Thermodynamic Patterns of Life: Emergent Phenomena in Reaction
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Climate Models and Their Evaluation
8 Climate Models and Their Evaluation Coordinating Lead Authors: David A. Randall (USA), Richard A. Wood (UK) Lead Authors: Sandrine Bony (France), Robert Colman (Australia), Thierry Fichefet (Belgium), John Fyfe (Canada), Vladimir Kattsov (Russian Federation), Andrew Pitman (Australia), Jagadish Shukla (USA), Jayaraman Srinivasan (India), Ronald J. Stouffer (USA), Akimasa Sumi (Japan), Karl E. Taylor (USA) Contributing Authors: K. AchutaRao (USA), R. Allan (UK), A. Berger (Belgium), H. Blatter (Switzerland), C. Bonfi ls (USA, France), A. Boone (France, USA), C. Bretherton (USA), A. Broccoli (USA), V. Brovkin (Germany, Russian Federation), W. Cai (Australia), M. Claussen (Germany), P. Dirmeyer (USA), C. Doutriaux (USA, France), H. Drange (Norway), J.-L. Dufresne (France), S. Emori (Japan), P. Forster (UK), A. Frei (USA), A. Ganopolski (Germany), P. Gent (USA), P. Gleckler (USA), H. Goosse (Belgium), R. Graham (UK), J.M. Gregory (UK), R. Gudgel (USA), A. Hall (USA), S. Hallegatte (USA, France), H. Hasumi (Japan), A. Henderson-Sellers (Switzerland), H. Hendon (Australia), K. Hodges (UK), M. Holland (USA), A.A.M. Holtslag (Netherlands), E. Hunke (USA), P. Huybrechts (Belgium), W. Ingram (UK), F. Joos (Switzerland), B. Kirtman (USA), S. Klein (USA), R. Koster (USA), P. Kushner (Canada), J. Lanzante (USA), M. Latif (Germany), N.-C. Lau (USA), M. Meinshausen (Germany), A. Monahan (Canada), J.M. Murphy (UK), T. Osborn (UK), T. Pavlova (Russian Federationi), V. Petoukhov (Germany), T. Phillips (USA), S. Power (Australia), S. Rahmstorf (Germany), S.C.B. Raper (UK), H. Renssen (Netherlands), D. Rind (USA), M. Roberts (UK), A. Rosati (USA), C. Schär (Switzerland), A. Schmittner (USA, Germany), J. Scinocca (Canada), D. Seidov (USA), A.G. -
Computational Medical Bioinformatics
MOJ Applied Bionics and Biomechanics Mini Review Open Access Computational medical bioinformatics Abstract Volume 2 Issue 4 - 2018 Biotechnology is a technological discipline based on Biology and applied to meet the Rodrigo Arturo Marquet Rivera, Guillermo needs of human life. Which can be considered essential, as is health. This discipline has developed in the last decades a series of medical applications that are interrelated Urriolagoitia Sosa, Rosa Alicia Hernández with other fields of science, which are not precisely those inherent in the health Vázquez, Beatriz Romero Ángeles, Juan sciences. One of the main ones is Computational Bioinformatics, which has become Alejandro Vázquez Feijoo, Guillermo a useful tool in the practice of the different medical areas through the generation of Urriolagoitia-Calderón biomodels. Instituto Politécnico Nacional, México Correspondence: Guillermo Urriolagoitia Sosa, Instituto Politécnico Nacional, Escuela Superior de Ingeniería Mecánica y Eléctrica, Sección de Estudios de Posgrado e Investigación Unidad Profesional Adolfo López Mateos, Zacatenco. Av. IPN s/n Edificio 5, 2° piso Col. Lindavista, Delegación Gustavo A. Madero, C.P. 07320, México, Email [email protected] Received: June 30, 2018 | Published: August 17, 2018 Introduction the images obtained from them allow a visualization and manipulation that offers better results (Figure 1). Computational Bioinformatics is a novel tool that can be applied in the study of the behaviour presented by the different levels of Proposal organization of living matter (cells, tissues and organs), under the effects of stimuli and external agents, such as burdens mechanical, With the images obtained from the imaging studies, it is possible to which influence the behaviour of cellular metabolism.1 Through generate biomodels that allow a better exploration of the anatomical the generation of anatomical biomodels, is interested in solving structures to be treated, observe them with greater precision and biological problems in a multidisciplinary and interdisciplinary way. -
Documentation and Software User’S Manual, Version 4.1
