1,004 research outputs found
GFF Utilities: GffRead and GffCompare
No full textclassify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFFPlease cite as:
Pertea G and Pertea M. "GFF Utilities: GffRead and GffCompare". F1000Research 2020, 9:304 DOI: 10.12688/f1000research.23297.
GffCompare
No full textclassify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFFPlease cite as: Pertea G and Pertea M. "GFF Utilities: GffRead and GffCompare". F1000Research 2020, 9:304 DOI: 10.12688/f1000research.23297.
Geo-engineering: A co-production of applied earth sciences and civil engineering - 2nd phase
No full textGeo-engineerin
Variable-schaal geo-informatie [1]
No full textDigitale kaarten worden tegenwoordig overal gebruikt van desktop tot mobiele telefoon en het gebruik is meer en meer interactief en gebaseerd op zoomen en pannen. Kaartgeneralisatie onderzoek kijkt naar generalisatie zonder vaste schalen (‘continue generaliseren’). Hoewel er een aantal eerste resultaten zijn (van Kreveld, 2001; Sester and Brenner, 2005), is de optimale oplossing nog niet gevonden. Dit artikel introduceert de eerste echte variable-schaal structuur voor geografische informatie: een kleine stap in de schaal dimensie heeft een kleine verandering in de kaart tot gevolg. Op basis hiervan kan (geanimeerd) geleidelijk zoomen worden ondersteundOTB ResearchOTB Research Institute for the Built Environmen
Investigating the use of semantic technologies in spatial mapping applications
No full textSemantic Web Technologies are ideally suited to build context-aware information retrieval applications. However, the geospatial aspect of context awareness presents unique challenges such as the semantic modelling of geographical references for efficient handling of spatial queries, the reconciliation of the heterogeneity at the semantic and geo-representation levels, maintaining the quality of service and scalability of communicating, and the efficient rendering of the spatial queries' results. In this paper, we describe the modelling decisions taken to solve these challenges by analysing our implementation of an intelligent planning and recommendation tool that provides location-aware advice for a specific application domain. This paper contributes to the methodology of integrating heterogeneous geo-referenced data into semantic knowledgebases, and also proposes mechanisms for efficient spatial interrogation of the semantic knowledgebase and optimising the rendering of the dynamically retrieved context-relevant information on a web frontend
Dynamic Geo-Fencing for Polycentric Congestion Management: A Simulation-Based Analysis
No full textOur cities are growing at an unprecedented pace. The flexible use of metropolitan infrastructures is the key to maintaining, if not increasing, the current quality of life. The combined use of geo-fence technology and connected vehicles can be the tool to achieve this flexibility. In this paper, we take a first step in the evaluation of the benefits that dynamic geo-fencing could bring. In a simulation-based environment, we employ a computer vision approach to dynamically identify congested areas in a given transportation network. We then compare the performance of perimeter control based on dynamic geo-fencing vs conventional perimeter strategies, based on a fixed, pre-determined area-a scenario mimicking traffic management approaches currently deployed in large metropolitan areas worldwide. Simulation results highlight a reduction of more than 20% of the Total Time Spent in a regular Manhattan grid network, encouraging further efforts to validate the efficiency of dynamic geo-fencing in addressing externalities (congestion, pollution, noise, etc.) in more realistic scenarios.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Transport and PlanningTransport and Plannin
Detection of lineage-specific evolutionary changes among primate species
No full textAbstract Background Comparison of the human genome with other primates offers the opportunity to detect evolutionary events that created the diverse phenotypes among the primate species. Because the primate genomes are highly similar to one another, methods developed for analysis of more divergent species do not always detect signs of evolutionary selection. Results We have developed a new method, called DivE, specifically designed to find regions that have evolved either more or less rapidly than expected, for any clade within a set of very closely related species. Unlike some previous methods, DivE does not rely on rates of synonymous and nonsynonymous substitution, which enables it to detect evolutionary events in noncoding regions. We demonstrate using simulated data that DivE compares favorably to alternative methods, and we then apply DivE to the ENCODE regions in 14 primate species. We identify thousands of regions in these primates, ranging from 50 to >10000 bp in length, that appear to have experienced either constrained or accelerated rates of evolution. In particular, we detected 4942 regions that have potentially undergone positive selection in one or more primate species. Most of these regions occur outside of protein-coding genes, although we identified 20 proteins that have experienced positive selection. Conclusions DivE provides an easy-to-use method to predict both positive and negative selection in noncoding DNA, that is particularly well-suited to detecting lineage-specific selection in large genomes.</p
Moving objects in a geo-DBMS: Structuring, indexing, querying and visualizing moving point objects in a geo-DBMS context
