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Sample records for computational biology research

  1. The applications of computers in biological research

    NASA Technical Reports Server (NTRS)

    Wei, Jennifer

    1988-01-01

    Research in many fields could not be done without computers. There is often a great deal of technical data, even in the biological fields, that need to be analyzed. These data, unfortunately, previously absorbed much of every researcher's time. Now, due to the steady increase in computer technology, biological researchers are able to make incredible advances in their work without the added worries of tedious and difficult tasks such as the many mathematical calculations involved in today's research and health care.

  2. 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. 2015 S. Karger AG, Basel.

  3. 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. Copyright © 2013 Wiley Periodicals, Inc.

  4. Towards a lightweight generic computational grid framework for biological research

    PubMed Central

    Halling-Brown, Mark D; Moss, David S; Shepherd, Adrian J

    2008-01-01

    Background An increasing number of scientific research projects require access to large-scale computational resources. This is particularly true in the biological field, whether to facilitate the analysis of large high-throughput data sets, or to perform large numbers of complex simulations – a characteristic of the emerging field of systems biology. Results In this paper we present a lightweight generic framework for combining disparate computational resources at multiple sites (ranging from local computers and clusters to established national Grid services). A detailed guide describing how to set up the framework is available from the following URL: . Conclusion This approach is particularly (but not exclusively) appropriate for large-scale biology projects with multiple collaborators working at different national or international sites. The framework is relatively easy to set up, hides the complexity of Grid middleware from the user, and provides access to resources through a single, uniform interface. It has been developed as part of the European ImmunoGrid project. PMID:18831735

  5. All biology is computational biology.

    PubMed

    Markowetz, Florian

    2017-03-01

    Here, I argue that computational thinking and techniques are so central to the quest of understanding life that today all biology is computational biology. Computational biology brings order into our understanding of life, it makes biological concepts rigorous and testable, and it provides a reference map that holds together individual insights. The next modern synthesis in biology will be driven by mathematical, statistical, and computational methods being absorbed into mainstream biological training, turning biology into a quantitative science.

  6. All biology is computational biology

    PubMed Central

    2017-01-01

    Here, I argue that computational thinking and techniques are so central to the quest of understanding life that today all biology is computational biology. Computational biology brings order into our understanding of life, it makes biological concepts rigorous and testable, and it provides a reference map that holds together individual insights. The next modern synthesis in biology will be driven by mathematical, statistical, and computational methods being absorbed into mainstream biological training, turning biology into a quantitative science. PMID:28278152

  7. 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…

  8. 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…

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

    PubMed Central

    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).

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

    PubMed Central

    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). PMID:26097686

  11. 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).

  12. Computational Systems Chemical Biology

    PubMed Central

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

    2013-01-01

    There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically-based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology, SCB (Oprea et al., 2007). 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. PMID:20838980

  13. 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.

  14. 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.

  15. 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

  16. Promoting synergistic research and education in computational biology and drug design.

    PubMed

    Jesneck, Jonathan L; Yang, Jack Y

    2008-01-01

    Supported by US National Science Foundation (NSF) and the International Society of Intelligent Biological Medicine (ISIBM), the IEEE 7th International Conference on Bioinformatics and Bioengineering at Harvard Medical School was designed dynamically in response to the cutting edge synergistic research and education. One of the key components of this academic event is the poster presentation focusing on specific topics to foster collaboration between the computational biology and drug design domains. The Harvard meeting attracted over five hundred scientists, researchers and medical doctors world-wide to present, discuss and exchange their research. The synergies between computational biology and drug design research had been well observed by participants. The poster sessions had been designed to be responsive to the need for synergistic inter/multidisciplinary research and education. A panel of judges was formed to decide the best posters. The papers in this special issue were selected for runners-up of the best poster award by a panel of judges. Authors were then invited to expand their posters into full research papers. Submitted papers were required to contain significant additional scientific detail and were rigorously reviewed by at least three external reviewers. Detailed information regarding the academic event can be found at the White Paper of the IEEE 7th International Conference on Bioinformatics and Bioengineering at Harvard Medical School at BMC Genomics http://www.biomedcentral.com/1471-2164/9/S2/I1.

  17. 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.

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

    PubMed Central

    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. PMID:20810969

  19. 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.

  20. 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.

  1. 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

  2. Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology.

    PubMed

    Schmidt, Henning; Jirstrand, Mats

    2006-02-15

    We present a Systems Biology Toolbox for the widely used general purpose mathematical software MATLAB. The toolbox offers systems biologists an open and extensible environment, in which to explore ideas, prototype and share new algorithms, and build applications for the analysis and simulation of biological and biochemical systems. Additionally it is well suited for educational purposes. The toolbox supports the Systems Biology Markup Language (SBML) by providing an interface for import and export of SBML models. In this way the toolbox connects nicely to other SBML-enabled modelling packages. Models are represented in an internal model format and can be described either by entering ordinary differential equations or, more intuitively, by entering biochemical reaction equations. The toolbox contains a large number of analysis methods, such as deterministic and stochastic simulation, parameter estimation, network identification, parameter sensitivity analysis and bifurcation analysis.

  3. 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.

  4. 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…

  5. 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…

  6. 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.

  7. Message from the ISCB: 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

    2015-02-15

    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 and three-dimensional 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$2000, at its July 2016 annual meeting (ISCB Intelligent Systems for Molecular Biology 2016, Orlando, FL). dkovats@iscb.org or rost@in.tum.de. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  8. 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.

  9. High Performance Computing and Storage Requirements for Biological and Environmental Research Target 2017

    SciTech Connect

    Gerber, Richard; Wasserman, Harvey

    2013-05-01

    The National Energy Research Scientific Computing Center (NERSC) is the primary computing center for the DOE Office of Science, serving approximately 4,500 users working on some 650 projects that involve nearly 600 codes in a wide variety of scientific disciplines. In addition to large-­scale computing and storage resources NERSC provides support and expertise that help scientists make efficient use of its systems. The latest review revealed several key requirements, in addition to achieving its goal of characterizing BER computing and storage needs.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. GPU computing for systems biology.

    PubMed

    Dematté, Lorenzo; Prandi, Davide

    2010-05-01

    The development of detailed, coherent, models of complex biological systems is recognized as a key requirement for integrating the increasing amount of experimental data. In addition, in-silico simulation of bio-chemical models provides an easy way to test different experimental conditions, helping in the discovery of the dynamics that regulate biological systems. However, the computational power required by these simulations often exceeds that available on common desktop computers and thus expensive high performance computing solutions are required. An emerging alternative is represented by general-purpose scientific computing on graphics processing units (GPGPU), which offers the power of a small computer cluster at a cost of approximately $400. Computing with a GPU requires the development of specific algorithms, since the programming paradigm substantially differs from traditional CPU-based computing. In this paper, we review some recent efforts in exploiting the processing power of GPUs for the simulation of biological systems.

  17. 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'.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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…

  3. 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…

  4. 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

  5. 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.

  6. 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.

  7. Focus issue: series on computational and systems biology.

    PubMed

    Gough, Nancy R

    2011-09-06

    The application of computational biology and systems biology is yielding quantitative insight into cellular regulatory phenomena. For the month of September, Science Signaling highlights research featuring computational approaches to understanding cell signaling and investigation of signaling networks, a series of Teaching Resources from a course in systems biology, and various other articles and resources relevant to the application of computational biology and systems biology to the study of signal transduction.

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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.

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

    PubMed

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

    2017-09-01

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

  18. The new biology and computational statistical physics

    NASA Astrophysics Data System (ADS)

    Rintoul, Mark D.

    2002-06-01

    While it has historically been an exploratory, descriptive, and empirical science, in the past 100 years, biology has become more discovery- and mechanism-oriented. There are a number of ways in which this new paradigm is driving much of the current biological research toward statistical physics. This is happening at a molecular level due to the very large nature of biological molecules, such as proteins and nucleic acids. It is also occurring at the cellular level where random processes play an important role in cell function. There are even examples that describe the behavior of large numbers of individual organisms within one or more species. Finally, this trend has been accelerated with the advent of high-throughput experimental techniques that are driving biology towards information science. Analysis and discovery of the information gained from such experiments will rely heavily on techniques that have traditionally been applied in statistical physics. This paper will focus on examples of how statistical physics techniques are being applied and hope to be applied to biological problems, with an emphasis on high-performance computing. We will also speculate on what we feel are the necessary computing requirements to solve many of the outstanding problems in computational biology using the techniques that will be discussed.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Data integration in biological research: an overview.

    PubMed

    Lapatas, Vasileios; Stefanidakis, Michalis; Jimenez, Rafael C; Via, Allegra; Schneider, Maria Victoria

    2015-12-01

    Data sharing, integration and annotation are essential to ensure the reproducibility of the analysis and interpretation of the experimental findings. Often these activities are perceived as a role that bioinformaticians and computer scientists have to take with no or little input from the experimental biologist. On the contrary, biological researchers, being the producers and often the end users of such data, have a big role in enabling biological data integration. The quality and usefulness of data integration depend on the existence and adoption of standards, shared formats, and mechanisms that are suitable for biological researchers to submit and annotate the data, so it can be easily searchable, conveniently linked and consequently used for further biological analysis and discovery. Here, we provide background on what is data integration from a computational science point of view, how it has been applied to biological research, which key aspects contributed to its success and future directions.

  5. Computers in biology: the future is today.

    PubMed

    Prilusky, J

    1986-01-01

    Which are the applications of microcomputers in biology today? Some areas where the work with microcomputers is becoming increasingly important are considered: laboratory applications, event simulation and word processing. Almost all laboratory computer applications can be described as one of the following functions: 1. control of experiments, including timing and synchronizing external voltages; 2. data acquisition, usually through digital conversion of analog electrical signals; 3. data storage and, 4. data analysis. Event simulation is considered both as a research tool and as an important element in the educational area. Word processing and the automatic creation of literature references lists is considered as an ignored role of the microcomputers in the laboratory field. What about the influence of biology in computer technology? As specialized magazines say, many laboratories of biotechnologist are working hard to build a molecular computer. That is, an artificially designed ultramicroscopic machine built of proteins, nucleic acids, metals and non-metals in a planned arrangement. And this is not the end. The latest application able to expand our horizon in the biological field may be starting to be used at this moment.

  6. 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.

  7. 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)

  8. 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)

  9. A First Attempt to Bring Computational Biology into Advanced High School Biology Classrooms

    PubMed Central

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

    2011-01-01

    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. PMID:22046118

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. Computational Tools for Stem Cell Biology.

    PubMed

    Bian, Qin; Cahan, Patrick

    2016-12-01

    For over half a century, the field of developmental biology has leveraged computation to explore mechanisms of developmental processes. More recently, computational approaches have been critical in the translation of high throughput data into knowledge of both developmental and stem cell biology. In the past several years, a new subdiscipline of computational stem cell biology has emerged that synthesizes the modeling of systems-level aspects of stem cells with high-throughput molecular data. In this review, we provide an overview of this new field and pay particular attention to the impact that single cell transcriptomics is expected to have on our understanding of development and our ability to engineer cell fate.

  20. Computer vision in cell biology.

    PubMed

    Danuser, Gaudenz

    2011-11-23

    Computer vision refers to the theory and implementation of artificial systems that extract information from images to understand their content. Although computers are widely used by cell biologists for visualization and measurement, interpretation of image content, i.e., the selection of events worth observing and the definition of what they mean in terms of cellular mechanisms, is mostly left to human intuition. This Essay attempts to outline roles computer vision may play and should play in image-based studies of cellular life. Copyright © 2011 Elsevier Inc. All rights reserved.

  1. Optical Computing Research.

    DTIC Science & Technology

    1985-06-01

    D i No 24 15 December 1984 • . .A AD-A162 272 OPTICAL COMPUTING RESEARCH(U) STANFORD UNIV CA 2 / 2 INFORMATION SYSTEMS... 2 - .. reconstruction is quite general, independent of chemical d , processing and film type. Fig. 9. Generalized optical Fourier transform geometry...I I Bearn / Expander B n R2{ Laser Fig. 9. Optical system for recording A- ’. produces its Fourier transform, a 2 - D sinc function, on (a) the

  2. Computer Science, Biology and Biomedical Informatics academy: Outcomes from 5 years of Immersing High-school Students into Informatics Research

    PubMed Central

    King, Andrew J.; Fisher, Arielle M.; Becich, Michael J.; Boone, David N.

    2017-01-01

    The University of Pittsburgh's Department of Biomedical Informatics and Division of Pathology Informatics created a Science, Technology, Engineering, and Mathematics (STEM) pipeline in 2011 dedicated to providing cutting-edge informatics research and career preparatory experiences to a diverse group of highly motivated high-school students. In this third editorial installment describing the program, we provide a brief overview of the pipeline, report on achievements of the past scholars, and present results from self-reported assessments by the 2015 cohort of scholars. The pipeline continues to expand with the 2015 addition of the innovation internship, and the introduction of a program in 2016 aimed at offering first-time research experiences to undergraduates who are underrepresented in pathology and biomedical informatics. Achievements of program scholars include authorship of journal articles, symposium and summit presentations, and attendance at top 25 universities. All of our alumni matriculated into higher education and 90% remain in STEM majors. The 2015 high-school program had ten participating scholars who self-reported gains in confidence in their research abilities and understanding of what it means to be a scientist. PMID:28400991

  3. Computer Science, Biology and Biomedical Informatics academy: Outcomes from 5 years of Immersing High-school Students into Informatics Research.

    PubMed

    King, Andrew J; Fisher, Arielle M; Becich, Michael J; Boone, David N

    2017-01-01

    The University of Pittsburgh's Department of Biomedical Informatics and Division of Pathology Informatics created a Science, Technology, Engineering, and Mathematics (STEM) pipeline in 2011 dedicated to providing cutting-edge informatics research and career preparatory experiences to a diverse group of highly motivated high-school students. In this third editorial installment describing the program, we provide a brief overview of the pipeline, report on achievements of the past scholars, and present results from self-reported assessments by the 2015 cohort of scholars. The pipeline continues to expand with the 2015 addition of the innovation internship, and the introduction of a program in 2016 aimed at offering first-time research experiences to undergraduates who are underrepresented in pathology and biomedical informatics. Achievements of program scholars include authorship of journal articles, symposium and summit presentations, and attendance at top 25 universities. All of our alumni matriculated into higher education and 90% remain in STEM majors. The 2015 high-school program had ten participating scholars who self-reported gains in confidence in their research abilities and understanding of what it means to be a scientist.

  4. 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)

  5. 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)

  6. 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.

  7. 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

  8. CSBB: synthetic biology research at Newcastle University.

    PubMed

    Goñi-Moreno, Angel; Wipat, Anil; Krasnogor, Natalio

    2017-06-15

    The Centre for Synthetic Biology and the Bioeconomy (CSBB) brings together a far-reaching multidisciplinary community across all Newcastle University's faculties - Medical Sciences, Science, Agriculture and Engineering, and Humanities, Arts and Social Sciences. The CSBB focuses on many different areas of Synthetic Biology, including bioprocessing, computational design and in vivo computation, as well as improving understanding of basic molecular machinery. Such breadth is supported by major national and international research funding, a range of industrial partners in the North East of England and beyond, as well as a large number of doctoral and post-doctoral researchers. The CSBB trains the next generation of scientists through a 1-year MSc in Synthetic Biology. © 2017 The Author(s).

