Kurth, Winfried

[["dc.bibliographiccitation.firstpage","480"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Methods in Ecology and Evolution"],["dc.bibliographiccitation.lastpage","483"],["dc.bibliographiccitation.volume","3"],["dc.contributor.author","Thiele, Jan C."],["dc.contributor.author","Kurth, Winfried"],["dc.contributor.author","Grimm, Volker"],["dc.date.accessioned","2018-11-07T09:09:50Z"],["dc.date.available","2018-11-07T09:09:50Z"],["dc.date.issued","2012"],["dc.description.abstract","1. NetLogo is a free software platform for implementing individual-based and agent-based models. However, NetLogos support of systematic design, performance and analysis of simulation experiments is limited. The statistics software R includes such support. 2. RNetLogo is an R package that links R and NetLogo: any NetLogo program can be controlled and run from R and model results can be transferred back to R for statistical analyses. RNetLogo includes 16 functions, which are explained and demonstrated in the user manual and tutorial. The design of RNetLogo was inspired by a similar link between Mathematica and NetLogo. 3. RNetLogo is a powerful tool for making individual-based modelling more efficient and less ad hoc. It links two fast growing user communities and constitutes a new interface for integrating descriptive statistical analyses and individual-based modelling."],["dc.identifier.doi","10.1111/j.2041-210X.2011.00180.x"],["dc.identifier.isi","000304902500005"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/26354"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Wiley-blackwell"],["dc.relation.issn","2041-210X"],["dc.title","RNetLogo: an R package for running and exploring individual-based models implemented in NetLogo"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1"],["dc.bibliographiccitation.journal","Computers and Electronics in Agriculture"],["dc.bibliographiccitation.lastpage","8"],["dc.bibliographiccitation.volume","92"],["dc.contributor.author","Hemmerling, Reinhard"],["dc.contributor.author","Evers, Jochem B."],["dc.contributor.author","Smolenova, Katarina"],["dc.contributor.author","Buck-Sorlin, Gerhard H."],["dc.contributor.author","Kurth, Winfried"],["dc.date.accessioned","2018-11-07T09:27:26Z"],["dc.date.available","2018-11-07T09:27:26Z"],["dc.date.issued","2013"],["dc.description.abstract","In simulation models of plant development, physiological processes taking place in plants are typically described in terms of ODEs (Ordinary Differential Equations). On the one hand, those processes drive the development of the plant structure and on the other hand, the developed structure again influences these processes (e.g., photosynthesis, hormone synthesis and transport, and allocation of carbon, nitrogen, etc.). To study this dependence, simulation models, termed functional-structural plant models (FSPMs), are developed. Such models usually operate at the organ scale, considering the topology and the geometry of organs, while being validated at the scale of the plant individual. The open source modelling platform GroIMP was designed for the purpose of creating FSPMs. In GroIMP, the structure of a plant is described by the eXtended L-system language (XL) which is an extension of the Java programming language and works on a general graph structure. It is general enough to be used for many biological problems that can be described by graphs. Until now, to specify and solve ODEs, Java code had to be used and there was no general solution for doing this easily and conveniently in XL Here we propose an extension to the XL language that allows the user to easily specify ODEs in terms of rule applications. Furthermore, their specification is separated from the numerical solution, with the possibility to choose between different integration methods. The new framework is illustrated with examples of auxin transport in Arabidopsis and gibberellic acid signal transduction in barley and compared with the conventional approach in FSPMs (Euler method). We show that besides the user-friendly specification of ODEs within rules by using a special operator, the results are computed faster, are more stable and accurate. The new framework is also compared with the mathematical formalism of differential L-systems (dL-systems). (C) 2013 Elsevier B.V. All rights reserved."],["dc.description.sponsorship","DFG [Ku 847/8-1]"],["dc.identifier.doi","10.1016/j.compag.2012.12.007"],["dc.identifier.isi","000316592000001"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/30538"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Elsevier Sci Ltd"],["dc.relation.issn","0168-1699"],["dc.title","Extension of the GroIMP modelling platform to allow easy specification of differential equations describing biological processes within plant