The Canadian Seasonal to Interannual Prediction System version 2 (CanSIPSv2) Canadian Meteorological Centre Technical Note H. Lin1, W. J. Merryfield2, R. Muncaster1, G. Smith1, M. Markovic3, A. Erfani3, S. Kharin2, W.-S. Lee2, M. Charron1 1-Meteorological Research Division 2-Canadian Centre for Climate Modelling and Analysis (CCCma) 3-Canadian Meteorological Centre (CMC) 7 May 2019 i Revisions Version Date Authors Remarks 1.0 2019/04/22 Hai Lin First draft 1.1 2019/04/26 Hai Lin Corrected the bias figures. Comments from Ryan Muncaster, Bill Merryfield 1.2 2019/05/01 Hai Lin Figures of CanSIPSv2 uses CanCM4i plus GEM-NEMO 1.3 2019/05/03 Bill Merrifield Added CanCM4i information, sea ice Hai Lin verification, 6.6 and 9 1.4 2019/05/06 Hai Lin All figures of CanSIPSv2 with CanCM4i and GEM-NEMO, made available by Slava Kharin ii © Environment and Climate Change Canada, 2019 Table of Contents 1 Introduction ............................................................................................................................. 4 2 Modifications to models .......................................................................................................... 6 2.1 CanCM4i .......................................................................................................................... 6 2.2 GEM-NEMO .................................................................................................................... 6 3 Forecast initialization ............................................................................................................. -
Data Extraction for the Reaction Kinetics Database SABIO-RK$
Perspectives in Science (]]]]) ], ]]]–]]] Available online at www.sciencedirect.com www.elsevier.com/locate/pisc REVIEW Data extraction for the reaction kinetics database SABIO-RK$ Ulrike Wittign, Renate Kania, Meik Bittkowski, Elina Wetsch, Lei Shi, Lenneke Jong, Martin Golebiewski, Maja Rey, Andreas Weidemann, Isabel Rojas, Wolfgang Müller Scientific Databases and Visualization Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany Received 5 March 2013; accepted 4 November 2013; Available online XX, XX, 2014 KEYWORDS Abstract Database; SABIO-RK (http://sabio.h-its.org/) is a web-accessible, manually curated database that has Reaction kinetics; been established as a resource for biochemical reactions and their kinetic properties with a Biocuration; focus on supporting the computational modeling to create models of biochemical reaction Ontology networks. SABIO-RK data are mainly extracted from literature but also directly submitted from lab experiments. In most cases the information in the literature is distributed across the whole publication, insufficiently structured and often described without standard terminology. Therefore the manual extraction of knowledge from the literature requires biological experts to understand the paper and interpret the data. The database offers the literature data in a structured format including annotations to controlled vocabularies, ontologies and external databases which supports modellers, as well as experimentalists, in the very time consuming process of collecting information from different publications. Here we describe the data extraction and curation efforts needed for SABIO-RK and give recommendations for publishing kinetic data in a complete and structured manner. & 2014 The Authors. Published by Elsevier GmbH. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/3.0/). -
Artificial Intelligence in Biological Modelling François Fages
Artificial Intelligence in Biological Modelling François Fages To cite this version: François Fages. Artificial Intelligence in Biological Modelling. A Guided Tour of Artificial Intelligence Research, 2020, Volume III: Interfaces and Applications of Artificial Intelligence, 978-3-030-06170-8_8. 10.1007/978-3-030-06170-8_8. hal-01409753v2 HAL Id: hal-01409753 https://hal.inria.fr/hal-01409753v2 Submitted on 11 May 2017 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. AI in Biological Modelling François Fages Abstract Systems Biology aims at elucidating the high-level functions of the cell from their biochemical basis at the molecular level. A lot of work has been done for collecting genomic and post-genomic data, making them available in databases and ontologies, building dynamical models of cell metabolism, signalling, division cy- cle, apoptosis, and publishing them in model repositories. In this chapter we review different applications of AI to biological systems modelling. We focus on cell pro- cesses at the unicellular level which constitutes most of the work achieved in the last two decades in the domain of Systems Biology. We show how rule-based languages and logical methods have played an important role in the study of molecular inter- action networks and of their emergent properties responsible for cell behaviours. -