  9. 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.

  10. 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

  11. Computer Animation In Perception Research

    NASA Technical Reports Server (NTRS)

    Kaiser, Mary K.; Proffitt, Dennis R.

    1990-01-01

    Artificiality of images apparent to subjects and influences experimental results. Report evalutes computer-generated animation in research on perception of motion. Such research programs not pursued without computer animation, report notes. Computer-generated displays afford variability and control almost impossible to achieve otherwise. Medium limited in that computer-generated images present simplified approximations of dynamics of natural events.

  12. [DEVELOPMENT RESEARCH OF BIOLOGICAL DRESSING].

    PubMed

    Zhang, Jinfeng; Hao, Jianbo; Zhang, Jinpeng; Luo, Bo; Liu, Peng

    2015-02-01

    To review the research progress of modern biological dressings. The related literature at home and abroad was reviewed, analyzed, and summarized in the progress of biological dressing situation and various types of biological dressing research. Compared with the traditional dressing, the biological dressing can greatly promote wound healing. Biological dressings are mainly divided into the natural materials, artificial synthetic materials, and drug loaded dressings. The natural material dressings are mainly the alginate dressing, this kind of dressing can promote wound healing, which has been confirmed by a large number of studies. The artificial synthetic materials include film dressings, liquid, water colloids, gels, and foam, each has its own advantages and disadvantages, which can be chosen according to need. The drug dressing can play the role of drug loading, and further promote the wound healing; using microcapsule technology to construct the dressing and choosing Chinese medicine as drugs is the research direction of load. The experiment and clinical application of biological dressing are many types, clinical application prospect is wide, but each has its own advantages and disadvantages, further study is needed to improve its efficacy.

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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. © 2015 John Wiley & Sons, Ltd.

  18. Computer Science Research in India.

    DTIC Science & Technology

    1995-10-07

    This paper begins with a discussion of the nature of Computer Science Research in India. The type of institutions in which Computer Science research...Finally we study the influence on Indian Computer Science research of the phenomenal growth in exports by the Indian software industry and the arrival

  19. AHPCRC - Army High Performance Computing Research Center

    DTIC Science & Technology

    2008-01-01

    materials “from the atoms up” or to model biological systems at the molecular level. The speed and capacity of massively parallel computers are key...Streamlined, massively parallel high performance computing structural codes allow researchers to examine many relevant physical factors simultaneously...expenditure of energy, so that the drones can carry their load of sensors, communications devices, and fuel. AHPCRC researchers are using massively

  20. Advances in systems biology: computational algorithms and applications.

    PubMed

    Huang, Yufei; Zhao, Zhongming; Xu, Hua; Shyr, Yu; Zhang, Bing

    2012-01-01

    The 2012 International Conference on Intelligent Biology and Medicine (ICIBM 2012) was held on April 22-24, 2012 in Nashville, Tennessee, USA. The conference featured six technical sessions, one tutorial session, one workshop, and 3 keynote presentations that covered state-of-the-art research activities in genomics, systems biology, and intelligent computing. In addition to a major emphasis on the next generation sequencing (NGS)-driven informatics, ICIBM 2012 aligned significant interests in systems biology and its applications in medicine. We highlight in this editorial the selected papers from the meeting that address the developments of novel algorithms and applications in systems biology.

  1. Standards and ontologies in computational systems biology.

    PubMed

    Sauro, Herbert M; Bergmann, Frank T

    2008-01-01

    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 the present chapter two chief model exchange standards, SBML (Systems Biology Markup Language) 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 modelling languages and visualization tools in systems biology.

  2. 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.

  3. 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.

  4. [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.

  5. 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.

  6. 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)

  7. 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.…

  8. 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)

  9. 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

  10. 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

  11. 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.

  12. 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

  13. Understanding Biological Computation: Reliable Learning and Recognition

    NASA Astrophysics Data System (ADS)

    Hogg, T.; Huberman, B. A.

    1984-11-01

    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 selfrepair, adaptation to the environment, recognition and discrimination of fuzzy inputs, and conditional learning, properties that are commonly associated with biological computation.

  14. [Progress in molecular biology study of DNA computer].

    PubMed

    Zhang, Zhi-Zhou; Zhao, Jian; He, Lin

    2003-09-01

    DNA (deoxyribonucleotide acids) computer is an emerging new study area that basically combines molecular biology study of DNA molecules and computational study on how to employ these specific molecules to calculate. In 1994 Adleman described his pioneering research on DNA computing in Science. This is the first experimental report on DNA computer study. In 2001 Benenson et al published a paper in Nature regarding a programmable and autonomous DNA computing device. Because of its Turing-like functions, the device is regarded as another milestone progress for DNA computer study. The main features of DNA computer are massively parallel computing ability and potential enormous data storage capacity. Comparing with conventional electronic computers, DNA molecules provide conceptually a revolution in computing, and more and more implications have been found in various disciplines. DNA computer studies have brought great progress not only in its own computing mechanisms, but also in DNA manipulation technologies especially nano-technology. This article presents the basic principles of DNA computer, its applications, its important relationship with genomic research and our comments on all above issues.

  15. Ranked retrieval of Computational Biology models

    PubMed Central

    2010-01-01

    Background The study of biological systems demands computational support. If targeting a biological problem, the reuse of existing computational models can save time and effort. Deciding for potentially suitable models, however, becomes more challenging with the increasing number of computational models available, and even more when considering the models' growing complexity. Firstly, among a set of potential model candidates it is difficult to decide for the model that best suits ones needs. Secondly, it is hard to grasp the nature of an unknown model listed in a search result set, and to judge how well it fits for the particular problem one has in mind. Results Here we present an improved search approach for computational models of biological processes. It is based on existing retrieval and ranking methods from Information Retrieval. The approach incorporates annotations suggested by MIRIAM, and additional meta-information. It is now part of the search engine of BioModels Database, a standard repository for computational models. Conclusions The introduced concept and implementation are, to our knowledge, the first application of Information Retrieval techniques on model search in Computational Systems Biology. Using the example of BioModels Database, it was shown that the approach is feasible and extends the current possibilities to search for relevant models. The advantages of our system over existing solutions are that we incorporate a rich set of meta-information, and that we provide the user with a relevance ranking of the models found for a query. Better search capabilities in model databases are expected to have a positive effect on the reuse of existing models. PMID:20701772

  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. 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

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

    PubMed

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

    2009-09-01

    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.

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

    PubMed

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

    2010-04-01

    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.

  20. 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

  1. International Conference in Computational Cell Biology: From the Past to the Future

    DTIC Science & Technology

    2016-09-12

    International Conference in Computational Cell Biology : from the past to the future The first International Conference on Computational Cell... Biology (ICCCB) was successfully held at Blacksburg, Virginia from August 14th to 16th, 2013. Over 100 researchers were gathered at Blacksburg to present...their latest research and discussed challenges in computational cell biology research and education. The views, opinions and/or findings contained in

  2. 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.

  3. 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.

  4. 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

  5. Research in Computer Forensics

    DTIC Science & Technology

    2002-06-01

    mails . Forged Email Trusted MTA Mails with Spoofed Sender Identity Forged Emails 491 Email Forgery Forging an email on SMTP (Simple Mail Transport...As such, the discipline of computer forensic analysis has emerged to meet such needs. Computers can contain evidence in many ways, in electronic mail ...shortcut files, registry entries, printer spool and operating system logs for the system events, internet information server, Exchange mail server

  6. Mathematical and Computational Modeling in Complex Biological Systems

    PubMed Central

    Li, Wenyang; Zhu, Xiaoliang

    2017-01-01

    The biological process and molecular functions involved in the cancer progression remain difficult to understand for biologists and clinical doctors. Recent developments in high-throughput technologies urge the systems biology to achieve more precise models for complex diseases. Computational and mathematical models are gradually being used to help us understand the omics data produced by high-throughput experimental techniques. The use of computational models in systems biology allows us to explore the pathogenesis of complex diseases, improve our understanding of the latent molecular mechanisms, and promote treatment strategy optimization and new drug discovery. Currently, it is urgent to bridge the gap between the developments of high-throughput technologies and systemic modeling of the biological process in cancer research. In this review, we firstly studied several typical mathematical modeling approaches of biological systems in different scales and deeply analyzed their characteristics, advantages, applications, and limitations. Next, three potential research directions in systems modeling were summarized. To conclude, this review provides an update of important solutions using computational modeling approaches in systems biology. PMID:28386558

  7. Computational Biology: Modeling Chronic Renal Allograft Injury

    PubMed Central

    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. PMID:26284070

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. Research in parallel computing

    NASA Technical Reports Server (NTRS)

    Ortega, James M.; Henderson, Charles

    1994-01-01

    This report summarizes work on parallel computations for NASA Grant NAG-1-1529 for the period 1 Jan. - 30 June 1994. Short summaries on highly parallel preconditioners, target-specific parallel reductions, and simulation of delta-cache protocols are provided.

  14. 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.

  15. 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.

  16. 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

  17. Structuring Research Opportunities for All Biology Majors.

    ERIC Educational Resources Information Center

    Lewis, Susan E.; Conley, Lisa K.; Horst, Cynthia J.

    2003-01-01

    Describes a required research experience program for all biology majors instituted in the biology department of Carroll College. Discusses successes and challenges of coordinating a program that involves 20-40 research projects each year. (Author/NB)

  18. 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.

  19. 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.

  20. Optical computing research

    NASA Astrophysics Data System (ADS)

    Goodman, Joseph W.

    1987-10-01

    Work Accomplished: OPTICAL INTERCONNECTIONS - the powerful interconnect abilities of optical beams have led much optimism about the possible roles for optics in solving interconnect problems at various levels of computer architecture. Examined were the powerful requirements of optical interconnects at the gate-to-gate and chip-to-chip levels. OPTICAL NEUTRAL NETWORKS - basic studies of the convergence properties on the Holfield model, based on mathematical approach - graph theory. OPTICS AND ARTIFICIAL INTELLIGENCE - review the field of optical processing and artificial intelligence, with the aim of finding areas that might be particularly attractive for future investigation(s).

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. 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

  7. Computer Applications in the Biological Sciences

    DTIC Science & Technology

    1975-02-01

    accessible to so large a number of separate terminals and users at minimal cost. Computer systems such as PROPHET. MIRACLE , CHEMCON. and CRYSNET are...specific research needs is difficult and requires interdisciplinary efforts and support. Successful merging of the common interests of these two gro

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Quantitative Pathway Logic for Computational Biology

    NASA Astrophysics Data System (ADS)

    Baggi, Michele; Ballis, Demis; Falaschi, Moreno

    This paper presents an extension of Pathway Logic, called Quantitative Pathway Logic (QPL), which allows one to reason about quantitative aspects of biological processes, such as element concentrations and reactions kinetics. Besides, it supports the modeling of inhibitors, that is, chemicals which may block a given reaction whenever their concentration exceeds a certain threshold. QPL models can be specified and directly simulated using rewriting logic or can be translated into Discrete Functional Petri Nets (DFPN) which are a subclass of Hybrid Functional Petri Nets in which only discrete transitions are allowed. Under some constraints over the anonymous variables appearing in the QPL models, the transformation between the two computational models is shown to preserve computations. By using the DFPN representation our models can be graphically visualized and simulated by means of well known tools (e.g. Cell Illustrator); moreover standard Petri net analyses (e.g. topological analysis, forward/backward reachability, etc.) may be performed on the net model. An executable framework for QPL and for the translation of QPL models into DFPNs has been implemented using the rewriting-based language Maude. We have tested this system on several examples.

  17. Cambridge Healthtech Institute's Fourth Annual In silico Biology Conference "Modeling Systems Biology for Research and Target Prioritization"

    SciTech Connect

    Forst, C.

    2002-01-01

    In silico biology, the computer aided analysis of biological systems, is a relatively young research area. It first has been coined in the late 1990's and emerged from Theoretical and Computational Biology. As in other fields before, biology experiences an increased use of systems mathematics and computer simulation. With the human genome sequence available, with an exponentially growing number of completely sequenced genomes from various model organisms and with expression and proteomic data at hand, the research paradigm is shifted towards systems analysis and simulation. Computer aided modeling of complex biomolecules and assemblies are already routinely performed. Nowadays, theoretical description and computer simulation of cellular components in larger intra- and inter-cellular networks is of growing importance. Together with classic biological and clinical experiments as well as data from functional genomics, in silico biology will take the leading role in the analysis of biological systems.

  18. 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)

  19. Individualizing Instruction in Large Undergraduate Biology Laboratories. II. Computers and Investigation

    ERIC Educational Resources Information Center

    Norberg, Ann Marie

    1975-01-01

    Describes the following uses of computers in college biology laboratories: (1) to organize and analyze research data and (2) to simulate biological systems. Also being developed are computer simulations to systematically prepare students for independent investigations. (See also SE 515 092.) (LS)

  20. 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.

  1. 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…

  2. 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…

  3. The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology.

    PubMed

    Hucka, M; Finney, A; Sauro, H M; Bolouri, H; Doyle, J; Kitano, H

    2002-01-01

    Researchers in computational biology today make use of a large number of different software packages for modeling, analysis, and data manipulation and visualization. In this paper, we describe the ERATO Systems Biology Workbench (SBW), a software framework that allows these heterogeneous application components--written in diverse programming languages and running on different platforms--to communicate and use each others' data and algorithmic capabilities. Our goal is to create a simple, open-source software infrastructure which is effective, easy to implement and easy to understand. SBW uses a broker-based architecture and enables applications (potentially running on separate, distributed computers) to communicate via a simple network protocol. The interfaces to the system are encapsulated in client-side libraries that we provide for different programming languages. We describe the SBW architecture and the current set of modules, as well as alternative implementation technologies.

  4. P43-S Computational Biology Applications Suite for High-Performance Computing (BioHPC.net)

    PubMed Central

    Pillardy, J.

    2007-01-01

    One of the challenges of high-performance computing (HPC) is user accessibility. At the Cornell University Computational Biology Service Unit, which is also a Microsoft HPC institute, we have developed a computational biology application suite that allows researchers from biological laboratories to submit their jobs to the parallel cluster through an easy-to-use Web interface. Through this system, we are providing users with popular bioinformatics tools including BLAST, HMMER, InterproScan, and MrBayes. The system is flexible and can be easily customized to include other software. It is also scalable; the installation on our servers currently processes approximately 8500 job submissions per year, many of them requiring massively parallel computations. It also has a built-in user management system, which can limit software and/or database access to specified users. TAIR, the major database of the plant model organism Arabidopsis, and SGN, the international tomato genome database, are both using our system for storage and data analysis. The system consists of a Web server running the interface (ASP.NET C#), Microsoft SQL server (ADO.NET), compute cluster running Microsoft Windows, ftp server, and file server. Users can interact with their jobs and data via a Web browser, ftp, or e-mail. The interface is accessible at http://cbsuapps.tc.cornell.edu/.

