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Sample records for bioinformatics system built

  1. ebTrack: an environmental bioinformatics system built upon ArrayTrack™

    PubMed Central

    Chen, Minjun; Martin, Jackson; Fang, Hong; Isukapalli, Sastry; Georgopoulos, Panos G; Welsh, William J; Tong, Weida

    2009-01-01

    ebTrack is being developed as an integrated bioinformatics system for environmental research and analysis by addressing the issues of integration, curation, management, first level analysis and interpretation of environmental and toxicological data from diverse sources. It is based on enhancements to the US FDA developed ArrayTrack™ system through additional analysis modules for gene expression data as well as through incorporation and linkages to modules for analysis of proteomic and metabonomic datasets that include tandem mass spectra. ebTrack uses a client-server architecture with the free and open source PostgreSQL as its database engine, and java tools for user interface, analysis, visualization, and web-based deployment. Several predictive tools that are critical for environmental health research are currently supported in ebTrack, including Significance Analysis of Microarray (SAM). Furthermore, new tools are under continuous integration, and interfaces to environmental health risk analysis tools are being developed in order to make ebTrack widely usable. These health risk analysis tools include the Modeling ENvironment for TOtal Risk studies (MENTOR) for source-to-dose exposure modeling and the DOse Response Information ANalysis system (DORIAN) for health outcome modeling. The design of ebTrack is presented in detail and steps involved in its application are summarized through an illustrative application. PMID:19278561

  2. Systems Biology, Bioinformatics, and Biomarkers in Neuropsychiatry

    PubMed Central

    Alawieh, Ali; Zaraket, Fadi A.; Li, Jian-Liang; Mondello, Stefania; Nokkari, Amaly; Razafsha, Mahdi; Fadlallah, Bilal; Boustany, Rose-Mary; Kobeissy, Firas H.

    2012-01-01

    Although neuropsychiatric (NP) disorders are among the top causes of disability worldwide with enormous financial costs, they can still be viewed as part of the most complex disorders that are of unknown etiology and incomprehensible pathophysiology. The complexity of NP disorders arises from their etiologic heterogeneity and the concurrent influence of environmental and genetic factors. In addition, the absence of rigid boundaries between the normal and diseased state, the remarkable overlap of symptoms among conditions, the high inter-individual and inter-population variations, and the absence of discriminative molecular and/or imaging biomarkers for these diseases makes difficult an accurate diagnosis. Along with the complexity of NP disorders, the practice of psychiatry suffers from a “top-down” method that relied on symptom checklists. Although checklist diagnoses cost less in terms of time and money, they are less accurate than a comprehensive assessment. Thus, reliable and objective diagnostic tools such as biomarkers are needed that can detect and discriminate among NP disorders. The real promise in understanding the pathophysiology of NP disorders lies in bringing back psychiatry to its biological basis in a systemic approach which is needed given the NP disorders’ complexity to understand their normal functioning and response to perturbation. This approach is implemented in the systems biology discipline that enables the discovery of disease-specific NP biomarkers for diagnosis and therapeutics. Systems biology involves the use of sophisticated computer software “omics”-based discovery tools and advanced performance computational techniques in order to understand the behavior of biological systems and identify diagnostic and prognostic biomarkers specific for NP disorders together with new targets of therapeutics. In this review, we try to shed light on the need of systems biology, bioinformatics, and biomarkers in neuropsychiatry, and

  3. SNPTrack™ : an integrated bioinformatics system for genetic association studies.

    PubMed

    Xu, Joshua; Kelly, Reagan; Zhou, Guangxu; Turner, Steven A; Ding, Don; Harris, Stephen C; Hong, Huixiao; Fang, Hong; Tong, Weida

    2012-01-01

    A genetic association study is a complicated process that involves collecting phenotypic data, generating genotypic data, analyzing associations between genotypic and phenotypic data, and interpreting genetic biomarkers identified. SNPTrack is an integrated bioinformatics system developed by the US Food and Drug Administration (FDA) to support the review and analysis of pharmacogenetics data resulting from FDA research or submitted by sponsors. The system integrates data management, analysis, and interpretation in a single platform for genetic association studies. Specifically, it stores genotyping data and single-nucleotide polymorphism (SNP) annotations along with study design data in an Oracle database. It also integrates popular genetic analysis tools, such as PLINK and Haploview. SNPTrack provides genetic analysis capabilities and captures analysis results in its database as SNP lists that can be cross-linked for biological interpretation to gene/protein annotations, Gene Ontology, and pathway analysis data. With SNPTrack, users can do the entire stream of bioinformatics jobs for genetic association studies. SNPTrack is freely available to the public at http://www.fda.gov/ScienceResearch/BioinformaticsTools/SNPTrack/default.htm. PMID:23245293

  4. Built-In Diagnostics (BID) Of Equipment/Systems

    NASA Technical Reports Server (NTRS)

    Granieri, Michael N.; Giordano, John P.; Nolan, Mary E.

    1995-01-01

    Diagnostician(TM)-on-Chip (DOC) technology identifies faults and commands systems reconfiguration. Smart microcontrollers operating in conjunction with other system-control circuits, command self-correcting system/equipment actions in real time. DOC microcontroller generates commands for associated built-in test equipment to stimulate unit of equipment diagnosed, collects and processes response data obtained by built-in test equipment, and performs diagnostic reasoning on response data, using diagnostic knowledge base derived from design data.

  5. Stroke of GENEous: A Tool for Teaching Bioinformatics to Information Systems Majors

    ERIC Educational Resources Information Center

    Tikekar, Rahul

    2006-01-01

    A tool for teaching bioinformatics concepts to information systems majors is described. Biological data are available from numerous sources and a good knowledge of biology is needed to understand much of these data. As the subject of bioinformatics gains popularity among computer and information science course offerings, it will become essential…

  6. Using Attributes of Natural Systems to Plan the Built Environment

    EPA Science Inventory

    The concept of 'protection' is possible only before something is lost, however, development of the built environment to meet human needs also compromises the environmental systems that sustain human life. Because maintaining an environment that is able to sustain human life requi...

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  9. Transformers: Shape-Changing Space Systems Built with Robotic Textiles

    NASA Technical Reports Server (NTRS)

    Stoica, Adrian

    2013-01-01

    Prior approaches to transformer-like robots had only very limited success. They suffer from lack of reliability, ability to integrate large surfaces, and very modest change in overall shape. Robots can now be built from two-dimensional (2D) layers of robotic fabric. These transformers, a new kind of robotic space system, are dramatically different from current systems in at least two ways. First, the entire transformer is built from a single, thin sheet; a flexible layer of a robotic fabric (ro-fabric); or robotic textile (ro-textile). Second, the ro-textile layer is foldable to small volume and self-unfolding to adapt shape and function to mission phases.

  10. Bioinformatics for transporter pharmacogenomics and systems biology: data integration and modeling with UML.

    PubMed

    Yan, Qing

    2010-01-01

    Bioinformatics is the rational study at an abstract level that can influence the way we understand biomedical facts and the way we apply the biomedical knowledge. Bioinformatics is facing challenges in helping with finding the relationships between genetic structures and functions, analyzing genotype-phenotype associations, and understanding gene-environment interactions at the systems level. One of the most important issues in bioinformatics is data integration. The data integration methods introduced here can be used to organize and integrate both public and in-house data. With the volume of data and the high complexity, computational decision support is essential for integrative transporter studies in pharmacogenomics, nutrigenomics, epigenetics, and systems biology. For the development of such a decision support system, object-oriented (OO) models can be constructed using the Unified Modeling Language (UML). A methodology is developed to build biomedical models at different system levels and construct corresponding UML diagrams, including use case diagrams, class diagrams, and sequence diagrams. By OO modeling using UML, the problems of transporter pharmacogenomics and systems biology can be approached from different angles with a more complete view, which may greatly enhance the efforts in effective drug discovery and development. Bioinformatics resources of membrane transporters and general bioinformatics databases and tools that are frequently used in transporter studies are also collected here. An informatics decision support system based on the models presented here is available at http://www.pharmtao.com/transporter . The methodology developed here can also be used for other biomedical fields. PMID:20419428

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

    PubMed Central

    Chen, Bor-Sen; Wu, Chia-Chou

    2013-01-01

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

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

    PubMed

    Chen, Bor-Sen; Wu, Chia-Chou

    2013-01-01

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

  13. NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology.

    PubMed

    Romano, Paolo; Cordero, Francesca

    2016-01-01

    The fourteenth NETTAB workshop, NETTAB 2014, was devoted to a range of disciplines going from structural bioinformatics, to proteomics and to integrative systems biology. The topics of the workshop were centred around bioinformatics methods, tools, applications, and perspectives for models, standards and management of high-throughput biological data, structural bioinformatics, functional proteomics, mass spectrometry, drug discovery, and systems biology.43 scientific contributions were presented at NETTAB 2014, including keynote, special guest and tutorial talks, oral communications, and posters. Full papers from some of the best contributions presented at the workshop were later submitted to a special Call for this Supplement.Here, we provide an overview of the workshop and introduce manuscripts that have been accepted for publication in this Supplement. PMID:26960985

  14. Digital camera system built on JPEG2000 compression and decompression

    NASA Astrophysics Data System (ADS)

    Atsumi, Eiji

    2003-05-01

    Processing architecture for digital camera has been built on JPEG2000 compression system. Concerns are to minimize processing power and data traffic inside (data-bandwidth at interface) and out-side (compression efficiency) of camera system. Key idea is to decompose Bayer matrix data given from image sensor into four half-resolution planes instead of interpolating to three full-resolution planes. With a new compression standard, JPEG2000, capable of handling multi-component image, the four-plane representation can be encoded into a single bit-stream. The representation saves data traffic between image reconstruction stage and compression stage by 1/3 to 1/2 compared to the Bayer-interpolated data. Not only reduced processing power prior to and during compression but also competitive or superior compression efficiency is achieved. On reconstruction to full resolution is Bayer-interpolation and/or edge-enhancement required as a post-processing to a standard decoder, while half or smaller resolution image is reconstructed without a post-processing. For mobile terminals with an integrated camera (image reconstruction in camera h/w and compression in terminal processor), this scheme helps to accommodate increased resolution with all the limited data-bandwidth from camera to terminal processor and limited processing capability.

  15. Integration of Proteomics, Bioinformatics, and Systems Biology in Traumatic Brain Injury Biomarker Discovery

    PubMed Central

    Guingab-Cagmat, J.D.; Cagmat, E.B.; Hayes, R.L.; Anagli, J.

    2013-01-01

    Traumatic brain injury (TBI) is a major medical crisis without any FDA-approved pharmacological therapies that have been demonstrated to improve functional outcomes. It has been argued that discovery of disease-relevant biomarkers might help to guide successful clinical trials for TBI. Major advances in mass spectrometry (MS) have revolutionized the field of proteomic biomarker discovery and facilitated the identification of several candidate markers that are being further evaluated for their efficacy as TBI biomarkers. However, several hurdles have to be overcome even during the discovery phase which is only the first step in the long process of biomarker development. The high-throughput nature of MS-based proteomic experiments generates a massive amount of mass spectral data presenting great challenges in downstream interpretation. Currently, different bioinformatics platforms are available for functional analysis and data mining of MS-generated proteomic data. These tools provide a way to convert data sets to biologically interpretable results and functional outcomes. A strategy that has promise in advancing biomarker development involves the triad of proteomics, bioinformatics, and systems biology. In this review, a brief overview of how bioinformatics and systems biology tools analyze, transform, and interpret complex MS datasets into biologically relevant results is discussed. In addition, challenges and limitations of proteomics, bioinformatics, and systems biology in TBI biomarker discovery are presented. A brief survey of researches that utilized these three overlapping disciplines in TBI biomarker discovery is also presented. Finally, examples of TBI biomarkers and their applications are discussed. PMID:23750150

  16. Airborne fibre and asbestos concentrations in system built schools

    NASA Astrophysics Data System (ADS)

    Burdett, Garry; Cottrell, Steve; Taylor, Catherine

    2009-02-01

    This paper summarises the airborne fibre concentration data measured in system built schools that contained asbestos insulation board (AIB) enclosed in the support columns by a protective steel casing. The particular focus of this work was the CLASP (Consortium of Local Authorities Special Programme) system buildings. A variety of air monitoring tests were carried out to assess the potential for fibres to be released into the classroom. A peak release testing protocol was adopted that involved static sampling, while simulating direct impact disturbances to selected columns. This was carried out before remediation, after sealing gaps and holes in and around the casing visible in the room (i.e. below ceiling level) and additionally round the tops of the columns, which extended into the suspended ceiling void. Simulated and actual measurements of worker exposures were also undertaken, while sealing columns, carrying out cleaning and maintenance work in the ceiling voids. Routine analysis of these air samples was carried out by phase contrast microscopy (PCM) with a limited amount of analytical transmission electron microscopy (TEM) analysis to confirm whether the fibres visible by PCM were asbestos or non-asbestos. The PCM fibre concentrations data from the peak release tests showed that while direct releases of fibres to the room air can occur from gaps and holes in and around the column casings, sealing is an effective way of minimising releases to below the limit of quantification (0.01 f/ml) of the PCM method for some 95% of the tests carried out. Sealing with silicone filler and taping any gaps and seams visible on the column casing in the room, also gave concentrations below the limit of quantification (LOQ) of the PCM method for 95% of the tests carried out. The data available did not show any significant difference between the PCM fibre concentrations in the room air for columns that had or had not been sealed in the ceiling void, as well as in the room

  17. Advances in Omics and Bioinformatics Tools for Systems Analyses of Plant Functions

    PubMed Central

    Mochida, Keiichi; Shinozaki, Kazuo

    2011-01-01

    Omics and bioinformatics are essential to understanding the molecular systems that underlie various plant functions. Recent game-changing sequencing technologies have revitalized sequencing approaches in genomics and have produced opportunities for various emerging analytical applications. Driven by technological advances, several new omics layers such as the interactome, epigenome and hormonome have emerged. Furthermore, in several plant species, the development of omics resources has progressed to address particular biological properties of individual species. Integration of knowledge from omics-based research is an emerging issue as researchers seek to identify significance, gain biological insights and promote translational research. From these perspectives, we provide this review of the emerging aspects of plant systems research based on omics and bioinformatics analyses together with their associated resources and technological advances. PMID:22156726

  18. A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing

    PubMed Central

    Cantacessi, Cinzia; Jex, Aaron R.; Hall, Ross S.; Young, Neil D.; Campbell, Bronwyn E.; Joachim, Anja; Nolan, Matthew J.; Abubucker, Sahar; Sternberg, Paul W.; Ranganathan, Shoba; Mitreva, Makedonka; Gasser, Robin B.

    2010-01-01

    Transcriptomics (at the level of single cells, tissues and/or whole organisms) underpins many fields of biomedical science, from understanding the basic cellular function in model organisms, to the elucidation of the biological events that govern the development and progression of human diseases, and the exploration of the mechanisms of survival, drug-resistance and virulence of pathogens. Next-generation sequencing (NGS) technologies are contributing to a massive expansion of transcriptomics in all fields and are reducing the cost, time and performance barriers presented by conventional approaches. However, bioinformatic tools for the analysis of the sequence data sets produced by these technologies can be daunting to researchers with limited or no expertise in bioinformatics. Here, we constructed a semi-automated, bioinformatic workflow system, and critically evaluated it for the analysis and annotation of large-scale sequence data sets generated by NGS. We demonstrated its utility for the exploration of differences in the transcriptomes among various stages and both sexes of an economically important parasitic worm (Oesophagostomum dentatum) as well as the prediction and prioritization of essential molecules (including GTPases, protein kinases and phosphatases) as novel drug target candidates. This workflow system provides a practical tool for the assembly, annotation and analysis of NGS data sets, also to researchers with a limited bioinformatic expertise. The custom-written Perl, Python and Unix shell computer scripts used can be readily modified or adapted to suit many different applications. This system is now utilized routinely for the analysis of data sets from pathogens of major socio-economic importance and can, in principle, be applied to transcriptomics data sets from any organism. PMID:20682560

  19. Role of remote sensing, geographical information system (GIS) and bioinformatics in kala-azar epidemiology.

    PubMed

    Bhunia, Gouri Sankar; Dikhit, Manas Ranjan; Kesari, Shreekant; Sahoo, Ganesh Chandra; Das, Pradeep

    2011-11-01

    Visceral leishmaniasis or kala-azar is a potent parasitic infection causing death of thousands of people each year. Medicinal compounds currently available for the treatment of kala-azar have serious side effects and decreased efficacy owing to the emergence of resistant strains. The type of immune reaction is also to be considered in patients infected with Leishmania donovani (L. donovani). For complete eradication of this disease, a high level modern research is currently being applied both at the molecular level as well as at the field level. The computational approaches like remote sensing, geographical information system (GIS) and bioinformatics are the key resources for the detection and distribution of vectors, patterns, ecological and environmental factors and genomic and proteomic analysis. Novel approaches like GIS and bioinformatics have been more appropriately utilized in determining the cause of visearal leishmaniasis and in designing strategies for preventing the disease from spreading from one region to another. PMID:23554714

  20. Role of remote sensing, geographical information system (GIS) and bioinformatics in kala-azar epidemiology

    PubMed Central

    Bhunia, Gouri Sankar; Dikhit, Manas Ranjan; Kesari, Shreekant; Sahoo, Ganesh Chandra; Das, Pradeep

    2011-01-01

    Visceral leishmaniasis or kala-azar is a potent parasitic infection causing death of thousands of people each year. Medicinal compounds currently available for the treatment of kala-azar have serious side effects and decreased efficacy owing to the emergence of resistant strains. The type of immune reaction is also to be considered in patients infected with Leishmania donovani (L. donovani). For complete eradication of this disease, a high level modern research is currently being applied both at the molecular level as well as at the field level. The computational approaches like remote sensing, geographical information system (GIS) and bioinformatics are the key resources for the detection and distribution of vectors, patterns, ecological and environmental factors and genomic and proteomic analysis. Novel approaches like GIS and bioinformatics have been more appropriately utilized in determining the cause of visearal leishmaniasis and in designing strategies for preventing the disease from spreading from one region to another. PMID:23554714

  1. Quantitative Analysis of the Trends Exhibited by the Three Interdisciplinary Biological Sciences: Biophysics, Bioinformatics, and Systems Biology

    PubMed Central

    Kang, Jonghoon; Park, Seyeon; Venkat, Aarya; Gopinath, Adarsh

    2015-01-01

    New interdisciplinary biological sciences like bioinformatics, biophysics, and systems biology have become increasingly relevant in modern science. Many papers have suggested the importance of adding these subjects, particularly bioinformatics, to an undergraduate curriculum; however, most of their assertions have relied on qualitative arguments. In this paper, we will show our metadata analysis of a scientific literature database (PubMed) that quantitatively describes the importance of the subjects of bioinformatics, systems biology, and biophysics as compared with a well-established interdisciplinary subject, biochemistry. Specifically, we found that the development of each subject assessed by its publication volume was well described by a set of simple nonlinear equations, allowing us to characterize them quantitatively. Bioinformatics, which had the highest ratio of publications produced, was predicted to grow between 77% and 93% by 2025 according to the model. Due to the large number of publications produced in bioinformatics, which nearly matches the number published in biochemistry, it can be inferred that bioinformatics is almost equal in significance to biochemistry. Based on our analysis, we suggest that bioinformatics be added to the standard biology undergraduate curriculum. Adding this course to an undergraduate curriculum will better prepare students for future research in biology. PMID:26753026

  2. Quantitative Analysis of the Trends Exhibited by the Three Interdisciplinary Biological Sciences: Biophysics, Bioinformatics, and Systems Biology.

    PubMed

    Kang, Jonghoon; Park, Seyeon; Venkat, Aarya; Gopinath, Adarsh

    2015-12-01

    New interdisciplinary biological sciences like bioinformatics, biophysics, and systems biology have become increasingly relevant in modern science. Many papers have suggested the importance of adding these subjects, particularly bioinformatics, to an undergraduate curriculum; however, most of their assertions have relied on qualitative arguments. In this paper, we will show our metadata analysis of a scientific literature database (PubMed) that quantitatively describes the importance of the subjects of bioinformatics, systems biology, and biophysics as compared with a well-established interdisciplinary subject, biochemistry. Specifically, we found that the development of each subject assessed by its publication volume was well described by a set of simple nonlinear equations, allowing us to characterize them quantitatively. Bioinformatics, which had the highest ratio of publications produced, was predicted to grow between 77% and 93% by 2025 according to the model. Due to the large number of publications produced in bioinformatics, which nearly matches the number published in biochemistry, it can be inferred that bioinformatics is almost equal in significance to biochemistry. Based on our analysis, we suggest that bioinformatics be added to the standard biology undergraduate curriculum. Adding this course to an undergraduate curriculum will better prepare students for future research in biology. PMID:26753026

  3. Edge Bioinformatics

    Energy Science and Technology Software Center (ESTSC)

    2015-08-03

    Edge Bioinformatics is a developmental bioinformatics and data management platform which seeks to supply laboratories with bioinformatics pipelines for analyzing data associated with common samples case goals. Edge Bioinformatics enables sequencing as a solution and forward-deployed situations where human-resources, space, bandwidth, and time are limited. The Edge bioinformatics pipeline was designed based on following USE CASES and specific to illumina sequencing reads. 1. Assay performance adjudication (PCR): Analysis of an existing PCR assay in amore » genomic context, and automated design of a new assay to resolve conflicting results; 2. Clinical presentation with extreme symptoms: Characterization of a known pathogen or co-infection with a. Novel emerging disease outbreak or b. Environmental surveillance« less

  4. Edge Bioinformatics

    SciTech Connect

    Lo, Chien-Chi

    2015-08-03

    Edge Bioinformatics is a developmental bioinformatics and data management platform which seeks to supply laboratories with bioinformatics pipelines for analyzing data associated with common samples case goals. Edge Bioinformatics enables sequencing as a solution and forward-deployed situations where human-resources, space, bandwidth, and time are limited. The Edge bioinformatics pipeline was designed based on following USE CASES and specific to illumina sequencing reads. 1. Assay performance adjudication (PCR): Analysis of an existing PCR assay in a genomic context, and automated design of a new assay to resolve conflicting results; 2. Clinical presentation with extreme symptoms: Characterization of a known pathogen or co-infection with a. Novel emerging disease outbreak or b. Environmental surveillance

  5. Early Warning System: a juridical notion to be built

    NASA Astrophysics Data System (ADS)

    Lucarelli, A.

    2007-12-01

    Early warning systems (EWS) are becoming effective tools for real time mitigation of the harmful effects arising from widely different hazards, which range from famine to financial crisis, malicious attacks, industrial accidents, natural catastrophes, etc. Early warning of natural catastrophic events allows to implement both alert systems and real time prevention actions for the safety of people and goods exposed to the risk However the effective implementation of early warning methods is hindered by the lack of a specific juridical frame. Under a juridical point of view, in fact, EWS and in general all the activities of prevention need a careful regulation, mainly with regards to responsibility and possible compensation for damage caused by the implemented actions. A preventive alarm, in fact, has an active influence on infrastructures in control of public services which in turn will suffer suspensions or interruptions because of the early warning actions. From here it is necessary to possess accurate normative references related to the typology of structures or infrastructures upon which the activity of readiness acts; the progressive order of suspension of public services; the duration of these suspensions; the corporate bodies or administrations that are competent to assume such decisions; the actors responsible for the consequences of false alarm, missed or delayed alarms; the mechanisms of compensation for damage; the insurance systems; etc In the European Union EWS are often quoted as preventive methods of mitigation of the risk. Nevertheless, a juridical notion of EWS of general use is not available. In fact, EW is a concept that finds application in many different circles, each of which require specific adaptations, and may concern subjects for which the European Union doesn't have exclusive competence as may be the responsibility of the member states to assign the necessary regulations. In so far as the juridical arrangement of the EWS, this must be

  6. A bioinformatics expert system linking functional data to anatomical outcomes in limb regeneration

    PubMed Central

    Lobo, Daniel; Feldman, Erica B.; Shah, Michelle; Malone, Taylor J.

    2014-01-01

    Abstract Amphibians and molting arthropods have the remarkable capacity to regenerate amputated limbs, as described by an extensive literature of experimental cuts, amputations, grafts, and molecular techniques. Despite a rich history of experimental effort, no comprehensive mechanistic model exists that can account for the pattern regulation observed in these experiments. While bioinformatics algorithms have revolutionized the study of signaling pathways, no such tools have heretofore been available to assist scientists in formulating testable models of large‐scale morphogenesis that match published data in the limb regeneration field. Major barriers to preventing an algorithmic approach are the lack of formal descriptions for experimental regenerative information and a repository to centralize storage and mining of functional data on limb regeneration. Establishing a new bioinformatics of shape would significantly accelerate the discovery of key insights into the mechanisms that implement complex regeneration. Here, we describe a novel mathematical ontology for limb regeneration to unambiguously encode phenotype, manipulation, and experiment data. Based on this formalism, we present the first centralized formal database of published limb regeneration experiments together with a user‐friendly expert system tool to facilitate its access and mining. These resources are freely available for the community and will assist both human biologists and artificial intelligence systems to discover testable, mechanistic models of limb regeneration. PMID:25729585

  7. Towards a career in bioinformatics

    PubMed Central

    2009-01-01

    The 2009 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation from 1998, was organized as the 8th International Conference on Bioinformatics (InCoB), Sept. 9-11, 2009 at Biopolis, Singapore. InCoB has actively engaged researchers from the area of life sciences, systems biology and clinicians, to facilitate greater synergy between these groups. To encourage bioinformatics students and new researchers, tutorials and student symposium, the Singapore Symposium on Computational Biology (SYMBIO) were organized, along with the Workshop on Education in Bioinformatics and Computational Biology (WEBCB) and the Clinical Bioinformatics (CBAS) Symposium. However, to many students and young researchers, pursuing a career in a multi-disciplinary area such as bioinformatics poses a Himalayan challenge. A collection to tips is presented here to provide signposts on the road to a career in bioinformatics. An overview of the application of bioinformatics to traditional and emerging areas, published in this supplement, is also presented to provide possible future avenues of bioinformatics investigation. A case study on the application of e-learning tools in undergraduate bioinformatics curriculum provides information on how to go impart targeted education, to sustain bioinformatics in the Asia-Pacific region. The next InCoB is scheduled to be held in Tokyo, Japan, Sept. 26-28, 2010. PMID:19958508

  8. An approach to built-in test for shipboard machinery systems

    NASA Astrophysics Data System (ADS)

    Hegner, H. R.

    This paper presents an approach for incorporating built-in test (BIT) into shipboard machinery systems. BIT, as used herein, denotes both built-in test and on-line monitoring. Since sensors are a key element to a successful machinery monitoring system, an assessment of shipboard sensors is included in the paper. Specific design examples are also presented for a marine diesel engine, gas turbine engine, and air conditioning plant.

  9. Bioinformatics and systems biology: bridging the gap between heterogeneous student backgrounds.

    PubMed

    Abeln, Sanne; Molenaar, Douwe; Feenstra, K Anton; Hoefsloot, Huub C J; Teusink, Bas; Heringa, Jaap

    2013-09-01

    Teaching students with very diverse backgrounds can be extremely challenging. This article uses the Bioinformatics and Systems Biology MSc in Amsterdam as a case study to describe how the knowledge gap for students with heterogeneous backgrounds can be bridged. We show that a mix in backgrounds can be turned into an advantage by creating a stimulating learning environment for the students. In the MSc Programme, conversion classes help to bridge differences between students, by mending initial knowledge and skill gaps. Mixing students from different backgrounds in a group to solve a complex task creates an opportunity for the students to reflect on their own abilities. We explain how a truly interdisciplinary approach to teaching helps students of all backgrounds to achieve the MSc end terms. Moreover, transferable skills obtained by the students in such a mixed study environment are invaluable for their later careers. PMID:23603092

  10. Analyses of Brucella Pathogenesis, Host Immunity, and Vaccine Targets using Systems Biology and Bioinformatics

    PubMed Central

    He, Yongqun

    2011-01-01

    Brucella is a Gram-negative, facultative intracellular bacterium that causes zoonotic brucellosis in humans and various animals. Out of 10 classified Brucella species, B. melitensis, B. abortus, B. suis, and B. canis are pathogenic to humans. In the past decade, the mechanisms of Brucella pathogenesis and host immunity have been extensively investigated using the cutting edge systems biology and bioinformatics approaches. This article provides a comprehensive review of the applications of Omics (including genomics, transcriptomics, and proteomics) and bioinformatics technologies for the analysis of Brucella pathogenesis, host immune responses, and vaccine targets. Based on more than 30 sequenced Brucella genomes, comparative genomics is able to identify gene variations among Brucella strains that help to explain host specificity and virulence differences among Brucella species. Diverse transcriptomics and proteomics gene expression studies have been conducted to analyze gene expression profiles of wild type Brucella strains and mutants under different laboratory conditions. High throughput Omics analyses of host responses to infections with virulent or attenuated Brucella strains have been focused on responses by mouse and cattle macrophages, bovine trophoblastic cells, mouse and boar splenocytes, and ram buffy coat. Differential serum responses in humans and rams to Brucella infections have been analyzed using high throughput serum antibody screening technology. The Vaxign reverse vaccinology has been used to predict many Brucella vaccine targets. More than 180 Brucella virulence factors and their gene interaction networks have been identified using advanced literature mining methods. The recent development of community-based Vaccine Ontology and Brucellosis Ontology provides an efficient way for Brucella data integration, exchange, and computer-assisted automated reasoning. PMID:22919594

  11. Specifying, Installing and Maintaining Built-Up and Modified Bitumen Roofing Systems.

    ERIC Educational Resources Information Center

    Hobson, Joseph W.

    2000-01-01

    Examines built-up, modified bitumen, and hybrid combinations of the two roofing systems and offers advise on how to assure high- quality performance and durability when using them. Included is a glossary of commercial roofing terms and asphalt roofing resources to aid in making decisions on roofing and systems product selection. (GR)

  12. KDE Bioscience: platform for bioinformatics analysis workflows.

    PubMed

    Lu, Qiang; Hao, Pei; Curcin, Vasa; He, Weizhong; Li, Yuan-Yuan; Luo, Qing-Ming; Guo, Yi-Ke; Li, Yi-Xue

    2006-08-01

    Bioinformatics is a dynamic research area in which a large number of algorithms and programs have been developed rapidly and independently without much consideration so far of the need for standardization. The lack of such common standards combined with unfriendly interfaces make it difficult for biologists to learn how to use these tools and to translate the data formats from one to another. Consequently, the construction of an integrative bioinformatics platform to facilitate biologists' research is an urgent and challenging task. KDE Bioscience is a java-based software platform that collects a variety of bioinformatics tools and provides a workflow mechanism to integrate them. Nucleotide and protein sequences from local flat files, web sites, and relational databases can be entered, annotated, and aligned. Several home-made or 3rd-party viewers are built-in to provide visualization of annotations or alignments. KDE Bioscience can also be deployed in client-server mode where simultaneous execution of the same workflow is supported for multiple users. Moreover, workflows can be published as web pages that can be executed from a web browser. The power of KDE Bioscience comes from the integrated algorithms and data sources. With its generic workflow mechanism other novel calculations and simulations can be integrated to augment the current sequence analysis functions. Because of this flexible and extensible architecture, KDE Bioscience makes an ideal integrated informatics environment for future bioinformatics or systems biology research. PMID:16260186

  13. Agile parallel bioinformatics workflow management using Pwrake

    PubMed Central

    2011-01-01

    Background In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error. Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. Findings We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Conclusions Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability

  14. A systems approach to resilience in the built environment: the case of Cuba.

    PubMed

    Lizarralde, Gonzalo; Valladares, Arturo; Olivera, Andres; Bornstein, Lisa; Gould, Kevin; Barenstein, Jennifer Duyne

    2015-01-01

    Through its capacity to evoke systemic adaptation before and after disasters, resilience has become a seductive theory in disaster management. Several studies have linked the concept with systems theory; however, they have been mostly based on theoretical models with limited empirical support. The study of the Cuban model of resilience sheds light on the variables that create systemic resilience in the built environment and its relations with the social and natural environments. Cuba is vulnerable to many types of hazard, yet the country's disaster management benefits from institutional, health and education systems that develop social capital, knowledge and other assets that support construction industry and housing development, systematic urban and regional planning, effective alerts, and evacuation plans. The Cuban political context is specific, but the study can nonetheless contribute to systemic improvements to the resilience of built environments in other contexts. PMID:25494958

  15. Autonomic Nervous System Responses to Viewing Green and Built Settings: Differentiating Between Sympathetic and Parasympathetic Activity.

    PubMed

    van den Berg, Magdalena M H E; Maas, Jolanda; Muller, Rianne; Braun, Anoek; Kaandorp, Wendy; van Lien, René; van Poppel, Mireille N M; van Mechelen, Willem; van den Berg, Agnes E

    2015-12-01

    This laboratory study explored buffering and recovery effects of viewing urban green and built spaces on autonomic nervous system activity. Forty-six students viewed photos of green and built spaces immediately following, and preceding acute stress induction. Simultaneously recorded electrocardiogram and impedance cardiogram signal was used to derive respiratory sinus arrhythmia (RSA) and pre-ejection period (PEP), indicators of respectively parasympathetic and sympathetic activity. The findings provide support for greater recovery after viewing green scenes, as marked by a stronger increase in RSA as a marker of parasympathetic activity. There were no indications for greater recovery after viewing green scenes in PEP as a marker of sympathetic activity, and there were also no indications of greater buffering effects of green space in neither RSA nor PEP. Overall, our findings are consistent with a predominant role of the parasympathetic nervous system in restorative effects of viewing green space. PMID:26694426

  16. Autonomic Nervous System Responses to Viewing Green and Built Settings: Differentiating Between Sympathetic and Parasympathetic Activity

    PubMed Central

    van den Berg, Magdalena M.H.E.; Maas, Jolanda; Muller, Rianne; Braun, Anoek; Kaandorp, Wendy; van Lien, René; van Poppel, Mireille N.M.; van Mechelen, Willem; van den Berg, Agnes E.

    2015-01-01

    This laboratory study explored buffering and recovery effects of viewing urban green and built spaces on autonomic nervous system activity. Forty-six students viewed photos of green and built spaces immediately following, and preceding acute stress induction. Simultaneously recorded electrocardiogram and impedance cardiogram signal was used to derive respiratory sinus arrhythmia (RSA) and pre-ejection period (PEP), indicators of respectively parasympathetic and sympathetic activity. The findings provide support for greater recovery after viewing green scenes, as marked by a stronger increase in RSA as a marker of parasympathetic activity. There were no indications for greater recovery after viewing green scenes in PEP as a marker of sympathetic activity, and there were also no indications of greater buffering effects of green space in neither RSA nor PEP. Overall, our findings are consistent with a predominant role of the parasympathetic nervous system in restorative effects of viewing green space. PMID:26694426

  17. Design and Implementation of a Custom Built Optical Projection Tomography System

    PubMed Central

    Wong, Michael D.; Dazai, Jun; Walls, Johnathon R.; Gale, Nicholas W.; Henkelman, R. Mark

    2013-01-01

    Optical projection tomography (OPT) is an imaging modality that has, in the last decade, answered numerous biological questions owing to its ability to view gene expression in 3 dimensions (3D) at high resolution for samples up to several cm3. This has increased demand for a cabinet OPT system, especially for mouse embryo phenotyping, for which OPT was primarily designed for. The Medical Research Council (MRC) Technology group (UK) released a commercial OPT system, constructed by Skyscan, called the Bioptonics OPT 3001 scanner that was installed in a limited number of locations. The Bioptonics system has been discontinued and currently there is no commercial OPT system available. Therefore, a few research institutions have built their own OPT system, choosing parts and a design specific to their biological applications. Some of these custom built OPT systems are preferred over the commercial Bioptonics system, as they provide improved performance based on stable translation and rotation stages and up to date CCD cameras coupled with objective lenses of high numerical aperture, increasing the resolution of the images. Here, we present a detailed description of a custom built OPT system that is robust and easy to build and install. Included is a hardware parts list, instructions for assembly, a description of the acquisition software and a free download site, and methods for calibration. The described OPT system can acquire a full 3D data set in 10 minutes at 6.7 micron isotropic resolution. The presented guide will hopefully increase adoption of OPT throughout the research community, for the OPT system described can be implemented by personnel with minimal expertise in optics or engineering who have access to a machine shop. PMID:24023880

  18. Design and implementation of a custom built optical projection tomography system.

    PubMed

    Wong, Michael D; Dazai, Jun; Walls, Johnathon R; Gale, Nicholas W; Henkelman, R Mark

    2013-01-01

    Optical projection tomography (OPT) is an imaging modality that has, in the last decade, answered numerous biological questions owing to its ability to view gene expression in 3 dimensions (3D) at high resolution for samples up to several cm(3). This has increased demand for a cabinet OPT system, especially for mouse embryo phenotyping, for which OPT was primarily designed for. The Medical Research Council (MRC) Technology group (UK) released a commercial OPT system, constructed by Skyscan, called the Bioptonics OPT 3001 scanner that was installed in a limited number of locations. The Bioptonics system has been discontinued and currently there is no commercial OPT system available. Therefore, a few research institutions have built their own OPT system, choosing parts and a design specific to their biological applications. Some of these custom built OPT systems are preferred over the commercial Bioptonics system, as they provide improved performance based on stable translation and rotation stages and up to date CCD cameras coupled with objective lenses of high numerical aperture, increasing the resolution of the images. Here, we present a detailed description of a custom built OPT system that is robust and easy to build and install. Included is a hardware parts list, instructions for assembly, a description of the acquisition software and a free download site, and methods for calibration. The described OPT system can acquire a full 3D data set in 10 minutes at 6.7 micron isotropic resolution. The presented guide will hopefully increase adoption of OPT throughout the research community, for the OPT system described can be implemented by personnel with minimal expertise in optics or engineering who have access to a machine shop. PMID:24023880

  19. Tank Monitoring and Document control System (TMACS) As Built Software Design Document

    SciTech Connect

    GLASSCOCK, J.A.

    2000-01-27

    This document describes the software design for the Tank Monitor and Control System (TMACS). This document captures the existing as-built design of TMACS as of November 1999. It will be used as a reference document to the system maintainers who will be maintaining and modifying the TMACS functions as necessary. The heart of the TMACS system is the ''point-processing'' functionality where a sample value is received from the field sensors and the value is analyzed, logged, or alarmed as required. This Software Design Document focuses on the point-processing functions.

  20. The study of calibration and epipolar geometry for the stereo vision system built by fisheye lenses

    NASA Astrophysics Data System (ADS)

    Zhang, Baofeng; Lu, Chunfang; Röning, Juha; Feng, Weijia

    2015-01-01

    Fish-eye lens is a kind of short focal distance (f=6~16mm) camera. The field of view (FOV) of it is near or even exceeded 180×180 degrees. A lot of literatures show that the multiple view geometry system built by fish-eye lens will get larger stereo field than traditional stereo vision system which based on a pair of perspective projection images. Since a fish-eye camera usually has a wider-than-hemispherical FOV, the most of image processing approaches based on the pinhole camera model for the conventional stereo vision system are not satisfied to deal with the applications of this category of stereo vision which built by fish-eye lenses. This paper focuses on discussing the calibration and the epipolar rectification method for a novel machine vision system set up by four fish-eye lenses, which is called Special Stereo Vision System (SSVS). The characteristic of SSVS is that it can produce 3D coordinate information from the whole global observation space and acquiring no blind area 360º×360º panoramic image simultaneously just using single vision equipment with one time static shooting. Parameters calibration and epipolar rectification is the basic for SSVS to realize 3D reconstruction and panoramic image generation.

  1. Factory Built-in Type Simplified OCT System for Industrial Application

    NASA Astrophysics Data System (ADS)

    Shiina, Tatsuo; Miyazaki, Satoshi; Honda, Toshio

    Factory built-in type simplified optical coherence tomography (OCT) system was developed for industrial use. The system design was supposed for check of the laser-welded resin. As a first approach, the current simplified OCT system for plant measurement was applied for the validation of the industrial sample; plastic resin. The industrial-use OCT was designed in response to the results. The performances of the measurement speed and range of the developed OCT system were 50scan/s and 5mm, respectively. The low coherence of 18.9μm could clearly distinguish the gap of 2 laser-welded resins. The system became compact and low price, and has the flexibility of epi-optics.

  2. Home-built magnetic resonance imaging system (0.3 T) with a complete digital spectrometer

    NASA Astrophysics Data System (ADS)

    Jie, Shen; Qin, Xu; Ying, Liu; Gengying, Li

    2005-10-01

    A home-built magnetic resonance imaging (MRI) system with a complete digital spectrometer has been designed for investigation of plants and animals. With the application of the latest digital integrated circuit technology, the digital spectrometer is greatly simplified without the loss of flexibility and performance. A powerful pulse sequence compiler with a graphical editor can allow the user to edit the pulse sequence more easily and more conveniently than ever before. Moreover, a permanent magnet capable of producing a 180 mm diam spherical homogeneous region is employed in our MRI system to ensure a comparatively large image size. Compared with previous work, our MRI system has the features of flexibility, relatively large imaging size, and low cost. Experimental results obtained with the proposed system are presented in this article.

  3. MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics

    PubMed Central

    2014-01-01

    Background Optimization is the key to solving many problems in computational biology. Global optimization methods, which provide a robust methodology, and metaheuristics in particular have proven to be the most efficient methods for many applications. Despite their utility, there is a limited availability of metaheuristic tools. Results We present MEIGO, an R and Matlab optimization toolbox (also available in Python via a wrapper of the R version), that implements metaheuristics capable of solving diverse problems arising in systems biology and bioinformatics. The toolbox includes the enhanced scatter search method (eSS) for continuous nonlinear programming (cNLP) and mixed-integer programming (MINLP) problems, and variable neighborhood search (VNS) for Integer Programming (IP) problems. Additionally, the R version includes BayesFit for parameter estimation by Bayesian inference. The eSS and VNS methods can be run on a single-thread or in parallel using a cooperative strategy. The code is supplied under GPLv3 and is available at http://www.iim.csic.es/~gingproc/meigo.html. Documentation and examples are included. The R package has been submitted to BioConductor. We evaluate MEIGO against optimization benchmarks, and illustrate its applicability to a series of case studies in bioinformatics and systems biology where it outperforms other state-of-the-art methods. Conclusions MEIGO provides a free, open-source platform for optimization that can be applied to multiple domains of systems biology and bioinformatics. It includes efficient state of the art metaheuristics, and its open and modular structure allows the addition of further methods. PMID:24885957

  4. Bioinformatic Indications That COPI- and Clathrin-Based Transport Systems Are Not Present in Chloroplasts: An Arabidopsis Model

    PubMed Central

    Aronsson, Henrik

    2014-01-01

    Coated vesicle transport occurs in the cytosol of yeast, mammals and plants. It consists of three different transport systems, the COPI, COPII and clathrin coated vesicles (CCV), all of which participate in the transfer of proteins and lipids between different cytosolic compartments. There are also indications that chloroplasts have a vesicle transport system. Several putative chloroplast-localized proteins, including CPSAR1 and CPRabA5e with similarities to cytosolic COPII transport-related proteins, were detected in previous experimental and bioinformatics studies. These indications raised the hypothesis that a COPI- and/or CCV-related system may be present in chloroplasts, in addition to a COPII-related system. To test this hypothesis we bioinformatically searched for chloroplast proteins that may have similar functions to known cytosolic COPI and CCV components in the model plants Arabidopsis thaliana and Oryza sativa (subsp. japonica) (rice). We found 29 such proteins, based on domain similarity, in Arabidopsis, and 14 in rice. However, many components could not be identified and among the identified most have assigned roles that are not related to either COPI or CCV transport. We conclude that COPII is probably the only active vesicle system in chloroplasts, at least in the model plants. The evolutionary implications of the findings are discussed. PMID:25137124

  5. Crowdsourcing for bioinformatics

    PubMed Central

    Good, Benjamin M.; Su, Andrew I.

    2013-01-01

    Motivation: Bioinformatics is faced with a variety of problems that require human involvement. Tasks like genome annotation, image analysis, knowledge-base population and protein structure determination all benefit from human input. In some cases, people are needed in vast quantities, whereas in others, we need just a few with rare abilities. Crowdsourcing encompasses an emerging collection of approaches for harnessing such distributed human intelligence. Recently, the bioinformatics community has begun to apply crowdsourcing in a variety of contexts, yet few resources are available that describe how these human-powered systems work and how to use them effectively in scientific domains. Results: Here, we provide a framework for understanding and applying several different types of crowdsourcing. The framework considers two broad classes: systems for solving large-volume ‘microtasks’ and systems for solving high-difficulty ‘megatasks’. Within these classes, we discuss system types, including volunteer labor, games with a purpose, microtask markets and open innovation contests. We illustrate each system type with successful examples in bioinformatics and conclude with a guide for matching problems to crowdsourcing solutions that highlights the positives and negatives of different approaches. Contact: bgood@scripps.edu PMID:23782614

  6. Expert systems built by the Expert: An evaluation of OPS5

    NASA Technical Reports Server (NTRS)

    Jackson, Robert

    1987-01-01

    Two expert systems were written in OPS5 by the expert, a Ph.D. astronomer with no prior experience in artificial intelligence or expert systems, without the use of a knowledge engineer. The first system was built from scratch and uses 146 rules to check for duplication of scientific information within a pool of prospective observations. The second system was grafted onto another expert system and uses 149 additional rules to estimate the spacecraft and ground resources consumed by a set of prospective observations. The small vocabulary, the IF this occurs THEN do that logical structure of OPS5, and the ability to follow program execution allowed the expert to design and implement these systems with only the data structures and rules of another OPS5 system as an example. The modularity of the rules in OPS5 allowed the second system to modify the rulebase of the system onto which it was grafted without changing the code or the operation of that system. These experiences show that experts are able to develop their own expert systems due to the ease of programming and code reusability in OPS5.

  7. Finding the next-best scanner position for as-built modeling of piping systems

    NASA Astrophysics Data System (ADS)

    Kawashima, K.; Yamanishi, S.; Kanai, S.; Date, H.

    2014-06-01

    Renovation of plant equipment of petroleum refineries or chemical factories have recently been frequent, and the demand for 3D asbuilt modelling of piping systems is increasing rapidly. Terrestrial laser scanners are used very often in the measurement for as-built modelling. However, the tangled structures of the piping systems results in complex occluded areas, and these areas must be captured from different scanner positions. For efficient and exhaustive measurement of the piping system, the scanner should be placed at optimum positions where the occluded parts of the piping system are captured as much as possible in less scans. However, this "nextbest" scanner positions are usually determined by experienced operators, and there is no guarantee that these positions fulfil the optimum condition. Therefore, this paper proposes a computer-aided method of the optimal sequential view planning for object recognition in plant piping systems using a terrestrial laser scanner. In the method, a sequence of next-best positions of a terrestrial laser scanner specialized for as-built modelling of piping systems can be found without any a priori information of piping objects. Different from the conventional approaches for the next-best-view (NBV) problem, in the proposed method, piping objects in the measured point clouds are recognized right after an every scan, local occluded spaces occupied by the unseen piping systems are then estimated, and the best scanner position can be found so as to minimize these local occluded spaces. The simulation results show that our proposed method outperforms a conventional approach in recognition accuracy, efficiency and computational time.

  8. Enabling high-throughput data management systems biology: The Bioinformatics Resource Manager

    SciTech Connect

    Shah, Anuj R.; Singhal, Mudita; Klicker, Kyle R.; Stephan, Eric G.; Wiley, H. S.; Waters, Katrina M.

    2007-02-25

    The Bioinformatics Resource Manager (BRM) is a problem-solving environment that provides the user with data retrieval, management, analysis and visualization capabilities through all aspects of an experimental study. Designed in collaboration with biologists, BRM simplifies the integration of experimental data across platforms and with other publicly available information from external data sources. An analysis pipeline is facilitated within BRM by the seamless connectivity of user data with visual analytics tools, through reformatting of the data for easy import. BRM is developed using JAVATM and other open source technologies so that it can be freely distributable.

  9. Bioinformatics for Exploration

    NASA Technical Reports Server (NTRS)

    Johnson, Kathy A.

    2006-01-01

    For the purpose of this paper, bioinformatics is defined as the application of computer technology to the management of biological information. It can be thought of as the science of developing computer databases and algorithms to facilitate and expedite biological research. This is a crosscutting capability that supports nearly all human health areas ranging from computational modeling, to pharmacodynamics research projects, to decision support systems within autonomous medical care. Bioinformatics serves to increase the efficiency and effectiveness of the life sciences research program. It provides data, information, and knowledge capture which further supports management of the bioastronautics research roadmap - identifying gaps that still remain and enabling the determination of which risks have been addressed.

  10. Exploring the immunogenome with bioinformatics.

    PubMed

    de Bono, Bernard; Trowsdale, John

    2003-08-01

    A better description of the immune system can be afforded if the latest developments in bioinformatics are applied to integrate sequence with structure and function. Clear guidelines for the upgrade of the bioinformatic capability of the immunogenetics laboratory are discussed in the light of more powerful methods to detect homology, combined approaches to predict the three dimensional properties of a protein and a robust strategy to represent the biological role of a gene. PMID:14690048

  11. Initial clinical testing of a multi-spectral imaging system built on a smartphone platform

    NASA Astrophysics Data System (ADS)

    Mink, Jonah W.; Wexler, Shraga; Bolton, Frank J.; Hummel, Charles; Kahn, Bruce S.; Levitz, David

    2016-03-01

    Multi-spectral imaging systems are often expensive and bulky. An innovative multi-spectral imaging system was fitted onto a mobile colposcope, an imaging system built around a smartphone in order to image the uterine cervix from outside the body. The multi-spectral mobile colposcope (MSMC) acquires images at different wavelengths. This paper presents the clinical testing of MSMC imaging (technical validation of the MSMC system is described elsewhere 1 ). Patients who were referred to colposcopy following abnormal screening test (Pap or HPV DNA test) according to the standard of care were enrolled. Multi-spectral image sets of the cervix were acquired, consisting of images from the various wavelengths. Image acquisition took 1-2 sec. Areas suspected for dysplasia under white light imaging were biopsied, according to the standard of care. Biopsied sites were recorded on a clockface map of the cervix. Following the procedure, MSMC data was processed from the sites of biopsied sites. To date, the initial histopathological results are still outstanding. Qualitatively, structures in the cervical images were sharper at lower wavelengths than higher wavelengths. Patients tolerated imaging well. The result suggests MSMC holds promise for cervical imaging.

  12. Design of a built-in health monitoring system for bolted thermal protection panels

    NASA Astrophysics Data System (ADS)

    Yang, Jinkyu; Chang, Fu-Kuo; Derriso, Mark M.

    2003-08-01

    Space vehicles require high performance thermal protection systems (TPS) that provide high temperature insulation capability with lower weight, high strength, and reliable integration with the existing system. Carbon-carbon panels mounted with bracket joints are potential future thermal protection systems with light weight, low creep, and high stiffness at high temperatures. However, the thermal protection system experiences a very harsh high-temperature and aerodynamic environment in addition to foreign object impacts. Damage or failure of panels without being detected can lead to catastrophe. Therefore, knowledge of the integrity of the thermal protection system before each launch and reentry is essential to the success of the mission. The objective of the study is to develop a built-in diagnostic system to assess the integrity of TPS panels as well as to lower inspection and maintenance time and costs. An integrated structural health monitoring system is being developed to monitor the TPS panels. The technology includes investigation of the loosening of bolts which connects TPS panels to the supporting structure, and potentially, identifying the location of damage on the panel caused by external impacts from micrometeorites and other objects. The first generation prototype was manufactured and tested in an acoustic chamber which simulated a re-entry environment to investigate the feasibility of the health monitoring system focusing on its survivability and sensitivity. The preliminary results were very promising. Based on the test results, the second generation design was proposed to improve the performance of the first generation design. To put a reliable and accurate decision on the diagnostics of the TPS panels, an advanced algorithm was developed with the aid of a wavelet transform technique.

  13. An Undergraduate-Built Prototype Altitude Determination System (PADS) for High Altitude Research Balloons.

    NASA Astrophysics Data System (ADS)

    Verner, E.; Bruhweiler, F. C.; Abot, J.; Casarotto, V.; Dichoso, J.; Doody, E.; Esteves, F.; Morsch Filho, E.; Gonteski, D.; Lamos, M.; Leo, A.; Mulder, N.; Matubara, F.; Schramm, P.; Silva, R.; Quisberth, J.; Uritsky, G.; Kogut, A.; Lowe, L.; Mirel, P.; Lazear, J.

    2014-12-01

    In this project a multi-disciplinary undergraduate team from CUA, comprising majors in Physics, Mechanical Engineering, Electrical Engineering, and Biology, design, build, test, fly, and analyze the data from a prototype attitude determination system (PADS). The goal of the experiment is to determine if an inexpensive attitude determination system could be built for high altitude research balloons using MEMS gyros. PADS is a NASA funded project, built by students with the cooperation of CUA faculty, Verner, Bruhweiler, and Abot, along with the contributed expertise of researchers and engineers at NASA/GSFC, Kogut, Lowe, Mirel, and Lazear. The project was initiated through a course taught in CUA's School of Engineering, which was followed by a devoted effort by students during the summer of 2014. The project is an experiment to use 18 MEMS gyros, similar to those used in many smartphones, to produce an averaged positional error signal that could be compared with the motion of the fixed optical system as recorded through a string of optical images of stellar fields to be stored on a hard drive flown with the experiment. The optical system, camera microprocessor, and hard drive are enclosed in a pressure vessel, which maintains approximately atmospheric pressure throughout the balloon flight. The experiment uses multiple microprocessors to control the camera exposures, record gyro data, and provide thermal control. CUA students also participated in NASA-led design reviews. Four students traveled to NASA's Columbia Scientific Balloon Facility in Palestine, Texas to integrate PADS into a large balloon gondola containing other experiments, before being shipped, then launched in mid-August at Ft. Sumner, New Mexico. The payload is to fly at a float altitude of 40-45,000 m, and the flight last approximately 15 hours. The payload is to return to earth by parachute and the retrieved data are to be analyzed by CUA undergraduates. A description of the instrument is presented

  14. Measurement of airflow and pressure characteristics of a fan built in a car ventilation system

    NASA Astrophysics Data System (ADS)

    Pokorný, Jan; Poláček, Filip; Fojtlín, Miloš; Fišer, Jan; Jícha, Miroslav

    2016-03-01

    The aim of this study was to identify a set of operating points of a fan built in ventilation system of our test car. These operating points are given by the fan pressure characteristics and are defined by a pressure drop of the HVAC system (air ducts and vents) and volumetric flow rate of ventilation air. To cover a wide range of pressure drops situations, four cases of vent flaps setup were examined: (1) all vents opened, (2) only central vents closed (3) only central vents opened and (4) all vents closed. To cover a different volumetric flows, the each case was measured at least for four different speeds of fan defined by the fan voltage. It was observed that the pressure difference of the fan is proportional to the fan voltage and strongly depends on the throttling of the air distribution system by the settings of the vents flaps. In case of our test car we identified correlations between volumetric flow rate of ventilation air, fan pressure difference and fan voltage. These correlations will facilitate and reduce time costs of the following experiments with this test car.

  15. Note: Design and implementation of a home-built imaging system with low jitter for cold atom experiments.

    PubMed

    Hachtel, A J; Gillette, M C; Clements, E R; Zhong, S; Weeks, M R; Bali, S

    2016-05-01

    A novel home-built system for imaging cold atom samples is presented using a readily available astronomy camera which has the requisite sensitivity but no timing-control. We integrate the camera with LabVIEW achieving fast, low-jitter imaging with a convenient user-defined interface. We show that our system takes precisely timed millisecond exposures and offers significant improvements in terms of system jitter and readout time over previously reported home-built systems. Our system rivals current commercial "black box" systems in performance and user-friendliness. PMID:27250483

  16. Experimental Identification of Smartphones Using Fingerprints of Built-In Micro-Electro Mechanical Systems (MEMS)

    PubMed Central

    Baldini, Gianmarco; Steri, Gary; Dimc, Franc; Giuliani, Raimondo; Kamnik, Roman

    2016-01-01

    The correct identification of smartphones has various applications in the field of security or the fight against counterfeiting. As the level of sophistication in counterfeit electronics increases, detection procedures must become more accurate but also not destructive for the smartphone under testing. Some components of the smartphone are more likely to reveal their authenticity even without a physical inspection, since they are characterized by hardware fingerprints detectable by simply examining the data they provide. This is the case of MEMS (Micro Electro-Mechanical Systems) components like accelerometers and gyroscopes, where tiny differences and imprecisions in the manufacturing process determine unique patterns in the data output. In this paper, we present the experimental evaluation of the identification of smartphones through their built-in MEMS components. In our study, three different phones of the same model are subject to repeatable movements (composing a repeatable scenario) using an high precision robotic arm. The measurements from MEMS for each repeatable scenario are collected and analyzed. The identification algorithm is based on the extraction of the statistical features of the collected data for each scenario. The features are used in a support vector machine (SVM) classifier to identify the smartphone. The results of the evaluation are presented for different combinations of features and Inertial Measurement Unit (IMU) outputs, which show that detection accuracy of higher than 90% is achievable. PMID:27271630

  17. Experimental Identification of Smartphones Using Fingerprints of Built-In Micro-Electro Mechanical Systems (MEMS).

    PubMed

    Baldini, Gianmarco; Steri, Gary; Dimc, Franc; Giuliani, Raimondo; Kamnik, Roman

    2016-01-01

    The correct identification of smartphones has various applications in the field of security or the fight against counterfeiting. As the level of sophistication in counterfeit electronics increases, detection procedures must become more accurate but also not destructive for the smartphone under testing. Some components of the smartphone are more likely to reveal their authenticity even without a physical inspection, since they are characterized by hardware fingerprints detectable by simply examining the data they provide. This is the case of MEMS (Micro Electro-Mechanical Systems) components like accelerometers and gyroscopes, where tiny differences and imprecisions in the manufacturing process determine unique patterns in the data output. In this paper, we present the experimental evaluation of the identification of smartphones through their built-in MEMS components. In our study, three different phones of the same model are subject to repeatable movements (composing a repeatable scenario) using an high precision robotic arm. The measurements from MEMS for each repeatable scenario are collected and analyzed. The identification algorithm is based on the extraction of the statistical features of the collected data for each scenario. The features are used in a support vector machine (SVM) classifier to identify the smartphone. The results of the evaluation are presented for different combinations of features and Inertial Measurement Unit (IMU) outputs, which show that detection accuracy of higher than 90% is achievable. PMID:27271630

  18. Handheld electrocardiogram measurement instrument using a new peak quantification method algorithm built on a system-on-chip embedded system

    NASA Astrophysics Data System (ADS)

    Chang Chien, Jia-Ren; Tai, Cheng-Chi

    2006-09-01

    This article reports on the new design and development of an electrocardiogram (ECG) measurement instrument built on a system-on-chip (SOC) embedded system. A new approach using the peak quantification method (PQM) for measuring the human heart rate is described. A computer, some medical equipment, and other facilities are often required for conducting the traditional ECG measurements. However, the monitors of such instruments have some disadvantages, e.g., bulky, not very easy to transport, expensive, and so forth. Hence, we propose a new design for ECG measurement which is built on an embedded system. Our system adopts a SOC and ECG detection circuits to carry out a real-time, low-cost, and compact ECG measurement system. Regarding heart rate computation, the experimental results show that the new PQM algorithm, when applied to heart rate measurements, yields error smaller than 1bpm. In addition, the correlation coefficient between the measured and actual heartbeats can reach 0.94 when the heart rate is less than 153bpm. It shows that the use of the PQM algorithm gives an extremely high degree of accuracy.

  19. Recommendation Systems for Geoscience Data Portals Built by Analyzing Usage Patterns

    NASA Astrophysics Data System (ADS)

    Crosby, C.; Nandigam, V.; Baru, C.

