Superimposé: a 3D structural superposition server

The Superimposé webserver performs structural similarity searches with a preference towards 3D structure-based methods. Similarities can be detected between small molecules (e.g. drugs), parts of large structures (e.g. binding sites of proteins) and entire proteins. For this purpose, a number of algorithms were implemented and various databases are provided. Superimposé assists the user regarding the selection of a suitable combination of algorithm and database. After the computation on our server infrastructure, a visual assessment of the results is provided. The structure-based in silico screening for similar drug-like compounds enables the detection of scaffold-hoppers with putatively similar effects. The possibility to find similar binding sites can be of special interest in the functional analysis of proteins. The search for structurally similar proteins allows the detection of similar folds with different backbone topology. The Superimposé server is available at: http://bioinformatics.charite.de/superimpose

Biodiversity Databases

Computing and database management has shifted from cottage industry-style methods — the small independent researcher keeping records for a particular project — to state-of-the-art file storage systems, presentation, and distribution over the Internet. New and emerging techniques for recognition, compilation, and data management have made managing data a discipline in its own right. Covering all aspects of this data management, Biodiversity Databases: Techniques, Politics, and Applications brings together input from social scientists, programmers, database designers, and information specialists to delineate the political setting and give institutions platforms for the dissemination of taxonomic information. A practical and logical guide to complex issues, the book explores the changes and challenges of the information age. It discusses projects developed to provide better access to all available biodiversity information. The chapters make the case for the need for representation of concepts in taxonomic databases. They explore issues involved in connecting databases with different user interfaces, the technical demands of linking databases that are not entirely uniform in structure, and the problems of user access and the control of data quality. The book highlights different approaches to addressing concerns associated with the taxonomic impediment and the low reproducibility of taxonomic data. It provides an in-depth examination of the challenge of making taxonomic information more widely available to users in the wider scientific community, in government, and the general population

Interoperability between heterogeneous and distributed biodiversity data sources in structured data networks

The extensive capturing of biodiversity data and storing them in heterogeneous information systems that are accessible on the internet across the globe has created many interoperability problems. One is that the data providers are independent of others and they can run systems which were developed on different platforms at different times using different software products to respond to different needs of information. A second arises from the data modelling used to convert the real world data into a computerised data structure which is not conditioned by a universal standard. Most importantly the need for interoperation between these disparate data sources is to get accurate and useful information for further analysis and decision making. The software representation of a universal or a single data definition structure for depicting a biodiversity entity is ideal. But this is not necessarily possible when integrating data from independently developed systems. The different perspectives of the real-world entity when being modelled by independent teams will result in the use of different terminologies, definition and representation of attributes and operations for the same real-world entity. The research in this thesis is concerned with designing and developing an interoperable flexible framework that allows data integration between various distributed and heterogeneous biodiversity data sources that adopt XML standards for data communication. In particular the problems of scope and representational heterogeneity among the various XML data schemas are addressed. To demonstrate this research a prototype system called BUFFIE (Biodiversity Users‘ Flexible Framework for Interoperability Experiments) was designed using a hybrid of Object-oriented and Functional design principles. This system accepts the query information from the user in a web form, and designs an XML query. This request query is enriched and is made more specific to data providers using the data provider information stored in a repository. These requests are sent to the different heterogeneous data resources across the internet using HTTP protocol. The responses received are in varied XML formats which are integrated using knowledge mapping rules defined in XSLT & XML. The XML mappings are derived from a biodiversity domain knowledgebase defined for schema mappings of different data exchange protocols. The integrated results are presented to users or client programs to do further analysis. The main results of this thesis are: (1) A framework model that allows interoperation between the heterogeneous data source systems. (2) Enriched querying improves the accuracy of responses by finding the correct information existing among autonomous, distributed and heterogeneous data resources. (3) A methodology that provides a foundation for extensibility as any new network data standards in XML can be added to the existing protocols. The presented approach shows that (1) semi automated mapping and integration of datasets from the heterogeneous and autonomous data providers is feasible. (2) Query enriching and integrating the data allows the querying and harvesting of useful data from various data providers for helpful analysis.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Interoperability between heterogeneous and distributed biodiversity data sources in structured data networks

The extensive capturing of biodiversity data and storing them in heterogeneous information systems that are accessible on the internet across the globe has created many interoperability problems. One is that the data providers are independent of others and they can run systems which were developed on different platforms at different times using different software products to respond to different needs of information. A second arises from the data modelling used to convert the real world data into a computerised data structure which is not conditioned by a universal standard. Most importantly the need for interoperation between these disparate data sources is to get accurate and useful information for further analysis and decision making. The software representation of a universal or a single data definition structure for depicting a biodiversity entity is ideal. But this is not necessarily possible when integrating data from independently developed systems. The different perspectives of the real-world entity when being modelled by independent teams will result in the use of different terminologies, definition and representation of attributes and operations for the same real-world entity. The research in this thesis is concerned with designing and developing an interoperable flexible framework that allows data integration between various distributed and heterogeneous biodiversity data sources that adopt XML standards for data communication. In particular the problems of scope and representational heterogeneity among the various XML data schemas are addressed. To demonstrate this research a prototype system called BUFFIE (Biodiversity Users‘ Flexible Framework for Interoperability Experiments) was designed using a hybrid of Object-oriented and Functional design principles. This system accepts the query information from the user in a web form, and designs an XML query. This request query is enriched and is made more specific to data providers using the data provider information stored in a repository. These requests are sent to the different heterogeneous data resources across the internet using HTTP protocol. The responses received are in varied XML formats which are integrated using knowledge mapping rules defined in XSLT & XML. The XML mappings are derived from a biodiversity domain knowledgebase defined for schema mappings of different data exchange protocols. The integrated results are presented to users or client programs to do further analysis. The main results of this thesis are: (1) A framework model that allows interoperation between the heterogeneous data source systems. (2) Enriched querying improves the accuracy of responses by finding the correct information existing among autonomous, distributed and heterogeneous data resources. (3) A methodology that provides a foundation for extensibility as any new network data standards in XML can be added to the existing protocols. The presented approach shows that (1) semi automated mapping and integration of datasets from the heterogeneous and autonomous data providers is feasible. (2) Query enriching and integrating the data allows the querying and harvesting of useful data from various data providers for helpful analysis