  5. 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

  6. Computational studies of gene regulatory networks: in numero molecular biology.

    PubMed

    Hasty, J; McMillen, D; Isaacs, F; Collins, J J

    2001-04-01

    Remarkable progress in genomic research is leading to a complete map of the building blocks of biology. Knowledge of this map is, in turn, setting the stage for a fundamental description of cellular function at the DNA level. Such a description will entail an understanding of gene regulation, in which proteins often regulate their own production or that of other proteins in a complex web of interactions. The implications of the underlying logic of genetic networks are difficult to deduce through experimental techniques alone, and successful approaches will probably involve the union of new experiments and computational modelling techniques.

  7. Computer Science Research Funding: How Much Is Too Little?

    DTIC Science & Technology

    2009-06-01

    Bioinformatics Parallel computing Computational biology Principles of programming Computational neuroscience Real-time and embedded systems Scientific...National Security Agency ( NSA ) • Missile Defense Agency (MDA) and others The various research programs have been coordinated through the DDR&E...DOD funding included only DARPA and OSD programs. FY07 and FY08 PBR funding included DARPA, NSA , some of the Services’ basic and applied research

  8. 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.

  9. 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

  10. 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

  11. 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. 2015 S. Karger AG, Basel.

  12. Biological Dual-Use Research and Synthetic Biology of Yeast.

    PubMed

    Cirigliano, Angela; Cenciarelli, Orlando; Malizia, Andrea; Bellecci, Carlo; Gaudio, Pasquale; Lioj, Michele; Rinaldi, Teresa

    2017-04-01

    In recent years, the publication of the studies on the transmissibility in mammals of the H5N1 influenza virus and synthetic genomes has triggered heated and concerned debate within the community of scientists on biological dual-use research; these papers have raised the awareness that, in some cases, fundamental research could be directed to harmful experiments, with the purpose of developing a weapon that could be used by a bioterrorist. Here is presented an overview regarding the dual-use concept and its related international agreements which underlines the work of the Australia Group (AG) Export Control Regime. It is hoped that the principles and activities of the AG, that focuses on export control of chemical and biological dual-use materials, will spread and become well known to academic researchers in different countries, as they exchange biological materials (i.e. plasmids, strains, antibodies, nucleic acids) and scientific papers. To this extent, and with the aim of drawing the attention of the scientific community that works with yeast to the so called Dual-Use Research of Concern, this article reports case studies on biological dual-use research and discusses a synthetic biology applied to the yeast Saccharomyces cerevisiae, namely the construction of the first eukaryotic synthetic chromosome of yeast and the use of yeast cells as a factory to produce opiates. Since this organism is considered harmless and is not included in any list of biological agents, yeast researchers should take simple actions in the future to avoid the sharing of strains and advanced technology with suspicious individuals.

  13. 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…

  14. 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…

  15. Textual data compression in computational biology: a synopsis.

    PubMed

    Giancarlo, Raffaele; Scaturro, Davide; Utro, Filippo

    2009-07-01

    Textual data compression, and the associated techniques coming from information theory, are often perceived as being of interest for data communication and storage. However, they are also deeply related to classification and data mining and analysis. In recent years, a substantial effort has been made for the application of textual data compression techniques to various computational biology tasks, ranging from storage and indexing of large datasets to comparison and reverse engineering of biological networks. The main focus of this review is on a systematic presentation of the key areas of bioinformatics and computational biology where compression has been used. When possible, a unifying organization of the main ideas and techniques is also provided. It goes without saying that most of the research results reviewed here offer software prototypes to the bioinformatics community. The Supplementary Material provides pointers to software and benchmark datasets for a range of applications of broad interest. In addition to provide reference to software, the Supplementary Material also gives a brief presentation of some fundamental results and techniques related to this paper. It is at: http://www.math.unipa.it/ approximately raffaele/suppMaterial/compReview/

  16. 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

  17. Computing Platforms for Big Biological Data Analytics: Perspectives and Challenges.

    PubMed

    Yin, Zekun; Lan, Haidong; Tan, Guangming; Lu, Mian; Vasilakos, Athanasios V; Liu, Weiguo

    2017-01-01

    The last decade has witnessed an explosion in the amount of available biological sequence data, due to the rapid progress of high-throughput sequencing projects. However, the biological data amount is becoming so great that traditional data analysis platforms and methods can no longer meet the need to rapidly perform data analysis tasks in life sciences. As a result, both biologists and computer scientists are facing the challenge of gaining a profound insight into the deepest biological functions from big biological data. This in turn requires massive computational resources. Therefore, high performance computing (HPC) platforms are highly needed as well as efficient and scalable algorithms that can take advantage of these platforms. In this paper, we survey the state-of-the-art HPC platforms for big biological data analytics. We first list the characteristics of big biological data and popular computing platforms. Then we provide a taxonomy of different biological data analysis applications and a survey of the way they have been mapped onto various computing platforms. After that, we present a case study to compare the efficiency of different computing platforms for handling the classical biological sequence alignment problem. At last we discuss the open issues in big biological data analytics.

  18. 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...

  19. 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...

  20. 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

  1. 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

  2. [Comparison study between biological vision and computer vision].

    PubMed

    Liu, W; Yuan, X G; Yang, C X; Liu, Z Q; Wang, R

    2001-08-01

    The development and bearing of biology vision in structure and mechanism were discussed, especially on the aspects including anatomical structure of biological vision, tentative classification of reception field, parallel processing of visual information, feedback and conformity effect of visual cortical, and so on. The new advance in the field was introduced through the study of the morphology of biological vision. Besides, comparison between biological vision and computer vision was made, and their similarities and differences were pointed out.

  3. 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).

  4. 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

  5. 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

  6. Tutoring in School Biology by Computer Conference.

    ERIC Educational Resources Information Center

    Baggott, Linda; Wright, Bruce

    1997-01-01

    Describes an exploration of the use of digitized images in teaching biology to school students via the new digital communications channel, the Integrated Services Digital Network (ISDN). Contains 23 references. (DDR)

  7. Community-driven computational biology with Debian Linux.

    PubMed

    Möller, Steffen; Krabbenhöft, Hajo Nils; Tille, Andreas; Paleino, David; Williams, Alan; Wolstencroft, Katy; Goble, Carole; Holland, Richard; Belhachemi, Dominique; Plessy, Charles

    2010-12-21

    The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources for research. In order to feed the steady demand for updates on software and associated data, a service infrastructure is required for sharing and providing these tools to heterogeneous computing environments. The Debian Med initiative provides ready and coherent software packages for medical informatics and bioinformatics. These packages can be used together in Taverna workflows via the UseCase plugin to manage execution on local or remote machines. If such packages are available in cloud computing environments, the underlying hardware and the analysis pipelines can be shared along with the software. Debian Med closes the gap between developers and users. It provides a simple method for offering new releases of software and data resources, thus provisioning a local infrastructure for computational biology. For geographically distributed teams it can ensure they are working on the same versions of tools, in the same conditions. This contributes to the world-wide networking of researchers.

  8. Community-driven computational biology with Debian Linux

    PubMed Central

    2010-01-01

    Background The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources for research. In order to feed the steady demand for updates on software and associated data, a service infrastructure is required for sharing and providing these tools to heterogeneous computing environments. Results The Debian Med initiative provides ready and coherent software packages for medical informatics and bioinformatics. These packages can be used together in Taverna workflows via the UseCase plugin to manage execution on local or remote machines. If such packages are available in cloud computing environments, the underlying hardware and the analysis pipelines can be shared along with the software. Conclusions Debian Med closes the gap between developers and users. It provides a simple method for offering new releases of software and data resources, thus provisioning a local infrastructure for computational biology. For geographically distributed teams it can ensure they are working on the same versions of tools, in the same conditions. This contributes to the world-wide networking of researchers. PMID:21210984

  9. 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…

  10. 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…

  11. Session on computation in biological pathways

    SciTech Connect

    Karp, P.D.; Riley, M.

    1996-12-31

    The papers in this session focus on the development of pathway databases and computational tools for pathway analysis. The discussion involves existing databases of sequenced genomes, as well as techniques for studying regulatory pathways.

  12. Mapping an expanding territory: computer simulations in evolutionary biology.

    PubMed

    Huneman, Philippe

    2014-08-01

    The pervasive use of computer simulations in the sciences brings novel epistemological issues discussed in the philosophy of science literature since about a decade. Evolutionary biology strongly relies on such simulations, and in relation to it there exists a research program (Artificial Life) that mainly studies simulations themselves. This paper addresses the specificity of computer simulations in evolutionary biology, in the context (described in Sect. 1) of a set of questions about their scope as explanations, the nature of validation processes and the relation between simulations and true experiments or mathematical models. After making distinctions, especially between a weak use where simulations test hypotheses about the world, and a strong use where they allow one to explore sets of evolutionary dynamics not necessarily extant in our world, I argue in Sect. 2 that (weak) simulations are likely to represent in virtue of the fact that they instantiate specific features of causal processes that may be isomorphic to features of some causal processes in the world, though the latter are always intertwined with a myriad of different processes and hence unlikely to be directly manipulated and studied. I therefore argue that these simulations are merely able to provide candidate explanations for real patterns. Section 3 ends up by placing strong and weak simulations in Levins' triangle, that conceives of simulations as devices trying to fulfil one or two among three incompatible epistemic values (precision, realism, genericity).

  13. 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.

  14. 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.

  15. Research on orchid biology and biotechnology.

    PubMed

    Hsiao, Yu-Yun; Pan, Zhao-Jun; Hsu, Chia-Chi; Yang, Ya-Ping; Hsu, Yi-Chin; Chuang, Yu-Chen; Shih, Hsing-Hui; Chen, Wen-Huei; Tsai, Wen-Chieh; Chen, Hong-Hwa

    2011-09-01

    Orchidaceae constitute one of the largest families of angiosperms. They are one of the most ecological and evolutionary significant plants and have successfully colonized almost every habitat on earth. Because of the significance of plant biology, market needs and the current level of breeding technologies, basic research into orchid biology and the application of biotechnology in the orchid industry are continually endearing scientists to orchids in Taiwan. In this introductory review, we give an overview of the research activities in orchid biology and biotechnology, including the status of genomics, transformation technology, flowering regulation, molecular regulatory mechanisms of floral development, scent production and color presentation. This information will provide a broad scope for study of orchid biology and serve as a starting point for uncovering the mysteries of orchid evolution.

  16. 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.

  17. 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, SW...

  18. 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

  19. Biological Agent Neutralization/Computational Modeling Studies

    DTIC Science & Technology

    2010-09-01

    Computational Results • Solution of the Navier - Stokes equations for the flow inside the device has been obtained by the GASP solver. • 3rd order of...flkv:.lD ENTERPRISE I OFFICE I PHONE: Ali) -Eugene Stokes / 767-2826 / flL DATE: tt4 PUBLIC AFFAIRS: KJtJJ/,1.1/~A. !ffi / ~ ~ ~uwc:- DATE:’ ti{fr._(-u...to temperatures from 165C to 275C for times between 25ms and 100ms. The data was used to anchor computational fluid dynamics (CFD) flow modeling of

  20. 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…

  1. Using Computer Technology to Create a Revolutionary New Style of Biology.

    ERIC Educational Resources Information Center

    Monaghan, Peter

    1993-01-01

    A $13-million gift of William Gates III to the University of Washington has enabled establishment of the country's first department in molecular biotechnology, a combination of medicine and molecular biology to be practiced by researchers versed in a variety of fields, including computer science, computation, applied physics, and engineering. (MSE)

  2. 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…

  3. 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.

  4. 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.…

  5. 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.…

  6. Using Computers To Enhance Action Research.

    ERIC Educational Resources Information Center

    Adamy, Peter

    This paper outlines the potential benefits of using computers to enhance the action research process for classroom teachers. An argument is made for classifying action research as a type of qualitative methodology. This argument is then used to apply the literature on computer use in qualitative research to its use in action research; advantages…

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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…

  12. 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…

  13. Coarse-graining methods for computational biology.

    PubMed

    Saunders, Marissa G; Voth, Gregory A

    2013-01-01

    Connecting the molecular world to biology requires understanding how molecular-scale dynamics propagate upward in scale to define the function of biological structures. To address this challenge, multiscale approaches, including coarse-graining methods, become necessary. We discuss here the theoretical underpinnings and history of coarse-graining and summarize the state of the field, organizing key methodologies based on an emerging paradigm for multiscale theory and modeling of biomolecular systems. This framework involves an integrated, iterative approach to couple information from different scales. The primary steps, which coincide with key areas of method development, include developing first-pass coarse-grained models guided by experimental results, performing numerous large-scale coarse-grained simulations, identifying important interactions that drive emergent behaviors, and finally reconnecting to the molecular scale by performing all-atom molecular dynamics simulations guided by the coarse-grained results. The coarse-grained modeling can then be extended and refined, with the entire loop repeated iteratively if necessary.

  14. 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.

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

    PubMed Central

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

    2011-01-01

    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. PMID:22081221

  16. 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

  17. 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.

  18. Computational science for energy research

    NASA Astrophysics Data System (ADS)

    Abgrall, Rémi; Koren, Barry

    2017-09-01

    Computational science complements theory and experiments. It can deliver knowledge and understanding in application areas where the latter two can not. Computational science is particularly important for the simulation of various energy-related processes, ranging from classical energy processes as combustion and subsurface oil-reservoir flows to more modern processes as wind-farm aerodynamics, photovoltaics and - very challenging from a computational perspective - tokamak-plasma physics.

  19. Continued research on computer-based testing.

    PubMed Central

    Clyman, S. G.; Julian, E. R.; Orr, N. A.; Dillon, G. F.; Cotton, K. E.

    1991-01-01

    The National Board of Medical Examiners has developed computer-based examination formats for use in evaluating physicians in training. This paper describes continued research on these formats including attitudes about computers and effects of factors not related to the trait being measured; differences between paper-administered and computer-administered multiple-choice questions; and the characteristics of simulation formats. The implications for computer-based testing and further research are discussed. PMID:1807703

  20. 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.

  1. Molecular biology research in neuropsychiatry: India's contribution.

    PubMed

    Sathyanarayana Rao, T S; Ramesh, B N; Vasudevaraju, P; Rao, K S J

    2010-01-01

    Neuropsychiatric disorders represent the second largest cause of morbidity worldwide. These disorders have complex etiology and patho-physiology. The major lacunae in the biology of the psychiatric disorders include genomics, biomarkers and drug discovery, for the early detection of the disease, and have great application in the clinical management of disease. Indian psychiatrists and scientists played a significant role in filling the gaps. The present annotation provides in depth information related to research contributions on the molecular biology research in neuropsychiatric disorders in India. There is a great need for further research in this direction as to understand the genetic association of the neuropsychiatric disorders; molecular biology has a tremendous role to play. The alterations in gene expression are implicated in the pathogenesis of several neuropsychiatric disorders, including drug addiction and depression. The development of transgenic neuropsychiatric animal models is of great thrust areas. No studies from India in this direction. Biomarkers in neuropsychiatric disorders are of great help to the clinicians for the early diagnosis of the disorders. The studies related to gene-environment interactions, DNA instability, oxidative stress are less studied in neuropsychiatric disorders and making efforts in this direction will lead to pioneers in these areas of research in India. In conclusion, we provided an insight for future research direction in molecular understanding of neuropsychiatry disorders.