    2009-04-01

    Since its launch five years ago, the National Science Foundation-funded GEON Project (www.geongrid.org) has been providing access to a variety of geoscience data sets such as geologic maps and other geographic information system (GIS)-oriented data, paleontologic databases, gravity and magnetics data and LiDAR topography via its online portal interface. In addition to data, the GEON Portal also provides web-based tools and other resources that enable users to process and interact with data. Examples of these tools include functions to dynamically map and integrate GIS data, compute synthetic seismograms, and to produce custom digital elevation models (DEMs) with user defined parameters such as resolution. The GEON portal built on the Gridsphere-portal framework allows us to capture user interaction with the system. In addition to the site access statistics captured by tools like Google Analystics which capture hits per unit time, search key words, operating systems, browsers, and referring sites, we also record additional statistics such as which data sets are being downloaded and in what formats, processing parameters, and navigation pathways through the portal. With over four years of data now available from the GEON Portal, this record of usage is a rich resource for exploring how earth scientists discover and utilize online data sets. Furthermore, we propose that this data could ultimately be harnessed to optimize the way users interact with the data portal, design intelligent processing and data management systems, and to make recommendations on algorithm settings and other available relevant data. The paradigm of integrating popular and commonly used patterns to make recommendations to a user is well established in the world of e-commerce where users receive suggestions on books, music and other products that they may find interesting based on their website browsing and purchasing history, as well as the patterns of fellow users who have made similar

  20. Experiences with Testing the Largest Ground System NASA Has Ever Built

    NASA Technical Reports Server (NTRS)

    Lehtonen, Ken; Messerly, Robert

    2003-01-01

    In the 1980s, the National Aeronautics and Space Administration (NASA) embarked upon a major Earth-focused program called Mission to Planet Earth. The Goddard Space Flight Center (GSFC) was selected to manage and develop a key component - the Earth Observing System (EOS). The EOS consisted of four major missions designed to monitor the Earth. The missions included 4 spacecraft. Terra (launched December 1999), Aqua (launched May 2002), ICESat (Ice, Cloud, and Land Elevation Satellite, launched January 2003), and Aura (scheduled for launch January 2004). The purpose of these missions was to provide support for NASA s long-term research effort for determining how human-induced and natural changes affect our global environment. The EOS Data and Information System (EOSDIS), a globally distributed, large-scale scientific system, was built to support EOS. Its primary function is to capture, collect, process, and distribute the most voluminous set of remotely sensed scientific data to date estimated to be 350 Gbytes per day. The EOSDIS is composed of a diverse set of elements with functional capabilities that require the implementation of a complex set of computers, high-speed networks, mission-unique equipment, and associated Information Technology (IT) software along with mission-specific software. All missions are constrained by schedule, budget, and staffing resources, and rigorous testing has been shown to be critical to the success of each mission. This paper addresses the challenges associated with the planning, test definition. resource scheduling, execution, and discrepancy reporting involved in the mission readiness testing of a ground system on the scale of EOSDIS. The size and complexity of the mission systems supporting the Aqua flight operations, for example, combined with the limited resources available, prompted the project to challenge the prevailing testing culture. The resulting success of the Aqua Mission Readiness Testing (MRT) program was due in no

  1. Pattern recognition in bioinformatics.

    PubMed

    de Ridder, Dick; de Ridder, Jeroen; Reinders, Marcel J T

    2013-09-01

    Pattern recognition is concerned with the development of systems that learn to solve a given problem using a set of example instances, each represented by a number of features. These problems include clustering, the grouping of similar instances; classification, the task of assigning a discrete label to a given instance; and dimensionality reduction, combining or selecting features to arrive at a more useful representation. The use of statistical pattern recognition algorithms in bioinformatics is pervasive. Classification and clustering are often applied to high-throughput measurement data arising from microarray, mass spectrometry and next-generation sequencing experiments for selecting markers, predicting phenotype and grouping objects or genes. Less explicitly, classification is at the core of a wide range of tools such as predictors of genes, protein function, functional or genetic interactions, etc., and used extensively in systems biology. A course on pattern recognition (or machine learning) should therefore be at the core of any bioinformatics education program. In this review, we discuss the main elements of a pattern recognition course, based on material developed for courses taught at the BSc, MSc and PhD levels to an audience of bioinformaticians, computer scientists and life scientists. We pay attention to common problems and pitfalls encountered in applications and in interpretation of the results obtained. PMID:23559637

  2. Bioinformatics and genomic medicine.

    PubMed

    Kim, Ju Han

    2002-01-01

    Bioinformatics is a rapidly emerging field of biomedical research. A flood of large-scale genomic and postgenomic data means that many of the challenges in biomedical research are now challenges in computational science. Clinical informatics has long developed methodologies to improve biomedical research and clinical care by integrating experimental and clinical information systems. The informatics revolution in both bioinformatics and clinical informatics will eventually change the current practice of medicine, including diagnostics, therapeutics, and prognostics. Postgenome informatics, powered by high-throughput technologies and genomic-scale databases, is likely to transform our biomedical understanding forever, in much the same way that biochemistry did a generation ago. This paper describes how these technologies will impact biomedical research and clinical care, emphasizing recent advances in biochip-based functional genomics and proteomics. Basic data preprocessing with normalization and filtering, primary pattern analysis, and machine-learning algorithms are discussed. Use of integrative biochip informatics technologies, including multivariate data projection, gene-metabolic pathway mapping, automated biomolecular annotation, text mining of factual and literature databases, and the integrated management of biomolecular databases, are also discussed. PMID:12544491

  3. Using Geographic Information Systems (GIS) to assess the role of the built environment in influencing obesity: a glossary

    PubMed Central

    2011-01-01

    Features of the built environment are increasingly being recognised as potentially important determinants of obesity. This has come about, in part, because of advances in methodological tools such as Geographic Information Systems (GIS). GIS has made the procurement of data related to the built environment easier and given researchers the flexibility to create a new generation of environmental exposure measures such as the travel time to the nearest supermarket or calculations of the amount of neighbourhood greenspace. Given the rapid advances in the availability of GIS data and the relative ease of use of GIS software, a glossary on the use of GIS to assess the built environment is timely. As a case study, we draw on aspects the food and physical activity environments as they might apply to obesity, to define key GIS terms related to data collection, concepts, and the measurement of environmental features. PMID:21722367

  4. [Construction and application of bioinformatic analysis platform for aquatic pathogen based on the MilkyWay-2 supercomputer].

    PubMed

    Xiang, Fang; Ningqiu, Li; Xiaozhe, Fu; Kaibin, Li; Qiang, Lin; Lihui, Liu; Cunbin, Shi; Shuqin, Wu

    2015-07-01

    As a key component of life science, bioinformatics has been widely applied in genomics, transcriptomics, and proteomics. However, the requirement of high-performance computers rather than common personal computers for constructing a bioinformatics platform significantly limited the application of bioinformatics in aquatic science. In this study, we constructed a bioinformatic analysis platform for aquatic pathogen based on the MilkyWay-2 supercomputer. The platform consisted of three functional modules, including genomic and transcriptomic sequencing data analysis, protein structure prediction, and molecular dynamics simulations. To validate the practicability of the platform, we performed bioinformatic analysis on aquatic pathogenic organisms. For example, genes of Flavobacterium johnsoniae M168 were identified and annotated via Blast searches, GO and InterPro annotations. Protein structural models for five small segments of grass carp reovirus HZ-08 were constructed by homology modeling. Molecular dynamics simulations were performed on out membrane protein A of Aeromonas hydrophila, and the changes of system temperature, total energy, root mean square deviation and conformation of the loops during equilibration were also observed. These results showed that the bioinformatic analysis platform for aquatic pathogen has been successfully built on the MilkyWay-2 supercomputer. This study will provide insights into the construction of bioinformatic analysis platform for other subjects. PMID:26351170

  5. Computational intelligence techniques in bioinformatics.

    PubMed

    Hassanien, Aboul Ella; Al-Shammari, Eiman Tamah; Ghali, Neveen I

    2013-12-01

    Computational intelligence (CI) is a well-established paradigm with current systems having many of the characteristics of biological computers and capable of performing a variety of tasks that are difficult to do using conventional techniques. It is a methodology involving adaptive mechanisms and/or an ability to learn that facilitate intelligent behavior in complex and changing environments, such that the system is perceived to possess one or more attributes of reason, such as generalization, discovery, association and abstraction. The objective of this article is to present to the CI and bioinformatics research communities some of the state-of-the-art in CI applications to bioinformatics and motivate research in new trend-setting directions. In this article, we present an overview of the CI techniques in bioinformatics. We will show how CI techniques including neural networks, restricted Boltzmann machine, deep belief network, fuzzy logic, rough sets, evolutionary algorithms (EA), genetic algorithms (GA), swarm intelligence, artificial immune systems and support vector machines, could be successfully employed to tackle various problems such as gene expression clustering and classification, protein sequence classification, gene selection, DNA fragment assembly, multiple sequence alignment, and protein function prediction and its structure. We discuss some representative methods to provide inspiring examples to illustrate how CI can be utilized to address these problems and how bioinformatics data can be characterized by CI. Challenges to be addressed and future directions of research are also presented and an extensive bibliography is included. PMID:23891719

  6. A knowledge-based decision support system in bioinformatics: an application to protein complex extraction

    PubMed Central

    2013-01-01

    Background We introduce a Knowledge-based Decision Support System (KDSS) in order to face the Protein Complex Extraction issue. Using a Knowledge Base (KB) coding the expertise about the proposed scenario, our KDSS is able to suggest both strategies and tools, according to the features of input dataset. Our system provides a navigable workflow for the current experiment and furthermore it offers support in the configuration and running of every processing component of that workflow. This last feature makes our system a crossover between classical DSS and Workflow Management Systems. Results We briefly present the KDSS' architecture and basic concepts used in the design of the knowledge base and the reasoning component. The system is then tested using a subset of Saccharomyces cerevisiae Protein-Protein interaction dataset. We used this subset because it has been well studied in literature by several research groups in the field of complex extraction: in this way we could easily compare the results obtained through our KDSS with theirs. Our system suggests both a preprocessing and a clustering strategy, and for each of them it proposes and eventually runs suited algorithms. Our system's final results are then composed of a workflow of tasks, that can be reused for other experiments, and the specific numerical results for that particular trial. Conclusions The proposed approach, using the KDSS' knowledge base, provides a novel workflow that gives the best results with regard to the other workflows produced by the system. This workflow and its numeric results have been compared with other approaches about PPI network analysis found in literature, offering similar results. PMID:23368995

  7. The origins of bioinformatics.

    PubMed

    Hagen, J B

    2000-12-01

    Bioinformatics is often described as being in its infancy, but computers emerged as important tools in molecular biology during the early 1960s. A decade before DNA sequencing became feasible, computational biologists focused on the rapidly accumulating data from protein biochemistry. Without the benefits of super computers or computer networks, these scientists laid important conceptual and technical foundations for bioinformatics today. PMID:11252753

  8. BioSig: A bioinformatic system for studying the mechanism of intra-cell signaling

    SciTech Connect

    Parvin, B.; Cong, G.; Fontenay, G.; Taylor, J.; Henshall, R.; Barcellos-Hoff, M.H.

    2000-12-15

    Mapping inter-cell signaling pathways requires an integrated view of experimental and informatic protocols. BioSig provides the foundation of cataloging inter-cell responses as a function of particular conditioning, treatment, staining, etc. for either in vivo or in vitro experiments. This paper outlines the system architecture, a functional data model for representing experimental protocols, algorithms for image analysis, and the required statistical analysis. The architecture provides remote shared operation of an inverted optical microscope, and couples instrument operation with images acquisition and annotation. The information is stored in an object-oriented database. The algorithms extract structural information such as morphology and organization, and map it to functional information such as inter-cellular responses. An example of usage of this system is included.

  9. Component-Based Approach for Educating Students in Bioinformatics

    ERIC Educational Resources Information Center

    Poe, D.; Venkatraman, N.; Hansen, C.; Singh, G.

    2009-01-01

    There is an increasing need for an effective method of teaching bioinformatics. Increased progress and availability of computer-based tools for educating students have led to the implementation of a computer-based system for teaching bioinformatics as described in this paper. Bioinformatics is a recent, hybrid field of study combining elements of…

  10. Integration of systems glycobiology with bioinformatics toolboxes, glycoinformatics resources, and glycoproteomics data.

    PubMed

    Liu, Gang; Neelamegham, Sriram

    2015-01-01

    The glycome constitutes the entire complement of free carbohydrates and glycoconjugates expressed on whole cells or tissues. 'Systems Glycobiology' is an emerging discipline that aims to quantitatively describe and analyse the glycome. Here, instead of developing a detailed understanding of single biochemical processes, a combination of computational and experimental tools are used to seek an integrated or 'systems-level' view. This can explain how multiple biochemical reactions and transport processes interact with each other to control glycome biosynthesis and function. Computational methods in this field commonly build in silico reaction network models to describe experimental data derived from structural studies that measure cell-surface glycan distribution. While considerable progress has been made, several challenges remain due to the complex and heterogeneous nature of this post-translational modification. First, for the in silico models to be standardized and shared among laboratories, it is necessary to integrate glycan structure information and glycosylation-related enzyme definitions into the mathematical models. Second, as glycoinformatics resources grow, it would be attractive to utilize 'Big Data' stored in these repositories for model construction and validation. Third, while the technology for profiling the glycome at the whole-cell level has been standardized, there is a need to integrate mass spectrometry derived site-specific glycosylation data into the models. The current review discusses progress that is being made to resolve the above bottlenecks. The focus is on how computational models can bridge the gap between 'data' generated in wet-laboratory studies with 'knowledge' that can enhance our understanding of the glycome. PMID:25871730

  11. Clinical Bioinformatics: challenges and opportunities

    PubMed Central

    2012-01-01

    Background Network Tools and Applications in Biology (NETTAB) Workshops are a series of meetings focused on the most promising and innovative ICT tools and to their usefulness in Bioinformatics. The NETTAB 2011 workshop, held in Pavia, Italy, in October 2011 was aimed at presenting some of the most relevant methods, tools and infrastructures that are nowadays available for Clinical Bioinformatics (CBI), the research field that deals with clinical applications of bioinformatics. Methods In this editorial, the viewpoints and opinions of three world CBI leaders, who have been invited to participate in a panel discussion of the NETTAB workshop on the next challenges and future opportunities of this field, are reported. These include the development of data warehouses and ICT infrastructures for data sharing, the definition of standards for sharing phenotypic data and the implementation of novel tools to implement efficient search computing solutions. Results Some of the most important design features of a CBI-ICT infrastructure are presented, including data warehousing, modularity and flexibility, open-source development, semantic interoperability, integrated search and retrieval of -omics information. Conclusions Clinical Bioinformatics goals are ambitious. Many factors, including the availability of high-throughput "-omics" technologies and equipment, the widespread availability of clinical data warehouses and the noteworthy increase in data storage and computational power of the most recent ICT systems, justify research and efforts in this domain, which promises to be a crucial leveraging factor for biomedical research. PMID:23095472

  12. Volarea - a bioinformatics tool to calculate the surface area and the volume of molecular systems.

    PubMed

    Ribeiro, João V; Tamames, Juan A C; Cerqueira, Nuno M F S A; Fernandes, Pedro A; Ramos, Maria J

    2013-12-01

    We have developed a computer program named 'VolArea' that allows for a rapid and fully automated analysis of molecular structures. The software calculates the surface area and the volume of molecular structures, as well as the volume of molecular cavities. The surface area facility can be used to calculate the solvent-exposed surface area of a molecule or the contact area between two molecules. The volume algorithm can be used to predict not only the space occupied by any molecular structure, but also the volume of cavities, such as tunnels or clefts. The software finds wide application in the characterization of systems, such as protein/ligand complexes, enzyme active sites, protein/protein interfaces, enzyme channels, membrane pores, solvent tunnels, among others. Some examples are given to illustrate its potential. VolArea is as a plug-in of the widely distributed software Visual Molecular Dynamics (VMD) and is freely available at http://www.fc.up.pt/PortoBioComp/Software/Volarea/Home.html. PMID:24164915

  13. Crimean-Congo Hemorrhagic Fever Virus Gn Bioinformatic Analysis and Construction of a Recombinant Bacmid in Order to Express Gn by Baculovirus Expression System

    PubMed Central

    Rahpeyma, Mehdi; Fotouhi, Fatemeh; Makvandi, Manouchehr; Ghadiri, Ata; Samarbaf-Zadeh, Alireza

    2015-01-01

    Background Crimean-Congo hemorrhagic fever virus (CCHFV) is a member of the nairovirus, a genus in the Bunyaviridae family, which causes a life threatening disease in human. Currently, there is no vaccine against CCHFV and detailed structural analysis of CCHFV proteins remains undefined. The CCHFV M RNA segment encodes two viral surface glycoproteins known as Gn and Gc. Viral glycoproteins can be considered as key targets for vaccine development. Objectives The current study aimed to investigate structural bioinformatics of CCHFV Gn protein and design a construct to make a recombinant bacmid to express by baculovirus system. Materials and Methods To express the Gn protein in insect cells that can be used as antigen in animal model vaccine studies. Bioinformatic analysis of CCHFV Gn protein was performed and designed a construct and cloned into pFastBacHTb vector and a recombinant Gn-bacmid was generated by Bac to Bac system. Results Primary, secondary, and 3D structure of CCHFV Gn were obtained and PCR reaction with M13 forward and reverse primers confirmed the generation of recombinant bacmid DNA harboring Gn coding region under polyhedron promoter. Conclusions Characterization of the detailed structure of CCHFV Gn by bioinformatics software provides the basis for development of new experiments and construction of a recombinant bacmid harboring CCHFV Gn, which is valuable for designing a recombinant vaccine against deadly pathogens like CCHFV. PMID:26862379

  14. Systems based on photogrammetry to evaluation of built heritage: tentative guidelines and control parameters

    NASA Astrophysics Data System (ADS)

    Valença, J.

    2014-06-01

    Technological innovations based on close-range imaging have arisen. The developments are related with both the advances in mathematical algorithms and acquisition equipment. This evolution allows to acquire data with large and powerful sensors and the fast and efficient processing of data. In general, the preservation of built heritage have applied these technological innovations very successfully in their different areas of intervention, namely, photogrammetry, digital image processing and multispectral image analysis. Furthermore, commercial packages of software and hardware have emerged. Thus, guidelines to best-practice procedures and to validate the results usually obtained should be established. Therefore, simple and easy to understand concepts, even for nonexperts in the field, should relate the characteristics of: (i) objects under study; (ii) acquisition conditions; (iii) methods applied; and (iv) equipment applied. In this scope, the limits of validity of the methods and a comprehensive protocol to achieve the required precision and accuracy for structural analysis is a mandatory task. Application of close-range photogrammetry to build 3D geometric models and for evaluation of displacements are herein presented. Parameters such as distance-to-object, sensor size and focal length, are correlated to the precision and accuracy achieved for displacement in both experimental and on site environment. This paper shows an early stage study. The aim consist in defining simple expressions to estimate the characteristics of the equipment and/or the conditions for image acquisition, depending on the required precision and accuracy. The results will be used to define tentative guidelines considered the all procedure, from image acquisition to final results of coordinates and displacements.

  15. As-built design specification for CAMS Development Dot Data System (CDDDS)

    NASA Technical Reports Server (NTRS)

    Wehmanen, O. A.

    1979-01-01

    The CAMS development dot data system is described. Listings and flow charts of the eight programs used to maintain the data base and the 15 subroutines used in FORTRAN programs to process the data are presented.

  16. Geochemistry of rare earth elements in a passive treatment system built for acid mine drainage remediation.

    PubMed

    Prudêncio, Maria Isabel; Valente, Teresa; Marques, Rosa; Sequeira Braga, Maria Amália; Pamplona, Jorge

    2015-11-01

    Rare earth elements (REE) were used to assess attenuation processes in a passive system for acid mine drainage treatment (Jales, Portugal). Hydrochemical parameters and REE contents in water, soils and sediments were obtained along the treatment system, after summer and winter. A decrease of REE contents in the water resulting from the interaction with limestone after summer occurs; in the wetlands REE are significantly released by the soil particles to the water. After winter, a higher water dynamics favors the AMD treatment effectiveness and performance since REE contents decrease along the system; La and Ce are preferentially sequestered by ochre sludge but released to the water in the wetlands, influencing the REE pattern of the creek water. Thus, REE fractionation occurs in the passive treatment systems and can be used as tracer to follow up and understand the geochemical processes that promote the remediation of AMD. PMID:26247412

  17. A Wearable Context-Aware ECG Monitoring System Integrated with Built-in Kinematic Sensors of the Smartphone.

    PubMed

    Miao, Fen; Cheng, Yayu; He, Yi; He, Qingyun; Li, Ye

    2015-01-01

    Continuously monitoring the ECG signals over hours combined with activity status is very important for preventing cardiovascular diseases. A traditional ECG holter is often inconvenient to carry because it has many electrodes attached to the chest and because it is heavy. This work proposes a wearable, low power context-aware ECG monitoring system integrated built-in kinetic sensors of the smartphone with a self-designed ECG sensor. The wearable ECG sensor is comprised of a fully integrated analog front-end (AFE), a commercial micro control unit (MCU), a secure digital (SD) card, and a Bluetooth module. The whole sensor is very small with a size of only 58 × 50 × 10 mm for wearable monitoring application due to the AFE design, and the total power dissipation in a full round of ECG acquisition is only 12.5 mW. With the help of built-in kinetic sensors of the smartphone, the proposed system can compute and recognize user's physical activity, and thus provide context-aware information for the continuous ECG monitoring. The experimental results demonstrated the performance of proposed system in improving diagnosis accuracy for arrhythmias and identifying the most common abnormal ECG patterns in different activities. In conclusion, we provide a wearable, accurate and energy-efficient system for long-term and context-aware ECG monitoring without any extra cost on kinetic sensor design but with the help of the widespread smartphone. PMID:25996508

  18. A Wearable Context-Aware ECG Monitoring System Integrated with Built-in Kinematic Sensors of the Smartphone

    PubMed Central

    Miao, Fen; Cheng, Yayu; He, Yi; He, Qingyun; Li, Ye

    2015-01-01

    Continuously monitoring the ECG signals over hours combined with activity status is very important for preventing cardiovascular diseases. A traditional ECG holter is often inconvenient to carry because it has many electrodes attached to the chest and because it is heavy. This work proposes a wearable, low power context-aware ECG monitoring system integrated built-in kinetic sensors of the smartphone with a self-designed ECG sensor. The wearable ECG sensor is comprised of a fully integrated analog front-end (AFE), a commercial micro control unit (MCU), a secure digital (SD) card, and a Bluetooth module. The whole sensor is very small with a size of only 58 × 50 × 10 mm for wearable monitoring application due to the AFE design, and the total power dissipation in a full round of ECG acquisition is only 12.5 mW. With the help of built-in kinetic sensors of the smartphone, the proposed system can compute and recognize user’s physical activity, and thus provide context-aware information for the continuous ECG monitoring. The experimental results demonstrated the performance of proposed system in improving diagnosis accuracy for arrhythmias and identifying the most common abnormal ECG patterns in different activities. In conclusion, we provide a wearable, accurate and energy-efficient system for long-term and context-aware ECG monitoring without any extra cost on kinetic sensor design but with the help of the widespread smartphone. PMID:25996508

  19. The ClimaGrowing Footprint of Climate Change: Can Systems Built Today Cope with Tomorrow's Weather Extremes?

    SciTech Connect

    Kintner-Meyer, Michael CW; Kraucunas, Ian P.

    2013-07-11

    This article describes how current climate conditions--with increasingly extreme storms, droughts, and heat waves and their ensuing effects on water quality and levels--are adding stress to an already aging power grid. Moreover, it explains how evaluations of said grid, built upon past weather patterns, are inaqeduate for measuring if the nation's energy systems can cope with future climate changes. The authors make the case for investing in the development of robust, integrated electricity planning tools that account for these climate change factors as a means for enhancing electricity infrastructure resilience.

  20. A Bioinformatics Facility for NASA

    NASA Technical Reports Server (NTRS)

    Schweighofer, Karl; Pohorille, Andrew

    2006-01-01

    Building on an existing prototype, we have fielded a facility with bioinformatics technologies that will help NASA meet its unique requirements for biological research. This facility consists of a cluster of computers capable of performing computationally intensive tasks, software tools, databases and knowledge management systems. Novel computational technologies for analyzing and integrating new biological data and already existing knowledge have been developed. With continued development and support, the facility will fulfill strategic NASA s bioinformatics needs in astrobiology and space exploration. . As a demonstration of these capabilities, we will present a detailed analysis of how spaceflight factors impact gene expression in the liver and kidney for mice flown aboard shuttle flight STS-108. We have found that many genes involved in signal transduction, cell cycle, and development respond to changes in microgravity, but that most metabolic pathways appear unchanged.

  1. Humidity compensation of bad-smell sensing system using a detector tube and a built-in camera

    NASA Astrophysics Data System (ADS)

    Hirano, Hiroyuki; Nakamoto, Takamichi

    2011-09-01

    We developed a low-cost sensing system robust against humidity change for detecting and estimating concentration of bad smell, such as hydrogen sulfide and ammonia. In the previous study, we developed automated measurement system for a gas detector tube using a built-in camera instead of the conventional manual inspection of the gas detector tube. Concentration detectable by the developed system ranges from a few tens of ppb to a few tens of ppm. However, we previously found that the estimated concentration depends not only on actual concentration, but on humidity. Here, we established the method to correct the influence of humidity by creating regression function with its inputs of discoloration rate and humidity. We studied 2 methods (Backpropagation, Radial basis function network) to get regression function and evaluated them. Consequently, the system successfully estimated the concentration on a practical level even when humidity changes.

  2. Dynamics of Complex Systems Built as Coupled Physical, Communication and Decision Layers

    PubMed Central

    Kühnlenz, Florian; Nardelli, Pedro H. J.

    2016-01-01

    This paper proposes a simple model to capture the complexity of multilayer systems where their constituent layers affect, and are affected by, each other. The physical layer is a circuit composed by a power source and resistors in parallel. Every individual agent aims at maximizing its own delivered power by adding, removing or keeping the resistors it has; the delivered power is in turn a non-linear function that depends on the other agents’ behavior, its own internal state, its global state perception, the information received from its neighbors via the communication network and a randomized selfishness. We develop an agent-based simulation to analyze the effects of number of agents (system size), communication network topology, communication errors and the minimum power gain that triggers a behavioral change on the system dynamic. Our results show that a wave-like behavior at macro-level (caused by individual changes in the decision layer) can only emerge for a specific system size. The ratio between cooperators and defectors depends on the minimum gain assumed—lower minimal gains lead to less cooperation, and vice-versa. Different communication network topologies imply different levels of power utilization and fairness at the physical layer, and a certain level of error in the communication layer induces more cooperation. PMID:26730590

  3. Dynamics of Complex Systems Built as Coupled Physical, Communication and Decision Layers.

    PubMed

    Kühnlenz, Florian; Nardelli, Pedro H J

    2016-01-01

    This paper proposes a simple model to capture the complexity of multilayer systems where their constituent layers affect, and are affected by, each other. The physical layer is a circuit composed by a power source and resistors in parallel. Every individual agent aims at maximizing its own delivered power by adding, removing or keeping the resistors it has; the delivered power is in turn a non-linear function that depends on the other agents' behavior, its own internal state, its global state perception, the information received from its neighbors via the communication network and a randomized selfishness. We develop an agent-based simulation to analyze the effects of number of agents (system size), communication network topology, communication errors and the minimum power gain that triggers a behavioral change on the system dynamic. Our results show that a wave-like behavior at macro-level (caused by individual changes in the decision layer) can only emerge for a specific system size. The ratio between cooperators and defectors depends on the minimum gain assumed-lower minimal gains lead to less cooperation, and vice-versa. Different communication network topologies imply different levels of power utilization and fairness at the physical layer, and a certain level of error in the communication layer induces more cooperation. PMID:26730590

  4. Teaching Folder Management System for the Enhancement of Engineering and Built Environment Faculty Program

    ERIC Educational Resources Information Center

    Ab-Rahman, Mohammad Syuhaimi; Mustaffa, Muhamad Azrin Mohd; Abdul, Nasrul Amir; Yusoff, Abdul Rahman Mohd; Hipni, Afiq

    2015-01-01

    A strong, systematic and well-executed management system will be able to minimize and coordinate workload. A number of committees need to be developed, which are joined by the department staffs to achieve the objectives that have been set. Another important aspect is the monitoring department in order to ensure that the work done is correct and in…

  5. Microbial bioinformatics 2020.

    PubMed

    Pallen, Mark J

    2016-09-01

    Microbial bioinformatics in 2020 will remain a vibrant, creative discipline, adding value to the ever-growing flood of new sequence data, while embracing novel technologies and fresh approaches. Databases and search strategies will struggle to cope and manual curation will not be sustainable during the scale-up to the million-microbial-genome era. Microbial taxonomy will have to adapt to a situation in which most microorganisms are discovered and characterised through the analysis of sequences. Genome sequencing will become a routine approach in clinical and research laboratories, with fresh demands for interpretable user-friendly outputs. The "internet of things" will penetrate healthcare systems, so that even a piece of hospital plumbing might have its own IP address that can be integrated with pathogen genome sequences. Microbiome mania will continue, but the tide will turn from molecular barcoding towards metagenomics. Crowd-sourced analyses will collide with cloud computing, but eternal vigilance will be the price of preventing the misinterpretation and overselling of microbial sequence data. Output from hand-held sequencers will be analysed on mobile devices. Open-source training materials will address the need for the development of a skilled labour force. As we boldly go into the third decade of the twenty-first century, microbial sequence space will remain the final frontier! PMID:27471065

  6. String Mining in Bioinformatics

    NASA Astrophysics Data System (ADS)

    Abouelhoda, Mohamed; Ghanem, Moustafa

    Sequence analysis is a major area in bioinformatics encompassing the methods and techniques for studying the biological sequences, DNA, RNA, and proteins, on the linear structure level. The focus of this area is generally on the identification of intra- and inter-molecular similarities. Identifying intra-molecular similarities boils down to detecting repeated segments within a given sequence, while identifying inter-molecular similarities amounts to spotting common segments among two or multiple sequences. From a data mining point of view, sequence analysis is nothing but string- or pattern mining specific to biological strings. For a long time, this point of view, however, has not been explicitly embraced neither in the data mining nor in the sequence analysis text books, which may be attributed to the co-evolution of the two apparently independent fields. In other words, although the word “data-mining” is almost missing in the sequence analysis literature, its basic concepts have been implicitly applied. Interestingly, recent research in biological sequence analysis introduced efficient solutions to many problems in data mining, such as querying and analyzing time series [49,53], extracting information from web pages [20], fighting spam mails [50], detecting plagiarism [22], and spotting duplications in software systems [14].

  7. String Mining in Bioinformatics

    NASA Astrophysics Data System (ADS)

    Abouelhoda, Mohamed; Ghanem, Moustafa

    Sequence analysis is a major area in bioinformatics encompassing the methods and techniques for studying the biological sequences, DNA, RNA, and proteins, on the linear structure level. The focus of this area is generally on the identification of intra- and inter-molecular similarities. Identifying intra-molecular similarities boils down to detecting repeated segments within a given sequence, while identifying inter-molecular similarities amounts to spotting common segments among two or multiple sequences. From a data mining point of view, sequence analysis is nothing but string- or pattern mining specific to biological strings. For a long time, this point of view, however, has not been explicitly embraced neither in the data mining nor in the sequence analysis text books, which may be attributed to the co-evolution of the two apparently independent fields. In other words, although the word "data-mining" is almost missing in the sequence analysis literature, its basic concepts have been implicitly applied. Interestingly, recent research in biological sequence analysis introduced efficient solutions to many problems in data mining, such as querying and analyzing time series [49,53], extracting information from web pages [20], fighting spam mails [50], detecting plagiarism [22], and spotting duplications in software systems [14].

  8. A Survey of Scholarly Literature Describing the Field of Bioinformatics Education and Bioinformatics Educational Research

    PubMed Central

    Taleyarkhan, Manaz; Alvarado, Daniela Rivera; Kane, Michael; Springer, John; Clase, Kari

    2014-01-01

    Bioinformatics education can be broadly defined as the teaching and learning of the use of computer and information technology, along with mathematical and statistical analysis for gathering, storing, analyzing, interpreting, and integrating data to solve biological problems. The recent surge of genomics, proteomics, and structural biology in the potential advancement of research and development in complex biomedical systems has created a need for an educated workforce in bioinformatics. However, effectively integrating bioinformatics education through formal and informal educational settings has been a challenge due in part to its cross-disciplinary nature. In this article, we seek to provide an overview of the state of bioinformatics education. This article identifies: 1) current approaches of bioinformatics education at the undergraduate and graduate levels; 2) the most common concepts and skills being taught in bioinformatics education; 3) pedagogical approaches and methods of delivery for conveying bioinformatics concepts and skills; and 4) assessment results on the impact of these programs, approaches, and methods in students’ attitudes or learning. Based on these findings, it is our goal to describe the landscape of scholarly work in this area and, as a result, identify opportunities and challenges in bioinformatics education. PMID:25452484

  9. A survey of scholarly literature describing the field of bioinformatics education and bioinformatics educational research.

    PubMed

    Magana, Alejandra J; Taleyarkhan, Manaz; Alvarado, Daniela Rivera; Kane, Michael; Springer, John; Clase, Kari

    2014-01-01

    Bioinformatics education can be broadly defined as the teaching and learning of the use of computer and information technology, along with mathematical and statistical analysis for gathering, storing, analyzing, interpreting, and integrating data to solve biological problems. The recent surge of genomics, proteomics, and structural biology in the potential advancement of research and development in complex biomedical systems has created a need for an educated workforce in bioinformatics. However, effectively integrating bioinformatics education through formal and informal educational settings has been a challenge due in part to its cross-disciplinary nature. In this article, we seek to provide an overview of the state of bioinformatics education. This article identifies: 1) current approaches of bioinformatics education at the undergraduate and graduate levels; 2) the most common concepts and skills being taught in bioinformatics education; 3) pedagogical approaches and methods of delivery for conveying bioinformatics concepts and skills; and 4) assessment results on the impact of these programs, approaches, and methods in students' attitudes or learning. Based on these findings, it is our goal to describe the landscape of scholarly work in this area and, as a result, identify opportunities and challenges in bioinformatics education. PMID:25452484

  10. Physical Realization of a Supervised Learning System Built with Organic Memristive Synapses

    PubMed Central

    Lin, Yu-Pu; Bennett, Christopher H.; Cabaret, Théo; Vodenicarevic, Damir; Chabi, Djaafar; Querlioz, Damien; Jousselme, Bruno; Derycke, Vincent; Klein, Jacques-Olivier

    2016-01-01

    Multiple modern applications of electronics call for inexpensive chips that can perform complex operations on natural data with limited energy. A vision for accomplishing this is implementing hardware neural networks, which fuse computation and memory, with low cost organic electronics. A challenge, however, is the implementation of synapses (analog memories) composed of such materials. In this work, we introduce robust, fastly programmable, nonvolatile organic memristive nanodevices based on electrografted redox complexes that implement synapses thanks to a wide range of accessible intermediate conductivity states. We demonstrate experimentally an elementary neural network, capable of learning functions, which combines four pairs of organic memristors as synapses and conventional electronics as neurons. Our architecture is highly resilient to issues caused by imperfect devices. It tolerates inter-device variability and an adaptable learning rule offers immunity against asymmetries in device switching. Highly compliant with conventional fabrication processes, the system can be extended to larger computing systems capable of complex cognitive tasks, as demonstrated in complementary simulations. PMID:27601088

  11. European built core data management system for the Russian Service Module

    NASA Astrophysics Data System (ADS)

    Brandt, G.; Schneider, W.; Urban, G.; Branets, V.; Reimers, C.

    1996-02-01

    In frame of the European-Russian cooperation within the International Space Station Program a Fault Tolerant Computer assembly with associated crew-control station is under development in European industry. The on-board equipment, which is supposed to be accommodated within the data management and guidance navigation control system of the Russian Service Module, is complemented with a complete set of ground hard- and software required for the application software development and verification process as well as Service Module System integration and check-out. For the on-board fault tolerant computer state of the art technology will be implemented. The mechanism, that provides the required two failure tolerant feature, is based on the so-called Byzantine Failure algorithm. The fault detection and recovery algorithm, the data input/output and the application software are implemented on separate layers each containing its own processing capability, such that the application program runs independent of any failure calculations and data input/output. Hardware realization is based on state of the art microcircuits, in particular transputer processors to provide compact equipment size and fast data exchange mechanism.

  12. Physical Realization of a Supervised Learning System Built with Organic Memristive Synapses.

    PubMed

    Lin, Yu-Pu; Bennett, Christopher H; Cabaret, Théo; Vodenicarevic, Damir; Chabi, Djaafar; Querlioz, Damien; Jousselme, Bruno; Derycke, Vincent; Klein, Jacques-Olivier

    2016-01-01

    Multiple modern applications of electronics call for inexpensive chips that can perform complex operations on natural data with limited energy. A vision for accomplishing this is implementing hardware neural networks, which fuse computation and memory, with low cost organic electronics. A challenge, however, is the implementation of synapses (analog memories) composed of such materials. In this work, we introduce robust, fastly programmable, nonvolatile organic memristive nanodevices based on electrografted redox complexes that implement synapses thanks to a wide range of accessible intermediate conductivity states. We demonstrate experimentally an elementary neural network, capable of learning functions, which combines four pairs of organic memristors as synapses and conventional electronics as neurons. Our architecture is highly resilient to issues caused by imperfect devices. It tolerates inter-device variability and an adaptable learning rule offers immunity against asymmetries in device switching. Highly compliant with conventional fabrication processes, the system can be extended to larger computing systems capable of complex cognitive tasks, as demonstrated in complementary simulations. PMID:27601088

  13. Dynamical energy analysis for built-up acoustic systems at high frequencies.

    PubMed

    Chappell, D J; Giani, S; Tanner, G

    2011-09-01

    Standard methods for describing the intensity distribution of mechanical and acoustic wave fields in the high frequency asymptotic limit are often based on flow transport equations. Common techniques are statistical energy analysis, employed mostly in the context of vibro-acoustics, and ray tracing, a popular tool in architectural acoustics. Dynamical energy analysis makes it possible to interpolate between standard statistical energy analysis and full ray tracing, containing both of these methods as limiting cases. In this work a version of dynamical energy analysis based on a Chebyshev basis expansion of the Perron-Frobenius operator governing the ray dynamics is introduced. It is shown that the technique can efficiently deal with multi-component systems overcoming typical geometrical limitations present in statistical energy analysis. Results are compared with state-of-the-art hp-adaptive discontinuous Galerkin finite element simulations. PMID:21895083

  14. Development of a purpose built landfill system for the control of methane emissions from municipal solid waste.

    PubMed

    Yedla, Sudhakar; Parikh, Jyoti K

    2002-01-01

    In the present paper, a new system of purpose built landfill (PBLF) has been proposed for the control of methane emissions from municipal solid waste (MSW), by considering all favourable conditions for improved methane generation in tropical climates. Based on certain theoretical considerations multivariate functional models (MFMs) are developed to estimate methane mitigation and energy generating potential of the proposed system. Comparison was made between the existing waste management system and proposed PBLF system. It has been found that the proposed methodology not only controlled methane emissions to the atmosphere but also could yield considerable energy in terms of landfill gas (LFG). Economic feasibility of the proposed system has been tested by comparing unit cost of waste disposal in conventional as well as PBLF systems. In a case study of MSW management in Mumbai (INDIA), it was found that the unit cost of waste disposal with PBLF system is seven times lesser than that of the conventional waste management system. The proposed system showed promising energy generation potential with production of methane worth of Rs. 244 millions/y ($5.2 million/y). Thus, the new waste management methodology could give an adaptable solution for the conflict between development, environmental degradation and natural resources depletion. PMID:12092759

  15. An Online Bioinformatics Curriculum

    PubMed Central

    Searls, David B.

    2012-01-01

    Online learning initiatives over the past decade have become increasingly comprehensive in their selection of courses and sophisticated in their presentation, culminating in the recent announcement of a number of consortium and startup activities that promise to make a university education on the internet, free of charge, a real possibility. At this pivotal moment it is appropriate to explore the potential for obtaining comprehensive bioinformatics training with currently existing free video resources. This article presents such a bioinformatics curriculum in the form of a virtual course catalog, together with editorial commentary, and an assessment of strengths, weaknesses, and likely future directions for open online learning in this field. PMID:23028269

  16. Bioinformatics and School Biology

    ERIC Educational Resources Information Center

    Dalpech, Roger

    2006-01-01

    The rapidly changing field of bioinformatics is fuelling the need for suitably trained personnel with skills in relevant biological "sub-disciplines" such as proteomics, transcriptomics and metabolomics, etc. But because of the complexity--and sheer weight of data--associated with these new areas of biology, many school teachers feel…

  17. An Arch-Shaped Intraoral Tongue Drive System with Built-in Tongue-Computer Interfacing SoC

    PubMed Central

    Park, Hangue; Ghovanloo, Maysam

    2014-01-01

    We present a new arch-shaped intraoral Tongue Drive System (iTDS) designed to occupy the buccal shelf in the user's mouth. The new arch-shaped iTDS, which will be referred to as the iTDS-2, incorporates a system-on-a-chip (SoC) that amplifies and digitizes the raw magnetic sensor data and sends it wirelessly to an external TDS universal interface (TDS-UI) via an inductive coil or a planar inverted-F antenna. A built-in transmitter (Tx) employs a dual-band radio that operates at either 27 MHz or 432 MHz band, according to the wireless link quality. A built-in super-regenerative receiver (SR-Rx) monitors the wireless link quality and switches the band if the link quality is below a predetermined threshold. An accompanying ultra-low power FPGA generates data packets for the Tx and handles digital control functions. The custom-designed TDS-UI receives raw magnetic sensor data from the iTDS-2, recognizes the intended user commands by the sensor signal processing (SSP) algorithm running in a smartphone, and delivers the classified commands to the target devices, such as a personal computer or a powered wheelchair. We evaluated the iTDS-2 prototype using center-out and maze navigation tasks on two human subjects, which proved its functionality. The subjects' performance with the iTDS-2 was improved by 22% over its predecessor, reported in our earlier publication. PMID:25405513

  18. In the Spotlight: Bioinformatics

    PubMed Central

    Wang, May Dongmei

    2016-01-01

    During 2012, next generation sequencing (NGS) has attracted great attention in the biomedical research community, especially for personalized medicine. Also, third generation sequencing has become available. Therefore, state-of-art sequencing technology and analysis are reviewed in this Bioinformatics spotlight on 2012. Next-generation sequencing (NGS) is high-throughput nucleic acid sequencing technology with wide dynamic range and single base resolution. The full promise of NGS depends on the optimization of NGS platforms, sequence alignment and assembly algorithms, data analytics, novel algorithms for integrating NGS data with existing genomic, proteomic, or metabolomic data, and quantitative assessment of NGS technology in comparing to more established technologies such as microarrays. NGS technology has been predicated to become a cornerstone of personalized medicine. It is argued that NGS is a promising field for motivated young researchers who are looking for opportunities in bioinformatics. PMID:23192635

  19. Phylogenetic trees in bioinformatics

    SciTech Connect

    Burr, Tom L

    2008-01-01

    Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding the best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.

  20. The resilience of structure built around the predicate: Homesign gesture systems in Turkish and American deaf children

    PubMed Central

    Goldin-Meadow, Susan; Namboodiripad, Savithry; Mylander, Carolyn; Özyürek, Aslı; Sancar, Burcu

    2013-01-01

    Deaf children whose hearing losses prevent them from accessing spoken language and whose hearing parents have not exposed them to sign language develop gesture systems, called homesigns, that have many of the properties of natural language—the so-called resilient properties of language. We explored the resilience of structure built around the predicate—in particular, how manner and path are mapped onto the verb—in homesign systems developed by deaf children in Turkey and the United States. We also asked whether the Turkish homesigners exhibit sentence-level structures previously identified as resilient in American and Chinese homesigners. We found that the Turkish and American deaf children used not only the same production probability and ordering patterns to indicate who does what to whom, but also the same segmentation and conflation patterns to package manner and path. The gestures that the hearing parents produced did not, for the most part, display the patterns found in the children’s gestures. Although co-speech gesture may provide the building blocks for homesign, it does not provide the blueprint for these resilient properties of language. PMID:25663828

  1. [An overview of feature selection algorithm in bioinformatics].

    PubMed

    Li, Xin; Ma, Li; Wang, Jinjia; Zhao, Chun

    2011-04-01

    Feature selection (FS) techniques have become an important tool in bioinformatics field. The core algorithm of it is to select the hidden significant data with low-dimension from high-dimensional data space, and thus to analyse the basic built-in rule of the data. The data of bioinformatics fields are always with high-dimension and small samples, so the research of FS algorithm in the bioinformatics fields has great foreground. In this article, we make the interested reader aware of the possibilities of feature selection, provide basic properties of feature selection techniques, and discuss their uses in the sequence analysis, microarray analysis, mass spectra analysis etc. Finally, the current problems and the prospects of feature selection algorithm in the application of bioinformatics is also discussed. PMID:21604512

  2. The potential of translational bioinformatics approaches for pharmacology research.

    PubMed

    Li, Lang

    2015-10-01

    The field of bioinformatics has allowed the interpretation of massive amounts of biological data, ushering in the era of 'omics' to biomedical research. Its potential impact on pharmacology research is enormous and it has shown some emerging successes. A full realization of this potential, however, requires standardized data annotation for large health record databases and molecular data resources. Improved standardization will further stimulate the development of system pharmacology models, using translational bioinformatics methods. This new translational bioinformatics paradigm is highly complementary to current pharmacological research fields, such as personalized medicine, pharmacoepidemiology and drug discovery. In this review, I illustrate the application of transformational bioinformatics to research in numerous pharmacology subdisciplines. PMID:25753093

  3. Bioinformatics-Driven New Immune Target Discovery in Disease.

    PubMed

    Yang, C; Chen, P; Zhang, W; Du, H

    2016-08-01

    Biomolecular network analysis has been widely applied in the discovery of cancer driver genes and molecular mechanism anatomization of many diseases on the genetic level. However, the application of such approach in the potential antigen discovery of autoimmune diseases remains largely unexplored. Here, we describe a previously uncharacterized region, with disease-associated autoantigens, to build antigen networks with three bioinformatics tools, namely NetworkAnalyst, GeneMANIA and ToppGene. First, we identified histone H2AX as an antigen of systemic lupus erythematosus by comparing highly ranked genes from all the built network-derived gene lists, and then a new potential biomarker for Behcet's disease, heat shock protein HSP 90-alpha (HSP90AA1), was further screened out. Moreover, 130 confirmed patients were enrolled and a corresponding enzyme-linked immunosorbent assay, mass spectrum analysis and immunoprecipitation were performed to further confirm the bioinformatics results with real-world clinical samples in succession. Our findings demonstrate that the combination of multiple molecular network approaches is a promising tool to discover new immune targets in diseases. PMID:27226232

  4. Making sense of genomes of parasitic worms: Tackling bioinformatic challenges.

    PubMed

    Korhonen, Pasi K; Young, Neil D; Gasser, Robin B

    2016-01-01

    Billions of people and animals are infected with parasitic worms (helminths). Many of these worms cause diseases that have a major socioeconomic impact worldwide, and are challenging to control because existing treatment methods are often inadequate. There is, therefore, a need to work toward developing new intervention methods, built on a sound understanding of parasitic worms at molecular level, the relationships that they have with their animal hosts and/or the diseases that they cause. Decoding the genomes and transcriptomes of these parasites brings us a step closer to this goal. The key focus of this article is to critically review and discuss bioinformatic tools used for the assembly and annotation of these genomes and transcriptomes, as well as various post-genomic analyses of transcription profiles, biological pathways, synteny, phylogeny, biogeography and the prediction and prioritisation of drug target candidates. Bioinformatic pipelines implemented and established recently provide practical and efficient tools for the assembly and annotation of genomes of parasitic worms, and will be applicable to a wide range of other parasites and eukaryotic organisms. Future research will need to assess the utility of long-read sequence data sets for enhanced genomic assemblies, and develop improved algorithms for gene prediction and post-genomic analyses, to enable comprehensive systems biology explorations of parasitic organisms. PMID:26956711

  5. Efficient azo dye decolorization in a continuous stirred tank reactor (CSTR) with built-in bioelectrochemical system.

    PubMed

    Cui, Min-Hua; Cui, Dan; Gao, Lei; Cheng, Hao-Yi; Wang, Ai-Jie

    2016-10-01

    A continuous stirred tank reactor with built-in bioelectrochemical system (CSTR-BES) was developed for azo dye Alizarin Yellow R (AYR) containing wastewater treatment. The decolorization efficiency (DE) of the CSTR-BES was 97.04±0.06% for 7h with sludge concentration of 3000mg/L and initial AYR concentration of 100mg/L, which was superior to that of the sole CSTR mode (open circuit: 54.87±4.34%) and the sole BES mode (without sludge addition: 91.37±0.44%). The effects of sludge concentration and sodium acetate (NaAc) concentration on azo dye decolorization were investigated. The highest DE of CSTR-BES for 4h was 87.66±2.93% with sludge concentration of 12,000mg/L, NaAc concentration of 2000mg/L and initial AYR concentration of 100mg/L. The results in this study indicated that CSTR-BES could be a practical strategy for upgrading conventional anaerobic facilities against refractory wastewater treatment. PMID:27497830

  6. Computer Simulation of Embryonic Systems: What can a virtual embryo teach us about developmental toxicity? (LA Conference on Computational Biology & Bioinformatics)

    EPA Science Inventory

    This presentation will cover work at EPA under the CSS program for: (1) Virtual Tissue Models built from the known biology of an embryological system and structured to recapitulate key cell signals and responses; (2) running the models with real (in vitro) or synthetic (in silico...

  7. Bioinformatics of prokaryotic RNAs

    PubMed Central

    Backofen, Rolf; Amman, Fabian; Costa, Fabrizio; Findeiß, Sven; Richter, Andreas S; Stadler, Peter F

    2014-01-01

    The genome of most prokaryotes gives rise to surprisingly complex transcriptomes, comprising not only protein-coding mRNAs, often organized as operons, but also harbors dozens or even hundreds of highly structured small regulatory RNAs and unexpectedly large levels of anti-sense transcripts. Comprehensive surveys of prokaryotic transcriptomes and the need to characterize also their non-coding components is heavily dependent on computational methods and workflows, many of which have been developed or at least adapted specifically for the use with bacterial and archaeal data. This review provides an overview on the state-of-the-art of RNA bioinformatics focusing on applications to prokaryotes. PMID:24755880

  8. Bioinformatics of prokaryotic RNAs.

    PubMed

    Backofen, Rolf; Amman, Fabian; Costa, Fabrizio; Findeiß, Sven; Richter, Andreas S; Stadler, Peter F

    2014-01-01

    The genome of most prokaryotes gives rise to surprisingly complex transcriptomes, comprising not only protein-coding mRNAs, often organized as operons, but also harbors dozens or even hundreds of highly structured small regulatory RNAs and unexpectedly large levels of anti-sense transcripts. Comprehensive surveys of prokaryotic transcriptomes and the need to characterize also their non-coding components is heavily dependent on computational methods and workflows, many of which have been developed or at least adapted specifically for the use with bacterial and archaeal data. This review provides an overview on the state-of-the-art of RNA bioinformatics focusing on applications to prokaryotes. PMID:24755880

  9. Molecular characterization and bioinformatics analysis of Ncoa7B, a novel ovulation-associated and reproduction system-specific Ncoa7 isoform.

    PubMed

    Shkolnik, Ketty; Ben-Dor, Shifra; Galiani, Dalia; Hourvitz, Ariel; Dekel, Nava

    2008-03-01

    In the present work, we employed bioinformatics search tools to select ovulation-associated cDNA clones with a preference for those representing putative novel genes. Detailed characterization of one of these transcripts, 6C3, by real-time PCR and RACE analyses led to identification of a novel ovulation-associated gene, designated Ncoa7B. This gene was found to exhibit a significant homology to the Ncoa7 gene that encodes a conserved tissue-specific nuclear receptor coactivator. Unlike Ncoa7, Ncoa7B possesses a unique and highly conserved exon at the 5' end and encodes a protein with a unique N-terminal sequence. Extensive bioinformatics analysis has revealed that Ncoa7B has one identifiable domain, TLDc, which has recently been suggested to be involved in protection from oxidative DNA damage. An alignment of TLDc domain containing proteins was performed, and the closest relative identified was OXR1, which also has a corresponding, highly related short isoform, with just a TLDc domain. Moreover, Ncoa7B expression, as seen to date, seems to be restricted to mammals, while other TLDc family members have no such restriction. Multiple tissue analysis revealed that unlike Ncoa7, which was abundant in a variety of tissues with the highest expression in the brain, Ncoa7B mRNA expression is restricted to the reproductive system organs, particularly the uterus and the ovary. The ovarian expression of Ncoa7B was stimulated by human chorionic gonadotropin. Additionally, using real-time PCR, we demonstrated the involvement of multiple signaling pathways for Ncoa7B expression on preovulatory follicles. PMID:18299425

  10. Temporal Patterns in Sheep Fetal Heart Rate Variability Correlate to Systemic Cytokine Inflammatory Response: A Methodological Exploration of Monitoring Potential Using Complex Signals Bioinformatics

    PubMed Central

    Wu, Hau-Tieng; Durosier, Lucien D.; Desrochers, André; Fecteau, Gilles; Seely, Andrew J. E.; Frasch, Martin G.

    2016-01-01

    Fetal inflammation is associated with increased risk for postnatal organ injuries. No means of early detection exist. We hypothesized that systemic fetal inflammation leads to distinct alterations of fetal heart rate variability (fHRV). We tested this hypothesis deploying a novel series of approaches from complex signals bioinformatics. In chronically instrumented near-term fetal sheep, we induced an inflammatory response with lipopolysaccharide (LPS) injected intravenously (n = 10) observing it over 54 hours; seven additional fetuses served as controls. Fifty-one fHRV measures were determined continuously every 5 minutes using Continuous Individualized Multi-organ Variability Analysis (CIMVA). CIMVA creates an fHRV measures matrix across five signal-analytical domains, thus describing complementary properties of fHRV. We implemented, validated and tested methodology to obtain a subset of CIMVA fHRV measures that matched best the temporal profile of the inflammatory cytokine IL-6. In the LPS group, IL-6 peaked at 3 hours. For the LPS, but not control group, a sharp increase in standardized difference in variability with respect to baseline levels was observed between 3 h and 6 h abating to baseline levels, thus tracking closely the IL-6 inflammatory profile. We derived fHRV inflammatory index (FII) consisting of 15 fHRV measures reflecting the fetal inflammatory response with prediction accuracy of 90%. Hierarchical clustering validated the selection of 14 out of 15 fHRV measures comprising FII. We developed methodology to identify a distinctive subset of fHRV measures that tracks inflammation over time. The broader potential of this bioinformatics approach is discussed to detect physiological responses encoded in HRV measures. PMID:27100089

  11. Temporal Patterns in Sheep Fetal Heart Rate Variability Correlate to Systemic Cytokine Inflammatory Response: A Methodological Exploration of Monitoring Potential Using Complex Signals Bioinformatics.

    PubMed

    Herry, Christophe L; Cortes, Marina; Wu, Hau-Tieng; Durosier, Lucien D; Cao, Mingju; Burns, Patrick; Desrochers, André; Fecteau, Gilles; Seely, Andrew J E; Frasch, Martin G

    2016-01-01

    Fetal inflammation is associated with increased risk for postnatal organ injuries. No means of early detection exist. We hypothesized that systemic fetal inflammation leads to distinct alterations of fetal heart rate variability (fHRV). We tested this hypothesis deploying a novel series of approaches from complex signals bioinformatics. In chronically instrumented near-term fetal sheep, we induced an inflammatory response with lipopolysaccharide (LPS) injected intravenously (n = 10) observing it over 54 hours; seven additional fetuses served as controls. Fifty-one fHRV measures were determined continuously every 5 minutes using Continuous Individualized Multi-organ Variability Analysis (CIMVA). CIMVA creates an fHRV measures matrix across five signal-analytical domains, thus describing complementary properties of fHRV. We implemented, validated and tested methodology to obtain a subset of CIMVA fHRV measures that matched best the temporal profile of the inflammatory cytokine IL-6. In the LPS group, IL-6 peaked at 3 hours. For the LPS, but not control group, a sharp increase in standardized difference in variability with respect to baseline levels was observed between 3 h and 6 h abating to baseline levels, thus tracking closely the IL-6 inflammatory profile. We derived fHRV inflammatory index (FII) consisting of 15 fHRV measures reflecting the fetal inflammatory response with prediction accuracy of 90%. Hierarchical clustering validated the selection of 14 out of 15 fHRV measures comprising FII. We developed methodology to identify a distinctive subset of fHRV measures that tracks inflammation over time. The broader potential of this bioinformatics approach is discussed to detect physiological responses encoded in HRV measures. PMID:27100089

  12. 4273π: Bioinformatics education on low cost ARM hardware

    PubMed Central

    2013-01-01

    Background Teaching bioinformatics at universities is complicated by typical computer classroom settings. As well as running software locally and online, students should gain experience of systems administration. For a future career in biology or bioinformatics, the installation of software is a useful skill. We propose that this may be taught by running the course on GNU/Linux running on inexpensive Raspberry Pi computer hardware, for which students may be granted full administrator access. Results We release 4273π, an operating system image for Raspberry Pi based on Raspbian Linux. This includes minor customisations for classroom use and includes our Open Access bioinformatics course, 4273π Bioinformatics for Biologists. This is based on the final-year undergraduate module BL4273, run on Raspberry Pi computers at the University of St Andrews, Semester 1, academic year 2012–2013. Conclusions 4273π is a means to teach bioinformatics, including systems administration tasks, to undergraduates at low cost. PMID:23937194

  13. The influence of the built environment on outcomes from a "walking school bus study": a cross-sectional analysis using geographical information systems.

    PubMed

    Oreskovic, Nicolas M; Blossom, Jeff; Robinson, Alyssa I; Chen, Minghua L; Uscanga, Doris K; Mendoza, Jason A

    2014-11-01

    Active commuting to school increases children's daily physical activity. The built environment is associated with children's physical activity levels in cross-sectional studies. This study examined the role of the built environment on the outcomes of a "walking school bus" study. Geographical information systems was used to map out and compare the built environments around schools participating in a pilot walking school bus randomised controlled trial, as well as along school routes. Multi-level modelling was used to determine the built environment attributes associated with the outcomes of active commuting to school and accelerometer-determined moderate-to-vigorous physical activity (MPVA). There were no differences in the surrounding built environments of control (n = 4) and intervention (n = 4) schools participating in the walking school bus study. Among school walking routes, park space was inversely associated with active commuting to school (β = -0.008, SE = 0.004, P = 0.03), while mixed-land use was positively associated with daily MPVA (β = 60.0, SE = 24.3, P = 0.02). There was effect modification such that high traffic volume and high street connectivity were associated with greater moderate-to-vigorous physical activity. The results of this study suggest that the built environment may play a role in active school commuting outcomes and daily physical activity. PMID:25545924

  14. The influence of the built environment on outcomes from a “walking school bus study”: a cross-sectional analysis using geographical information systems

    PubMed Central

    Oreskovic, Nicolas M.; Blossom, Jeff; Robinson, Alyssa I.; Chen, Minghua L.; Uscanga, Doris K.; Mendoza, Jason A.

    2015-01-01

    Active commuting to school increases children’s daily physical activity. The built environment is associated with children’s physical activity levels in cross-sectional studies. This study examined the role of the built environment on the outcomes of a “walking school bus” study. Geographical information systems was used to map out and compare the built environments around schools participating in a pilot walking school bus randomised controlled trial, as well as along school routes. Multi-level modelling was used to determine the built environment attributes associated with the outcomes of active commuting to school and accelerometer-determined moderate-to-vigorous physical activity (MPVA). There were no differences in the surrounding built environments of control (n = 4) and intervention (n = 4) schools participating in the walking school bus study. Among school walking routes, park space was inversely associated with active commuting to school (β = −0.008, SE = 0.004, P = 0.03), while mixed-land use was positively associated with daily MPVA (β = 60.0, SE = 24.3, P = 0.02). There was effect modification such that high traffic volume and high street connectivity were associated with greater moderate-to-vigorous physical activity. The results of this study suggest that the built environment may play a role in active school commuting outcomes and daily physical activity. PMID:25545924

  15. Bioinformatics-Aided Venomics

    PubMed Central

    Kaas, Quentin; Craik, David J.

