohl, Alain; Pondeville, Emilie; Schnettler, Esther; Crisanti, Andrea; Supparo, Clelia; Christophides, George K; Kersey, Paul J; Maslen, Gareth L; Takken, Willem; Koenraadt, Constantianus J M; Oliva, Clelia F; Busquets, Núria; Abad, F Xavier; Failloux, Anna-Bella; Levashina, Elena A; Wilson, Anthony J; Veronesi, Eva; Pichard, Maëlle; Arnaud Marsh, Sarah; Simard, Frédéric; Vernick, Kenneth D

    2016-01-01

    Vector-borne pathogens impact public health, animal production, and animal welfare. Research on arthropod vectors such as mosquitoes, ticks, sandflies, and midges which transmit pathogens to humans and economically important animals is crucial for development of new control measures that target transmission by the vector. While insecticides are an important part of this arsenal, appearance of resistance mechanisms is increasingly common. Novel tools for genetic manipulation of vectors, use of Wolbachia endosymbiotic bacteria, and other biological control mechanisms to prevent pathogen transmission have led to promising new intervention strategies, adding to strong interest in vector biology and genetics as well as vector-pathogen interactions. Vector research is therefore at a crucial juncture, and strategic decisions on future research directions and research infrastructure investment should be informed by the research community. A survey initiated by the European Horizon 2020 INFRAVEC-2 consortium set out to canvass priorities in the vector biology research community and to determine key activities that are needed for researchers to efficiently study vectors, vector-pathogen interactions, as well as access the structures and services that allow such activities to be carried out. We summarize the most important findings of the survey which in particular reflect the priorities of researchers in European countries, and which will be of use to stakeholders that include researchers, government, and research organizations. PMID:27677378

  4. Educational Outcomes and Research from 1:1 Computing Settings

    ERIC Educational Resources Information Center

    Bebell, Damian; O'Dwyer, Laura M.

    2010-01-01

    Despite the growing interest in 1:1 computing initiatives, relatively little empirical research has focused on the outcomes of these investments. The current special edition of the Journal of Technology and Assessment presents four empirical studies of K-12 1:1 computing programs and one review of key themes in the conversation about 1:1 computing…

  5. A Research and Development Strategy for High Performance Computing.

    ERIC Educational Resources Information Center

    Office of Science and Technology Policy, Washington, DC.

    This report is the result of a systematic review of the status and directions of high performance computing and its relationship to federal research and development. Conducted by the Federal Coordinating Council for Science, Engineering, and Technology (FCCSET), the review involved a series of workshops attended by numerous computer scientists and…

  6. THE LEARNING RESEARCH AND DEVELOPMENT CENTER'S COMPUTER ASSISTED LABORATORY.

    ERIC Educational Resources Information Center

    RAGSDALE, RONALD G.

    THIS PAPER DESCRIBES THE OPERATION AND PLANNED APPLICATIONS OF A COMPUTER ASSISTED LABORATORY FOR SOCIAL SCIENCE RESEARCH. THE LAB CENTERS AROUND AN 8K PDP-7 COMPUTER AND ITS SPECIAL PERIPHERAL EQUIPMENT. SPECIAL DEVICES INCLUDE RANDOM ACCESS AUDIO AND VIDEO, GRAPHICAL INPUT, AND TOUCH-SENSITIVE AND BLOCK-MANIPULATION INPUTS. THE SYSTEM MAY BE…

  7. National Energy Research Scientific Computing Center 2007 Annual Report

    SciTech Connect

    Hules, John A.; Bashor, Jon; Wang, Ucilia; Yarris, Lynn; Preuss, Paul

    2008-10-23

    This report presents highlights of the research conducted on NERSC computers in a variety of scientific disciplines during the year 2007. It also reports on changes and upgrades to NERSC's systems and services aswell as activities of NERSC staff.

  8. Research on the Use of Computer-Assisted Instruction.

    ERIC Educational Resources Information Center

    Craft, C. O.

    1982-01-01

    Reviews recent research studies related to computer assisted instruction (CAI). The studies concerned program effectiveness, teaching of psychomotor skills, tool availability, and factors affecting the adoption of CAI. (CT)

  9. Computational Science Guides and Accelerates Hydrogen Research (Fact Sheet)

    SciTech Connect

    Not Available

    2010-12-01

    This fact sheet describes NREL's accomplishments in using computational science to enhance hydrogen-related research and development in areas such as storage and photobiology. Work was performed by NREL's Chemical and Materials Science Center and Biosciences Center.