  2. 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.

  3. 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.

  4. [Practice relevant research in biological psychiatry].

    PubMed

    Meyer-Lindenberg, A

    2015-11-01

    The practice of psychiatry would be unthinkable without modern psychopharmacology. Drug treatment, especially of severe psychiatric disorders, is often a precondition of community participation, societal reintegration and recovery. Seen in this context it is understandable that biological psychiatry has long been primarily defined by its close interconnection with psychopharmacology and has been perceived this way by practicing physicians. In recent years, however, the concept of what is "biological" has markedly expanded and so has the outreach of this approach into the practice of psychiatry. This article discusses examples showing that biological research methods provide new impulses for individualized medicine, psychotherapy and understanding environmental risks and therefore provide the basis for a preemptive and preventive approach that will be the key to master the challenges posed by the severe burden of mental illness.

  5. 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.

  6. 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.

  7. 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.

  8. Biological defense research program. Final report

    SciTech Connect

    Not Available

    1989-04-01

    The proposed action, and subject of this Final Environmental Impact Statement (FEIS), is continuation of the Biological Defense Research Program (BDRP). The BDRP is a research, development, test and evaluation (RDT E) program conducted by the Department of Defense (DoD), with the Department of the Army (DA) serving as the executive agent. This FEIS addresses the ongoing program and provides a basis for evaluating future BDRP activities. The objectives of the BDRP are to develop measures for detection, treatment, protection and decontamination of potential biological warfare threat agents. Development of medical defensive measures, such as prophylactic vaccines and drugs, therapeutic measures, and patient treatment and management protocols are important components of the program. The purpose of the BDRP is to maintain and promote a solid national defense posture with respect to potential biological warfare threats. The BDRP supports RDT E efforts necessary for the maintenance and development of defensive measures and materiel to meet these threats. In addition to promoting the national defense posture, the BDRP benefits the scientific community in general through its research and development efforts, and benefits the global population in the development of diagnostic methods, and vaccine and drug therapies for the treatment of diseases.

  9. 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.

  10. [Cremation--biological source for gender research].

    PubMed

    Grosskopf, Birgit; Gramsch, Alexander

    2004-09-01

    This article presents a project designed for prehistoric gender research. It focuses on the late Bronze Age to early Iron Age urnfield in Cottbus "Alvensleben-Kaserne", Brandenburg. The cremation remains were emptied from the urns layer by layer. This provided excellent conditions for a critical reconstruction of the funeral rituals related to the cremation. Detailed recording of each bone fragment in each layer made possible the discovery of the ritual deposition of burnt bones according to the anatomical order. Cremated bones, a primarily biological source, are also a substantial resource for cultural historical research, e.g., on funeral practices as well as social structures.

  11. 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.

  12. 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.

  13. [Computational radiofrequency electromagnetic field dosimetry in evaluation of biological effects].

    PubMed

    Perov, S Iu; Kudryashov, Iu B; Rubtsova, N B

    2012-01-01

    Given growing computational resources, radiofrequency electromagnetic field dosimetry is becoming more vital in the study of biological effects of non-ionizing electromagnetic radiation. The study analyzes numerical methods which are used in theoretical dosimetry to assess the exposure level and specific absorption rate distribution. The advances of theoretical dosimetry are shown. Advantages and disadvantages of different methods are analyzed in respect to electromagnetic field biological effects. The finite-difference time-domain method was implemented in detail; also evaluated were possible uncertainties of complex biological structure simulation for bioelectromagnetic investigations.

  14. Research on Computers and Problem Solving.

    ERIC Educational Resources Information Center

    Burton, John K.; And Others

    1988-01-01

    Eight articles review and report on research involving computers and problem solving skills. Topics discussed include research design; problem solving skills and programing languages, including BASIC and LOGO; computer anxiety; diagnostic programs for arithmetic problems; and relationships between ability and problem solving scores and between…

  15. Research in computational fluid dynamics

    NASA Technical Reports Server (NTRS)

    Murman, Earll M.

    1987-01-01

    The numerical integration of quasi-one-dimensional unsteady flow problems which involve finite rate chemistry are discussed, and are expressed in terms of conservative form Euler and species conservation equations. Hypersonic viscous calculations for delta wing geometries is also examined. The conical Navier-Stokes equations model was selected in order to investigate the effects of viscous-inviscid interations. The more complete three-dimensional model is beyond the available computing resources. The flux vector splitting method with van Leer's MUSCL differencing is being used. Preliminary results were computed for several conditions.

  16. 77 FR 55201 - Biological and Environmental Research Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-07

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

  17. 78 FR 12043 - Biological and Environmental Research Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-21

    ... Biological and Environmental Research Advisory Committee AGENCY: Office of Science, Department of Energy... and Environmental Research Advisory Committee (BERAC). The Federal Advisory Committee Act (Pub. L. No... Science, Office of Biological and Environmental Research, SC-23/Germantown Building, 1000 Independence...

  18. 78 FR 34088 - Biological and Environmental Research Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-06

    ... Office of Biological and Environmental Research News from the Biological Systems Science and Climate and... Biological and Environmental Research Advisory Committee AGENCY: Office of Science, Department of Energy..., Office of Science, Office of Biological and Environmental Research, SC-23/Germantown Building, 1000...

  19. 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.

  20. Reproducible research in computational science.

    PubMed

    Peng, Roger D

    2011-12-02

    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.

  1. 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)

  2. 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)

  3. COMPUTER-AIDED WORD RESEARCH.

    ERIC Educational Resources Information Center

    SILIAKUS, H.J.

    IN PREPARATION FOR THE DEVELOPMENT OF A GENERAL FREQUENCY WORD LIST IN GERMAN DESIGNED TO MEET THE NEEDS OF THE INTERMEDIATE AND ADVANCED LEVELS OF READING IN THE GERMAN CURRICULUM, A COMPUTER-BASED WORD COUNT WAS BEGUN IN AUSTRALIA'S UNIVERSITY OF ADELAIDE. USING MAGNETIC TAPES CONTAINING (1) A TEXT OF OVER 100,000 RUNNING WORDS, (2) 1,000 MOST…

  4. Understanding diseases by mouse click: the promise and potential of computational approaches in Systems Biology.

    PubMed

    Klauschen, F; Angermann, B R; Meier-Schellersheim, M

    2007-09-01

    Computational modelling approaches can nowadays build large-scale simulations of cellular behaviour based on data describing detailed molecular level interactions, thus performing the space- and time-scale integrations that would be impossible just by intuition. Recent progress in the development of both experimental methods and computational tools has provided the means to generate the necessary quantitative data and has made computational methods accessible even to non-theorists, thereby removing a major hurdle that has in the past made many experimentalists hesitate to invest serious effort in formulating quantitative models. We describe how computational biology differs from classical bioinformatics, how it emerged from mathematical biology and elucidate the role it plays for the integration of traditionally separated areas of biomedical research within the larger framework of Systems Biology.

  5. Understanding diseases by mouse click: the promise and potential of computational approaches in Systems Biology

    PubMed Central

    Klauschen, F; Angermann, B R; Meier-Schellersheim, M

    2007-01-01

    Computational modelling approaches can nowadays build large-scale simulations of cellular behaviour based on data describing detailed molecular level interactions, thus performing the space- and time-scale integrations that would be impossible just by intuition. Recent progress in the development of both experimental methods and computational tools has provided the means to generate the necessary quantitative data and has made computational methods accessible even to non-theorists, thereby removing a major hurdle that has in the past made many experimentalists hesitate to invest serious effort in formulating quantitative models. We describe how computational biology differs from classical bioinformatics, how it emerged from mathematical biology and elucidate the role it plays for the integration of traditionally separated areas of biomedical research within the larger framework of Systems Biology. PMID:17666096

  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. 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…

  8. 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…

  9. Evaluating Computer Lab Modules for Large Biology Courses.

    ERIC Educational Resources Information Center

    Eichinger, David C.; And Others

    This paper describes the first phase of a study to investigate students' evaluations of computer laboratory modules in a university-level, non-majors biology course. The National Science Foundation-funded project has two primary goals: (1) to develop programmable, multifunctional Bio LabStations for data collection and analysis, lab extensions,…

  10. 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.

  11. 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.

  12. 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.

  13. Synergy between medicinal chemistry and biological research.

    PubMed

    Moncada, Salvador; Coaker, Hannah

    2014-09-01

    Salvador Moncada studied medicine at the University of El Salvador (El Salvador) before coming to the UK in 1971 to work on a PhD with Professor John Vane at the Institute of Basic Medical Sciences, Royal College of Surgeons (UK). After a short period of research at the University of Honduras (Honduras), he joined the Wellcome Research Laboratories (UK) where he became Head of the Department of Prostaglandin Research and later, Director of Research. He returned to academic life in 1996 as founder and director of the Wolfson Institute for Biomedical Research at University College London (UK). Moncada played a role in the discovery of the mechanism of action of aspirin-like drugs and later led the teams which discover prostacyclin and identified nitric oxide as a biological mediator. In his role as a Director of Research of the Wellcome Laboratories, he oversaw the discovery and development of medicines for epilepsy, migraine, malaria and cancer. Currently, he is working on the regulation of cell proliferation as Director of the Institute of Cancer Sciences at the University of Manchester (UK). Moncada has won numerous awards from the international scientific community and in 2010, he received a knighthood from Her Majesty Queen Elizabeth II for his services to science.

  14. Biological research on a Space Station

    NASA Technical Reports Server (NTRS)

    Krikorian, A. D.; Johnson, Catherine C.

    1990-01-01

    A Space Station can provide reliable, long duration access to ug environments for basic and applied biological research. The uniqueness of access to near-weightless environments to probe fundamental questions of significance to gravitational and Space biologists can be exploited from many vantage points. Access to centrifuge facilities that can provide 1 g and hypo-g controls will permit identification of gravity-dependent or primary effects. Understanding secondary effects of the ug environment as well will allow a fuller exploitation of the Space environment.

  15. 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 ...

  16. 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 ...

  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. 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.

  19. 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

  20. Race in biological and biomedical research.

    PubMed

    Cooper, Richard S

    2013-11-01

    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.

  1. Research Guidelines for Computer-Assisted Instruction.

    ERIC Educational Resources Information Center

    Hickey, Albert E.

    Prepared for the Defense Advanced Research Projects Agency (ARPA), this report contains 59 recommendations for research and development in support of computer-assisted instruction (CAI). The guidelines were derived from interviews with 14 leading education researchers. They cover the following learning and instruction variables: (1) learning…

  2. Research Techniques Made Simple: Bioinformatics for Genome-Scale Biology.

    PubMed

    Foulkes, Amy C; Watson, David S; Griffiths, Christopher E M; Warren, Richard B; Huber, Wolfgang; Barnes, Michael R

    2017-09-01

    High-throughput biology presents unique opportunities and challenges for dermatological research. Drawing on a small handful of exemplary studies, we review some of the major lessons of these new technologies. We caution against several common errors and introduce helpful statistical concepts that may be unfamiliar to researchers without experience in bioinformatics. We recommend specific software tools that can aid dermatologists at varying levels of computational literacy, including platforms with command line and graphical user interfaces. The future of dermatology lies in integrative research, in which clinicians, laboratory scientists, and data analysts come together to plan, execute, and publish their work in open forums that promote critical discussion and reproducibility. In this article, we offer guidelines that we hope will steer researchers toward best practices for this new and dynamic era of data intensive dermatology. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  3. [Animal experimentation, computer simulation and surgical research].

    PubMed

    Carpentier, Alain

    2009-11-01

    We live in a digital world In medicine, computers are providing new tools for data collection, imaging, and treatment. During research and development of complex technologies and devices such as artificial hearts, computer simulation can provide more reliable information than experimentation on large animals. In these specific settings, animal experimentation should serve more to validate computer models of complex devices than to demonstrate their reliability.

  4. Optical Computing Research at NASA

    NASA Technical Reports Server (NTRS)

    Abdeldayem, H. A.; Paley, Mark S.

    1999-01-01

    Scientists at the Marshall Space Flight Center (NASA), Universities Space Research Association (USRA), the University of Alabama in Huntsville (UAH), and the Alliance for Nonlinear Optics (ANLO) are working to develop thin-film organic-based materials useful for making optical devices. These devices can use photons exclusively to transmit data, or use both photons and electrons to form electronic/optical hybrids called electrooptic devices.

  5. 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.

  6. 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...

  7. 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...

  8. The Learning of Biology: A Structural Basis for Future Research

    ERIC Educational Resources Information Center

    Murray, Darrel L.

    1977-01-01

    This article reviews recent research studies and experiences relating the learning theories of Ausubel to biology instruction. Also some suggestions are made for future research on the learning of biology. (MR)

  9. The Learning of Biology: A Structural Basis for Future Research

    ERIC Educational Resources Information Center

    Murray, Darrel L.

    1977-01-01

    This article reviews recent research studies and experiences relating the learning theories of Ausubel to biology instruction. Also some suggestions are made for future research on the learning of biology. (MR)

  10. 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

  11. 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

  12. Teaching Computer Applications in Historical Research.

    ERIC Educational Resources Information Center

    Allwsang, John M.

    1992-01-01

    Contends that courses designed to help students learn about the application of computers to historical study can be prepared and taught in a number of ways. Describes a college-level course that combines an introduction to computer applications with a student research project. (CFR)

  13. 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.

  14. 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.

  15. Natural computing for mechanical systems research: A tutorial overview

    NASA Astrophysics Data System (ADS)

    Worden, Keith; Staszewski, Wieslaw J.; Hensman, James J.

    2011-01-01

    A great many computational algorithms developed over the past half-century have been motivated or suggested by biological systems or processes, the most well-known being the artificial neural networks. These algorithms are commonly grouped together under the terms soft or natural computing. A property shared by most natural computing algorithms is that they allow exploration of, or learning from, data. This property has proved extremely valuable in the solution of many diverse problems in science and engineering. The current paper is intended as a tutorial overview of the basic theory of some of the most common methods of natural computing as they are applied in the context of mechanical systems research. The application of some of the main algorithms is illustrated using case studies. The paper also attempts to give some indication as to which of the algorithms emerging now from the machine learning community are likely to be important for mechanical systems research in the future.

  16. 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.)

  17. 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)

  18. 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.

  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. 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.

  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. 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

  3. 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... 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...

  4. 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 beginning...

  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... to the Director, Office of Science on the biological and environmental research programs..., notice is hereby given that the Biological and Environmental Research Advisory Committee will be renewed...

  6. 75 FR 53685 - Biological and Environmental Research Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-01

    ... Doc No: 2010-21673] DEPARTMENT OF ENERGY Biological and Environmental Research Advisory Committee... announces a meeting of the Biological and Environmental Research Advisory Committee (BERAC). The Federal.... Department of Energy, Office of Science, Office of Biological and Environmental Research, SC-23/Germantown...