    2015-01-01

    Venomics is a modern approach that combines transcriptomics and proteomics to explore the toxin content of venoms. This review will give an overview of computational approaches that have been created to classify and consolidate venomics data, as well as algorithms that have helped discovery and analysis of toxin nucleic acid and protein sequences, toxin three-dimensional structures and toxin functions. Bioinformatics is used to tackle specific challenges associated with the identification and annotations of toxins. Recognizing toxin transcript sequences among second generation sequencing data cannot rely only on basic sequence similarity because toxins are highly divergent. Mass spectrometry sequencing of mature toxins is challenging because toxins can display a large number of post-translational modifications. Identifying the mature toxin region in toxin precursor sequences requires the prediction of the cleavage sites of proprotein convertases, most of which are unknown or not well characterized. Tracing the evolutionary relationships between toxins should consider specific mechanisms of rapid evolution as well as interactions between predatory animals and prey. Rapidly determining the activity of toxins is the main bottleneck in venomics discovery, but some recent bioinformatics and molecular modeling approaches give hope that accurate predictions of toxin specificity could be made in the near future. PMID:26110505

  16. Comprehensive Decision Tree Models in Bioinformatics

    PubMed Central

    Stiglic, Gregor; Kocbek, Simon; Pernek, Igor; Kokol, Peter

    2012-01-01

    Purpose Classification is an important and widely used machine learning technique in bioinformatics. Researchers and other end-users of machine learning software often prefer to work with comprehensible models where knowledge extraction and explanation of reasoning behind the classification model are possible. Methods This paper presents an extension to an existing machine learning environment and a study on visual tuning of decision tree classifiers. The motivation for this research comes from the need to build effective and easily interpretable decision tree models by so called one-button data mining approach where no parameter tuning is needed. To avoid bias in classification, no classification performance measure is used during the tuning of the model that is constrained exclusively by the dimensions of the produced decision tree. Results The proposed visual tuning of decision trees was evaluated on 40 datasets containing classical machine learning problems and 31 datasets from the field of bioinformatics. Although we did not expected significant differences in classification performance, the results demonstrate a significant increase of accuracy in less complex visually tuned decision trees. In contrast to classical machine learning benchmarking datasets, we observe higher accuracy gains in bioinformatics datasets. Additionally, a user study was carried out to confirm the assumption that the tree tuning times are significantly lower for the proposed method in comparison to manual tuning of the decision tree. Conclusions The empirical results demonstrate that by building simple models constrained by predefined visual boundaries, one not only achieves good comprehensibility, but also very good classification performance that does not differ from usually more complex models built using default settings of the classical decision tree algorithm. In addition, our study demonstrates the suitability of visually tuned decision trees for datasets with binary class

  17. Virtual Bioinformatics Distance Learning Suite

    ERIC Educational Resources Information Center

    Tolvanen, Martti; Vihinen, Mauno

    2004-01-01

    Distance learning as a computer-aided concept allows students to take courses from anywhere at any time. In bioinformatics, computers are needed to collect, store, process, and analyze massive amounts of biological and biomedical data. We have applied the concept of distance learning in virtual bioinformatics to provide university course material…

  18. Channelrhodopsins: a bioinformatics perspective.

    PubMed

    Del Val, Coral; Royuela-Flor, José; Milenkovic, Stefan; Bondar, Ana-Nicoleta

    2014-05-01

    Channelrhodopsins are microbial-type rhodopsins that function as light-gated cation channels. Understanding how the detailed architecture of the protein governs its dynamics and specificity for ions is important, because it has the potential to assist in designing site-directed channelrhodopsin mutants for specific neurobiology applications. Here we use bioinformatics methods to derive accurate alignments of channelrhodopsin sequences, assess the sequence conservation patterns and find conserved motifs in channelrhodopsins, and use homology modeling to construct three-dimensional structural models of channelrhodopsins. The analyses reveal that helices C and D of channelrhodopsins contain Cys, Ser, and Thr groups that can engage in both intra- and inter-helical hydrogen bonds. We propose that these polar groups participate in inter-helical hydrogen-bonding clusters important for the protein conformational dynamics and for the local water interactions. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks. PMID:24252597

  19. Bioinformatics and Moonlighting Proteins

    PubMed Central

    Hernández, Sergio; Franco, Luís; Calvo, Alejandra; Ferragut, Gabriela; Hermoso, Antoni; Amela, Isaac; Gómez, Antonio; Querol, Enrique; Cedano, Juan

    2015-01-01

    Multitasking or moonlighting is the capability of some proteins to execute two or more biochemical functions. Usually, moonlighting proteins are experimentally revealed by serendipity. For this reason, it would be helpful that Bioinformatics could predict this multifunctionality, especially because of the large amounts of sequences from genome projects. In the present work, we analyze and describe several approaches that use sequences, structures, interactomics, and current bioinformatics algorithms and programs to try to overcome this problem. Among these approaches are (a) remote homology searches using Psi-Blast, (b) detection of functional motifs and domains, (c) analysis of data from protein–protein interaction databases (PPIs), (d) match the query protein sequence to 3D databases (i.e., algorithms as PISITE), and (e) mutation correlation analysis between amino acids by algorithms as MISTIC. Programs designed to identify functional motif/domains detect mainly the canonical function but usually fail in the detection of the moonlighting one, Pfam and ProDom being the best methods. Remote homology search by Psi-Blast combined with data from interactomics databases (PPIs) has the best performance. Structural information and mutation correlation analysis can help us to map the functional sites. Mutation correlation analysis can only be used in very specific situations – it requires the existence of multialigned family protein sequences – but can suggest how the evolutionary process of second function acquisition took place. The multitasking protein database MultitaskProtDB (http://wallace.uab.es/multitask/), previously published by our group, has been used as a benchmark for the all of the analyses. PMID:26157797

  20. Bioinformatics and Moonlighting Proteins.

    PubMed

    Hernández, Sergio; Franco, Luís; Calvo, Alejandra; Ferragut, Gabriela; Hermoso, Antoni; Amela, Isaac; Gómez, Antonio; Querol, Enrique; Cedano, Juan

    2015-01-01

    Multitasking or moonlighting is the capability of some proteins to execute two or more biochemical functions. Usually, moonlighting proteins are experimentally revealed by serendipity. For this reason, it would be helpful that Bioinformatics could predict this multifunctionality, especially because of the large amounts of sequences from genome projects. In the present work, we analyze and describe several approaches that use sequences, structures, interactomics, and current bioinformatics algorithms and programs to try to overcome this problem. Among these approaches are (a) remote homology searches using Psi-Blast, (b) detection of functional motifs and domains, (c) analysis of data from protein-protein interaction databases (PPIs), (d) match the query protein sequence to 3D databases (i.e., algorithms as PISITE), and (e) mutation correlation analysis between amino acids by algorithms as MISTIC. Programs designed to identify functional motif/domains detect mainly the canonical function but usually fail in the detection of the moonlighting one, Pfam and ProDom being the best methods. Remote homology search by Psi-Blast combined with data from interactomics databases (PPIs) has the best performance. Structural information and mutation correlation analysis can help us to map the functional sites. Mutation correlation analysis can only be used in very specific situations - it requires the existence of multialigned family protein sequences - but can suggest how the evolutionary process of second function acquisition took place. The multitasking protein database MultitaskProtDB (http://wallace.uab.es/multitask/), previously published by our group, has been used as a benchmark for the all of the analyses. PMID:26157797

  1. The 2015 Bioinformatics Open Source Conference (BOSC 2015).

    PubMed

    Harris, Nomi L; Cock, Peter J A; Lapp, Hilmar; Chapman, Brad; Davey, Rob; Fields, Christopher; Hokamp, Karsten; Munoz-Torres, Monica

    2016-02-01

    The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included "Data Science;" "Standards and Interoperability;" "Open Science and Reproducibility;" "Translational Bioinformatics;" "Visualization;" and "Bioinformatics Open Source Project Updates". In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled "Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community," that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule. PMID:26914653

  2. ncRDeathDB: A comprehensive bioinformatics resource for deciphering network organization of the ncRNA-mediated cell death system.

    PubMed

    Wu, Deng; Huang, Yan; Kang, Juanjuan; Li, Kongning; Bi, Xiaoman; Zhang, Ting; Jin, Nana; Hu, Yongfei; Tan, Puwen; Zhang, Lu; Yi, Ying; Shen, Wenjun; Huang, Jian; Li, Xiaobo; Li, Xia; Xu, Jianzhen; Wang, Dong

    2015-01-01

    Programmed cell death (PCD) is a critical biological process involved in many important processes, and defects in PCD have been linked with numerous human diseases. In recent years, the protein architecture in different PCD subroutines has been explored, but our understanding of the global network organization of the noncoding RNA (ncRNA)-mediated cell death system is limited and ambiguous. Hence, we developed the comprehensive bioinformatics resource (ncRDeathDB, www.rna-society.org/ncrdeathdb ) to archive ncRNA-associated cell death interactions. The current version of ncRDeathDB documents a total of more than 4600 ncRNA-mediated PCD entries in 12 species. ncRDeathDB provides a user-friendly interface to query, browse and manipulate these ncRNA-associated cell death interactions. Furthermore, this resource will help to visualize and navigate current knowledge of the noncoding RNA component of cell death and autophagy, to uncover the generic organizing principles of ncRNA-associated cell death systems, and to generate valuable biological hypotheses. PMID:26431463

  3. Combining chemoinformatics with bioinformatics: in silico prediction of bacterial flavor-forming pathways by a chemical systems biology approach "reverse pathway engineering".

    PubMed

    Liu, Mengjin; Bienfait, Bruno; Sacher, Oliver; Gasteiger, Johann; Siezen, Roland J; Nauta, Arjen; Geurts, Jan M W

    2014-01-01

    The incompleteness of genome-scale metabolic models is a major bottleneck for systems biology approaches, which are based on large numbers of metabolites as identified and quantified by metabolomics. Many of the revealed secondary metabolites and/or their derivatives, such as flavor compounds, are non-essential in metabolism, and many of their synthesis pathways are unknown. In this study, we describe a novel approach, Reverse Pathway Engineering (RPE), which combines chemoinformatics and bioinformatics analyses, to predict the "missing links" between compounds of interest and their possible metabolic precursors by providing plausible chemical and/or enzymatic reactions. We demonstrate the added-value of the approach by using flavor-forming pathways in lactic acid bacteria (LAB) as an example. Established metabolic routes leading to the formation of flavor compounds from leucine were successfully replicated. Novel reactions involved in flavor formation, i.e. the conversion of alpha-hydroxy-isocaproate to 3-methylbutanoic acid and the synthesis of dimethyl sulfide, as well as the involved enzymes were successfully predicted. These new insights into the flavor-formation mechanisms in LAB can have a significant impact on improving the control of aroma formation in fermented food products. Since the input reaction databases and compounds are highly flexible, the RPE approach can be easily extended to a broad spectrum of applications, amongst others health/disease biomarker discovery as well as synthetic biology. PMID:24416282

  4. Combining Chemoinformatics with Bioinformatics: In Silico Prediction of Bacterial Flavor-Forming Pathways by a Chemical Systems Biology Approach “Reverse Pathway Engineering”

    PubMed Central

    Liu, Mengjin; Bienfait, Bruno; Sacher, Oliver; Gasteiger, Johann; Siezen, Roland J.; Nauta, Arjen; Geurts, Jan M. W.

    2014-01-01

    The incompleteness of genome-scale metabolic models is a major bottleneck for systems biology approaches, which are based on large numbers of metabolites as identified and quantified by metabolomics. Many of the revealed secondary metabolites and/or their derivatives, such as flavor compounds, are non-essential in metabolism, and many of their synthesis pathways are unknown. In this study, we describe a novel approach, Reverse Pathway Engineering (RPE), which combines chemoinformatics and bioinformatics analyses, to predict the “missing links” between compounds of interest and their possible metabolic precursors by providing plausible chemical and/or enzymatic reactions. We demonstrate the added-value of the approach by using flavor-forming pathways in lactic acid bacteria (LAB) as an example. Established metabolic routes leading to the formation of flavor compounds from leucine were successfully replicated. Novel reactions involved in flavor formation, i.e. the conversion of alpha-hydroxy-isocaproate to 3-methylbutanoic acid and the synthesis of dimethyl sulfide, as well as the involved enzymes were successfully predicted. These new insights into the flavor-formation mechanisms in LAB can have a significant impact on improving the control of aroma formation in fermented food products. Since the input reaction databases and compounds are highly flexible, the RPE approach can be easily extended to a broad spectrum of applications, amongst others health/disease biomarker discovery as well as synthetic biology. PMID:24416282

  5. Translational bioinformatics in psychoneuroimmunology: methods and applications.

    PubMed

    Yan, Qing

    2012-01-01

    Translational bioinformatics plays an indispensable role in transforming psychoneuroimmunology (PNI) into personalized medicine. It provides a powerful method to bridge the gaps between various knowledge domains in PNI and systems biology. Translational bioinformatics methods at various systems levels can facilitate pattern recognition, and expedite and validate the discovery of systemic biomarkers to allow their incorporation into clinical trials and outcome assessments. Analysis of the correlations between genotypes and phenotypes including the behavioral-based profiles will contribute to the transition from the disease-based medicine to human-centered medicine. Translational bioinformatics would also enable the establishment of predictive models for patient responses to diseases, vaccines, and drugs. In PNI research, the development of systems biology models such as those of the neurons would play a critical role. Methods based on data integration, data mining, and knowledge representation are essential elements in building health information systems such as electronic health records and computerized decision support systems. Data integration of genes, pathophysiology, and behaviors are needed for a broad range of PNI studies. Knowledge discovery approaches such as network-based systems biology methods are valuable in studying the cross-talks among pathways in various brain regions involved in disorders such as Alzheimer's disease. PMID:22933157

  6. Global computing for bioinformatics.

    PubMed

    Loewe, Laurence

    2002-12-01

    Global computing, the collaboration of idle PCs via the Internet in a SETI@home style, emerges as a new way of massive parallel multiprocessing with potentially enormous CPU power. Its relations to the broader, fast-moving field of Grid computing are discussed without attempting a review of the latter. This review (i) includes a short table of milestones in global computing history, (ii) lists opportunities global computing offers for bioinformatics, (iii) describes the structure of problems well suited for such an approach, (iv) analyses the anatomy of successful projects and (v) points to existing software frameworks. Finally, an evaluation of the various costs shows that global computing indeed has merit, if the problem to be solved is already coded appropriately and a suitable global computing framework can be found. Then, either significant amounts of computing power can be recruited from the general public, or--if employed in an enterprise-wide Intranet for security reasons--idle desktop PCs can substitute for an expensive dedicated cluster. PMID:12511066

  7. Bioinformatics in protein analysis.

    PubMed

    Persson, B

    2000-01-01

    The chapter gives an overview of bioinformatic techniques of importance in protein analysis. These include database searches, sequence comparisons and structural predictions. Links to useful World Wide Web (WWW) pages are given in relation to each topic. Databases with biological information are reviewed with emphasis on databases for nucleotide sequences (EMBL, GenBank, DDBJ), genomes, amino acid sequences (Swissprot, PIR, TrEMBL, GenePept), and three-dimensional structures (PDB). Integrated user interfaces for databases (SRS and Entrez) are described. An introduction to databases of sequence patterns and protein families is also given (Prosite, Pfam, Blocks). Furthermore, the chapter describes the widespread methods for sequence comparisons, FASTA and BLAST, and the corresponding WWW services. The techniques involving multiple sequence alignments are also reviewed: alignment creation with the Clustal programs, phylogenetic tree calculation with the Clustal or Phylip packages and tree display using Drawtree, njplot or phylo_win. Finally, the chapter also treats the issue of structural prediction. Different methods for secondary structure predictions are described (Chou-Fasman, Garnier-Osguthorpe-Robson, Predator, PHD). Techniques for predicting membrane proteins, antigenic sites and postranslational modifications are also reviewed. PMID:10803381

  8. MEMOSys: Bioinformatics platform for genome-scale metabolic models

    PubMed Central

    2011-01-01

    Background Recent advances in genomic sequencing have enabled the use of genome sequencing in standard biological and biotechnological research projects. The challenge is how to integrate the large amount of data in order to gain novel biological insights. One way to leverage sequence data is to use genome-scale metabolic models. We have therefore designed and implemented a bioinformatics platform which supports the development of such metabolic models. Results MEMOSys (MEtabolic MOdel research and development System) is a versatile platform for the management, storage, and development of genome-scale metabolic models. It supports the development of new models by providing a built-in version control system which offers access to the complete developmental history. Moreover, the integrated web board, the authorization system, and the definition of user roles allow collaborations across departments and institutions. Research on existing models is facilitated by a search system, references to external databases, and a feature-rich comparison mechanism. MEMOSys provides customizable data exchange mechanisms using the SBML format to enable analysis in external tools. The web application is based on the Java EE framework and offers an intuitive user interface. It currently contains six annotated microbial metabolic models. Conclusions We have developed a web-based system designed to provide researchers a novel application facilitating the management and development of metabolic models. The system is freely available at http://www.icbi.at/MEMOSys. PMID:21276275

  9. Development of a 3D Underground Cadastral System with Indoor Mapping for As-Built BIM: The Case Study of Gangnam Subway Station in Korea.

    PubMed

    Kim, Sangmin; Kim, Jeonghyun; Jung, Jaehoon; Heo, Joon

    2015-01-01

    The cadastral system provides land ownership information by registering and representing land boundaries on a map. The current cadastral system in Korea, however, focuses mainly on the management of 2D land-surface boundaries. It is not yet possible to provide efficient or reliable land administration, as this 2D system cannot support or manage land information on 3D properties (including architectures and civil infrastructures) for both above-ground and underground facilities. A geometrical model of the 3D parcel, therefore, is required for registration of 3D properties. This paper, considering the role of the cadastral system, proposes a framework for a 3D underground cadastral system that can register various types of 3D underground properties using indoor mapping for as-built Building Information Modeling (BIM). The implementation consists of four phases: (1) geometric modeling of a real underground infrastructure using terrestrial laser scanning data; (2) implementation of as-built BIM based on geometric modeling results; (3) accuracy assessment for created as-built BIM using reference points acquired by total station; and (4) creation of three types of 3D underground cadastral map to represent underground properties. The experimental results, based on indoor mapping for as-built BIM, show that the proposed framework for a 3D underground cadastral system is able to register the rights, responsibilities, and restrictions corresponding to the 3D underground properties. In this way, clearly identifying the underground physical situation enables more reliable and effective decision-making in all aspects of the national land administration system. PMID:26690174

  10. Development of a 3D Underground Cadastral System with Indoor Mapping for As-Built BIM: The Case Study of Gangnam Subway Station in Korea

    PubMed Central

    Kim, Sangmin; Kim, Jeonghyun; Jung, Jaehoon; Heo, Joon

    2015-01-01

    The cadastral system provides land ownership information by registering and representing land boundaries on a map. The current cadastral system in Korea, however, focuses mainly on the management of 2D land-surface boundaries. It is not yet possible to provide efficient or reliable land administration, as this 2D system cannot support or manage land information on 3D properties (including architectures and civil infrastructures) for both above-ground and underground facilities. A geometrical model of the 3D parcel, therefore, is required for registration of 3D properties. This paper, considering the role of the cadastral system, proposes a framework for a 3D underground cadastral system that can register various types of 3D underground properties using indoor mapping for as-built Building Information Modeling (BIM). The implementation consists of four phases: (1) geometric modeling of a real underground infrastructure using terrestrial laser scanning data; (2) implementation of as-built BIM based on geometric modeling results; (3) accuracy assessment for created as-built BIM using reference points acquired by total station; and (4) creation of three types of 3D underground cadastral map to represent underground properties. The experimental results, based on indoor mapping for as-built BIM, show that the proposed framework for a 3D underground cadastral system is able to register the rights, responsibilities, and restrictions corresponding to the 3D underground properties. In this way, clearly identifying the underground physical situation enables more reliable and effective decision-making in all aspects of the national land administration system. PMID:26690174

  11. Engineering bioinformatics: building reliability, performance and productivity into bioinformatics software

    PubMed Central

    Lawlor, Brendan; Walsh, Paul

    2015-01-01

    There is a lack of software engineering skills in bioinformatic contexts. We discuss the consequences of this lack, examine existing explanations and remedies to the problem, point out their shortcomings, and propose alternatives. Previous analyses of the problem have tended to treat the use of software in scientific contexts as categorically different from the general application of software engineering in commercial settings. In contrast, we describe bioinformatic software engineering as a specialization of general software engineering, and examine how it should be practiced. Specifically, we highlight the difference between programming and software engineering, list elements of the latter and present the results of a survey of bioinformatic practitioners which quantifies the extent to which those elements are employed in bioinformatics. We propose that the ideal way to bring engineering values into research projects is to bring engineers themselves. We identify the role of Bioinformatic Engineer and describe how such a role would work within bioinformatic research teams. We conclude by recommending an educational emphasis on cross-training software engineers into life sciences, and propose research on Domain Specific Languages to facilitate collaboration between engineers and bioinformaticians. PMID:25996054

  12. Engineering bioinformatics: building reliability, performance and productivity into bioinformatics software.

    PubMed

    Lawlor, Brendan; Walsh, Paul

    2015-01-01

    There is a lack of software engineering skills in bioinformatic contexts. We discuss the consequences of this lack, examine existing explanations and remedies to the problem, point out their shortcomings, and propose alternatives. Previous analyses of the problem have tended to treat the use of software in scientific contexts as categorically different from the general application of software engineering in commercial settings. In contrast, we describe bioinformatic software engineering as a specialization of general software engineering, and examine how it should be practiced. Specifically, we highlight the difference between programming and software engineering, list elements of the latter and present the results of a survey of bioinformatic practitioners which quantifies the extent to which those elements are employed in bioinformatics. We propose that the ideal way to bring engineering values into research projects is to bring engineers themselves. We identify the role of Bioinformatic Engineer and describe how such a role would work within bioinformatic research teams. We conclude by recommending an educational emphasis on cross-training software engineers into life sciences, and propose research on Domain Specific Languages to facilitate collaboration between engineers and bioinformaticians. PMID:25996054

  13. Survey of MapReduce frame operation in bioinformatics.

    PubMed

    Zou, Quan; Li, Xu-Bin; Jiang, Wen-Rui; Lin, Zi-Yu; Li, Gui-Lin; Chen, Ke

    2014-07-01

    Bioinformatics is challenged by the fact that traditional analysis tools have difficulty in processing large-scale data from high-throughput sequencing. The open source Apache Hadoop project, which adopts the MapReduce framework and a distributed file system, has recently given bioinformatics researchers an opportunity to achieve scalable, efficient and reliable computing performance on Linux clusters and on cloud computing services. In this article, we present MapReduce frame-based applications that can be employed in the next-generation sequencing and other biological domains. In addition, we discuss the challenges faced by this field as well as the future works on parallel computing in bioinformatics. PMID:23396756

  14. VLSI Microsystem for Rapid Bioinformatic Pattern Recognition

    NASA Technical Reports Server (NTRS)

    Fang, Wai-Chi; Lue, Jaw-Chyng

    2009-01-01

    A system comprising very-large-scale integrated (VLSI) circuits is being developed as a means of bioinformatics-oriented analysis and recognition of patterns of fluorescence generated in a microarray in an advanced, highly miniaturized, portable genetic-expression-assay instrument. Such an instrument implements an on-chip combination of polymerase chain reactions and electrochemical transduction for amplification and detection of deoxyribonucleic acid (DNA).

  15. The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets.

    PubMed

    Droege, Marcus; Hill, Brendon

    2008-08-31

    The Genome Sequencer FLX System (GS FLX), powered by 454 Sequencing, is a next-generation DNA sequencing technology featuring a unique mix of long reads, exceptional accuracy, and ultra-high throughput. It has been proven to be the most versatile of all currently available next-generation sequencing technologies, supporting many high-profile studies in over seven applications categories. GS FLX users have pursued innovative research in de novo sequencing, re-sequencing of whole genomes and target DNA regions, metagenomics, and RNA analysis. 454 Sequencing is a powerful tool for human genetics research, having recently re-sequenced the genome of an individual human, currently re-sequencing the complete human exome and targeted genomic regions using the NimbleGen sequence capture process, and detected low-frequency somatic mutations linked to cancer. PMID:18616967

  16. Autophagy Regulatory Network — A systems-level bioinformatics resource for studying the mechanism and regulation of autophagy

    PubMed Central

    Türei, Dénes; Földvári-Nagy, László; Fazekas, Dávid; Módos, Dezső; Kubisch, János; Kadlecsik, Tamás; Demeter, Amanda; Lenti, Katalin; Csermely, Péter; Vellai, Tibor; Korcsmáros, Tamás

    2015-01-01

    Autophagy is a complex cellular process having multiple roles, depending on tissue, physiological, or pathological conditions. Major post-translational regulators of autophagy are well known, however, they have not yet been collected comprehensively. The precise and context-dependent regulation of autophagy necessitates additional regulators, including transcriptional and post-transcriptional components that are listed in various datasets. Prompted by the lack of systems-level autophagy-related information, we manually collected the literature and integrated external resources to gain a high coverage autophagy database. We developed an online resource, Autophagy Regulatory Network (ARN; http://autophagy-regulation.org), to provide an integrated and systems-level database for autophagy research. ARN contains manually curated, imported, and predicted interactions of autophagy components (1,485 proteins with 4,013 interactions) in humans. We listed 413 transcription factors and 386 miRNAs that could regulate autophagy components or their protein regulators. We also connected the above-mentioned autophagy components and regulators with signaling pathways from the SignaLink 2 resource. The user-friendly website of ARN allows researchers without computational background to search, browse, and download the database. The database can be downloaded in SQL, CSV, BioPAX, SBML, PSI-MI, and in a Cytoscape CYS file formats. ARN has the potential to facilitate the experimental validation of novel autophagy components and regulators. In addition, ARN helps the investigation of transcription factors, miRNAs and signaling pathways implicated in the control of the autophagic pathway. The list of such known and predicted regulators could be important in pharmacological attempts against cancer and neurodegenerative diseases. PMID:25635527

  17. Adapting bioinformatics curricula for big data.

    PubMed

    Greene, Anna C; Giffin, Kristine A; Greene, Casey S; Moore, Jason H

    2016-01-01

    Modern technologies are capable of generating enormous amounts of data that measure complex biological systems. Computational biologists and bioinformatics scientists are increasingly being asked to use these data to reveal key systems-level properties. We review the extent to which curricula are changing in the era of big data. We identify key competencies that scientists dealing with big data are expected to possess across fields, and we use this information to propose courses to meet these growing needs. While bioinformatics programs have traditionally trained students in data-intensive science, we identify areas of particular biological, computational and statistical emphasis important for this era that can be incorporated into existing curricula. For each area, we propose a course structured around these topics, which can be adapted in whole or in parts into existing curricula. In summary, specific challenges associated with big data provide an important opportunity to update existing curricula, but we do not foresee a wholesale redesign of bioinformatics training programs. PMID:25829469

  18. Adapting bioinformatics curricula for big data

    PubMed Central

    Greene, Anna C.; Giffin, Kristine A.; Greene, Casey S.

    2016-01-01

    Modern technologies are capable of generating enormous amounts of data that measure complex biological systems. Computational biologists and bioinformatics scientists are increasingly being asked to use these data to reveal key systems-level properties. We review the extent to which curricula are changing in the era of big data. We identify key competencies that scientists dealing with big data are expected to possess across fields, and we use this information to propose courses to meet these growing needs. While bioinformatics programs have traditionally trained students in data-intensive science, we identify areas of particular biological, computational and statistical emphasis important for this era that can be incorporated into existing curricula. For each area, we propose a course structured around these topics, which can be adapted in whole or in parts into existing curricula. In summary, specific challenges associated with big data provide an important opportunity to update existing curricula, but we do not foresee a wholesale redesign of bioinformatics training programs. PMID:25829469

  19. Chapter 16: text mining for translational bioinformatics.

    PubMed

    Cohen, K Bretonnel; Hunter, Lawrence E

    2013-04-01

    Text mining for translational bioinformatics is a new field with tremendous research potential. It is a subfield of biomedical natural language processing that concerns itself directly with the problem of relating basic biomedical research to clinical practice, and vice versa. Applications of text mining fall both into the category of T1 translational research-translating basic science results into new interventions-and T2 translational research, or translational research for public health. Potential use cases include better phenotyping of research subjects, and pharmacogenomic research. A variety of methods for evaluating text mining applications exist, including corpora, structured test suites, and post hoc judging. Two basic principles of linguistic structure are relevant for building text mining applications. One is that linguistic structure consists of multiple levels. The other is that every level of linguistic structure is characterized by ambiguity. There are two basic approaches to text mining: rule-based, also known as knowledge-based; and machine-learning-based, also known as statistical. Many systems are hybrids of the two approaches. Shared tasks have had a strong effect on the direction of the field. Like all translational bioinformatics software, text mining software for translational bioinformatics can be considered health-critical and should be subject to the strictest standards of quality assurance and software testing. PMID:23633944

  20. Chapter 16: Text Mining for Translational Bioinformatics

    PubMed Central

    Cohen, K. Bretonnel; Hunter, Lawrence E.

    2013-01-01

    Text mining for translational bioinformatics is a new field with tremendous research potential. It is a subfield of biomedical natural language processing that concerns itself directly with the problem of relating basic biomedical research to clinical practice, and vice versa. Applications of text mining fall both into the category of T1 translational research—translating basic science results into new interventions—and T2 translational research, or translational research for public health. Potential use cases include better phenotyping of research subjects, and pharmacogenomic research. A variety of methods for evaluating text mining applications exist, including corpora, structured test suites, and post hoc judging. Two basic principles of linguistic structure are relevant for building text mining applications. One is that linguistic structure consists of multiple levels. The other is that every level of linguistic structure is characterized by ambiguity. There are two basic approaches to text mining: rule-based, also known as knowledge-based; and machine-learning-based, also known as statistical. Many systems are hybrids of the two approaches. Shared tasks have had a strong effect on the direction of the field. Like all translational bioinformatics software, text mining software for translational bioinformatics can be considered health-critical and should be subject to the strictest standards of quality assurance and software testing. PMID:23633944

  1. Bioinformatic pipelines in Python with Leaf

    PubMed Central

    2013-01-01

    Background An incremental, loosely planned development approach is often used in bioinformatic studies when dealing with custom data analysis in a rapidly changing environment. Unfortunately, the lack of a rigorous software structuring can undermine the maintainability, communicability and replicability of the process. To ameliorate this problem we propose the Leaf system, the aim of which is to seamlessly introduce the pipeline formality on top of a dynamical development process with minimum overhead for the programmer, thus providing a simple layer of software structuring. Results Leaf includes a formal language for the definition of pipelines with code that can be transparently inserted into the user’s Python code. Its syntax is designed to visually highlight dependencies in the pipeline structure it defines. While encouraging the developer to think in terms of bioinformatic pipelines, Leaf supports a number of automated features including data and session persistence, consistency checks between steps of the analysis, processing optimization and publication of the analytic protocol in the form of a hypertext. Conclusions Leaf offers a powerful balance between plan-driven and change-driven development environments in the design, management and communication of bioinformatic pipelines. Its unique features make it a valuable alternative to other related tools. PMID:23786315

  2. Generations of interdisciplinarity in bioinformatics

    PubMed Central

    Bartlett, Andrew; Lewis, Jamie; Williams, Matthew L.

    2016-01-01

    Bioinformatics, a specialism propelled into relevance by the Human Genome Project and the subsequent -omic turn in the life science, is an interdisciplinary field of research. Qualitative work on the disciplinary identities of bioinformaticians has revealed the tensions involved in work in this “borderland.” As part of our ongoing work on the emergence of bioinformatics, between 2010 and 2011, we conducted a survey of United Kingdom-based academic bioinformaticians. Building on insights drawn from our fieldwork over the past decade, we present results from this survey relevant to a discussion of disciplinary generation and stabilization. Not only is there evidence of an attitudinal divide between the different disciplinary cultures that make up bioinformatics, but there are distinctions between the forerunners, founders and the followers; as inter/disciplines mature, they face challenges that are both inter-disciplinary and inter-generational in nature. PMID:27453689

  3. No moving parts safe & arm apparatus and method with monitoring and built-in-test for optical firing of explosive systems

    DOEpatents

    Hendrix, J.L.

    1995-04-11

    A laser initiated ordnance controller apparatus which provides a safe and arm scheme with no moving parts. The safe & arm apparatus provides isolation of firing energy to explosive devices using a combination of polarization isolation and control through acousto-optical deviation of laser energy pulses. The apparatus provides constant monitoring of the systems status and performs 100% built-in-test at any time prior to ordnance ignition without the risk of premature ignition or detonation. The apparatus has a computer controller, a solid state laser, an acousto-optic deflector and RF drive circuitry, built-in-test optics and electronics, and system monitoring capabilities. The optical system is completed from the laser beam power source to the pyrotechnic ordnance through fiber optic cabling, optical splitters and optical connectors. During operation of the apparatus, a command is provided by the computer controller and, simultaneous with laser flashlamp fire, the safe & arm device is opened for approximately 200 microseconds which allows the laser pulse to transmit through the device. The arm signal also energizes the laser power supply and activates the acousto-optical deflector. When the correct fire format command is received, the acousto-optic deflector moves to the selected event channel, and the channel is verified to ensure the system is pointing to the correct position. Laser energy is transmitted through the fiber where an ignitor or detonator designed to be sensitive to optical pulses is fired at the end of the fiber channel. Simultaneous event channels may also be utilized by optically splitting a single event channel. The built-in-test may be performed anytime prior to ordnance ignition. 6 figures.

  4. No moving parts safe & arm apparatus and method with monitoring and built-in-test for optical firing of explosive systems

    DOEpatents

    Hendrix, James L.

    1995-01-01

    A laser initiated ordnance controller apparatus which provides a safe and m scheme with no moving parts. The safe & arm apparatus provides isolation of firing energy to explosive devices using a combination of polarization isolation and control through acousto-optical deviation of laser energy pulses. The apparatus provides constant monitoring of the systems status and performs 100% built-in-test at any time prior to ordnance ignition without the risk of premature ignition or detonation. The apparatus has a computer controller, a solid state laser, an acousto-optic deflector and RF drive circuitry, built-in-test optics and electronics, and system monitoring capabilities. The optical system is completed from the laser beam power source to the pyrotechnic ordnance through fiber optic cabling, optical splitters and optical connectors. During operation of the apparatus, a command is provided by the computer controller and, simultaneous with laser flashlamp fire, the safe & arm device is opened for approximately 200 microseconds which allows the laser pulse to transmit through the device. The arm signal also energizes the laser power supply and activates the acousto-optical deflector. When the correct fire format command is received, the acousto-optic deflector moves to the selected event channel, and the channel is verified to ensure the system is pointing to the correct position. Laser energy is transmitted through the fiber where an ignitor or detonator designed to be sensitive to optical pulses is fired at the end of the fiber channel. Simultaneous event channels may also be utilized by optically splitting a single event channel. The built-in-test may be performed anytime prior to ordnance ignition.

  5. No moving parts safe and arm apparatus and method with monitoring and built-in-test for optical firing of explosive systems

    SciTech Connect

    Hendrix, J.L.

    1994-12-31

    A laser initiated ordnance controller apparatus which provides a safe and arm scheme with no moving parts. The safe and arm apparatus provides isolation of firing energy to explosive devices using a combination of polarization isolation and control through acousto-optical deviation of laser energy pulses. The apparatus provides constant monitoring of the systems status and performs 100% built-in-test at any time prior to ordnance ignition without the risk of premature ignition or detonation. The apparatus has a computer controller, a solid state laser, an acousto-optic deflector and RF drive circuitry, built-in-test optics and electronics, and system monitoring capabilities. The optical system is completed from the laser beam power source to the pyrotechnic ordnance through fiber optic cabling, optical splitters and optical connectors. During operation of the apparatus, a command is provided by the computer controller and, simultaneous with laser flashlamp fire, the safe and arm device is opened for approximately 200 microseconds which allows the laser pulse to transmit through the device. The arm signal also energizes the laser power supply and activated the acousto-optical deflector. When the correct fire format command is received, the acousto-optic deflector moves to the selected event channel and the channel is verified to ensure the system is pointing to the correct position. Laser energy is transmitted through the fiber where an ignitor or detonator designed to be sensitive to optical pulses is fired at the end of the fiber channel.

  6. The vibro-acoustic analysis of built-up systems using a hybrid method with parametric and non-parametric uncertainties

    NASA Astrophysics Data System (ADS)

    Cicirello, Alice; Langley, Robin S.

    2013-04-01

    An existing hybrid finite element (FE)/statistical energy analysis (SEA) approach to the analysis of the mid- and high frequency vibrations of a complex built-up system is extended here to a wider class of uncertainty modeling. In the original approach, the constituent parts of the system are considered to be either deterministic, and modeled using FE, or highly random, and modeled using SEA. A non-parametric model of randomness is employed in the SEA components, based on diffuse wave theory and the Gaussian Orthogonal Ensemble (GOE), and this enables the mean and variance of second order quantities such as vibrational energy and response cross-spectra to be predicted. In the present work the assumption that the FE components are deterministic is relaxed by the introduction of a parametric model of uncertainty in these components. The parametric uncertainty may be modeled either probabilistically, or by using a non-probabilistic approach such as interval analysis, and it is shown how these descriptions can be combined with the non-parametric uncertainty in the SEA subsystems to yield an overall assessment of the performance of the system. The method is illustrated by application to an example built-up plate system which has random properties, and benchmark comparisons are made with full Monte Carlo simulations.

  7. The 2015 Bioinformatics Open Source Conference (BOSC 2015)

    PubMed Central

    Harris, Nomi L.; Cock, Peter J. A.; Lapp, Hilmar

    2016-01-01

    The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included “Data Science;” “Standards and Interoperability;” “Open Science and Reproducibility;” “Translational Bioinformatics;” “Visualization;” and “Bioinformatics Open Source Project Updates”. In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled “Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community,” that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule. PMID:26914653

  8. The Space Launch System -The Biggest, Most Capable Rocket Ever Built, for Entirely New Human Exploration Missions Beyond Earth's Orbit

    NASA Technical Reports Server (NTRS)

    Shivers, C. Herb

    2012-01-01

    NASA is developing the Space Launch System -- an advanced heavy-lift launch vehicle that will provide an entirely new capability for human exploration beyond Earth's orbit. The Space Launch System will provide a safe, affordable and sustainable means of reaching beyond our current limits and opening up new discoveries from the unique vantage point of space. The first developmental flight, or mission, is targeted for the end of 2017. The Space Launch System, or SLS, will be designed to carry the Orion Multi-Purpose Crew Vehicle, as well as important cargo, equipment and science experiments to Earth's orbit and destinations beyond. Additionally, the SLS will serve as a backup for commercial and international partner transportation services to the International Space Station. The SLS rocket will incorporate technological investments from the Space Shuttle Program and the Constellation Program in order to take advantage of proven hardware and cutting-edge tooling and manufacturing technology that will significantly reduce development and operations costs. The rocket will use a liquid hydrogen and liquid oxygen propulsion system, which will include the RS-25D/E from the Space Shuttle Program for the core stage and the J-2X engine for the upper stage. SLS will also use solid rocket boosters for the initial development flights, while follow-on boosters will be competed based on performance requirements and affordability considerations.

  9. The Resilience of Structure Built around the Predicate: Homesign Gesture Systems in Turkish and American Deaf Children

    ERIC Educational Resources Information Center

    Goldin-Meadow, Susan; Namboodiripad, Savithry; Mylander, Carolyn; Özyürek, Asli; Sancar, Burcu

    2015-01-01

    Deaf children whose hearing losses prevent them from accessing spoken language and whose hearing parents have not exposed them to sign language develop gesture systems, called "homesigns", which have many of the properties of natural language--the so-called resilient properties of language. We explored the resilience of structure built…

  10. The detection method for small molecules coupled with a molecularly imprinted polymer/quantum dot chip using a home-built optical system.

    PubMed

    Liu, Yixi; Wang, Yong; Liu, Le; He, Yonghong; He, Qinghua; Ji, Yanhong

    2016-07-01

    A method to detect small molecules with a molecularly imprinted polymer/quantum dot (MIP-QD) chip using a home-built optical fluidic system was first proposed in this study. Ractopamine (RAC) was used as the model molecule to demonstrate its feasibility. The sensing of the target molecule is based on the quenching amount of the quantum dots. The method is facile, cost-saving, easy for miniaturization and avoids the cumbersome steps that are needed to get the fluorescent quenching curve using a spectrofluorometer. Most importantly, more details and accurate response time can be obtained by use of this method. The experimental results show that the prepared chips with low cost are highly selective and the home-built detection system allows the fast binding kinetics. The recorded quenching process was used to study the kinetic uptake of RAC onto the MIP-QD chip and the specificity towards RAC. The system can further be utilized to study the effect of the solvent, pH and temperature on the selectivity of the prepared MIP. The methodology could be extended to other similar studies with different molecules. Graphical abstract Schematic illustration of the molecularly imprinted polymer/quantum dot chip capturing the target molecule. PMID:27235159

  11. Towards an International Planetary Community Built on Open Source Software: the Evolution of the Planetary Data System

    NASA Astrophysics Data System (ADS)

    Crichton, D. J.; Ramirez, P.; Hardman, S.; Hughes, J. S.

    2012-12-01

    Access to the worldwide planetary science research results from robotic exploration of the solar system has become a key driver in internationalizing the data standards from the Planetary Data System. The Planetary Data System, through international agency collaborations with the International Planetary Data Alliance (IPDA), has been developing a next generation set of data standards and technical implementation known as PDS4. PDS4 modernizes the PDS towards a world-wide online data system providing data and technical standards for improving access and interoperability among planetary archives. Since 2006, the IPDA has been working with the PDS to ensure that the next generation PDS is capable of allowing agency autonomy in building compatible archives while providing mechanisms to link the archive together. At the 7th International Planetary Data Alliance (IPDA) Meeting in Bangalore, India, the IPDA discussed and passed a resolution paving the way to adopt the PDS4 data standards. While the PDS4 standards have matured, another effort has been underway to move the PDS, a set of distributed discipline oriented science nodes, into a fully, online, service-oriented architecture. In order to accomplish this goal, the PDS has been developing a core set of software components that form the basis for many of the functions needed by a data system. These include the ability to harvest, validate, register, search and distribute the data products defined by the PDS4 data standards. Rather than having each group build their own independent implementations, the intention is to ultimately govern the implementation of this software through an open source community. This will enable not only sharing of software among U.S. planetary science nodes, but also has the potential of improving collaboration not only on core data management software, but also the tools by the international community. This presentation will discuss the progress in developing an open source infrastructure

  12. Mathematics and evolutionary biology make bioinformatics education comprehensible

    PubMed Central

    Weisstein, Anton E.

    2013-01-01

    The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes—the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software—the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a ‘two-culture’ problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses. PMID:23821621

  13. Bioinformatics and the Undergraduate Curriculum

    ERIC Educational Resources Information Center

    Maloney, Mark; Parker, Jeffrey; LeBlanc, Mark; Woodard, Craig T.; Glackin, Mary; Hanrahan, Michael

    2010-01-01

    Recent advances involving high-throughput techniques for data generation and analysis have made familiarity with basic bioinformatics concepts and programs a necessity in the biological sciences. Undergraduate students increasingly need training in methods related to finding and retrieving information stored in vast databases. The rapid rise of…

  14. Reproducible Bioinformatics Research for Biologists

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This book chapter describes the current Big Data problem in Bioinformatics and the resulting issues with performing reproducible computational research. The core of the chapter provides guidelines and summaries of current tools/techniques that a noncomputational researcher would need to learn to pe...

  15. Visualising "Junk" DNA through Bioinformatics

    ERIC Educational Resources Information Center

    Elwess, Nancy L.; Latourelle, Sandra M.; Cauthorn, Olivia

    2005-01-01

    One of the hottest areas of science today is the field in which biology, information technology,and computer science are merged into a single discipline called bioinformatics. This field enables the discovery and analysis of biological data, including nucleotide and amino acid sequences that are easily accessed through the use of computers. As…

  16. Highly Flexible Home-built ND:YVO4 Modelocked Laser System for Trapped Ion Qubit Raman Transitions

    NASA Astrophysics Data System (ADS)

    Sakrejda, Tomasz; Wright, John; Graham, Richard; Zhou, Zichao; Blinov, Boris

    2014-05-01

    A passively mode-locked ND:YVO4 laser system for driving Raman transitions in Ba+ and Yb+ is constructed and evaluated. Based on on a commercial CW laser platform, we make straightforward modifications to the cavity to effect passive mode locking. With 20 W of 808 nm diode pump light, we achieve over 4 W 1064 nm output power, 150 MHz repetition rate, and 17 ps pulse duration. Laser cavity parameters can be easily modified to facilitate changes in pulse duration or repetition rate. Stable mode locking is achieved at start-up with no perturbations to the cavity resonator. The output 1064 nm light can frequency-doubled in an external LBO crystal to generate up to 130 mW of 532 nm light in a single pass. The 532 nm light is close enough to the 493 nm line in Ba+ to drive ground state qubit flips with a single laser pulse. We plan to use this laser to drive qubit gates in both Ba 138+ and, with a third harmonic (355 nm) generation system, in 171Yb+. Supported by MUSIQC/IARPA.

  17. Natural and built environmental exposures on children's active school travel: A Dutch global positioning system-based cross-sectional study.

    PubMed

    Helbich, Marco; Emmichoven, Maarten J Zeylmans van; Dijst, Martin J; Kwan, Mei-Po; Pierik, Frank H; Vries, Sanne I de

    2016-05-01

    Physical inactivity among children is on the rise. Active transport to school (ATS), namely walking and cycling there, adds to children's activity level. Little is known about how exposures along actual routes influence children's transport behavior. This study examined how natural and built environments influence mode choice among Dutch children aged 6-11 years. 623 school trips were tracked with global positioning system. Natural and built environmental exposures were determined by means of a geographic information system and their associations with children's active/passive mode choice were analyzed using mixed models. The actual commuted distance is inversely associated with ATS when only personal, traffic safety, and weather features are considered. When the model is adjusted for urban environments, the results are reversed and distance is no longer significant, whereas well-connected streets and cycling lanes are positively associated with ATS. Neither green space nor weather is significant. As distance is not apparent as a constraining travel determinant when moving through urban landscapes, planning authorities should support children's ATS by providing well-designed cities. PMID:27010106

  18. Development of Kinematic 3D Laser Scanning System for Indoor Mapping and As-Built BIM Using Constrained SLAM

    PubMed Central

    Jung, Jaehoon; Yoon, Sanghyun; Ju, Sungha; Heo, Joon

    2015-01-01

    The growing interest and use of indoor mapping is driving a demand for improved data-acquisition facility, efficiency and productivity in the era of the Building Information Model (BIM). The conventional static laser scanning method suffers from some limitations on its operability in complex indoor environments, due to the presence of occlusions. Full scanning of indoor spaces without loss of information requires that surveyors change the scanner position many times, which incurs extra work for registration of each scanned point cloud. Alternatively, a kinematic 3D laser scanning system, proposed herein, uses line-feature-based Simultaneous Localization and Mapping (SLAM) technique for continuous mapping. Moreover, to reduce the uncertainty of line-feature extraction, we incorporated constrained adjustment based on an assumption made with respect to typical indoor environments: that the main structures are formed of parallel or orthogonal line features. The superiority of the proposed constrained adjustment is its reduction for uncertainties of the adjusted lines, leading to successful data association process. In the present study, kinematic scanning with and without constrained adjustment were comparatively evaluated in two test sites, and the results confirmed the effectiveness of the proposed system. The accuracy of the 3D mapping result was additionally evaluated by comparison with the reference points acquired by a total station: the Euclidean average distance error was 0.034 m for the seminar room and 0.043 m for the corridor, which satisfied the error tolerance for point cloud acquisition (0.051 m) according to the guidelines of the General Services Administration for BIM accuracy. PMID:26501292

  19. Development of kinematic 3D laser scanning system for indoor mapping and as-built BIM using constrained SLAM.

    PubMed

    Jung, Jaehoon; Yoon, Sanghyun; Ju, Sungha; Heo, Joon

    2015-01-01

    The growing interest and use of indoor mapping is driving a demand for improved data-acquisition facility, efficiency and productivity in the era of the Building Information Model (BIM). The conventional static laser scanning method suffers from some limitations on its operability in complex indoor environments, due to the presence of occlusions. Full scanning of indoor spaces without loss of information requires that surveyors change the scanner position many times, which incurs extra work for registration of each scanned point cloud. Alternatively, a kinematic 3D laser scanning system, proposed herein, uses line-feature-based Simultaneous Localization and Mapping (SLAM) technique for continuous mapping. Moreover, to reduce the uncertainty of line-feature extraction, we incorporated constrained adjustment based on an assumption made with respect to typical indoor environments: that the main structures are formed of parallel or orthogonal line features. The superiority of the proposed constrained adjustment is its reduction for uncertainties of the adjusted lines, leading to successful data association process. In the present study, kinematic scanning with and without constrained adjustment were comparatively evaluated in two test sites, and the results confirmed the effectiveness of the proposed system. The accuracy of the 3D mapping result was additionally evaluated by comparison with the reference points acquired by a total station: the Euclidean average distance error was 0.034 m for the seminar room and 0.043 m for the corridor, which satisfied the error tolerance for point cloud acquisition (0.051 m) according to the guidelines of the General Services Administration for BIM accuracy. PMID:26501292

  20. An agent-based multilayer architecture for bioinformatics grids.

    PubMed

    Bartocci, Ezio; Cacciagrano, Diletta; Cannata, Nicola; Corradini, Flavio; Merelli, Emanuela; Milanesi, Luciano; Romano, Paolo

    2007-06-01

    Due to the huge volume and complexity of biological data available today, a fundamental component of biomedical research is now in silico analysis. This includes modelling and simulation of biological systems and processes, as well as automated bioinformatics analysis of high-throughput data. The quest for bioinformatics resources (including databases, tools, and knowledge) becomes therefore of extreme importance. Bioinformatics itself is in rapid evolution and dedicated Grid cyberinfrastructures already offer easier access and sharing of resources. Furthermore, the concept of the Grid is progressively interleaving with those of Web Services, semantics, and software agents. Agent-based systems can play a key role in learning, planning, interaction, and coordination. Agents constitute also a natural paradigm to engineer simulations of complex systems like the molecular ones. We present here an agent-based, multilayer architecture for bioinformatics Grids. It is intended to support both the execution of complex in silico experiments and the simulation of biological systems. In the architecture a pivotal role is assigned to an "alive" semantic index of resources, which is also expected to facilitate users' awareness of the bioinformatics domain. PMID:17695749

  1. Mobyle: a new full web bioinformatics framework

    PubMed Central

    Néron, Bertrand; Ménager, Hervé; Maufrais, Corinne; Joly, Nicolas; Maupetit, Julien; Letort, Sébastien; Carrere, Sébastien; Tuffery, Pierre; Letondal, Catherine

    2009-01-01

    Motivation: For the biologist, running bioinformatics analyses involves a time-consuming management of data and tools. Users need support to organize their work, retrieve parameters and reproduce their analyses. They also need to be able to combine their analytic tools using a safe data flow software mechanism. Finally, given that scientific tools can be difficult to install, it is particularly helpful for biologists to be able to use these tools through a web user interface. However, providing a web interface for a set of tools raises the problem that a single web portal cannot offer all the existing and possible services: it is the user, again, who has to cope with data copy among a number of different services. A framework enabling portal administrators to build a network of cooperating services would therefore clearly be beneficial. Results: We have designed a system, Mobyle, to provide a flexible and usable Web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using a hierarchical typing system. Mobyle offers invocation of services distributed over remote Mobyle servers, thus enabling a federated network of curated bioinformatics portals without the user having to learn complex concepts or to install sophisticated software. While being focused on the end user, the Mobyle system also addresses the need, for the bioinfomatician, to automate remote services execution: PlayMOBY is a companion tool that automates the publication of BioMOBY web services, using Mobyle program definitions. Availability: The Mobyle system is distributed under the terms of the GNU GPLv2 on the project web site (http://bioweb2.pasteur.fr/projects/mobyle/). It is already deployed on three servers: http://mobyle.pasteur.fr, http://mobyle.rpbs.univ-paris-diderot.fr and http://lipm-bioinfo.toulouse.inra.fr/Mobyle. The PlayMOBY companion is distributed under the

  2. Robust Bioinformatics Recognition with VLSI Biochip Microsystem

    NASA Technical Reports Server (NTRS)

    Lue, Jaw-Chyng L.; Fang, Wai-Chi

    2006-01-01

    A microsystem architecture for real-time, on-site, robust bioinformatic patterns recognition and analysis has been proposed. This system is compatible with on-chip DNA analysis means such as polymerase chain reaction (PCR)amplification. A corresponding novel artificial neural network (ANN) learning algorithm using new sigmoid-logarithmic transfer function based on error backpropagation (EBP) algorithm is invented. Our results show the trained new ANN can recognize low fluorescence patterns better than the conventional sigmoidal ANN does. A differential logarithmic imaging chip is designed for calculating logarithm of relative intensities of fluorescence signals. The single-rail logarithmic circuit and a prototype ANN chip are designed, fabricated and characterized.

  3. Bioinformatics in the information age

    SciTech Connect

    Spengler, Sylvia J.

    2000-02-01

    There is a well-known story about the blind man examining the elephant: the part of the elephant examined determines his perception of the whole beast. Perhaps bioinformatics--the shotgun marriage between biology and mathematics, computer science, and engineering--is like an elephant that occupies a large chair in the scientific living room. Given the demand for and shortage of researchers with the computer skills to handle large volumes of biological data, where exactly does the bioinformatics elephant sit? There are probably many biologists who feel that a major product of this bioinformatics elephant is large piles of waste material. If you have tried to plow through Web sites and software packages in search of a specific tool for analyzing and collating large amounts of research data, you may well feel the same way. But there has been progress with major initiatives to develop more computing power, educate biologists about computers, increase funding, and set standards. For our purposes, bioinformatics is not simply a biologically inclined rehash of information theory (1) nor is it a hodgepodge of computer science techniques for building, updating, and accessing biological data. Rather bioinformatics incorporates both of these capabilities into a broad interdisciplinary science that involves both conceptual and practical tools for the understanding, generation, processing, and propagation of biological information. As such, bioinformatics is the sine qua non of 21st-century biology. Analyzing gene expression using cDNA microarrays immobilized on slides or other solid supports (gene chips) is set to revolutionize biology and medicine and, in so doing, generate vast quantities of data that have to be accurately interpreted (Fig. 1). As discussed at a meeting a few months ago (Microarray Algorithms and Statistical Analysis: Methods and Standards; Tahoe City, California; 9-12 November 1999), experiments with cDNA arrays must be subjected to quality control

  4. Built to disappear.

    PubMed

    Bauer, Siegfried; Kaltenbrunner, Martin

    2014-06-24

    Microelectronics dominates the technological and commercial landscape of today's electronics industry; ultrahigh density integrated circuits on rigid silicon provide the computing power for smart appliances that help us organize our daily lives. Integrated circuits function flawlessly for decades, yet we like to replace smart phones and tablet computers every year. Disposable electronics, built to disappear in a controlled fashion after the intended lifespan, may be one of the potential applications of transient single-crystalline silicon nanomembranes, reported by Hwang et al. in this issue of ACS Nano. We briefly outline the development of this latest branch of electronics research, and we present some prospects for future developments. Electronics is steadily evolving, and 20 years from now we may find it perfectly normal for smart appliances to be embedded everywhere, on textiles, on our skin, and even in our body. PMID:24892500

  5. Tools and collaborative environments for bioinformatics research

    PubMed Central

    Giugno, Rosalba; Pulvirenti, Alfredo

    2011-01-01

    Advanced research requires intensive interaction among a multitude of actors, often possessing different expertise and usually working at a distance from each other. The field of collaborative research aims to establish suitable models and technologies to properly support these interactions. In this article, we first present the reasons for an interest of Bioinformatics in this context by also suggesting some research domains that could benefit from collaborative research. We then review the principles and some of the most relevant applications of social networking, with a special attention to networks supporting scientific collaboration, by also highlighting some critical issues, such as identification of users and standardization of formats. We then introduce some systems for collaborative document creation, including wiki systems and tools for ontology development, and review some of the most interesting biological wikis. We also review the principles of Collaborative Development Environments for software and show some examples in Bioinformatics. Finally, we present the principles and some examples of Learning Management Systems. In conclusion, we try to devise some of the goals to be achieved in the short term for the exploitation of these technologies. PMID:21984743

  6. Using Bioinformatics Approach to Explore the Pharmacological Mechanisms of Multiple Ingredients in Shuang-Huang-Lian

    PubMed Central

    Zhang, Bai-xia; Li, Jian; Gu, Hao; Li, Qiang; Zhang, Qi; Zhang, Tian-jiao; Wang, Yun; Cai, Cheng-ke

    2015-01-01

    Due to the proved clinical efficacy, Shuang-Huang-Lian (SHL) has developed a variety of dosage forms. However, the in-depth research on targets and pharmacological mechanisms of SHL preparations was scarce. In the presented study, the bioinformatics approaches were adopted to integrate relevant data and biological information. As a result, a PPI network was built and the common topological parameters were characterized. The results suggested that the PPI network of SHL exhibited a scale-free property and modular architecture. The drug target network of SHL was structured with 21 functional modules. According to certain modules and pharmacological effects distribution, an antitumor effect and potential drug targets were predicted. A biological network which contained 26 subnetworks was constructed to elucidate the antipneumonia mechanism of SHL. We also extracted the subnetwork to explicitly display the pathway where one effective component acts on the pneumonia related targets. In conclusions, a bioinformatics approach was established for exploring the drug targets, pharmacological activity distribution, effective components of SHL, and its mechanism of antipneumonia. Above all, we identified the effective components and disclosed the mechanism of SHL from the view of system. PMID:26495421

  7. Using Bioinformatics Approach to Explore the Pharmacological Mechanisms of Multiple Ingredients in Shuang-Huang-Lian.

    PubMed

    Zhang, Bai-xia; Li, Jian; Gu, Hao; Li, Qiang; Zhang, Qi; Zhang, Tian-jiao; Wang, Yun; Cai, Cheng-ke

    2015-01-01

    Due to the proved clinical efficacy, Shuang-Huang-Lian (SHL) has developed a variety of dosage forms. However, the in-depth research on targets and pharmacological mechanisms of SHL preparations was scarce. In the presented study, the bioinformatics approaches were adopted to integrate relevant data and biological information. As a result, a PPI network was built and the common topological parameters were characterized. The results suggested that the PPI network of SHL exhibited a scale-free property and modular architecture. The drug target network of SHL was structured with 21 functional modules. According to certain modules and pharmacological effects distribution, an antitumor effect and potential drug targets were predicted. A biological network which contained 26 subnetworks was constructed to elucidate the antipneumonia mechanism of SHL. We also extracted the subnetwork to explicitly display the pathway where one effective component acts on the pneumonia related targets. In conclusions, a bioinformatics approach was established for exploring the drug targets, pharmacological activity distribution, effective components of SHL, and its mechanism of antipneumonia. Above all, we identified the effective components and disclosed the mechanism of SHL from the view of system. PMID:26495421

  8. Bioinformatic Insights from Metagenomics through Visualization

    SciTech Connect

    Havre, Susan L.; Webb-Robertson, Bobbie-Jo M.; Shah, Anuj; Posse, Christian; Gopalan, Banu; Brockman, Fred J.

    2005-08-10

    Revised abstract: (remove current and replace with this) Cutting-edge biological and bioinformatics research seeks a systems perspective through the analysis of multiple types of high-throughput and other experimental data for the same sample. Systems-level analysis requires the integration and fusion of such data, typically through advanced statistics and mathematics. Visualization is a complementary com-putational approach that supports integration and analysis of complex data or its derivatives. We present a bioinformatics visualization prototype, Juxter, which depicts categorical information derived from or assigned to these diverse data for the purpose of comparing patterns across categorizations. The visualization allows users to easily discern correlated and anomalous patterns in the data. These patterns, which might not be detected automatically by algorithms, may reveal valuable information leading to insight and discovery. We describe the visualization and interaction capabilities and demonstrate its utility in a new field, metagenomics, which combines molecular biology and genetics to identify and characterize genetic material from multi-species microbial samples.

  9. A reliable, low-cost picture archiving and communications system for small and medium veterinary practices built using open-source technology.