models"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","11"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Journal of Artificial Societies and Social Simulation"],["dc.bibliographiccitation.volume","17"],["dc.contributor.author","Thiele, Jan Christoph"],["dc.contributor.author","Kurth, Winfried"],["dc.contributor.author","Grimm, Volker"],["dc.date.accessioned","2018-11-07T09:38:43Z"],["dc.date.available","2018-11-07T09:38:43Z"],["dc.date.issued","2014"],["dc.description.abstract","Agent-based models are increasingly used to address questions regarding real-world phenomena and mechanisms; therefore, the calibration of model parameters to certain data sets and patterns is often needed. Furthermore, sensitivity analysis is an important part of the development and analysis of any simulation model. By exploring the sensitivity of model output to changes in parameters, we learn about the relative importance of the various mechanisms represented in the model and how robust the model output is to parameter uncertainty. These insights foster the understanding of models and their use for theory development and applications. Both steps of the model development cycle require massive repetitions of simulation runs with varying parameter values. To facilitate parameter estimation and sensitivity analysis for agent-based modellers, we show how to use a suite of important established methods. Because NetLogo and R are widely used in agent-based modelling and for statistical analyses, we use a simple model implemented in NetLogo as an example, packages in R that implement the respective methods, and the RNetLogo package, which links R and NetLogo. We briefly introduce each method and provide references for further reading. We then list the packages in R that may be used for implementing the methods, provide short code examples demonstrating how the methods can be applied in R, and present and discuss the corresponding outputs. The Supplementary Material includes full, adaptable code samples for using the presented methods with R and NetLogo. Our overall aim is to make agent-based modellers aware of existing methods and tools for parameter estimation and sensitivity analysis and to provide accessible tools for using these methods. In this way, we hope to contribute to establishing an advanced culture of relating agent-based models to data and patterns observed in real systems and to foster rigorous and structured analyses of agent-based models."],["dc.identifier.isi","000339121300018"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/33127"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.relatedmaterial.fulltext","https://www.jasss.org/17/3/11.html"],["dc.relation.issn","1460-7425"],["dc.relation.orgunit","Abteilung Ökoinformatik, Biometrie und Waldwachstum"],["dc.title","Facilitating Parameter Estimation and Sensitivity Analysis of Agent-Based Models: A Cookbook Using Net Logo and R"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","813"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Annals of Botany"],["dc.bibliographiccitation.lastpage","827"],["dc.bibliographiccitation.volume","114"],["dc.contributor.author","Ong, Yongzhi"],["dc.contributor.author","Streit, Katarina"],["dc.contributor.author","Henke, Michael"],["dc.contributor.author","Kurth, Winfried"],["dc.date.accessioned","2018-11-07T09:35:41Z"],["dc.date.available","2018-11-07T09:35:41Z"],["dc.date.issued","2014"],["dc.description.abstract","Background and Aims Functional-structural plant models (FSPMs) simulate biological processes at different spatial scales. Methods exist for multiscale data representation and modification, but the advantages of using multiple scales in the dynamic aspects of FSPMs remain unclear. Results from multiscale models in various other areas of science that share fundamental modelling issues with FSPMs suggest that potential advantages do exist, and this study therefore aims to introduce an approach to multiscale modelling in FSPMs. Methods A three-part graph data structure and grammar is revisited, and presented with a conceptual framework for multiscale modelling. The framework is used for identifying roles, categorizing and describing scale-to-scale interactions, thus allowing alternative approaches to model development as opposed to correlation-based modelling at a single scale. Reverse information flow(from macro-to micro-scale) is catered for in the framework. The methods are implemented within the programming language XL. Key Results Three example models are implemented using the proposed multiscale graph model and framework. The first illustrates the fundamental usage of the graph data structure and grammar, the second uses probabilistic modelling for organs at the fine scale in order to derive crown growth, and the third combines multiscale plant topology with ozone trends and metabolic network simulations in order to model juvenile