  7. 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

  8. Natural computing and biological evolution: a new paradigm.

    PubMed

    Giuditta, Antonio

    2008-01-01

    After a brief outline of the available hypotheses on the mechanism of biological evolution, attention is called on the global nature of the variations leading to the generation of new species. Integrated changes may hardly be attributed to beneficial random mutations of single traits even if assisted by a phylogenetic elimination of poorly adapted individuals. Rather, integrated variations are likely to reflect the outcome of cybernetic algorithms (natural computing) operating on organism's resources and impending environmental changes. As all organisms are endowed with computing capacities that modulate and integrate ontogenetic development and maintenance of biological functions, structures, and behaviors, these capacities are assumed to have moulded the evolutionary variations of organisms, and their transfer to the progeny.

  9. A biological solution to a fundamental distributed computing problem.

    PubMed

    Afek, Yehuda; Alon, Noga; Barad, Omer; Hornstein, Eran; Barkai, Naama; Bar-Joseph, Ziv

    2011-01-14

    Computational and biological systems are often distributed so that processors (cells) jointly solve a task, without any of them receiving all inputs or observing all outputs. Maximal independent set (MIS) selection is a fundamental distributed computing procedure that seeks to elect a set of local leaders in a network. A variant of this problem is solved during the development of the fly's nervous system, when sensory organ precursor (SOP) cells are chosen. By studying SOP selection, we derived a fast algorithm for MIS selection that combines two attractive features. First, processors do not need to know their degree; second, it has an optimal message complexity while only using one-bit messages. Our findings suggest that simple and efficient algorithms can be developed on the basis of biologically derived insights.

  10. 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

  11. Computational biology of cardiac myocytes: proposed standards for the physiome

    PubMed Central

    Smith, Nicolas P.; Crampin, Edmund J.; Niederer, Steven A.; Bassingthwaighte, James B.; Beard, Daniel A.

    2010-01-01

    Summary Predicting information about human physiology and pathophysiology from genomic data is a compelling, but unfulfilled goal of post-genomic biology. This is the aim of the so-called Physiome Project and is, undeniably, an ambitious goal. Yet if we can exploit even a small proportion of the rich and varied experimental data currently available, significant insights into clinically important aspects of human physiology will follow. To achieve this requires the integration of data from disparate sources into a common framework. Extrapolation of available data across species, laboratory techniques and conditions requires a quantitative approach. Mathematical models allow us to integrate molecular information into cellular, tissue and organ-level, and ultimately clinically relevant scales. In this paper we argue that biophysically detailed computational modelling provides the essential tool for this process and, furthermore, that an appropriate framework for annotating, databasing and critiquing these models will be essential for the development of integrative computational biology. PMID:17449822

  12. Computational intelligence approaches for pattern discovery in biological systems.

    PubMed

    Fogel, Gary B

    2008-07-01

    Biology, chemistry and medicine are faced by tremendous challenges caused by an overwhelming amount of data and the need for rapid interpretation. Computational intelligence (CI) approaches such as artificial neural networks, fuzzy systems and evolutionary computation are being used with increasing frequency to contend with this problem, in light of noise, non-linearity and temporal dynamics in the data. Such methods can be used to develop robust models of processes either on their own or in combination with standard statistical approaches. This is especially true for database mining, where modeling is a key component of scientific understanding. This review provides an introduction to current CI methods, their application to biological problems, and concludes with a commentary about the anticipated impact of these approaches in bioinformatics.

  13. Exploiting Graphics Processing Units for Computational Biology and Bioinformatics

    PubMed Central

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

    2010-01-01

    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 general-purpose 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. PMID:20658333

  14. 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.

  15. A Computer Solution to Clinical and Research Computing Needs

    PubMed Central

    London, Jack W.

    1985-01-01

    A computer cluster is a recent advance in network technology in which a group of processors have simultaneous read and write access to the same records on one or more disk drives. The mass storage is associated with all the processors on the cluster, rather than any single processor. When combined with an intelligent terminal port selector, the computer cluster offers significant advantages in a hospital environment. Further benefits accrue when there exists a need for sharing data between hospital information and scientific research applications. A description of the hardware and software elements of a computer cluster and the use of a cluster at a medical center comprised of a hospital and research institute will be presented. The advantages and limitations of this approach will be discussed.

  16. 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

  17. Topological properties of robust biological and computational networks.

    PubMed

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

    2014-07-06

    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.

  18. 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.

  19. 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.

  20. 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.

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

    PubMed Central

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

    2011-01-01

    The twentieth century was marked by extraordinary advances in our understanding of microbes and infectious disease, but pandemics remain, food and waterborne illnesses are frequent, multidrug-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 twenty-first 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. PMID:21285433

  2. 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. Copyright © 2012 Elsevier Ltd. All rights reserved.

  3. HPC AND GRID COMPUTING FOR INTEGRATIVE BIOMEDICAL RESEARCH

    PubMed Central

    Kurc, Tahsin; Hastings, Shannon; Kumar, Vijay; Langella, Stephen; Sharma, Ashish; Pan, Tony; Oster, Scott; Ervin, David; Permar, Justin; Narayanan, Sivaramakrishnan; Gil, Yolanda; Deelman, Ewa; Hall, Mary; Saltz, Joel

    2010-01-01

    Integrative biomedical research projects query, analyze, and integrate many different data types and make use of datasets obtained from measurements or simulations of structure and function at multiple biological scales. With the increasing availability of high-throughput and high-resolution instruments, the integrative biomedical research imposes many challenging requirements on software middleware systems. In this paper, we look at some of these requirements using example research pattern templates. We then discuss how middleware systems, which incorporate Grid and high-performance computing, could be employed to address the requirements. PMID:20107625

  4. 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.

  5. 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.

  6. Mathematical and computational challenges in population biology and ecosystems science.

    PubMed

    Levin, S A; Grenfell, B; Hastings, A; Perelson, A S

    1997-01-17

    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.

  7. Advanced Computer Simulations Of Nanomaterials And Stochastic Biological Processes

    NASA Astrophysics Data System (ADS)

    Minakova, Maria S.

    This dissertation consists of several parts. The first two chapters are devoted to of study of dynamic processes in cellular organelles called filopodia. A stochastic kinetics approach is used to describe non-equilibrium evolution of the filopodial system from nano- to micro scales. Dynamic coupling between chemistry and mechanics is also taken into account in order to investigate the influence of focal adhesions on cell motility. The second chapter explores the possibilities and effects of motor enhanced delivery of actin monomers to the polymerizing tips of filopodia, and how the steady-state filopodial length can exceed the limit set by pure diffusion. Finally, we also challenge the currently existing view of active transport and propose a new theoretical model that accurately describes the motor dynamics and concentration profiles seen in experiments in a physically meaningful way. The third chapter is a result of collaboration between three laboratories, as a part of Energy Frontier Research Center at the University of North Carolina at Chapel Hill. The work presented here unified the fields of synthetic chemistry, photochemistry, and computational physical chemistry in order to investigate a novel bio-synthetic compound and its energy transfer capabilities. This particular peptide-based design has never been studied via Molecular Dynamics with high precision, and it is the first attempt known to us to simulate the whole chromophore-peptide complex in solution in order to gain detailed information about its structural and dynamic features. The fourth chapter deals with the non-equilibrium relaxation induced transport of water molecules in a microemulsion. This problem required a different set of methodologies and a more detailed, all-atomistic treatment of the system. We found interesting water clustering effects and elucidated the most probable mechanism of water transfer through oil under the condition of saturated Langmuir monolayers. Together these

  8. Application of Computational Methods in Planaria Research: A Current Update.

    PubMed

    Ghosh, Shyamasree

    2017-07-06

    Planaria is a member of the Phylum Platyhelminthes including flatworms. Planarians possess the unique ability of regeneration from adult stem cells or neoblasts and finds importance as a model organism for regeneration and developmental studies. Although research is being actively carried out globally through conventional methods to understand the process of regeneration from neoblasts, biology of development, neurobiology and immunology of Planaria, there are many thought provoking questions related to stem cell plasticity, and uniqueness of regenerative potential in Planarians amongst other members of Phylum Platyhelminthes. The complexity of receptors and signalling mechanisms, immune system network, biology of repair, responses to injury are yet to be understood in Planaria. Genomic and transcriptomic studies have generated a vast repository of data, but their availability and analysis is a challenging task. Data mining, computational approaches of gene curation, bioinformatics tools for analysis of transcriptomic data, designing of databases, application of algorithms in deciphering changes of morphology by RNA interference (RNAi) approaches, understanding regeneration experiments is a new venture in Planaria research that is helping researchers across the globe in understanding the biology. We highlight the applications of Hidden Markov models (HMMs) in designing of computational tools and their applications in Planaria decoding their complex biology.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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)

  14. 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)

  15. 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, Office...

  16. 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.

  17. Frontiers of research in advanced computations

    SciTech Connect

    1996-07-01

    The principal mission of the Institute for Scientific Computing Research is to foster interactions among LLNL researchers, universities, and industry on selected topics in scientific computing. In the area of computational physics, the Institute has developed a new algorithm, GaPH, to help scientists understand the chemistry of turbulent and driven plasmas or gases at far less cost than other methods. New low-frequency electromagnetic models better describe the plasma etching and deposition characteristics of a computer chip in the making. A new method for modeling realistic curved boundaries within an orthogonal mesh is resulting in a better understanding of the physics associated with such boundaries and much quicker solutions. All these capabilities are being developed for massively parallel implementation, which is an ongoing focus of Institute researchers. Other groups within the Institute are developing novel computational methods to address a range of other problems. Examples include feature detection and motion recognition by computer, improved monitoring of blood oxygen levels, and entirely new models of human joint mechanics and prosthetic devices.

  18. A framework to establish credibility of computational models in biology.

    PubMed

    Patterson, Eann A; Whelan, Maurice P

    2016-10-01

    Computational models in biology and biomedical science are often constructed to aid people's understanding of phenomena or to inform decisions with socioeconomic consequences. Model credibility is the willingness of people to trust a model's predictions and is often difficult to establish for computational biology models. A 3 × 3 matrix has been proposed to allow such models to be categorised with respect to their testability and epistemic foundation in order to guide the selection of an appropriate process of validation to supply evidence to establish credibility. Three approaches to validation are identified that can be deployed depending on whether a model is deemed untestable, testable or lies somewhere in between. In the latter two cases, the validation process involves the quantification of uncertainty which is a key output. The issues arising due to the complexity and inherent variability of biological systems are discussed and the creation of 'digital twins' proposed as a means to alleviate the issues and provide a more robust, transparent and traceable route to model credibility and acceptance.

  19. 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

  20. 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…

  1. 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…

  2. 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.

  3. 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

  4. 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

  5. MACBenAbim: A Multi-platform Mobile Application for searching keyterms in Computational Biology and Bioinformatics.

    PubMed

    Oluwagbemi, Olugbenga O; Adewumi, Adewole; Esuruoso, Abimbola

    2012-01-01

    Computational biology and bioinformatics are gradually gaining grounds in Africa and other developing nations of the world. However, in these countries, some of the challenges of computational biology and bioinformatics education are inadequate infrastructures, and lack of readily-available complementary and motivational tools to support learning as well as research. This has lowered the morale of many promising undergraduates, postgraduates and researchers from aspiring to undertake future study in these fields. In this paper, we developed and described MACBenAbim (Multi-platform Mobile Application for Computational Biology and Bioinformatics), a flexible user-friendly tool to search for, define and describe the meanings of keyterms in computational biology and bioinformatics, thus expanding the frontiers of knowledge of the users. This tool also has the capability of achieving visualization of results on a mobile multi-platform context. MACBenAbim is available from the authors for non-commercial purposes.

  6. 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.

  7. 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.

  8. 76 FR 8357 - Biological and Environmental Research Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-14

    ... Biological and Environmental Research Advisory Committee AGENCY: Department of Energy; Office of Science... News from the Biological Systems Science and Climate and Environmental Sciences Divisions Discussions on the Climate and Environmental Sciences Division Committee of Visitors Response and the...

  9. A Computational Architecture for Programmable Automation Research

    NASA Astrophysics Data System (ADS)

    Taylor, Russell H.; Korein, James U.; Maier, Georg E.; Durfee, Lawrence F.

    1987-03-01

    This short paper describes recent work at the IBM T. J. Watson Research Center directed at developing a highly flexible computational architecture for research on sensor-based programmable automation. The system described here has been designed with a focus on dynamic configurability, layered user inter-faces and incorporation of sensor-based real time operations into new commands. It is these features which distinguish it from earlier work. The system is cur-rently being implemented at IBM for research purposes and internal use and is an outgrowth of programmable automation research which has been ongoing since 1972 [e.g., 1, 2, 3, 4, 5, 6] .

  10. 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)

  11. 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)

  12. hackseq: Catalyzing collaboration between biological and computational scientists via hackathon

    PubMed Central

    2017-01-01

    hackseq ( http://www.hackseq.com) was a genomics hackathon with the aim of bringing together a diverse set of biological and computational scientists to work on collaborative bioinformatics projects. In October 2016, 66 participants from nine nations came together for three days for hackseq and collaborated on nine projects ranging from data visualization to algorithm development. The response from participants was overwhelmingly positive with 100% (n = 54) of survey respondents saying they would like to participate in future hackathons. We detail key steps for others interested in organizing a successful hackathon and report excerpts from each project. PMID:28417000

  13. Computational adaptive optics for live three-dimensional biological imaging

    PubMed Central

    Kam, Z.; Hanser, B.; Gustafsson, M. G. L.; Agard, D. A.; Sedat, J. W.

    2001-01-01

    Light microscopy of thick biological samples, such as tissues, is often limited by aberrations caused by refractive index variations within the sample itself. This problem is particularly severe for live imaging, a field of great current excitement due to the development of inherently fluorescent proteins. We describe a method of removing such aberrations computationally by mapping the refractive index of the sample using differential interference contrast microscopy, modeling the aberrations by ray tracing through this index map, and using space-variant deconvolution to remove aberrations. This approach will open possibilities to study weakly labeled molecules in difficult-to-image live specimens. PMID:11274396

  14. Is there a future for computational chemistry in drug research?

    NASA Astrophysics Data System (ADS)

    Maggiora, Gerald M.

    2012-01-01

    Improvements in computational chemistry methods have had a growing impact on drug research. But will incremental improvements be sufficient to ensure this continues? Almost all existing efforts to discover new drugs depend on the classic one target, one drug paradigm, although the situation is changing slowly. A new paradigm that focuses on a more systems biology approach and takes account of the reality that most drugs exhibit some level of polypharmacology is beginning to emerge. This will bring about dramatic changes that can significantly influence the role that computational methods play in future drug research. But these changes require that current methods be augmented with those from bioinformatics and engineering if the field is to have a significant impact on future drug research.

  15. Biological networks 101: computational modeling for molecular biologists.

    PubMed

    Scholma, Jetse; Schivo, Stefano; Urquidi Camacho, Ricardo A; van de Pol, Jaco; Karperien, Marcel; Post, Janine N

    2014-01-01

    Computational modeling of biological networks permits the comprehensive analysis of cells and tissues to define molecular phenotypes and novel hypotheses. Although a large number of software tools have been developed, the versatility of these tools is limited by mathematical complexities that prevent their broad adoption and effective use by molecular biologists. This study clarifies the basic aspects of molecular modeling, how to convert data into useful input, as well as the number of time points and molecular parameters that should be considered for molecular regulatory models with both explanatory and predictive potential. We illustrate the necessary experimental preconditions for converting data into a computational model of network dynamics. This model requires neither a thorough background in mathematics nor precise data on intracellular concentrations, binding affinities or reaction kinetics. Finally, we show how an interactive model of crosstalk between signal transduction pathways in primary human articular chondrocytes allows insight into processes that regulate gene expression.

