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  • INDISIM-Saccha, an individual-based model to tackle Saccharomyces cerevisiae fermentations

     Portell Canal, Xavier; Gras Moreu, Anna Maria; Ginovart Gisbert, Marta
    Ecological modelling
    Date of publication: 2014-05-10
    Journal article

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    This contribution develops and implements INDISIM-Saccha, a spatially explicit IBM model to analyze the dynamics of Saccharomyces cerevisiae anaerobic cultures evolving in a liquid medium with glucose as a main carbon source and organic and inorganic nitrogen sources. The model has been parameterized, calibrated and its adequacy assessed using available experimental data. The growth of the yeast population and the glucose depletion were simulated, and changes in the ethanol production kinetics resulting from differences in the size distribution of the cells making up the inocula were examined in silico. Uncertainty on the initial estimated values of the model parameters was reduced by means of an iterative process involving a computational full factorial experiment, and the parameter values reproducing simultaneously glucose depletion and growth curves of batch cultures in two initial glucose concentrations were selected. The model adequacy was assessed with multiple both individual and population patterns not previously used in the calibration process carried out. Three virtual experiments were conducted from inocula with different cell size distributions. The maximum yeast cell number, the specific growth rate and the time to achieve the maximum ethanol produced were studied. Although the ethanol obtained was similar in the three studied situations, the time required to achieve it was significantly different, fermentations started by inocula made up of greater cells showed increased productivity. Due to the importance of S. cerevisiae in both fundamental research and industrial production contexts, having a calibrated computational model capable of studying the structures of this yeast population and the profiles of the fermentations carried out by it represents a noteworthy advancement in the field of microbial ecology. (C) 2014 Elsevier B.V. All rights reserved.

  • The microbial individual-based model INDISIM-YEAST ready to be used in the free access NetLogo modelling environment

     Portell Canal, Xavier; Gras Moreu, Anna Maria; Prats Soler, Clara; Ginovart Gisbert, Marta
    Date of publication: 2014
    Book chapter

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  • An individual-based model for the study of Paracoccus denitrificans, a denitrifying bacterium

     Araujo Granda, Pablo Alejandro; Gras Moreu, Anna Maria; Ginovart Gisbert, Marta
    Date of publication: 2014
    Book chapter

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  • Discovering the Power of Individual-Based Modelling in Teaching and Learning: The Study of a Predator-Prey System

     Ginovart Gisbert, Marta
    Journal of science education and technology
    Date of publication: 2014-08-01
    Journal article

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    The general aim is to promote the use of individual-based models (biological agent-based models) in teaching and learning contexts in life sciences and to make their progressive incorporation into academic curricula easier, complementing other existing modelling strategies more frequently used in the classroom. Modelling activities for the study of a predator-prey system for a mathematics classroom in the first year of an undergraduate program in biosystems engineering have been designed and implemented. These activities were designed to put two modelling approaches side by side, an individual-based model and a set of ordinary differential equations. In order to organize and display this, a system with wolves and sheep in a confined domain was considered and studied. With the teaching material elaborated and a computer to perform the numerical resolutions involved and the corresponding individual-based simulations, the students answered questions and completed exercises to achieve the learning goals set. Students' responses regarding the modelling of biological systems and these two distinct methodologies applied to the study of a predator-prey system were collected via questionnaires, open-ended queries and face-to-face dialogues. Taking into account the positive responses of the students when they were doing these activities, it was clear that using a discrete individual-based model to deal with a predator-prey system jointly with a set of ordinary differential equations enriches the understanding of the modelling process, adds new insights and opens novel perspectives of what can be done with computational models versus other models. The complementary views given by the two modelling approaches were very well assessed by students.

    The general aim is to promote the use of individual- based models (biological agent-based models) in teaching and learning contexts in life sciences and to make their progressive incorporation into academic curricula easier, complementing other existing modelling strategies more frequently used in the classroom. Modelling activities for the study of a predator–prey system for a mathematics classroom in the first year of an undergraduate program in biosystems engineering have been designed and implemented. These activities were designed to put two modelling approaches side by side, an individual-based model and a set of ordinary differential equations. In order to organize and display this, a system with wolves and sheep in a confined domain was considered and studied. With the teaching material elaborated and a computer to perform the numerical resolutions involved and the corresponding individual-based simulations, the students answered questions and completed exercises to achieve the learning goals set. Students’ responses regarding the modelling of biological systems and these two distinct methodologies applied to the study of a predator–prey system were collected via questionnaires, open-ended queries and face-toface dialogues. Taking into account the positive responses of the students when they were doing these activities, it was clear that using a discrete individual-based model to deal with a predator–prey system jointly with a set of ordinary differential equations enriches the understanding of the modelling process, adds new insights and opens novel perspectives of what can be done with computational models versus other models. The complementary views given by the two modelling approaches were very well assessed by students.