Expanding Horizons to Include More Modelling Approaches and Formats Mihai Glont1, Tung V
D1248–D1253 Nucleic Acids Research, 2018, Vol. 46, Database issue Published online 2 November 2017 doi: 10.1093/nar/gkx1023 BioModels: expanding horizons to include more modelling approaches and formats Mihai Glont1, Tung V. N. Nguyen1, Martin Graesslin2, Robert Halke¨ 3,RazaAli1, Jochen Schramm2, Sarala M. Wimalaratne1, Varun B. Kothamachu1,4, Nicolas Rodriguez4, Maciej J. Swat1, Jurgen Eils2, Roland Eils2, Camille Laibe1, Rahuman S. Malik-Sheriff1,*, Vijayalakshmi Chelliah1, Nicolas Le Novere` 4,* and Henning Hermjakob1,* 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK, 2Department of Bioinformatics and Functional Genomics, Biomedical Computer Vision Group, University of Heidelberg, BioQuant, IPMB and DKFZ Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany, 3University of Rostock, Rostock, Germany and 4Babraham Institute, Cambridge CB22 3AT, UK Received September 25, 2017; Editorial Decision October 17, 2017; Accepted October 18, 2017 ABSTRACT a resource that facilitates the exchange, reuse and repurpos- ing of the models. Since its inception, BioModels’ content BioModels serves as a central repository of mathe- has been steadily increasing, making it a central portal that matical models representing biological processes. It provides reproducible, high-quality, freely accessible mod- offers a platform to make mathematical models easily els published in the scientific literature. BioModels hosts shareable across the systems modelling community, over 8400 models from the scientific literature submitted thereby supporting model reuse. To facilitate host- by authors as well as internal and external BioModels cu- ing a broader range of model formats derived from rators. This includes a recent submission of 6750 patient- diverse modelling approaches and tools, a new in- specific genome-scale metabolic models derived from tu- frastructure for BioModels has been developed that mour samples of individual patients (2). -
Atmospheric Dispersion of Radioactive Material in Radiological Risk Assessment and Emergency Response
Progress in NUCLEAR SCIENCE and TECHNOLOGY, Vol. 1, p.7-13 (2011) REVIEW Atmospheric Dispersion of Radioactive Material in Radiological Risk Assessment and Emergency Response YAO Rentai * China Institute for Radiation Protection, P.O.Box 120, Taiyuan, Shanxi 030006, China The purpose of a consequence assessment system is to assess the consequences of specific hazards on people and the environment. In this paper, the studies on technique and method of atmospheric dispersion modeling of radioactive material in radiological risk assessment and emergency response are reviewed in brief. Some current statuses of nuclear accident consequences assessment in China were introduced. In the future, extending the dispersion modeling scales such as urban building scale, establishing high quality experiment dataset and method of model evaluation, improved methods of real-time modeling using limited inputs, and so on, should be promoted with high priority of doing much more work. KEY WORDS: atmospheric model, risk assessment, emergency response, nuclear accident 11) I. Introduction from U.S. NOAA, and SPEEDI/WSPEEDI from The studies and developments of techniques and methods Japan/JAERI. However, the needs of emergency of atmospheric dispersion modeling of radioactive material management may not be well satisfied by existing models in radiological risk assessment and emergency response which are not well designed and confronted with difficulty have evolved over the past 50-60 years. The three marked in detailed constructions of local wind and turbulence -
Organigramm Des Rektorats Einrichtungen Des Rektorats Der
