Sebastian Bauer - Böcker

Introduction to Bio-Ontologies explores the computational background of ontologies. Emphasizing computational and algorithmic issues surrounding bio-ontologies, this self-contained text helps readers understand ontological algorithms and their applications.The first part of the book defines ontology and bio-ontologies. It also explains the importance of mathematical logic for understanding concepts of inference in bio-ontologies, discusses the probability and statistics topics necessary for understanding ontology algorithms, and describes ontology languages, including OBO (the preeminent language for bio-ontologies), RDF, RDFS, and OWL.The second part covers significant bio-ontologies and their applications. The book presents the Gene Ontology; upper-level ontologies, such as the Basic Formal Ontology and the Relation Ontology; and current bio-ontologies, including several anatomy ontologies, Chemical Entities of Biological Interest, Sequence Ontology, Mammalian Phenotype Ontology, and Human Phenotype Ontology.The third part of the text introduces the major graph-based algorithms for bio-ontologies. The authors discuss how these algorithms are used in overrepresentation analysis, model-based procedures, semantic similarity analysis, and Bayesian networks for molecular biology and biomedical applications.With a focus on computational reasoning topics, the final part describes the ontology languages of the Semantic Web and their applications for inference. It covers the formal semantics of RDF and RDFS, OWL inference rules, a key inference algorithm, the SPARQL query language, and the state of the art for querying OWL ontologies.Web ResourceSoftware and data designed to complement material in the text are available on the book’s website: http://bio-ontologies-book.org The site provides the R Robo package developed for the book, along with a compressed archive of data and ontology files used in some of the exercises. It also offers teaching/presentation slides and links to other relevant websites.This book provides readers with the foundation to use ontologies as a starting point for new bioinformatics research projects or to support current molecular genetics research projects. By supplying a self-contained introduction to OBO ontologies and the Semantic Web, it bridges the gap between both fields and helps readers see what each can contribute to the analysis and understanding of biomedical data.

Energy Geotechnics includes 97 technical papers presented at the 1st International Conference on Energy Geotechnics (ICEGT 2016, Kiel, Germany, 29-31 August 2016). The contributions provides significant advances and critical challenges facing the areas of fundamentals, constitutive and numerical modelling, testing techniques and energy geotechnics applications. Energy Geotechnics contains seven regular sessions and six minisymposia, with contributions on discrete and continuum based modelling as well as investigations based on experimental studies at various scales. The papers on discrete and continuum based modelling examine the behaviour of gas hydrate sediments, cyclic and Themo-Hydro-Mechanical (T-H-M) modelling of energy piles, non-linear behaviour of energy geo-storage and geo-structures, deformation of geomaterials, modelling of borehole heat exchangers and energy walls, analysis of hydraulic fracturing and discontinuities in reservoirs, engineering problems involving gas hydrates sediments, and modelling of environmental impact of energy geotechnical processes.

Introduction to Bio-Ontologies explores the computational background of ontologies. Emphasizing computational and algorithmic issues surrounding bio-ontologies, this self-contained text helps readers understand ontological algorithms and their applications.The first part of the book defines ontology and bio-ontologies. It also explains the importance of mathematical logic for understanding concepts of inference in bio-ontologies, discusses the probability and statistics topics necessary for understanding ontology algorithms, and describes ontology languages, including OBO (the preeminent language for bio-ontologies), RDF, RDFS, and OWL.The second part covers significant bio-ontologies and their applications. The book presents the Gene Ontology; upper-level ontologies, such as the Basic Formal Ontology and the Relation Ontology; and current bio-ontologies, including several anatomy ontologies, Chemical Entities of Biological Interest, Sequence Ontology, Mammalian Phenotype Ontology, and Human Phenotype Ontology.The third part of the text introduces the major graph-based algorithms for bio-ontologies. The authors discuss how these algorithms are used in overrepresentation analysis, model-based procedures, semantic similarity analysis, and Bayesian networks for molecular biology and biomedical applications.With a focus on computational reasoning topics, the final part describes the ontology languages of the Semantic Web and their applications for inference. It covers the formal semantics of RDF and RDFS, OWL inference rules, a key inference algorithm, the SPARQL query language, and the state of the art for querying OWL ontologies.Web ResourceSoftware and data designed to complement material in the text are available on the book’s website: http://bio-ontologies-book.org The site provides the R Robo package developed for the book, along with a compressed archive of data and ontology files used in some of the exercises. It also offers teaching/presentation slides and links to other relevant websites.This book provides readers with the foundation to use ontologies as a starting point for new bioinformatics research projects or to support current molecular genetics research projects. By supplying a self-contained introduction to OBO ontologies and the Semantic Web, it bridges the gap between both fields and helps readers see what each can contribute to the analysis and understanding of biomedical data.