  • A connection between discrete individual-based and continuous population-based models: A forest modelling case study

     Gómez Mourelo, Pablo; Ginovart Gisbert, Marta
    Artificial Intelligence Research
    Date of publication: 2013
    Journal article

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  • A free accessible individual-based simulator enabling virtual experiments on soil organic matter processes in classroom  Open access

     Gras Moreu, Anna Maria; Cañadas Lorenzo, Juan Carlos; Ginovart Gisbert, Marta
    Journal of technology and science education
    Date of publication: 2013
    Journal article

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    This work addresses and aims to fulfil a very clear need in teaching biosystem engineering. When introducing students to the complexity of soil processes, one of the frustrations that teachers ofen experience is the impossibility to demonstrate practically, in the lab, some of the concepts and processes discussed in class. Either the experiments take far longer than a typical laboratory session or they require access to specific equipment. To deal with this situation, it would be ideal for students to be able to do virtual experiments. The purpose of this work is to display the individual-based simulation model INDISIM-SOM, available free from a website, and to show how it can be used in experiments or as a teaching-learning instrument in the classroom. The computational model has been designed specifically for the study of soil organic matter and is based mainly on the activity conducted by two diferent prototypes of microorganisms. One option of using INDISIMSOM is as a way to introduce the individual-based model as a methodology to improve understanding of the agents involved in soil microbial system and their processes. Another option is to develop the ability to work with simulators by connecting concepts and helping students in the development of modelling competence. Virtual experiments were carried out as an example of what may be expected from using the INDISIM-SOM web simulator. Temporal evolutions of five virtual soils with diferent organic C content and proportional content in organic N, easily hidrolyzable N, nitrate and ammonia were generated and discussed.

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    Modelización y simulación discreta para tratar con problemas de toma de decisiones: El problema del Bar El Farol  Open access

     Ginovart Gisbert, Marta
    Revista MSEL (Modeling in science education and learning)
    Date of publication: 2013
    Journal article

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    >Se puede utilizar la modelizacion y simulacion discreta para investigar como \razonan", \piensan" o \deciden" los individuos en situaciones \complejas" y no perfectamente delimitadas o controladas? Para dar alguna respuesta a esta pregunta, planteamos una \situacion real" para trabajar con los estudiantes. Se introduce en el aula la modelizacion y simulacion discreta como una herramienta para investigar la toma de decisiones y los sistemas adaptativos a traves de un conjunto de tareas que giran entorno al siguiente contexto: la ocupacion semanal por parte de una poblacion de un recurso publico a partir de la decision individual de ir o no a utilizarlo, con el proposito o deseo de no coincidir con un numero excesivo de individuos y siendo la ocupacion historica de este recurso en semanas previas la unica informacion disponible para la toma de esa decision. Se desarrollan y analizan distintas estrategias de modelizacion y simulacion discreta para implementar en una hoja de calculo y se generan con ellas experimentos com- putacionales o simulaciones para tratar con esta situacion. Constatando las limitaciones que este tipo de simulacion exhibe, se introduce un entorno de programacion especco para modelos basados en el indi- viduo (NetLogo) que permitira proseguir con el estudio de esta situacion a partir del problema del Bar El Farol. La valoracion nal de los estudiantes de esta actividad fue muy positiva, pues descubrieron que lo que pareca inicialmente un problema \intratable", con la ayuda del ordenador, pasaba a ser un problema abordable, y posible de investigar y analizar.

    Se puede utilizar la modelizaci on y simulaci on discreta para investigar como razonan, piensan o deciden los individuos en situaciones complejas" y no perfectamente delimitadas o controladas. Para dar alguna respuesta a esta pregunta, planteamos una situaci on real para trabajar con los estudiantes. Se introduce en el aula la modelizaci on y simulaci on discreta como una herramienta para investigar la toma de decisiones y los sistemas adaptativos a trav es de un conjunto de tareas que giran entorno al siguiente contexto: la ocupaci on semanal por parte de una poblaci on de un recurso p ublico a partir de la decisi on individual de ir o no a utilizarlo, con el prop osito o deseo de no coincidir con un n umero excesivo de individuos y siendo la ocupaci on hist orica de este recurso en semanas previas la unica informaci on disponible para la toma de esa decisi on. Se desarrollan y analizan distintas estrategias de modelizaci on y simulaci on discreta para implementar en una hoja de c alculo y se generan con ellas experimentos computacionales o simulaciones para tratar con esta situaci on. Constatando las limitaciones que este tipo de simulaci on exhibe, se introduce un entorno de programaci on espec co para modelos basados en el individuo (NetLogo) que permitir a proseguir con el estudio de esta situaci on a partir del problema del Bar El Farol. La valoraci on nal de los estudiantes de esta actividad fue muy positiva, pues descubrieron que lo que parec a inicialmente un problema intratable, con la ayuda del ordenador, pasaba a ser un problema abordable, y posible de investigar y analizar.