beech stands under exposure to a toxic trace gas. Conclusions The graph data structure supports data representation and grammar operations at multiple scales. The results demonstrate that multiscale modelling is a viable method in FSPM and an alternative to correlation-based modelling. Advantages and disadvantages of multiscale modelling are illustrated by comparisons with single-scale implementations, leading to motivations for further research in sensitivity analysis and run-time efficiency for these models."],["dc.identifier.doi","10.1093/aob/mcu155"],["dc.identifier.isi","000343039600018"],["dc.identifier.pmid","25134929"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/32443"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Oxford Univ Press"],["dc.relation.issn","1095-8290"],["dc.relation.issn","0305-7364"],["dc.title","An approach to multiscale modelling with graph grammars"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","117"],["dc.bibliographiccitation.issue","2-3"],["dc.bibliographiccitation.journal","Tree Physiology"],["dc.bibliographiccitation.lastpage","128"],["dc.bibliographiccitation.volume","21"],["dc.contributor.author","Oppelt, A. L."],["dc.contributor.author","Kurth, W."],["dc.contributor.author","Godbold, Douglas L."],["dc.date.accessioned","2018-11-07T09:26:35Z"],["dc.date.available","2018-11-07T09:26:35Z"],["dc.date.issued","2001"],["dc.description.abstract","Aspects of root architecture, including topology, link length, diameter and scaling relations, were analyzed in excavated coarse root systems of three field-grown fruit tree species (Strychnos cocculoides Bak., Strychnos spinosa Lam. and Vangueria infausta Burch) and the fruit-bearing shrub Grewia flava DC. We investigated the root systems using semi-automatic digitizing and computer-based 3-D reconstruction techniques. Topological analysis was carried out to investigate branching patterns as basic determinants of root architecture. New topological indices were developed and revealed significant differences among the species. The different architectural strategies can be explained in terms of cost-benefit relations and efficiency in soil resource exploration and exploitation. In addition, some well-known hypotheses about geometry and scaling, most of them previously unverified by empirical observations on root systems, were tested. For practical applications, the main emphasis is on the relationship between proximal root diameter, an easily determined parameter, and several parameters describing the size of the whole root system. We also tested the \"pipe stem\" theory, essentially dating back to Leonardo da Vinci, which underlies many models and which we found conformed to our measurement data with reasonable accuracy. A physiological consequence of the \"constant cross-sectional area rule\" may be a certain homogeneity of hydraulic architecture throughout root systems."],["dc.identifier.isi","000166829300007"],["dc.identifier.pmid","11303642"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/30333"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Heron Publishing"],["dc.publisher.place","Victoria"],["dc.relation.conference","2nd IUFRO International Symposium on Dynamics of Physiological Processes in Woody Roots"],["dc.relation.eventlocation","NANCY, FRANCE"],["dc.relation.issn","0829-318X"],["dc.title","Topology, scaling relations and Leonardo's rule in root systems from African tree species"],["dc.type","conference_paper"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1103"],["dc.bibliographiccitation.issue","6"],["dc.bibliographiccitation.journal","Frontiers of Computer Science"],["dc.bibliographiccitation.lastpage","1117"],["dc.bibliographiccitation.volume","10"],["dc.contributor.author","Henke, Michael"],["dc.contributor.author","Kurth, Winfried"],["dc.contributor.author","Buck-Sorlin, Gerhard H."],["dc.date.accessioned","2018-11-07T10:05:36Z"],["dc.date.available","2018-11-07T10:05:36Z"],["dc.date.issued","2016"],["dc.description.abstract","In the last decade, functional-structural plant modelling (FSPM) has become a more widely accepted paradigm in crop and tree production, as 3D models for the most important crops have been proposed. Given the wider portfolio of available models, it is now appropriate to enter the next level in FSPM development, by introducing more efficient methods for model development. This includes the consideration of model reuse (by modularisation), combination and comparison, and the enhancement of existing models. To facilitate this process, standards for design and communication need to be defined and established. We present a first step towards an efficient and general, i.e., not speciesspecific FSPM, presently restricted to annual or bi-annual plants, but with the potential for extension and further generalization. Model structure is hierarchical