    PubMed

    Iotti, Bryan; Valazza, Alberto

    2014-10-01

    Picture Archiving and Communications Systems (PACS) are the most needed system in a modern hospital. As an integral part of the Digital Imaging and Communications in Medicine (DICOM) standard, they are charged with the responsibility for secure storage and accessibility of the diagnostic imaging data. These machines need to offer high performance, stability, and security while proving reliable and ergonomic in the day-to-day and long-term storage and retrieval of the data they safeguard. This paper reports the experience of the authors in developing and installing a compact and low-cost solution based on open-source technologies in the Veterinary Teaching Hospital for the University of Torino, Italy, during the course of the summer of 2012. The PACS server was built on low-cost x86-based hardware and uses an open source operating system derived from Oracle OpenSolaris (Oracle Corporation, Redwood City, CA, USA) to host the DCM4CHEE PACS DICOM server (DCM4CHEE, http://www.dcm4che.org ). This solution features very high data security and an ergonomic interface to provide easy access to a large amount of imaging data. The system has been in active use for almost 2 years now and has proven to be a scalable, cost-effective solution for practices ranging from small to very large, where the use of different hardware combinations allows scaling to the different deployments, while the use of paravirtualization allows increased security and easy migrations and upgrades. PMID:24793019

  10. Using bioinformatics for drug target identification from the genome.

    PubMed

    Jiang, Zhenran; Zhou, Yanhong

    2005-01-01

    Genomics and proteomics technologies have created a paradigm shift in the drug discovery process, with bioinformatics having a key role in the exploitation of genomic, transcriptomic, and proteomic data to gain insights into the molecular mechanisms that underlie disease and to identify potential drug targets. We discuss the current state of the art for some of the bioinformatic approaches to identifying drug targets, including identifying new members of successful target classes and their functions, predicting disease relevant genes, and constructing gene networks and protein interaction networks. In addition, we introduce drug target discovery using the strategy of systems biology, and discuss some of the data resources for the identification of drug targets. Although bioinformatics tools and resources can be used to identify putative drug targets, validating targets is still a process that requires an understanding of the role of the gene or protein in the disease process and is heavily dependent on laboratory-based work. PMID:16336003

  11. ExPASy: SIB bioinformatics resource portal

    PubMed Central

    Artimo, Panu; Jonnalagedda, Manohar; Arnold, Konstantin; Baratin, Delphine; Csardi, Gabor; de Castro, Edouard; Duvaud, Séverine; Flegel, Volker; Fortier, Arnaud; Gasteiger, Elisabeth; Grosdidier, Aurélien; Hernandez, Céline; Ioannidis, Vassilios; Kuznetsov, Dmitry; Liechti, Robin; Moretti, Sébastien; Mostaguir, Khaled; Redaschi, Nicole; Rossier, Grégoire; Xenarios, Ioannis; Stockinger, Heinz

    2012-01-01

    ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It has now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can henceforth access seamlessly a wide range of resources in many different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics, etc. The individual resources (databases, web-based and downloadable software tools) are hosted in a ‘decentralized’ way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions. Specifically, a single web portal provides a common entry point to a wide range of resources developed and operated by different SIB groups and external institutions. The portal features a search function across ‘selected’ resources. Additionally, the availability and usage of resources are monitored. The portal is aimed for both expert users and people who are not familiar with a specific domain in life sciences. The new web interface provides, in particular, visual guidance for newcomers to ExPASy. PMID:22661580

  12. Bioinformatics in Africa: The Rise of Ghana?

    PubMed

    Karikari, Thomas K

    2015-09-01

    Until recently, bioinformatics, an important discipline in the biological sciences, was largely limited to countries with advanced scientific resources. Nonetheless, several developing countries have lately been making progress in bioinformatics training and applications. In Africa, leading countries in the discipline include South Africa, Nigeria, and Kenya. However, one country that is less known when it comes to bioinformatics is Ghana. Here, I provide a first description of the development of bioinformatics activities in Ghana and how these activities contribute to the overall development of the discipline in Africa. Over the past decade, scientists in Ghana have been involved in publications incorporating bioinformatics analyses, aimed at addressing research questions in biomedical science and agriculture. Scarce research funding and inadequate training opportunities are some of the challenges that need to be addressed for Ghanaian scientists to continue developing their expertise in bioinformatics. PMID:26378921

  13. Bioinformatics in Africa: The Rise of Ghana?

    PubMed Central

    Karikari, Thomas K.

    2015-01-01

    Until recently, bioinformatics, an important discipline in the biological sciences, was largely limited to countries with advanced scientific resources. Nonetheless, several developing countries have lately been making progress in bioinformatics training and applications. In Africa, leading countries in the discipline include South Africa, Nigeria, and Kenya. However, one country that is less known when it comes to bioinformatics is Ghana. Here, I provide a first description of the development of bioinformatics activities in Ghana and how these activities contribute to the overall development of the discipline in Africa. Over the past decade, scientists in Ghana have been involved in publications incorporating bioinformatics analyses, aimed at addressing research questions in biomedical science and agriculture. Scarce research funding and inadequate training opportunities are some of the challenges that need to be addressed for Ghanaian scientists to continue developing their expertise in bioinformatics. PMID:26378921

  14. Active vision and image/video understanding systems built upon network-symbolic models for perception-based navigation of mobile robots in real-world environments

    NASA Astrophysics Data System (ADS)

    Kuvich, Gary

    2004-12-01

    To be completely successful, robots need to have reliable perceptual systems that are similar to human vision. It is hard to use geometric operations for processing of natural images. Instead, the brain builds a relational network-symbolic structure of visual scene, using different clues to set up the relational order of surfaces and objects with respect to the observer and to each other. Feature, symbol, and predicate are equivalent in the biologically inspired Network-Symbolic systems. A linking mechanism binds these features/symbols into coherent structures, and image converts from a "raster" into a "vector" representation. View-based object recognition is a hard problem for traditional algorithms that directly match a primary view of an object to a model. In Network-Symbolic Models, the derived structure, not the primary view, is a subject for recognition. Such recognition is not affected by local changes and appearances of the object as seen from a set of similar views. Once built, the model of visual scene changes slower then local information in the visual buffer. It allows for disambiguating visual information and effective control of actions and navigation via incremental relational changes in visual buffer. Network-Symbolic models can be seamlessly integrated into the NIST 4D/RCS architecture and better interpret images/video for situation awareness, target recognition, navigation and actions.

  15. Effect of electrode position on azo dye removal in an up-flow hybrid anaerobic digestion reactor with built-in bioelectrochemical system

    PubMed Central

    Cui, Min-Hua; Cui, Dan; Lee, Hyung-Sool; Liang, Bin; Wang, Ai-Jie; Cheng, Hao-Yi

    2016-01-01

    In this study, two modes of hybrid anaerobic digestion (AD) bioreactor with built-in BESs (electrodes installed in liquid phase (R1) and sludge phase (R2)) were tested for identifying the effect of electrodes position on azo dye wastewater treatment. Alizarin yellow R (AYR) was used as a model dye. Decolorization efficiency of R1 was 90.41 ± 6.20% at influent loading rate of 800 g-AYR/ m3·d, which was 39% higher than that of R2. The contribution of bioelectrochemical reduction to AYR decolorization (16.23 ± 1.86% for R1 versus 22.24 ± 2.14% for R2) implied that although azo dye was mainly removed in sludge zone, BES further improved the effluent quality, especially for R1 where electrodes were installed in liquid phase. The microbial communities in the electrode biofilms (dominant by Enterobacter) and sludge (dominant by Enterococcus) were well distinguished in R1, but they were similar in R2. These results suggest that electrodes installed in liquid phase in the anaerobic hybrid system are more efficient than that in sludge phase for azo dye removal, which give great inspirations for the application of AD-BES hybrid process for various refractory wastewaters treatment. PMID:27121278

  16. Effect of electrode position on azo dye removal in an up-flow hybrid anaerobic digestion reactor with built-in bioelectrochemical system.

    PubMed

    Cui, Min-Hua; Cui, Dan; Lee, Hyung-Sool; Liang, Bin; Wang, Ai-Jie; Cheng, Hao-Yi

    2016-01-01

    In this study, two modes of hybrid anaerobic digestion (AD) bioreactor with built-in BESs (electrodes installed in liquid phase (R1) and sludge phase (R2)) were tested for identifying the effect of electrodes position on azo dye wastewater treatment. Alizarin yellow R (AYR) was used as a model dye. Decolorization efficiency of R1 was 90.41 ± 6.20% at influent loading rate of 800 g-AYR/ m(3)·d, which was 39% higher than that of R2. The contribution of bioelectrochemical reduction to AYR decolorization (16.23 ± 1.86% for R1 versus 22.24 ± 2.14% for R2) implied that although azo dye was mainly removed in sludge zone, BES further improved the effluent quality, especially for R1 where electrodes were installed in liquid phase. The microbial communities in the electrode biofilms (dominant by Enterobacter) and sludge (dominant by Enterococcus) were well distinguished in R1, but they were similar in R2. These results suggest that electrodes installed in liquid phase in the anaerobic hybrid system are more efficient than that in sludge phase for azo dye removal, which give great inspirations for the application of AD-BES hybrid process for various refractory wastewaters treatment. PMID:27121278

  17. Optimisation and analysis of microreactor designs for microfluidic gradient generation using a purpose built optical detection system for entire chip imaging.

    PubMed

    Abdulla Yusuf, Hayat; Baldock, Sara J; Barber, Robert W; Fielden, Peter R; Goddard, Nick J; Mohr, Stephan; Treves Brown, Bernard J

    2009-07-01

    This paper presents and fully characterises a novel simplification approach for the development of microsystem based concentration gradient generators with significantly reduced microfluidic networks. Three microreactors are presented; a pair of two-inlet six-outlet (2-6) networks and a two-inlet eleven-outlet (2-11) network design. The mathematical approach has been validated experimentally using a purpose built optical detection system. The experimental results are shown to be in very good agreement with the theoretical predictions from the model. The developed networks are proven to deliver precise linear concentration gradients (R(2) = 0.9973 and 0.9991 for the (2-6) designs) and the simplified networks are shown to provide enhanced performance over conventional designs, overcoming some of the practical issues associated with traditional networks. The optical measurements were precise enough to validate the linearity in each level of the conventional (2-6) networks (R(2) ranged from 0.9999 to 0.9973) compared to R(2) = 1 for the theoretical model. CFD results show that there is an effective upper limit on the operating flow rate. The new simplified (2-11) design was able to maintain a linear outlet profile up to 0.8 microl/s per inlet (R(2) = 0.9992). The proposed approach is widely applicable for the production of linear and arbitrary concentration profiles, with the potential for high throughput applications that span a wide range of chemical and biological studies. PMID:19532963

  18. Nuclear reactors built, being built, or planned 1992

    SciTech Connect

    Not Available

    1993-07-01

    Nuclear Reactors Built, Being Built, or Planned contains unclassified information about facilities built, being built, or planned in the United States for domestic use or export as of December 31, 1992. The Office of Scientific and Technical Information, US Department of Energy, gathers this information annually from Washington headquarters and field offices of DOE from the US Nuclear Regulatory Commission (NRC); from the US reactor manufacturers who are the principal nuclear contractors for foreign reactor locations; from US and foreign embassies; and from foreign governmental nuclear departments. Information is presented on five parts: Civilian, Production, Military, Export and Critical Assembly.

  19. Genomics and Bioinformatics Resources for Crop Improvement

    PubMed Central

    Mochida, Keiichi; Shinozaki, Kazuo

    2010-01-01

    Recent remarkable innovations in platforms for omics-based research and application development provide crucial resources to promote research in model and applied plant species. A combinatorial approach using multiple omics platforms and integration of their outcomes is now an effective strategy for clarifying molecular systems integral to improving plant productivity. Furthermore, promotion of comparative genomics among model and applied plants allows us to grasp the biological properties of each species and to accelerate gene discovery and functional analyses of genes. Bioinformatics platforms and their associated databases are also essential for the effective design of approaches making the best use of genomic resources, including resource integration. We review recent advances in research platforms and resources in plant omics together with related databases and advances in technology. PMID:20208064

  20. Postgenomics: Proteomics and Bioinformatics in Cancer Research

    PubMed Central

    2003-01-01

    Now that the human genome is completed, the characterization of the proteins encoded by the sequence remains a challenging task. The study of the complete protein complement of the genome, the “proteome,” referred to as proteomics, will be essential if new therapeutic drugs and new disease biomarkers for early diagnosis are to be developed. Research efforts are already underway to develop the technology necessary to compare the specific protein profiles of diseased versus nondiseased states. These technologies provide a wealth of information and rapidly generate large quantities of data. Processing the large amounts of data will lead to useful predictive mathematical descriptions of biological systems which will permit rapid identification of novel therapeutic targets and identification of metabolic disorders. Here, we present an overview of the current status and future research approaches in defining the cancer cell's proteome in combination with different bioinformatics and computational biology tools toward a better understanding of health and disease. PMID:14615629

  1. Rapid Development of Bioinformatics Education in China

    ERIC Educational Resources Information Center

    Zhong, Yang; Zhang, Xiaoyan; Ma, Jian; Zhang, Liang

    2003-01-01

    As the Human Genome Project experiences remarkable success and a flood of biological data is produced, bioinformatics becomes a very "hot" cross-disciplinary field, yet experienced bioinformaticians are urgently needed worldwide. This paper summarises the rapid development of bioinformatics education in China, especially related undergraduate…

  2. Biology in 'silico': The Bioinformatics Revolution.

    ERIC Educational Resources Information Center

    Bloom, Mark

    2001-01-01

    Explains the Human Genome Project (HGP) and efforts to sequence the human genome. Describes the role of bioinformatics in the project and considers it the genetics Swiss Army Knife, which has many different uses, for use in forensic science, medicine, agriculture, and environmental sciences. Discusses the use of bioinformatics in the high school…

  3. Online Bioinformatics Tutorials | Office of Cancer Genomics

    Cancer.gov

    Bioinformatics is a scientific discipline that applies computer science and information technology to help understand biological processes. The NIH provides a list of free online bioinformatics tutorials, either generated by the NIH Library or other institutes, which includes introductory lectures and "how to" videos on using various tools.

  4. Fuzzy Logic in Medicine and Bioinformatics

    PubMed Central

    Torres, Angela; Nieto, Juan J.

    2006-01-01

    The purpose of this paper is to present a general view of the current applications of fuzzy logic in medicine and bioinformatics. We particularly review the medical literature using fuzzy logic. We then recall the geometrical interpretation of fuzzy sets as points in a fuzzy hypercube and present two concrete illustrations in medicine (drug addictions) and in bioinformatics (comparison of genomes). PMID:16883057

  5. A Mathematical Optimization Problem in Bioinformatics

    ERIC Educational Resources Information Center

    Heyer, Laurie J.

    2008-01-01

    This article describes the sequence alignment problem in bioinformatics. Through examples, we formulate sequence alignment as an optimization problem and show how to compute the optimal alignment with dynamic programming. The examples and sample exercises have been used by the author in a specialized course in bioinformatics, but could be adapted…

  6. Using "Arabidopsis" Genetic Sequences to Teach Bioinformatics

    ERIC Educational Resources Information Center

    Zhang, Xiaorong

    2009-01-01

    This article describes a new approach to teaching bioinformatics using "Arabidopsis" genetic sequences. Several open-ended and inquiry-based laboratory exercises have been designed to help students grasp key concepts and gain practical skills in bioinformatics, using "Arabidopsis" leucine-rich repeat receptor-like kinase (LRR RLK) genetic…

  7. Nuclear reactors built, being built, or planned 1993

    SciTech Connect

    Not Available

    1993-08-01

    Nuclear Reactors Built, Being Built, or Planned contains unclassified information about facilities built, being built, or planned in the United States for domestic use or export as of December 31, 1993. The Office of Scientific and Technical Information, US Department of Energy, gathers this information annually from Washington headquarters and field offices of DOE; from the US Nuclear Regulatory Commission (NRC); from the US reactor manufacturers who are the principal nuclear embassies; and from foreign governmental nuclear departments. The book consists of three divisions, as follows: (1) a commercial reactor locator map and tables of the characteristic and statistical data that follow; a table of abbreviations; (2) tables of data for reactors operating, being built, or planned; and (3) tables of data for reactors that have been shut down permanently or dismantled. The reactors are subdivided into the following parts: civilian, production, military, export, and critical assembly.

  8. Bioinformatics clouds for big data manipulation

    PubMed Central

    2012-01-01

    Abstract As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computing infrastructure into utility-supplied cloud computing delivered over the Internet, in order to handle the vast quantities of biological data generated by high-throughput experimental technologies. Albeit relatively new, cloud computing promises to address big data storage and analysis issues in the bioinformatics field. Here we review extant cloud-based services in bioinformatics, classify them into Data as a Service (DaaS), Software as a Service (SaaS), Platform as a Service (PaaS), and Infrastructure as a Service (IaaS), and present our perspectives on the adoption of cloud computing in bioinformatics. Reviewers This article was reviewed by Frank Eisenhaber, Igor Zhulin, and Sandor Pongor. PMID:23190475

  9. Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

    SciTech Connect

    Ditty, Jayna L.; Kvaal, Christopher A.; Goodner, Brad; Freyermuth, Sharyn K.; Bailey, Cheryl; Britton, Robert A.; Gordon, Stuart G.; Heinhorst, Sabine; Reed, Kelynne; Xu, Zhaohui; Sanders-Lorenz, Erin R.; Axen, Seth; Kim, Edwin; Johns, Mitrick; Scott, Kathleen; Kerfeld, Cheryl A.

    2011-08-01

    courses or independent research projects requires infrastructure for organizing and assessing student work. Here, we present a new platform for faculty to keep current with the rapidly changing field of bioinformatics, the Integrated Microbial Genomes Annotation Collaboration Toolkit (IMG-ACT). It was developed by instructors from both research-intensive and predominately undergraduate institutions in collaboration with the Department of Energy-Joint Genome Institute (DOE-JGI) as a means to innovate and update undergraduate education and faculty development. The IMG-ACT program provides a cadre of tools, including access to a clearinghouse of genome sequences, bioinformatics databases, data storage, instructor course management, and student notebooks for organizing the results of their bioinformatic investigations. In the process, IMG-ACT makes it feasible to provide undergraduate research opportunities to a greater number and diversity of students, in contrast to the traditional mentor-to-student apprenticeship model for undergraduate research, which can be too expensive and time-consuming to provide for every undergraduate. The IMG-ACT serves as the hub for the network of faculty and students that use the system for microbial genome analysis. Open access of the IMG-ACT infrastructure to participating schools ensures that all types of higher education institutions can utilize it. With the infrastructure in place, faculty can focus their efforts on the pedagogy of bioinformatics, involvement of students in research, and use of this tool for their own research agenda. What the original faculty members of the IMG-ACT development team present here is an overview of how the IMG-ACT program has affected our development in terms of teaching and research with the hopes that it will inspire more faculty to get involved.

  10. 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

  11. Bioinformatic challenges in targeted proteomics.

    PubMed

    Reker, Daniel; Malmström, Lars

    2012-09-01

    Selected reaction monitoring mass spectrometry is an emerging targeted proteomics technology that allows for the investigation of complex protein samples with high sensitivity and efficiency. It requires extensive knowledge about the sample for the many parameters needed to carry out the experiment to be set appropriately. Most studies today rely on parameter estimation from prior studies, public databases, or from measuring synthetic peptides. This is efficient and sound, but in absence of prior data, de novo parameter estimation is necessary. Computational methods can be used to create an automated framework to address this problem. However, the number of available applications is still small. This review aims at giving an orientation on the various bioinformatical challenges. To this end, we state the problems in classical machine learning and data mining terms, give examples of implemented solutions and provide some room for alternatives. This will hopefully lead to an increased momentum for the development of algorithms and serve the needs of the community for computational methods. We note that the combination of such methods in an assisted workflow will ease both the usage of targeted proteomics in experimental studies as well as the further development of computational approaches. PMID:22866949

  12. An approach to regional wetland digital elevation model development using a differential global positioning system and a custom-built helicopter-based surveying system

    USGS Publications Warehouse

    Jones, J.W.; Desmond, G.B.; Henkle, C.; Glover, R.

    2012-01-01

    Accurate topographic data are critical to restoration science and planning for the Everglades region of South Florida, USA. They are needed to monitor and simulate water level, water depth and hydroperiod and are used in scientific research on hydrologic and biologic processes. Because large wetland environments and data acquisition challenge conventional ground-based and remotely sensed data collection methods, the United States Geological Survey (USGS) adapted a classical data collection instrument to global positioning system (GPS) and geographic information system (GIS) technologies. Data acquired with this instrument were processed using geostatistics to yield sub-water level elevation values with centimetre accuracy (??15 cm). The developed database framework, modelling philosophy and metadata protocol allow for continued, collaborative model revision and expansion, given additional elevation or other ancillary data. ?? 2012 Taylor & Francis.

  13. Smart built-in test

    NASA Technical Reports Server (NTRS)

    Richards, Dale W.

    1990-01-01

    The work which built-in test (BIT) is asked to perform in today's electronic systems increases with every insertion of new technology or introduction of tighter performance criteria. Yet the basic purpose remains unchanged -- to determine with high confidence the operational capability of that equipment. Achievement of this level of BIT performance requires the management and assimilation of a large amount of data, both realtime and historical. Smart BIT has taken advantage of advanced techniques from the field of artificial intelligence (AI) in order to meet these demands. The Smart BIT approach enhances traditional functional BIT by utilizing AI techniques to incorporate environmental stress data, temporal BIT information and maintenance data, and realtime BIT reports into an integrated test methodology for increased BIT effectiveness and confidence levels. Future research in this area will incorporate onboard fault-logging of BIT output, stress data and Smart BIT decision criteria in support of a singular, integrated and complete test and maintenance capability. The state of this research is described along with a discussion of directions for future development.

  14. Bioinformatics and the undergraduate curriculum essay.

    PubMed

    Maloney, Mark; Parker, Jeffrey; Leblanc, Mark; Woodard, Craig T; Glackin, Mary; Hanrahan, Michael

    2010-01-01

    Recent advances involving high-throughput techniques for data generation and analysis have made familiarity with basic bioinformatics concepts and programs a necessity in the biological sciences. Undergraduate students increasingly need training in methods related to finding and retrieving information stored in vast databases. The rapid rise of bioinformatics as a new discipline has challenged many colleges and universities to keep current with their curricula, often in the face of static or dwindling resources. On the plus side, many bioinformatics modules and related databases and software programs are free and accessible online, and interdisciplinary partnerships between existing faculty members and their support staff have proved advantageous in such efforts. We present examples of strategies and methods that have been successfully used to incorporate bioinformatics content into undergraduate curricula. PMID:20810947

  15. Bioinformatics Visualisation Tools: An Unbalanced Picture.

    PubMed

    Broască, Laura; Ancuşa, Versavia; Ciocârlie, Horia

    2016-01-01

    Visualization tools represent a key element in triggering human creativity while being supported with the analysis power of the machine. This paper analyzes free network visualization tools for bioinformatics, frames them in domain specific requirements and compares them. PMID:27577488

  16. Bioinformatics in Italy: BITS2011, the Eighth Annual Meeting of the Italian Society of Bioinformatics

    PubMed Central

    2012-01-01

    The BITS2011 meeting, held in Pisa on June 20-22, 2011, brought together more than 120 Italian researchers working in the field of Bioinformatics, as well as students in Bioinformatics, Computational Biology, Biology, Computer Sciences, and Engineering, representing a landscape of Italian bioinformatics research. This preface provides a brief overview of the meeting and introduces the peer-reviewed manuscripts that were accepted for publication in this Supplement. PMID:22536954

  17. Nuclear reactors built, being built, or planned, 1991

    SciTech Connect

    Simpson, B.

    1992-07-01

    This document contains unclassified information about facilities built, being built, or planned in the United States for domestic use or export as of December 31, 1991. The book is divided into three major sections: Section 1 consists of a reactor locator map and reactor tables; Section 2 includes nuclear reactors that are operating, being built, or planned; and Section 3 includes reactors that have been shut down permanently or dismantled. Sections 2 and 3 contain the following classification of reactors: Civilian, Production, Military, Export, and Critical Assembly. Export reactor refers to a reactor for which the principal nuclear contractor is an American company -- working either independently or in cooperation with a foreign company (Part 4, in each section). Critical assembly refers to an assembly of fuel and assembly of fuel and moderator that requires an external source of neutrons to initiate and maintain fission. A critical assembly is used for experimental measurements (Part 5).

  18. Nuclear reactors built, being built, or planned 1996

    SciTech Connect

    1997-08-01

    This publication contains unclassified information about facilities, built, being built, or planned in the United States for domestic use or export as of December 31, 1996. The Office of Scientific and Technical Information, U.S. Department of Energy, gathers this information annually from Washington headquarters, and field offices of DOE; from the U.S. Nuclear Regulatory Commission (NRC); from the U. S. reactor manufacturers who are the principal nuclear contractors for foreign reactor locations; from U.S. and foreign embassies; and from foreign governmental nuclear departments. The book consists of three divisions, as follows: (1) a commercial reactor locator map and tables of the characteristic and statistical data that follow; a table of abbreviations; (2) tables of data for reactors operating, being built, or planned; and (3) tables of data for reactors that have been shut down permanently or dismantled.

  19. Multichannel Analyzer Built from a Microcomputer.

    ERIC Educational Resources Information Center

    Spencer, C. D.; Mueller, P.

    1979-01-01

    Describes a multichannel analyzer built using eight-bit S-100 bus microcomputer hardware. The output modes are an oscilloscope display, print data, and send data to another computer. Discusses the system's hardware, software, costs, and advantages relative to commercial multichannels. (Author/GA)

  20. Bioinformatics process management: information flow via a computational journal

    PubMed Central

    Feagan, Lance; Rohrer, Justin; Garrett, Alexander; Amthauer, Heather; Komp, Ed; Johnson, David; Hock, Adam; Clark, Terry; Lushington, Gerald; Minden, Gary; Frost, Victor

    2007-01-01

    This paper presents the Bioinformatics Computational Journal (BCJ), a framework for conducting and managing computational experiments in bioinformatics and computational biology. These experiments often involve series of computations, data searches, filters, and annotations which can benefit from a structured environment. Systems to manage computational experiments exist, ranging from libraries with standard data models to elaborate schemes to chain together input and output between applications. Yet, although such frameworks are available, their use is not widespread–ad hoc scripts are often required to bind applications together. The BCJ explores another solution to this problem through a computer based environment suitable for on-site use, which builds on the traditional laboratory notebook paradigm. It provides an intuitive, extensible paradigm designed for expressive composition of applications. Extensive features facilitate sharing data, computational methods, and entire experiments. By focusing on the bioinformatics and computational biology domain, the scope of the computational framework was narrowed, permitting us to implement a capable set of features for this domain. This report discusses the features determined critical by our system and other projects, along with design issues. We illustrate the use of our implementation of the BCJ on two domain-specific examples. PMID:18053179

  1. ESF AS-BUILT CONFIGURATION

    SciTech Connect

    NA

    2005-03-17

    The calculations contained in this document were developed by the ''Mining Group of the Design & Engineering Organization'' and are intended solely for the use of the ''Design & Engineering Organization'' in its work regarding the subsurface repository. Yucca Mountain Project personnel from the ''Mining Group'' should be consulted before use of the calculations for purposes other than those stated herein or use by individuals other than authorized personnel in the ''Design & Engineering Organization''. The purpose of this calculation is to provide design inputs that can be used to develop an as-built drawing of the Exploratory Studies Facility (ESF) for the planning and development of the subsurface repository. This document includes subsurface as-built surveys, recommendation to complete as-built surveys, and Management and Operating Contractor (M&O) Subsurface Design Drawings as inputs. This calculation is used to provide data and information for an as-built ESF subsurface drawing and is not used in the development of results or conclusions, therefore all inputs are considered as indirect.

  2. A Guide to Bioinformatics for Immunologists

    PubMed Central

    Whelan, Fiona J.; Yap, Nicholas V. L.; Surette, Michael G.; Golding, G. Brian; Bowdish, Dawn M. E.

    2013-01-01

    Bioinformatics includes a suite of methods, which are cheap, approachable, and many of which are easily accessible without any sort of specialized bioinformatic training. Yet, despite this, bioinformatic tools are under-utilized by immunologists. Herein, we review a representative set of publicly available, easy-to-use bioinformatic tools using our own research on an under-annotated human gene, SCARA3, as an example. SCARA3 shares an evolutionary relationship with the class A scavenger receptors, but preliminary research showed that it was divergent enough that its function remained unclear. In our quest for more information about this gene – did it share gene sequence similarities to other scavenger receptors? Did it contain conserved protein domains? Where was it expressed in the human body? – we discovered the power and informative potential of publicly available bioinformatic tools designed for the novice in mind, which allowed us to hypothesize on the regulation, structure, and function of this protein. We argue that these tools are largely applicable to many facets of immunology research. PMID:24363654

  3. Carving a niche: establishing bioinformatics collaborations

    PubMed Central

    Lyon, Jennifer A.; Tennant, Michele R.; Messner, Kevin R.; Osterbur, David L.

    2006-01-01

    Objectives: The paper describes collaborations and partnerships developed between library bioinformatics programs and other bioinformatics-related units at four academic institutions. Methods: A call for information on bioinformatics partnerships was made via email to librarians who have participated in the National Center for Biotechnology Information's Advanced Workshop for Bioinformatics Information Specialists. Librarians from Harvard University, the University of Florida, the University of Minnesota, and Vanderbilt University responded and expressed willingness to contribute information on their institutions, programs, services, and collaborating partners. Similarities and differences in programs and collaborations were identified. Results: The four librarians have developed partnerships with other units on their campuses that can be categorized into the following areas: knowledge management, instruction, and electronic resource support. All primarily support freely accessible electronic resources, while other campus units deal with fee-based ones. These demarcations are apparent in resource provision as well as in subsequent support and instruction. Conclusions and Recommendations: Through environmental scanning and networking with colleagues, librarians who provide bioinformatics support can develop fruitful collaborations. Visibility is key to building collaborations, as is broad-based thinking in terms of potential partners. PMID:16888668

  4. Nuclear reactors built, being built, or planned, 1994

    SciTech Connect

    1995-07-01

    This document contains unclassified information about facilities built, being built, or planned in the United States for domestic use or export as of December 31, 1994. The Office of Scientific and Technical Information, US Department of Energy, gathers this information annually from Washington headquarters and field offices of DOE; from the US Nuclear Regulatory Commission (NRC); from the US reactor manufacturers who are the principal nuclear contractors for foreign reactor locations; from US and foreign embassies; and from foreign governmental nuclear departments. The book consists of three divisions, as follows: a commercial reactor locator map and tables of the characteristic and statistical data that follow; a table of abbreviations; tables of data for reactors operating, being built, or planned; and tables of data for reactors that have been shut down permanently or dismantled. The reactors are subdivided into the following parts: Civilian, Production, Military, Export, and Critical Assembly. Export reactor refers to a reactor for which the principal nuclear contractor is a US company -- working either independently or in cooperation with a foreign company (Part 4). Critical assembly refers to an assembly of fuel and moderator that requires an external source of neutrons to initiate and maintain fission. A critical assembly is used for experimental measurements (Part 5).

  5. Nuclear reactors built, being built, or planned: 1995

    SciTech Connect

    1996-08-01

    This report contains unclassified information about facilities built, being built, or planned in the US for domestic use or export as of December 31, 1995. The Office of Scientific and Technical Information, US Department of Energy, gathers this information annually from Washington headquarters and field offices of DOE; from the US Nuclear Regulatory Commission (NRC); from the US reactor manufacturers who are the principal nuclear contractors for foreign reactor locations; from US and foreign embassies; and from foreign governmental nuclear departments. The book consists of three divisions, as follows: (1) a commercial reactor locator map and tables of the characteristic and statistical data that follow; a table of abbreviations; (2) tables of data for reactors operating, being built, or planned; and (3) tables of data for reactors that have been shut down permanently or dismantled. The reactors are subdivided into the following parts: Civilian, Production, Military, Export, and Critical Assembly. Export reactor refers to a reactor for which the principal nuclear contractor is a US company--working either independently or in cooperation with a foreign company (Part 4). Critical assembly refers to an assembly of fuel and moderator that requires an external source of neutrons to initiate and maintain fission. A critical assembly is used for experimental measurements (Part 5).

  6. Bioinformatics-enabled identification of the HrpL regulon and type III secretion system effector proteins of Pseudomonas syringae pv. phaseolicola 1448A

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The ability of Pseudomonas syringae pv. phaseolicola to cause halo blight of bean is dependent on its ability to translocate effector proteins into host cells via the Hrp type III secretion system (T3SS). To identity genes encoding type III effectors and other potential virulence factors that are r...

  7. A Quick Guide for Building a Successful Bioinformatics Community

    PubMed Central

    Budd, Aidan; Corpas, Manuel; Brazas, Michelle D.; Fuller, Jonathan C.; Goecks, Jeremy; Mulder, Nicola J.; Michaut, Magali; Ouellette, B. F. Francis; Pawlik, Aleksandra; Blomberg, Niklas

    2015-01-01

    “Scientific community” refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding activities; (iv) interactions and engagement with professionals from other fields; and (v) other activities beneficial to individual participants, communities, and the scientific field as a whole. It is thus beneficial at many different levels to understand the general features of successful, high-impact bioinformatics communities; how individual participants can contribute to the success of these communities; and the role of education and training within these communities. We present here a quick guide to building and maintaining a successful, high-impact bioinformatics community, along with an overview of the general benefits of participating in such communities. This article grew out of contributions made by organizers, presenters, panelists, and other participants of the ISMB/ECCB 2013 workshop “The ‘How To Guide’ for Establishing a Successful Bioinformatics Network” at the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 12th European Conference on Computational Biology (ECCB). PMID:25654371

  8. A quick guide for building a successful bioinformatics community.

    PubMed

    Budd, Aidan; Corpas, Manuel; Brazas, Michelle D; Fuller, Jonathan C; Goecks, Jeremy; Mulder, Nicola J; Michaut, Magali; Ouellette, B F Francis; Pawlik, Aleksandra; Blomberg, Niklas

    2015-02-01

    "Scientific community" refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding activities; (iv) interactions and engagement with professionals from other fields; and (v) other activities beneficial to individual participants, communities, and the scientific field as a whole. It is thus beneficial at many different levels to understand the general features of successful, high-impact bioinformatics communities; how individual participants can contribute to the success of these communities; and the role of education and training within these communities. We present here a quick guide to building and maintaining a successful, high-impact bioinformatics community, along with an overview of the general benefits of participating in such communities. This article grew out of contributions made by organizers, presenters, panelists, and other participants of the ISMB/ECCB 2013 workshop "The 'How To Guide' for Establishing a Successful Bioinformatics Network" at the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 12th European Conference on Computational Biology (ECCB). PMID:25654371

  9. Built Environment Wind Turbine Roadmap

    SciTech Connect

    Smith, J.; Forsyth, T.; Sinclair, K.; Oteri, F.

    2012-11-01

    The market currently encourages BWT deployment before the technology is ready for full-scale commercialization. To address this issue, industry stakeholders convened a Rooftop and Built-Environment Wind Turbine Workshop on August 11 - 12, 2010, at the National Wind Technology Center, located at the U.S. Department of Energy’s National Renewable Energy Laboratory in Boulder, Colorado. This report summarizes the workshop.

  10. Response of mollusc assemblages to climate variability and anthropogenic activities: a 4000-year record from a shallow bar-built lagoon system.

    PubMed

    Cerrato, Robert M; Locicero, Philip V; Goodbred, Steven L

    2013-10-01

    With their position at the interface between land and ocean and their fragile nature, lagoons are sensitive to environmental change, and it is reasonable to expect these changes would be recorded in well-preserved taxa such as molluscs. To test this, the 4000-year history of molluscs in Great South Bay, a bar-built lagoon, was reconstructed from 24 vibracores. Using x-radiography to identify shell layers, faunal counts, shell condition, organic content, and sediment type were measured in 325 samples. Sample age was estimated by interpolating 40 radiocarbon dates. K-means cluster analysis identified three molluscan assemblages, corresponding to sand-associated and mud-associated groups, and the third associated with inlet areas. Redundancy and regression tree analyses indicated that significant transitions from the sand-associated to mud-associated assemblage occurred over large portions of the bay about 650 and 294 years bp. The first date corresponds to the transition from the Medieval Warm Period to the Little Ice Age; this change in climate reduced the frequency of strong storms, likely leading to reduced barrier island breaching, greater bay enclosure, and fine-grained sediment accumulation. The second date marks the initiation of clear cutting by European settlers, an activity that would have increased runoff of fine-grained material. The occurrence of the inlet assemblage in the western and eastern ends of the bay is consistent with a history of inlets in these areas, even though prior to Hurricane Sandy in 2012, no inlet was present in the eastern bay in almost 200 years. The mud dominant, Mulinia lateralis, is a bivalve often associated with environmental disturbances. Its increased frequency over the past 300 years suggests that disturbances are more common in the bay than in the past. Management activities maintaining the current barrier island state may be contributing to the sand-mud transition and to the bay's susceptibility to disturbances. PMID

  11. Implementing bioinformatic workflows within the bioextract server

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Computational workflows in bioinformatics are becoming increasingly important in the achievement of scientific advances. These workflows typically require the integrated use of multiple, distributed data sources and analytic tools. The BioExtract Server (http://bioextract.org) is a distributed servi...

  12. Bioinformatics in Undergraduate Education: Practical Examples

    ERIC Educational Resources Information Center

    Boyle, John A.

    2004-01-01

    Bioinformatics has emerged as an important research tool in recent years. The ability to mine large databases for relevant information has become increasingly central to many different aspects of biochemistry and molecular biology. It is important that undergraduates be introduced to the available information and methodologies. We present a…

  13. SPECIES DATABASES AND THE BIOINFORMATICS REVOLUTION.

    EPA Science Inventory

    Biological databases are having a growth spurt. Much of this results from research in genetics and biodiversity, coupled with fast-paced developments in information technology. The revolution in bioinformatics, defined by Sugden and Pennisi (2000) as the "tools and techniques for...

  14. Privacy Preserving PCA on Distributed Bioinformatics Datasets

    ERIC Educational Resources Information Center

    Li, Xin

    2011-01-01

    In recent years, new bioinformatics technologies, such as gene expression microarray, genome-wide association study, proteomics, and metabolomics, have been widely used to simultaneously identify a huge number of human genomic/genetic biomarkers, generate a tremendously large amount of data, and dramatically increase the knowledge on human…

  15. Bioinformatics: A History of Evolution "In Silico"

    ERIC Educational Resources Information Center

    Ondrej, Vladan; Dvorak, Petr

    2012-01-01

    Bioinformatics, biological databases, and the worldwide use of computers have accelerated biological research in many fields, such as evolutionary biology. Here, we describe a primer of nucleotide sequence management and the construction of a phylogenetic tree with two examples; the two selected are from completely different groups of organisms:…

  16. "Extreme Programming" in a Bioinformatics Class

    ERIC Educational Resources Information Center

    Kelley, Scott; Alger, Christianna; Deutschman, Douglas

    2009-01-01

    The importance of Bioinformatics tools and methodology in modern biological research underscores the need for robust and effective courses at the college level. This paper describes such a course designed on the principles of cooperative learning based on a computer software industry production model called "Extreme Programming" (EP). The…

  17. 2010 Translational bioinformatics year in review

    PubMed Central

    Miller, Katharine S

    2011-01-01

    A review of 2010 research in translational bioinformatics provides much to marvel at. We have seen notable advances in personal genomics, pharmacogenetics, and sequencing. At the same time, the infrastructure for the field has burgeoned. While acknowledging that, according to researchers, the members of this field tend to be overly optimistic, the authors predict a bright future. PMID:21672905

  18. Navigating the changing learning landscape: perspective from bioinformatics.ca

    PubMed Central

    Ouellette, B. F. Francis

    2013-01-01

    With the advent of YouTube channels in bioinformatics, open platforms for problem solving in bioinformatics, active web forums in computing analyses and online resources for learning to code or use a bioinformatics tool, the more traditional continuing education bioinformatics training programs have had to adapt. Bioinformatics training programs that solely rely on traditional didactic methods are being superseded by these newer resources. Yet such face-to-face instruction is still invaluable in the learning continuum. Bioinformatics.ca, which hosts the Canadian Bioinformatics Workshops, has blended more traditional learning styles with current online and social learning styles. Here we share our growing experiences over the past 12 years and look toward what the future holds for bioinformatics training programs. PMID:23515468

  19. Navigating the changing learning landscape: perspective from bioinformatics.ca.

    PubMed

    Brazas, Michelle D; Ouellette, B F Francis

    2013-09-01

    With the advent of YouTube channels in bioinformatics, open platforms for problem solving in bioinformatics, active web forums in computing analyses and online resources for learning to code or use a bioinformatics tool, the more traditional continuing education bioinformatics training programs have had to adapt. Bioinformatics training programs that solely rely on traditional didactic methods are being superseded by these newer resources. Yet such face-to-face instruction is still invaluable in the learning continuum. Bioinformatics.ca, which hosts the Canadian Bioinformatics Workshops, has blended more traditional learning styles with current online and social learning styles. Here we share our growing experiences over the past 12 years and look toward what the future holds for bioinformatics training programs. PMID:23515468

  20. A Bioinformatics Reference Model: Towards a Framework for Developing and Organising Bioinformatic Resources

    NASA Astrophysics Data System (ADS)

    Hiew, Hong Liang; Bellgard, Matthew

    2007-11-01

    Life Science research faces the constant challenge of how to effectively handle an ever-growing body of bioinformatics software and online resources. The users and developers of bioinformatics resources have a diverse set of competing demands on how these resources need to be developed and organised. Unfortunately, there does not exist an adequate community-wide framework to integrate such competing demands. The problems that arise from this include unstructured standards development, the emergence of tools that do not meet specific needs of researchers, and often times a communications gap between those who use the tools and those who supply them. This paper presents an overview of the different functions and needs of bioinformatics stakeholders to determine what may be required in a community-wide framework. A Bioinformatics Reference Model is proposed as a basis for such a framework. The reference model outlines the functional relationship between research usage and technical aspects of bioinformatics resources. It separates important functions into multiple structured layers, clarifies how they relate to each other, and highlights the gaps that need to be addressed for progress towards a diverse, manageable, and sustainable body of resources. The relevance of this reference model to the bioscience research community, and its implications in progress for organising our bioinformatics resources, are discussed.

  1. Bioinformatic characterization of plant networks

    SciTech Connect

    McDermott, Jason E.; Samudrala, Ram

    2008-06-30

    Cells and organisms are governed by networks of interactions, genetic, physical and metabolic. Large-scale experimental studies of interactions between components of biological systems have been performed for a variety of eukaryotic organisms. However, there is a dearth of such data for plants. Computational methods for prediction of relationships between proteins, primarily based on comparative genomics, provide a useful systems-level view of cellular functioning and can be used to extend information about other eukaryotes to plants. We have predicted networks for Arabidopsis thaliana, Oryza sativa indica and japonica and several plant pathogens using the Bioverse (http://bioverse.compbio.washington.edu) and show that they are similar to experimentally-derived interaction networks. Predicted interaction networks for plants can be used to provide novel functional annotations and predictions about plant phenotypes and aid in rational engineering of biosynthesis pathways.

  2. Composable languages for bioinformatics: the NYoSh experiment.

    PubMed

    Simi, Manuele; Campagne, Fabien

    2014-01-01

    Language WorkBenches (LWBs) are software engineering tools that help domain experts develop solutions to various classes of problems. Some of these tools focus on non-technical users and provide languages to help organize knowledge while other workbenches provide means to create new programming languages. A key advantage of language workbenches is that they support the seamless composition of independently developed languages. This capability is useful when developing programs that can benefit from different levels of abstraction. We reasoned that language workbenches could be useful to develop bioinformatics software solutions. In order to evaluate the potential of language workbenches in bioinformatics, we tested a prominent workbench by developing an alternative to shell scripting. To illustrate what LWBs and Language Composition can bring to bioinformatics, we report on our design and development of NYoSh (Not Your ordinary Shell). NYoSh was implemented as a collection of languages that can be composed to write programs as expressive and concise as shell scripts. This manuscript offers a concrete illustration of the advantages and current minor drawbacks of using the MPS LWB. For instance, we found that we could implement an environment-aware editor for NYoSh that can assist the programmers when developing scripts for specific execution environments. This editor further provides semantic error detection and can be compiled interactively with an automatic build and deployment system. In contrast to shell scripts, NYoSh scripts can be written in a modern development environment, supporting context dependent intentions and can be extended seamlessly by end-users with new abstractions and language constructs. We further illustrate language extension and composition with LWBs by presenting a tight integration of NYoSh scripts with the GobyWeb system. The NYoSh Workbench prototype, which implements a fully featured integrated development environment for NYoSh is

  3. Composable languages for bioinformatics: the NYoSh experiment

    PubMed Central

    Simi, Manuele

    2014-01-01

    Language WorkBenches (LWBs) are software engineering tools that help domain experts develop solutions to various classes of problems. Some of these tools focus on non-technical users and provide languages to help organize knowledge while other workbenches provide means to create new programming languages. A key advantage of language workbenches is that they support the seamless composition of independently developed languages. This capability is useful when developing programs that can benefit from different levels of abstraction. We reasoned that language workbenches could be useful to develop bioinformatics software solutions. In order to evaluate the potential of language workbenches in bioinformatics, we tested a prominent workbench by developing an alternative to shell scripting. To illustrate what LWBs and Language Composition can bring to bioinformatics, we report on our design and development of NYoSh (Not Your ordinary Shell). NYoSh was implemented as a collection of languages that can be composed to write programs as expressive and concise as shell scripts. This manuscript offers a concrete illustration of the advantages and current minor drawbacks of using the MPS LWB. For instance, we found that we could implement an environment-aware editor for NYoSh that can assist the programmers when developing scripts for specific execution environments. This editor further provides semantic error detection and can be compiled interactively with an automatic build and deployment system. In contrast to shell scripts, NYoSh scripts can be written in a modern development environment, supporting context dependent intentions and can be extended seamlessly by end-users with new abstractions and language constructs. We further illustrate language extension and composition with LWBs by presenting a tight integration of NYoSh scripts with the GobyWeb system. The NYoSh Workbench prototype, which implements a fully featured integrated development environment for NYoSh is

  4. Platinum-related deep levels in silicon and their passivation by atomic hydrogen using a home-built automated DLTS system

    NASA Astrophysics Data System (ADS)

    Reddy, B. P. N.; Reddy, P. N.; Pandu Rangaiah, S. V.

    1996-09-01

    An inexpensive automated DLTS system has been developed in modular form consisting of modules such as a capacitance meter, pulse generator, DLTS system timing controller, data acquisition system, PID temperature controller, cryostat with LN2 flow control facility, etc. These modules, except the capacitance meter and pulse generator, have been designed and fabricated in the laboratory. Further they are integrated and interfaced to PC AT/386 computer. Software has been developed to run the spectrometer, collect data and off-line data processing for the deep level parameters such as activation energy, capture cross-section and density. The system has been used to study the deep levels of platinum in n-type silicon and their passivation by atomic hydrogen. The estimated activation energy of the two acceptor levels are Ec-0.280 eV and Ec-0.522 eV and their capture cross sections are 2.2E-15 cm-2 and 4.3E-15 cm-2 respectively. These levels are found to be reactivated when the hydrogenated samples are annealed in the temperature range 350 - 500 degrees Celsius. The mechanism of passivation and reactivation of these levels are discussed.

  5. A toolbox for developing bioinformatics software

    PubMed Central

    Potrzebowski, Wojciech; Puton, Tomasz; Rother, Magdalena; Wywial, Ewa; Bujnicki, Janusz M.

    2012-01-01

    Creating useful software is a major activity of many scientists, including bioinformaticians. Nevertheless, software development in an academic setting is often unsystematic, which can lead to problems associated with maintenance and long-term availibility. Unfortunately, well-documented software development methodology is difficult to adopt, and technical measures that directly improve bioinformatic programming have not been described comprehensively. We have examined 22 software projects and have identified a set of practices for software development in an academic environment. We found them useful to plan a project, support the involvement of experts (e.g. experimentalists), and to promote higher quality and maintainability of the resulting programs. This article describes 12 techniques that facilitate a quick start into software engineering. We describe 3 of the 22 projects in detail and give many examples to illustrate the usage of particular techniques. We expect this toolbox to be useful for many bioinformatics programming projects and to the training of scientific programmers. PMID:21803787

  6. A toolbox for developing bioinformatics software.

    PubMed

    Rother, Kristian; Potrzebowski, Wojciech; Puton, Tomasz; Rother, Magdalena; Wywial, Ewa; Bujnicki, Janusz M

    2012-03-01

    Creating useful software is a major activity of many scientists, including bioinformaticians. Nevertheless, software development in an academic setting is often unsystematic, which can lead to problems associated with maintenance and long-term availibility. Unfortunately, well-documented software development methodology is difficult to adopt, and technical measures that directly improve bioinformatic programming have not been described comprehensively. We have examined 22 software projects and have identified a set of practices for software development in an academic environment. We found them useful to plan a project, support the involvement of experts (e.g. experimentalists), and to promote higher quality and maintainability of the resulting programs. This article describes 12 techniques that facilitate a quick start into software engineering. We describe 3 of the 22 projects in detail and give many examples to illustrate the usage of particular techniques. We expect this toolbox to be useful for many bioinformatics programming projects and to the training of scientific programmers. PMID:21803787

  7. Novel bioinformatic developments for exome sequencing.

    PubMed

    Lelieveld, Stefan H; Veltman, Joris A; Gilissen, Christian

    2016-06-01

    With the widespread adoption of next generation sequencing technologies by the genetics community and the rapid decrease in costs per base, exome sequencing has become a standard within the repertoire of genetic experiments for both research and diagnostics. Although bioinformatics now offers standard solutions for the analysis of exome sequencing data, many challenges still remain; especially the increasing scale at which exome data are now being generated has given rise to novel challenges in how to efficiently store, analyze and interpret exome data of this magnitude. In this review we discuss some of the recent developments in bioinformatics for exome sequencing and the directions that this is taking us to. With these developments, exome sequencing is paving the way for the next big challenge, the application of whole genome sequencing. PMID:27075447

  8. Translational bioinformatics applications in genome medicine

    PubMed Central

    2009-01-01

    Although investigators using methodologies in bioinformatics have always been useful in genomic experimentation in analytic, engineering, and infrastructure support roles, only recently have bioinformaticians been able to have a primary scientific role in asking and answering questions on human health and disease. Here, I argue that this shift in role towards asking questions in medicine is now the next step needed for the field of bioinformatics. I outline four reasons why bioinformaticians are newly enabled to drive the questions in primary medical discovery: public availability of data, intersection of data across experiments, commoditization of methods, and streamlined validation. I also list four recommendations for bioinformaticians wishing to get more involved in translational research. PMID:19566916

  9. Bioinformatics in New Generation Flavivirus Vaccines

    PubMed Central

    Koraka, Penelope; Martina, Byron E. E.; Osterhaus, Albert D. M. E.

    2010-01-01

    Flavivirus infections are the most prevalent arthropod-borne infections world wide, often causing severe disease especially among children, the elderly, and the immunocompromised. In the absence of effective antiviral treatment, prevention through vaccination would greatly reduce morbidity and mortality associated with flavivirus infections. Despite the success of the empirically developed vaccines against yellow fever virus, Japanese encephalitis virus and tick-borne encephalitis virus, there is an increasing need for a more rational design and development of safe and effective vaccines. Several bioinformatic tools are available to support such rational vaccine design. In doing so, several parameters have to be taken into account, such as safety for the target population, overall immunogenicity of the candidate vaccine, and efficacy and longevity of the immune responses triggered. Examples of how bio-informatics is applied to assist in the rational design and improvements of vaccines, particularly flavivirus vaccines, are presented and discussed. PMID:20467477

  10. Discovery and Classification of Bioinformatics Web Services

    SciTech Connect

    Rocco, D; Critchlow, T

    2002-09-02

    The transition of the World Wide Web from a paradigm of static Web pages to one of dynamic Web services provides new and exciting opportunities for bioinformatics with respect to data dissemination, transformation, and integration. However, the rapid growth of bioinformatics services, coupled with non-standardized interfaces, diminish the potential that these Web services offer. To face this challenge, we examine the notion of a Web service class that defines the functionality provided by a collection of interfaces. These descriptions are an integral part of a larger framework that can be used to discover, classify, and wrapWeb services automatically. We discuss how this framework can be used in the context of the proliferation of sites offering BLAST sequence alignment services for specialized data sets.

  11. Development and experimental evaluation of a thermography measurement system for real-time monitoring of comfort and heat rate exchange in the built environment

    NASA Astrophysics Data System (ADS)

    Revel, G. M.; Sabbatini, E.; Arnesano, M.

    2012-03-01

    A measurement system based on infrared (IR) thermovision technique (ITT) is developed for real-time estimation of room thermal variations and comfort conditions in office-type environment as a part of a feasibility study in the EU FP7 project ‘INTUBE’. An IR camera installed on the ceiling allows thermal image acquisition and post-processing is performed to derive mean surface temperatures, number of occupants and presence of other heat sources (e.g. computer) through detecting algorithms. A lumped parameter model of the room, developed in the Matlab/Simulink environment, receives as input the information extracted from image processing to compute room exchanged heat rate, air temperature and thermal comfort (PMV). The aim is to provide in real time the room thermal balance and comfort information for energy-saving purposes in an improved way with respect to traditional thermostats. Instantaneous information can be displayed for the users or eventually used for automatic HVAC control. The system is based on custom adaptation of a surveillance low-cost IR system with dedicated radiometric calibration. Experimental results show average absolute discrepancies in the order of 0.4 °C between calculated and measured air temperature during a time period of a day. A sensitivity analysis is performed in order to identify main uncertainty sources.

  12. Quantum Bio-Informatics IV

    NASA Astrophysics Data System (ADS)

    Accardi, Luigi; Freudenberg, Wolfgang; Ohya, Masanori

    2011-01-01

    The QP-DYN algorithms / L. Accardi, M. Regoli and M. Ohya -- Study of transcriptional regulatory network based on Cis module database / S. Akasaka ... [et al.] -- On Lie group-Lie algebra correspondences of unitary groups in finite von Neumann algebras / H. Ando, I. Ojima and Y. Matsuzawa -- On a general form of time operators of a Hamiltonian with purely discrete spectrum / A. Arai -- Quantum uncertainty and decision-making in game theory / M. Asano ... [et al.] -- New types of quantum entropies and additive information capacities / V. P. Belavkin -- Non-Markovian dynamics of quantum systems / D. Chruscinski and A. Kossakowski -- Self-collapses of quantum systems and brain activities / K.-H. Fichtner ... [et al.] -- Statistical analysis of random number generators / L. Accardi and M. Gabler -- Entangled effects of two consecutive pairs in residues and its use in alignment / T. Ham, K. Sato and M. Ohya -- The passage from digital to analogue in white noise analysis and applications / T. Hida -- Remarks on the degree of entanglement / D. Chruscinski ... [et al.] -- A completely discrete particle model derived from a stochastic partial differential equation by point systems / K.-H. Fichtner, K. Inoue and M. Ohya -- On quantum algorithm for exptime problem / S. Iriyama and M. Ohya -- On sufficient algebraic conditions for identification of quantum states / A. Jamiolkowski -- Concurrence and its estimations by entanglement witnesses / J. Jurkowski -- Classical wave model of quantum-like processing in brain / A. Khrennikov -- Entanglement mapping vs. quantum conditional probability operator / D. Chruscinski ... [et al.] -- Constructing multipartite entanglement witnesses / M. Michalski -- On Kadison-Schwarz property of quantum quadratic operators on M[symbol](C) / F. Mukhamedov and A. Abduganiev -- On phase transitions in quantum Markov chains on Cayley Tree / L. Accardi, F. Mukhamedov and M. Saburov -- Space(-time) emergence as symmetry breaking effect / I. Ojima

  13. Bioinformatics Approach in Plant Genomic Research.

    PubMed

    Ong, Quang; Nguyen, Phuc; Thao, Nguyen Phuong; Le, Ly

    2016-08-01

    The advance in genomics technology leads to the dramatic change in plant biology research. Plant biologists now easily access to enormous genomic data to deeply study plant high-density genetic variation at molecular level. Therefore, fully understanding and well manipulating bioinformatics tools to manage and analyze these data are essential in current plant genome research. Many plant genome databases have been established and continued expanding recently. Meanwhile, analytical methods based on bioinformatics are also well developed in many aspects of plant genomic research including comparative genomic analysis, phylogenomics and evolutionary analysis, and genome-wide association study. However, constantly upgrading in computational infrastructures, such as high capacity data storage and high performing analysis software, is the real challenge for plant genome research. This review paper focuses on challenges and opportunities which knowledge and skills in bioinformatics can bring to plant scientists in present plant genomics era as well as future aspects in critical need for effective tools to facilitate the translation of knowledge from new sequencing data to enhancement of plant productivity. PMID:27499685

  14. Bioinformatics tools for analysing viral genomic data.

    PubMed

    Orton, R J; Gu, Q; Hughes, J; Maabar, M; Modha, S; Vattipally, S B; Wilkie, G S; Davison, A J

    2016-04-01

    The field of viral genomics and bioinformatics is experiencing a strong resurgence due to high-throughput sequencing (HTS) technology, which enables the rapid and cost-effective sequencing and subsequent assembly of large numbers of viral genomes. In addition, the unprecedented power of HTS technologies has enabled the analysis of intra-host viral diversity and quasispecies dynamics in relation to important biological questions on viral transmission, vaccine resistance and host jumping. HTS also enables the rapid identification of both known and potentially new viruses from field and clinical samples, thus adding new tools to the fields of viral discovery and metagenomics. Bioinformatics has been central to the rise of HTS applications because new algorithms and software tools are continually needed to process and analyse the large, complex datasets generated in this rapidly evolving area. In this paper, the authors give a brief overview of the main bioinformatics tools available for viral genomic research, with a particular emphasis on HTS technologies and their main applications. They summarise the major steps in various HTS analyses, starting with quality control of raw reads and encompassing activities ranging from consensus and de novo genome assembly to variant calling and metagenomics, as well as RNA sequencing. PMID:27217183

  15. Bioinformatics on the Cloud Computing Platform Azure

    PubMed Central

    Shanahan, Hugh P.; Owen, Anne M.; Harrison, Andrew P.

    2014-01-01

    We discuss the applicability of the Microsoft cloud computing platform, Azure, for bioinformatics. We focus on the usability of the resource rather than its performance. We provide an example of how R can be used on Azure to analyse a large amount of microarray expression data deposited at the public database ArrayExpress. We provide a walk through to demonstrate explicitly how Azure can be used to perform these analyses in Appendix S1 and we offer a comparison with a local computation. We note that the use of the Platform as a Service (PaaS) offering of Azure can represent a steep learning curve for bioinformatics developers who will usually have a Linux and scripting language background. On the other hand, the presence of an additional set of libraries makes it easier to deploy software in a parallel (scalable) fashion and explicitly manage such a production run with only a few hundred lines of code, most of which can be incorporated from a template. We propose that this environment is best suited for running stable bioinformatics software by users not involved with its development. PMID:25050811

  16. Bioinformatics on the cloud computing platform Azure.

    PubMed

    Shanahan, Hugh P; Owen, Anne M; Harrison, Andrew P

    2014-01-01

    We discuss the applicability of the Microsoft cloud computing platform, Azure, for bioinformatics. We focus on the usability of the resource rather than its performance. We provide an example of how R can be used on Azure to analyse a large amount of microarray expression data deposited at the public database ArrayExpress. We provide a walk through to demonstrate explicitly how Azure can be used to perform these analyses in Appendix S1 and we offer a comparison with a local computation. We note that the use of the Platform as a Service (PaaS) offering of Azure can represent a steep learning curve for bioinformatics developers who will usually have a Linux and scripting language background. On the other hand, the presence of an additional set of libraries makes it easier to deploy software in a parallel (scalable) fashion and explicitly manage such a production run with only a few hundred lines of code, most of which can be incorporated from a template. We propose that this environment is best suited for running stable bioinformatics software by users not involved with its development. PMID:25050811

  17. Application of Bioinformatics in Chronobiology Research

    PubMed Central

    Lopes, Robson da Silva; Resende, Nathalia Maria; Honorio-França, Adenilda Cristina; França, Eduardo Luzía

    2013-01-01

    Bioinformatics and other well-established sciences, such as molecular biology, genetics, and biochemistry, provide a scientific approach for the analysis of data generated through “omics” projects that may be used in studies of chronobiology. The results of studies that apply these techniques demonstrate how they significantly aided the understanding of chronobiology. However, bioinformatics tools alone cannot eliminate the need for an understanding of the field of research or the data to be considered, nor can such tools replace analysts and researchers. It is often necessary to conduct an evaluation of the results of a data mining effort to determine the degree of reliability. To this end, familiarity with the field of investigation is necessary. It is evident that the knowledge that has been accumulated through chronobiology and the use of tools derived from bioinformatics has contributed to the recognition and understanding of the patterns and biological rhythms found in living organisms. The current work aims to develop new and important applications in the near future through chronobiology research. PMID:24187519

  18. Parallel algorithm research on several important open problems in bioinformatics.

    PubMed

    Niu, Bei-Fang; Lang, Xian-Yu; Lu, Zhong-Hua; Chi, Xue-Bin

    2009-09-01

    High performance computing has opened the door to using bioinformatics and systems biology to explore complex relationships among data, and created the opportunity to tackle very large and involved simulations of biological systems. Many supercomputing centers have jumped on the bandwagon because the opportunities for significant impact in this field is infinite. Development of new algorithms, especially parallel algorithms and software to mine new biological information and to assess different relationships among the members of a large biological data set, is becoming very important. This article presents our work on the design and development of parallel algorithms and software to solve some important open problems arising from bioinformatics, such as structure alignment of RNA sequences, finding new genes, alternative splicing, gene expression clustering and so on. In order to make these parallel software available to a wide audience, the grid computing service interfaces to these software have been deployed in China National Grid (CNGrid). Finally, conclusions and some future research directions are presented. PMID:20640837

  19. Shared bioinformatics databases within the Unipro UGENE platform.

    PubMed

    Protsyuk, Ivan V; Grekhov, German A; Tiunov, Alexey V; Fursov, Mikhail Y

    2015-01-01

    Unipro UGENE is an open-source bioinformatics toolkit that integrates popular tools along with original instruments for molecular biologists within a unified user interface. Nowadays, most bioinformatics desktop applications, including UGENE, make use of a local data model while processing different types of data. Such an approach causes an inconvenience for scientists working cooperatively and relying on the same data. This refers to the need of making multiple copies of certain files for every workplace and maintaining synchronization between them in case of modifications. Therefore, we focused on delivering a collaborative work into the UGENE user experience. Currently, several UGENE installations can be connected to a designated shared database and users can interact with it simultaneously. Such databases can be created by UGENE users and be used at their discretion. Objects of each data type, supported by UGENE such as sequences, annotations, multiple alignments, etc., can now be easily imported from or exported to a remote storage. One of the main advantages of this system, compared to existing ones, is the almost simultaneous access of client applications to shared data regardless of their volume. Moreover, the system is capable of storing millions of objects. The storage itself is a regular database server so even an inexpert user is able to deploy it. Thus, UGENE may provide access to shared data for users located, for example, in the same laboratory or institution. UGENE is available at: http://ugene.net/download.html. PMID:26527191

  20. Doublet III beamline: as-built

    SciTech Connect

    Harder, C.R.; Holland, M.M.; Parker, J.W.; Gunn, J.; Resnick, L.