  • Influence of tillage on soil macropore size, shape of top layer and crop development in a sub-humid environment

     Josa March, Ramon Peñafort; Gorchs Altarriba, Gil; Ginovart Gisbert, Marta; Solé Benet, Albert
    Biología
    Date of publication: 2013-12-01
    Journal article

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    Topsoil macropores of two plots under no-tillage and conventional tillage were analyzed. A leguminous-cereal rotation was applied for six cycles under dry-land farming system (crop residues were removed). The clay-loam soil shows some vertic characteristics. The main goal is to identify the relationship between the top soil macro and meso-pore distribution for the two tillage systems (at the end of sixth cycle of cultivation) with the annual crop production (rainfall in normal growing period and crop production values are included). Unaltered topsoil samples were taken from 0 to 60 mm (row and interrow positions) and from the immediate depth (60 to 110 mm) in both plots (conventional and no-tillage). The morphometric analyses of 66 polished slices were carried out with the aim to identify differences in soil macro and meso-pore organisation.

  • Influence of tillage on soil macropore size and shape of top layer and crop development in a sub-humid environment

     Josa March, Ramon Peñafort; Gorchs Altarriba, Gil; Ginovart Gisbert, Marta; Solé Bénet, Albert
    Biohydrology
    Presentation's date: 2013-05-21
    Presentation of work at congresses

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    Topsoil macropores of two plots under no-tillage and conventional tillage were analyzed with crop residues removal in a leguminous- cereal rotation during six cycles under dry-land farming system (soil is clay-loam). Sixty six slices coming from both plots were obtained from three topsoil positions: row and interrow positions (0 to 60 mm) and the immediate depth (60 to 110 mm). Soil macropores were classified by size (area) and elongation ratio and by form factor and equivalent pore diameter. No appreciable differences were observed. Soil macro and meso pore distributions of samples were also compared. The presence of larger macropores was higher in conventional tillage with regard to no tillage. Samples coming on row and deeper positions of conventional tillage show a somewhat higher amount of macropores in the range between 2 to 2.3 mm equivalent pore diameter. Soil macropores contribute to increase soil aeration and soil drying when topsoil is too wet in critical periods of crop development.

  • The individual-based soil organic matter model INDISIM-SOM in NetLogo - open to new users and data

     Gras Moreu, Anna Maria; Banitz, Thomas; Ginovart Gisbert, Marta
    Federation of European Microbiological Societies Congress
    Presentation's date: 2013
    Presentation of work at congresses

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  • Stability of ripe sourdough acidity during propagation and use

     Gordun Quiles, Elena; Carbo Moliner, Rosa; Ginovart Gisbert, Marta
    International Conference on Environmental, Industrial and Applied Microbiology
    Presentation's date: 2013
    Presentation of work at congresses

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  • An individual-based model for the study of Paracoccus denitrificans, a denitrifying bacterium

     Araujo Granda, Pablo Alejandro; Gras Moreu, Anna Maria; Ginovart Gisbert, Marta
    International Conference on Environmental, Industrial and Applied Microbiology
    Presentation's date: 2013
    Presentation of work at congresses

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  • Effect of aerobic and microaerophilic conditions on the growth of Saccharomyces cerevisiae

     Carbo Moliner, Rosa; Portell Canal, Xavier; Ginovart Gisbert, Marta
    International Conference on Environmental, Industrial and Applied Microbiology
    Presentation's date: 2013
    Presentation of work at congresses

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  • The microbial individual-based model INDISIM-YEAST ready to be used in the free access NetLogo modelling environment

     Portell Canal, Xavier; Gras Moreu, Anna Maria; Prats Soler, Clara; Ginovart Gisbert, Marta
    International Conference on Environmental, Industrial and Applied Microbiology
    Presentation's date: 2013
    Presentation of work at congresses

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    INDISIM-YEAST:Saccha, an individual-based model to tackle Saccharomyces cerevisiae batch cultures  Open access

     Portell Canal, Xavier; Gras Moreu, Anna Maria; Carbo Moliner, Rosa; Ginovart Gisbert, Marta
    Federation of European Microbiological Societies Congress
    Presentation's date: 2013
    Presentation of work at congresses

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  • On how Moodle quizzes can contribute to the formative e-assessment of first-year engineering students in mathematics courses

     Blanco Abellan, Monica; Ginovart Gisbert, Marta
    Revista de Universidad y Sociedad del Conocimiento, RUSC
    Date of publication: 2012-01
    Journal article