The book comprises the 3rd collection of benchmarks and examples for porous and fractured media mechanics. The 3rd THMC benchmark book also introduces benchmark-based tutorials, therefore the subtitle is selected as “From Benchmarking to Tutoring”.

The present book provides guidance to understanding complicated coupled processes based on the experimental data available and implementation of developed algorithms in numerical codes. Results of selected test cases in the fields of closed-form solutions (e.g., deformation processes), single processes (such as groundwater flow) as well as coupled processes are presented.It is part of the OpenGeoSys initiative - an open source project to share knowledge and experience in environmental analysis and scientific computation with the community.

This book presents a new suite of benchmarks for and examples of porous media mechanics collected over the last two years. It continues the assembly of benchmarks and examples for porous media mechanics published in 2014. The book covers various applications in the geosciences, geotechnics, geothermal energy, and geological waste deposition. The analysis of thermo-hydro-mechanical-chemical (THMC) processes is essential to many applications in environmental engineering, such as geological waste deposition, geothermal energy utilisation, carbon capture and storage, water resources management, hydrology, and even climate change. In order to assess the feasibility and safety of geotechnical applications, process-based modelling is the only tool that can effectively quantify future scenarios, a fact which also creates a huge burden of responsibility concerning the reliability of computational tools. The book shows that benchmarking offers a suitable methodology for verifying the quality of modelling tools based on best practices, and together with code comparison fosters community efforts. It also  provides a brief introduction to the DECOVALEX, SeSBench and MOMAS initiatives. This benchmark book is part of the OpenGeoSys initiative – an open source project designed to share knowledge and experience in environmental analysis and scientific computation.

The present book provides guidance to understanding complicated coupled processes based on the experimental data available and implementation of developed algorithms in numerical codes. Results of selected test cases in the fields of closed-form solutions (e.g., deformation processes), single processes (such as groundwater flow) as well as coupled processes are presented.It is part of the OpenGeoSys initiative - an open source project to share knowledge and experience in environmental analysis and scientific computation with the community.

This book explores the application of the open-source software OpenGeoSys (OGS) for hydrological numerical simulations concerning conservative and reactive transport modeling. It provides general information on the hydrological and groundwater flow modeling of a real case study and step-by-step model set-up with OGS, while also highlighting related components such as the OGS Data Explorer. The material is based on unpublished manuals and the results of a collaborative project between China and Germany (SUSTAIN H2O). Though the book is primarily intended for graduate students and applied scientists who deal with hydrological modeling, it also offers a valuable source of information for professional geoscientists wishing to expand their knowledge of the numerical modeling of hydrological processes including nitrate reactive transport modeling. This book is the second in a series that showcases further applications of computational modeling in hydrological science.

The book comprises the 3rd  collection of benchmarks and examples for porous and fractured media mechanics. Analysis of thermo-hydro-mechanical-chemical (THMC) processes is essential to a wide area of applications in environmental engineering, such as geological waste deposition, geothermal energy utilization (shallow and deep systems), carbon capture and storage (CCS) as well as water resources management and hydrology. In order to assess the feasibility, safety as well as sustainability of geoenvironmental applications, model-based simulation is the only way to quantify future scenarios. This charges a huge responsibility concerning the reliability of conceptual models and computational tools. Benchmarking is an appropriate methodology to verify the quality and validate the concept of models based on best practices. Moreover, benchmarking and code comparison are building strong community links. The 3rd THMC benchmark book also introduces benchmark-based tutorials, therefore the subtitle is selected as “From Benchmarking to Tutoring”. The benchmark book is part of the OpenGeoSys initiative - an open source project to share knowledge and experience in environmental analysis and scientific computation. The new version of OGS-6 is introduced and first benchmarks are presented therein (see appendices).

This book presents a new suite of benchmarks for and examples of porous media mechanics collected over the last two years.

Das Buch richtet sich an Studierende und Lehrende des Lehramts der Sekundarstufe sowie an Lehrerinnen und Lehrer der Sekundarstufe.