Kurth, Winfried

[["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.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","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","1109"],["dc.bibliographiccitation.issue","8"],["dc.bibliographiccitation.journal","Annals of Botany"],["dc.bibliographiccitation.lastpage","1123"],["dc.bibliographiccitation.volume","101"],["dc.contributor.author","Buck-Sorlin, Gerhard H."],["dc.contributor.author","Hemmerling, Reinhard"],["dc.contributor.author","Kniemeyer, Ole"],["dc.contributor.author","Burema, Benno"],["dc.contributor.author","Kurth, Winfried"],["dc.date.accessioned","2018-11-07T11:15:17Z"],["dc.date.available","2018-11-07T11:15:17Z"],["dc.date.issued","2008"],["dc.description.abstract","Background and Aims Functional-structural plant models (FSPM) constitute a paradigm in plant modelling that combines 3D structural and graphical modelling with the simulation of plant processes. While structural aspects of plant development could so far be represented using rule-based formalisms such as Lindenmayer systems, process models were traditionally written using a procedural code. The faithful representation of structures interacting with functions across scales, however, requires a new modelling formalism. Therefore relational growth grammars (RGG) were developed on the basis of Lindenmayer systems. Methods In order to implement and test RGG, a new modelling language, the eXtended L-system language (XL) was created. Models using XL are interpreted by the interactive, Java-based modelling platform GroIMP. Three models, a semi-quantitative gibberellic acid (GA) signal transduction model, and a phytochrome-based shade detection and object avoidance model, both coupled to an existing morphogenetic structural model of barley (Hordeum vulgare L.), serve as examples to demonstrate the versatility and suitability of RGG and XL to represent the interaction of diverse biological processes across hierarchical scales. Key Results The dynamics of the concentrations in the signal transduction network could be modelled qualitatively and the phenotypes of GA-response mutants faithfully reproduced. The light model used here was simple to use yet effective enough to carry out local measurement of red:far-red ratios. Suppression of tillering at low red:far-red ratios could be simulated. Conclusions The RGG formalism is suitable for implementation of multi-scaled FSPM of plants interacting with their environment via hormonal control. However, their ensuing complexity requires careful design. On the positive side, such an FSPM displays knowledge gaps better thereby guiding future experimental design."],["dc.identifier.doi","10.1093/aob/mcm172"],["dc.identifier.isi","000255524800005"],["dc.identifier.pmid","17766311"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/54335"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Oxford Univ Press"],["dc.relation.issn","0305-7364"],["dc.title","A rule-based model of barley morphogenesis, with special respect to shading and gibberellic acid signal transduction"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","739"],["dc.bibliographiccitation.issue","9-10"],["dc.bibliographiccitation.journal","Functional Plant Biology"],["dc.bibliographiccitation.lastpage","750"],["dc.bibliographiccitation.volume","35"],["dc.contributor.author","Hemmerling, Reinhard"],["dc.contributor.author","Kniemeyer, Ole"],["dc.contributor.author","Lanwert, Dirk"],["dc.contributor.author","Kurth, Winfried"],["dc.contributor.author","Buck-Sorlin, Gerhard H."],["dc.date.accessioned","2018-11-07T11:19:57Z"],["dc.date.available","2018-11-07T11:19:57Z"],["dc.date.issued","2008"],["dc.description.abstract","The programming language XL ('eXtended L-system language') is an extension of Java, which supports the specification and execution of relational growth grammars, a variant of parallel graph grammars. XL is a powerful generalisation of the well-known L-system approach to functional-structural plant modelling. Some features of XL are discussed that are particularly useful for combining structure and function and for querying plant architectural data, and an exemplary functional-structural plant model of young beech trees is presented that is implemented in XL and includes PAR distribution, assimilate allocation and morphological plasticity. Together with a simpler model of spruce trees, this beech model is included in a virtual landscape with a mixed-species forest stand where competition for light occurs. The open-source platform GroIMP was used for the complete model development process and for visualising the results."],["dc.identifier.doi","10.1071/FP08052"],["dc.identifier.isi","000260794000002"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/55412"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Csiro Publishing"],["dc.publisher.place","Collingwood"],["dc.relation.conference","5th International Workshop on Functional Structural Plant Models"],["dc.relation.eventlocation","Napier, NEW ZEALAND"],["dc.relation.issn","1445-4408"],["dc.title","The rule-based language XL and the modelling environment GroIMP illustrated with simulated tree competition"],["dc.type","conference_paper"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","49"],["dc.bibliographiccitation.issue","1-2"],["dc.bibliographiccitation.journal","Plant and Soil"],["dc.bibliographiccitation.lastpage","62"],["dc.bibliographiccitation.volume","385"],["dc.contributor.author","Henke, Michael"],["dc.contributor.author","Sarlikioti, Vaia"],["dc.contributor.author","Kurth, Winfried"],["dc.contributor.author","Buck-Sorlin, Gerhard H."],["dc.contributor.author","Pages, Loic"],["dc.date.accessioned","2018-11-07T09:32:16Z"],["dc.date.available","2018-11-07T09:32:16Z"],["dc.date.issued","2014"],["dc.description.abstract","Background and aims Root plasticity is a key process affecting the root system foraging capacity while itself being affected by the nutrient availability around the root environment. Root system architecture is determined by three types of plastic responses: chemotropism, spacing of lateral roots, hierarchy between laterals and their mother root. Methods We attempt a systematic comparison of the effect of each mechanism on the whole root plasticity when the root is grown under four distinct nutrient distribution scenarios using a functional-structural root model. Nutrient distributions included i) a completely random distribution, ii) a layered distribution, iii) a patch distribution, and iv) a gradient distribution. Root length, volume, total uptake, uptake efficiency as well as the soil profiles are given as model outputs. Results Root uptake was more efficient in a soil with a gradient nutrient distribution and less so in a patch distribution for all mechanisms. In terms of mechanisms uptake was more efficient for the spacing (elongation) mechanism than the hierarchy (branching) mechanism. Conclusions Root mechanisms play a different role in the foraging of the root with chemotropism being a global tracking mechanism, whereas spacing and hierarchy are ways to proliferate in a zone with locally available nutrients."],["dc.description.sponsorship","French National Institute of Agronomic Research (INRA, EA department"],["dc.identifier.doi","10.1007/s11104-014-2221-7"],["dc.identifier.isi","000345283400004"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/31717"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Springer"],["dc.relation.issn","1573-5036"],["dc.relation.issn","0032-079X"],["dc.title","Exploring root developmental plasticity to nitrogen with a three-dimensional architectural model"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]