Knowledge Accumulation of Microbial Data Aiming at a Dynamic Taxonomic Framework

Deze thesis is een poging om precies dit onderzoeksgebied te overbruggen dat ligt tussen ruw gegeven en abstract concept, tussen praktijk en theorie, binnen het kader van de hedendaagse bacteriële taxonomie. Als gevolg hiervan is het een kruisbestuiving geworden tussen microbiologie, wiskunde en computerwetenschappen. De kunst om het landschap van de bacteriële diversiteit uit te tekenen, gebruikt als een metafoor voor het modelleren van de taxonomie, vereist het bepalen van een representatieve waaier aan reproduceerbare en vergelijkbare experimentele kenmerken van een verzameling bacteriën (microbiologie/taxonomie), het ontwerpen en implementeren van objectieve classificatiemethodes voor het groeperen van gegevens op een niet gecoördineerde manier (wiskunde/classificatie) en het consolideren van experimentele gegevens en hun verschillende onderverdelingen via een uniforme en weldoordachte aanpak (computerwetenschappen/kennisbeheer). Men kan zich gemakkelijk een globaal kennissysteem voor de geest halen dat de vellen vol experimentele gegevens die voortspruiten uit de microbiologische onderzoeksverrichtingen op een gestructureerde en geüniformiseerde manier kan absorberen. Een dergelijk kennisbeheersysteem zou een ongelofelijke vooruitgang betekenen voor de mogelijke toepassing van intelligente en goed gefundeerde methodes voor het ontginnen van de gegevens, ingezet als hulpmiddel om het afbakenen van objectieve en universele taxonomische consensusmodellen op een betere manier te stroomlijnen en te automatiseren. Bovendien kunnen dergelijke inferentiesystemen in staat worden geacht om ogenblikkelijk te reageren op een toevloed van nieuwe gegevens en interactief te communiceren met de buitenwereld indien noodzakelijke stukken voor het vervolledigen van de taxonomische puzzel zouden ontbreken. De geldigheid van nieuwe inzichten of hypothesen omtrent het leven en de evolutie van bacteriën zou onmiddellijk kunnen getoetst worden aan deze vergaarbakken vol kennis, mogelijks met een directe aanpassing van bestaande taxonomische modellen tot gevolg. Vooraleer de betrachtingen van een autodidactisch inferentiesysteem voor het uittekenen van het landschap van de bacteriële diversiteit kunnen gerealiseerd worden, moeten belangrijke technische en organisatorische hindernissen overwonnen worden. Dit vraagt het verleggen van de grenzen van een mondiale uitwisseling van gegevens, het nasporen en invullen van de hiaten in de waarnemingen, en het verkennen van de mogelijkheden van nieuwe technieken voor het ontginnen van gegevens, ten voordele van een beter inzicht in het leven en de evolutie van bacteriën. Spijts de nog vele onopgeloste kwesties, kunnen de ideeën die worden aangebracht in deze verhandeling als stimulans en leidraad dienen bij het integreren en exploiteren van microbiële gegevens, in plaats van het blijvend koesteren van een ijdele hoo

Bodies of Water

This book is available as open access through the Bloomsbury Open Access programme and is available on www.bloomsburycollections.com. Water is the element that, more than any other, ties human beings in to the world around them – from the oceans that surround us to the water that makes up most of our bodies. Exploring the cultural and philosophical implications of this fact, Bodies of Water develops an innovative new mode of posthuman feminist phenomenology that understands our bodies as being fundamentally part of the natural world and not separate from or privileged to it. Building on the works by Luce Irigaray, Maurice Merleau-Ponty and Gilles Deleuze, Astrida Neimanis’s book is a landmark study that brings a new feminist perspective to bear on ideas of embodiment and ecological ethics in the posthuman critical moment

Social work with airports passengers

Social work at the airport is in to offer to passengers social services. The main methodological position is that people are under stress, which characterized by a particular set of characteristics in appearance and behavior. In such circumstances passenger attracts in his actions some attention. Only person whom he trusts can help him with the documents or psychologically

Study on open science: The general state of the play in Open Science principles and practices at European life sciences institutes

Nowadays, open science is a hot topic on all levels and also is one of the priorities of the European Research Area. Components that are commonly associated with open science are open access, open data, open methodology, open source, open peer review, open science policies and citizen science. Open science may a great potential to connect and influence the practices of researchers, funding institutions and the public. In this paper, we evaluate the level of openness based on public surveys at four European life sciences institute