    1980-03-01

    In order to fully exploit Doublet III capabilities and to study new plasma physics regimes, a Neutral Beam Injector System has been constructed. Initially, a two beamline system will supply 7 MW of heat to the plasma. The system is currently being expanded to inject approx. 20 MW of power (6 beamlines). Each beamline is equipped with two Lawrence Berkeley Laboratory type rectangular ion sources with 10 cm x 40 cm extraction grids. These sources will accelerate hydrogen ions to 80 keV, with extracted beam currents in excess of 80 A per source expected. The first completed source is currently being tested and conditioned on the High Voltage Test Stand at Lawrence Livermore Laboratory. This paper pictorially reviews the as-built Doublet III neutral beamline with emphasis on component relation and configuration relative to spatial and source imposed design constraints.

  1. Bioinformatics for the synthetic biology of natural products: integrating across the Design-Build-Test cycle.

    PubMed

    Carbonell, Pablo; Currin, Andrew; Jervis, Adrian J; Rattray, Nicholas J W; Swainston, Neil; Yan, Cunyu; Takano, Eriko; Breitling, Rainer

    2016-08-27

    Covering: 2000 to 2016Progress in synthetic biology is enabled by powerful bioinformatics tools allowing the integration of the design, build and test stages of the biological engineering cycle. In this review we illustrate how this integration can be achieved, with a particular focus on natural products discovery and production. Bioinformatics tools for the DESIGN and BUILD stages include tools for the selection, synthesis, assembly and optimization of parts (enzymes and regulatory elements), devices (pathways) and systems (chassis). TEST tools include those for screening, identification and quantification of metabolites for rapid prototyping. The main advantages and limitations of these tools as well as their interoperability capabilities are highlighted. PMID:27185383

  2. Translational Bioinformatics Approaches to Drug Development

    PubMed Central

    Readhead, Ben; Dudley, Joel

    2013-01-01

    Significance A majority of therapeutic interventions occur late in the pathological process, when treatment outcome can be less predictable and effective, highlighting the need for new precise and preventive therapeutic development strategies that consider genomic and environmental context. Translational bioinformatics is well positioned to contribute to the many challenges inherent in bridging this gap between our current reactive methods of healthcare delivery and the intent of precision medicine, particularly in the areas of drug development, which forms the focus of this review. Recent Advances A variety of powerful informatics methods for organizing and leveraging the vast wealth of available molecular measurements available for a broad range of disease contexts have recently emerged. These include methods for data driven disease classification, drug repositioning, identification of disease biomarkers, and the creation of disease network models, each with significant impacts on drug development approaches. Critical Issues An important bottleneck in the application of bioinformatics methods in translational research is the lack of investigators who are versed in both biomedical domains and informatics. Efforts to nurture both sets of competencies within individuals and to increase interfield visibility will help to accelerate the adoption and increased application of bioinformatics in translational research. Future Directions It is possible to construct predictive, multiscale network models of disease by integrating genotype, gene expression, clinical traits, and other multiscale measures using causal network inference methods. This can enable the identification of the “key drivers” of pathology, which may represent novel therapeutic targets or biomarker candidates that play a more direct role in the etiology of disease. PMID:24527359

  3. Microbial bioinformatics for food safety and production

    PubMed Central

    Alkema, Wynand; Boekhorst, Jos; Wels, Michiel

    2016-01-01

    In the production of fermented foods, microbes play an important role. Optimization of fermentation processes or starter culture production traditionally was a trial-and-error approach inspired by expert knowledge of the fermentation process. Current developments in high-throughput ‘omics’ technologies allow developing more rational approaches to improve fermentation processes both from the food functionality as well as from the food safety perspective. Here, the authors thematically review typical bioinformatics techniques and approaches to improve various aspects of the microbial production of fermented food products and food safety. PMID:26082168

  4. Critical Issues in Bioinformatics and Computing

    PubMed Central

    Kesh, Someswa; Raghupathi, Wullianallur

    2004-01-01

    This article provides an overview of the field of bioinformatics and its implications for the various participants. Next-generation issues facing developers (programmers), users (molecular biologists), and the general public (patients) who would benefit from the potential applications are identified. The goal is to create awareness and debate on the opportunities (such as career paths) and the challenges such as privacy that arise. A triad model of the participants' roles and responsibilities is presented along with the identification of the challenges and possible solutions. PMID:18066389

  5. Translational Bioinformatics: Past, Present, and Future

    PubMed Central

    Tenenbaum, Jessica D.

    2016-01-01

    Though a relatively young discipline, translational bioinformatics (TBI) has become a key component of biomedical research in the era of precision medicine. Development of high-throughput technologies and electronic health records has caused a paradigm shift in both healthcare and biomedical research. Novel tools and methods are required to convert increasingly voluminous datasets into information and actionable knowledge. This review provides a definition and contextualization of the term TBI, describes the discipline’s brief history and past accomplishments, as well as current foci, and concludes with predictions of future directions in the field. PMID:26876718

  6. Bioinformatics in proteomics: application, terminology, and pitfalls.

    PubMed

    Wiemer, Jan C; Prokudin, Alexander

    2004-01-01

    Bioinformatics applies data mining, i.e., modern computer-based statistics, to biomedical data. It leverages on machine learning approaches, such as artificial neural networks, decision trees and clustering algorithms, and is ideally suited for handling huge data amounts. In this article, we review the analysis of mass spectrometry data in proteomics, starting with common pre-processing steps and using single decision trees and decision tree ensembles for classification. Special emphasis is put on the pitfall of overfitting, i.e., of generating too complex single decision trees. Finally, we discuss the pros and cons of the two different decision tree usages. PMID:15237926

  7. A Survey of Scholarly Literature Describing the Field of Bioinformatics Education and Bioinformatics Educational Research

    ERIC Educational Resources Information Center

    Magana, Alejandra J.; Taleyarkhan, Manaz; Alvarado, Daniela Rivera; Kane, Michael; Springer, John; Clase, Kari

    2014-01-01

    Bioinformatics education can be broadly defined as the teaching and learning of the use of computer and information technology, along with mathematical and statistical analysis for gathering, storing, analyzing, interpreting, and integrating data to solve biological problems. The recent surge of genomics, proteomics, and structural biology in the…

  8. OpenHelix: bioinformatics education outside of a different box.

    PubMed

    Williams, Jennifer M; Mangan, Mary E; Perreault-Micale, Cynthia; Lathe, Scott; Sirohi, Neeraj; Lathe, Warren C

    2010-11-01

    The amount of biological data is increasing rapidly, and will continue to increase as new rapid technologies are developed. Professionals in every area of bioscience will have data management needs that require publicly available bioinformatics resources. Not all scientists desire a formal bioinformatics education but would benefit from more informal educational sources of learning. Effective bioinformatics education formats will address a broad range of scientific needs, will be aimed at a variety of user skill levels, and will be delivered in a number of different formats to address different learning styles. Informal sources of bioinformatics education that are effective are available, and will be explored in this review. PMID:20798181

  9. Translational Bioinformatics: Linking the Molecular World to the Clinical World

    PubMed Central

    Altman, RB

    2014-01-01

    Translational bioinformatics represents the union of translational medicine and bioinformatics. Translational medicine moves basic biological discoveries from the research bench into the patient-care setting and uses clinical observations to inform basic biology. It focuses on patient care, including the creation of new diagnostics, prognostics, prevention strategies, and therapies based on biological discoveries. Bioinformatics involves algorithms to represent, store, and analyze basic biological data, including DNA sequence, RNA expression, and protein and small-molecule abundance within cells. Translational bioinformatics spans these two fields; it involves the development of algorithms to analyze basic molecular and cellular data with an explicit goal of affecting clinical care. PMID:22549287

  10. OpenHelix: bioinformatics education outside of a different box

    PubMed Central

    Mangan, Mary E.; Perreault-Micale, Cynthia; Lathe, Scott; Sirohi, Neeraj; Lathe, Warren C.

    2010-01-01

    The amount of biological data is increasing rapidly, and will continue to increase as new rapid technologies are developed. Professionals in every area of bioscience will have data management needs that require publicly available bioinformatics resources. Not all scientists desire a formal bioinformatics education but would benefit from more informal educational sources of learning. Effective bioinformatics education formats will address a broad range of scientific needs, will be aimed at a variety of user skill levels, and will be delivered in a number of different formats to address different learning styles. Informal sources of bioinformatics education that are effective are available, and will be explored in this review. PMID:20798181

  11. Receptor-binding sites: bioinformatic approaches.

    PubMed

    Flower, Darren R

    2006-01-01

    It is increasingly clear that both transient and long-lasting interactions between biomacromolecules and their molecular partners are the most fundamental of all biological mechanisms and lie at the conceptual heart of protein function. In particular, the protein-binding site is the most fascinating and important mechanistic arbiter of protein function. In this review, I examine the nature of protein-binding sites found in both ligand-binding receptors and substrate-binding enzymes. I highlight two important concepts underlying the identification and analysis of binding sites. The first is based on knowledge: when one knows the location of a binding site in one protein, one can "inherit" the site from one protein to another. The second approach involves the a priori prediction of a binding site from a sequence or a structure. The full and complete analysis of binding sites will necessarily involve the full range of informatic techniques ranging from sequence-based bioinformatic analysis through structural bioinformatics to computational chemistry and molecular physics. Integration of both diverse experimental and diverse theoretical approaches is thus a mandatory requirement in the evaluation of binding sites and the binding events that occur within them. PMID:16671408

  12. Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN

    PubMed Central

    2010-01-01

    Background Brucella spp. are Gram-negative, facultative intracellular bacteria that cause brucellosis, one of the commonest zoonotic diseases found worldwide in humans and a variety of animal species. While several animal vaccines are available, there is no effective and safe vaccine for prevention of brucellosis in humans. VIOLIN (http://www.violinet.org) is a web-based vaccine database and analysis system that curates, stores, and analyzes published data of commercialized vaccines, and vaccines in clinical trials or in research. VIOLIN contains information for 454 vaccines or vaccine candidates for 73 pathogens. VIOLIN also contains many bioinformatics tools for vaccine data analysis, data integration, and vaccine target prediction. To demonstrate the applicability of VIOLIN for vaccine research, VIOLIN was used for bioinformatics analysis of existing Brucella vaccines and prediction of new Brucella vaccine targets. Results VIOLIN contains many literature mining programs (e.g., Vaxmesh) that provide in-depth analysis of Brucella vaccine literature. As a result of manual literature curation, VIOLIN contains information for 38 Brucella vaccines or vaccine candidates, 14 protective Brucella antigens, and 68 host response studies to Brucella vaccines from 97 peer-reviewed articles. These Brucella vaccines are classified in the Vaccine Ontology (VO) system and used for different ontological applications. The web-based VIOLIN vaccine target prediction program Vaxign was used to predict new Brucella vaccine targets. Vaxign identified 14 outer membrane proteins that are conserved in six virulent strains from B. abortus, B. melitensis, and B. suis that are pathogenic in humans. Of the 14 membrane proteins, two proteins (Omp2b and Omp31-1) are not present in B. ovis, a Brucella species that is not pathogenic in humans. Brucella vaccine data stored in VIOLIN were compared and analyzed using the VIOLIN query system. Conclusions Bioinformatics curation and ontological

  13. The House That Jones Built.

    ERIC Educational Resources Information Center

    Rist, Marilee C.

    1992-01-01

    Describes lifelong commitment of middle-school principal and major W.J. Jones to Coahoma, a small town in Mississippi Delta. Thanks to his efforts, town recently acquired a sewage system, blacktopped roads, and new housing (through Habitat for Humanity and World Vision). Although town elementary school fell victim to consolidation and children are…

  14. Discovery of novel xylosides in co-culture of basidiomycetes Trametes versicolor and Ganoderma applanatum by integrated metabolomics and bioinformatics.

    PubMed

    Yao, Lu; Zhu, Li-Ping; Xu, Xiao-Yan; Tan, Ling-Ling; Sadilek, Martin; Fan, Huan; Hu, Bo; Shen, Xiao-Ting; Yang, Jie; Qiao, Bin; Yang, Song

    2016-01-01

    Transcriptomic analysis of cultured fungi suggests that many genes for secondary metabolite synthesis are presumably silent under standard laboratory condition. In order to investigate the expression of silent genes in symbiotic systems, 136 fungi-fungi symbiotic systems were built up by co-culturing seventeen basidiomycetes, among which the co-culture of Trametes versicolor and Ganoderma applanatum demonstrated the strongest coloration of confrontation zones. Metabolomics study of this co-culture discovered that sixty-two features were either newly synthesized or highly produced in the co-culture compared with individual cultures. Molecular network analysis highlighted a subnetwork including two novel xylosides (compounds 2 and 3). Compound 2 was further identified as N-(4-methoxyphenyl)formamide 2-O-β-D-xyloside and was revealed to have the potential to enhance the cell viability of human immortalized bronchial epithelial cell line of Beas-2B. Moreover, bioinformatics and transcriptional analysis of T. versicolor revealed a potential candidate gene (GI: 636605689) encoding xylosyltransferases for xylosylation. Additionally, 3-phenyllactic acid and orsellinic acid were detected for the first time in G. applanatum, which may be ascribed to response against T.versicolor stress. In general, the described co-culture platform provides a powerful tool to discover novel metabolites and help gain insights into the mechanism of silent gene activation in fungal defense. PMID:27616058

  15. Built for the road ahead.

    PubMed

    Mansour, Alexander

    2015-10-01

    Henry Ford Health System in Detroit is seeking new ways to lower and cover costs for the large, low-income population it serves in southeastern Michigan. Employing a strategy that couples the federal 340B Drug Pricing Program with a prescription assistance program of its own creation, Henry Ford has seen improvement in the following areas: Increased medication adherence. Reduced readmissions. Cost savings that are sufficient to expand services where expansion otherwise would not have been feasible. PMID:26595980

  16. First results for custom-built low-temperature (4.2 K) scanning tunneling microscope/molecular beam epitaxy and pulsed laser epitaxy system designed for spin-polarized measurements

    NASA Astrophysics Data System (ADS)

    Foley, Andrew; Alam, Khan; Lin, Wenzhi; Wang, Kangkang; Chinchore, Abhijit; Corbett, Joseph; Savage, Alan; Chen, Tianjiao; Shi, Meng; Pak, Jeongihm; Smith, Arthur

    2014-03-01

    A custom low-temperature (4.2 K) scanning tunneling microscope system has been developed which is combined directly with a custom molecular beam epitaxy facility (and also including pulsed laser epitaxy) for the purpose of studying surface nanomagnetism of complex spintronic materials down to the atomic scale. For purposes of carrying out spin-polarized STM measurements, the microscope is built into a split-coil, 4.5 Tesla superconducting magnet system where the magnetic field can be applied normal to the sample surface; since, as a result, the microscope does not include eddy current damping, vibration isolation is achieved using a unique combination of two stages of pneumatic isolators along with an acoustical noise shield, in addition to the use of a highly stable as well as modular `Pan'-style STM design with a high Q factor. First 4.2 K results reveal, with clear atomic resolution, various reconstructions on wurtzite GaN c-plane surfaces grown by MBE, including the c(6x12) on N-polar GaN(0001). Details of the system design and functionality will be presented.

  17. Bioinformatics and the Politics of Innovation in the Life Sciences

    PubMed Central

    Zhou, Yinhua; Datta, Saheli; Salter, Charlotte

    2016-01-01

    The governments of China, India, and the United Kingdom are unanimous in their belief that bioinformatics should supply the link between basic life sciences research and its translation into health benefits for the population and the economy. Yet at the same time, as ambitious states vying for position in the future global bioeconomy they differ considerably in the strategies adopted in pursuit of this goal. At the heart of these differences lies the interaction between epistemic change within the scientific community itself and the apparatus of the state. Drawing on desk-based research and thirty-two interviews with scientists and policy makers in the three countries, this article analyzes the politics that shape this interaction. From this analysis emerges an understanding of the variable capacities of different kinds of states and political systems to work with science in harnessing the potential of new epistemic territories in global life sciences innovation. PMID:27546935

  18. Bioinformatic and biometric methods in plant morphology1

    PubMed Central

    Punyasena, Surangi W.; Smith, Selena Y.

    2014-01-01

    Recent advances in microscopy, imaging, and data analyses have permitted both the greater application of quantitative methods and the collection of large data sets that can be used to investigate plant morphology. This special issue, the first for Applications in Plant Sciences, presents a collection of papers highlighting recent methods in the quantitative study of plant form. These emerging biometric and bioinformatic approaches to plant sciences are critical for better understanding how morphology relates to ecology, physiology, genotype, and evolutionary and phylogenetic history. From microscopic pollen grains and charcoal particles, to macroscopic leaves and whole root systems, the methods presented include automated classification and identification, geometric morphometrics, and skeleton networks, as well as tests of the limits of human assessment. All demonstrate a clear need for these computational and morphometric approaches in order to increase the consistency, objectivity, and throughput of plant morphological studies.

  19. Assessment of a Bioinformatics across Life Science Curricula Initiative

    ERIC Educational Resources Information Center

    Howard, David R.; Miskowski, Jennifer A.; Grunwald, Sandra K.; Abler, Michael L.

    2007-01-01

    At the University of Wisconsin-La Crosse, we have undertaken a program to integrate the study of bioinformatics across the undergraduate life science curricula. Our efforts have included incorporating bioinformatics exercises into courses in the biology, microbiology, and chemistry departments, as well as coordinating the efforts of faculty within…

  20. Evaluating an Inquiry-Based Bioinformatics Course Using Q Methodology

    ERIC Educational Resources Information Center

    Ramlo, Susan E.; McConnell, David; Duan, Zhong-Hui; Moore, Francisco B.

    2008-01-01

    Faculty at a Midwestern metropolitan public university recently developed a course on bioinformatics that emphasized collaboration and inquiry. Bioinformatics, essentially the application of computational tools to biological data, is inherently interdisciplinary. Thus part of the challenge of creating this course was serving the needs and…

  1. Generative Topic Modeling in Image Data Mining and Bioinformatics Studies

    ERIC Educational Resources Information Center

    Chen, Xin

    2012-01-01

    Probabilistic topic models have been developed for applications in various domains such as text mining, information retrieval and computer vision and bioinformatics domain. In this thesis, we focus on developing novel probabilistic topic models for image mining and bioinformatics studies. Specifically, a probabilistic topic-connection (PTC) model…

  2. Quantum Bio-Informatics II From Quantum Information to Bio-Informatics

    NASA Astrophysics Data System (ADS)

    Accardi, L.; Freudenberg, Wolfgang; Ohya, Masanori

    2009-02-01

    The problem of quantum-like representation in economy cognitive science, and genetics / L. Accardi, A. Khrennikov and M. Ohya -- Chaotic behavior observed in linea dynamics / M. Asano, T. Yamamoto and Y. Togawa -- Complete m-level quantum teleportation based on Kossakowski-Ohya scheme / M. Asano, M. Ohya and Y. Tanaka -- Towards quantum cybernetics: optimal feedback control in quantum bio informatics / V. P. Belavkin -- Quantum entanglement and circulant states / D. Chruściński -- The compound Fock space and its application in brain models / K. -H. Fichtner and W. Freudenberg -- Characterisation of beam splitters / L. Fichtner and M. Gäbler -- Application of entropic chaos degree to a combined quantum baker's map / K. Inoue, M. Ohya and I. V. Volovich -- On quantum algorithm for multiple alignment of amino acid sequences / S. Iriyama and M. Ohya --Quantum-like models for decision making in psychology and cognitive science / A. Khrennikov -- On completely positive non-Markovian evolution of a d-level system / A. Kossakowski and R. Rebolledo -- Measures of entanglement - a Hilbert space approach / W. A. Majewski -- Some characterizations of PPT states and their relation / T. Matsuoka -- On the dynamics of entanglement and characterization ofentangling properties of quantum evolutions / M. Michalski -- Perspective from micro-macro duality - towards non-perturbative renormalization scheme / I. Ojima -- A simple symmetric algorithm using a likeness with Introns behavior in RNA sequences / M. Regoli -- Some aspects of quadratic generalized white noise functionals / Si Si and T. Hida -- Analysis of several social mobility data using measure of departure from symmetry / K. Tahata ... [et al.] -- Time in physics and life science / I. V. Volovich -- Note on entropies in quantum processes / N. Watanabe -- Basics of molecular simulation and its application to biomolecules / T. Ando and I. Yamato -- Theory of proton-induced superionic conduction in hydrogen-bonded systems

  3. Relax with CouchDB - Into the non-relational DBMS era of Bioinformatics

    PubMed Central

    Manyam, Ganiraju; Payton, Michelle A.; Roth, Jack A.; Abruzzo, Lynne V.; Coombes, Kevin R.

    2012-01-01

    With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. PMID:22609849

  4. Relax with CouchDB--into the non-relational DBMS era of bioinformatics.

    PubMed

    Manyam, Ganiraju; Payton, Michelle A; Roth, Jack A; Abruzzo, Lynne V; Coombes, Kevin R

    2012-07-01

    With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. PMID:22609849

  5. The European Bioinformatics Institute's data resources 2014.

    PubMed

    Brooksbank, Catherine; Bergman, Mary Todd; Apweiler, Rolf; Birney, Ewan; Thornton, Janet

    2014-01-01

    Molecular Biology has been at the heart of the 'big data' revolution from its very beginning, and the need for access to biological data is a common thread running from the 1965 publication of Dayhoff's 'Atlas of Protein Sequence and Structure' through the Human Genome Project in the late 1990s and early 2000s to today's population-scale sequencing initiatives. The European Bioinformatics Institute (EMBL-EBI; http://www.ebi.ac.uk) is one of three organizations worldwide that provides free access to comprehensive, integrated molecular data sets. Here, we summarize the principles underpinning the development of these public resources and provide an overview of EMBL-EBI's database collection to complement the reviews of individual databases provided elsewhere in this issue. PMID:24271396

  6. Bioinformatics by Example: From Sequence to Target

    NASA Astrophysics Data System (ADS)

    Kossida, Sophia; Tahri, Nadia; Daizadeh, Iraj

    2002-12-01

    With the completion of the human genome, and the imminent completion of other large-scale sequencing and structure-determination projects, computer-assisted bioscience is aimed to become the new paradigm for conducting basic and applied research. The presence of these additional bioinformatics tools stirs great anxiety for experimental researchers (as well as for pedagogues), since they are now faced with a wider and deeper knowledge of differing disciplines (biology, chemistry, physics, mathematics, and computer science). This review targets those individuals who are interested in using computational methods in their teaching or research. By analyzing a real-life, pharmaceutical, multicomponent, target-based example the reader will experience this fascinating new discipline.

  7. Bioinformatics Resources for MicroRNA Discovery

    PubMed Central

    Moore, Alyssa C.; Winkjer, Jonathan S.; Tseng, Tsai-Tien

    2015-01-01

    Biomarker identification is often associated with the diagnosis and evaluation of various diseases. Recently, the role of microRNA (miRNA) has been implicated in the development of diseases, particularly cancer. With the advent of next-generation sequencing, the amount of data on miRNA has increased tremendously in the last decade, requiring new bioinformatics approaches for processing and storing new information. New strategies have been developed in mining these sequencing datasets to allow better understanding toward the actions of miRNAs. As a result, many databases have also been established to disseminate these findings. This review focuses on several curated databases of miRNAs and their targets from both predicted and validated sources. PMID:26819547

  8. Survey: Translational Bioinformatics embraces Big Data

    PubMed Central

    Shah, Nigam H.

    2015-01-01

    Summary We review the latest trends and major developments in translational bioinformatics in the year 2011–2012. Our emphasis is on highlighting the key events in the field and pointing at promising research areas for the future. The key take-home points are: Translational informatics is ready to revolutionize human health and healthcare using large-scale measurements on individuals.Data–centric approaches that compute on massive amounts of data (often called “Big Data”) to discover patterns and to make clinically relevant predictions will gain adoption.Research that bridges the latest multimodal measurement technologies with large amounts of electronic healthcare data is increasing; and is where new breakthroughs will occur. PMID:22890354

  9. Bioinformatics and molecular modeling in glycobiology

    PubMed Central

    Schloissnig, Siegfried

    2010-01-01

    The field of glycobiology is concerned with the study of the structure, properties, and biological functions of the family of biomolecules called carbohydrates. Bioinformatics for glycobiology is a particularly challenging field, because carbohydrates exhibit a high structural diversity and their chains are often branched. Significant improvements in experimental analytical methods over recent years have led to a tremendous increase in the amount of carbohydrate structure data generated. Consequently, the availability of databases and tools to store, retrieve and analyze these data in an efficient way is of fundamental importance to progress in glycobiology. In this review, the various graphical representations and sequence formats of carbohydrates are introduced, and an overview of newly developed databases, the latest developments in sequence alignment and data mining, and tools to support experimental glycan analysis are presented. Finally, the field of structural glycoinformatics and molecular modeling of carbohydrates, glycoproteins, and protein–carbohydrate interaction are reviewed. PMID:20364395

  10. Bioinformatics Analysis of Estrogen-Responsive Genes.

    PubMed

    Handel, Adam E

    2016-01-01

    Estrogen is a steroid hormone that plays critical roles in a myriad of intracellular pathways. The expression of many genes is regulated through the steroid hormone receptors ESR1 and ESR2. These bind to DNA and modulate the expression of target genes. Identification of estrogen target genes is greatly facilitated by the use of transcriptomic methods, such as RNA-seq and expression microarrays, and chromatin immunoprecipitation with massively parallel sequencing (ChIP-seq). Combining transcriptomic and ChIP-seq data enables a distinction to be drawn between direct and indirect estrogen target genes. This chapter discusses some methods of identifying estrogen target genes that do not require any expertise in programming languages or complex bioinformatics. PMID:26585125

  11. Biology and bioinformatics of myeloma cell.

    PubMed

    Abroun, Saeid; Saki, Najmaldin; Fakher, Rahim; Asghari, Farahnaz

    2012-12-01

    Multiple myeloma (MM) is a plasma cell disorder that occurs in about 10% of all hematologic cancers. The majority of patients (99%) are over 50 years of age when diagnosed. In the bone marrow (BM), stromal and hematopoietic stem cells (HSCs) are responsible for the production of blood cells. Therefore any destruction or/and changes within the BM undesirably impacts a wide range of hematopoiesis, causing diseases and influencing patient survival. In order to establish an effective therapeutic strategy, recognition of the biology and evaluation of bioinformatics models for myeloma cells are necessary to assist in determining suitable methods to cure or prevent disease complications in patients. This review presents the evaluation of molecular and cellular aspects of MM such as genetic translocation, genetic analysis, cell surface marker, transcription factors, and chemokine signaling pathways. It also briefly reviews some of the mechanisms involved in MM in order to develop a better understanding for use in future studies. PMID:23253865

  12. Bioinformatics for Next Generation Sequencing Data

    PubMed Central

    Magi, Alberto; Benelli, Matteo; Gozzini, Alessia; Girolami, Francesca; Torricelli, Francesca; Brandi, Maria Luisa

    2010-01-01

    The emergence of next-generation sequencing (NGS) platforms imposes increasing demands on statistical methods and bioinformatic tools for the analysis and the management of the huge amounts of data generated by these technologies. Even at the early stages of their commercial availability, a large number of softwares already exist for analyzing NGS data. These tools can be fit into many general categories including alignment of sequence reads to a reference, base-calling and/or polymorphism detection, de novo assembly from paired or unpaired reads, structural variant detection and genome browsing. This manuscript aims to guide readers in the choice of the available computational tools that can be used to face the several steps of the data analysis workflow. PMID:24710047

  13. Comparison of Online and Onsite Bioinformatics Instruction for a Fully Online Bioinformatics Master’s Program

    PubMed Central

    Obom, Kristina M.; Cummings, Patrick J.

    2007-01-01

    The completely online Master of Science in Bioinformatics program differs from the onsite program only in the mode of content delivery. Analysis of student satisfaction indicates no statistically significant difference between most online and onsite student responses, however, online and onsite students do differ significantly in their responses to a few questions on the course evaluation queries. Analysis of student exam performance using three assessments indicates that there was no significant difference in grades earned by students in online and onsite courses. These results suggest that our model for online bioinformatics education provides students with a rigorous course of study that is comparable to onsite course instruction and possibly provides a more rigorous course load and more opportunities for participation. PMID:23653816

  14. LXtoo: an integrated live Linux distribution for the bioinformatics community

    PubMed Central

    2012-01-01

    Background Recent advances in high-throughput technologies dramatically increase biological data generation. However, many research groups lack computing facilities and specialists. This is an obstacle that remains to be addressed. Here, we present a Linux distribution, LXtoo, to provide a flexible computing platform for bioinformatics analysis. Findings Unlike most of the existing live Linux distributions for bioinformatics limiting their usage to sequence analysis and protein structure prediction, LXtoo incorporates a comprehensive collection of bioinformatics software, including data mining tools for microarray and proteomics, protein-protein interaction analysis, and computationally complex tasks like molecular dynamics. Moreover, most of the programs have been configured and optimized for high performance computing. Conclusions LXtoo aims to provide well-supported computing environment tailored for bioinformatics research, reducing duplication of efforts in building computing infrastructure. LXtoo is distributed as a Live DVD and freely available at http://bioinformatics.jnu.edu.cn/LXtoo. PMID:22813356

  15. Built Environment Education in Art Education.

    ERIC Educational Resources Information Center

    Guilfoil, Joanne K., Ed.; Sandler, Alan R., Ed.

    This anthology brings the study of the built environment, its design, social and cultural functions, and the criticism thereof into focus. Following a preface and introduction, 22 essays are organized in three parts. Part 1 includes: (1) "Landscape Art and the Role of the Natural Environment in Built Environment Education" (Heather Anderson); (2)…

  16. The Zebrafish DVD Exchange Project: a bioinformatics initiative.

    PubMed

    Cooper, Mark S; Sommers-Herivel, Greg; Poage, Cara T; McCarthy, Matthew B; Crawford, Bryan D; Phillips, Carey

    2004-01-01

    Scientists who study zebrafish currently have an acute need to increase the rate of visual data exchange within their international community. Although the Internet has provided a revolutionary transformation of information exchange, the Internet is at present unable to serve as a vehicle for the efficient exchange of massive amounts of visual information. Much like an overburdened public water system, the Internet has inherent limits to the services it can provide. It is possible, however, for zebrafishologists to develop and use virtual intranets (such as the approach we outlined in this chapter) to adapt to the growing informatics need of our expanding research community. We need to assess qualitatively the economics of visual bioinformatics in our research community and evaluate the benefit:investment ratio of our collective information-sharing activities. The development of the World Wide Web started in the early 1990s by particle physicists who needed to rapidly exchange visual information within their collaborations. However, because of current limitations in information bandwidth, the World Wide Web cannot be used to easily exchange gigabytes of visual information. The Zebrafish DVD Exchange Project is aimed at by-passing these limitations. Scientists are curiosity-driven tool makers as well as curiosity-driven tool users. We have the capacity to assimilate new tools, as well as to develop new innovations, to serve our collective research needs. As a proactive research community, we need to create new data transfer methodologies (e.g., the Zebrafish DVD Exchange Project) to stay ahead of our bioinformatics needs. PMID:15602926

  17. Bioinformatics for Diagnostics, Forensics, and Virulence Characterization and Detection

    SciTech Connect

    Gardner, S; Slezak, T

    2005-04-05

    We summarize four of our group's high-risk/high-payoff research projects funded by the Intelligence Technology Innovation Center (ITIC) in conjunction with our DHS-funded pathogen informatics activities. These are (1) quantitative assessment of genomic sequencing needs to predict high quality DNA and protein signatures for detection, and comparison of draft versus finished sequences for diagnostic signature prediction; (2) development of forensic software to identify SNP and PCR-RFLP variations from a large number of viral pathogen sequences and optimization of the selection of markers for maximum discrimination of those sequences; (3) prediction of signatures for the detection of virulence, antibiotic resistance, and toxin genes and genetic engineering markers in bacteria; (4) bioinformatic characterization of virulence factors to rapidly screen genomic data for potential genes with similar functions and to elucidate potential health threats in novel organisms. The results of (1) are being used by policy makers to set national sequencing priorities. Analyses from (2) are being used in collaborations with the CDC to genotype and characterize many variola strains, and reports from these collaborations have been made to the President. We also determined SNPs for serotype and strain discrimination of 126 foot and mouth disease virus (FMDV) genomes. For (3), currently >1000 probes have been predicted for the specific detection of >4000 virulence, antibiotic resistance, and genetic engineering vector sequences, and we expect to complete the bioinformatic design of a comprehensive ''virulence detection chip'' by August 2005. Results of (4) will be a system to rapidly predict potential virulence pathways and phenotypes in organisms based on their genomic sequences.

  18. Bioinformatic Analysis of HIV-1 Entry and Pathogenesis

    PubMed Central

    Aiamkitsumrit, Benjamas; Dampier, Will; Antell, Gregory; Rivera, Nina; Martin-Garcia, Julio; Pirrone, Vanessa; Nonnemacher, Michael R.; Wigdahl, Brian

    2015-01-01

    The evolution of human immunodeficiency virus type 1 (HIV-1) with respect to co-receptor utilization has been shown to be relevant to HIV-1 pathogenesis and disease. The CCR5-utilizing (R5) virus has been shown to be important in the very early stages of transmission and highly prevalent during asymptomatic infection and chronic disease. In addition, the R5 virus has been proposed to be involved in neuroinvasion and central nervous system (CNS) disease. In contrast, the CXCR4-utilizing (X4) virus is more prevalent during the course of disease progression and concurrent with the loss of CD4+ T cells. The dual-tropic virus is able to utilize both co-receptors (CXCR4 and CCR5) and has been thought to represent an intermediate transitional virus that possesses properties of both X4 and R5 viruses that can be encountered at many stages of disease. The use of computational tools and bioinformatic approaches in the prediction of HIV-1 co-receptor usage has been growing in importance with respect to understanding HIV-1 pathogenesis and disease, developing diagnostic tools, and improving the efficacy of therapeutic strategies focused on blocking viral entry. Current strategies have enhanced the sensitivity, specificity, and reproducibility relative to the prediction of co-receptor use; however, these technologies need to be improved with respect to their efficient and accurate use across the HIV-1 subtypes. The most effective approach may center on the combined use of different algorithms involving sequences within and outside of the env-V3 loop. This review focuses on the HIV-1 entry process and on co-receptor utilization, including bioinformatic tools utilized in the prediction of co-receptor usage. It also provides novel preliminary analyses for enabling identification of linkages between amino acids in V3 with other components of the HIV-1 genome and demonstrates that these linkages are different between X4 and R5 viruses. PMID:24862329

  19. Design of Wrapper Integration Within the DataFoundry Bioinformatics Application

    SciTech Connect

    Anderson, J; Critchlow, T

    2002-08-20

    The DataFoundry bioinformatics application was designed to enable scientists to directly interact with large datasets, gathered from multiple remote data sources, through a graphical, interactive interface. Gathering information from multiple data sources, integrating that data, and providing an interface to the accumulated data is non-trivial. Advanced techniques are required to develop a solution that adequately completes this task. One possible solution to this problem involves the use of specialized information access programs that are able to access information and transmute that information to a form usable by a single application. These information access programs, called wrappers, were decided to be the most appropriate way to extend the DataFoundry bioinformatics application to support data integration from multiple sources. By adding wrapper support into the DataFoundry application, it is hoped that this system will be able to provide a single access point to bioinformatics data for scientists. We describe some of the computer science concepts, design, and the implementation of adding wrapper support into the DataFoundry bioinformatics application, and then discuss issues of performance.

  20. Bioinformatic approaches to augment study of epithelial-to-mesenchymal transition in lung cancer.

    PubMed

    Beck, Tim N; Chikwem, Adaeze J; Solanki, Nehal R; Golemis, Erica A

    2014-10-01

    Bioinformatic approaches are intended to provide systems level insight into the complex biological processes that underlie serious diseases such as cancer. In this review we describe current bioinformatic resources, and illustrate how they have been used to study a clinically important example: epithelial-to-mesenchymal transition (EMT) in lung cancer. Lung cancer is the leading cause of cancer-related deaths and is often diagnosed at advanced stages, leading to limited therapeutic success. While EMT is essential during development and wound healing, pathological reactivation of this program by cancer cells contributes to metastasis and drug resistance, both major causes of death from lung cancer. Challenges of studying EMT include its transient nature, its molecular and phenotypic heterogeneity, and the complicated networks of rewired signaling cascades. Given the biology of lung cancer and the role of EMT, it is critical to better align the two in order to advance the impact of precision oncology. This task relies heavily on the application of bioinformatic resources. Besides summarizing recent work in this area, we use four EMT-associated genes, TGF-β (TGFB1), NEDD9/HEF1, β-catenin (CTNNB1) and E-cadherin (CDH1), as exemplars to demonstrate the current capacities and limitations of probing bioinformatic resources to inform hypothesis-driven studies with therapeutic goals. PMID:25096367

  1. A scalable neuristor built with Mott memristors

    NASA Astrophysics Data System (ADS)

    Pickett, Matthew D.; Medeiros-Ribeiro, Gilberto; Williams, R. Stanley

    2013-02-01

    The Hodgkin-Huxley model for action potential generation in biological axons is central for understanding the computational capability of the nervous system and emulating its functionality. Owing to the historical success of silicon complementary metal-oxide-semiconductors, spike-based computing is primarily confined to software simulations and specialized analogue metal-oxide-semiconductor field-effect transistor circuits. However, there is interest in constructing physical systems that emulate biological functionality more directly, with the goal of improving efficiency and scale. The neuristor was proposed as an electronic device with properties similar to the Hodgkin-Huxley axon, but previous implementations were not scalable. Here we demonstrate a neuristor built using two nanoscale Mott memristors, dynamical devices that exhibit transient memory and negative differential resistance arising from an insulating-to-conducting phase transition driven by Joule heating. This neuristor exhibits the important neural functions of all-or-nothing spiking with signal gain and diverse periodic spiking, using materials and structures that are amenable to extremely high-density integration with or without silicon transistors.

  2. A scalable neuristor built with Mott memristors.

    PubMed

    Pickett, Matthew D; Medeiros-Ribeiro, Gilberto; Williams, R Stanley

    2013-02-01

    The Hodgkin-Huxley model for action potential generation in biological axons is central for understanding the computational capability of the nervous system and emulating its functionality. Owing to the historical success of silicon complementary metal-oxide-semiconductors, spike-based computing is primarily confined to software simulations and specialized analogue metal-oxide-semiconductor field-effect transistor circuits. However, there is interest in constructing physical systems that emulate biological functionality more directly, with the goal of improving efficiency and scale. The neuristor was proposed as an electronic device with properties similar to the Hodgkin-Huxley axon, but previous implementations were not scalable. Here we demonstrate a neuristor built using two nanoscale Mott memristors, dynamical devices that exhibit transient memory and negative differential resistance arising from an insulating-to-conducting phase transition driven by Joule heating. This neuristor exhibits the important neural functions of all-or-nothing spiking with signal gain and diverse periodic spiking, using materials and structures that are amenable to extremely high-density integration with or without silicon transistors. PMID:23241533

  3. Bi{sub 2}O{sub 3}–CuO–P{sub 2}O{sub 5} system: Two novel compounds built from the intergrowths oxocentered polycationic 1D-ribbons

    SciTech Connect

    Colmont, Marie; Endara, Diana; Aliev, Almaz; Terryn, Christine; Huvé, Marielle; Mentré, Olivier

    2013-07-15

    Single crystals of two novel bismuth copper oxyphosphates were grown from a unique melt. They have been structurally characterized by means of single crystal X-Ray Diffraction (XRD). Bi{sub 29.4}Cu{sub 9.29}O{sub 32}(PO{sub 4}){sub 16}Cu{sub 2.63} (1) is orthorhombic, space group Pca2{sub 1}, a=33.0549(2)A, b=11.6991(4)A and c=5.2902(2)A, R{sub 1}=0.059 and wR{sub 2}=0.061. Bi{sub 37.2}Cu{sub 18.8}O{sub 44}(PO{sub 4}){sub 24}Cu{sub 5} (2) is orthorhombic, space group Pna2{sub 1}, a=11.6010(3)A, b=47.4384(5)A and c=5.267(2)A, R{sub 1}=0.0940 and wR{sub 2}=0.0981. Both compounds are formed of similar 1D building units (BUs) organized into two different 3D regular intergrowths mediated by phosphate groups. Here, the so-called 1D-BUs are infinite ribbons formed by edge-sharing O(Bi,M){sub 4} tetrahedra with n=4 and n=3 tetrahedra-wide units. Both compounds were analyzed from the viewpoint of their relationship with the parent δ-Bi{sub 2}O{sub 3} fluorite-like structure, where phosphorus atoms substitutes for some Bi sites. A non-exhaustive review of the related structural types is given. We have checked by second harmonic generacy (SHG) microscopy that the two non-centrosymmetric structures (despite polar subunits) lead to SHG before the samples are irreversibly damaged. - Graphical abstract: This paper reports the crystal structure of two new bismuth oxophosphate compounds. Both are built on the association of n=3 and 4 building unit ribbons surrounded by isolated PO4 tetrahedra and tunnels hosting Cu{sup 2+} cations. They come in addition to the numerous Bi-based compounds already pointed out. Once more, this is the proof of the richness of this crystal system. - Highlights: • Two new bismuth oxophosphates were synthesized. • Crystal structure were solved thanks to single crystal X-Ray diffraction. • They show two different associations of n=3 and 4 ribbons built on [O,(Bi,M){sub 4}] tetrahedral sharing edges and surrounded by isolated PO4 groups. • SHG

  4. Continuing Education Workshops in Bioinformatics Positively Impact Research and Careers

    PubMed Central

    Brazas, Michelle D.; Ouellette, B. F. Francis

    2016-01-01

    Bioinformatics.ca has been hosting continuing education programs in introductory and advanced bioinformatics topics in Canada since 1999 and has trained more than 2,000 participants to date. These workshops have been adapted over the years to keep pace with advances in both science and technology as well as the changing landscape in available learning modalities and the bioinformatics training needs of our audience. Post-workshop surveys have been a mandatory component of each workshop and are used to ensure appropriate adjustments are made to workshops to maximize learning. However, neither bioinformatics.ca nor others offering similar training programs have explored the long-term impact of bioinformatics continuing education training. Bioinformatics.ca recently initiated a look back on the impact its workshops have had on the career trajectories, research outcomes, publications, and collaborations of its participants. Using an anonymous online survey, bioinformatics.ca analyzed responses from those surveyed and discovered its workshops have had a positive impact on collaborations, research, publications, and career progression. PMID:27281025

  5. Continuing Education Workshops in Bioinformatics Positively Impact Research and Careers.

    PubMed

    Brazas, Michelle D; Ouellette, B F Francis

    2016-06-01

    Bioinformatics.ca has been hosting continuing education programs in introductory and advanced bioinformatics topics in Canada since 1999 and has trained more than 2,000 participants to date. These workshops have been adapted over the years to keep pace with advances in both science and technology as well as the changing landscape in available learning modalities and the bioinformatics training needs of our audience. Post-workshop surveys have been a mandatory component of each workshop and are used to ensure appropriate adjustments are made to workshops to maximize learning. However, neither bioinformatics.ca nor others offering similar training programs have explored the long-term impact of bioinformatics continuing education training. Bioinformatics.ca recently initiated a look back on the impact its workshops have had on the career trajectories, research outcomes, publications, and collaborations of its participants. Using an anonymous online survey, bioinformatics.ca analyzed responses from those surveyed and discovered its workshops have had a positive impact on collaborations, research, publications, and career progression. PMID:27281025

  6. Online Tools for Bioinformatics Analyses in Nutrition Sciences12

    PubMed Central

    Malkaram, Sridhar A.; Hassan, Yousef I.; Zempleni, Janos

    2012-01-01

    Recent advances in “omics” research have resulted in the creation of large datasets that were generated by consortiums and centers, small datasets that were generated by individual investigators, and bioinformatics tools for mining these datasets. It is important for nutrition laboratories to take full advantage of the analysis tools to interrogate datasets for information relevant to genomics, epigenomics, transcriptomics, proteomics, and metabolomics. This review provides guidance regarding bioinformatics resources that are currently available in the public domain, with the intent to provide a starting point for investigators who want to take advantage of the opportunities provided by the bioinformatics field. PMID:22983844

  7. Built Environment Analysis Tool: April 2013

    SciTech Connect

    Porter, C.

    2013-05-01

    This documentation describes the tool development. It was created to evaluate the effects of built environment scenarios on transportation energy and greenhouse gas (GHG) emissions. This documentation also provides guidance on how to apply the tool.

  8. Principles of As-Built Engineering

    SciTech Connect

    Dolin, R.M.; Hefele, J.

    1996-11-01

    As-Built Engineering is a product realization methodology founded on the notion that life-cycle engineering should be based on what is actually produced and not on what is nominally designed. As-Built Engineering is a way of thinking about the production realization process that enables customization in mass production environments. It questions the relevance of nominal based methods of engineering and the role that tolerancing plays in product realization. As-Built Engineering recognizes that there will always be errors associated with manufacturing that cannot be controlled and therefore need to be captured in order to fully characterize each individual product`s unique attributes. One benefit of As-Built Engineering is the ability to provide actual product information to designers and analysts enabling them to verify their assumptions using actual part and assembly data. Another benefit is the ability to optimize new and re-engineered assemblies.

  9. A lightweight, flow-based toolkit for parallel and distributed bioinformatics pipelines

    PubMed Central

    2011-01-01

    Background Bioinformatic analyses typically proceed as chains of data-processing tasks. A pipeline, or 'workflow', is a well-defined protocol, with a specific structure defined by the topology of data-flow interdependencies, and a particular functionality arising from the data transformations applied at each step. In computer science, the dataflow programming (DFP) paradigm defines software systems constructed in this manner, as networks of message-passing components. Thus, bioinformatic workflows can be naturally mapped onto DFP concepts. Results To enable the flexible creation and execution of bioinformatics dataflows, we have written a modular framework for parallel pipelines in Python ('PaPy'). A PaPy workflow is created from re-usable components connected by data-pipes into a directed acyclic graph, which together define nested higher-order map functions. The successive functional transformations of input data are evaluated on flexibly pooled compute resources, either local or remote. Input items are processed in batches of adjustable size, all flowing one to tune the trade-off between parallelism and lazy-evaluation (memory consumption). An add-on module ('NuBio') facilitates the creation of bioinformatics workflows by providing domain specific data-containers (e.g., for biomolecular sequences, alignments, structures) and functionality (e.g., to parse/write standard file formats). Conclusions PaPy offers a modular framework for the creation and deployment of parallel and distributed data-processing workflows. Pipelines derive their functionality from user-written, data-coupled components, so PaPy also can be viewed as a lightweight toolkit for extensible, flow-based bioinformatics data-processing. The simplicity and flexibility of distributed PaPy pipelines may help users bridge the gap between traditional desktop/workstation and grid computing. PaPy is freely distributed as open-source Python code at http://muralab.org/PaPy, and includes extensive

  10. Bioinformatics construction of the human cell surfaceome

    PubMed Central

    da Cunha, J. P. C.; Galante, P. A. F.; de Souza, J. E.; de Souza, R. F.; Carvalho, P. M.; Ohara, D. T.; Moura, R. P.; Oba-Shinja, S. M.; Marie, S. K. N.; Silva, W. A.; Perez, R. O.; Stransky, B.; Pieprzyk, M.; Moore, J.; Caballero, O.; Gama-Rodrigues, J.; Habr-Gama, A.; Kuo, W. P.; Simpson, A. J.; Camargo, A. A.; Old, Lloyd J.; de Souza, S. J.

    2009-01-01

    Cell surface proteins are excellent targets for diagnostic and therapeutic interventions. By using bioinformatics tools, we generated a catalog of 3,702 transmembrane proteins located at the surface of human cells (human cell surfaceome). We explored the genetic diversity of the human cell surfaceome at different levels, including the distribution of polymorphisms, conservation among eukaryotic species, and patterns of gene expression. By integrating expression information from a variety of sources, we were able to identify surfaceome genes with a restricted expression in normal tissues and/or differential expression in tumors, important characteristics for putative tumor targets. A high-throughput and efficient quantitative real-time PCR approach was used to validate 593 surfaceome genes selected on the basis of their expression pattern in normal and tumor samples. A number of candidates were identified as potential diagnostic and therapeutic targets for colorectal tumors and glioblastoma. Several candidate genes were also identified as coding for cell surface cancer/testis antigens. The human cell surfaceome will serve as a reference for further studies aimed at characterizing tumor targets at the surface of human cells. PMID:19805368

  11. Bioinformatic tools for microRNA dissection

    PubMed Central

    Akhtar, Most Mauluda; Micolucci, Luigina; Islam, Md Soriful; Olivieri, Fabiola; Procopio, Antonio Domenico

    2016-01-01

    Recently, microRNAs (miRNAs) have emerged as important elements of gene regulatory networks. MiRNAs are endogenous single-stranded non-coding RNAs (∼22-nt long) that regulate gene expression at the post-transcriptional level. Through pairing with mRNA, miRNAs can down-regulate gene expression by inhibiting translation or stimulating mRNA degradation. In some cases they can also up-regulate the expression of a target gene. MiRNAs influence a variety of cellular pathways that range from development to carcinogenesis. The involvement of miRNAs in several human diseases, particularly cancer, makes them potential diagnostic and prognostic biomarkers. Recent technological advances, especially high-throughput sequencing, have led to an exponential growth in the generation of miRNA-related data. A number of bioinformatic tools and databases have been devised to manage this growing body of data. We analyze 129 miRNA tools that are being used in diverse areas of miRNA research, to assist investigators in choosing the most appropriate tools for their needs. PMID:26578605

  12. CAPweb: a bioinformatics CGH array Analysis Platform.

    PubMed

    Liva, Stéphane; Hupé, Philippe; Neuvial, Pierre; Brito, Isabel; Viara, Eric; La Rosa, Philippe; Barillot, Emmanuel

    2006-07-01

    Assessing variations in DNA copy number is crucial for understanding constitutional or somatic diseases, particularly cancers. The recently developed array-CGH (comparative genomic hybridization) technology allows this to be investigated at the genomic level. We report the availability of a web tool for analysing array-CGH data. CAPweb (CGH array Analysis Platform on the Web) is intended as a user-friendly tool enabling biologists to completely analyse CGH arrays from the raw data to the visualization and biological interpretation. The user typically performs the following bioinformatics steps of a CGH array project within CAPweb: the secure upload of the results of CGH array image analysis and of the array annotation (genomic position of the probes); first level analysis of each array, including automatic normalization of the data (for correcting experimental biases), breakpoint detection and status assignment (gain, loss or normal); validation or deletion of the analysis based on a summary report and quality criteria; visualization and biological analysis of the genomic profiles and results through a user-friendly interface. CAPweb is accessible at http://bioinfo.curie.fr/CAPweb. PMID:16845053

  13. Parallel evolutionary computation in bioinformatics applications.

    PubMed

    Pinho, Jorge; Sobral, João Luis; Rocha, Miguel

    2013-05-01

    A large number of optimization problems within the field of Bioinformatics require methods able to handle its inherent complexity (e.g. NP-hard problems) and also demand increased computational efforts. In this context, the use of parallel architectures is a necessity. In this work, we propose ParJECoLi, a Java based library that offers a large set of metaheuristic methods (such as Evolutionary Algorithms) and also addresses the issue of its efficient execution on a wide range of parallel architectures. The proposed approach focuses on the easiness of use, making the adaptation to distinct parallel environments (multicore, cluster, grid) transparent to the user. Indeed, this work shows how the development of the optimization library can proceed independently of its adaptation for several architectures, making use of Aspect-Oriented Programming. The pluggable nature of parallelism related modules allows the user to easily configure its environment, adding parallelism modules to the base source code when needed. The performance of the platform is validated with two case studies within biological model optimization. PMID:23127284

  14. Structural bioinformatics of the human spliceosomal proteome

    PubMed Central

    Korneta, Iga; Magnus, Marcin; Bujnicki, Janusz M.

    2012-01-01

    In this work, we describe the results of a comprehensive structural bioinformatics analysis of the spliceosomal proteome. We used fold recognition analysis to complement prior data on the ordered domains of 252 human splicing proteins. Examples of newly identified domains include a PWI domain in the U5 snRNP protein 200K (hBrr2, residues 258–338), while examples of previously known domains with a newly determined fold include the DUF1115 domain of the U4/U6 di-snRNP protein 90K (hPrp3, residues 540–683). We also established a non-redundant set of experimental models of spliceosomal proteins, as well as constructed in silico models for regions without an experimental structure. The combined set of structural models is available for download. Altogether, over 90% of the ordered regions of the spliceosomal proteome can be represented structurally with a high degree of confidence. We analyzed the reduced spliceosomal proteome of the intron-poor organism Giardia lamblia, and as a result, we proposed a candidate set of ordered structural regions necessary for a functional spliceosome. The results of this work will aid experimental and structural analyses of the spliceosomal proteins and complexes, and can serve as a starting point for multiscale modeling of the structure of the entire spliceosome. PMID:22573172

  15. Identifiying human MHC supertypes using bioinformatic methods.

    PubMed

    Doytchinova, Irini A; Guan, Pingping; Flower, Darren R

    2004-04-01

    Classification of MHC molecules into supertypes in terms of peptide-binding specificities is an important issue, with direct implications for the development of epitope-based vaccines with wide population coverage. In view of extremely high MHC polymorphism (948 class I and 633 class II HLA alleles) the experimental solution of this task is presently impossible. In this study, we describe a bioinformatics strategy for classifying MHC molecules into supertypes using information drawn solely from three-dimensional protein structure. Two chemometric techniques-hierarchical clustering and principal component analysis-were used independently on a set of 783 HLA class I molecules to identify supertypes based on structural similarities and molecular interaction fields calculated for the peptide binding site. Eight supertypes were defined: A2, A3, A24, B7, B27, B44, C1, and C4. The two techniques gave 77% consensus, i.e., 605 HLA class I alleles were classified in the same supertype by both methods. The proposed strategy allowed "supertype fingerprints" to be identified. Thus, the A2 supertype fingerprint is Tyr(9)/Phe(9), Arg(97), and His(114) or Tyr(116); the A3-Tyr(9)/Phe(9)/Ser(9), Ile(97)/Met(97) and Glu(114) or Asp(116); the A24-Ser(9) and Met(97); the B7-Asn(63) and Leu(81); the B27-Glu(63) and Leu(81); for B44-Ala(81); the C1-Ser(77); and the C4-Asn(77). PMID:15034046

  16. Bacterial bioinformatics: pathogenesis and the genome.

    PubMed

    Paine, Kelly; Flower, Darren R

    2002-07-01

    As the number of completed microbial genome sequences continues to grow, there is a pressing need for the exploitation of this wealth of data through a synergistic interaction between the well-established science of bacteriology and the emergent discipline of bioinformatics. Antibiotic resistance and pathogenicity in virulent bacteria has become an increasing problem, with even the strongest drugs useless against some species, such as multi-drug resistant Enterococcus faecium and Mycobacterium tuberculosis. The global spread of Human Immunodeficiency Virus (HIV) and Acquired Immune Deficiency Syndrome (AIDS) has contributed to the re-emergence of tuberculosis and the threat from new and emergent diseases. To address these problems, bacterial pathogenicity requires redefinition as Koch's postulates become obsolete. This review discusses how the use of bacterial genomic information, and the in silico tools available at present, may aid in determining the definition of a current pathogen. The combination of both fields should provide a rapid and efficient way of assisting in the future development of antimicrobial therapies. PMID:12125816

  17. The Built Environment Predicts Observed Physical Activity

    PubMed Central

    Kelly, Cheryl; Wilson, Jeffrey S.; Schootman, Mario; Clennin, Morgan; Baker, Elizabeth A.; Miller, Douglas K.

    2014-01-01

    Background: In order to improve our understanding of the relationship between the built environment and physical activity, it is important to identify associations between specific geographic characteristics and physical activity behaviors. Purpose: Examine relationships between observed physical activity behavior and measures of the built environment collected on 291 street segments in Indianapolis and St. Louis. Methods: Street segments were selected using a stratified geographic sampling design to ensure representation of neighborhoods with different land use and socioeconomic characteristics. Characteristics of the built environment on-street segments were audited using two methods: in-person field audits and audits based on interpretation of Google Street View imagery with each method blinded to results from the other. Segments were dichotomized as having a particular characteristic (e.g., sidewalk present or not) based on the two auditing methods separately. Counts of individuals engaged in different forms of physical activity on each segment were assessed using direct observation. Non-parametric statistics were used to compare counts of physically active individuals on each segment with built environment characteristic. Results: Counts of individuals engaged in physical activity were significantly higher on segments with mixed land use or all non-residential land use, and on segments with pedestrian infrastructure (e.g., crosswalks and sidewalks) and public transit. Conclusion: Several micro-level built environment characteristics were associated with physical activity. These data provide support for theories that suggest changing the built environment and related policies may encourage more physical activity. PMID:24904916

  18. Intrageneric primer design: Bringing bioinformatics tools to the class.

    PubMed

    Lima, André O S; Garcês, Sérgio P S

    2006-09-01

    Bioinformatics is one of the fastest growing scientific areas over the last decade. It focuses on the use of informatics tools for the organization and analysis of biological data. An example of their importance is the availability nowadays of dozens of software programs for genomic and proteomic studies. Thus, there is a growing field (private and academic) with a need for bachelor of science students with bioinformatics skills. In consideration of this need, described here is a problem-based class in which students are asked to design a set of intrageneric primers for PCR. The exercise is divided into five classes of 1 h each, in which students use freeware bioinformatics tools and data bases available through the Internet. Besides designing the set of primers, the students will consequently learn the significance and use of the major bioinformatics procedures, such as searching a data base, conducting and analyzing sequence multialignment, comparing sequences with a data base, and selecting primers. PMID:21638710

  19. Creating Bioinformatic Workflows within the BioExtract Server

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Computational workflows in bioinformatics are becoming increasingly important in the achievement of scientific advances. These workflows generally require access to multiple, distributed data sources and analytic tools. The requisite data sources may include large public data repositories, community...

  20. Survey of Natural Language Processing Techniques in Bioinformatics.

    PubMed

    Zeng, Zhiqiang; Shi, Hua; Wu, Yun; Hong, Zhiling

    2015-01-01

    Informatics methods, such as text mining and natural language processing, are always involved in bioinformatics research. In this study, we discuss text mining and natural language processing methods in bioinformatics from two perspectives. First, we aim to search for knowledge on biology, retrieve references using text mining methods, and reconstruct databases. For example, protein-protein interactions and gene-disease relationship can be mined from PubMed. Then, we analyze the applications of text mining and natural language processing techniques in bioinformatics, including predicting protein structure and function, detecting noncoding RNA. Finally, numerous methods and applications, as well as their contributions to bioinformatics, are discussed for future use by text mining and natural language processing researchers. PMID:26525745

  1. Survey of Natural Language Processing Techniques in Bioinformatics

    PubMed Central

    Zeng, Zhiqiang; Shi, Hua; Wu, Yun; Hong, Zhiling

    2015-01-01

    Informatics methods, such as text mining and natural language processing, are always involved in bioinformatics research. In this study, we discuss text mining and natural language processing methods in bioinformatics from two perspectives. First, we aim to search for knowledge on biology, retrieve references using text mining methods, and reconstruct databases. For example, protein-protein interactions and gene-disease relationship can be mined from PubMed. Then, we analyze the applications of text mining and natural language processing techniques in bioinformatics, including predicting protein structure and function, detecting noncoding RNA. Finally, numerous methods and applications, as well as their contributions to bioinformatics, are discussed for future use by text mining and natural language processing researchers. PMID:26525745

  2. Bioinformatics opportunities for identification and study of medicinal plants

    PubMed Central

    Sharma, Vivekanand

    2013-01-01

    Plants have been used as a source of medicine since historic times and several commercially important drugs are of plant-based origin. The traditional approach towards discovery of plant-based drugs often times involves significant amount of time and expenditure. These labor-intensive approaches have struggled to keep pace with the rapid development of high-throughput technologies. In the era of high volume, high-throughput data generation across the biosciences, bioinformatics plays a crucial role. This has generally been the case in the context of drug designing and discovery. However, there has been limited attention to date to the potential application of bioinformatics approaches that can leverage plant-based knowledge. Here, we review bioinformatics studies that have contributed to medicinal plants research. In particular, we highlight areas in medicinal plant research where the application of bioinformatics methodologies may result in quicker and potentially cost-effective leads toward finding plant-based remedies. PMID:22589384

  3. Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond

    PubMed Central

    Hiraoka, Satoshi; Yang, Ching-chia; Iwasaki, Wataru

    2016-01-01

    Metagenomic approaches are now commonly used in microbial ecology to study microbial communities in more detail, including many strains that cannot be cultivated in the laboratory. Bioinformatic analyses make it possible to mine huge metagenomic datasets and discover general patterns that govern microbial ecosystems. However, the findings of typical metagenomic and bioinformatic analyses still do not completely describe the ecology and evolution of microbes in their environments. Most analyses still depend on straightforward sequence similarity searches against reference databases. We herein review the current state of metagenomics and bioinformatics in microbial ecology and discuss future directions for the field. New techniques will allow us to go beyond routine analyses and broaden our knowledge of microbial ecosystems. We need to enrich reference databases, promote platforms that enable meta- or comprehensive analyses of diverse metagenomic datasets, devise methods that utilize long-read sequence information, and develop more powerful bioinformatic methods to analyze data from diverse perspectives. PMID:27383682

  4. The Foundations of Lifelong Health Are Built in Early Childhood

    ERIC Educational Resources Information Center

    National Forum on Early Childhood Policy and Programs, 2010

    2010-01-01

    A vital and productive society with a prosperous and sustainable future is built on a foundation of healthy child development. Health in the earliest years--beginning with the future mother's well-being before she becomes pregnant--lays the groundwork for a lifetime of vitality. When developing biological systems are strengthened by positive early…

  5. An Interactive Multimedia Learning Environment for VLSI Built with COSMOS

    ERIC Educational Resources Information Center

    Angelides, Marios C.; Agius, Harry W.