Organizational chart of the University of Veterinary Medicine, Vienna Governing Bodies of the University Senate Rectorate University Council Research and Teaching Department 1 Department 2 Department 3 Department 4 Department 5 ________________________________________________________ ________________________________________________________ ________________________________________________________ ________________________________________________________ ________________________________________________________ Department of Biomedical Sciences Department of Pathobiology Department/University Clinic for Farm Department/University Clinic for Department of Interdisciplinary Life Animals and Veterinary Public Health Companion Animals and Horses Sciences Institute of Computational Medicine Institute of Morphology Institute for in-vivo and in-vitro models Institute of Microbiology Institute of Food Safety, Food Technology and University Clinic* for Small Animals Research Institute of Wildlife Ecology Institute of Medical Biochemistry Functional Microbiology Veterinary Public Health Anaesthesiology and perioperative Intensive- Conservation Medicine Institute of Pharmacology and Toxicology Institute of Immunology Food Microbiology Care Medicine Konrad Lorenz Institute of Ethology Clinical Pharmacology Institute of Parasitology Food Hygiene and Technology Diagnostic Imaging Ornithology Institute of Physiology, Patho physiology and Institute of Pathology Veterinary Public Health and Epidemiology Obstetrics, Gynaecology and Andrology -
Lecture 29. Introduction to Atmospheric Chemical Transport Models
Lecture 29. Introduction to atmospheric chemical transport models. Part 1. Objectives: 1. Model types. 2. Box models. 3. One-dimensional models. 4. Two-dimensional models. 5. Three-dimensional models. Readings: Graedel T. and P.Crutzen. “Atmospheric change: an earth system perspective”. Chapter 15.”Bulding environmental chemical models”, 1992. 1. Model types. Mathematical models provide the necessary framework for integration of our understanding of individual atmospheric processes and study of their interactions. Note, that atmosphere is a complex reactive system in which numerous physical and chemical processes occur simultaneously. • Atmospheric chemical transport models are defined according to their spatial scale: Model Typical domain scale Typical resolution Microscale 200x200x100 m 5 m Mesoscale(urban) 100x100x5 km 2 km Regional 1000x1000x10 km 20 km Synoptic(continental) 3000x3000x20 km 80 km Global 65000x65000x20km 50x50 1 Figure 29.1 Components of a chemical transport model (Seinfeld and Pandis, 1998). 2 • Domain of the atmospheric model is the area that is simulated. The computation domain consists of an array of computational cells, each having uniform chemical composition. The size of cells determines the spatial resolution of the model. • Atmospheric chemical transport models are also characterized by their dimensionality: zero-dimensional (box) model; one-dimensional (column) model; two-dimensional model; and three-dimensional model. • Model time scale depends on a specific application varying from hours (e.g., air quality model) to hundreds of years (e.g., climate models) 3 Two principal approaches to simulate changes in the chemical composition of a given air parcel: 1) Lagrangian approach: air parcel moves with the local wind so that there is no mass exchange that is allowed to enter the air parcel and its surroundings (except of species emissions). -
A Brief Summary of Plans for the GMAO Core Priorities and Initiatives for the Next 5 Years
A Brief Summary of Plans for the GMAO Core Priorities and Initiatives for the Next 5 years Provided as information for ROSES 2012 A.13 – MAP Developments in the GMAO are focused on the next generation systems, GEOS-6, and an Integrated Earth System Analysis and the associated modeling system that supports that analysis. GEOS-6 and IESA (1) The GEOS-6 system will be built around the next generation, non-hydrostatic atmospheric model with aerosol-cloud microphysics (advances upon the Morrison-Gettelman cloud microphysics and the Modal Aerosol Model (MAM) aerosol microphysics module for the inclusion of aerosol indirect effects) and an accompanying hybrid (ensemble-variational) 4DVar atmospheric assimilation system. (2) IESA capabilities