  10. Low Charge-State AMS for Biological Research

    SciTech Connect

    Vogel, J S; Ognibene, T; Roberts, M; Brown, T; Clifford, A; Espinosa, D; Lin, Y

    2001-03-01

    University collaborations and internal research programs that trace isotopically labeled compounds in natural biological systems have grown significantly in the past few years. New research in molecular nutrition, protein sequencing, immunoassays, and toxicology now require hundreds to thousands of sample analyses per project. The goal of this effort was to strengthen this Laboratory and University health related research by the expansion of AMS access. This was achieved by our design and implementation of an AMS spectrometer that analyzes isotopic ions at lower energies in a more compact spectrometer without sacrificing precision or throughput. The decrease in ion energies is accompanied by a significant reduction in size and cost of the spectrometer. Our successful reduction in spectrometer cost, operation, and space will make this technology more appealing to research institutions, including industrial research centers. While others have also developed smaller spectrometers, these are limited in precision and throughput by the much lower intensities of ion beams that can be transmitted through them without differential loss of isotope species. The primary challenge in this project was mating the LLNL-designed high intensity negative ion source (Roberts, et al. 1994; Southon & Roberts, 2000) to available accelerator components and then showing that the precision and throughput would remain high enough to serve the research that needs large numbers of AMS analyses. The project also required reduction in operating complexity so that scientists and students would not require technical specialists to make their measurements. This report describes the experiments done to assure the needed spectrometer performance.

  11. [Research under reduced gravity. Part I: bases of gravitational biology].

    PubMed

    Volkmann, D; Sievers, A

    1992-02-01

    The orientation of organisms in space and their morphogenesis in relation to the gravitational field of the Earth are the main topics of research in the field of gravitational biology. For more than 100 years clinostats provided the only possibility to simulate physiological weightlessness. In contrast to animals, plants are characterized by intracellular gravireceptors. Nevertheless, there are some indications, e.g., the minimal energy of approx. 10(-18) J triggering a gravity-dependent response, for similar mechanisms of gravity perception. Stretch-activated ion channels might be the common structural basis. PMID:11536493

  12. Impact of Interdisciplinary Undergraduate Research in Mathematics and Biology on the Development of a New Course Integrating Five STEM Disciplines

    ERIC Educational Resources Information Center

    Caudill, Lester; Hill, April; Hoke, Kathy; Lipan, Ovidiu

    2010-01-01

    Funded by innovative programs at the National Science Foundation and the Howard Hughes Medical Institute, University of Richmond faculty in biology, chemistry, mathematics, physics, and computer science teamed up to offer first- and second-year students the opportunity to contribute to vibrant, interdisciplinary research projects. The result was…

  13. 3-D visualization and identification of biological microorganisms using partially temporal incoherent light in-line computational holographic imaging.

    PubMed

    Moon, Inkyu; Javidi, Bahram

    2008-12-01

    We present a new method for three-dimensional (3-D) visualization and identification of biological microorganisms using partially temporal incoherent light in-line (PTILI) computational holographic imaging and multivariate statistical methods. For 3-D data acquisition of biological microorganisms, the band-pass filtered white light is used to illuminate a biological sample. The transversely and longitudinally diffracted pattern of the biological sample is magnified by microscope objective (MO) and is optically recorded with an image sensor array interfaced with a computer. Three-dimensional reconstruction of the biological sample from the diffraction pattern is accomplished by using computational Fresnel propagation method. Principal components analysis and nonparametric inference algorithms are applied to the 3-D complex amplitude biological sample for identification purposes. Experiments indicate that the proposed system can be useful for identifying biological microorganisms. To the best of our knowledge, this is the first report on using PTILI computational holographic microscopy for identification of biological microorganisms.