    2002-01-01

    This paper presents Bigger Bits, an interactive multimedia learning environment that teaches students about VLSI within the context of computer electronics. The system was built with COSMOS (Content Oriented semantic Modelling Overlay Scheme), which is a modelling scheme that we developed for enabling the semantic content of multimedia to be used…

  6. 28. MAP SHOWING LOCATION OF ARVFS FACILITY AS BUILT. SHOWS ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    28. MAP SHOWING LOCATION OF ARVFS FACILITY AS BUILT. SHOWS LINCOLN BOULEVARD, BIG LOST RIVER, AND NAVAL REACTORS FACILITY. F.C. TORKELSON DRAWING NUMBER 842-ARVFS-101-2. DATED OCTOBER 12, 1965. INEL INDEX CODE NUMBER: 075 0101 851 151969. - Idaho National Engineering Laboratory, Advanced Reentry Vehicle Fusing System, Scoville, Butte County, ID

  7. Skate Genome Project: Cyber-Enabled Bioinformatics Collaboration

    PubMed Central

    Vincent, J.

    2011-01-01

    The Skate Genome Project, a pilot project of the North East Cyber infrastructure Consortium, aims to produce a draft genome sequence of Leucoraja erinacea, the Little Skate. The pilot project was designed to also develop expertise in large scale collaborations across the NECC region. An overview of the bioinformatics and infrastructure challenges faced during the first year of the project will be presented. Results to date and lessons learned from the perspective of a bioinformatics core will be highlighted.

  8. Profiling, Bioinformatic, and Functional Data on the Developing Olfactory/GnRH System Reveal Cellular and Molecular Pathways Essential for This Process and Potentially Relevant for the Kallmann Syndrome

    PubMed Central

    Garaffo, Giulia; Provero, Paolo; Molineris, Ivan; Pinciroli, Patrizia; Peano, Clelia; Battaglia, Cristina; Tomaiuolo, Daniela; Etzion, Talya; Gothilf, Yoav; Santoro, Massimo; Merlo, Giorgio R.

    2013-01-01

    During embryonic development, immature neurons in the olfactory epithelium (OE) extend axons through the nasal mesenchyme, to contact projection neurons in the olfactory bulb. Axon navigation is accompanied by migration of the GnRH+ neurons, which enter the anterior forebrain and home in the septo-hypothalamic area. This process can be interrupted at various points and lead to the onset of the Kallmann syndrome (KS), a disorder characterized by anosmia and central hypogonadotropic hypogonadism. Several genes has been identified in human and mice that cause KS or a KS-like phenotype. In mice a set of transcription factors appears to be required for olfactory connectivity and GnRH neuron migration; thus we explored the transcriptional network underlying this developmental process by profiling the OE and the adjacent mesenchyme at three embryonic ages. We also profiled the OE from embryos null for Dlx5, a homeogene that causes a KS-like phenotype when deleted. We identified 20 interesting genes belonging to the following categories: (1) transmembrane adhesion/receptor, (2) axon-glia interaction, (3) scaffold/adapter for signaling, (4) synaptic proteins. We tested some of them in zebrafish embryos: the depletion of five (of six) Dlx5 targets affected axonal extension and targeting, while three (of three) affected GnRH neuron position and neurite organization. Thus, we confirmed the importance of cell–cell and cell-matrix interactions and identified new molecules needed for olfactory connection and GnRH neuron migration. Using available and newly generated data, we predicted/prioritized putative KS-disease genes, by building conserved co-expression networks with all known disease genes in human and mouse. The results show the overall validity of approaches based on high-throughput data and predictive bioinformatics to identify genes potentially relevant for the molecular pathogenesis of KS. A number of candidate will be discussed, that should be tested in future

  9. Which craft is best in bioinformatics?

    PubMed

    Attwood, T K; Miller, C J

    2001-07-01

    'Silicon-based' biology has gathered momentum as the world-wide sequencing projects have made possible the investigation and comparative analysis of complete genomes. Central to the quest to elucidate and characterise the genes and gene products encoded within genomes are pivotal concepts concerning the processes of evolution, the mechanisms of protein folding, and, crucially, the manifestation of protein function. Our use of computers to model such concepts is limited by, and must be placed in the context of, the current limits of our understanding of these biological processes. It is important to recognise that we do not have a common understanding of what constitutes a gene; we cannot invariably say that a particular sequence or fold has arisen via divergence or convergence; we do not fully understand the rules of protein folding, so we cannot predict protein structure; and we cannot invariably diagnose protein function, given knowledge only of its sequence or structure in isolation. Accepting what we cannot do with computers plays an essential role in forming an appreciation of what we can do. Without this understanding, it is easy to be misled, as spurious arguments are often used to promote over-enthusiastic notions of what particular programs can achieve. There are valuable lessons to be learned here from the field of artificial intelligence, principal among which is the realisation that capturing and representing complex knowledge is time consuming, expensive and hard. If bioinformatics is to tackle biological complexity meaningfully, the road ahead must therefore be paved with caution, rigour and pragmatism. PMID:11459349

  10. Bioinformatics Approaches for Predicting Disordered Protein Motifs.

    PubMed

    Bhowmick, Pallab; Guharoy, Mainak; Tompa, Peter

    2015-01-01

    Short, linear motifs (SLiMs) in proteins are functional microdomains consisting of contiguous residue segments along the protein sequence, typically not more than 10 consecutive amino acids in length with less than 5 defined positions. Many positions are 'degenerate' thus offering flexibility in terms of the amino acid types allowed at those positions. Their short length and degenerate nature confers evolutionary plasticity meaning that SLiMs often evolve convergently. Further, SLiMs have a propensity to occur within intrinsically unstructured protein segments and this confers versatile functionality to unstructured regions of the proteome. SLiMs mediate multiple types of protein interactions based on domain-peptide recognition and guide functions including posttranslational modifications, subcellular localization of proteins, and ligand binding. SLiMs thus behave as modular interaction units that confer versatility to protein function and SLiM-mediated interactions are increasingly being recognized as therapeutic targets. In this chapter we start with a brief description about the properties of SLiMs and their interactions and then move on to discuss algorithms and tools including several web-based methods that enable the discovery of novel SLiMs (de novo motif discovery) as well as the prediction of novel occurrences of known SLiMs. Both individual amino acid sequences as well as sets of protein sequences can be scanned using these methods to obtain statistically overrepresented sequence patterns. Lists of putatively functional SLiMs are then assembled based on parameters such as evolutionary sequence conservation, disorder scores, structural data, gene ontology terms and other contextual information that helps to assess the functional credibility or significance of these motifs. These bioinformatics methods should certainly guide experiments aimed at motif discovery. PMID:26387106

  11. Interoperability of GADU in using heterogeneous Grid resources for bioinformatics applications.

    SciTech Connect

    Sulakhe, D.; Rodriguez, A.; Wilde, M.; Foster, I.; Maltsev, N.; Univ. of Chicago

    2008-03-01

    Bioinformatics tools used for efficient and computationally intensive analysis of genetic sequences require large-scale computational resources to accommodate the growing data. Grid computational resources such as the Open Science Grid and TeraGrid have proved useful for scientific discovery. The genome analysis and database update system (GADU) is a high-throughput computational system developed to automate the steps involved in accessing the Grid resources for running bioinformatics applications. This paper describes the requirements for building an automated scalable system such as GADU that can run jobs on different Grids. The paper describes the resource-independent configuration of GADU using the Pegasus-based virtual data system that makes high-throughput computational tools interoperable on heterogeneous Grid resources. The paper also highlights the features implemented to make GADU a gateway to computationally intensive bioinformatics applications on the Grid. The paper will not go into the details of problems involved or the lessons learned in using individual Grid resources as it has already been published in our paper on genome analysis research environment (GNARE) and will focus primarily on the architecture that makes GADU resource independent and interoperable across heterogeneous Grid resources.

  12. Atlas – a data warehouse for integrative bioinformatics

    PubMed Central

    Shah, Sohrab P; Huang, Yong; Xu, Tao; Yuen, Macaire MS; Ling, John; Ouellette, BF Francis

    2005-01-01

    Background We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. Description The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL) calls that are implemented in a set of Application Programming Interfaces (APIs). The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD), Biomolecular Interaction Network Database (BIND), Database of Interacting Proteins (DIP), Molecular Interactions Database (MINT), IntAct, NCBI Taxonomy, Gene Ontology (GO), Online Mendelian Inheritance in Man (OMIM), LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations. Conclusion The Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First, Atlas stores data of

  13. Bioinformatics Analysis of MAPKKK Family Genes in Medicago truncatula

    PubMed Central

    Li, Wei; Xu, Hanyun; Liu, Ying; Song, Lili; Guo, Changhong; Shu, Yongjun

    2016-01-01

    Mitogen-activated protein kinase kinase kinase (MAPKKK) is a component of the MAPK cascade pathway that plays an important role in plant growth, development, and response to abiotic stress, the functions of which have been well characterized in several plant species, such as Arabidopsis, rice, and maize. In this study, we performed genome-wide and systemic bioinformatics analysis of MAPKKK family genes in Medicago truncatula. In total, there were 73 MAPKKK family members identified by search of homologs, and they were classified into three subfamilies, MEKK, ZIK, and RAF. Based on the genomic duplication function, 72 MtMAPKKK genes were located throughout all chromosomes, but they cluster in different chromosomes. Using microarray data and high-throughput sequencing-data, we assessed their expression profiles in growth and development processes; these results provided evidence for exploring their important functions in developmental regulation, especially in the nodulation process. Furthermore, we investigated their expression in abiotic stresses by RNA-seq, which confirmed their critical roles in signal transduction and regulation processes under stress. In summary, our genome-wide, systemic characterization and expressional analysis of MtMAPKKK genes will provide insights that will be useful for characterizing the molecular functions of these genes in M. truncatula. PMID:27049397

  14. Bioinformatics Analysis of MAPKKK Family Genes in Medicago truncatula.

    PubMed

    Li, Wei; Xu, Hanyun; Liu, Ying; Song, Lili; Guo, Changhong; Shu, Yongjun

    2016-01-01

    Mitogen-activated protein kinase kinase kinase (MAPKKK) is a component of the MAPK cascade pathway that plays an important role in plant growth, development, and response to abiotic stress, the functions of which have been well characterized in several plant species, such as Arabidopsis, rice, and maize. In this study, we performed genome-wide and systemic bioinformatics analysis of MAPKKK family genes in Medicago truncatula. In total, there were 73 MAPKKK family members identified by search of homologs, and they were classified into three subfamilies, MEKK, ZIK, and RAF. Based on the genomic duplication function, 72 MtMAPKKK genes were located throughout all chromosomes, but they cluster in different chromosomes. Using microarray data and high-throughput sequencing-data, we assessed their expression profiles in growth and development processes; these results provided evidence for exploring their important functions in developmental regulation, especially in the nodulation process. Furthermore, we investigated their expression in abiotic stresses by RNA-seq, which confirmed their critical roles in signal transduction and regulation processes under stress. In summary, our genome-wide, systemic characterization and expressional analysis of MtMAPKKK genes will provide insights that will be useful for characterizing the molecular functions of these genes in M. truncatula. PMID:27049397

  15. Built Environment Energy Analysis Tool Overview (Presentation)

    SciTech Connect

    Porter, C.

    2013-04-01

    This presentation provides an overview of the Built Environment Energy Analysis Tool, which is designed to assess impacts of future land use/built environment patterns on transportation-related energy use and greenhouse gas (GHG) emissions. The tool can be used to evaluate a range of population distribution and urban design scenarios for 2030 and 2050. This tool was produced as part of the Transportation Energy Futures (TEF) project, a Department of Energy-sponsored multi-agency project initiated to pinpoint underexplored strategies for abating GHGs and reducing petroleum dependence related to transportation.

  16. The microbiome of the built environment and mental health.

    PubMed

    Hoisington, Andrew J; Brenner, Lisa A; Kinney, Kerry A; Postolache, Teodor T; Lowry, Christopher A

    2015-01-01

    The microbiome of the built environment (MoBE) is a relatively new area of study. While some knowledge has been gained regarding impacts of the MoBE on the human microbiome and disease vulnerability, there is little knowledge of the impacts of the MoBE on mental health. Depending on the specific microbial species involved, the transfer of microorganisms from the built environment to occupant's cutaneous or mucosal membranes has the potential to increase or disrupt immunoregulation and/or exaggerate or suppress inflammation. Preclinical evidence highlighting the influence of the microbiota on systemic inflammation supports the assertion that microorganisms, including those originating from the built environment, have the potential to either increase or decrease the risk of inflammation-induced psychiatric conditions and their symptom severity. With advanced understanding of both the ecology of the built environment, and its influence on the human microbiome, it may be possible to develop bioinformed strategies for management of the built environment to promote mental health. Here we present a brief summary of microbiome research in both areas and highlight two interdependencies including the following: (1) effects of the MoBE on the human microbiome and (2) potential opportunities for manipulation of the MoBE in order to improve mental health. In addition, we propose future research directions including strategies for assessment of changes in the microbiome of common areas of built environments shared by multiple human occupants, and associated cohort-level changes in the mental health of those who spend time in the buildings. Overall, our understanding of the fields of both the MoBE and influence of host-associated microorganisms on mental health are advancing at a rapid pace and, if linked, could offer considerable benefit to health and wellness. PMID:26674771

  17. Integrating bioinformatics into senior high school: design principles and implications.

    PubMed

    Machluf, Yossy; Yarden, Anat

    2013-09-01

    Bioinformatics is an integral part of modern life sciences. It has revolutionized and redefined how research is carried out and has had an enormous impact on biotechnology, medicine, agriculture and related areas. Yet, it is only rarely integrated into high school teaching and learning programs, playing almost no role in preparing the next generation of information-oriented citizens. Here, we describe the design principles of bioinformatics learning environments, including our own, that are aimed at introducing bioinformatics into senior high school curricula through engaging learners in scientifically authentic inquiry activities. We discuss the bioinformatics-related benefits and challenges that high school teachers and students face in the course of the implementation process, in light of previous studies and our own experience. Based on these lessons, we present a new approach for characterizing the questions embedded in bioinformatics teaching and learning units, based on three criteria: the type of domain-specific knowledge required to answer each question (declarative knowledge, procedural knowledge, strategic knowledge, situational knowledge), the scientific approach from which each question stems (biological, bioinformatics, a combination of the two) and the associated cognitive process dimension (remember, understand, apply, analyze, evaluate, create). We demonstrate the feasibility of this approach using a learning environment, which we developed for the high school level, and suggest some of its implications. This review sheds light on unique and critical characteristics related to broader integration of bioinformatics in secondary education, which are also relevant to the undergraduate level, and especially on curriculum design, development of suitable learning environments and teaching and learning processes. PMID:23665511

  18. Proteomic and bioinformatic analyses of spinal cord injury‑induced skeletal muscle atrophy in rats.

    PubMed

    Wei, Zhi-Jian; Zhou, Xian-Hu; Fan, Bao-You; Lin, Wei; Ren, Yi-Ming; Feng, Shi-Qing

    2016-07-01

    Spinal cord injury (SCI) may result in skeletal muscle atrophy. Identifying diagnostic biomarkers and effective targets for treatment is an important challenge in clinical work. The aim of the present study is to elucidate potential biomarkers and therapeutic targets for SCI‑induced muscle atrophy (SIMA) using proteomic and bioinformatic analyses. The protein samples from rat soleus muscle were collected at different time points following SCI injury and separated by two‑dimensional gel electrophoresis and compared with the sham group. The identities of these protein spots were analyzed by mass spectrometry (MS). MS demonstrated that 20 proteins associated with muscle atrophy were differentially expressed. Bioinformatic analyses indicated that SIMA changed the expression of proteins associated with cellular, developmental, immune system and metabolic processes, biological adhesion and localization. The results of the present study may be beneficial in understanding the molecular mechanisms of SIMA and elucidating potential biomarkers and targets for the treatment of muscle atrophy. PMID:27177391

  19. Proteomic and bioinformatic analyses of spinal cord injury-induced skeletal muscle atrophy in rats

    PubMed Central

    WEI, ZHI-JIAN; ZHOU, XIAN-HU; FAN, BAO-YOU; LIN, WEI; REN, YI-MING; FENG, SHI-QING

    2016-01-01

    Spinal cord injury (SCI) may result in skeletal muscle atrophy. Identifying diagnostic biomarkers and effective targets for treatment is an important challenge in clinical work. The aim of the present study is to elucidate potential biomarkers and therapeutic targets for SCI-induced muscle atrophy (SIMA) using proteomic and bioinformatic analyses. The protein samples from rat soleus muscle were collected at different time points following SCI injury and separated by two-dimensional gel electrophoresis and compared with the sham group. The identities of these protein spots were analyzed by mass spectrometry (MS). MS demonstrated that 20 proteins associated with muscle atrophy were differentially expressed. Bioinformatic analyses indicated that SIMA changed the expression of proteins associated with cellular, developmental, immune system and metabolic processes, biological adhesion and localization. The results of the present study may be beneficial in understanding the molecular mechanisms of SIMA and elucidating potential biomarkers and targets for the treatment of muscle atrophy. PMID:27177391

  20. "Anarchy and a Built-In Gyro"

    ERIC Educational Resources Information Center

    Healy, Timothy S.

    1978-01-01

    Any good college resists rule, but it also has a built-in self-correcting apparatus, suggests this university president. Trustees should ask themselves: Does your college surprise you? Do you trust it? Do you wish you could be more a part of it? (Author/LBH)

  1. Schooling Built on the Multiple Intelligences

    ERIC Educational Resources Information Center

    Kunkel, Christine D.

    2009-01-01

    This article features a school built on multiple intelligences. As the first multiple intelligences school in the world, the Key Learning Community shapes its students' days to include significant time in the musical, spatial and bodily-kinesthetic intelligences, as well as the more traditional areas of logical-mathematical and linguistics. In…

  2. From Molecules to Patients: The Clinical Applications of Translational Bioinformatics

    PubMed Central

    Regan, K.

    2015-01-01

    Summary Objective In order to realize the promise of personalized medicine, Translational Bioinformatics (TBI) research will need to continue to address implementation issues across the clinical spectrum. In this review, we aim to evaluate the expanding field of TBI towards clinical applications, and define common themes and current gaps in order to motivate future research. Methods Here we present the state-of-the-art of clinical implementation of TBI-based tools and resources. Our thematic analyses of a targeted literature search of recent TBI-related articles ranged across topics in genomics, data management, hypothesis generation, molecular epidemiology, diagnostics, therapeutics and personalized medicine. Results Open areas of clinically-relevant TBI research identified in this review include developing data standards and best practices, publicly available resources, integrative systems-level approaches, user-friendly tools for clinical support, cloud computing solutions, emerging technologies and means to address pressing legal, ethical and social issues. Conclusions There is a need for further research bridging the gap from foundational TBI-based theories and methodologies to clinical implementation. We have organized the topic themes presented in this review into four conceptual foci – domain analyses, knowledge engineering, computational architectures and computation methods alongside three stages of knowledge development in order to orient future TBI efforts to accelerate the goals of personalized medicine. PMID:26293863

  3. Vignettes: diverse library staff offering diverse bioinformatics services*

    PubMed Central

    Osterbur, David L.; Alpi, Kristine; Canevari, Catharine; Corley, Pamela M.; Devare, Medha; Gaedeke, Nicola; Jacobs, Donna K.; Kirlew, Peter; Ohles, Janet A.; Vaughan, K.T.L.; Wang, Lili; Wu, Yongchun; Geer, Renata C.

    2006-01-01

    Objectives: The paper gives examples of the bioinformatics services provided in a variety of different libraries by librarians with a broad range of educational background and training. Methods: Two investigators sent an email inquiry to attendees of the “National Center for Biotechnology Information's (NCBI) Introduction to Molecular Biology Information Resources” or “NCBI Advanced Workshop for Bioinformatics Information Specialists (NAWBIS)” courses. The thirty-five-item questionnaire addressed areas such as educational background, library setting, types and numbers of users served, and bioinformatics training and support services provided. Answers were compiled into program vignettes. Discussion: The bioinformatics support services addressed in the paper are based in libraries with academic and clinical settings. Services have been established through different means: in collaboration with biology faculty as part of formal courses, through teaching workshops in the library, through one-on-one consultations, and by other methods. Librarians with backgrounds from art history to doctoral degrees in genetics have worked to establish these programs. Conclusion: Successful bioinformatics support programs can be established in libraries in a variety of different settings and by staff with a variety of different backgrounds and approaches. PMID:16888664

  4. Knowledge-driven enhancements for task composition in bioinformatics

    PubMed Central

    Sutherland, Karen; McLeod, Kenneth; Ferguson, Gus; Burger, Albert

    2009-01-01

    Background A key application area of semantic technologies is the fast-developing field of bioinformatics. Sealife was a project within this field with the aim of creating semantics-based web browsing capabilities for the Life Sciences. This includes meaningfully linking significant terms from the text of a web page to executable web services. It also involves the semantic mark-up of biological terms, linking them to biomedical ontologies, then discovering and executing services based on terms that interest the user. Results A system was produced which allows a user to identify terms of interest on a web page and subsequently connects these to a choice of web services which can make use of these inputs. Elements of Artificial Intelligence Planning build on this to present a choice of higher level goals, which can then be broken down to construct a workflow. An Argumentation System was implemented to evaluate the results produced by three different gene expression databases. An evaluation of these modules was carried out on users from a variety of backgrounds. Users with little knowledge of web services were able to achieve tasks that used several services in much less time than they would have taken to do this manually. The Argumentation System was also considered a useful resource and feedback was collected on the best way to present results. Conclusion Overall the system represents a move forward in helping users to both construct workflows and analyse results by incorporating specific domain knowledge into the software. It also provides a mechanism by which web pages can be linked to web services. However, this work covers a specific domain and much co-ordinated effort is needed to make all web services available for use in such a way, i.e. the integration of underlying knowledge is a difficult but essential task. PMID:19796396

  5. Bioinformatics tools help molecular characterization of Perkinsus olseni differentially expressed genes.

    PubMed

    Ascenso, Rita M T

    2011-01-01

    In the 80ies, in Southern Europe and in particular in Ria Formosa there was an episode of heavy mortality of the economically relevant clam Ruditapes (R.) decussatus associated with a debilitating disease (Perkinsosis) caused by Perkinsus olseni. This protozoan parasite was poorly known concerning its' differential transcriptome in response to its host, R. decussatus. This laboratory available protozoan system was used to identify parasite genes related to host interaction. Beyond the application of molecular biology technologies and methodologies, only the help of Bioinformatics tools allowed to analyze the results of the study. The strategy started with SSH technique, allowing the identification of parasite up-regulated genes in response to its natural host, then a macroarray was constructed and hybridized to characterize the parasite genes expression when exposed to bivalves hemolymph from permissive host (R. decussatus), resistant host (R. philippinarum) and non permissive bivalve (Donax trunculus) that cohabit in the same or adjacent habitats in Southern Portugal. Genes and respective peptides full molecular characterization depended on several Bioinformatic tools application. Also a new Bioinformatic tool was developed. PMID:21926442

  6. Embracing the Future: Bioinformatics for High School Women

    NASA Astrophysics Data System (ADS)

    Zales, Charlotte Rappe; Cronin, Susan J.

    Sixteen high school women participated in a 5-week residential summer program designed to encourage female and minority students to choose careers in scientific fields. Students gained expertise in bioinformatics through problem-based learning in a complex learning environment of content instruction, speakers, labs, and trips. Innovative hands-on activities filled the program. Students learned biological principles in context and sophisticated bioinformatics tools for processing data. Students additionally mastered a variety of information-searching techniques. Students completed creative individual and group projects, demonstrating the successful integration of biology, information technology, and bioinformatics. Discussions with female scientists allowed students to see themselves in similar roles. Summer residential aspects fostered an atmosphere in which students matured in interacting with others and in their views of diversity.

  7. Bioinformatics Projects Supporting Life-Sciences Learning in High Schools

    PubMed Central

    Marques, Isabel; Almeida, Paulo; Alves, Renato; Dias, Maria João; Godinho, Ana; Pereira-Leal, José B.

    2014-01-01

    The interdisciplinary nature of bioinformatics makes it an ideal framework to develop activities enabling enquiry-based learning. We describe here the development and implementation of a pilot project to use bioinformatics-based research activities in high schools, called “Bioinformatics@school.” It includes web-based research projects that students can pursue alone or under teacher supervision and a teacher training program. The project is organized so as to enable discussion of key results between students and teachers. After successful trials in two high schools, as measured by questionnaires, interviews, and assessment of knowledge acquisition, the project is expanding by the action of the teachers involved, who are helping us develop more content and are recruiting more teachers and schools. PMID:24465192

  8. Developing expertise in bioinformatics for biomedical research in Africa

    PubMed Central

    Karikari, Thomas K.; Quansah, Emmanuel; Mohamed, Wael M.Y.

    2015-01-01

    Research in bioinformatics has a central role in helping to advance biomedical research. However, its introduction to Africa has been met with some challenges (such as inadequate infrastructure, training opportunities, research funding, human resources, biorepositories and databases) that have contributed to the slow pace of development in this field across the continent. Fortunately, recent improvements in areas such as research funding, infrastructural support and capacity building are helping to develop bioinformatics into an important discipline in Africa. These contributions are leading to the establishment of world-class research facilities, biorepositories, training programmes, scientific networks and funding schemes to improve studies into disease and health in Africa. With increased contribution from all stakeholders, these developments could be further enhanced. Here, we discuss how the recent developments are contributing to the advancement of bioinformatics in Africa. PMID:26767162

  9. Bioinformatic Identification of Conserved Cis-Sequences in Coregulated Genes.

    PubMed

    Bülow, Lorenz; Hehl, Reinhard

    2016-01-01

    Bioinformatics tools can be employed to identify conserved cis-sequences in sets of coregulated plant genes because more and more gene expression and genomic sequence data become available. Knowledge on the specific cis-sequences, their enrichment and arrangement within promoters, facilitates the design of functional synthetic plant promoters that are responsive to specific stresses. The present chapter illustrates an example for the bioinformatic identification of conserved Arabidopsis thaliana cis-sequences enriched in drought stress-responsive genes. This workflow can be applied for the identification of cis-sequences in any sets of coregulated genes. The workflow includes detailed protocols to determine sets of coregulated genes, to extract the corresponding promoter sequences, and how to install and run a software package to identify overrepresented motifs. Further bioinformatic analyses that can be performed with the results are discussed. PMID:27557771

  10. Measuring the Built Environment for Physical Activity

    PubMed Central

    Brownson, Ross C.; Hoehner, Christine M.; Day, Kristen; Forsyth, Ann; Sallis, James F.

    2009-01-01

    Physical inactivity is one of the most important public health issues in the U.S. and internationally. Increasingly, links are being identified between various elements of the physical—or built—environment and physical activity. To understand the impact of the built environment on physical activity, the development of high-quality measures is essential. Three categories of built environment data are being used: (1) perceived measures obtained by telephone interview or self-administered questionnaires; (2) observational measures obtained using systematic observational methods (audits); and (3) archival data sets that are often layered and analyzed with GIS. This review provides a critical assessment of these three types of built-environment measures relevant to the study of physical activity. Among perceived measures, 19 questionnaires were reviewed, ranging in length from 7 to 68 questions. Twenty audit tools were reviewed that cover community environments (i.e., neighborhoods, cities), parks, and trails. For GIS-derived measures, more than 50 studies were reviewed. A large degree of variability was found in the operationalization of common GIS measures, which include population density, land-use mix, access to recreational facilities, and street pattern. This first comprehensive examination of built-environment measures demonstrates considerable progress over the past decade, showing diverse environmental variables available that use multiple modes of assessment. Most can be considered first-generation measures, so further development is needed. In particular, further research is needed to improve the technical quality of measures, understand the relevance to various population groups, and understand the utility of measures for science and public health. PMID:19285216

  11. Built-Environment Wind Turbine Roadmap

    SciTech Connect

    Smith, J.; Forsyth, T.; Sinclair, K.; Oteri, F.

    2012-11-01

    Although only a small contributor to total electricity production needs, built-environment wind turbines (BWTs) nonetheless have the potential to influence the public's consideration of renewable energy, and wind energy in particular. Higher population concentrations in urban environments offer greater opportunities for project visibility and an opportunity to acquaint large numbers of people to the advantages of wind projects on a larger scale. However, turbine failures will be equally visible and could have a negative effect on public perception of wind technology. This roadmap provides a framework for achieving the vision set forth by the attendees of the Built-Environment Wind Turbine Workshop on August 11 - 12, 2010, at the U.S. Department of Energy's National Renewable Energy Laboratory. The BWT roadmap outlines the stakeholder actions that could be taken to overcome the barriers identified. The actions are categorized as near-term (0 - 3 years), medium-term (4 - 7 years), and both near- and medium-term (requiring immediate to medium-term effort). To accomplish these actions, a strategic approach was developed that identifies two focus areas: understanding the built-environment wind resource and developing testing and design standards. The authors summarize the expertise and resources required in these areas.

  12. Contributions of built environment to childhood obesity.

    PubMed

    Rahman, Tamanna; Cushing, Rachel A; Jackson, Richard J

    2011-01-01

    As childhood obesity has reached epidemic proportions, it is critical to devise interventions that target the root causes of obesity and its risk factors. The two main components of childhood obesity are physical inactivity and improper nutrition, and it is becoming increasingly evident that the built environment can determine the level of exposure to these risk factors. Through a multidisciplinary literature review, we investigated the association between various built environment attributes and childhood obesity. We found that neighborhood features such as walkability/bikeability, mixed land use, accessible destinations, and transit increase resident physical activity; also that access to high-caloric foods and convenience stores increases risk of overweight and obesity, whereas the presence of neighborhood supermarkets and farmers' markets is associated with lower childhood body mass index and overweight status. It is evident that a child's built environment impacts his access to nutritious foods and physical activity. In order for children, as well as adults, to prevent onset of overweight or obesity, they need safe places to be active and local markets that offer affordable, healthy food options. Interventions that are designed to provide safe, walkable neighborhoods with access to necessary destinations will be effective in combating the epidemic of obesity. PMID:21259262

  13. Mobility disability and the urban built environment.

    PubMed

    Clarke, Philippa; Ailshire, Jennifer A; Bader, Michael; Morenoff, Jeffrey D; House, James S

    2008-09-01

    Research on the effects of the built environment in the pathway from impairment to disability has been largely absent. Using data from the Chicago Community Adult Health Study (2001-2003), the authors examined the effect of built environment characteristics on mobility disability among adults aged 45 or more years (n = 1,195) according to their level of lower extremity physical impairment. Built environment characteristics were assessed by using systematic social observation to independently rate street and sidewalk quality in the block surrounding each respondent's residence in the city of Chicago (Illinois). Using multinomial logistic regression, the authors found that street conditions had no effect on outdoor mobility among adults with only mild or no physical impairment. However, among adults with more severe impairment in neuromuscular and movement-related functions, the difference in the odd ratios for reporting severe mobility disability was over four times greater when at least one street was in fair or poor condition (characterized by cracks, potholes, or broken curbs). When all streets were in good condition, the odds of reporting mobility disability were attenuated in those with lower extremity impairment. If street quality could be improved, even somewhat, for those adults at greatest risk for disability in outdoor mobility, the disablement process could be slowed or even reversed. PMID:18667526

  14. 2. EAST ELEVATION OF IPA FACTORY; TWOSTORY SECTION BUILT IN ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. EAST ELEVATION OF IPA FACTORY; TWO-STORY SECTION BUILT IN 1892 AND PARTIALLY DESTROYED PARAPET SECTION BUILT CA. 1948. BRICK CHIMNEY ALSO BUILT CA. 1948. - Illinois Pure Aluminum Company, 109 Holmes Street, Lemont, Cook County, IL

  15. One Bedroom Units: Floor Plan, South Elevation (As Built), North ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    One Bedroom Units: Floor Plan, South Elevation (As Built), North Elevation (As Built), Section A-A (As Built), Section AA (Existing) - Aluminum City Terrace, East Hill Drive, New Kensington, Westmoreland County, PA

  16. Bioinformatic scaling of allosteric interactions in biomedical isozymes

    NASA Astrophysics Data System (ADS)

    Phillips, J. C.

    2016-09-01

    Allosteric (long-range) interactions can be surprisingly strong in proteins of biomedical interest. Here we use bioinformatic scaling to connect prior results on nonsteroidal anti-inflammatory drugs to promising new drugs that inhibit cancer cell metabolism. Many parallel features are apparent, which explain how even one amino acid mutation, remote from active sites, can alter medical results. The enzyme twins involved are cyclooxygenase (aspirin) and isocitrate dehydrogenase (IDH). The IDH results are accurate to 1% and are overdetermined by adjusting a single bioinformatic scaling parameter. It appears that the final stage in optimizing protein functionality may involve leveling of the hydrophobic limits of the arms of conformational hydrophilic hinges.

  17. Bioinformatic analysis of expression data to identify effector candidates.

    PubMed

    Reid, Adam J; Jones, John T

    2014-01-01

    Pathogens produce effectors that manipulate the host to the benefit of the pathogen. These effectors are often secreted proteins that are upregulated during the early phases of infection. These properties can be used to identify candidate effectors from genomes and transcriptomes of pathogens. Here we describe commonly used bioinformatic approaches that (1) allow identification of genes encoding predicted secreted proteins within a genome and (2) allow the identification of genes encoding predicted secreted proteins that are upregulated at important stages of the life cycle. Other approaches for bioinformatic identification of effector candidates, including OrthoMCL analysis to identify expanded gene families, are also described. PMID:24643549

  18. Georgia Power Company solar as-built drawings (Engineering Materials)

    SciTech Connect

    Not Available

    1980-04-30

    This package consists of a set of sepia reproducibles of the Final As-Built document of the Georgia Power Company solar heating and cooling system. The system utilizes 1482 DEL concentrating parabolic trough collectors (23,712 ft/sup 2/). The solar array is designed as a combination of series and parallel circuits circulating water as the heat transfer fluid. The system will displace 18.6% of the heating and cooling energy for the building. Reference DOE/AL/12548--T1.

  19. Bioinformatics education--perspectives and challenges out of Africa.

    PubMed

    Tastan Bishop, Özlem; Adebiyi, Ezekiel F; Alzohairy, Ahmed M; Everett, Dean; Ghedira, Kais; Ghouila, Amel; Kumuthini, Judit; Mulder, Nicola J; Panji, Sumir; Patterton, Hugh-G

    2015-03-01

    The discipline of bioinformatics has developed rapidly since the complete sequencing of the first genomes in the 1990s. The development of many high-throughput techniques during the last decades has ensured that bioinformatics has grown into a discipline that overlaps with, and is required for, the modern practice of virtually every field in the life sciences. This has placed a scientific premium on the availability of skilled bioinformaticians, a qualification that is extremely scarce on the African continent. The reasons for this are numerous, although the absence of a skilled bioinformatician at academic institutions to initiate a training process and build sustained capacity seems to be a common African shortcoming. This dearth of bioinformatics expertise has had a knock-on effect on the establishment of many modern high-throughput projects at African institutes, including the comprehensive and systematic analysis of genomes from African populations, which are among the most genetically diverse anywhere on the planet. Recent funding initiatives from the National Institutes of Health and the Wellcome Trust are aimed at ameliorating this shortcoming. In this paper, we discuss the problems that have limited the establishment of the bioinformatics field in Africa, as well as propose specific actions that will help with the education and training of bioinformaticians on the continent. This is an absolute requirement in anticipation of a boom in high-throughput approaches to human health issues unique to data from African populations. PMID:24990350

  20. Learning Genetics through an Authentic Research Simulation in Bioinformatics

    ERIC Educational Resources Information Center

    Gelbart, Hadas; Yarden, Anat

    2006-01-01

    Following the rationale that learning is an active process of knowledge construction as well as enculturation into a community of experts, we developed a novel web-based learning environment in bioinformatics for high-school biology majors in Israel. The learning environment enables the learners to actively participate in a guided inquiry process…

  1. An International Bioinformatics Infrastructure to Underpin the Arabidopsis Community

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The future bioinformatics needs of the Arabidopsis community as well as those of other scientific communities that depend on Arabidopsis resources were discussed at a pair of recent meetings held by the Multinational Arabidopsis Steering Committee (MASC) and the North American Arabidopsis Steering C...

  2. Technical phosphoproteomic and bioinformatic tools useful in cancer research.

    PubMed

    López, Elena; Wesselink, Jan-Jaap; López, Isabel; Mendieta, Jesús; Gómez-Puertas, Paulino; Muñoz, Sarbelio Rodríguez

    2011-01-01

    Reversible protein phosphorylation is one of the most important forms of cellular regulation. Thus, phosphoproteomic analysis of protein phosphorylation in cells is a powerful tool to evaluate cell functional status. The importance of protein kinase-regulated signal transduction pathways in human cancer has led to the development of drugs that inhibit protein kinases at the apex or intermediary levels of these pathways. Phosphoproteomic analysis of these signalling pathways will provide important insights for operation and connectivity of these pathways to facilitate identification of the best targets for cancer therapies. Enrichment of phosphorylated proteins or peptides from tissue or bodily fluid samples is required. The application of technologies such as phosphoenrichments, mass spectrometry (MS) coupled to bioinformatics tools is crucial for the identification and quantification of protein phosphorylation sites for advancing in such relevant clinical research. A combination of different phosphopeptide enrichments, quantitative techniques and bioinformatic tools is necessary to achieve good phospho-regulation data and good structural analysis of protein studies. The current and most useful proteomics and bioinformatics techniques will be explained with research examples. Our aim in this article is to be helpful for cancer research via detailing proteomics and bioinformatic tools. PMID:21967744

  3. Bioinformatics Education—Perspectives and Challenges out of Africa

    PubMed Central

    Adebiyi, Ezekiel F.; Alzohairy, Ahmed M.; Everett, Dean; Ghedira, Kais; Ghouila, Amel; Kumuthini, Judit; Mulder, Nicola J.; Panji, Sumir; Patterton, Hugh-G.

    2015-01-01

    The discipline of bioinformatics has developed rapidly since the complete sequencing of the first genomes in the 1990s. The development of many high-throughput techniques during the last decades has ensured that bioinformatics has grown into a discipline that overlaps with, and is required for, the modern practice of virtually every field in the life sciences. This has placed a scientific premium on the availability of skilled bioinformaticians, a qualification that is extremely scarce on the African continent. The reasons for this are numerous, although the absence of a skilled bioinformatician at academic institutions to initiate a training process and build sustained capacity seems to be a common African shortcoming. This dearth of bioinformatics expertise has had a knock-on effect on the establishment of many modern high-throughput projects at African institutes, including the comprehensive and systematic analysis of genomes from African populations, which are among the most genetically diverse anywhere on the planet. Recent funding initiatives from the National Institutes of Health and the Wellcome Trust are aimed at ameliorating this shortcoming. In this paper, we discuss the problems that have limited the establishment of the bioinformatics field in Africa, as well as propose specific actions that will help with the education and training of bioinformaticians on the continent. This is an absolute requirement in anticipation of a boom in high-throughput approaches to human health issues unique to data from African populations. PMID:24990350

  4. Bioinformatic-driven search for metabolic biomarkers in disease

    PubMed Central

    2011-01-01

    The search and validation of novel disease biomarkers requires the complementary power of professional study planning and execution, modern profiling technologies and related bioinformatics tools for data analysis and interpretation. Biomarkers have considerable impact on the care of patients and are urgently needed for advancing diagnostics, prognostics and treatment of disease. This survey article highlights emerging bioinformatics methods for biomarker discovery in clinical metabolomics, focusing on the problem of data preprocessing and consolidation, the data-driven search, verification, prioritization and biological interpretation of putative metabolic candidate biomarkers in disease. In particular, data mining tools suitable for the application to omic data gathered from most frequently-used type of experimental designs, such as case-control or longitudinal biomarker cohort studies, are reviewed and case examples of selected discovery steps are delineated in more detail. This review demonstrates that clinical bioinformatics has evolved into an essential element of biomarker discovery, translating new innovations and successes in profiling technologies and bioinformatics to clinical application. PMID:21884622

  5. A BIOINFORMATIC STRATEGY TO RAPIDLY CHARACTERIZE CDNA LIBRARIES

    EPA Science Inventory

    A Bioinformatic Strategy to Rapidly Characterize cDNA Libraries

    G. Charles Ostermeier1, David J. Dix2 and Stephen A. Krawetz1.
    1Departments of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, & Institute for Scientific Computing, Wayne State Univer...

  6. Incorporation of Bioinformatics Exercises into the Undergraduate Biochemistry Curriculum

    ERIC Educational Resources Information Center

    Feig, Andrew L.; Jabri, Evelyn

    2002-01-01

    The field of bioinformatics is developing faster than most biochemistry textbooks can adapt. Supplementing the undergraduate biochemistry curriculum with data-mining exercises is an ideal way to expose the students to the common databases and tools that take advantage of this vast repository of biochemical information. An integrated collection of…

  7. Design and bioinformatics analysis of genome-wide CLIP experiments

    PubMed Central

    Wang, Tao; Xiao, Guanghua; Chu, Yongjun; Zhang, Michael Q.; Corey, David R.; Xie, Yang

    2015-01-01

    The past decades have witnessed a surge of discoveries revealing RNA regulation as a central player in cellular processes. RNAs are regulated by RNA-binding proteins (RBPs) at all post-transcriptional stages, including splicing, transportation, stabilization and translation. Defects in the functions of these RBPs underlie a broad spectrum of human pathologies. Systematic identification of RBP functional targets is among the key biomedical research questions and provides a new direction for drug discovery. The advent of cross-linking immunoprecipitation coupled with high-throughput sequencing (genome-wide CLIP) technology has recently enabled the investigation of genome-wide RBP–RNA binding at single base-pair resolution. This technology has evolved through the development of three distinct versions: HITS-CLIP, PAR-CLIP and iCLIP. Meanwhile, numerous bioinformatics pipelines for handling the genome-wide CLIP data have also been developed. In this review, we discuss the genome-wide CLIP technology and focus on bioinformatics analysis. Specifically, we compare the strengths and weaknesses, as well as the scopes, of various bioinformatics tools. To assist readers in choosing optimal procedures for their analysis, we also review experimental design and procedures that affect bioinformatics analyses. PMID:25958398

  8. Technical phosphoproteomic and bioinformatic tools useful in cancer research

    PubMed Central

    2011-01-01

    Reversible protein phosphorylation is one of the most important forms of cellular regulation. Thus, phosphoproteomic analysis of protein phosphorylation in cells is a powerful tool to evaluate cell functional status. The importance of protein kinase-regulated signal transduction pathways in human cancer has led to the development of drugs that inhibit protein kinases at the apex or intermediary levels of these pathways. Phosphoproteomic analysis of these signalling pathways will provide important insights for operation and connectivity of these pathways to facilitate identification of the best targets for cancer therapies. Enrichment of phosphorylated proteins or peptides from tissue or bodily fluid samples is required. The application of technologies such as phosphoenrichments, mass spectrometry (MS) coupled to bioinformatics tools is crucial for the identification and quantification of protein phosphorylation sites for advancing in such relevant clinical research. A combination of different phosphopeptide enrichments, quantitative techniques and bioinformatic tools is necessary to achieve good phospho-regulation data and good structural analysis of protein studies. The current and most useful proteomics and bioinformatics techniques will be explained with research examples. Our aim in this article is to be helpful for cancer research via detailing proteomics and bioinformatic tools. PMID:21967744

  9. Omics-bioinformatics in the context of clinical data.

    PubMed

    Mayer, Gert; Heinze, Georg; Mischak, Harald; Hellemons, Merel E; Heerspink, Hiddo J Lambers; Bakker, Stephan J L; de Zeeuw, Dick; Haiduk, Martin; Rossing, Peter; Oberbauer, Rainer

    2011-01-01

    The Omics revolution has provided the researcher with tools and methodologies for qualitative and quantitative assessment of a wide spectrum of molecular players spanning from the genome to the meta-bolome level. As a consequence, explorative analysis (in contrast to purely hypothesis driven research procedures) has become applicable. However, numerous issues have to be considered for deriving meaningful results from Omics, and bioinformatics has to respect these in data analysis and interpretation. Aspects include sample type and quality, concise definition of the (clinical) question, and selection of samples ideally coming from thoroughly defined sample and data repositories. Omics suffers from a principal shortcoming, namely unbalanced sample-to-feature matrix denoted as "curse of dimensionality", where a feature refers to a specific gene or protein among the many thousands assayed in parallel in an Omics experiment. This setting makes the identification of relevant features with respect to a phenotype under analysis error prone from a statistical perspective. From this sample size calculation for screening studies and for verification of results from Omics, bioinformatics is essential. Here we present key elements to be considered for embedding Omics bioinformatics in a quality controlled workflow for Omics screening, feature identification, and validation. Relevant items include sample and clinical data management, minimum sample quality requirements, sample size estimates, and statistical procedures for computing the significance of findings from Omics bioinformatics in validation studies. PMID:21370098

  10. Bioinformatics for Undergraduates: Steps toward a Quantitative Bioscience Curriculum

    ERIC Educational Resources Information Center

    Chapman, Barbara S.; Christmann, James L.; Thatcher, Eileen F.

    2006-01-01

    We describe an innovative bioinformatics course developed under grants from the National Science Foundation and the California State University Program in Research and Education in Biotechnology for undergraduate biology students. The project has been part of a continuing effort to offer students classroom experiences focused on principles and…

  11. Intrageneric Primer Design: Bringing Bioinformatics Tools to the Class

    ERIC Educational Resources Information Center

    Lima, Andre O. S.; Garces, Sergio P. S.

    2006-01-01

    Bioinformatics is one of the fastest growing scientific areas over the last decade. It focuses on the use of informatics tools for the organization and analysis of biological data. An example of their importance is the availability nowadays of dozens of software programs for genomic and proteomic studies. Thus, there is a growing field (private…

  12. Pladipus Enables Universal Distributed Computing in Proteomics Bioinformatics.

    PubMed

    Verheggen, Kenneth; Maddelein, Davy; Hulstaert, Niels; Martens, Lennart; Barsnes, Harald; Vaudel, Marc

    2016-03-01

    The use of proteomics bioinformatics substantially contributes to an improved understanding of proteomes, but this novel and in-depth knowledge comes at the cost of increased computational complexity. Parallelization across multiple computers, a strategy termed distributed computing, can be used to handle this increased complexity; however, setting up and maintaining a distributed computing infrastructure requires resources and skills that are not readily available to most research groups. Here we propose a free and open-source framework named Pladipus that greatly facilitates the establishment of distributed computing networks for proteomics bioinformatics tools. Pladipus is straightforward to install and operate thanks to its user-friendly graphical interface, allowing complex bioinformatics tasks to be run easily on a network instead of a single computer. As a result, any researcher can benefit from the increased computational efficiency provided by distributed computing, hence empowering them to tackle more complex bioinformatics challenges. Notably, it enables any research group to perform large-scale reprocessing of publicly available proteomics data, thus supporting the scientific community in mining these data for novel discoveries. PMID:26510693

  13. Automatic Discovery and Inferencing of Complex Bioinformatics Web Interfaces

    SciTech Connect

    Ngu, A; Rocco, D; Critchlow, T; Buttler, D

    2003-12-22

    The World Wide Web provides a vast resource to genomics researchers in the form of web-based access to distributed data sources--e.g. BLAST sequence homology search interfaces. However, the process for seeking the desired scientific information is still very tedious and frustrating. While there are several known servers on genomic data (e.g., GeneBank, EMBL, NCBI), that are shared and accessed frequently, new data sources are created each day in laboratories all over the world. The sharing of these newly discovered genomics results are hindered by the lack of a common interface or data exchange mechanism. Moreover, the number of autonomous genomics sources and their rate of change out-pace the speed at which they can be manually identified, meaning that the available data is not being utilized to its full potential. An automated system that can find, classify, describe and wrap new sources without tedious and low-level coding of source specific wrappers is needed to assist scientists to access to hundreds of dynamically changing bioinformatics web data sources through a single interface. A correct classification of any kind of Web data source must address both the capability of the source and the conversation/interaction semantics which is inherent in the design of the Web data source. In this paper, we propose an automatic approach to classify Web data sources that takes into account both the capability and the conversational semantics of the source. The ability to discover the interaction pattern of a Web source leads to increased accuracy in the classification process. At the same time, it facilitates the extraction of process semantics, which is necessary for the automatic generation of wrappers that can interact correctly with the sources.

  14. Candidate genes for nicotine dependence via linkage, epistasis, and bioinformatics.

    PubMed

    Sullivan, Patrick F; Neale, Benjamin M; van den Oord, Edwin; Miles, Michael F; Neale, Michael C; Bulik, Cynthia M; Joyce, Peter R; Straub, Richard E; Kendler, Kenneth S

    2004-04-01

    Many smoking-related phenotypes are substantially heritable. One genome scan of nicotine dependence (ND) has been published and several others are in progress and should be completed in the next 5 years. The goal of this hypothesis-generating study was two-fold. First, we present further analyses of our genome scan data for ND published by Straub et al. [1999: Mol Psychiatry 4:129-144] (PMID: 10208445). Second, we used the method described by Cox et al. [1999: Nat Genet 21:213-215] (PMID: 9988276) to search for epistatic loci across the markers used in the genome scan. The overall results of the genome scan nearly reached the rigorous Lander and Kruglyak [1995: Nat Genet 11:241-247] criteria for "significant" linkage with the best findings on chromosomes 10 and 2. We then looked for correspondence between genes located in the 10 regions implicated in affected sibling pair (ASP) and epistatic linkage analyses with a list of genes suggested by microarray studies of experimental nicotine exposure and candidate genes from the literature. We found correspondence between linkage and microarray/candidate gene studies for genes involved with the mitogen-activated protein kinase (MAPK) signaling system, nuclear factor kappa B (NFKB) complex, neuropeptide Y (NPY) neurotransmission, a nicotinic receptor subunit (CHRNA2), the vesicular monoamine transporter (SLC18A2), genes in pathways implicated in human anxiety (HTR7, TDO2, and the endozepine-related protein precursor, DKFZP434A2417), and the micro 1-opioid receptor (OPRM1). Although the hypotheses resulting from these linkage and bioinformatic analyses are plausible and intriguing, their ultimate worth depends on replication in additional linkage samples and in future experimental studies. PMID:15048644

  15. Cell buffer with built-in test

    NASA Technical Reports Server (NTRS)

    Ott, William E. (Inventor)

    2004-01-01

    A cell buffer with built-in testing mechanism is provided. The cell buffer provides the ability to measure voltage provided by a power cell. The testing mechanism provides the ability to test whether the cell buffer is functioning properly and thus providing an accurate voltage measurement. The testing mechanism includes a test signal-provider to provide a test signal to the cell buffer. During normal operation, the test signal is disabled and the cell buffer operates normally. During testing, the test signal is enabled and changes the output of the cell buffer in a defined way. The change in the cell buffer output can then be monitored to determine if the cell buffer is functioning correctly. Specifically, if the voltage output of the cell buffer changes in a way that corresponds to the provided test signal, then the functioning of the cell buffer is confirmed. If the voltage output of the cell buffer does not change correctly, then the cell buffer is known not to be operating correctly. Thus, the built in testing mechanism provides the ability to quickly and accurately determine if the cell buffer is operating correctly. Furthermore, the testing mechanism provides this functionality without requiring excessive device size and complexity.

  16. Missing "Links" in Bioinformatics Education: Expanding Students' Conceptions of Bioinformatics Using a Biodiversity Database of Living and Fossil Reef Corals

    ERIC Educational Resources Information Center

    Nehm, Ross H.; Budd, Ann F.

    2006-01-01

    NMITA is a reef coral biodiversity database that we use to introduce students to the expansive realm of bioinformatics beyond genetics. We introduce a series of lessons that have students use this database, thereby accessing real data that can be used to test hypotheses about biodiversity and evolution while targeting the "National Science …

  17. Applying Instructional Design Theories to Bioinformatics Education in Microarray Analysis and Primer Design Workshops

    ERIC Educational Resources Information Center

    Shachak, Aviv; Ophir, Ron; Rubin, Eitan

    2005-01-01

    The need to support bioinformatics training has been widely recognized by scientists, industry, and government institutions. However, the discussion of instructional methods for teaching bioinformatics is only beginning. Here we report on a systematic attempt to design two bioinformatics workshops for graduate biology students on the basis of…

  18. Design and Implementation of an Interdepartmental Bioinformatics Program across Life Science Curricula

    ERIC Educational Resources Information Center

    Miskowski, Jennifer A.; Howard, David R.; Abler, Michael L.; Grunwald, Sandra K.

    2007-01-01

    Over the past 10 years, there has been a technical revolution in the life sciences leading to the emergence of a new discipline called bioinformatics. In response, bioinformatics-related topics have been incorporated into various undergraduate courses along with the development of new courses solely focused on bioinformatics. This report describes…

  19. Introductory Bioinformatics Exercises Utilizing Hemoglobin and Chymotrypsin to Reinforce the Protein Sequence-Structure-Function Relationship

    ERIC Educational Resources Information Center

    Inlow, Jennifer K.; Miller, Paige; Pittman, Bethany

    2007-01-01

    We describe two bioinformatics exercises intended for use in a computer laboratory setting in an upper-level undergraduate biochemistry course. To introduce students to bioinformatics, the exercises incorporate several commonly used bioinformatics tools, including BLAST, that are freely available online. The exercises build upon the students'…

  20. Report on the EMBER Project--A European Multimedia Bioinformatics Educational Resource

    ERIC Educational Resources Information Center

    Attwood, Terri K.; Selimas, Ioannis; Buis, Rob; Altenburg, Ruud; Herzog, Robert; Ledent, Valerie; Ghita, Viorica; Fernandes, Pedro; Marques, Isabel; Brugman, Marc

    2005-01-01

    EMBER was a European project aiming to develop bioinformatics teaching materials on the Web and CD-ROM to help address the recognised skills shortage in bioinformatics. The project grew out of pilot work on the development of an interactive web-based bioinformatics tutorial and the desire to repackage that resource with the help of a professional…

  1. Vertical and Horizontal Integration of Bioinformatics Education: A Modular, Interdisciplinary Approach

    ERIC Educational Resources Information Center

    Furge, Laura Lowe; Stevens-Truss, Regina; Moore, D. Blaine; Langeland, James A.

    2009-01-01

    Bioinformatics education for undergraduates has been approached primarily in two ways: introduction of new courses with largely bioinformatics focus or introduction of bioinformatics experiences into existing courses. For small colleges such as Kalamazoo, creation of new courses within an already resource-stretched setting has not been an option.…

  2. Tester-assisted built in test

    NASA Astrophysics Data System (ADS)

    Guntheroth, Kurt

    It is noted that board makers invest considerable time and money writing extensive self-tests and that this investment can be multiplied by selecting ATE (automatic test equipment) that complements and extends the power of the self-test. The tester can diagnose boards in situations where a fault prevents the self-test from running. If the tester monitors such resources as processor, memory, and I/O, confidence in test results is improved. The tester can be used during development of the self-test and to turn on prototypes before the self-test is complete. The author argues that emulative functional testers outperform other types of ATE on boards with BIST (built-in self-test) and lists features of emulative functional testers that are most important to users of BIST.

  3. The Large Built Water Clock Of Amphiaraeion.

    NASA Astrophysics Data System (ADS)

    Theodossiou, E.; Katsiotis, M.; Manimanis, V. N.; Mantarakis, P.

    A very well preserved ancient water clock was discovered during excavations at the Amphiaraeion, in Oropos, Greece. The Amphiaraeion, a famous religious and oracle center of the deified healer Amphiaraus, was active from the pre-classic period until the replacement of the ancient religion by Christianity in the 5th Century A.D.. The foretelling was supposedly done through dreams sent by the god to the believers sleeping in a special gallery. In these dreams the god suggesting to them the therapy for their illness or the solution to their problems. The patients, then threw coins into a spring of the sanctuary. In such a place, the measurement of time was a necessity. Therefore, time was kept with both a conical sundial and a water clock in the form of a fountain. According to archeologists, the large built structure that measured the time for the sanctuary dates from the 4th Century B.C.

  4. Photocatalytic oxide films in the built environment

    NASA Astrophysics Data System (ADS)

    Österlund, Lars; Topalian, Zareh

    2014-11-01

    The possibility to increase human comfort in buildings is a powerful driving force for the introduction of new technology. Among other things our sense of comfort depends on air quality, temperature, lighting level, and the possibility of having visual contact between indoors and outdoors. Indeed there is an intimate connection between energy, comfort, and health issues in the built environment, leading to a need for intelligent building materials and green architecture. Photocatalytic materials can be applied as coatings, filters, and be embedded in building materials to provide self-cleaning, antibacterial, air cleaning, deodorizing, and water cleaning functions utilizing either solar light or artificial illumination sources - either already present in buildings, or by purposefully designed luminaries. Huge improvements in indoor comfort can thus be made, and also alleviate negative health effects associated with buildings, such as the sick-house syndrome. At the same time huge cost savings can be made by reducing maintenance costs. Photocatalytic oxides can be chemically modified by changing their acid-base surface properties, which can be used to overcome deactivation problems commonly encountered for TiO2 in air cleaning applications. In addition, the wetting properties of oxides can be tailored by surface chemical modifications and thus be made e.g. oleophobic and water repellent. Here we show results of surface acid modified TiO2 coatings on various substrates by means of photo-fixation of surface sulfate species by a method invented in our group. In particular, we show that such surface treatments of photocatalytic concrete made by mixing TiO2 nanoparticles in reactive concrete powders result in concrete surfaces with beneficial self-cleaning properties. We propose that such approaches are feasible for a number of applications in the built environment, including glass, tiles, sheet metals, plastics, etc.

  5. Potential Conservation of Circadian Clock Proteins in the phylum Nematoda as Revealed by Bioinformatic Searches

    PubMed Central

    Romanowski, Andrés; Garavaglia, Matías Javier; Goya, María Eugenia; Ghiringhelli, Pablo Daniel; Golombek, Diego Andrés

    2014-01-01

    Although several circadian rhythms have been described in C. elegans, its molecular clock remains elusive. In this work we employed a novel bioinformatic approach, applying probabilistic methodologies, to search for circadian clock proteins of several of the best studied circadian model organisms of different taxa (Mus musculus, Drosophila melanogaster, Neurospora crassa, Arabidopsis thaliana and Synechoccocus elongatus) in the proteomes of C. elegans and other members of the phylum Nematoda. With this approach we found that the Nematoda contain proteins most related to the core and accessory proteins of the insect and mammalian clocks, which provide new insights into the nematode clock and the evolution of the circadian system. PMID:25396739

  6. Biochip microsystem for bioinformatics recognition and analysis

    NASA Technical Reports Server (NTRS)

    Lue, Jaw-Chyng (Inventor); Fang, Wai-Chi (Inventor)

    2011-01-01

    A system with applications in pattern recognition, or classification, of DNA assay samples. Because DNA reference and sample material in wells of an assay may be caused to fluoresce depending upon dye added to the material, the resulting light may be imaged onto an embodiment comprising an array of photodetectors and an adaptive neural network, with applications to DNA analysis. Other embodiments are described and claimed.