and object-oriented, with plant organs being the base-level objects and plant individual and canopy the higher-level objects. Modules for the majority of physiological processes are incorporated, more than in other platforms that have a similar aim (e.g., photosynthesis, organ formation and growth). Simulation runs with several general parameter sets adopted from the literature show that the present prototypewas able to reproduce a plausible output range for different crops (rapeseed, barley, etc.) in terms of both the dynamics and final values (at harvest time) of model state variables such as assimilate production, organ biomass, leaf area and architecture."],["dc.identifier.doi","10.1007/s11704-015-4472-8"],["dc.identifier.isi","000385137600011"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/38926"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.relation.issn","2095-2236"],["dc.relation.issn","2095-2228"],["dc.relation.orgunit","Abteilung Ökoinformatik, Biometrie und Waldwachstum"],["dc.title","FSPM-P: towards a general functional-structural plant model for robust and comprehensive model development"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1577"],["dc.bibliographiccitation.issue","6"],["dc.bibliographiccitation.journal","Trees"],["dc.bibliographiccitation.lastpage","1588"],["dc.bibliographiccitation.volume","28"],["dc.contributor.author","Yoshimoto, Atsushi"],["dc.contributor.author","Surovy, Peter"],["dc.contributor.author","Konoshima, Masashi"],["dc.contributor.author","Kurth, Winfried"],["dc.date.accessioned","2018-11-07T09:32:16Z"],["dc.date.available","2018-11-07T09:32:16Z"],["dc.date.issued","2014"],["dc.description.abstract","Key message The main message of this work is the demonstration of possibility of creation of stem shape from digitized points using integer-programming approach. The points are digitized by magnetic motion tracker which in contrast to the laser scanning allows the reconstruction of complete cross-section of stem even in the \"hidden (invisible)\" part. Three-dimensional information on tree stem form plays an important role in understanding the structure and strength of a standing tree against the forces of wind, snow, and other natural pressure. It also contributes to precision in volume measurement compared to conventional two-dimensional measurement. We investigate approaches for obtaining three-dimensional information of tree stem form from partially organized surface measurements, acquired using a three-dimensional digitizing device (Polhemus FASTRAK(A (R)) motion tracking device). We then propose a new programming approach from discrete mathematics to construct tree stem form. Our method is based on an optimal connection of neighbor triangles for surface construction, which is created by locally possible combination of three digitized points on the stem surface. We compare the proposed method to the existing heuristic methods of contour tracing and region growing. Our analysis shows that the proposed method provides a consistent construction of tree stem form, for even stems with extremely irregular structure such as those from bent trees and mangrove trees with unique root spread, while the other methods are incapable for constructing such tree stems."],["dc.description.sponsorship","JSPS KAKENHI [22252002, 23.01400]; JSPS [P11400]"],["dc.identifier.doi","10.1007/s00468-014-1065-3"],["dc.identifier.isi","000345145100003"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/31719"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Springer"],["dc.relation.issn","1432-2285"],["dc.relation.issn","0931-1890"],["dc.title","Constructing tree stem form from digitized surface measurements by a programming approach within discrete mathematics"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","161"],["dc.bibliographiccitation.issue","8-9"],["dc.bibliographiccitation.journal","ALLGEMEINE FORST UND JAGDZEITUNG"],["dc.bibliographiccitation.lastpage","168"],["dc.bibliographiccitation.volume","172"],["dc.contributor.author","Knauft, F. J."],["dc.contributor.author","Sloboda, B."],["dc.contributor.author","Kurth, W."],["dc.date.accessioned","2018-11-07T08:46:25Z"],["dc.date.available","2018-11-07T08:46:25Z"],["dc.date.issued","2001"],["dc.identifier.isi","000170919800007"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/20685"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","J D Sauerlanders Verlag"],["dc.relation.issn","0002-5852"],["dc.title","Model integration for the generation of virtual forest landscapes"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","817"],["dc.bibliographiccitation.issue","5"],["dc.bibliographiccitation.journal","Annals of Botany"],["dc.bibliographiccitation.lastpage","828"],["dc.bibliographiccitation.volume","107"],["dc.contributor.author","Xu, L. F."],["dc.contributor.author","Henke, Michael"],["dc.contributor.author","Zhu, Jun"],["dc.contributor.author","Kurth, Winfried"],["dc.contributor.author","Buck-Sorlin, Gerhard