  14. Activities of the Research Institute for Advanced Computer Science

    NASA Technical Reports Server (NTRS)

    Oliger, Joseph

    1994-01-01

    The Research Institute for Advanced Computer Science (RIACS) was established by the Universities Space Research Association (USRA) at the NASA Ames Research Center (ARC) on June 6, 1983. RIACS is privately operated by USRA, a consortium of universities with research programs in the aerospace sciences, under contract with NASA. The primary mission of RIACS is to provide research and expertise in computer science and scientific computing to support the scientific missions of NASA ARC. The research carried out at RIACS must change its emphasis from year to year in response to NASA ARC's changing needs and technological opportunities. Research at RIACS is currently being done in the following areas: (1) parallel computing; (2) advanced methods for scientific computing; (3) high performance networks; and (4) learning systems. RIACS technical reports are usually preprints of manuscripts that have been submitted to research journals or conference proceedings. A list of these reports for the period January 1, 1994 through December 31, 1994 is in the Reports and Abstracts section of this report.

  15. G-LoSA: An efficient computational tool for local structure-centric biological studies and drug design.

    PubMed

    Lee, Hui Sun; Im, Wonpil

    2016-04-01

    Molecular recognition by protein mostly occurs in a local region on the protein surface. Thus, an efficient computational method for accurate characterization of protein local structural conservation is necessary to better understand biology and drug design. We present a novel local structure alignment tool, G-LoSA. G-LoSA aligns protein local structures in a sequence order independent way and provides a GA-score, a chemical feature-based and size-independent structure similarity score. Our benchmark validation shows the robust performance of G-LoSA to the local structures of diverse sizes and characteristics, demonstrating its universal applicability to local structure-centric comparative biology studies. In particular, G-LoSA is highly effective in detecting conserved local regions on the entire surface of a given protein. In addition, the applications of G-LoSA to identifying template ligands and predicting ligand and protein binding sites illustrate its strong potential for computer-aided drug design. We hope that G-LoSA can be a useful computational method for exploring interesting biological problems through large-scale comparison of protein local structures and facilitating drug discovery research and development. G-LoSA is freely available to academic users at http://im.compbio.ku.edu/GLoSA/. PMID:26813336

  16. The opportunities for space biology research on the Space Station

    NASA Technical Reports Server (NTRS)

    Ballard, Rodney W.; Souza, Kenneth A.

    1987-01-01

    The goals of space biology research to be conducted aboard the Space Station in 1990s include long-term studies of reproduction, development, growth, physiology, behavior, and aging in both animals and plants. They also include studies of the mechanisms by which gravitational stimuli are sensed, processed, and transmitted to a responsive site, and of the effect of microgravity on each component. The Space Station configuration will include a life sciences research facility, where experiment cyles will be on a 90-day basis (since the Space Station missions planned for the 1990s call for 90-day intervals). A modular approach is taken to accomodate animal habitats, plant growth chambers, and other specimen holding facilities; the modular habitats would be transportable between the launch systems, habitat racks, a workbench, and a variable-gravity centrifuge (included for providing artificial gravity and accurately controlled acceleration levels aboard Space Station).

  17. BCTR: Biological and Chemical Technologies Research 1994 annual summary report

    SciTech Connect

    Petersen, G.

    1995-02-01

    The annual summary report presents the fiscal year (FY) 1994 research activities and accomplishments for the United States Department of Energy (DOE) Biological and Chemical Technologies Research (BCTR) Program of the Advanced Industrial Concepts Division (AICD). This AICD program resides within the Office of Industrial Technologies (OIT) of the Office of Energy Efficiency and Renewable Energy (EE). Although the OIT was reorganized in 1991 and AICD no longer exists, this document reports on efforts conducted under the former structure. The annual summary report for 1994 (ASR 94) contains the following: program description (including BCTR program mission statement, historical background, relevance, goals and objectives); program structure and organization, selected technical and programmatic highlights for 1994; detailed descriptions of individual projects; a listing of program output, including a bibliography of published work; patents, and awards arising from work supported by BCTR.

  18. Experimental biological research on stem cells in fascia tissue.

    PubMed

    Ou, Yinghua; Qu, Rongmei; Dai, Jingxing

    2013-06-01

    The fascia tissue, derived from the mesoderm, is distributed in all parts of the human body. It consists of connective tissues and stem cells. The fascia tissue is also believed to be a functional system, like the digestive system, in the human body, controlling self-inspection, self-maintenance, support, and storage. In addition, much of the research relevant to fascia tissue has focused on adipose-derived stem cells (ADSCs), which mainly exist in adipose tissues. The aim of this review is to summarize the current research on ADSCs, including a brief introduction of their biological characteristics, the isolation and expansion methods, a conclusion on their multidifferentiation potential, new clinical applications, and the therapeutic strategies for treating tumors.