  7. Bioinformatics for precision medicine in oncology: principles and application to the SHIVA clinical trial

    PubMed Central

    Servant, Nicolas; Roméjon, Julien; Gestraud, Pierre; La Rosa, Philippe; Lucotte, Georges; Lair, Séverine; Bernard, Virginie; Zeitouni, Bruno; Coffin, Fanny; Jules-Clément, Gérôme; Yvon, Florent; Lermine, Alban; Poullet, Patrick; Liva, Stéphane; Pook, Stuart; Popova, Tatiana; Barette, Camille; Prud’homme, François; Dick, Jean-Gabriel; Kamal, Maud; Le Tourneau, Christophe; Barillot, Emmanuel; Hupé, Philippe

    2014-01-01

    Precision medicine (PM) requires the delivery of individually adapted medical care based on the genetic characteristics of each patient and his/her tumor. The last decade witnessed the development of high-throughput technologies such as microarrays and next-generation sequencing which paved the way to PM in the field of oncology. While the cost of these technologies decreases, we are facing an exponential increase in the amount of data produced. Our ability to use this information in daily practice relies strongly on the availability of an efficient bioinformatics system that assists in the translation of knowledge from the bench towards molecular targeting and diagnosis. Clinical trials and routine diagnoses constitute different approaches, both requiring a strong bioinformatics environment capable of (i) warranting the integration and the traceability of data, (ii) ensuring the correct processing and analyses of genomic data, and (iii) applying well-defined and reproducible procedures for workflow management and decision-making. To address the issues, a seamless information system was developed at Institut Curie which facilitates the data integration and tracks in real-time the processing of individual samples. Moreover, computational pipelines were developed to identify reliably genomic alterations and mutations from the molecular profiles of each patient. After a rigorous quality control, a meaningful report is delivered to the clinicians and biologists for the therapeutic decision. The complete bioinformatics environment and the key points of its implementation are presented in the context of the SHIVA clinical trial, a multicentric randomized phase II trial comparing targeted therapy based on tumor molecular profiling versus conventional therapy in patients with refractory cancer. The numerous challenges faced in practice during the setting up and the conduct of this trial are discussed as an illustration of PM application. PMID:24910641

  8. Progress in bioinformatics and the importance of being earnest.

    PubMed

    Attwood, T K; Miller, C J

    2002-01-01

    In silico biology has gathered momentum as, worldwide, scientists have united in a common quest to sequence, store and analyse complete genomes. This year, a pivotal achievement of this cooperative endeavour was realised in the release of a public draft of the human genome, and with it the promises to improve our understanding of diverse aspects of biology and to yield a healthier future with safe personalized medicines. Key to these goals will be the need to elucidate and characterise the genes and gene products encoded not just in the human genome, but in many genomes. These tasks are underpinned by the concepts and processes of genome and gene/protein evolution, regulation of gene expression, mechanisms of protein folding, the manifestation of protein function, and so on, all of which must be understood in the context of complex, dynamic biological systems. Our use of computers to model such concepts and systems must be placed in the context of the current limits of our understanding of them:- it is important to recognise, for example, that we don't have a common understanding either of what constitutes a gene or a protein function; we can't invariably say that a particular sequence or fold has arisen via divergent or convergent evolution; and we don't fully understand the rules of protein folding. Accepting what we can't do in silico is essential in appreciating what we can do. Without this understanding, it is easy to be misled, as notions of what particular computational approaches can achieve are sometimes rather optimistic. There are valuable lessons to be learned here from the field of Artificial Intelligence, principal among which is the realisation that capturing and representing complex knowledge is time consuming, expensive and hard. Thus, we argue here that if bioinformatics is to tackle biological complexity in earnest, it would be wise to absorb the experience distilled from decades of artificial intelligence research, and to approach the road ahead

  9. Meeting Review: 2002 O'Reilly Bioinformatics Technology Conference

    PubMed Central

    2002-01-01

    At the end of January I travelled to the States to speak at and attend the first O’Reilly Bioinformatics Technology Conference [14]. It was a large, well-organized and diverse meeting with an interesting history. Although the meeting was not a typical academic conference, its style will, I am sure, become more typical of meetings in both biological and computational sciences. Speakers at the event included prominent bioinformatics researchers such as Ewan Birney, Terry Gaasterland and Lincoln Stein; authors and leaders in the open source programming community like Damian Conway and Nat Torkington; and representatives from several publishing companies including the Nature Publishing Group, Current Science Group and the President of O’Reilly himself, Tim O’Reilly. There were presentations, tutorials, debates, quizzes and even a ‘jam session’ for musical bioinformaticists. PMID:18628852

  10. A review of estimation of distribution algorithms in bioinformatics

    PubMed Central

    Armañanzas, Rubén; Inza, Iñaki; Santana, Roberto; Saeys, Yvan; Flores, Jose Luis; Lozano, Jose Antonio; Peer, Yves Van de; Blanco, Rosa; Robles, Víctor; Bielza, Concha; Larrañaga, Pedro

    2008-01-01

    Evolutionary search algorithms have become an essential asset in the algorithmic toolbox for solving high-dimensional optimization problems in across a broad range of bioinformatics problems. Genetic algorithms, the most well-known and representative evolutionary search technique, have been the subject of the major part of such applications. Estimation of distribution algorithms (EDAs) offer a novel evolutionary paradigm that constitutes a natural and attractive alternative to genetic algorithms. They make use of a probabilistic model, learnt from the promising solutions, to guide the search process. In this paper, we set out a basic taxonomy of EDA techniques, underlining the nature and complexity of the probabilistic model of each EDA variant. We review a set of innovative works that make use of EDA techniques to solve challenging bioinformatics problems, emphasizing the EDA paradigm's potential for further research in this domain. PMID:18822112

  11. Rise and Demise of Bioinformatics? Promise and Progress

    PubMed Central

    Ouzounis, Christos A.

    2012-01-01

    The field of bioinformatics and computational biology has gone through a number of transformations during the past 15 years, establishing itself as a key component of new biology. This spectacular growth has been challenged by a number of disruptive changes in science and technology. Despite the apparent fatigue of the linguistic use of the term itself, bioinformatics has grown perhaps to a point beyond recognition. We explore both historical aspects and future trends and argue that as the field expands, key questions remain unanswered and acquire new meaning while at the same time the range of applications is widening to cover an ever increasing number of biological disciplines. These trends appear to be pointing to a redefinition of certain objectives, milestones, and possibly the field itself. PMID:22570600

  12. Bioinformatic Analysis of Toll-Like Receptor Sequences and Structures.

    PubMed

    Monie, Tom P; Gay, Nicholas J; Gangloff, Monique

    2016-01-01

    Continual advancements in computing power and sophistication, coupled with rapid increases in protein sequence and structural information, have made bioinformatic tools an invaluable resource for the molecular and structural biologist. With the degree of sequence information continuing to expand at an almost exponential rate, it is essential that scientists today have a basic understanding of how to utilise, manipulate and analyse this information for the benefit of their own experiments. In the context of Toll-Interleukin I Receptor domain containing proteins, we describe here a series of the more common and user-friendly bioinformatic tools available as Internet-based resources. These will enable the identification and alignment of protein sequences; the identification of functional motifs; the characterisation of protein secondary structure; the identification of protein structural folds and distantly homologous proteins; and the validation of the structural geometry of modelled protein structures. PMID:26803620

  13. A survey on evolutionary algorithm based hybrid intelligence in bioinformatics.

    PubMed

    Li, Shan; Kang, Liying; Zhao, Xing-Ming

    2014-01-01

    With the rapid advance in genomics, proteomics, metabolomics, and other types of omics technologies during the past decades, a tremendous amount of data related to molecular biology has been produced. It is becoming a big challenge for the bioinformatists to analyze and interpret these data with conventional intelligent techniques, for example, support vector machines. Recently, the hybrid intelligent methods, which integrate several standard intelligent approaches, are becoming more and more popular due to their robustness and efficiency. Specifically, the hybrid intelligent approaches based on evolutionary algorithms (EAs) are widely used in various fields due to the efficiency and robustness of EAs. In this review, we give an introduction about the applications of hybrid intelligent methods, in particular those based on evolutionary algorithm, in bioinformatics. In particular, we focus on their applications to three common problems that arise in bioinformatics, that is, feature selection, parameter estimation, and reconstruction of biological networks. PMID:24729969

  14. Current trends in antimicrobial agent research: chemo- and bioinformatics approaches.

    PubMed

    Hammami, Riadh; Fliss, Ismail

    2010-07-01

    Databases and chemo- and bioinformatics tools that contain genomic, proteomic and functional information have become indispensable for antimicrobial drug research. The combination of chemoinformatics tools, bioinformatics tools and relational databases provides means of analyzing, linking and comparing online search results. The development of computational tools feeds on a diversity of disciplines, including mathematics, statistics, computer science, information technology and molecular biology. The computational approach to antimicrobial agent discovery and design encompasses genomics, molecular simulation and dynamics, molecular docking, structural and/or functional class prediction, and quantitative structure-activity relationships. This article reviews progress in the development of computational methods, tools and databases used for organizing and extracting biological meaning from antimicrobial research. PMID:20546918

  15. Personalized medicine: challenges and opportunities for translational bioinformatics

    PubMed Central

    Overby, Casey Lynnette; Tarczy-Hornoch, Peter

    2013-01-01

    Personalized medicine can be defined broadly as a model of healthcare that is predictive, personalized, preventive and participatory. Two US President’s Council of Advisors on Science and Technology reports illustrate challenges in personalized medicine (in a 2008 report) and in use of health information technology (in a 2010 report). Translational bioinformatics is a field that can help address these challenges and is defined by the American Medical Informatics Association as “the development of storage, analytic and interpretive methods to optimize the transformation of increasing voluminous biomedical data into proactive, predictive, preventative and participatory health.” This article discusses barriers to implementing genomics applications and current progress toward overcoming barriers, describes lessons learned from early experiences of institutions engaged in personalized medicine and provides example areas for translational bioinformatics research inquiry. PMID:24039624

  16. Bioinformatics tools for small genomes, such as hepatitis B virus.

    PubMed

    Bell, Trevor G; Kramvis, Anna

    2015-02-01

    DNA sequence analysis is undertaken in many biological research laboratories. The workflow consists of several steps involving the bioinformatic processing of biological data. We have developed a suite of web-based online bioinformatic tools to assist with processing, analysis and curation of DNA sequence data. Most of these tools are genome-agnostic, with two tools specifically designed for hepatitis B virus sequence data. Tools in the suite are able to process sequence data from Sanger sequencing, ultra-deep amplicon resequencing (pyrosequencing) and chromatograph (trace files), as appropriate. The tools are available online at no cost and are aimed at researchers without specialist technical computer knowledge. The tools can be accessed at http://hvdr.bioinf.wits.ac.za/SmallGenomeTools, and the source code is available online at https://github.com/DrTrevorBell/SmallGenomeTools. PMID:25690798

  17. A Survey on Evolutionary Algorithm Based Hybrid Intelligence in Bioinformatics

    PubMed Central

    Li, Shan; Zhao, Xing-Ming

    2014-01-01

    With the rapid advance in genomics, proteomics, metabolomics, and other types of omics technologies during the past decades, a tremendous amount of data related to molecular biology has been produced. It is becoming a big challenge for the bioinformatists to analyze and interpret these data with conventional intelligent techniques, for example, support vector machines. Recently, the hybrid intelligent methods, which integrate several standard intelligent approaches, are becoming more and more popular due to their robustness and efficiency. Specifically, the hybrid intelligent approaches based on evolutionary algorithms (EAs) are widely used in various fields due to the efficiency and robustness of EAs. In this review, we give an introduction about the applications of hybrid intelligent methods, in particular those based on evolutionary algorithm, in bioinformatics. In particular, we focus on their applications to three common problems that arise in bioinformatics, that is, feature selection, parameter estimation, and reconstruction of biological networks. PMID:24729969

  18. Bioinformatics and Microarray Data Analysis on the Cloud.

    PubMed

    Calabrese, Barbara; Cannataro, Mario

    2016-01-01

    High-throughput platforms such as microarray, mass spectrometry, and next-generation sequencing are producing an increasing volume of omics data that needs large data storage and computing power. Cloud computing offers massive scalable computing and storage, data sharing, on-demand anytime and anywhere access to resources and applications, and thus, it may represent the key technology for facing those issues. In fact, in the recent years it has been adopted for the deployment of different bioinformatics solutions and services both in academia and in the industry. Although this, cloud computing presents several issues regarding the security and privacy of data, that are particularly important when analyzing patients data, such as in personalized medicine. This chapter reviews main academic and industrial cloud-based bioinformatics solutions; with a special focus on microarray data analysis solutions and underlines main issues and problems related to the use of such platforms for the storage and analysis of patients data. PMID:25863787

  19. Squid – a simple bioinformatics grid

    PubMed Central

    Carvalho, Paulo C; Glória, Rafael V; de Miranda, Antonio B; Degrave, Wim M

    2005-01-01

    Background BLAST is a widely used genetic research tool for analysis of similarity between nucleotide and protein sequences. This paper presents a software application entitled "Squid" that makes use of grid technology. The current version, as an example, is configured for BLAST applications, but adaptation for other computing intensive repetitive tasks can be easily accomplished in the open source version. This enables the allocation of remote resources to perform distributed computing, making large BLAST queries viable without the need of high-end computers. Results Most distributed computing / grid solutions have complex installation procedures requiring a computer specialist, or have limitations regarding operating systems. Squid is a multi-platform, open-source program designed to "keep things simple" while offering high-end computing power for large scale applications. Squid also has an efficient fault tolerance and crash recovery system against data loss, being able to re-route jobs upon node failure and recover even if the master machine fails. Our results show that a Squid application, working with N nodes and proper network resources, can process BLAST queries almost N times faster than if working with only one computer. Conclusion Squid offers high-end computing, even for the non-specialist, and is freely available at the project web site. Its open-source and binary Windows distributions contain detailed instructions and a "plug-n-play" instalation containing a pre-configured example. PMID:16078998

  20. Integration of bioinformatics into an undergraduate biology curriculum and the impact on development of mathematical skills.

    PubMed

    Wightman, Bruce; Hark, Amy T

    2012-01-01

    The development of fields such as bioinformatics and genomics has created new challenges and opportunities for undergraduate biology curricula. Students preparing for careers in science, technology, and medicine need more intensive study of bioinformatics and more sophisticated training in the mathematics on which this field is based. In this study, we deliberately integrated bioinformatics instruction at multiple course levels into an existing biology curriculum. Students in an introductory biology course, intermediate lab courses, and advanced project-oriented courses all participated in new course components designed to sequentially introduce bioinformatics skills and knowledge, as well as computational approaches that are common to many bioinformatics applications. In each course, bioinformatics learning was embedded in an existing disciplinary instructional sequence, as opposed to having a single course where all bioinformatics learning occurs. We designed direct and indirect assessment tools to follow student progress through the course sequence. Our data show significant gains in both student confidence and ability in bioinformatics during individual courses and as course level increases. Despite evidence of substantial student learning in both bioinformatics and mathematics, students were skeptical about the link between learning bioinformatics and learning mathematics. While our approach resulted in substantial learning gains, student "buy-in" and engagement might be better in longer project-based activities that demand application of skills to research problems. Nevertheless, in situations where a concentrated focus on project-oriented bioinformatics is not possible or desirable, our approach of integrating multiple smaller components into an existing curriculum provides an alternative. PMID:22987552

  1. GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training

    PubMed Central

    Atwood, Teresa K.; Bongcam-Rudloff, Erik; Brazas, Michelle E.; Corpas, Manuel; Gaudet, Pascale; Lewitter, Fran; Mulder, Nicola; Palagi, Patricia M.; Schneider, Maria Victoria; van Gelder, Celia W. G.

    2015-01-01

    In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy—paradoxically, many are actually closing “niche” bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all. PMID:25856076

  2. High-throughput protein analysis integrating bioinformatics and experimental assays.

    PubMed

    del Val, Coral; Mehrle, Alexander; Falkenhahn, Mechthild; Seiler, Markus; Glatting, Karl-Heinz; Poustka, Annemarie; Suhai, Sandor; Wiemann, Stefan

    2004-01-01

    The wealth of transcript information that has been made publicly available in recent years requires the development of high-throughput functional genomics and proteomics approaches for its analysis. Such approaches need suitable data integration procedures and a high level of automation in order to gain maximum benefit from the results generated. We have designed an automatic pipeline to analyse annotated open reading frames (ORFs) stemming from full-length cDNAs produced mainly by the German cDNA Consortium. The ORFs are cloned into expression vectors for use in large-scale assays such as the determination of subcellular protein localization or kinase reaction specificity. Additionally, all identified ORFs undergo exhaustive bioinformatic analysis such as similarity searches, protein domain architecture determination and prediction of physicochemical characteristics and secondary structure, using a wide variety of bioinformatic methods in combination with the most up-to-date public databases (e.g. PRINTS, BLOCKS, INTERPRO, PROSITE SWISSPROT). Data from experimental results and from the bioinformatic analysis are integrated and stored in a relational database (MS SQL-Server), which makes it possible for researchers to find answers to biological questions easily, thereby speeding up the selection of targets for further analysis. The designed pipeline constitutes a new automatic approach to obtaining and administrating relevant biological data from high-throughput investigations of cDNAs in order to systematically identify and characterize novel genes, as well as to comprehensively describe the function of the encoded proteins. PMID:14762202

  3. Bioinformatics: Current practice and future challenges for life science education.

    PubMed

    Hack, Catherine; Kendall, Gary

    2005-03-01

    It is widely predicted that the application of high-throughput technologies to the quantification and identification of biological molecules will cause a paradigm shift in the life sciences. However, if the biosciences are to evolve from a predominantly descriptive discipline to an information science, practitioners will require enhanced skills in mathematics, computing, and statistical analysis. Universities have responded to the widely perceived skills gap primarily by developing masters programs in bioinformatics, resulting in a rapid expansion in the provision of postgraduate bioinformatics education. There is, however, a clear need to improve the quantitative and analytical skills of life science undergraduates. This article reviews the response of academia in the United Kingdom and proposes the learning outcomes that graduates should achieve to cope with the new biology. While the analysis discussed here uses the development of bioinformatics education in the United Kingdom as an illustrative example, it is hoped that the issues raised will resonate with all those involved in curriculum development in the life sciences. PMID:21638550

  4. Using Grid technology for computationally intensive applied bioinformatics analyses.

    PubMed

    Andrade, Jorge; Berglund, Lisa; Uhlén, Mathias; Odeberg, Jacob

    2006-01-01

    For several applications and algorithms used in applied bioinformatics, a bottle neck in terms of computational time may arise when scaled up to facilitate analyses of large datasets and databases. Re-codification, algorithm modification or sacrifices in sensitivity and accuracy may be necessary to accommodate for limited computational capacity of single work stations. Grid computing offers an alternative model for solving massive computational problems by parallel execution of existing algorithms and software implementations. We present the implementation of a Grid-aware model for solving computationally intensive bioinformatic analyses exemplified by a blastp sliding window algorithm for whole proteome sequence similarity analysis, and evaluate the performance in comparison with a local cluster and a single workstation. Our strategy involves temporary installations of the BLAST executable and databases on remote nodes at submission, accommodating for dynamic Grid environments as it avoids the need of predefined runtime environments (preinstalled software and databases at specific Grid-nodes). Importantly, the implementation is generic where the BLAST executable can be replaced by other software tools to facilitate analyses suitable for parallelisation. This model should be of general interest in applied bioinformatics. Scripts and procedures are freely available from the authors. PMID:17518760

  5. Best practices in bioinformatics training for life scientists.

    PubMed

    Via, Allegra; Blicher, Thomas; Bongcam-Rudloff, Erik; Brazas, Michelle D; Brooksbank, Cath; Budd, Aidan; De Las Rivas, Javier; Dreyer, Jacqueline; Fernandes, Pedro L; van Gelder, Celia; Jacob, Joachim; Jimenez, Rafael C; Loveland, Jane; Moran, Federico; Mulder, Nicola; Nyrönen, Tommi; Rother, Kristian; Schneider, Maria Victoria; Attwood, Teresa K

    2013-09-01

    The mountains of data thrusting from the new landscape of modern high-throughput biology are irrevocably changing biomedical research and creating a near-insatiable demand for training in data management and manipulation and data mining and analysis. Among life scientists, from clinicians to environmental researchers, a common theme is the need not just to use, and gain familiarity with, bioinformatics tools and resources but also to understand their underlying fundamental theoretical and practical concepts. Providing bioinformatics training to empower life scientists to handle and analyse their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource-centric demos, using interactivity, problem-solving exercises and cooperative learning to substantially enhance training quality and learning outcomes. In this context, this article discusses various pragmatic criteria for identifying training needs and learning objectives, for selecting suitable trainees and trainers, for developing and maintaining training skills and evaluating training quality. Adherence to these criteria may help not only to guide course organizers and trainers on the path towards bioinformatics training excellence but, importantly, also to improve the training experience for life scientists. PMID:23803301

  6. GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training.

    PubMed

    Attwood, Teresa K; Atwood, Teresa K; Bongcam-Rudloff, Erik; Brazas, Michelle E; Corpas, Manuel; Gaudet, Pascale; Lewitter, Fran; Mulder, Nicola; Palagi, Patricia M; Schneider, Maria Victoria; van Gelder, Celia W G

    2015-04-01

    In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy--paradoxically, many are actually closing "niche" bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all. PMID:25856076

  7. A primer to frequent itemset mining for bioinformatics.

    PubMed

    Naulaerts, Stefan; Meysman, Pieter; Bittremieux, Wout; Vu, Trung Nghia; Vanden Berghe, Wim; Goethals, Bart; Laukens, Kris

    2015-03-01

    Over the past two decades, pattern mining techniques have become an integral part of many bioinformatics solutions. Frequent itemset mining is a popular group of pattern mining techniques designed to identify elements that frequently co-occur. An archetypical example is the identification of products that often end up together in the same shopping basket in supermarket transactions. A number of algorithms have been developed to address variations of this computationally non-trivial problem. Frequent itemset mining techniques are able to efficiently capture the characteristics of (complex) data and succinctly summarize it. Owing to these and other interesting properties, these techniques have proven their value in biological data analysis. Nevertheless, information about the bioinformatics applications of these techniques remains scattered. In this primer, we introduce frequent itemset mining and their derived association rules for life scientists. We give an overview of various algorithms, and illustrate how they can be used in several real-life bioinformatics application domains. We end with a discussion of the future potential and open challenges for frequent itemset mining in the life sciences. PMID:24162173

  8. Best practices in bioinformatics training for life scientists

    PubMed Central

    Blicher, Thomas; Bongcam-Rudloff, Erik; Brazas, Michelle D.; Brooksbank, Cath; Budd, Aidan; De Las Rivas, Javier; Dreyer, Jacqueline; Fernandes, Pedro L.; van Gelder, Celia; Jacob, Joachim; Jimenez, Rafael C.; Loveland, Jane; Moran, Federico; Mulder, Nicola; Nyrönen, Tommi; Rother, Kristian; Schneider, Maria Victoria; Attwood, Teresa K.

    2013-01-01

    The mountains of data thrusting from the new landscape of modern high-throughput biology are irrevocably changing biomedical research and creating a near-insatiable demand for training in data management and manipulation and data mining and analysis. Among life scientists, from clinicians to environmental researchers, a common theme is the need not just to use, and gain familiarity with, bioinformatics tools and resources but also to understand their underlying fundamental theoretical and practical concepts. Providing bioinformatics training to empower life scientists to handle and analyse their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource-centric demos, using interactivity, problem-solving exercises and cooperative learning to substantially enhance training quality and learning outcomes. In this context, this article discusses various pragmatic criteria for identifying training needs and learning objectives, for selecting suitable trainees and trainers, for developing and maintaining training skills and evaluating training quality. Adherence to these criteria may help not only to guide course organizers and trainers on the path towards bioinformatics training excellence but, importantly, also to improve the training experience for life scientists. PMID:23803301

  9. A primer to frequent itemset mining for bioinformatics

    PubMed Central

    Naulaerts, Stefan; Meysman, Pieter; Bittremieux, Wout; Vu, Trung Nghia; Vanden Berghe, Wim; Goethals, Bart

    2015-01-01

    Over the past two decades, pattern mining techniques have become an integral part of many bioinformatics solutions. Frequent itemset mining is a popular group of pattern mining techniques designed to identify elements that frequently co-occur. An archetypical example is the identification of products that often end up together in the same shopping basket in supermarket transactions. A number of algorithms have been developed to address variations of this computationally non-trivial problem. Frequent itemset mining techniques are able to efficiently capture the characteristics of (complex) data and succinctly summarize it. Owing to these and other interesting properties, these techniques have proven their value in biological data analysis. Nevertheless, information about the bioinformatics applications of these techniques remains scattered. In this primer, we introduce frequent itemset mining and their derived association rules for life scientists. We give an overview of various algorithms, and illustrate how they can be used in several real-life bioinformatics application domains. We end with a discussion of the future potential and open challenges for frequent itemset mining in the life sciences. PMID:24162173

  10. Inter-laboratory study of human in vitro toxicogenomics-based tests as alternative methods for evaluating chemical carcinogenicity: a bioinformatics perspective.

    PubMed

    Herwig, R; Gmuender, H; Corvi, R; Bloch, K M; Brandenburg, A; Castell, J; Ceelen, L; Chesne, C; Doktorova, T Y; Jennen, D; Jennings, P; Limonciel, A; Lock, E A; McMorrow, T; Phrakonkham, P; Radford, R; Slattery, C; Stierum, R; Vilardell, M; Wittenberger, T; Yildirimman, R; Ryan, M; Rogiers, V; Kleinjans, J

    2016-09-01

    The assessment of the carcinogenic potential of chemicals with alternative, human-based in vitro systems has become a major goal of toxicogenomics. The central read-out of these assays is the transcriptome, and while many studies exist that explored the gene expression responses of such systems, reports on robustness and reproducibility, when testing them independently in different laboratories, are still uncommon. Furthermore, there is limited knowledge about variability induced by the data analysis protocols. We have conducted an inter-laboratory study for testing chemical carcinogenicity evaluating two human in vitro assays: hepatoma-derived cells and hTERT-immortalized renal proximal tubule epithelial cells, representing liver and kidney as major target organs. Cellular systems were initially challenged with thirty compounds, genome-wide gene expression was measured with microarrays, and hazard classifiers were built from this training set. Subsequently, each system was independently established in three different laboratories, and gene expression measurements were conducted using anonymized compounds. Data analysis was performed independently by two separate groups applying different protocols for the assessment of inter-laboratory reproducibility and for the prediction of carcinogenic hazard. As a result, both workflows came to very similar conclusions with respect to (1) identification of experimental outliers, (2) overall assessment of robustness and inter-laboratory reproducibility and (3) re-classification of the unknown compounds to the respective toxicity classes. In summary, the developed bioinformatics workflows deliver accurate measures for inter-laboratory comparison studies, and the study can be used as guidance for validation of future carcinogenicity assays in order to implement testing of human in vitro alternatives to animal testing. PMID:26525393

  11. Monitoring the expansion of built-up areas in Seberang Perai region, Penang State, Malaysia

    NASA Astrophysics Data System (ADS)

    Samat, N.

    2014-02-01

    Rapid urbanization has caused land use transformation and encroachment of built environment into arable agriculture land. Uncontrolled expansion could bring negative impacts to society, space and the environment. Therefore, information on expansion and future spatial pattern of built-up areas would be useful for planners and decision makers in formulating policies towards managing and planning for sustainable urban development. This study demonstrates the usage of Geographic Information System in monitoring the expansion of built-up area in Seberang Perai region, Penang State, Malaysia. Built-up area has increased by approximately 20% between 1990 and 2001 and further increased by 12% between 2001 and 2007. New development is expected to continue encroach into existing open space and agriculture area since those are the only available land in this study area. The information on statistics of the expansion of built-up area and future spatial pattern of urban expansion were useful in planning and managing urban spatial growth.

  12. DETAIL OF TYPICAL GIRDER SPAN, PIER NUMBER 5 (BUILT IN ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    DETAIL OF TYPICAL GIRDER SPAN, PIER NUMBER 5 (BUILT IN 1922) AND PIER NUMBER 6 (BUILT IN 1929). VIEW TO NORTH. - Hassayampa Bridge, Spanning Hassayampa River at old U.S. Highway 80, Arlington, Maricopa County, AZ

  13. Sequestering CO2 in the Built Environment

    NASA Astrophysics Data System (ADS)

    Constantz, B. R.

    2009-12-01

    Calera’s Carbonate Mineralization by Aqueous Precipitation (CMAP) technology with beneficial reuse has been called, “game-changing” by Carl Pope, Director of the Sierra Club. Calera offers a solution to the scale of the carbon problem. By capturing carbon into the built environment through carbonate mineralization, Calera provides a sound and cost-effective alternative to Geologic Sequestration and Terrestrial Sequestration. The CMAP technology permanently converts carbon dioxide into a mineral form that can be stored above ground, or used as a building material. The process produces a suite of carbonate-containing minerals of various polymorphic forms. Calera product can be substituted into blends with ordinary Portland cements and used as aggregate to produce concrete with reduced carbon, carbon neutral, or carbon negative footprints. For each ton of product produced, approximately half a ton of carbon dioxide can be sequestered using the Calera process. Coal and natural gas are composed of predominately istopically light carbon, as the carbon in the fuel is plant-derived. Thus, power plant CO2 emissions have relatively low δ13C values.The carbon species throughout the CMAP process are identified through measuring the inorganic carbon content, δ13C values of the dissolved carbonate species, and the product carbonate minerals. Measuring δ13C allows for tracking the flue gas CO2 throughout the capture process. Initial analysis of the capture of propane flue gas (δ13C ˜ -25 ‰) with seawater (δ13C ˜ -10 ‰) and industrial brucite tailings from a retired magnesium oxide plant in Moss Landing, CA (δ13C ˜ -7 ‰ from residual calcite) produced carbonate mineral products with a δ13C value of ˜ -20 ‰. This isotopically light carbon, transformed from flue gas to stable carbonate minerals, can be transferred and tracked through the capture process, and finally to the built environment. CMAP provides an economical solution to global warming by producing

  14. Sources of airborne microorganisms in the built environment.

    PubMed

    Prussin, Aaron J; Marr, Linsey C

    2015-01-01

    Each day people are exposed to millions of bioaerosols, including whole microorganisms, which can have both beneficial and detrimental effects. The next chapter in understanding the airborne microbiome of the built environment is characterizing the various sources of airborne microorganisms and the relative contribution of each. We have identified the following eight major categories of sources of airborne bacteria, viruses, and fungi in the built environment: humans; pets; plants; plumbing systems; heating, ventilation, and air-conditioning systems; mold; dust resuspension; and the outdoor environment. Certain species are associated with certain sources, but the full potential of source characterization and source apportionment has not yet been realized. Ideally, future studies will quantify detailed emission rates of microorganisms from each source and will identify the relative contribution of each source to the indoor air microbiome. This information could then be used to probe fundamental relationships between specific sources and human health, to design interventions to improve building health and human health, or even to provide evidence for forensic investigations. PMID:26694197

  15. The OAuth 2.0 Web Authorization Protocol for the Internet Addiction Bioinformatics (IABio) Database.

    PubMed

    Choi, Jeongseok; Kim, Jaekwon; Lee, Dong Kyun; Jang, Kwang Soo; Kim, Dai-Jin; Choi, In Young

    2016-03-01

    Internet addiction (IA) has become a widespread and problematic phenomenon as smart devices pervade society. Moreover, internet gaming disorder leads to increases in social expenditures for both individuals and nations alike. Although the prevention and treatment of IA are getting more important, the diagnosis of IA remains problematic. Understanding the neurobiological mechanism of behavioral addictions is essential for the development of specific and effective treatments. Although there are many databases related to other addictions, a database for IA has not been developed yet. In addition, bioinformatics databases, especially genetic databases, require a high level of security and should be designed based on medical information standards. In this respect, our study proposes the OAuth standard protocol for database access authorization. The proposed IA Bioinformatics (IABio) database system is based on internet user authentication, which is a guideline for medical information standards, and uses OAuth 2.0 for access control technology. This study designed and developed the system requirements and configuration. The OAuth 2.0 protocol is expected to establish the security of personal medical information and be applied to genomic research on IA. PMID:27103887

  16. BioZone Exploting Source-Capability Information for Integrated Access to Multiple Bioinformatics Data Sources

    SciTech Connect

    Liu, L; Buttler, D; Paques, H; Pu, C; Critchlow

    2002-01-28

    Modern Bioinformatics data sources are widely used by molecular biologists for homology searching and new drug discovery. User-friendly and yet responsive access is one of the most desirable properties for integrated access to the rapidly growing, heterogeneous, and distributed collection of data sources. The increasing volume and diversity of digital information related to bioinformatics (such as genomes, protein sequences, protein structures, etc.) have led to a growing problem that conventional data management systems do not have, namely finding which information sources out of many candidate choices are the most relevant and most accessible to answer a given user query. We refer to this problem as the query routing problem. In this paper we introduce the notation and issues of query routing, and present a practical solution for designing a scalable query routing system based on multi-level progressive pruning strategies. The key idea is to create and maintain source-capability profiles independently, and to provide algorithms that can dynamically discover relevant information sources for a given query through the smart use of source profiles. Compared to the keyword-based indexing techniques adopted in most of the search engines and software, our approach offers fine-granularity of interest matching, thus it is more powerful and effective for handling queries with complex conditions.

  17. BioZoom: Exploiting Source-Capability Information for Integrated Access to Multiple Bioinformatics Data Sources

    SciTech Connect

    Liu, L; Buttler, D; Critchlow, T J; Han, W; Paques, H; Pu, C; Rocco, D

    2003-01-09

    Modern Bioinformatics data sources are widely used by molecular biologists for homology searching and new drug discovery. User-friendly and yet responsive access is one of the most desirable properties for integrated access to the rapidly growing, heterogeneous, and distributed collection of data sources. The increasing volume and diversity of digital information related to bioinformatics (such as genomes, protein sequences, protein structures, etc.) have led to a growing problem that conventional data management systems do not have, namely finding which information sources out of many candidate choices are the most relevant and most accessible to answer a given user query. We refer to this problem as the query routing problem. In this paper we introduce the notation and issues of query routing, and present a practical solution for designing a scalable query routing system based on multi-level progressive pruning strategies. The key idea is to create and maintain source-capability profiles independently, and to provide algorithms that can dynamically discover relevant information sources for a given query through the smart use of source profiles. Compared to the keyword-based indexing techniques adopted in most of the search engines and software, our approach offers fine-granularity of interest matching, thus it is more powerful and effective for handling queries with complex conditions.

  18. The OAuth 2.0 Web Authorization Protocol for the Internet Addiction Bioinformatics (IABio) Database

    PubMed Central

    Choi, Jeongseok; Kim, Jaekwon; Lee, Dong Kyun; Jang, Kwang Soo; Kim, Dai-Jin

    2016-01-01

    Internet addiction (IA) has become a widespread and problematic phenomenon as smart devices pervade society. Moreover, internet gaming disorder leads to increases in social expenditures for both individuals and nations alike. Although the prevention and treatment of IA are getting more important, the diagnosis of IA remains problematic. Understanding the neurobiological mechanism of behavioral addictions is essential for the development of specific and effective treatments. Although there are many databases related to other addictions, a database for IA has not been developed yet. In addition, bioinformatics databases, especially genetic databases, require a high level of security and should be designed based on medical information standards. In this respect, our study proposes the OAuth standard protocol for database access authorization. The proposed IA Bioinformatics (IABio) database system is based on internet user authentication, which is a guideline for medical information standards, and uses OAuth 2.0 for access control technology. This study designed and developed the system requirements and configuration. The OAuth 2.0 protocol is expected to establish the security of personal medical information and be applied to genomic research on IA. PMID:27103887

  19. 46 CFR 67.97 - United States built.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 2 2012-10-01 2012-10-01 false United States built. 67.97 Section 67.97 Shipping COAST... DOCUMENTATION OF VESSELS Build Requirements for Vessel Documentation § 67.97 United States built. To be considered built in the United States a vessel must meet both of the following criteria: (a) All...

  20. 46 CFR 67.97 - United States built.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 2 2014-10-01 2014-10-01 false United States built. 67.97 Section 67.97 Shipping COAST... DOCUMENTATION OF VESSELS Build Requirements for Vessel Documentation § 67.97 United States built. To be considered built in the United States a vessel must meet both of the following criteria: (a) All...

  1. 46 CFR 67.97 - United States built.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 2 2013-10-01 2013-10-01 false United States built. 67.97 Section 67.97 Shipping COAST... DOCUMENTATION OF VESSELS Build Requirements for Vessel Documentation § 67.97 United States built. To be considered built in the United States a vessel must meet both of the following criteria: (a) All...

  2. 47 CFR 15.23 - Home-built devices.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false Home-built devices. 15.23 Section 15.23 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES General § 15.23 Home-built... that the individual builder of home-built equipment may not possess the means to perform...

  3. 47 CFR 15.23 - Home-built devices.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 1 2011-10-01 2011-10-01 false Home-built devices. 15.23 Section 15.23 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES General § 15.23 Home-built... that the individual builder of home-built equipment may not possess the means to perform...

  4. 46 CFR 67.97 - United States built.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 2 2011-10-01 2011-10-01 false United States built. 67.97 Section 67.97 Shipping COAST... DOCUMENTATION OF VESSELS Build Requirements for Vessel Documentation § 67.97 United States built. To be considered built in the United States a vessel must meet both of the following criteria: (a) All...

  5. 47 CFR 15.23 - Home-built devices.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 1 2013-10-01 2013-10-01 false Home-built devices. 15.23 Section 15.23 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES General § 15.23 Home-built... that the individual builder of home-built equipment may not possess the means to perform...

  6. 47 CFR 15.23 - Home-built devices.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 1 2014-10-01 2014-10-01 false Home-built devices. 15.23 Section 15.23 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES General § 15.23 Home-built... that the individual builder of home-built equipment may not possess the means to perform...

  7. 47 CFR 15.23 - Home-built devices.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 1 2012-10-01 2012-10-01 false Home-built devices. 15.23 Section 15.23 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES General § 15.23 Home-built... that the individual builder of home-built equipment may not possess the means to perform...

  8. 46 CFR 67.97 - United States built.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 2 2010-10-01 2010-10-01 false United States built. 67.97 Section 67.97 Shipping COAST... DOCUMENTATION OF VESSELS Build Requirements for Vessel Documentation § 67.97 United States built. To be considered built in the United States a vessel must meet both of the following criteria: (a) All...

  9. YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry-based Proteomics Research

    PubMed Central

    Colangelo, Christopher M.; Shifman, Mark; Cheung, Kei-Hoi; Stone, Kathryn L.; Carriero, Nicholas J.; Gulcicek, Erol E.; Lam, TuKiet T.; Wu, Terence; Bjornson, Robert D.; Bruce, Can; Nairn, Angus C.; Rinehart, Jesse; Miller, Perry L.; Williams, Kenneth R.

    2015-01-01

    We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database (YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a single laboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography–tandem mass spectrometry (LC–MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring (MRM)/selective reaction monitoring (SRM) assay development. We have linked YPED’s database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results. PMID:25712262

  10. Sequential and Structural Aspects of Antifungal Peptides from Animals, Bacteria and Fungi Based on Bioinformatics Tools.

    PubMed

    Neelabh; Singh, Karuna; Rani, Jyoti

    2016-06-01

    Emerging drug resistance varieties and hyper-virulent strains of microorganisms have compelled the scientific fraternity to develop more potent and less harmful therapeutics. Antimicrobial peptides could be one of such therapeutics. This review is an attempt to explore antifungal peptides naturally produced by prokaryotes as well as eukaryotes. They are components of innate immune system providing first line of defence against microbial attacks, especially in eukaryotes. The present article concentrates on types, structures, sources and mode of action of gene-encoded antifungal peptides such as mammalian defensins, protegrins, tritrpticins, histatins, lactoferricins, antifungal peptides derived from birds, amphibians, insects, fungi, bacteria and their synthetic analogues such as pexiganan, omiganan, echinocandins and Novexatin. In silico drug designing, a major revolution in the area of therapeutics, facilitates drug development by exploiting different bioinformatics tools. With this view, bioinformatics tools were used to visualize the structural details of antifungal peptides and to predict their level of similarity. Current practices and recent developments in this area have also been discussed briefly. PMID:27060002

  11. Documenting the emergence of bio-ontologies: or, why researching bioinformatics requires HPSSB.

    PubMed

    Leonelli, Sabina

    2010-01-01

    This paper reflects on the analytic challenges emerging from the study of bioinformatic tools recently created to store and disseminate biological data, such as databases, repositories, and bio-ontologies. I focus my discussion on the Gene Ontology, a term that defines three entities at once: a classification system facilitating the distribution and use of genomic data as evidence towards new insights; an expert community specialised in the curation of those data; and a scientific institution promoting the use of this tool among experimental biologists. These three dimensions of the Gene Ontology can be clearly distinguished analytically, but are tightly intertwined in practice. I suggest that this is true of all bioinformatic tools: they need to be understood simultaneously as epistemic, social, and institutional entities, since they shape the knowledge extracted from data and at the same time regulate the organisation, development, and communication of research. This viewpoint has one important implication for the methodologies used to study these tools; that is, the need to integrate historical, philosophical, and sociological approaches. I illustrate this claim through examples of misunderstandings that may result from a narrowly disciplinary study of the Gene Ontology, as I experienced them in my own research. PMID:20848809

  12. Opportunities and challenges provided by cloud repositories for bioinformatics-enabled drug discovery.

    PubMed

    Dalpé, Gratien; Joly, Yann

    2014-09-01

    Healthcare-related bioinformatics databases are increasingly offering the possibility to maintain, organize, and distribute DNA sequencing data. Different national and international institutions are currently hosting such databases that offer researchers website platforms where they can obtain sequencing data on which they can perform different types of analysis. Until recently, this process remained mostly one-dimensional, with most analysis concentrated on a limited amount of data. However, newer genome sequencing technology is producing a huge amount of data that current computer facilities are unable to handle. An alternative approach has been to start adopting cloud computing services for combining the information embedded in genomic and model system biology data, patient healthcare records, and clinical trials' data. In this new technological paradigm, researchers use virtual space and computing power from existing commercial or not-for-profit cloud service providers to access, store, and analyze data via different application programming interfaces. Cloud services are an alternative to the need of larger data storage; however, they raise different ethical, legal, and social issues. The purpose of this Commentary is to summarize how cloud computing can contribute to bioinformatics-based drug discovery and to highlight some of the outstanding legal, ethical, and social issues that are inherent in the use of cloud services. PMID:25195583

  13. An Abstract Description Approach to the Discovery and Classification of Bioinformatics Web Sources

    SciTech Connect

    Rocco, D; Critchlow, T J

    2003-05-01

    The World Wide Web provides an incredible resource to genomics researchers in the form of dynamic data sources--e.g. BLAST sequence homology search interfaces. The growth rate of these sources outpaces the speed at which they can be manually classified, meaning that the available data is not being utilized to its full potential. Existing research has not addressed the problems of automatically locating, classifying, and integrating classes of bioinformatics data sources. This paper presents an overview of a system for finding classes of bioinformatics data sources and integrating them behind a unified interface. We examine an approach to classifying these sources automatically that relies on an abstract description format: the service class description. This format allows a domain expert to describe the important features of an entire class of services without tying that description to any particular Web source. We present the features of this description format in the context of BLAST sources to show how the service class description relates to Web sources that are being described. We then show how a service class description can be used to classify an arbitrary Web source to determine if that source is an instance of the described service. To validate the effectiveness of this approach, we have constructed a prototype that can correctly classify approximately two-thirds of the BLAST sources we tested. We then examine these results, consider the factors that affect correct automatic classification, and discuss future work.

  14. Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses

    PubMed Central

    Liu, Bo; Madduri, Ravi K; Sotomayor, Borja; Chard, Kyle; Lacinski, Lukasz; Dave, Utpal J; Li, Jianqiang; Liu, Chunchen; Foster, Ian T

    2014-01-01

    Due to the upcoming data deluge of genome data, the need for storing and processing large-scale genome data, easy access to biomedical analyses tools, efficient data sharing and retrieval has presented significant challenges. The variability in data volume results in variable computing and storage requirements, therefore biomedical researchers are pursuing more reliable, dynamic and convenient methods for conducting sequencing analyses. This paper proposes a Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses, which enables reliable and highly scalable execution of sequencing analyses workflows in a fully automated manner. Our platform extends the existing Galaxy workflow system by adding data management capabilities for transferring large quantities of data efficiently and reliably (via Globus Transfer), domain-specific analyses tools preconfigured for immediate use by researchers (via user-specific tools integration), automatic deployment on Cloud for on-demand resource allocation and pay-as-you-go pricing (via Globus Provision), a Cloud provisioning tool for auto-scaling (via HTCondor scheduler), and the support for validating the correctness of workflows (via semantic verification tools). Two bioinformatics workflow use cases as well as performance evaluation are presented to validate the feasibility of the proposed approach. PMID:24462600

  15. GITIRBio: A Semantic and Distributed Service Oriented-Architecture for Bioinformatics Pipeline.

    PubMed

    Castillo, Luis F; López-Gartner, Germán; Isaza, Gustavo A; Sánchez, Mariana; Arango, Jeferson; Agudelo-Valencia, Daniel; Castaño, Sergio

    2015-01-01

    The need to process large quantities of data generated from genomic sequencing has resulted in a difficult task for life scientists who are not familiar with the use of command-line operations or developments in high performance computing and parallelization. This knowledge gap, along with unfamiliarity with necessary processes, can hinder the execution of data processing tasks. Furthermore, many of the commonly used bioinformatics tools for the scientific community are presented as isolated, unrelated entities that do not provide an integrated, guided, and assisted interaction with the scheduling facilities of computational resources or distribution, processing and mapping with runtime analysis. This paper presents the first approximation of a Web Services platform-based architecture (GITIRBio) that acts as a distributed front-end system for autonomous and assisted processing of parallel bioinformatics pipelines that has been validated using multiple sequences. Additionally, this platform allows integration with semantic repositories of genes for search annotations. GITIRBio is available at: http://c-head.ucaldas.edu.co:8080/gitirbio. PMID:26527189

  16. Managing, analysing, and integrating big data in medical bioinformatics: open problems and future perspectives.

    PubMed

    Merelli, Ivan; Pérez-Sánchez, Horacio; Gesing, Sandra; D'Agostino, Daniele

    2014-01-01

    The explosion of the data both in the biomedical research and in the healthcare systems demands urgent solutions. In particular, the research in omics sciences is moving from a hypothesis-driven to a data-driven approach. Healthcare is additionally always asking for a tighter integration with biomedical data in order to promote personalized medicine and to provide better treatments. Efficient analysis and interpretation of Big Data opens new avenues to explore molecular biology, new questions to ask about physiological and pathological states, and new ways to answer these open issues. Such analyses lead to better understanding of diseases and development of better and personalized diagnostics and therapeutics. However, such progresses are directly related to the availability of new solutions to deal with this huge amount of information. New paradigms are needed to store and access data, for its annotation and integration and finally for inferring knowledge and making it available to researchers. Bioinformatics can be viewed as the "glue" for all these processes. A clear awareness of present high performance computing (HPC) solutions in bioinformatics, Big Data analysis paradigms for computational biology, and the issues that are still open in the biomedical and healthcare fields represent the starting point to win this challenge. PMID:25254202

  17. Managing, Analysing, and Integrating Big Data in Medical Bioinformatics: Open Problems and Future Perspectives

    PubMed Central

    Merelli, Ivan; Pérez-Sánchez, Horacio; Gesing, Sandra; D'Agostino, Daniele

    2014-01-01

    The explosion of the data both in the biomedical research and in the healthcare systems demands urgent solutions. In particular, the research in omics sciences is moving from a hypothesis-driven to a data-driven approach. Healthcare is additionally always asking for a tighter integration with biomedical data in order to promote personalized medicine and to provide better treatments. Efficient analysis and interpretation of Big Data opens new avenues to explore molecular biology, new questions to ask about physiological and pathological states, and new ways to answer these open issues. Such analyses lead to better understanding of diseases and development of better and personalized diagnostics and therapeutics. However, such progresses are directly related to the availability of new solutions to deal with this huge amount of information. New paradigms are needed to store and access data, for its annotation and integration and finally for inferring knowledge and making it available to researchers. Bioinformatics can be viewed as the “glue” for all these processes. A clear awareness of present high performance computing (HPC) solutions in bioinformatics, Big Data analysis paradigms for computational biology, and the issues that are still open in the biomedical and healthcare fields represent the starting point to win this challenge. PMID:25254202

  18. PyDPI: freely available python package for chemoinformatics, bioinformatics, and chemogenomics studies.

    PubMed

    Cao, Dong-Sheng; Liang, Yi-Zeng; Yan, Jun; Tan, Gui-Shan; Xu, Qing-Song; Liu, Shao

    2013-11-25

    The rapidly increasing amount of publicly available data in biology and chemistry enables researchers to revisit interaction problems by systematic integration and analysis of heterogeneous data. Herein, we developed a comprehensive python package to emphasize the integration of chemoinformatics and bioinformatics into a molecular informatics platform for drug discovery. PyDPI (drug-protein interaction with Python) is a powerful python toolkit for computing commonly used structural and physicochemical features of proteins and peptides from amino acid sequences, molecular descriptors of drug molecules from their topology, and protein-protein interaction and protein-ligand interaction descriptors. It computes 6 protein feature groups composed of 14 features that include 52 descriptor types and 9890 descriptors, 9 drug feature groups composed of 13 descriptor types that include 615 descriptors. In addition, it provides seven types of molecular fingerprint systems for drug molecules, including topological fingerprints, electro-topological state (E-state) fingerprints, MACCS keys, FP4 keys, atom pair fingerprints, topological torsion fingerprints, and Morgan/circular fingerprints. By combining different types of descriptors from drugs and proteins in different ways, interaction descriptors representing protein-protein or drug-protein interactions could be conveniently generated. These computed descriptors can be widely used in various fields relevant to chemoinformatics, bioinformatics, and chemogenomics. PyDPI is freely available via https://sourceforge.net/projects/pydpicao/. PMID:24047419

  19. Design component method for sensitivity analysis of built-up structures

    NASA Technical Reports Server (NTRS)

    Choi, Kyung K.; Seong, Hwai G.

    1986-01-01

    A 'design component method' that provides a unified and systematic organization of design sensitivity analysis for built-up structures is developed and implemented. Both conventional design variables, such as thickness and cross-sectional area, and shape design variables of components of built-up structures are considered. It is shown that design of components of built-up structures can be characterized and system design sensitivity expressions obtained by simply adding contributions from each component. The method leads to a systematic organization of computations for design sensitivity analysis that is similar to the way in which computations are organized within a finite element code.

  20. Integrated Bioinformatics Approach Reveals Crosstalk Between Tumor Stroma and Peripheral Blood Mononuclear Cells in Breast Cancer.

    PubMed

    He, Lang; Wang, Dan; Wei, Na; Guo, Zheng

    2016-01-01

    Breast cancer is now the leading cause of cancer death in women worldwide. Cancer progression is driven not only by cancer cell intrinsic alterations and interactions with tumor microenvironment, but also by systemic effects. Integration of multiple profiling data may provide insights into the underlying molecular mechanisms of complex systemic processes. We performed a bioinformatic analysis of two public available microarray datasets for breast tumor stroma and peripheral blood mononuclear cells, featuring integrated transcriptomics data, protein-protein interactions (PPIs) and protein subcellular localization, to identify genes and biological pathways that contribute to dialogue between tumor stroma and the peripheral circulation. Genes of the integrin family as well as CXCR4 proved to be hub nodes of the crosstalk network and may play an important role in response to stroma-derived chemoattractants. This study pointed to potential for development of therapeutic strategies that target systemic signals travelling through the circulation and interdict tumor cell recruitment. PMID:27039717

  1. Bioinformatics Approaches to Classifying Allergens and Predicting Cross-Reactivity

    PubMed Central

    Schein, Catherine H.; Ivanciuc, Ovidiu; Braun, Werner

    2007-01-01

    The major advances in understanding why patients respond to several seemingly different stimuli have been through the isolation, sequencing and structural analysis of proteins that induce an IgE response. The most significant finding is that allergenic proteins from very different sources can have nearly identical sequences and structures, and that this similarity can account for clinically observed cross-reactivity. The increasing amount of information on the sequence, structure and IgE epitopes of allergens is now available in several databases and powerful bioinformatics search tools allow user access to relevant information. Here, we provide an overview of these databases and describe state-of-the art bioinformatics tools to identify the common proteins that may be at the root of multiple allergy syndromes. Progress has also been made in quantitatively defining characteristics that discriminate allergens from non-allergens. Search and software tools for this purpose have been developed and implemented in the Structural Database of Allergenic Proteins (SDAP, http://fermi.utmb.edu/SDAP/). SDAP contains information for over 800 allergens and extensive bibliographic references in a relational database with links to other publicly available databases. SDAP is freely available on the Web to clinicians and patients, and can be used to find structural and functional relations among known allergens and to identify potentially cross-reacting antigens. Here we illustrate how these bioinformatics tools can be used to group allergens, and to detect areas that may account for common patterns of IgE binding and cross-reactivity. Such results can be used to guide treatment regimens for allergy sufferers. PMID:17276876

  2. SPOT--towards temporal data mining in medicine and bioinformatics.

    PubMed

    Tusch, Guenter; Bretl, Chris; O'Connor, Martin; Connor, Martin; Das, Amar

    2008-01-01

    Mining large clinical and bioinformatics databases often includes exploration of temporal data. E.g., in liver transplantation, researchers might look for patients with an unusual time pattern of potential complications of the liver. In Knowledge-based Temporal Abstraction time-stamped data points are transformed into an interval-based representation. We extended this framework by creating an open-source platform, SPOT. It supports the R statistical package and knowledge representation standards (OWL, SWRL) using the open source Semantic Web tool Protégé-OWL. PMID:18999225

  3. Bioinformatics pipeline for functional identification and characterization of proteins

    NASA Astrophysics Data System (ADS)

    Skarzyńska, Agnieszka; Pawełkowicz, Magdalena; Krzywkowski, Tomasz; Świerkula, Katarzyna; PlÄ der, Wojciech; Przybecki, Zbigniew

    2015-09-01

    The new sequencing methods, called Next Generation Sequencing gives an opportunity to possess a vast amount of data in short time. This data requires structural and functional annotation. Functional identification and characterization of predicted proteins could be done by in silico approches, thanks to a numerous computational tools available nowadays. However, there is a need to confirm the results of proteins function prediction using different programs and comparing the results or confirm experimentally. Here we present a bioinformatics pipeline for structural and functional annotation of proteins.

  4. Applications of Support Vector Machines In Chemo And Bioinformatics

    NASA Astrophysics Data System (ADS)

    Jayaraman, V. K.; Sundararajan, V.

    2010-10-01

    Conventional linear & nonlinear tools for classification, regression & data driven modeling are being replaced on a rapid scale by newer techniques & tools based on artificial intelligence and machine learning. While the linear techniques are not applicable for inherently nonlinear problems, newer methods serve as attractive alternatives for solving real life problems. Support Vector Machine (SVM) classifiers are a set of universal feed-forward network based classification algorithms that have been formulated from statistical learning theory and structural risk minimization principle. SVM regression closely follows the classification methodology. In this work recent applications of SVM in Chemo & Bioinformatics will be described with suitable illustrative examples.

  5. Biophysics and bioinformatics of transcription regulation in bacteria and bacteriophages

    NASA Astrophysics Data System (ADS)

    Djordjevic, Marko

    2005-11-01

    Due to rapid accumulation of biological data, bioinformatics has become a very important branch of biological research. In this thesis, we develop novel bioinformatic approaches and aid design of biological experiments by using ideas and methods from statistical physics. Identification of transcription factor binding sites within the regulatory segments of genomic DNA is an important step towards understanding of the regulatory circuits that control expression of genes. We propose a novel, biophysics based algorithm, for the supervised detection of transcription factor (TF) binding sites. The method classifies potential binding sites by explicitly estimating the sequence-specific binding energy and the chemical potential of a given TF. In contrast with the widely used information theory based weight matrix method, our approach correctly incorporates saturation in the transcription factor/DNA binding probability. This results in a significant reduction in the number of expected false positives, and in the explicit appearance---and determination---of a binding threshold. The new method was used to identify likely genomic binding sites for the Escherichia coli TFs, and to examine the relationship between TF binding specificity and degree of pleiotropy (number of regulatory targets). We next address how parameters of protein-DNA interactions can be obtained from data on protein binding to random oligos under controlled conditions (SELEX experiment data). We show that 'robust' generation of an appropriate data set is achieved by a suitable modification of the standard SELEX procedure, and propose a novel bioinformatic algorithm for analysis of such data. Finally, we use quantitative data analysis, bioinformatic methods and kinetic modeling to analyze gene expression strategies of bacterial viruses. We study bacteriophage Xp10 that infects rice pathogen Xanthomonas oryzae. Xp10 is an unusual bacteriophage, which has morphology and genome organization that most closely

  6. WU-Blast2 server at the European Bioinformatics Institute

    PubMed Central

    Lopez, Rodrigo; Silventoinen, Ville; Robinson, Stephen; Kibria, Asif; Gish, Warren

    2003-01-01

    Since 1995, the WU-BLAST programs (http://blast.wustl.edu) have provided a fast, flexible and reliable method for similarity searching of biological sequence databases. The software is in use at many locales and web sites. The European Bioinformatics Institute's WU-Blast2 (http://www.ebi.ac.uk/blast2/) server has been providing free access to these search services since 1997 and today supports many features that both enhance the usability and expand on the scope of the software. PMID:12824421

  7. Comprehensive bioinformatics analysis of cell-free protein synthesis: identification of multiple protein properties that correlate with successful expression.

    PubMed

    Kurotani, Atsushi; Takagi, Tetsuo; Toyama, Mitsutoshi; Shirouzu, Mikako; Yokoyama, Shigeyuki; Fukami, Yasuo; Tokmakov, Alexander A

    2010-04-01

    High-throughput cell-free protein synthesis is being used increasingly in structural/functional genomics projects. However, the factors determining expression success are poorly understood. Here, we evaluated the expression of 3066 human proteins and their domains in a bacterial cell-free system and analyzed the correlation of protein expression with 39 physicochemical and structural properties of proteins. As a result of the bioinformatics analysis performed, we determined the 18 most influential features that affect protein amenability to cell-free expression. They include protein length; hydrophobicity; pI; content of charged, nonpolar, and aromatic residues;, cysteine content; solvent accessibility; presence of coiled coil; content of intrinsically disordered and structured (alpha-helix and beta-sheet) sequence; number of disulfide bonds and functional domains; presence of transmembrane regions; PEST motifs; and signaling sequences. This study represents the first comprehensive bioinformatics analysis of heterologous protein synthesis in a cell-free system. The rules and correlations revealed here provide a plethora of important insights into rationalization of cell-free protein production and can be of practical use for protein engineering with the aim of increasing expression success.-Kurotani, A., Takagi, T., Toyama, M., Shirouzu, M., Yokoyama, S., Fukami, Y., Tokmakov, A. A. Comprehensive bioinformatics analysis of cell-free protein synthesis: identification of multiple protein properties that correlate with successful expression. PMID:19940260

  8. Development of a ``Built-in'' Scanning Near Field Microscope Head for an Atomic Force Microscope System and Stress Mapping of an Al2O3/ZrO2 Eutectic Composite

    NASA Astrophysics Data System (ADS)

    Nakagawa, Tatsuo; Fukura, Satoshi; Nakai, Munenori; Sugiyama, Kazumasa; Kokawa, Ryohei; Kagi, Hiroyuki

    2006-07-01

    We constructed a scanning near-field optical microscope (SNOM) on a commercially available atomic force microscopy (AFM) apparatus (SPM-9500J2; Shimadzu Corp.) to measure the stress distribution in ceramic composite materials. Features of our SNOM system are: (1) a compact SNOM head substituted for the original AFM head; (2) a wide scanning range (125 × 125 μm2) inherited from the original scanner; (3) use of conventional shear-force regulation; (4) an optical system for the illumination-collection (I-C) mode; (5) excitation by a 488 nm line of an Ar-ion laser, and (6) light detection by photon counting or a polychromator equipped with an electronically cooled charge coupled device (CCD). This SNOM system was used to measure the surface structure and stress distribution of an Al2O3/ZrO2 eutectic composite. We simultaneously measured topographic images and fluorescence spectra of an Al2O3/ZrO2 eutectic composite. We estimated its peak intensity, peak position, and peak width from the fluorescence spectrum during scanning, which respectively correspond to the abundance of Al2O3, stress in the grain, and the anisotropy of that stress. Mapping images showed that the stress and its anisotropy were weaker in the center of the Al2O3 grain than its boundary between Al2O3 and ZrO2. That observation suggests that Al2O3 underwent intense anisotropic stress induced by volume expansion in the phase transition of ZrO2 from the cubic phase to the monoclinic phase during preparation.