for other parts of the earth system, including atmospheric chemical constituents and aerosols, ocean circulation, land hydrology, and carbon budget will be built upon our existing separate assimilation capabilities. The GEOS Model Our modeling strategy is driven by the need to have a comprehensive global model valid for both weather and climate and for use in both simulation and assimilation. Our main task in atmospheric modeling during the next five years will be to make the transition to GEOS-6. This direction is driven by (i) the need to improve the representation of clouds and precipitation to enable use of cloud- and precipitation-contaminated satellite radiance observations in NWP, and (ii) the research goal of understanding and predicting weather- climate connections. Development will focus on 1km to 10km resolutions that will be needed for the data assimilation system (DAS). Climate resolutions (10-100km) will not be ignored, but developments for resolutions coarser than 50 km will have lower priority. -
SABIO-RK: a Data Warehouse for Biochemical Reactions and Their Kinetics
Journal of Integrative Bioinformatics 2007 http://journal.imbio.de/ SABIO-RK: A data warehouse for biochemical reactions and their kinetics. Olga Krebs*, Martin Golebiewski, Renate Kania, Saqib Mir, Jasmin Saric, Andreas Weidemann, Ulrike Wittig and Isabel Rojas Scientific Databases and Visualisation Group, EML Research gGmbH, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg, Germany Abstract Systems biology is an emerging field that aims at obtaining a system-level understanding of biological processes. The modelling and simulation of networks of biochemical reactions have great and promising application potential but require reliable kinetic data. In order to support the systems biology community with such data we have developed SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics), a curated database with information about biochemical reactions and their kinetic (http://creativecommons.org/licenses/by-nc-nd/3.0/). properties, which allows researchers to obtain and compare kinetic data and to integrate them into models of biochemical networks. SABIO-RK is freely available for academic License use at http://sabio.villa-bosch.de/SABIORK/. Unported 1 Introduction 3.0 Systems biology deals with the analysis and prediction of the dynamic behaviour of biological networks through mathematical modelling based on experimental data [1]. It focuses on the connections and interactions of the components in the cell and in general in the organism, all as part of one system. The modelling and simulation of biochemical reaction -
DJ Karoly Et
Supporting Online Material “Detection of a human influence on North American climate”, D. J. Karoly et al. (2003) Materials and Methods Description of the climate models GFDL R30 is a spectral atmospheric model with rhomboidal truncation at wavenumber 30 equivalent to 3.75° longitude × 2.2° latitude (96 × 80) with 14 levels in the vertical. The atmospheric model is coupled to an 18 level gridpoint (192 × 80) ocean model where two ocean grid boxes underlie each atmospheric grid box exactly. Both models are described by Delworth et al. (S1) and Dixon et al. (S2). HadCM2 and HadCM3 use the same atmospheric horizontal resolution, 3.75°× 2.5° (96 × 72) finite difference model (T42/R30 equivalent) with 19 levels in the atmosphere and 20 levels in the ocean (S3, S4). For HadCM2, the ocean horizontal grid lies exactly under that of the atmospheric model. The ocean component of HadCM3 uses much higher resolution (1.25° × 1.25°) with six ocean grid boxes for every atmospheric grid box. In the context of results shown here, the main difference between the two models is that HadCM3 includes improved representations of physical processes in the atmosphere and the ocean (S5). For example, HadCM3 employs a radiation scheme that explicitly represents the radiative effects of minor greenhouse gases as well as CO2, water vapor and ozone (S6), as well as a simple parametrization of background aerosol (S7). ECHAM4/OPYC3 is an atmospheric T42 spectral model equivalent to 2.8° longitude × 2.8° latitude (128 × 64) with 19 vertical layers. The ocean model OPYC3 uses isopycnals as the vertical coordinate system.