  19. A framework for integrating thermal biology into fragmentation research.

    PubMed

    Tuff, K T; Tuff, T; Davies, K F

    2016-04-01

    Habitat fragmentation changes thermal conditions in remnant patches, and thermal conditions strongly influence organism morphology, distribution, and activity patterns. However, few studies explore temperature as a mechanism driving ecological responses to fragmentation. Here we offer a conceptual framework that integrates thermal biology into fragmentation research to better understand individual, species, community, and ecosystem-level responses to fragmentation. Specifically, the framework addresses how fragmentation changes temperature and how the effects of those temperature changes spread through the ecosystem, from organism response via thermal sensitivity, to changes in species distribution and activity patterns, to shifts in community structure following species' responses, and ultimately to changes in ecosystem functions. We place a strong emphasis on future research directions by outlining "Critical gaps" for each step of the framework. Empirical efforts to apply and test this framework promise new understanding of fragmentation's ecological consequences and new strategies for conservation in an increasingly fragmented and warmer world. PMID:26892491

  20. An Analysis of 27 Years of Research into Computer Education Published in Australian Educational Computing

    ERIC Educational Resources Information Center

    Zagami, Jason

    2015-01-01

    Analysis of three decades of publications in Australian Educational Computing (AEC) provides insight into the historical trends in Australian educational computing, highlighting an emphasis on pedagogy, comparatively few articles on educational technologies, and strong research topic alignment with similar international journals. Analysis confirms…

  1. VirtualPlant: A Software Platform to Support Systems Biology Research1[W][OA

    PubMed Central

    Katari, Manpreet S.; Nowicki, Steve D.; Aceituno, Felipe F.; Nero, Damion; Kelfer, Jonathan; Thompson, Lee Parnell; Cabello, Juan M.; Davidson, Rebecca S.; Goldberg, Arthur P.; Shasha, Dennis E.; Coruzzi, Gloria M.; Gutiérrez, Rodrigo A.

    2010-01-01

    Data generation is no longer the limiting factor in advancing biological research. In addition, data integration, analysis, and interpretation have become key bottlenecks and challenges that biologists conducting genomic research face daily. To enable biologists to derive testable hypotheses from the increasing amount of genomic data, we have developed the VirtualPlant software platform. VirtualPlant enables scientists to visualize, integrate, and analyze genomic data from a systems biology perspective. VirtualPlant integrates genome-wide data concerning the known and predicted relationships among genes, proteins, and molecules, as well as genome-scale experimental measurements. VirtualPlant also provides visualization techniques that render multivariate information in visual formats that facilitate the extraction of biological concepts. Importantly, VirtualPlant helps biologists who are not trained in computer science to mine lists of genes, microarray experiments, and gene networks to address questions in plant biology, such as: What are the molecular mechanisms by which internal or external perturbations affect processes controlling growth and development? We illustrate the use of VirtualPlant with three case studies, ranging from querying a gene of interest to the identification of gene networks and regulatory hubs that control seed development. Whereas the VirtualPlant software was developed to mine Arabidopsis (Arabidopsis thaliana) genomic data, its data structures, algorithms, and visualization tools are designed in a species-independent way. VirtualPlant is freely available at www.virtualplant.org. PMID:20007449

  2. Applications of the Aurora parallel Prolog system to computational molecular biology

    SciTech Connect

    Lusk, E.L.; Overbeek, R.; Mudambi, S.; Szeredi, P.

    1993-09-01

    We describe an investigation into the use of the Aurora parallel Prolog system in two applications within the area of computational molecular biology. The computational requirements were large, due to the nature of the applications, and were large, due to the nature of the applications, and were carried out on a scalable parallel computer the BBN ``Butterfly`` TC-2000. Results include both a demonstration that logic programming can be effective in the context of demanding applications on large-scale parallel machines, and some insights into parallel programming in Prolog.