  16. 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.

  17. 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.

  18. Application of Computational Systems Biology to Explore Environmental Toxicity Hazards

    PubMed Central

    Grandjean, Philippe

    2011-01-01

    Background: Computer-based modeling is part of a new approach to predictive toxicology. Objectives: We investigated the usefulness of an integrated computational systems biology approach in a case study involving the isomers and metabolites of the pesticide dichlorodiphenyltrichloroethane (DDT) to ascertain their possible links to relevant adverse effects. Methods: We extracted chemical–protein association networks for each DDT isomer and its metabolites using ChemProt, a disease chemical biology database that includes both binding and gene expression data, and we explored protein–protein interactions using a human interactome network. To identify associated dysfunctions and diseases, we integrated protein–disease annotations into the protein complexes using the Online Mendelian Inheritance in Man database and the Comparative Toxicogenomics Database. Results: We found 175 human proteins linked to p,p´-DDT, and 187 to o,p´-DDT.Dichlorodiphenyldichloroethylene (p,p´-DDE) was the metabolite with the highest number of links, with 52. We grouped proteins for each compound based on their disease annotations. Although the two data sources differed in linkage to diseases, integrated results predicted that most diseases were linked to the two DDT isomers. Asthma was uniquely linked with p,p´-DDT, and autism with o,p´-DDT. Several reproductive and neurobehavioral outcomes and cancer types were linked to all three compounds. Conclusions: Computer-based modeling relies on available information. Although differences in linkages to proteins may be due to incomplete data, our results appear meaningful and suggest that the parent DDT compounds may be responsible for more disease connections than the metabolites. The findings illustrate the potential use of computational approaches to toxicology. PMID:21846611

  19. 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.

  20. Computer Files and the Research Library.

    ERIC Educational Resources Information Center

    Johnson, Margaret; And Others

    This report on a machine-readable data files workshop highlights unresolved issues related to innovative approaches to collecting, describing, and providing service for computer files in research libraries. The remarks of four of the workshop speakers are presented. Margaret Johnson of the University of Minnesota gives a comprehensive review of…

  1. 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.

  2. 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…

  3. 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…

  4. 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…

  5. 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.

  6. 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.

  7. Parameter Estimation and Model Selection in Computational Biology

    PubMed Central

    Lillacci, Gabriele; Khammash, Mustafa

    2010-01-01

    A central challenge in computational modeling of biological systems is the determination of the model parameters. Typically, only a fraction of the parameters (such as kinetic rate constants) are experimentally measured, while the rest are often fitted. The fitting process is usually based on experimental time course measurements of observables, which are used to assign parameter values that minimize some measure of the error between these measurements and the corresponding model prediction. The measurements, which can come from immunoblotting assays, fluorescent markers, etc., tend to be very noisy and taken at a limited number of time points. In this work we present a new approach to the problem of parameter selection of biological models. We show how one can use a dynamic recursive estimator, known as extended Kalman filter, to arrive at estimates of the model parameters. The proposed method follows. First, we use a variation of the Kalman filter that is particularly well suited to biological applications to obtain a first guess for the unknown parameters. Secondly, we employ an a posteriori identifiability test to check the reliability of the estimates. Finally, we solve an optimization problem to refine the first guess in case it should not be accurate enough. The final estimates are guaranteed to be statistically consistent with the measurements. Furthermore, we show how the same tools can be used to discriminate among alternate models of the same biological process. We demonstrate these ideas by applying our methods to two examples, namely a model of the heat shock response in E. coli, and a model of a synthetic gene regulation system. The methods presented are quite general and may be applied to a wide class of biological systems where noisy measurements are used for parameter estimation or model selection. PMID:20221262

  8. Parameter estimation and model selection in computational biology.

    PubMed

    Lillacci, Gabriele; Khammash, Mustafa

    2010-03-05

    A central challenge in computational modeling of biological systems is the determination of the model parameters. Typically, only a fraction of the parameters (such as kinetic rate constants) are experimentally measured, while the rest are often fitted. The fitting process is usually based on experimental time course measurements of observables, which are used to assign parameter values that minimize some measure of the error between these measurements and the corresponding model prediction. The measurements, which can come from immunoblotting assays, fluorescent markers, etc., tend to be very noisy and taken at a limited number of time points. In this work we present a new approach to the problem of parameter selection of biological models. We show how one can use a dynamic recursive estimator, known as extended Kalman filter, to arrive at estimates of the model parameters. The proposed method follows. First, we use a variation of the Kalman filter that is particularly well suited to biological applications to obtain a first guess for the unknown parameters. Secondly, we employ an a posteriori identifiability test to check the reliability of the estimates. Finally, we solve an optimization problem to refine the first guess in case it should not be accurate enough. The final estimates are guaranteed to be statistically consistent with the measurements. Furthermore, we show how the same tools can be used to discriminate among alternate models of the same biological process. We demonstrate these ideas by applying our methods to two examples, namely a model of the heat shock response in E. coli, and a model of a synthetic gene regulation system. The methods presented are quite general and may be applied to a wide class of biological systems where noisy measurements are used for parameter estimation or model selection.

  9. Computing life: Add logos to biology and bios to physics.

    PubMed

    Kolodkin, Alexey; Simeonidis, Evangelos; Westerhoff, Hans V

    2013-04-01

    This paper discusses the interrelations between physics and biology. Particularly, we analyse the approaches for reconstructing the emergent properties of physical or biological systems. We propose approaches to scale emergence according to the degree of state-dependency of the system's component properties. Since the component properties of biological systems are state-dependent to a high extent, biological emergence should be considered as very strong emergence - i.e. its reconstruction would require a lot of information about state-dependency of its component properties. However, due to its complexity and volume, this information cannot be handled in the naked human brain, or on the back of an envelope. To solve this problem, biological emergence can be reconstructed in silico based on experimentally determined rate laws and parameter values of the living cell. According to some rough calculations, the silicon human might comprise the mathematical descriptions of around 10(5) interactions. This is not a small number, but taking into account the exponentially increase of computational power, it should not prove to be our principal limitation. The bigger challenges will be located in different areas. For example they may be related to the observer effect - the limitation to measuring a system's component properties without affecting the system. Another obstacle may be hidden in the tradition of "shaving away" all "unnecessary" assumptions (the so-called Occam's razor) that, in fact, reflects the intention to model the system as simply as possible and thus to deem the emergence to be less strong than it possibly is. We argue here that that Occam's razor should be replaced with the law of completeness. Copyright © 2012 Elsevier Ltd. All rights reserved.

  10. 77 FR 4028 - Biological and Environmental Research Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-26

    ... and Environmental Research News from the Biological Systems Science and Climate and Environmental... 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...

  11. 78 FR 6087 - Biological and Environmental Research Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-29

    ... 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.... Department of Energy, Office of Science, Office of Biological and Environmental Research, SC-23/Germantown...

  12. 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, SC-23...

  13. Taking the example of computer systems engineering for the analysis of biological cell systems.

    PubMed

    Pronk, Tessa E; Pimentel, Andy D; Roos, Marco; Breit, Timo M

    2007-01-01

    In this paper, we discuss the potential for the use of engineering methods that were originally developed for the design of embedded computer systems, to analyse biological cell systems. For embedded systems as well as for biological cell systems, design is a feature that defines their identity. The assembly of different components in designs of both systems can vary widely. In contrast to the biology domain, the computer engineering domain has the opportunity to quickly evaluate design options and consequences of its systems by methods for computer aided design and in particular design space exploration. We argue that there are enough concrete similarities between the two systems to assume that the engineering methodology from the computer systems domain, and in particular that related to embedded systems, can be applied to the domain of cellular systems. This will help to understand the myriad of different design options cellular systems have. First we compare computer systems with cellular systems. Then, we discuss exactly what features of engineering methods could aid researchers with the analysis of cellular systems, and what benefits could be gained.

  14. 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.

  15. 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…

  16. 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

  17. 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.

  18. 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

  19. Systems biology driven software design for the research enterprise.

    PubMed

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

    2008-06-25

    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. 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. 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.

  20. 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.

  1. Convolutional Deep Belief Networks for Single-Cell/Object Tracking in Computational Biology and Computer Vision.

    PubMed

    Zhong, Bineng; Pan, Shengnan; Zhang, Hongbo; Wang, Tian; Du, Jixiang; Chen, Duansheng; Cao, Liujuan

    2016-01-01

    In this paper, we propose deep architecture to dynamically learn the most discriminative features from data for both single-cell and object tracking in computational biology and computer vision. Firstly, the discriminative features are automatically learned via a convolutional deep belief network (CDBN). Secondly, we design a simple yet effective method to transfer features learned from CDBNs on the source tasks for generic purpose to the object tracking tasks using only limited amount of training data. Finally, to alleviate the tracker drifting problem caused by model updating, we jointly consider three different types of positive samples. Extensive experiments validate the robustness and effectiveness of the proposed method.

  2. Convolutional Deep Belief Networks for Single-Cell/Object Tracking in Computational Biology and Computer Vision

    PubMed Central

    Pan, Shengnan; Zhang, Hongbo; Wang, Tian; Du, Jixiang; Chen, Duansheng; Cao, Liujuan

    2016-01-01

    In this paper, we propose deep architecture to dynamically learn the most discriminative features from data for both single-cell and object tracking in computational biology and computer vision. Firstly, the discriminative features are automatically learned via a convolutional deep belief network (CDBN). Secondly, we design a simple yet effective method to transfer features learned from CDBNs on the source tasks for generic purpose to the object tracking tasks using only limited amount of training data. Finally, to alleviate the tracker drifting problem caused by model updating, we jointly consider three different types of positive samples. Extensive experiments validate the robustness and effectiveness of the proposed method. PMID:27847827

  3. Hemlock woolly adelgid biological control research

    Treesearch

    Michael Montgomery; Nathan Havill; Carole Cheah; Mark McClure; Gabriella Zilahi-Balogh; Ashley Lamb; Scott Salom

    2003-01-01

    The hemlock woolly adelgid (HWA), Adelges tsugae Annand, is an introduced pest that causes mortality of hemlock in the eastern U. S. Three laboratories have imported and are evaluating predacious beetles for biological control of the adelgid.

  4. Integrating computational biology and forward genetics in Drosophila.

    PubMed

    Aerts, Stein; Vilain, Sven; Hu, Shu; Tranchevent, Leon-Charles; Barriot, Roland; Yan, Jiekun; Moreau, Yves; Hassan, Bassem A; Quan, Xiao-Jiang

    2009-01-01

    Genetic screens are powerful methods for the discovery of gene-phenotype associations. However, a systems biology approach to genetics must leverage the massive amount of "omics" data to enhance the power and speed of functional gene discovery in vivo. Thus far, few computational methods for gene function prediction have been rigorously tested for their performance on a genome-wide scale in vivo. In this work, we demonstrate that integrating genome-wide computational gene prioritization with large-scale genetic screening is a powerful tool for functional gene discovery. To discover genes involved in neural development in Drosophila, we extend our strategy for the prioritization of human candidate disease genes to functional prioritization in Drosophila. We then integrate this prioritization strategy with a large-scale genetic screen for interactors of the proneural transcription factor Atonal using genomic deficiencies and mutant and RNAi collections. Using the prioritized genes validated in our genetic screen, we describe a novel genetic interaction network for Atonal. Lastly, we prioritize the whole Drosophila genome and identify candidate gene associations for ten receptor-signaling pathways. This novel database of prioritized pathway candidates, as well as a web application for functional prioritization in Drosophila, called Endeavour-HighFly, and the Atonal network, are publicly available resources. A systems genetics approach that combines the power of computational predictions with in vivo genetic screens strongly enhances the process of gene function and gene-gene association discovery.

  5. 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.

  6. 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.

  7. 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

  8. Synthetic biology: an emerging research field in China.

    PubMed

    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. Copyright © 2011 Elsevier Inc. All rights reserved.

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. CERR: a computational environment for radiotherapy research.

    PubMed

    Deasy, Joseph O; Blanco, Angel I; Clark, Vanessa H

    2003-05-01

    A software environment is described, called the computational environment for radiotherapy research (CERR, pronounced "sir"). CERR partially addresses four broad needs in treatment planning research: (a) it provides a convenient and powerful software environment to develop and prototype treatment planning concepts, (b) it serves as a software integration environment to combine treatment planning software written in multiple languages (MATLAB, FORTRAN, C/C++, JAVA, etc.), together with treatment plan information (computed tomography scans, outlined structures, dose distributions, digital films, etc.), (c) it provides the ability to extract treatment plans from disparate planning systems using the widely available AAPM/RTOG archiving mechanism, and (d) it provides a convenient and powerful tool for sharing and reproducing treatment planning research results. The functional components currently being distributed, including source code, include: (1) an import program which converts the widely available AAPM/RTOG treatment planning format into a MATLAB cell-array data object, facilitating manipulation; (2) viewers which display axial, coronal, and sagittal computed tomography images, structure contours, digital films, and isodose lines or dose colorwash, (3) a suite of contouring tools to edit and/or create anatomical structures, (4) dose-volume and dose-surface histogram calculation and display tools, and (5) various predefined commands. CERR allows the user to retrieve any AAPM/RTOG key word information about the treatment plan archive. The code is relatively self-describing, because it relies on MATLAB structure field name definitions based on the AAPM/RTOG standard. New structure field names can be added dynamically or permanently. New components of arbitrary data type can be stored and accessed without disturbing system operation. CERR has been applied to aid research in dose-volume-outcome modeling, Monte Carlo dose calculation, and treatment planning optimization

  14. 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

  15. Computer Science Research Review 1974-75

    DTIC Science & Technology

    1975-08-01

    mwmmmimmm^m^mmmrm. : i i 1 Faculty and Visitors Mario Barbaccl Research Associate B.S., Universidad Nacional de Ingenieria , Lima, Peru (1966...Engineer, Universidad Nacional de Ingenieria , Lima, Peru (1968) Ph.D., Carnegie-Mellon University (1974) Carnegie. 1969: Design Automation...Compitational Complexity Jack R Buchanan Assistant Professor of Computer Science and Industrial Administration B.S., University of Utah (1965) M.A

  16. 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

  17. 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.

  18. [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.

  19. Computational cancer biology: education is a natural key to many locks.

    PubMed

    Emmert-Streib, Frank; Zhang, Shu-Dong; Hamilton, Peter

    2015-01-15

    Oncology is a field that profits tremendously from the genomic data generated by high-throughput technologies, including next-generation sequencing. However, in order to exploit, integrate, visualize and interpret such high-dimensional data efficiently, non-trivial computational and statistical analysis methods are required that need to be developed in a problem-directed manner. For this reason, computational cancer biology aims to fill this gap. Unfortunately, computational cancer biology is not yet fully recognized as a coequal field in oncology, leading to a delay in its maturation and, as an immediate consequence, an under-exploration of high-throughput data for translational research. Here we argue that this imbalance, favoring 'wet lab-based activities', will be naturally rectified over time, if the next generation of scientists receives an academic education that provides a fair and competent introduction to computational biology and its manifold capabilities. Furthermore, we discuss a number of local educational provisions that can be implemented on university level to help in facilitating the process of harmonization.