  9. Detecting evolution of bioinformatics with a content and co-authorship analysis.

    PubMed

    Song, Min; Yang, Christopher C; Tang, Xuning

    2013-12-01

    Bioinformatics is an interdisciplinary research field that applies advanced computational techniques to biological data. Bibliometrics analysis has recently been adopted to understand the knowledge structure of a research field by citation pattern. In this paper, we explore the knowledge structure of Bioinformatics from the perspective of a core open access Bioinformatics journal, BMC Bioinformatics with trend analysis, the content and co-authorship network similarity, and principal component analysis. Publications in four core journals including Bioinformatics - Oxford Journal and four conferences in Bioinformatics were harvested from DBLP. After converting publications into TF-IDF term vectors, we calculate the content similarity, and we also calculate the social network similarity based on the co-authorship network by utilizing the overlap measure between two co-authorship networks. Key terms is extracted and analyzed with PCA, visualization of the co-authorship network is conducted. The experimental results show that Bioinformatics is fast-growing, dynamic and diversified. The content analysis shows that there is an increasing overlap among Bioinformatics journals in terms of topics and more research groups participate in researching Bioinformatics according to the co-authorship network similarity. PMID:23710427

  10. Technosciences in Academia: Rethinking a Conceptual Framework for Bioinformatics Undergraduate Curricula

    NASA Astrophysics Data System (ADS)

    Symeonidis, Iphigenia Sofia

    This paper aims to elucidate guiding concepts for the design of powerful undergraduate bioinformatics degrees which will lead to a conceptual framework for the curriculum. "Powerful" here should be understood as having truly bioinformatics objectives rather than enrichment of existing computer science or life science degrees on which bioinformatics degrees are often based. As such, the conceptual framework will be one which aims to demonstrate intellectual honesty in regards to the field of bioinformatics. A synthesis/conceptual analysis approach was followed as elaborated by Hurd (1983). The approach takes into account the following: bioinfonnatics educational needs and goals as expressed by different authorities, five undergraduate bioinformatics degrees case-studies, educational implications of bioinformatics as a technoscience and approaches to curriculum design promoting interdisciplinarity and integration. Given these considerations, guiding concepts emerged and a conceptual framework was elaborated. The practice of bioinformatics was given a closer look, which led to defining tool-integration skills and tool-thinking capacity as crucial areas of the bioinformatics activities spectrum. It was argued, finally, that a process-based curriculum as a variation of a concept-based curriculum (where the concepts are processes) might be more conducive to the teaching of bioinformatics given a foundational first year of integrated science education as envisioned by Bialek and Botstein (2004). Furthermore, the curriculum design needs to define new avenues of communication and learning which bypass the traditional disciplinary barriers of academic settings as undertaken by Tador and Tidmor (2005) for graduate studies.

  11. MOWServ: a web client for integration of bioinformatic resources

    PubMed Central

    Ramírez, Sergio; Muñoz-Mérida, Antonio; Karlsson, Johan; García, Maximiliano; Pérez-Pulido, Antonio J.; Claros, M. Gonzalo; Trelles, Oswaldo

    2010-01-01

    The productivity of any scientist is affected by cumbersome, tedious and time-consuming tasks that try to make the heterogeneous web services compatible so that they can be useful in their research. MOWServ, the bioinformatic platform offered by the Spanish National Institute of Bioinformatics, was released to provide integrated access to databases and analytical tools. Since its release, the number of available services has grown dramatically, and it has become one of the main contributors of registered services in the EMBRACE Biocatalogue. The ontology that enables most of the web-service compatibility has been curated, improved and extended. The service discovery has been greatly enhanced by Magallanes software and biodataSF. User data are securely stored on the main server by an authentication protocol that enables the monitoring of current or already-finished user’s tasks, as well as the pipelining of successive data processing services. The BioMoby standard has been greatly extended with the new features included in the MOWServ, such as management of additional information (metadata such as extended descriptions, keywords and datafile examples), a qualified registry, error handling, asynchronous services and service replication. All of them have increased the MOWServ service quality, usability and robustness. MOWServ is available at http://www.inab.org/MOWServ/ and has a mirror at http://www.bitlab-es.com/MOWServ/. PMID:20525794

  12. Web services at the European Bioinformatics Institute-2009

    PubMed Central

    Mcwilliam, Hamish; Valentin, Franck; Goujon, Mickael; Li, Weizhong; Narayanasamy, Menaka; Martin, Jenny; Miyar, Teresa; Lopez, Rodrigo

    2009-01-01

    The European Bioinformatics Institute (EMBL-EBI) has been providing access to mainstream databases and tools in bioinformatics since 1997. In addition to the traditional web form based interfaces, APIs exist for core data resources such as EMBL-Bank, Ensembl, UniProt, InterPro, PDB and ArrayExpress. These APIs are based on Web Services (SOAP/REST) interfaces that allow users to systematically access databases and analytical tools. From the user's point of view, these Web Services provide the same functionality as the browser-based forms. However, using the APIs frees the user from web page constraints and are ideal for the analysis of large batches of data, performing text-mining tasks and the casual or systematic evaluation of mathematical models in regulatory networks. Furthermore, these services are widespread and easy to use; require no prior knowledge of the technology and no more than basic experience in programming. In the following we wish to inform of new and updated services as well as briefly describe planned developments to be made available during the course of 2009–2010. PMID:19435877

  13. Can bioinformatics help in the identification of moonlighting proteins?

    PubMed

    Hernández, Sergio; Calvo, Alejandra; Ferragut, Gabriela; Franco, Luís; Hermoso, Antoni; Amela, Isaac; Gómez, Antonio; Querol, Enrique; Cedano, Juan

    2014-12-01

    Protein multitasking or moonlighting is the capability of certain proteins to execute two or more unique biological functions. This ability to perform moonlighting functions helps us to understand one of the ways used by cells to perform many complex functions with a limited number of genes. Usually, moonlighting proteins are revealed experimentally by serendipity, and the proteins described probably represent just the tip of the iceberg. It would be helpful if bioinformatics could predict protein multifunctionality, especially because of the large amounts of sequences coming from genome projects. In the present article, we describe several approaches that use sequences, structures, interactomics and current bioinformatics algorithms and programs to try to overcome this problem. The sequence analysis has been performed: (i) by remote homology searches using PSI-BLAST, (ii) by the detection of functional motifs, and (iii) by the co-evolutionary relationship between amino acids. Programs designed to identify functional motifs/domains are basically oriented to detect the main function, but usually fail in the detection of secondary ones. Remote homology searches such as PSI-BLAST seem to be more versatile in this task, and it is a good complement for the information obtained from protein-protein interaction (PPI) databases. Structural information and mutation correlation analysis can help us to map the functional sites. Mutation correlation analysis can be used only in very restricted situations, but can suggest how the evolutionary process of the acquisition of the second function took place. PMID:25399591

  14. Translational Bioinformatics and Healthcare Informatics: Computational and Ethical Challenges

    PubMed Central

    Sethi, Prerna; Theodos, Kimberly

    2009-01-01

    Exponentially growing biological and bioinformatics data sets present a challenge and an opportunity for researchers to contribute to the understanding of the genetic basis of phenotypes. Due to breakthroughs in microarray technology, it is possible to simultaneously monitor the expressions of thousands of genes, and it is imperative that researchers have access to the clinical data to understand the genetics and proteomics of the diseased tissue. This technology could be a landmark in personalized medicine, which will provide storage for clinical and genetic data in electronic health records (EHRs). In this paper, we explore the computational and ethical challenges that emanate from the intersection of bioinformatics and healthcare informatics research. We describe the current situation of the EHR and its capabilities to store clinical and genetic data and then discuss the Genetic Information Nondiscrimination Act. Finally, we posit that the synergy obtained from the collaborative efforts between the genomics, clinical, and healthcare disciplines has potential to enhance and promote faster and more advanced breakthroughs in healthcare. PMID:20169020

  15. MOWServ: a web client for integration of bioinformatic resources.

    PubMed

    Ramírez, Sergio; Muñoz-Mérida, Antonio; Karlsson, Johan; García, Maximiliano; Pérez-Pulido, Antonio J; Claros, M Gonzalo; Trelles, Oswaldo

    2010-07-01

    The productivity of any scientist is affected by cumbersome, tedious and time-consuming tasks that try to make the heterogeneous web services compatible so that they can be useful in their research. MOWServ, the bioinformatic platform offered by the Spanish National Institute of Bioinformatics, was released to provide integrated access to databases and analytical tools. Since its release, the number of available services has grown dramatically, and it has become one of the main contributors of registered services in the EMBRACE Biocatalogue. The ontology that enables most of the web-service compatibility has been curated, improved and extended. The service discovery has been greatly enhanced by Magallanes software and biodataSF. User data are securely stored on the main server by an authentication protocol that enables the monitoring of current or already-finished user's tasks, as well as the pipelining of successive data processing services. The BioMoby standard has been greatly extended with the new features included in the MOWServ, such as management of additional information (metadata such as extended descriptions, keywords and datafile examples), a qualified registry, error handling, asynchronous services and service replication. All of them have increased the MOWServ service quality, usability and robustness. MOWServ is available at http://www.inab.org/MOWServ/ and has a mirror at http://www.bitlab-es.com/MOWServ/. PMID:20525794

  16. Integrating genomics, proteomics and bioinformatics in translational studies of molecular medicine.

    PubMed

    Ostrowski, Jerzy; Wyrwicz, Lucjan S

    2009-09-01

    Understanding the molecular mechanisms of disease requires the introduction of molecular diagnostics into medical practice. Current medicine employs only elements of molecular diagnostics, which are usually applied on the scale of single genes. Medicine in the postgenomic era will utilize thousands of disease-associated molecular markers provided by high-throughput sequencing and functional genomic, proteomic and metabolomic studies. Such a spectrum of techniques will link clinical medicine based on molecularly oriented diagnostics with the prediction and prevention of disease. To achieve this task, large-scale and genome-wide biological and medical data must be combined with biostatistical and bioinformatic analyses to model biological systems. Collecting, cataloging and comparing data from molecular studies, and the subsequent development of conclusions, creates the fundamentals of systems biology. This highly complex analytical process reflects a new scientific paradigm known as integrative genomics. PMID:19732006

  17. Bioinformatics visualization and integration with open standards: the Bluejay genomic browser.

    PubMed

    Turinsky, Andrei L; Ah-Seng, Andrew C; Gordon, Paul M K; Stromer, Julie N; Taschuk, Morgan L; Xu, Emily W; Sensen, Christoph W

    2005-01-01

    We have created a new Java-based integrated computational environment for the exploration of genomic data, called Bluejay. The system is capable of using almost any XML file related to genomic data. Non-XML data sources can be accessed via a proxy server. Bluejay has several features, which are new to Bioinformatics, including an unlimited semantic zoom capability, coupled with Scalable Vector Graphics (SVG) outputs; an implementation of the XLink standard, which features access to MAGPIE Genecards as well as any BioMOBY service accessible over the Internet; and the integration of gene chip analysis tools with the functional assignments. The system can be used as a signed web applet, Web Start, and a local stand-alone application, with or without connection to the Internet. It is available free of charge and as open source via http://bluejay.ucalgary.ca. PMID:15972014

  18. FY02 CBNP Annual Report Input: Bioinformatics Support for CBNP Research and Deployments

    SciTech Connect

    Slezak, T; Wolinsky, M

    2002-10-31

    The events of FY01 dynamically reprogrammed the objectives of the CBNP bioinformatics support team, to meet rapidly-changing Homeland Defense needs and requests from other agencies for assistance: Use computational techniques to determine potential unique DNA signature candidates for microbial and viral pathogens of interest to CBNP researcher and to our collaborating partner agencies such as the Centers for Disease Control and Prevention (CDC), U.S. Department of Agriculture (USDA), Department of Defense (DOD), and Food and Drug Administration (FDA). Develop effective electronic screening measures for DNA signatures to reduce the cost and time of wet-bench screening. Build a comprehensive system for tracking the development and testing of DNA signatures. Build a chain-of-custody sample tracking system for field deployment of the DNA signatures as part of the BASIS project. Provide computational tools for use by CBNP Biological Foundations researchers.

  19. AphidBase: A centralized bioinformatic resource for annotation of the pea aphid genome

    PubMed Central

    Legeai, Fabrice; Shigenobu, Shuji; Gauthier, Jean-Pierre; Colbourne, John; Rispe, Claude; Collin, Olivier; Richards, Stephen; Wilson, Alex C. C.; Tagu, Denis

    2015-01-01

    AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System designed to organize and distribute genomic data and annotations for a large international community was constructed using open source software tools from the Generic Model Organism Database (GMOD). The system includes Apollo and GBrowse utilities as well as a wiki, blast search capabilities and a full text search engine. AphidBase strongly supported community cooperation and coordination in the curation of gene models during community annotation of the pea aphid genome. AphidBase can be accessed at http://www.aphidbase.com. PMID:20482635

  20. APOLLO 13: The Spirit that Built America

    NASA Technical Reports Server (NTRS)

    1974-01-01

    APOLLO 13: Nixon commends the crew of APOLLO 13 From the film documentary 'APOLLO 13: 'Houston, We've got a problem'', part of a documentary series on the APOLLO missions made in the early '70's and narrated by Burgess Meredith. APOLO 13 : Third manned lunar landing attempt with James A. Lovell, Jr., John L. Swigert, Jr., and Fred w. Haise, Jr. Pressure lost in SM oxygen system; mission aborted; LM used for life support. Mission Duration 142hrs 54mins 41sec

  1. 5. Conveyors 'C' through 'K' (built 1940) south of Station, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. Conveyors 'C' through 'K' (built 1940) south of Station, looking northeast from hurricane barrier. - Manchester Street Generating Station, Conveyors, 460 Eddy Street, Providence, Providence County, RI

  2. Built-in-test by signature inspection (bitsi)

    DOEpatents

    Bergeson, Gary C.; Morneau, Richard A.

    1991-01-01

    A system and method for fault detection for electronic circuits. A stimulus generator sends a signal to the input of the circuit under test. Signature inspection logic compares the resultant signal from test nodes on the circuit to an expected signal. If the signals do not match, the signature inspection logic sends a signal to the control logic for indication of fault detection in the circuit. A data input multiplexer between the test nodes of the circuit under test and the signature inspection logic can provide for identification of the specific node at fault by the signature inspection logic. Control logic responsive to the signature inspection logic conveys information about fault detection for use in determining the condition of the circuit. When used in conjunction with a system test controller, the built-in test by signature inspection system and method can be used to poll a plurality of circuits automatically and continuous for faults and record the results of such polling in the system test controller.

  3. Bioinformatics in the secondary science classroom: A study of state content standards and students' perceptions of, and performance in, bioinformatics lessons

    NASA Astrophysics Data System (ADS)

    Wefer, Stephen H.

    The proliferation of bioinformatics in modern Biology marks a new revolution in science, which promises to influence science education at all levels. This thesis examined state standards for content that articulated bioinformatics, and explored secondary students' affective and cognitive perceptions of, and performance in, a bioinformatics mini-unit. The results are presented as three studies. The first study analyzed secondary science standards of 49 U.S States (Iowa has no science framework) and the District of Columbia for content related to bioinformatics at the introductory high school biology level. The bionformatics content of each state's Biology standards were categorized into nine areas and the prevalence of each area documented. The nine areas were: The Human Genome Project, Forensics, Evolution, Classification, Nucleotide Variations, Medicine, Computer Use, Agriculture/Food Technology, and Science Technology and Society/Socioscientific Issues (STS/SSI). Findings indicated a generally low representation of bioinformatics related content, which varied substantially across the different areas. Recommendations are made for reworking existing standards to incorporate bioinformatics and to facilitate the goal of promoting science literacy in this emerging new field among secondary school students. The second study examined thirty-two students' affective responses to, and content mastery of, a two-week bioinformatics mini-unit. The findings indicate that the students generally were positive relative to their interest level, the usefulness of the lessons, the difficulty level of the lessons, likeliness to engage in additional bioinformatics, and were overall successful on the assessments. A discussion of the results and significance is followed by suggestions for future research and implementation for transferability. The third study presents a case study of individual differences among ten secondary school students, whose cognitive and affective percepts were

  4. Bioinformatics Methods and Tools to Advance Clinical Care

    PubMed Central

    Lecroq, T.

    2015-01-01

    Summary Objectives To summarize excellent current research in the field of Bioinformatics and Translational Informatics with application in the health domain and clinical care. Method We provide a synopsis of the articles selected for the IMIA Yearbook 2015, from which we attempt to derive a synthetic overview of current and future activities in the field. As last year, a first step of selection was performed by querying MEDLINE with a list of MeSH descriptors completed by a list of terms adapted to the section. Each section editor has evaluated separately the set of 1,594 articles and the evaluation results were merged for retaining 15 articles for peer-review. Results The selection and evaluation process of this Yearbook’s section on Bioinformatics and Translational Informatics yielded four excellent articles regarding data management and genome medicine that are mainly tool-based papers. In the first article, the authors present PPISURV a tool for uncovering the role of specific genes in cancer survival outcome. The second article describes the classifier PredictSNP which combines six performing tools for predicting disease-related mutations. In the third article, by presenting a high-coverage map of the human proteome using high resolution mass spectrometry, the authors highlight the need for using mass spectrometry to complement genome annotation. The fourth article is also related to patient survival and decision support. The authors present datamining methods of large-scale datasets of past transplants. The objective is to identify chances of survival. Conclusions The current research activities still attest the continuous convergence of Bioinformatics and Medical Informatics, with a focus this year on dedicated tools and methods to advance clinical care. Indeed, there is a need for powerful tools for managing and interpreting complex, large-scale genomic and biological datasets, but also a need for user-friendly tools developed for the clinicians in their

  5. Students, Structures, Spaces: Activities in the Built Environment.

    ERIC Educational Resources Information Center

    Eriksen, Aase; Wintermute, Marjorie

    Built environment education, an innovative concept, is not a new subject in educational curricula, but rather an approach to traditional areas of study that can be integrated into existing curricula. The goals of built environment education as outlined and developed in this teachers guide are to develop an awareness of surroundings, senses,…

  6. Transformative Learning: Innovating Sustainability Education in Built Environment

    ERIC Educational Resources Information Center

    Iyer-Raniga, Usha; Andamon, Mary Myla

    2016-01-01

    Purpose: This paper aims to evaluate how transformative learning is key to innovating sustainability education in the built environment in the region's universities, in addition to reporting on the research project undertaken to integrate sustainability thinking and practice into engineering/built environment curricula in Asia-Pacific…

  7. 2. DETAIL OF BUILDER'S PLATE: 'SUPERSTRUCTURE BUILT BY STROBEL STEEL ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. DETAIL OF BUILDER'S PLATE: 'SUPERSTRUCTURE BUILT BY STROBEL STEEL CONSTRUCTION CO., CHICAGO, ILL., 1913, SUBSTRUCTURE BUILT BY FITZSIMONS & CONNELL D&D CO., CHICAGO, ILL.' - Chicago River Bascule Bridge, Grand Avenue, Spanning North Branch Chicago River at Grand Avenue, Chicago, Cook County, IL

  8. 49 CFR 41.117 - Buildings built with Federal assistance.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 1 2013-10-01 2013-10-01 false Buildings built with Federal assistance. 41.117 Section 41.117 Transportation Office of the Secretary of Transportation SEISMIC SAFETY § 41.117 Buildings built with Federal assistance. (a) Each DOT Operating Administration assisting in the financing,...

  9. 49 CFR 41.117 - Buildings built with Federal assistance.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 1 2011-10-01 2011-10-01 false Buildings built with Federal assistance. 41.117 Section 41.117 Transportation Office of the Secretary of Transportation SEISMIC SAFETY § 41.117 Buildings built with Federal assistance. (a) Each DOT Operating Administration assisting in the financing,...

  10. 49 CFR 41.117 - Buildings built with Federal assistance.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 1 2014-10-01 2014-10-01 false Buildings built with Federal assistance. 41.117 Section 41.117 Transportation Office of the Secretary of Transportation SEISMIC SAFETY § 41.117 Buildings built with Federal assistance. (a) Each DOT Operating Administration assisting in the financing,...

  11. 49 CFR 41.117 - Buildings built with Federal assistance.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 1 2010-10-01 2010-10-01 false Buildings built with Federal assistance. 41.117 Section 41.117 Transportation Office of the Secretary of Transportation SEISMIC SAFETY § 41.117 Buildings built with Federal assistance. (a) Each DOT Operating Administration assisting in the financing,...

  12. 49 CFR 41.117 - Buildings built with Federal assistance.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 1 2012-10-01 2012-10-01 false Buildings built with Federal assistance. 41.117 Section 41.117 Transportation Office of the Secretary of Transportation SEISMIC SAFETY § 41.117 Buildings built with Federal assistance. (a) Each DOT Operating Administration assisting in the financing,...

  13. Meeting Review: Bioinformatics and Medicine – From Molecules to Humans, Virtual and Real

    PubMed Central

    2002-01-01

    The Industrialization Workshop Series aims to promote and discuss integration, automation, simulation, quality, availability and standards in the high-throughput life sciences. The main issues addressed being the transformation of bioinformatics and bioinformaticsbased drug design into a robust discipline in industry, the government, research institutes and academia. The latest workshop emphasized the influence of the post-genomic era on medicine and healthcare with reference to advanced biological systems modeling and simulation, protein structure research, protein-protein interactions, metabolism and physiology. Speakers included Michael Ashburner, Kenneth Buetow, Francois Cambien, Cyrus Chothia, Jean Garnier, Francois Iris, Matthias Mann, Maya Natarajan, Peter Murray-Rust, Richard Mushlin, Barry Robson, David Rubin, Kosta Steliou, John Todd, Janet Thornton, Pim van der Eijk, Michael Vieth and Richard Ward. PMID:18628854

  14. Experimental Design and Bioinformatics Analysis for the Application of Metagenomics in Environmental Sciences and Biotechnology.

    PubMed

    Ju, Feng; Zhang, Tong

    2015-11-01

    Recent advances in DNA sequencing technologies have prompted the widespread application of metagenomics for the investigation of novel bioresources (e.g., industrial enzymes and bioactive molecules) and unknown biohazards (e.g., pathogens and antibiotic resistance genes) in natural and engineered microbial systems across multiple disciplines. This review discusses the rigorous experimental design and sample preparation in the context of applying metagenomics in environmental sciences and biotechnology. Moreover, this review summarizes the principles, methodologies, and state-of-the-art bioinformatics procedures, tools and database resources for metagenomics applications and discusses two popular strategies (analysis of unassembled reads versus assembled contigs/draft genomes) for quantitative or qualitative insights of microbial community structure and functions. Overall, this review aims to facilitate more extensive application of metagenomics in the investigation of uncultured microorganisms, novel enzymes, microbe-environment interactions, and biohazards in biotechnological applications where microbial communities are engineered for bioenergy production, wastewater treatment, and bioremediation. PMID:26451629

  15. Subcarrier multiplexing system with built-in dispersion reduction

    SciTech Connect

    Sargis, P.D.; Haigh, R.E.; McCammon, K.G.

    1995-09-08

    Dispersion is effectively reduced in a 1550-nm subcarrier-multiplexed fiber link by using optical pre-filtering at the receiver. Recent experimental results demonstrate transmission of two 2.5 Gbit/s data channels over 220 km of ordinary single-mode fiber.

  16. A Summer Program Designed to Educate College Students for Careers in Bioinformatics

    ERIC Educational Resources Information Center

    Krilowicz, Beverly; Johnston, Wendie; Sharp, Sandra B.; Warter-Perez, Nancy; Momand, Jamil

    2007-01-01

    A summer program was created for undergraduates and graduate students that teaches bioinformatics concepts, offers skills in professional development, and provides research opportunities in academic and industrial institutions. We estimate that 34 of 38 graduates (89%) are in a career trajectory that will use bioinformatics. Evidence from…

  17. Computer Programming and Biomolecular Structure Studies: A Step beyond Internet Bioinformatics

    ERIC Educational Resources Information Center

    Likic, Vladimir A.

    2006-01-01

    This article describes the experience of teaching structural bioinformatics to third year undergraduate students in a subject titled "Biomolecular Structure and Bioinformatics." Students were introduced to computer programming and used this knowledge in a practical application as an alternative to the well established Internet bioinformatics…

  18. BioStar: an online question & answer resource for the bioinformatics community

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although the era of big data has produced many bioinformatics tools and databases, using them effectively often requires specialized knowledge. Many groups lack bioinformatics expertise, and frequently find that software documentation is inadequate and local colleagues may be overburdened or unfamil...

  19. A Portable Bioinformatics Course for Upper-Division Undergraduate Curriculum in Sciences

    ERIC Educational Resources Information Center

    Floraino, Wely B.

    2008-01-01

    This article discusses the challenges that bioinformatics education is facing and describes a bioinformatics course that is successfully taught at the California State Polytechnic University, Pomona, to the fourth year undergraduate students in biological sciences, chemistry, and computer science. Information on lecture and computer practice…

  20. Bioinformatics and the allergy assessment of agricultural biotechnology products: industry practices and recommendations.

    PubMed

    Ladics, Gregory S; Cressman, Robert F; Herouet-Guicheney, Corinne; Herman, Rod A; Privalle, Laura; Song, Ping; Ward, Jason M; McClain, Scott

    2011-06-01

    Bioinformatic tools are being increasingly utilized to evaluate the degree of similarity between a novel protein and known allergens within the context of a larger allergy safety assessment process. Importantly, bioinformatics is not a predictive analysis that can determine if a novel protein will ''become" an allergen, but rather a tool to assess whether the protein is a known allergen or is potentially cross-reactive with an existing allergen. Bioinformatic tools are key components of the 2009 CodexAlimentarius Commission's weight-of-evidence approach, which encompasses a variety of experimental approaches for an overall assessment of the allergenic potential of a novel protein. Bioinformatic search comparisons between novel protein sequences, as well as potential novel fusion sequences derived from the genome and transgene, and known allergens are required by all regulatory agencies that assess the safety of genetically modified (GM) products. The objective of this paper is to identify opportunities for consensus in the methods of applying bioinformatics and to outline differences that impact a consistent and reliable allergy safety assessment. The bioinformatic comparison process has some critical features, which are outlined in this paper. One of them is a curated, publicly available and well-managed database with known allergenic sequences. In this paper, the best practices, scientific value, and food safety implications of bioinformatic analyses, as they are applied to GM food crops are discussed. Recommendations for conducting bioinformatic analysis on novel food proteins for potential cross-reactivity to known allergens are also put forth. PMID:21320564

  1. Bioinformatics in Middle East Program Curricula--A Focus on the Arabian Gulf

    ERIC Educational Resources Information Center

    Loucif, Samia

    2014-01-01

    The purpose of this paper is to investigate the inclusion of bioinformatics in program curricula in the Middle East, focusing on educational institutions in the Arabian Gulf. Bioinformatics is a multidisciplinary field which has emerged in response to the need for efficient data storage and retrieval, and accurate and fast computational and…

  2. The S-Star Trial Bioinformatics Course: An On-line Learning Success

    ERIC Educational Resources Information Center

    Lim, Yun Ping; Hoog, Jan-Olov; Gardner, Phyllis; Ranganathan, Shoba; Andersson, Siv; Subbiah, Subramanian; Tan, Tin Wee; Hide, Winston; Weiss, Anthony S.

    2003-01-01

    The S-Star Trial Bioinformatics on-line course (www.s-star.org) is a global experiment in bioinformatics distance education. Six universities from five continents have participated in this project. One hundred and fifty students participated in the first trial course of which 96 followed through the entire course and 70 fulfilled the overall…

  3. Incorporating a Collaborative Web-Based Virtual Laboratory in an Undergraduate Bioinformatics Course

    ERIC Educational Resources Information Center

    Weisman, David

    2010-01-01

    Face-to-face bioinformatics courses commonly include a weekly, in-person computer lab to facilitate active learning, reinforce conceptual material, and teach practical skills. Similarly, fully-online bioinformatics courses employ hands-on exercises to achieve these outcomes, although students typically perform this work offsite. Combining a…

  4. Integration of Bioinformatics into an Undergraduate Biology Curriculum and the Impact on Development of Mathematical Skills

    ERIC Educational Resources Information Center

    Wightman, Bruce; Hark, Amy T.

    2012-01-01

    The development of fields such as bioinformatics and genomics has created new challenges and opportunities for undergraduate biology curricula. Students preparing for careers in science, technology, and medicine need more intensive study of bioinformatics and more sophisticated training in the mathematics on which this field is based. In this…

  5. Bioinformatics in High School Biology Curricula: A Study of State Science Standards

    ERIC Educational Resources Information Center

    Wefer, Stephen H.; Sheppard, Keith

    2008-01-01

    The proliferation of bioinformatics in modern biology marks a modern revolution in science that promises to influence science education at all levels. This study analyzed secondary school science standards of 49 U.S. states (Iowa has no science framework) and the District of Columbia for content related to bioinformatics. The bioinformatics…

  6. Visualizing and Sharing Results in Bioinformatics Projects: GBrowse and GenBank Exports

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Effective tools for presenting and sharing data are necessary for collaborative projects, typical for bioinformatics. In order to facilitate sharing our data with other genomics, molecular biology, and bioinformatics researchers, we have developed software to export our data to GenBank and combined ...

  7. Teaching Bioinformatics and Neuroinformatics by Using Free Web-Based Tools

    ERIC Educational Resources Information Center

    Grisham, William; Schottler, Natalie A.; Valli-Marill, Joanne; Beck, Lisa; Beatty, Jackson

    2010-01-01

    This completely computer-based module's purpose is to introduce students to bioinformatics resources. We present an easy-to-adopt module that weaves together several important bioinformatic tools so students can grasp how these tools are used in answering research questions. Students integrate information gathered from websites dealing with…

  8. Making Bioinformatics Projects a Meaningful Experience in an Undergraduate Biotechnology or Biomedical Science Programme

    ERIC Educational Resources Information Center

    Sutcliffe, Iain C.; Cummings, Stephen P.

    2007-01-01

    Bioinformatics has emerged as an important discipline within the biological sciences that allows scientists to decipher and manage the vast quantities of data (such as genome sequences) that are now available. Consequently, there is an obvious need to provide graduates in biosciences with generic, transferable skills in bioinformatics. We present…

  9. Exploring Cystic Fibrosis Using Bioinformatics Tools: A Module Designed for the Freshman Biology Course

    ERIC Educational Resources Information Center

    Zhang, Xiaorong

    2011-01-01

    We incorporated a bioinformatics component into the freshman biology course that allows students to explore cystic fibrosis (CF), a common genetic disorder, using bioinformatics tools and skills. Students learn about CF through searching genetic databases, analyzing genetic sequences, and observing the three-dimensional structures of proteins…

  10. Data Compression Concepts and Algorithms and their Applications to Bioinformatics

    PubMed Central

    Nalbantog̃lu, Ö. U.; Russell, D.J.; Sayood, K.

    2009-01-01

    Data compression at its base is concerned with how information is organized in data. Understanding this organization can lead to efficient ways of representing the information and hence data compression. In this paper we review the ways in which ideas and approaches fundamental to the theory and practice of data compression have been used in the area of bioinformatics. We look at how basic theoretical ideas from data compression, such as the notions of entropy, mutual information, and complexity have been used for analyzing biological sequences in order to discover hidden patterns, infer phylogenetic relationships between organisms and study viral populations. Finally, we look at how inferred grammars for biological sequences have been used to uncover structure in biological sequences. PMID:20157640

  11. The European Bioinformatics Institute in 2016: Data growth and integration

    PubMed Central

    Cook, Charles E.; Bergman, Mary Todd; Finn, Robert D.; Cochrane, Guy; Birney, Ewan; Apweiler, Rolf

    2016-01-01

    New technologies are revolutionising biological research and its applications by making it easier and cheaper to generate ever-greater volumes and types of data. In response, the services and infrastructure of the European Bioinformatics Institute (EMBL-EBI, www.ebi.ac.uk) are continually expanding: total disk capacity increases significantly every year to keep pace with demand (75 petabytes as of December 2015), and interoperability between resources remains a strategic priority. Since 2014 we have launched two new resources: the European Variation Archive for genetic variation data and EMPIAR for two-dimensional electron microscopy data, as well as a Resource Description Framework platform. We also launched the Embassy Cloud service, which allows users to run large analyses in a virtual environment next to EMBL-EBI's vast public data resources. PMID:26673705

  12. Public Access for Teaching Genomics, Proteomics, and Bioinformatics

    PubMed Central

    Campbell, A. Malcolm

    2003-01-01

    When the human genome project was conceived, its leaders wanted all researchers to have equal access to the data and associated research tools. Their vision of equal access provides an unprecedented teaching opportunity. Teachers and students have free access to the same databases that researchers are using. Furthermore, the recent movement to deliver scientific publications freely has presented a second source of current information for teaching. I have developed a genomics course that incorporates many of the public-domain databases, research tools, and peer-reviewed journals. These online resources provide students with exciting entree into the new fields of genomics, proteomics, and bioinformatics. In this essay, I outline how these fields are especially well suited for inclusion in the undergraduate curriculum. Assessment data indicate that my students were able to utilize online information to achieve the educational goals of the course and that the experience positively influenced their perceptions of how they might contribute to biology. PMID:12888845

  13. The European Bioinformatics Institute in 2016: Data growth and integration.

    PubMed

    Cook, Charles E; Bergman, Mary Todd; Finn, Robert D; Cochrane, Guy; Birney, Ewan; Apweiler, Rolf

    2016-01-01

    New technologies are revolutionising biological research and its applications by making it easier and cheaper to generate ever-greater volumes and types of data. In response, the services and infrastructure of the European Bioinformatics Institute (EMBL-EBI, www.ebi.ac.uk) are continually expanding: total disk capacity increases significantly every year to keep pace with demand (75 petabytes as of December 2015), and interoperability between resources remains a strategic priority. Since 2014 we have launched two new resources: the European Variation Archive for genetic variation data and EMPIAR for two-dimensional electron microscopy data, as well as a Resource Description Framework platform. We also launched the Embassy Cloud service, which allows users to run large analyses in a virtual environment next to EMBL-EBI's vast public data resources. PMID:26673705

  14. The European Bioinformatics Institute’s data resources 2014

    PubMed Central

    Brooksbank, Catherine; Bergman, Mary Todd; Apweiler, Rolf; Birney, Ewan; Thornton, Janet

    2014-01-01

    Molecular Biology has been at the heart of the ‘big data’ revolution from its very beginning, and the need for access to biological data is a common thread running from the 1965 publication of Dayhoff’s ‘Atlas of Protein Sequence and Structure’ through the Human Genome Project in the late 1990s and early 2000s to today’s population-scale sequencing initiatives. The European Bioinformatics Institute (EMBL-EBI; http://www.ebi.ac.uk) is one of three organizations worldwide that provides free access to comprehensive, integrated molecular data sets. Here, we summarize the principles underpinning the development of these public resources and provide an overview of EMBL-EBI’s database collection to complement the reviews of individual databases provided elsewhere in this issue. PMID:24271396

  15. Serial analysis of gene expression (SAGE): unraveling the bioinformatics tools.

    PubMed

    Tuteja, Renu; Tuteja, Narendra

    2004-08-01

    Serial analysis of gene expression (SAGE) is a powerful technique that can be used for global analysis of gene expression. Its chief advantage over other methods is that it does not require prior knowledge of the genes of interest and provides qualitative and quantitative data of potentially every transcribed sequence in a particular cell or tissue type. This is a technique of expression profiling, which permits simultaneous, comparative and quantitative analysis of gene-specific, 9- to 13-basepair sequences. These short sequences, called SAGE tags, are linked together for efficient sequencing. The sequencing data are then analyzed to identify each gene expressed in the cell and the levels at which each gene is expressed. The main benefit of SAGE includes the digital output and the identification of novel genes. In this review, we present an outline of the method, various bioinformatics methods for data analysis and general applications of this important technology. PMID:15273993

  16. From Jobs to Work: Scheduling the Right Bioinformatics Tools

    PubMed Central

    Ries, James E.; Patrick, Timothy B.; Springer, Gordon K.

    2002-01-01

    A great deal of effort has been expended toward scheduling computationally intensive jobs on Grids1,2 and other collections of high performance computing resources. Bioinformatics computer jobs are of particular interest as they are often highly computationally intensive. However, the problem has not been addressed from the viewpoint of the overall work that should be done. Here, we make a distinction between jobs and work. Jobs are specifically bound computational tasks (e.g., a request to run NCBI's BLAST tool or the GCG FASTA program) versus work requests, which are more general (e.g., a request to compare a set of sequences for similarity). We contend that biology researchers often wish to accomplish work rather than run a particular job. With this idea in mind, it is possible to improve resource usage by mapping work to jobs with the goal of choosing appropriate jobs that can best be scheduled at a given time.

  17. Bioinformatics Tools for the Discovery of New Nonribosomal Peptides.

    PubMed

    Leclère, Valérie; Weber, Tilmann; Jacques, Philippe; Pupin, Maude

    2016-01-01

    This chapter helps in the use of bioinformatics tools relevant to the discovery of new nonribosomal peptides (NRPs) produced by microorganisms. The strategy described can be applied to draft or fully assembled genome sequences. It relies on the identification of the synthetase genes and the deciphering of the domain architecture of the nonribosomal peptide synthetases (NRPSs). In the next step, candidate peptides synthesized by these NRPSs are predicted in silico, considering the specificity of incorporated monomers together with their isomery. To assess their novelty, the two-dimensional structure of the peptides can be compared with the structural patterns of all known NRPs. The presented workflow leads to an efficient and rapid screening of genomic data generated by high throughput technologies. The exploration of such sequenced genomes may lead to the discovery of new drugs (i.e., antibiotics against multi-resistant pathogens or anti-tumors). PMID:26831711

  18. Why Polyphenols have Promiscuous Actions? An Investigation by Chemical Bioinformatics.

    PubMed

    Tang, Guang-Yan

    2016-05-01

    Despite their diverse pharmacological effects, polyphenols are poor for use as drugs, which have been traditionally ascribed to their low bioavailability. However, Baell and co-workers recently proposed that the redox potential of polyphenols also plays an important role in this, because redox reactions bring promiscuous actions on various protein targets and thus produce non-specific pharmacological effects. To investigate whether the redox reactivity behaves as a critical factor in polyphenol promiscuity, we performed a chemical bioinformatics analysis on the structure-activity relationships of twenty polyphenols. It was found that the gene expression profiles of human cell lines induced by polyphenols were not correlated with the presence or not of redox moieties in the polyphenols, but significantly correlated with their molecular structures. Therefore, it is concluded that the promiscuous actions of polyphenols are likely to result from their inherent structural features rather than their redox potential. PMID:27319142

  19. [Bioinformatics analysis of DNA demethylase genes in Lonicera japonica Thunb].

    PubMed

    Qi, Lin-jie; Yuan, Yuan; Wu, Chong; Huang, Lu-qi; Chen, Ping

    2015-03-01

    The DNA demethylase genes are widespread in plants. Four DNA demethylase genes (LJDME1, LJDME2, LJDME3 and LJDME4) were obtained from transcriptome dataset of Lonicera japonica Thunb by using bioinformatics methods and the proteins' physicochemical properties they encoded were predicted. The phylogenetic tree showed that the four DNA demethylase genes and Arabidopsis thaliana DME had a close relationship. The result of gene expression model showed that four DNA demethylase genes were different between species. The expression levels of LJDME1 and LJDME2 were even more higher in Lonicera japonica var. chinensis than those in L. japonica. LJDME] and LJDME2 maybe regulate the active compounds of L. japonica. This study aims to lay a foundation for further understanding of the function of DNA demethylase genes in L. japonica. PMID:26118119

  20. NMR structure improvement: A structural bioinformatics & visualization approach

    NASA Astrophysics Data System (ADS)

    Block, Jeremy N.

    The overall goal of this project is to enhance the physical accuracy of individual models in macromolecular NMR (Nuclear Magnetic Resonance) structures and the realism of variation within NMR ensembles of models, while improving agreement with the experimental data. A secondary overall goal is to combine synergistically the best aspects of NMR and crystallographic methodologies to better illuminate the underlying joint molecular reality. This is accomplished by using the powerful method of all-atom contact analysis (describing detailed sterics between atoms, including hydrogens); new graphical representations and interactive tools in 3D and virtual reality; and structural bioinformatics approaches to the expanded and enhanced data now available. The resulting better descriptions of macromolecular structure and its dynamic variation enhances the effectiveness of the many biomedical applications that depend on detailed molecular structure, such as mutational analysis, homology modeling, molecular simulations, protein design, and drug design.

  1. BioRuby: bioinformatics software for the Ruby programming language

    PubMed Central

    Goto, Naohisa; Prins, Pjotr; Nakao, Mitsuteru; Bonnal, Raoul; Aerts, Jan; Katayama, Toshiaki

    2010-01-01

    Summary: The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser. Availability: BioRuby is free and open source software, made available under the Ruby license. BioRuby runs on all platforms that support Ruby, including Linux, Mac OS X and Windows. And, with JRuby, BioRuby runs on the Java Virtual Machine. The source code is available from http://www.bioruby.org/. Contact: katayama@bioruby.org PMID:20739307

  2. Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders

    PubMed Central

    Hofmann-Apitius, Martin; Ball, Gordon; Gebel, Stephan; Bagewadi, Shweta; de Bono, Bernard; Schneider, Reinhard; Page, Matt; Kodamullil, Alpha Tom; Younesi, Erfan; Ebeling, Christian; Tegnér, Jesper; Canard, Luc

    2015-01-01

    Since the decoding of the Human Genome, techniques from bioinformatics, statistics, and machine learning have been instrumental in uncovering patterns in increasing amounts and types of different data produced by technical profiling technologies applied to clinical samples, animal models, and cellular systems. Yet, progress on unravelling biological mechanisms, causally driving diseases, has been limited, in part due to the inherent complexity of biological systems. Whereas we have witnessed progress in the areas of cancer, cardiovascular and metabolic diseases, the area of neurodegenerative diseases has proved to be very challenging. This is in part because the aetiology of neurodegenerative diseases such as Alzheimer´s disease or Parkinson´s disease is unknown, rendering it very difficult to discern early causal events. Here we describe a panel of bioinformatics and modeling approaches that have recently been developed to identify candidate mechanisms of neurodegenerative diseases based on publicly available data and knowledge. We identify two complementary strategies—data mining techniques using genetic data as a starting point to be further enriched using other data-types, or alternatively to encode prior knowledge about disease mechanisms in a model based framework supporting reasoning and enrichment analysis. Our review illustrates the challenges entailed in integrating heterogeneous, multiscale and multimodal information in the area of neurology in general and neurodegeneration in particular. We conclude, that progress would be accelerated by increasing efforts on performing systematic collection of multiple data-types over time from each individual suffering from neurodegenerative disease. The work presented here has been driven by project AETIONOMY; a project funded in the course of the Innovative Medicines Initiative (IMI); which is a public-private partnership of the European Federation of Pharmaceutical Industry Associations (EFPIA) and the European

  3. Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders.

    PubMed

    Hofmann-Apitius, Martin; Ball, Gordon; Gebel, Stephan; Bagewadi, Shweta; de Bono, Bernard; Schneider, Reinhard; Page, Matt; Kodamullil, Alpha Tom; Younesi, Erfan; Ebeling, Christian; Tegnér, Jesper; Canard, Luc

    2015-01-01

    Since the decoding of the Human Genome, techniques from bioinformatics, statistics, and machine learning have been instrumental in uncovering patterns in increasing amounts and types of different data produced by technical profiling technologies applied to clinical samples, animal models, and cellular systems. Yet, progress on unravelling biological mechanisms, causally driving diseases, has been limited, in part due to the inherent complexity of biological systems. Whereas we have witnessed progress in the areas of cancer, cardiovascular and metabolic diseases, the area of neurodegenerative diseases has proved to be very challenging. This is in part because the aetiology of neurodegenerative diseases such as Alzheimer´s disease or Parkinson´s disease is unknown, rendering it very difficult to discern early causal events. Here we describe a panel of bioinformatics and modeling approaches that have recently been developed to identify candidate mechanisms of neurodegenerative diseases based on publicly available data and knowledge. We identify two complementary strategies-data mining techniques using genetic data as a starting point to be further enriched using other data-types, or alternatively to encode prior knowledge about disease mechanisms in a model based framework supporting reasoning and enrichment analysis. Our review illustrates the challenges entailed in integrating heterogeneous, multiscale and multimodal information in the area of neurology in general and neurodegeneration in particular. We conclude, that progress would be accelerated by increasing efforts on performing systematic collection of multiple data-types over time from each individual suffering from neurodegenerative disease. The work presented here has been driven by project AETIONOMY; a project funded in the course of the Innovative Medicines Initiative (IMI); which is a public-private partnership of the European Federation of Pharmaceutical Industry Associations (EFPIA) and the European

  4. Bioinformatics approaches to single-cell analysis in developmental biology.

    PubMed

    Yalcin, Dicle; Hakguder, Zeynep M; Otu, Hasan H

    2016-03-01

    Individual cells within the same population show various degrees of heterogeneity, which may be better handled with single-cell analysis to address biological and clinical questions. Single-cell analysis is especially important in developmental biology as subtle spatial and temporal differences in cells have significant associations with cell fate decisions during differentiation and with the description of a particular state of a cell exhibiting an aberrant phenotype. Biotechnological advances, especially in the area of microfluidics, have led to a robust, massively parallel and multi-dimensional capturing, sorting, and lysis of single-cells and amplification of related macromolecules, which have enabled the use of imaging and omics techniques on single cells. There have been improvements in computational single-cell image analysis in developmental biology regarding feature extraction, segmentation, image enhancement and machine learning, handling limitations of optical resolution to gain new perspectives from the raw microscopy images. Omics approaches, such as transcriptomics, genomics and epigenomics, targeting gene and small RNA expression, single nucleotide and structural variations and methylation and histone modifications, rely heavily on high-throughput sequencing technologies. Although there are well-established bioinformatics methods for analysis of sequence data, there are limited bioinformatics approaches which address experimental design, sample size considerations, amplification bias, normalization, differential expression, coverage, clustering and classification issues, specifically applied at the single-cell level. In this review, we summarize biological and technological advancements, discuss challenges faced in the aforementioned data acquisition and analysis issues and present future prospects for application of single-cell analyses to developmental biology. PMID:26358759

  5. Hydroxysteroid dehydrogenases (HSDs) in bacteria: a bioinformatic perspective.

    PubMed

    Kisiela, Michael; Skarka, Adam; Ebert, Bettina; Maser, Edmund

    2012-03-01

    Steroidal compounds including cholesterol, bile acids and steroid hormones play a central role in various physiological processes such as cell signaling, growth, reproduction, and energy homeostasis. Hydroxysteroid dehydrogenases (HSDs), which belong to the superfamily of short-chain dehydrogenases/reductases (SDR) or aldo-keto reductases (AKR), are important enzymes involved in the steroid hormone metabolism. HSDs function as an enzymatic switch that controls the access of receptor-active steroids to nuclear hormone receptors and thereby mediate a fine-tuning of the steroid response. The aim of this study was the identification of classified functional HSDs and the bioinformatic annotation of these proteins in all complete sequenced bacterial genomes followed by a phylogenetic analysis. For the bioinformatic annotation we constructed specific hidden Markov models in an iterative approach to provide a reliable identification for the specific catalytic groups of HSDs. Here, we show a detailed phylogenetic analysis of 3α-, 7α-, 12α-HSDs and two further functional related enzymes (3-ketosteroid-Δ(1)-dehydrogenase, 3-ketosteroid-Δ(4)(5α)-dehydrogenase) from the superfamily of SDRs. For some bacteria that have been previously reported to posses a specific HSD activity, we could annotate the corresponding HSD protein. The dominating phyla that were identified to express HSDs were that of Actinobacteria, Proteobacteria, and Firmicutes. Moreover, some evolutionarily more ancient microorganisms (e.g., Cyanobacteria and Euryachaeota) were found as well. A large number of HSD-expressing bacteria constitute the normal human gastro-intestinal flora. Another group of bacteria were originally isolated from natural habitats like seawater, soil, marine and permafrost sediments. These bacteria include polycyclic aromatic hydrocarbons-degrading species such as Pseudomonas, Burkholderia and Rhodococcus. In conclusion, HSDs are found in a wide variety of microorganisms including

  6. Bioinformatics analysis of the epitope regions for norovirus capsid protein

    PubMed Central

    2013-01-01

    Background Norovirus is the major cause of nonbacterial epidemic gastroenteritis, being highly prevalent in both developing and developed countries. Despite of the available monoclonal antibodies (MAbs) for different sub-genogroups, a comprehensive epitope analysis based on various bioinformatics technology is highly desired for future potential antibody development in clinical diagonosis and treatment. Methods A total of 18 full-length human norovirus capsid protein sequences were downloaded from GenBank. Protein modeling was performed with program Modeller 9.9. The modeled 3D structures of capsid protein of norovirus were submitted to the protein antigen spatial epitope prediction webserver (SEPPA) for predicting the possible spatial epitopes with the default threshold. The results were processed using the Biosoftware. Results Compared with GI, we found that the GII genogroup had four deletions and two special insertions in the VP1 region. The predicted conformational epitope regions mainly concentrated on N-terminal (1~96), Middle Part (298~305, 355~375) and C-terminal (560~570). We find two common epitope regions on sequences for GI and GII genogroup, and also found an exclusive epitope region for GII genogroup. Conclusions The predicted conformational epitope regions of norovirus VP1 mainly concentrated on N-terminal, Middle Part and C-terminal. We find two common epitope regions on sequences for GI and GII genogroup, and also found an exclusive epitope region for GII genogroup. The overlapping with experimental epitopes indicates the important role of latest computational technologies. With the fast development of computational immunology tools, the bioinformatics pipeline will be more and more critical to vaccine design. PMID:23514273

  7. Evolving Strategies for the Incorporation of Bioinformatics Within the Undergraduate Cell Biology Curriculum

    PubMed Central

    Honts, Jerry E.

    2003-01-01

    Recent advances in genomics and structural biology have resulted in an unprecedented increase in biological data available from Internet-accessible databases. In order to help students effectively use this vast repository of information, undergraduate biology students at Drake University were introduced to bioinformatics software and databases in three courses, beginning with an introductory course in cell biology. The exercises and projects that were used to help students develop literacy in bioinformatics are described. In a recently offered course in bioinformatics, students developed their own simple sequence analysis tool using the Perl programming language. These experiences are described from the point of view of the instructor as well as the students. A preliminary assessment has been made of the degree to which students had developed a working knowledge of bioinformatics concepts and methods. Finally, some conclusions have been drawn from these courses that may be helpful to instructors wishing to introduce bioinformatics within the undergraduate biology curriculum. PMID:14673489

  8. The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community

    PubMed Central

    D'Elia, Domenica; Gisel, Andreas; Eriksson, Nils-Einar; Kossida, Sophia; Mattila, Kimmo; Klucar, Lubos; Bongcam-Rudloff, Erik

    2009-01-01

    The EMBnet Conference 2008, focusing on 'Leading Applications and Technologies in Bioinformatics', was organized by the European Molecular Biology network (EMBnet) to celebrate its 20th anniversary. Since its foundation in 1988, EMBnet has been working to promote collaborative development of bioinformatics services and tools to serve the European community of molecular biology laboratories. This conference was the first meeting organized by the network that was open to the international scientific community outside EMBnet. The conference covered a broad range of research topics in bioinformatics with a main focus on new achievements and trends in emerging technologies supporting genomics, transcriptomics and proteomics analyses such as high-throughput sequencing and data managing, text and data-mining, ontologies and Grid technologies. Papers selected for publication, in this supplement to BMC Bioinformatics, cover a broad range of the topics treated, providing also an overview of the main bioinformatics research fields that the EMBnet community is involved in. PMID:19534734

  9. Bioinformatics Goes to School—New Avenues for Teaching Contemporary Biology

    PubMed Central

    Wood, Louisa; Gebhardt, Philipp

    2013-01-01

    Since 2010, the European Molecular Biology Laboratory's (EMBL) Heidelberg laboratory and the European Bioinformatics Institute (EMBL-EBI) have jointly run bioinformatics training courses developed specifically for secondary school science teachers within Europe and EMBL member states. These courses focus on introducing bioinformatics, databases, and data-intensive biology, allowing participants to explore resources and providing classroom-ready materials to support them in sharing this new knowledge with their students. In this article, we chart our progress made in creating and running three bioinformatics training courses, including how the course resources are received by participants and how these, and bioinformatics in general, are subsequently used in the classroom. We assess the strengths and challenges of our approach, and share what we have learned through our interactions with European science teachers. PMID:23785266

  10. A decade of web server updates at the bioinformatics links directory: 2003–2012

    PubMed Central

    Brazas, Michelle D.; Yim, David; Yeung, Winston; Ouellette, B. F. Francis

    2012-01-01

    The 2012 Bioinformatics Links Directory update marks the 10th special Web Server issue from Nucleic Acids Research. Beginning with content from their 2003 publication, the Bioinformatics Links Directory in collaboration with Nucleic Acids Research has compiled and published a comprehensive list of freely accessible, online tools, databases and resource materials for the bioinformatics and life science research communities. The past decade has exhibited significant growth and change in the types of tools, databases and resources being put forth, reflecting both technology changes and the nature of research over that time. With the addition of 90 web server tools and 12 updates from the July 2012 Web Server issue of Nucleic Acids Research, the Bioinformatics Links Directory at http://bioinformatics.ca/links_directory/ now contains an impressive 134 resources, 455 databases and 1205 web server tools, mirroring the continued activity and efforts of our field. PMID:22700703

  11. The bioinformatics of nucleotide sequence coding for proteins requiring metal coenzymes and proteins embedded with metals

    NASA Astrophysics Data System (ADS)

    Tremberger, G.; Dehipawala, Sunil; Cheung, E.; Holden, T.; Sullivan, R.; Nguyen, A.; Lieberman, D.; Cheung, T.

    2015-09-01

    All metallo-proteins need post-translation metal incorporation. In fact, the isotope ratio of Fe, Cu, and Zn in physiology and oncology have emerged as an important tool. The nickel containing F430 is the prosthetic group of the enzyme methyl coenzyme M reductase which catalyzes the release of methane in the final step of methano-genesis, a prime energy metabolism candidate for life exploration space mission in the solar system. The 3.5 Gyr early life sulfite reductase as a life switch energy metabolism had Fe-Mo clusters. The nitrogenase for nitrogen fixation 3 billion years ago had Mo. The early life arsenite oxidase needed for anoxygenic photosynthesis energy metabolism 2.8 billion years ago had Mo and Fe. The selection pressure in metal incorporation inside a protein would be quantifiable in terms of the related nucleotide sequence complexity with fractal dimension and entropy values. Simulation model showed that the studied metal-required energy metabolism sequences had at least ten times more selection pressure relatively in comparison to the horizontal transferred sequences in Mealybug, guided by the outcome histogram of the correlation R-sq values. The metal energy metabolism sequence group was compared to the circadian clock KaiC sequence group using magnesium atomic level bond shifting mechanism in the protein, and the simulation model would suggest a much higher selection pressure for the energy life switch sequence group. The possibility of using Kepler 444 as an example of ancient life in Galaxy with the associated exoplanets has been proposed and is further discussed in this report. Examples of arsenic metal bonding shift probed by Synchrotron-based X-ray spectroscopy data and Zn controlled FOXP2 regulated pathways in human and chimp brain studied tissue samples are studied in relationship to the sequence bioinformatics. The analysis results suggest that relatively large metal bonding shift amount is associated with low probability correlation R

  12. Towards a bioinformatics of patterning: a computational approach to understanding regulative morphogenesis

    PubMed Central

    Lobo, Daniel; Malone, Taylor J.; Levin, Michael

    2013-01-01

    Summary The mechanisms underlying the regenerative abilities of certain model species are of central importance to the basic understanding of pattern formation. Complex organisms such as planaria and salamanders exhibit an exceptional capacity to regenerate complete body regions and organs from amputated pieces. However, despite the outstanding bottom-up efforts of molecular biologists and bioinformatics focused at the level of gene sequence, no comprehensive mechanistic model exists that can account for more than one or two aspects of regeneration. The development of computational approaches that help scientists identify constructive models of pattern regulation is held back by the lack of both flexible morphological representations and a repository for the experimental procedures and their results (altered pattern formation). No formal representation or computational tools exist to efficiently store, search, or mine the available knowledge from regenerative experiments, inhibiting fundamental insights from this huge dataset. To overcome these problems, we present here a new class of ontology to encode formally and unambiguously a very wide range of possible morphologies, manipulations, and experiments. This formalism will pave the way for top-down approaches for the discovery of comprehensive models of regeneration. We chose the planarian regeneration dataset to illustrate a proof-of-principle of this novel bioinformatics of shape; we developed a software tool to facilitate the formalization and mining of the planarian experimental knowledge, and cured a database containing all of the experiments from the principal publications on planarian regeneration. These resources are freely available for the regeneration community and will readily assist researchers in identifying specific functional data in planarian experiments. More importantly, these applications illustrate the presented framework for formalizing knowledge about functional perturbations of

  13. Built Environment and Elderly Population Health: A Comprehensive Literature Review

    PubMed Central

    Garin, Noe; Olaya, Beatriz; Miret, Marta; Ayuso-Mateos, Jose Luis; Power, Michael; Bucciarelli, Paola; Haro, Josep Maria

    2014-01-01

    Global population aging over recent years has been linked to poorer health outcomes and higher healthcare expenditure. Policies focusing on healthy aging are currently being developed but a complete understanding of health determinants is needed to guide these efforts. The built environment and other external factors have been added to the International Classification of Functioning as important determinants of health and disability. Although the relationship between the built environment and health has been widely examined in working age adults, research focusing on elderly people is relatively recent. In this review, we provide a comprehensive synthesis of the evidence on the built environment and health in the elderly. PMID:25356084

  14. Introduction of electrodehydrators with built-in jet mixers

    SciTech Connect

    Gershuni, S.S.; Baimbetov, A.M.; Idrisova, T.S.; Makhov, A.F.

    1985-09-01

    This paper describes an effective technique of crude oil desalting which is recirculation of water within the electrodehydrator by means of built-in jet mixers. Vertical electrodehydrators with built-in jet mixers have been tested and approved at the Novo-Ufa refinery. Design and operation of the vessel is described. Results from analyses of the oil during the test period are summarized. Retrofitting of electrodehydrators with built-in jet mixers proved increased capacity and the consumption of water and electric power in desalting was cut in half while oil loss in the electric desalting units was reduced substantially.

  15. Site Plans (2008 As Built) Oklahoma City Civic Center, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Site Plans (2008 As Built) - Oklahoma City Civic Center, Bounded by N. Shartel Avenue to the West, N. Hudson Avenue to the East, Couch Drive to the North, and Colcord Drive to the South, Oklahoma City, Oklahoma County, OK

  16. Main elevation of Lincoln School (built 1928) utilized by the ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Main elevation of Lincoln School (built 1928) utilized by the children of Lincoln Mill workers living the surrounding mill housing neighborhood - Lincoln School, 1110 Meridian Street, Huntsville, Madison County, AL

  17. VIEW OF FORMER WINDBER ELECTRIC COMPANY BUILDING, BUILT 1925, LOOKING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    VIEW OF FORMER WINDBER ELECTRIC COMPANY BUILDING, BUILT 1925, LOOKING NORTH, LOCATED ON THE NORTH SIDE OF 15TH STREET, NOW BERWIND-WILMORE DIVISION OFFICES AND REITZ COAL COMPANY - Windber Electric Building, 509 Fifteenth Street, Windber, Somerset County, PA

  18. 4. J. E. HERMAN HOUSE, built 1899, of SOFT CLAYLIKE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    4. J. E. HERMAN HOUSE, built 1899, of SOFT CLAY-LIKE MATERIAL THAT WAS QUARRIED AND THEN HARDENED ON CONTACT WITH AIR AND SUNSHINE. IT HAS NO DOORWAY TO STREET. - Town of Liebenthal, Liebenthal, Rush County, KS

  19. 26. INTERIOR VIEW SHOWING ROW OF TIMBER SUPPORT TOWERS BUILT ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    26. INTERIOR VIEW SHOWING ROW OF TIMBER SUPPORT TOWERS BUILT AS TEMPORARY TRUSS REINFORCEMENT (NOTE STEEL STRUCTURES ATOP TIMBER BRACING) - Oakland Army Base, Transit Shed, East of Dunkirk Street & South of Burma Road, Oakland, Alameda County, CA

  20. Northeast end of Pier 22, looking southeast, the partially built ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Northeast end of Pier 22, looking southeast, the partially built towers of the new Carquinez Straits Bridge are visible in the distance - Mare Island Naval Shipyard, Finger Piers 22 & 23, Railroad Avenue near Eighteenth Street, Vallejo, Solano County, CA