  3. 2010 Tetrapyrroles, Chemistry & Biology of Gordon Research Conference

    SciTech Connect

    Angela Wilks

    2010-07-30

    The objective of the Chemistry & Biology of Tetrapyrroles Gordon Conference is to bring together researchers from diverse disciplines that otherwise would not interact. By bringing biologists, chemists, engineers and clinicians with a common interest in tetrapyrroles the conference provides a forum for cross-disciplinary ideas and collaboration. The perspective provided by biologists, chemists, and clinicians working in fields such as newly discovered defects in human porphyrin metabolism, the myriad of strategies for light harvesting in photosynthetic organisms, novel tetrapyrroles that serve as auxiliary chromophores or enzyme cofactors, synthetic strategies in the design of novel tetrapyrrole scaffolds, and tetrapyrrole based cell signaling and regulatory systems, makes this conference unique in the field. Over the years the growing evidence for the role of tetrapyrroles and their reactive intermediates in cell signaling and regulation has been of increasing importance at this conference. The 2010 conference on Chemistry & Biology of Tetrapyrroles will focus on many of these new frontiers as outlined in the preliminary program listed. Speakers will emphasize unpublished results and new findings in the field. The oral sessions will be followed by the highly interactive afternoon poster sessions. The poster sessions provide all conferees with the opportunity to present their latest research and to exchange ideas in a more informal setting. As in the past, this opportunity will continue during the nightly social gathering that takes place in the poster hall following the evening lectures. All conferees are encouraged to submit and present posters. At the conference the best poster in the areas of biology, chemistry and medicine will be selected by a panel of previous conference chairs.

  4. Using a Computer Simulation To Teach Science Process Skills to College Biology and Elementary Education Majors.

    ERIC Educational Resources Information Center

    Lee, Aimee T.; Hairston, Rosalina V.; Thames, Rachel; Lawrence, Tonya; Herron, Sherry S.

    2002-01-01

    Describes the Lateblight computer simulation implemented in the general biology laboratory and science methods course for elementary teachers to reinforce the processes of science and allow students to engage, explore, explain, elaborate, and evaluate the methods of building concepts in science. (Author/KHR)

  5. Problem-Solving Inquiry-Oriented Biology Tasks Integrating Practical Laboratory and Computer.

    ERIC Educational Resources Information Center

    Friedler, Yael; And Others

    1992-01-01

    Presents results of a study that examines the development and use of computer simulations for high school science instruction and for integrated laboratory and computerized tests that are part of the biology matriculation examination in Israel. Eleven implications for teaching are presented. (MDH)

  6. Effects of Computer-Assisted Instruction on Performance of Senior High School Biology Students in Ghana

    ERIC Educational Resources Information Center

    Owusu, K. A.; Monney, K. A.; Appiah, J. Y.; Wilmot, E. M.

    2010-01-01

    This study investigated the comparative efficiency of computer-assisted instruction (CAI) and conventional teaching method in biology on senior high school students. A science class was selected in each of two randomly selected schools. The pretest-posttest non equivalent quasi experimental design was used. The students in the experimental group…

  7. Effects of Constructivist and Computer-Facilitated Strategies on Achievement in Heterogeneous Secondary Biology.

    ERIC Educational Resources Information Center

    Duffy, Maryellen; Barowy, William

    This paper describes the effects of the implementation of constructivist techniques with interactive computer simulations on conceptual understanding of plant nutrition and critical thinking skills in heterogeneously grouped secondary biology classrooms. The study focused on three strategies for teaching plant nutrition: (1) traditional; (2)…

  8. Supporting Representational Competence in High School Biology with Computer-Based Biomolecular Visualizations

    ERIC Educational Resources Information Center

    Wilder, Anna; Brinkerhoff, Jonathan

    2007-01-01

    This study assessed the effectiveness of computer-based biomolecular visualization activities on the development of high school biology students' representational competence as a means of understanding and visualizing protein structure/function relationships. Also assessed were students' attitudes toward these activities. Sixty-nine students…

  9. Computer Labs as Techno-Pedagogical Tools for Learning Biology--Exploring ICT Practices in India

    ERIC Educational Resources Information Center

    Nayark, Ajitha K.; Barker, Miles

    2014-01-01

    In Indian secondary schools, as in many countries, Information and Communication Technologies, ICT, are changing the image of learning places, the roles of teachers and students, and often the entire classroom learning ambience. This study investigates current practices for learning biology in school computer labs in India in the light of the…

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

    NASA Technical Reports Server (NTRS)

    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.

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

    NASA Technical Reports Server (NTRS)

    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.