H."],["dc.date.accessioned","2018-11-07T08:57:16Z"],["dc.date.available","2018-11-07T08:57:16Z"],["dc.date.issued","2011"],["dc.description.abstract","Background and Aims Although quantitative trait loci (QTL) analysis of yield-related traits for rice has developed rapidly, crop models using genotype information have been proposed only relatively recently. As a first step towards a generic genotype-phenotype model, we present here a three-dimensional functional-structural plant model (FSPM) of rice, in which some model parameters are controlled by functions describing the effect of main-effect and epistatic QTLs. Methods The model simulates the growth and development of rice based on selected ecophysiological processes, such as photosynthesis (source process) and organ formation, growth and extension (sink processes). It was devised using GroIMP, an interactive modelling platform based on the Relational Growth Grammar formalism (RGG). RGG rules describe the course of organ initiation and extension resulting in final morphology. The link between the phenotype (as represented by the simulated rice plant) and the QTL genotype was implemented via a data interface between the rice FSPM and the QTLNetwork software, which computes predictions of QTLs from map data and measured trait data. Key Results Using plant height and grain yield, it is shown how QTL information for a given trait can be used in an FSPM, computing and visualizing the phenotypes of different lines of a mapping population. Furthermore, we demonstrate how modification of a particular trait feeds back on the entire plant phenotype via the physiological processes considered. Conclusions We linked a rice FSPM to a quantitative genetic model, thereby employing QTL information to refine model parameters and visualizing the dynamics of development of the entire phenotype as a result of ecophysiological processes, including the trait(s) for which genetic information is available. Possibilities for further extension of the model, for example for the purposes of ideotype breeding, are discussed."],["dc.identifier.doi","10.1093/aob/mcq264"],["dc.identifier.isi","000289838400008"],["dc.identifier.pmid","21247905"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/23353"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Oxford Univ Press"],["dc.relation.issn","0305-7364"],["dc.title","A functional-structural model of rice linking quantitative genetic information with morphological development and physiological processes"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Agroforestry Systems"],["dc.bibliographiccitation.lastpage","11"],["dc.bibliographiccitation.volume","64"],["dc.contributor.author","Oppelt, A. L."],["dc.contributor.author","Kurth, W."],["dc.contributor.author","Jentschke, G."],["dc.contributor.author","Godbold, Douglas L."],["dc.date.accessioned","2018-11-07T08:33:02Z"],["dc.date.available","2018-11-07T08:33:02Z"],["dc.date.issued","2005"],["dc.description.abstract","To assess the possible degree of root competition from fruit trees which could potentially be used in agroforestry systems,. ne root density of fruit trees Strychnos cocculoides BAK., Strychnos spinosa LAM. (Loganiaceae) and Vangueria infausta BURCH. (Rubiaceae), as well as from the shrubby species, Grewia flava DC. (Tiliaceae) was investigated. Vangueria infausta had the highest. ne root densities in both vertical and horizontal extensions. In Vangueria infausta. ne root density decreased with increasing soil depth. For the other species in the 80 cm soil pro. le investigated, no significant changes in. ne root density with soil depth were found. For Strychnos cocculoides almost no. ne roots were detected in the upper soil horizon (0-20 cm). Using fine root surface area densities, exploration and exploitation indices were calculated. Vangueria infausta had the highest value of the exploration index compared to the other species. For use in agroforestry systems Vangueria infausta was estimated to be the most competitive of the investigated species, whereas Strychnos cocculoides seems to be the less competitive. Strychnos cocculoides has additionally spatial arrangements of. ne roots favourable for agroforestry, slowly increasing with depth and additionally low concentrations in upper soil layers."],["dc.identifier.doi","10.1007/s10457-005-2402-8"],["dc.identifier.isi","000229021900002"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/17480"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Springer"],["dc.relation.issn","0167-4366"],["dc.title","Contrasting rooting patterns of some arid-zone fruit tree species from Botswana - I. Fine root distribution"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]