  20. 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

  1. Patient radiation biological risk in computed tomography angiography procedure.

    PubMed

    Alkhorayef, M; Babikir, E; Alrushoud, A; Al-Mohammed, H; Sulieman, A

    2017-02-01

    Computed tomography angiography (CTA) has become the most valuable imaging modality for the diagnosis of blood vessel diseases; however, patients are exposed to high radiation doses and the probability of cancer and other biological effects is increased. The objectives of this study were to measure the patient radiation dose during a CTA procedure and to estimate the radiation dose and biological effects. The study was conducted in two radiology departments equipped with 64-slice CT machines (Aquilion) calibrated according to international protocols. A total of 152 patients underwent brain, lower limb, chest, abdomen, and pelvis examinations. The effective radiation dose was estimated using ImPACT scan software. Cancer and biological risks were estimated using the International Commission on Radiological Protection (ICRP) conversion factors. The mean patient dose value per procedure (dose length product [DLP], mGy·cm) for all examinations was 437.8 ± 166, 568.8 ± 194, 516.0 ± 228, 581.8 ± 175, and 1082.9 ± 290 for the lower limbs, pelvis, abdomen, chest, and cerebral, respectively. The lens of the eye, uterus, and ovaries received high radiation doses compared to thyroid and testis. The overall patient risk per CTA procedure ranged between 15 and 36 cancer risks per 1 million procedures. Patient risk from CTA procedures is high during neck and abdomen procedures. Special concern should be provided to the lens of the eye and thyroid during brain CTA procedures. Patient dose reduction is an important consideration; thus, staff should optimize the radiation dose during CTA procedures.

  2. 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

  3. 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.

  4. 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.

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

    PubMed Central

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

    2016-01-01

    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

  6. 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'. © 2016 The Author(s).

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  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. Biological Structures, Interactions, Function and Behavior: Research Opportunities for Physicists

    NASA Astrophysics Data System (ADS)

    Concepcion, Gisela P.

    2008-06-01

    Studies on marine biomolecules at the Marine Natural Products Laboratory (MNPL) and studies on biomedically relevant proteins at the Virtual Laboratory of Biomolecular Structures (VIRLS) of the University of the Philippines Marine Science Institute (UPMSI) are presented. These serve to illustrate some underlying principles of biological structures, interactions, function and behavior, and also to draw out some unresolved questions in biology of possible interest to non-biologists. The Biological Structures course offered at UPMSI, which aims to introduce underlying biological principles to non-biology majors and to promote trans-disciplinary research efforts, is also presented.

  13. 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.

  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.

  15. 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

  16. 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.

  17. 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.

  18. 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...

  19. 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...

  20. 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

  1. 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.

  2. 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.

  3. International Research: Its Role in Environmental Biology

    ERIC Educational Resources Information Center

    Higginson, John

    1970-01-01

    Proposes an international research laboratory to investigate environmental factors in human health. By international cooperation unnecessary duplication and waste of resources can be avoided and long-term studies can examine various world-wide environments. (JM)

  4. Computing fuzzy associations for the analysis of biological literature.

    PubMed

    Perez-Iratxeta, Carolina; Keer, Harindar S; Bork, Peer; Andrade, Miguel A

    2002-06-01

    The increase of information in biology makes it difficult for researchers in any field to keep current with the literature. The MEDLINE database of scientific abstracts can be quickly scanned using electronic mechanisms. Potentially interesting abstracts can be selected by matching words joined by Boolean operators. However this means of selecting documents is not optimal. Nonspecific queries have to be effected, resulting in large numbers of irrelevant abstracts that have to be manually scanned To facilitate this analysis, we have developed a system that compiles a summary of subjects and related documents on the results of a MEDLINE query. For this, we have applied a fuzzy binary relation formalism that deduces relations between words present in a set of abstracts preprocessed with a standard grammatical tagger. Those relations are used to derive ensembles of related words and their associated subsets of abstracts. The algorithm can be used publicly at http:// www.bork.embl-heidelberg.de/xplormed/.

  5. 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.

  6. 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…

  7. 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…

  8. [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.

  9. NCI RNA Biology 2017 symposium recap | Center for Cancer Research

    Cancer.gov

    The recent discovery of new classes of RNAs and the demonstration that alterations in RNA metabolism underlie numerous human cancers have resulted in enormous interest among CCR investigators in RNA biology. In order to share the latest research in this exciting field, the CCR Initiative in RNA Biology held its second international symposium April 23-24, 2017, in Natcher Auditorium. Learn more...

  10. Teaching and research on Developmental Biology in Portugal.

    PubMed

    Thorsteinsdóttir, Sólveig; Rodrigues, Gabriela; Crespo, Eduardo G

    2009-01-01

    Developmental Biology has established itself as a solid field of teaching and research in Portugal. Its history is recent, generally considered to have started with the pioneering work of Augusto Celestino da Costa at the beginning of the 20th century. However, research groups were very few and, until the early 1990s, teaching beyond morphological and comparative embryology was uncommon. In 1994, the first university course dedicated to Developmental Biology as a separate field from Embryology was created at the Faculty of Sciences of the University of Lisbon and a course on Plant Differentiation and Morphogenesis was also initiated. A Masters programme in Developmental Biology followed at the Lusofona University in 1996. Subsequently, modules of Developmental Biology were included in many Embryology courses and eventually more Developmental Biology courses were created. From 1999 onwards, the number of research groups working in Developmental Biology started to increase, many of which were initiated by researchers who had had the opportunity to pursue their PhD and/or post-doc studies abroad. The Instituto Gulbenkian de Cincia (Gulbenkian Institute of Science) became the first home of most of these groups, but several later spread to other institutions. This increased activity in turn has stimulated teaching of Developmental Biology and more students have been getting interested in the field. This positive feedback loop makes it a nice time to be teaching and working in Developmental Biology in Portugal.

  11. 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.

  12. High Performance Computing Assets for Ocean Acoustics Research

    DTIC Science & Technology

    2016-11-18

    Enclosed is the Final Report for ONR Grant No. NOOO 14-15-1-2840 entitled "High Performance Computing Assets for Ocean Acoustjc Research," Principal...distribution is unlimited. ONR DURIP Grant Final Report High Performance Computing Assets for Ocean Acoustics Research Timothy F. Dud a Applied Ocean ...computing equipment configured for our ocean acoustics research. This work benefits from a strong computational capability. Limits of computational accuracy

  13. A platform for biological sequence comparison on parallel computers.

    PubMed

    Deshpande, A S; Richards, D S; Pearson, W R

    1991-04-01

    We have written two programs for searching biological sequence databases that run on Intel hypercube computers. PSCANLIB compares a single sequence against a sequence library, and PCOMPLIB compares all the entries in one sequence library against a second library. The programs provide a general framework for similarity searching; they include functions for reading in query sequences, search parameters and library entries, and reporting the results of a search. We have isolated the code for the specific function that calculates the similarity score between the query and library sequence; alternative searching algorithms can be implemented by editing two files. We have implemented the rapid FASTA sequence comparison algorithm and the more rigorous Smith-Waterman algorithm within this framework. The PSCANLIB program on a 16 node iPSC/2 80386-based hypercube can compare a 229 amino acid protein sequence with a 3.4 million residue sequence library in approximately 16 s with the FASTA algorithm. Using the Smith-Waterman algorithm, the same search takes 35 min. The PCOMPLIB program can compare a 0.8 million amino acid protein sequence library with itself in 5.3 min with FASTA on a third-generation 32 node Intel iPSC/860 hypercube.

  14. 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

  15. Evolutionary Developmental Biology (Evo-Devo) Research in Latin America.

    PubMed

    Marcellini, Sylvain; González, Favio; Sarrazin, Andres F; Pabón-Mora, Natalia; Benítez, Mariana; Piñeyro-Nelson, Alma; Rezende, Gustavo L; Maldonado, Ernesto; Schneider, Patricia Neiva; Grizante, Mariana B; Da Fonseca, Rodrigo Nunes; Vergara-Silva, Francisco; Suaza-Gaviria, Vanessa; Zumajo-Cardona, Cecilia; Zattara, Eduardo E; Casasa, Sofia; Suárez-Baron, Harold; Brown, Federico D

    2017-01-01

    Famous for its blind cavefish and Darwin's finches, Latin America is home to some of the richest biodiversity hotspots of our planet. The Latin American fauna and flora inspired and captivated naturalists from the nineteenth and twentieth centuries, including such notable pioneers such as Fritz Müller, Florentino Ameghino, and Léon Croizat who made a significant contribution to the study of embryology and evolutionary thinking. But, what are the historical and present contributions of the Latin American scientific community to Evo-Devo? Here, we provide the first comprehensive overview of the Evo-Devo laboratories based in Latin America and describe current lines of research based on endemic species, focusing on body plans and patterning, systematics, physiology, computational modeling approaches, ecology, and domestication. Literature searches reveal that Evo-Devo in Latin America is still in its early days; while showing encouraging indicators of productivity, it has not stabilized yet, because it relies on few and sparsely distributed laboratories. Coping with the rapid changes in national scientific policies and contributing to solve social and health issues specific to each region are among the main challenges faced by Latin American researchers. The 2015 inaugural meeting of the Pan-American Society for Evolutionary Developmental Biology played a pivotal role in bringing together Latin American researchers eager to initiate and consolidate regional and worldwide collaborative networks. Such networks will undoubtedly advance research on the extremely high genetic and phenotypic biodiversity of Latin America, bound to be an almost infinite source of amazement and fascinating findings for the Evo-Devo community.

  16. 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

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. 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.

  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. Patenting inventions arising from biological research

    PubMed Central

    Latimer, Matthew T

    2005-01-01

    Patents are the most important way in which researchers can protect the income that might come from ideas or technologies they have developed. This article describes the steps involved and the considerations needed for successful granting of a patent. For instance, inventions must be novel and not obvious, adequately described, and useful, and they should not be disclosed publicly before a patent is applied for. PMID:15642107

  4. 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).

  5. Emerging Uses of Computer Technology in Qualitative Research.

    ERIC Educational Resources Information Center

    Parker, D. Randall

    The application of computer technology in qualitative research and evaluation ranges from simple word processing to doing sophisticated data sorting and retrieval. How computer software can be used for qualitative research is discussed. Researchers should consider the use of computers in data analysis in light of their own familiarity and comfort…

  6. Quantitative morphology for biologists and computer scientists: I. Computer-aided tutorial for biological stereology (version 1.0).

    PubMed

    Bolender, R P

    1992-06-01

    This paper describes a computer-aided tutorial for biological stereology. Stereology, a type of quantitative morphology, includes a collection of statistical methods that quantify the structural compartments that can be viewed in sections with light and electron microscopy. These methods provide volume, surface, length, shape, and number data, and help define the quantitative relationships among the structural compartments of biological hierarchies. Hierarchies, which connect structural data ranging in size from molecules to organs, serve as a central core to which the data of biological databases can be linked. The tutorial focuses on two objectives. It provides the user primarily interested in using quantitative morphology databases with background information, and offers a set of state-of-the-art tools to researchers wishing to use these methods in the laboratory. The main topics of the tutorial include: introduction to quantitative morphology, symbols/terms, data types, sampling, hierarchies, data interpretation, and utilities. The tutorial runs under the MS-DOS operating system and requires at least an IBM PC AT (or compatible), a color monitor (EGA, VGA), 540 KB of RAM, and 3 MB of hard disk space.

  7. 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.

  8. 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

  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. Computational approaches to selecting and optimising targets for structural biology

    PubMed Central

    Overton, Ian M.; Barton, Geoffrey J.

    2011-01-01

    Selection of protein targets for study is central to structural biology and may be influenced by numerous factors. A key aim is to maximise returns for effort invested by identifying proteins with the balance of biophysical properties that are conducive to success at all stages (e.g. solubility, crystallisation) in the route towards a high resolution structural model. Selected targets can be optimised through construct design (e.g. to minimise protein disorder), switching to a homologous protein, and selection of experimental methodology (e.g. choice of expression system) to prime for efficient progress through the structural proteomics pipeline. Here we discuss computational techniques in target selection and optimisation, with more detailed focus on tools developed within the Scottish Structural Proteomics Facility (SSPF); namely XANNpred, ParCrys, OB-Score (target selection) and TarO (target optimisation). TarO runs a large number of algorithms, searching for homologues and annotating the pool of possible alternative targets. This pool of putative homologues is presented in a ranked, tabulated format and results are also visualised as an automatically generated and annotated multiple sequence alignment. The target selection algorithms each predict the propensity of a selected protein target to progress through the experimental stages leading to diffracting crystals. This single predictor approach has advantages for target selection, when compared with an approach using two or more predictors that each predict for success at a single experimental stage. The tools described here helped SSPF achieve a high (21%) success rate in progressing cloned targets to diffraction-quality crystals. PMID:21906678

  11. 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…

  12. 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.

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

    PubMed Central

    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. PMID:25708611

  14. 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.

  15. 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

  16. 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…

  17. 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…

  18. 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…

  19. 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…

  20. 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.

  1. Factors associated with computer and Internet technology implementation in biology, chemistry, and physics education in Turkish secondary schools

    NASA Astrophysics Data System (ADS)

    Ozer, Melike

    The main purposes of the research were to identify computer and Internet use by biology, chemistry and physics teachers in Turkish secondary schools and identify factors associated with computer and Internet technology. To this end, survey documents were sent by the Provincial Directorate of National Education to 250 selected schools' administrators for further distribution. Administrators were asked to complete the "Computer and Internet Use: School Survey," and to distribute the "Science Teacher Computer and Internet Use" surveys to the two teachers who teach science class. Surveys were then returned to the General Directorate of Educational Technologies. Research findings showed that computer and Internet use has not occurred effectively. Computers were first introduced to Turkish schools in 1984; unfortunately the current situation of computer and Internet use in science education is not at the projected earlier point in time. Considering the fact that science teachers' participation in technology-related professional development program is higher than other subject teachers, the use of computer and Internet technologies in Turkish secondary schools is still at its early stages. Lack of computer knowledge and not knowing how to integrate computers into education were the major factors reported. With regard to computer and Internet use, a regression model for Turkish schools, which includes access and knowledge, explains a large part of the variance in study results. There was a significant relationship between computer attitude (computer liking, usefulness, and confidence) and computer and Internet use. Although there was a significant negative relationship between Internet and computer uses and the attitudinal component, computer anxiety, it did not deter individuals from expressing a desire to engage in computer use in education.

  2. Spacecraft computer technology at Southwest Research Institute

    NASA Technical Reports Server (NTRS)

    Shirley, D. J.