  12. Institute for Scientific Computing Research Annual Report: Fiscal Year 2004

    SciTech Connect

    Keyes, D E

    2005-02-07

    Large-scale scientific computation and all of the disciplines that support and help to validate it have been placed at the focus of Lawrence Livermore National Laboratory (LLNL) by the Advanced Simulation and Computing (ASC) program of the National Nuclear Security Administration (NNSA) and the Scientific Discovery through Advanced Computing (SciDAC) initiative of the Office of Science of the Department of Energy (DOE). The maturation of computational simulation as a tool of scientific and engineering research is underscored in the November 2004 statement of the Secretary of Energy that, ''high performance computing is the backbone of the nation's science and technology enterprise''. LLNL operates several of the world's most powerful computers--including today's single most powerful--and has undertaken some of the largest and most compute-intensive simulations ever performed. Ultrascale simulation has been identified as one of the highest priorities in DOE's facilities planning for the next two decades. However, computers at architectural extremes are notoriously difficult to use efficiently. Furthermore, each successful terascale simulation only points out the need for much better ways of interacting with the resulting avalanche of data. Advances in scientific computing research have, therefore, never been more vital to LLNL's core missions than at present. Computational science is evolving so rapidly along every one of its research fronts that to remain on the leading edge, LLNL must engage researchers at many academic centers of excellence. In Fiscal Year 2004, the Institute for Scientific Computing Research (ISCR) served as one of LLNL's main bridges to the academic community with a program of collaborative subcontracts, visiting faculty, student internships, workshops, and an active seminar series. The ISCR identifies researchers from the academic community for computer science and computational science collaborations with LLNL and hosts them for short- and

  13. Development of computational fluid dynamics at NASA Ames Research Center

    NASA Technical Reports Server (NTRS)

    Inouye, M.

    1984-01-01

    Ames Research Center has the lead role among NASA centers to conduct research in computational fluid dynamics. The past, the present, and the future prospects in this field are reviewed. Past accomplishments include pioneering computer simulations of fluid dynamics problems that have made computers valuable in complementing wind tunnels for aerodynamic research. The present facilities include the most powerful computers built in the United States. Three examples of viscous flow simulations are presented: an afterbody with an exhaust plume, a blunt fin mounted on a flat plate, and the Space Shuttle. The future prospects include implementation of the Numerical Aerodynamic Simulation Processing System that will provide the capability for solving the viscous flow field around an aircraft in a matter of minutes.

  14. Harnessing Polypharmacology with Computer-Aided Drug Design and Systems Biology.

    PubMed

    Wathieu, Henri; Issa, Naiem T; Byers, Stephen W; Dakshanamurthy, Sivanesan

    2016-01-01

    The ascent of polypharmacology in drug development has many implications for disease therapy, most notably in the efforts of drug discovery, drug repositioning, precision medicine and combination therapy. The single- target approach to drug development has encountered difficulties in predicting drugs that are both clinically efficacious and avoid toxicity. By contrast, polypharmacology offers the possibility of a controlled distribution of effects on a biological system. This review addresses possibilities and bottlenecks in the efficient computational application of polypharmacology. The two major areas we address are the discovery and prediction of multiple protein targets using the tools of computer-aided drug design, and the use of these protein targets in predicting therapeutic potential in the context of biological networks. The successful application of polypharmacology to systems biology and pharmacology has the potential to markedly accelerate the pace of development of novel therapies for multiple diseases, and has implications for the intellectual property landscape, likely requiring targeted changes in patent law. PMID:26907947

  15. Harnessing Polypharmacology with Computer-Aided Drug Design and Systems Biology.

    PubMed

    Wathieu, Henri; Issa, Naiem T; Byers, Stephen W; Dakshanamurthy, Sivanesan

    2016-01-01

    The ascent of polypharmacology in drug development has many implications for disease therapy, most notably in the efforts of drug discovery, drug repositioning, precision medicine and combination therapy. The single- target approach to drug development has encountered difficulties in predicting drugs that are both clinically efficacious and avoid toxicity. By contrast, polypharmacology offers the possibility of a controlled distribution of effects on a biological system. This review addresses possibilities and bottlenecks in the efficient computational application of polypharmacology. The two major areas we address are the discovery and prediction of multiple protein targets using the tools of computer-aided drug design, and the use of these protein targets in predicting therapeutic potential in the context of biological networks. The successful application of polypharmacology to systems biology and pharmacology has the potential to markedly accelerate the pace of development of novel therapies for multiple diseases, and has implications for the intellectual property landscape, likely requiring targeted changes in patent law.