No full textThe main question of this research is: What is the potential and performance of a geo-DBMS to structure, index, query and visualize spatiotemporal points clouds of moving objects? Some researchers have been developing spatiatemporal data structures. These structures have some disadvantages. For instance, the model made by Vazirgiannis and Wolfson is especially made for road networks and anoter data model (developed by Wolfson) is relatively complicated and can be used for objects that move freely in space like aircrafts. Some approaches have been the disadvantage that they a lot of redundant storage. To overcome these disadvantages, a new approach is introduced. Thi smodel could be used for every purpose that deals with moving point object data (this makes it generic) and it does noet contain any redundant storage. An efficient indexing method makes quering of the data in a DBMS faster. For many query tpes, indexing methods are available. In moving point object cases, most of these indexin gmethods are based on the R-tree. Often it is not known in advance whih queries are going to be done on a data set and which structure and which indexing methods are going to be chosen. So it needs to be investigated which indexing methods give the fastes access to the data. The main principle of this generix model is choosing a base table, from which, by using (materialized) views, three other data representations (based n different geometric data types) easily could be derived. In this way a set of four data representations is available for quering. These four data types are 2D points, 3D points, 2D lines and 3D lines. In the 2D representations time is regarded as an attribute. From tbis set, many queries cold be formulated, like the objects speed, direction or acceleration. After the model is introduced, an efficient querying and indexing needs to be found. BEcause in Oracle 9i Spatial only the 2D and the 3D R-tree are implemented, the only way to manipulate the efficiency of accessing the data by the user is by formulating efficient queries. To demonstrate that this generic model is fast and flexible, two chase studies have been done. In the first case, the data has been collected in advance and being analyzed afterwards. So, the data set is static. The second case deals with real-time data. The main conclusion is that the generic data model for storing moving point data in a geo-DBMS is flexible and efficient. The data can be accessed in a fast way, depending on the type of query and the moethod used for indexing.GIS technologyCivil Engineering and Geoscience
3D-GEM: Geo-technical extension towards an integrated 3D information model for infrastructural development
No full textIn infrastructural projects, communication as well as information exchange and (re-)use in and between involved parties is difficult. Mainly this is caused by a lack of information harmonisation. Various specialists are working together on the development of an infrastructural project and all use their own specific software and definitions for various information types. In addition, the lack of and/or differences in the use and definition of thematic semantic information regarding the various information types adds to the problem. Realistic 3D models describing and integrating parts of the earth already exist, but are generally neglecting the subsurface, and especially the aspects of geology and geo-technology. This paper summarises the research towards the extension of an existing integrated semantic information model to include surface as well as subsurface objects and in particular, subsurface geological and geotechnical objects. The major contributions of this research are the definition of geotechnical objects and the mechanism to link them with CityGML, GeoSciML and O&M standard models. The model is called 3D-GEM, short for 3D Geotechnical Extension Model.OTBArchitecture and The Built Environmen
Strategic position model Geo-ICT function: Facing the challenge of organizational alignment
No full textThis paper focuses on organizational aspects and aims to explain the dynamic alignment between the development of the internal Geo-ICT function, including the corporate SDI, of an organization and the interest of this organization in an SDI. It is proposed that a better understanding of the topic of alignment provides an insight into the qualitative and quantitative benefits of an SDI and can give direction to a further development of the SDI. The cooperation among the different public and private organizations involved in an SDI is complex and the success of the SDI is mainly based on the organizational aspects of the cooperation. The complexity of the cooperation among organizations in an SDI has also a dynamic aspect. Not only the organizations involved in the ongoing process of developing the SDI, also the SDI’s itself developed due to new initiatives. As a result of an ongoing study at the Delft University of Technology the Strategic Position Model Geo-ICT Function is developed. In this paper the Strategic Position Model Geo-ICT Function describes a theoretical approach on with it becomes possible to compare, analyze and explain the dynamic alignment between the internal Geo-ICT function, including the corporate SDI, of the organization and the different levels of SDI’s. At present several cases are selected to assess the utilization of this model in practice. When organizations are ’in alignment with the SDI’ and they can rely on an SDI, the SDI becomes an important cornerstone for the internal Geo-ICT function of each organization. In return, the investments, development and business decisions of organizations for their Geo- ICT function give an impulse to the interest and the use of an SDI. This interest can lead to further development of the SDI, so the community of all users drives a successful development of the SDI.OTB ResearchOTB Research Institute for the Built Environmen
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