    1993-01-01

    Southwest Research Institute (SwRI) has developed and delivered spacecraft computers for a number of different near-Earth-orbit spacecraft including shuttle experiments and SDIO free-flyer experiments. We describe the evolution of the basic SwRI spacecraft computer design from those weighing in at 20 to 25 lb and using 20 to 30 W to newer models weighing less than 5 lb and using only about 5 W, yet delivering twice the processing throughput. Because of their reduced size, weight, and power, these newer designs are especially applicable to planetary instrument requirements. The basis of our design evolution has been the availability of more powerful processor chip sets and the development of higher density packaging technology, coupled with more aggressive design strategies in incorporating high-density FPGA technology and use of high-density memory chips. In addition to reductions in size, weight, and power, the newer designs also address the necessity of survival in the harsh radiation environment of space. Spurred by participation in such programs as MSTI, LACE, RME, Delta 181, Delta Star, and RADARSAT, our designs have evolved in response to program demands to be small, low-powered units, radiation tolerant enough to be suitable for both Earth-orbit microsats and for planetary instruments. Present designs already include MIL-STD-1750 and Multi-Chip Module (MCM) technology with near-term plans to include RISC processors and higher-density MCM's. Long term plans include development of whole-core processors on one or two MCM's.

  3. Bibliometric analysis of original molecular biology research in anaesthesia.

    PubMed

    Schreiber, K; Girard, T; Kindler, C H

    2004-10-01

    Molecular biology has expanded the horizons of anaesthesia during the last 20 years and has led to an increase of basic science articles that are published in the specialised anaesthetic journals or originate in anaesthetic institutions. We searched for and analysed the specific features, such as year of publication, publishing journal, and country of origin, of all such molecular biology articles stored in the MEDLINE database during the period 1986-2002. We identified 1265 original articles that used molecular biology techniques; 223 (18%) of these articles were published in anaesthetic journals and 1042 (82%) articles in 556 other biomedical journals. While in the late 1980s only a few molecular biology articles were published each year by anaesthetic institutions, worldwide this number reached approximately 200 basic science articles by the end of 2002. The USA clearly dominates the field of anaesthesia with respect to molecular biology research with 839 (66%) such articles.

  4. 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.

  5. Analysis of Nonstationary Time Series for Biological Rhythms Research.

    PubMed

    Leise, Tanya L

    2017-06-01

    This article is part of a Journal of Biological Rhythms series exploring analysis and statistics topics relevant to researchers in biological rhythms and sleep research. The goal is to provide an overview of the most common issues that arise in the analysis and interpretation of data in these fields. In this article on time series analysis for biological rhythms, we describe some methods for assessing the rhythmic properties of time series, including tests of whether a time series is indeed rhythmic. Because biological rhythms can exhibit significant fluctuations in their period, phase, and amplitude, their analysis may require methods appropriate for nonstationary time series, such as wavelet transforms, which can measure how these rhythmic parameters change over time. We illustrate these methods using simulated and real time series.

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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…

  12. 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

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

    PubMed Central

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

    2014-01-01

    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. DOI: http://dx.doi.org/10.7554/eLife.04333.001 PMID:25490932

  14. 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.

  15. Considering sex as a biological variable in preclinical research.

    PubMed

    Miller, Leah R; Marks, Cheryl; Becker, Jill B; Hurn, Patricia D; Chen, Wei-Jung; Woodruff, Teresa; McCarthy, Margaret M; Sohrabji, Farida; Schiebinger, Londa; Wetherington, Cora Lee; Makris, Susan; Arnold, Arthur P; Einstein, Gillian; Miller, Virginia M; Sandberg, Kathryn; Maier, Susan; Cornelison, Terri L; Clayton, Janine A

    2017-01-01

    In June 2015, the National Institutes of Health (NIH) released a Guide notice (NOT-OD-15-102) that highlighted the expectation of the NIH that the possible role of sex as a biologic variable be factored into research design, analyses, and reporting of vertebrate animal and human studies. Anticipating these guidelines, the NIH Office of Research on Women's Health, in October 2014, convened key stakeholders to discuss methods and techniques for integrating sex as a biologic variable in preclinical research. The workshop focused on practical methods, experimental design, and approaches to statistical analyses in the use of both male and female animals, cells, and tissues in preclinical research. Workshop participants also considered gender as a modifier of biology. This article builds on the workshop and is meant as a guide to preclinical investigators as they consider methods and techniques for inclusion of both sexes in preclinical research and is not intended to prescribe exhaustive/specific approaches for compliance with the new NIH policy.-Miller, L. R., Marks, C., Becker, J. B., Hurn, P. D., Chen, W.-J., Woodruff, T., McCarthy, M. M., Sohrabji, F., Schiebinger, L., Wetherington, C. L., Makris, S., Arnold, A. P., Einstein, G., Miller, V. M., Sandberg, K., Maier, S., Cornelison, T. L., Clayton, J. A. Considering sex as a biological variable in preclinical research.

  16. 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.

  17. 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.

  18. [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.

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. 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…

  4. 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…

  5. Research in Optical Symbolic Computing Tasks

    DTIC Science & Technology

    1988-05-31

    the Integration of Optical Computing , we have developed an adaptive neural network based algorithm for a fundamental problem in image processing, viz...IEEE International Conference on Neural Networks, San Diego, July 1988. 5. B.K. Jenkins and C.L. Giles, "Superposition in Optical Computing ...Angeles, California, 10-15 January, 1988. " Neural Network Models for Optical Computing ", SPIE vol. 882. • -# - - Where M(k) and l(k) are the input

  6. Research on Computational Fluid Dynamics and Turbulence

    NASA Technical Reports Server (NTRS)

    1986-01-01

    Preconditioning matrices for Chebyshev derivative operators in several space dimensions; the Jacobi matrix technique in computational fluid dynamics; and Chebyshev techniques for periodic problems are discussed.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. The increasing urgency for standards in basic biologic research.

    PubMed

    Freedman, Leonard P; Inglese, James

    2014-08-01

    Research advances build upon the validity and reproducibility of previously published data and findings. Yet irreproducibility in basic biologic and preclinical research is pervasive in both academic and commercial settings. Lack of reproducibility has led to invalidated research breakthroughs, retracted articles, and aborted clinical trials. Concerns and requirements for transparent, reproducible, and translatable research are accelerated by the rapid growth of "post-publication peer review," open access publishing, and data sharing that facilitate the identification of irreproducible data/studies; they are magnified by the explosion of high-throughput technologies, genomics, and other data-intensive disciplines. Collectively, these changes and challenges are decreasing the effectiveness of traditional research quality mechanisms and are contributing to unacceptable-and unsustainable-levels of irreproducibility. The global oncology and basic biologic research communities can no longer tolerate or afford widespread irreproducible research. This article discusses (i) how irreproducibility in preclinical research can ultimately be traced to an absence of a unifying life science standards framework, and (ii) makes an urgent case for the expanded development and use of consensus-based standards to both enhance reproducibility and drive innovations in cancer research. ©2014 American Association for Cancer Research.

  13. 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

  14. 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

  15. A review on data mining and continuous optimization applications in computational biology and medicine.

    PubMed

    Weber, Gerhard-Wilhelm; Ozöğür-Akyüz, Süreyya; Kropat, Erik

    2009-06-01

    An emerging research area in computational biology and biotechnology is devoted to mathematical modeling and prediction of gene-expression patterns; it nowadays requests mathematics to deeply understand its foundations. This article surveys data mining and machine learning methods for an analysis of complex systems in computational biology. It mathematically deepens recent advances in modeling and prediction by rigorously introducing the environment and aspects of errors and uncertainty into the genetic context within the framework of matrix and interval arithmetics. Given the data from DNA microarray experiments and environmental measurements, we extract nonlinear ordinary differential equations which contain parameters that are to be determined. This is done by a generalized Chebychev approximation and generalized semi-infinite optimization. Then, time-discretized dynamical systems are studied. By a combinatorial algorithm which constructs and follows polyhedra sequences, the region of parametric stability is detected. In addition, we analyze the topological landscape of gene-environment networks in terms of structural stability. As a second strategy, we will review recent model selection and kernel learning methods for binary classification which can be used to classify microarray data for cancerous cells or for discrimination of other kind of diseases. This review is practically motivated and theoretically elaborated; it is devoted to a contribution to better health care, progress in medicine, a better education, and more healthy living conditions.

  16. 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.

  17. 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.

  18. Cardiac lineage selection: integrating biological complexity into computational models.

    PubMed

    Foley, Ann

    2009-01-01

    The emergence of techniques to study developmental processes using systems biology approaches offers exciting possibilities for the developmental biologist. In particular cardiac lineage selection may be particularly amenable to these types of studies since the heart is the first fully functional organ to form in vertebrates. However there are many technical obstacles that need to be overcome for these studies to proceed. Here we present a brief overview of cardiomyocyte lineage deterimination and discuss how different aspects of this process either benefit from or present unique challenges for the development of systems biology approaches.

  19. 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.

  20. 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.…

  1. 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.…

  2. 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…

  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. Biological field stations: research legacies and sites for serendipity

    Treesearch

    William K. Michener; Keith L. Bildstein; Arthur McKee; Robert R. Parmenter; William W. Hargrove; Deedra McClearn; Mark. Stromberg

    2009-01-01

    Biological field stations are distributed throughout North America, capturing much of the ecological variability present at the continental scale and encompassing many unique habitats. In addition to their role in supporting research and education, field stations offer legacies of data, specimens, and accumulated knowledge. Such legacies often provide the only...

  5. Progress in nucleic acid research and molecular biology

    SciTech Connect

    Cohn, W.E. . Biology Div.); Moldave, K. )

    1989-01-01

    This book contain the proceedings on progress in nucleic acid research and molecular biology. Topics covered include: polynucleotide-protein cross-links induced by ultraviolet light and their use for structural investigation of nucleoproteins; left-handed Z-DNA and genetic recombination, and structure and function of signal recognition particle RNA.

  6. 77 FR 28368 - Biological and Environmental Research Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-14

    ... Biological and Environmental Research Advisory Committee AGENCY: Office of Science, Department of Energy...: Dr. David Thomassen, Designated Federal Officer, BERAC, U.S. Department of Energy, Office of Science...., Washington, DC 20585-1290. Phone 301-903-9817; fax (301) 903-5051 or email: david.thomassen@science.doe.gov...

  7. 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…

  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. Computing biological functions using BioΨ, a formal description of biological processes based on elementary bricks of actions

    PubMed Central

    Pérès, Sabine; Felicori, Liza; Rialle, Stéphanie; Jobard, Elodie; Molina, Franck

    2010-01-01

    Motivation: In the available databases, biological processes are described from molecular and cellular points of view, but these descriptions are represented with text annotations that make it difficult to handle them for computation. Consequently, there is an obvious need for formal descriptions of biological processes. Results: We present a formalism that uses the BioΨ concepts to model biological processes from molecular details to networks. This computational approach, based on elementary bricks of actions, allows us to calculate on biological functions (e.g. process comparison, mapping structure–function relationships, etc.). We illustrate its application with two examples: the functional comparison of proteases and the functional description of the glycolysis network. This computational approach is compatible with detailed biological knowledge and can be applied to different kinds of systems of simulation. Availability: www.sysdiag.cnrs.fr/publications/supplementary-materials/BioPsi_Manager/ Contact: sabine.peres@sysdiag.cnrs.fr; franck.molina@sysdiag.cnrs.fr Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20448138

  10. RESEARCH ON COMPUTER-AUGMENTED INFORMATION MANAGEMENT

    DTIC Science & Technology

    information management . The report is, in itself a product of the project: With the exception of ’front matter,’ the entire report was composed, edited, and produced with on-line and off-line computer aids. For this project, the techniques of computer aids were applied to two areas: task monitoring and program design. The processes and techniques developed offer a promising beginning to computer-aided programming design extending from initial specification to final debugging in a unified design record that grows and evolves to complete final documentation. The

  11. PathCase-SB: integrating data sources and providing tools for systems biology research

    PubMed Central

    2012-01-01

    Background Integration of metabolic pathways resources and metabolic network models, and deploying new tools on the integrated platform can help perform more effective and more efficient systems biology research on understanding the regulation of metabolic networks. Therefore, the tasks of (a) integrating under a single database environment regulatory metabolic networks and existing models, and (b) building tools to help with modeling and analysis are desirable and intellectually challenging computational tasks. Results PathCase Systems Biology (PathCase-SB) is built and released. This paper describes PathCase-SB user interfaces developed to date. The current PathCase-SB system provides a database-enabled framework and web-based computational tools towards facilitating the development of kinetic models for biological systems. PathCase-SB aims to integrate systems biology models data and metabolic network data of selected biological data sources on the web (currently, BioModels Database and KEGG, respectively), and to provide more powerful and/or new capabilities via the new web-based integrative framework. Conclusions Each of the current four PathCase-SB interfaces, namely, Browser, Visualization, Querying, and Simulation interfaces, have expanded and new capabilities as compared with the original data sources. PathCase-SB is already available on the web and being used by researchers across the globe. PMID:22697505

  12. 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.

  13. Advances and Computational Tools towards Predictable Design in Biological Engineering

    PubMed Central

    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. PMID:25161694

  14. 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…

  15. 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.

  16. 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.

  17. [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.

  18. First steps in computational systems biology: A practical session in metabolic modeling and simulation.

    PubMed

    Reyes-Palomares, Armando; Sánchez-Jiménez, Francisca; Medina, Miguel Ángel

    2009-05-01

    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 faster numerical simulations of mathematical models. Mathematical modeling plays an essential role in new systems biology approaches. As a complex, integrated system, metabolism is a suitable topic of study for systems biology approaches. However, up until recently, this topic has not been properly covered in biochemistry courses. This communication reports the development and implementation of a practical lesson plan on metabolic modeling and simulation.

  19. DNASU plasmid and PSI:Biology-Materials repositories: resources to accelerate biological research.

    PubMed

    Seiler, Catherine Y; Park, Jin G; Sharma, Amit; Hunter, Preston; Surapaneni, Padmini; Sedillo, Casey; Field, James; Algar, Rhys; Price, Andrea; Steel, Jason; Throop, Andrea; Fiacco, Michael; LaBaer, Joshua

    2014-01-01

    The mission of the DNASU Plasmid Repository is to accelerate research by providing high-quality, annotated plasmid samples and online plasmid resources to the research community through the curated DNASU database, website and repository (http://dnasu.asu.edu or http://dnasu.org). The collection includes plasmids from grant-funded, high-throughput cloning projects performed in our laboratory, plasmids from external researchers, and large collections from consortia such as the ORFeome Collaboration and the NIGMS-funded Protein Structure Initiative: Biology (PSI:Biology). Through DNASU, researchers can search for and access detailed information about each plasmid such as the full length gene insert sequence, vector information, associated publications, and links to external resources that provide additional protein annotations and experimental protocols. Plasmids can be requested directly through the DNASU website. DNASU and the PSI:Biology-Materials Repositories were previously described in the 2010 NAR Database Issue (Cormier, C.Y., Mohr, S.E., Zuo, D., Hu, Y., Rolfs, A., Kramer, J., Taycher, E., Kelley, F., Fiacco, M., Turnbull, G. et al. (2010) Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community. Nucleic Acids Res., 38, D743-D749.). In this update we will describe the plasmid collection and highlight the new features in the website redesign, including new browse/search options, plasmid annotations and a dynamic vector mapping feature that was developed in collaboration with LabGenius. Overall, these plasmid resources continue to enable research with the goal of elucidating the role of proteins in both normal biological processes and disease.

  20. 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…