  16. Computational toxicology at the European Commission's Joint Research Centre.

    PubMed

    Mostrag-Szlichtyng, Aleksandra; Zaldívar Comenges, José-Manuel; Worth, Andrew P

    2010-07-01

    The methods and tools of computational toxicology form an essential and integrating pillar in the new paradigm of predictive toxicology, which seeks to develop more efficient and effective means of assessing chemical toxicity, while also reducing animal testing. The increasingly prominent role of computational toxicology in the implementation of European chemicals' legislation is described, along with initiatives by the European Commission's Joint Research Centre to promote the acceptance and use of computational methods. Outstanding needs and scientific challenges are also outlined. In recent years, there have been impressive scientific and technological advances in computational toxicology. However, considerable progress is still needed to increase the acceptance of computational methods, and in particular to develop a deeper and common understanding of how to apply computational toxicology in regulatory decision making.

  17. Computational Fluid Dynamics Program at NASA Ames Research Center

    NASA Technical Reports Server (NTRS)

    Holst, Terry L.

    1989-01-01

    The Computational Fluid Dynamics (CFD) Program at NASA Ames Research Center is reviewed and discussed. The technical elements of the CFD Program are listed and briefly discussed. These elements include algorithm research, research and pilot code development, scientific visualization, advanced surface representation, volume grid generation, and numerical optimization. Next, the discipline of CFD is briefly discussed and related to other areas of research at NASA Ames including experimental fluid dynamics, computer science research, computational chemistry, and numerical aerodynamic simulation. These areas combine with CFD to form a larger area of research, which might collectively be called computational technology. The ultimate goal of computational technology research at NASA Ames is to increase the physical understanding of the world in which we live, solve problems of national importance, and increase the technical capabilities of the aerospace community. Next, the major programs at NASA Ames that either use CFD technology or perform research in CFD are listed and discussed. Briefly, this list includes turbulent/transition physics and modeling, high-speed real gas flows, interdisciplinary research, turbomachinery demonstration computations, complete aircraft aerodynamics, rotorcraft applications, powered lift flows, high alpha flows, multiple body aerodynamics, and incompressible flow applications. Some of the individual problems actively being worked in each of these areas is listed to help define the breadth or extent of CFD involvement in each of these major programs. State-of-the-art examples of various CFD applications are presented to highlight most of these areas. The main emphasis of this portion of the presentation is on examples which will not otherwise be treated at this conference by the individual presentations. Finally, a list of principal current limitations and expected future directions is given.

  18. Biologically relevant molecular transducer with increased computing power and iterative abilities.

    PubMed

    Ratner, Tamar; Piran, Ron; Jonoska, Natasha; Keinan, Ehud

    2013-05-23

    As computing devices, which process data and interconvert information, transducers can encode new information and use their output for subsequent computing, offering high computational power that may be equivalent to a universal Turing machine. We report on an experimental DNA-based molecular transducer that computes iteratively and produces biologically relevant outputs. As a proof of concept, the transducer accomplished division of numbers by 3. The iterative power was demonstrated by a recursive application on an obtained output. This device reads plasmids as input and processes the information according to a predetermined algorithm, which is represented by molecular software. The device writes new information on the plasmid using hardware that comprises DNA-manipulating enzymes. The computation produces dual output: a quotient, represented by newly encoded DNA, and a remainder, represented by E. coli phenotypes. This device algorithmically manipulates genetic codes. PMID:23706637

  19. Computer Applications in Health Care. NCHSR Research Report Series.

    ERIC Educational Resources Information Center

    Medical Information Systems Cluster, Rockville, MD.

    This NCHSR research program in the application of computers in health care--conducted over the ten year span 1968-1978--identified two areas of application research, an inpatient care support system, and an outpatient care support system. Both of these systems were conceived as conceptual frameworks for a related network of projects and ideas that…

  20. The Importance of Computer Programming Skills to Educational Researchers.

    ERIC Educational Resources Information Center

    Lawson, Stephen

    The use of the modern computer has revolutionized the field of educational research. Software packages are currently available that allow almost anyone to analyze data efficiently and rapidly. Yet, caution must temper the widespread acceptance and use of these programs. It is recommended that the researcher not rely solely on the use of "canned"…