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  • Discovering the power of agent-based modelling to deal with complex systems in diverse contexts

     Ginovart Gisbert, Marta; Portell Canal, Xavier; Blanco Abellan, Monica
    Quaderni di Ricerca in Didattica/Mathematics (QRDM)
    Date of publication: 2012
    Journal article

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  • Modelización basada en el individuo: una metodología atractiva para el estudio de biosistemas

     Ginovart Gisbert, Marta; Blanco Abellan, Monica; Portell Canal, Xavier; Ferrer-Closas, Pol
    Enseñanza de las ciencias. Revista de investigación y experiencias didácticas
    Date of publication: 2012
    Journal article

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  • Effects of air-drying and rewetting on extractable organic carbon, microbial biomass, soil respiration and ß-Glucosidase and ß-Galactosidase activities of minimally disturbed soils under mediterranean conditions

     Marando, Graciela; Jimenez de Ridder, Patricia; Josa March, Ramon Peñafort; Julia Moli, Maria; Ginovart Gisbert, Marta; Bonmati Pont, Manuel
    Date of publication: 2012
    Book chapter

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  • Biochemical characterisation of minimally disturbed soils under mediterranean conditions

     Jimenez de Ridder, Patricia; Marando, Graciela; Josa March, Ramon Peñafort; Julia Moli, Maria; Ginovart Gisbert, Marta; Bonmati Pont, Manuel
    Date of publication: 2012
    Book chapter

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  • An individual-based model for dealing with organic amendments and mineral nitrogen soil fertilizations

     Gras Moreu, Anna Maria; Comas Angelet, Jordi; Ginovart Gisbert, Marta
    Date of publication: 2012
    Book chapter

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    Modelización y simulación discreta con la plataforma NetLogo: ¿por qué caen las hojas en otoño?  Open access

     Ginovart Gisbert, Marta; Catalina, Merche; Blanco Abellan, Monica
    Congrés Internacional de Docència Universitària i Innovació
    Presentation's date: 2012
    Presentation of work at congresses

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    Los modelos basados en agentes (ABMs) describen a los individuos o partes que configuran un sistema como entidades autónomas y discretas, y focalizan toda su atención en caracterizar estas partes (agentes) mediante reglas de comportamiento, permitiendo la interacción entre ellas y con el entorno en el que se hallan. Se presenta el material docente diseñado para una actividad a realizar de forma autónoma en aula informática, centrada en el modelo “Autumn” que se encuentra en la plataforma NetLogo (de acceso libre desde la Web). Se analizan los resultados obtenidos con su implementación en los estudios de grado en Ingeniería de Biosistemas de la Universitat Politècnica de Catalunya.

  • A Bacterial Individual-based Virtual Bioreactor to Test Handling Protocols in a NetLogo Platform

     Ginovart Gisbert, Marta; Prats Soler, Clara
    Vienna International Conference on Mathematical Modelling
    Presentation's date: 2012
    Presentation of work at congresses

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  • A simple discrete simulation model to explore in the classroom some rules involved in the decision-making process

     Ginovart Gisbert, Marta
    International Commission for the Study and Improvement of Mathematics
    Presentation's date: 2012
    Presentation of work at congresses

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  • Modelización y Simulación Discreta para tratar con problemas de toma de decisiones: El problema del Bar El Farol

     Ginovart Gisbert, Marta
    Jornadas de Modelización Matemática
    Presentation's date: 2012-06-07
    Presentation of work at congresses

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  • Differences in stationary-phase cells of a commercial Saccharomyces cerevisiae wine yeast grown in aerobic and microaerophilic batch cultures assessed by electric particle analysis, light diffraction and flow cytometry

     Portell Canal, Xavier; Ginovart Gisbert, Marta; Carbo Moliner, Rosa; Vives-Rego, Josep
    Journal of industrial microbiology and biotechnology
    Date of publication: 2011
    Journal article

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    Modelos basados en el individuo y la plataforma NetLogo  Open access

     Ginovart Gisbert, Marta; Portell Canal, Xavier; Ferrer-Closas, Pol; Blanco Abellan, Monica
    Unión. Revista Iberoamericana de educación matemática
    Date of publication: 2011
    Journal article

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    El objetivo general de este trabajo se enmarca en el deseo de dar a conocer la metodología de la modelización basada en el individuo y sus posibilidades para ser utilizada, entre otras metodologías, en la adquisición de la competencia de modelización en docencia. Para ello se presenta: i) una descripción de los elementos que permiten identificar, describir, comunicar e implementar los modelos basados en el individuo (IBMs), y como obtener resultados de simulación; y ii) un ejemplo-muestra de un IBM de NetLogo que ilustra con detalle la manera de proceder con este tipo de modelo

  • Exploring the lag phase and growth initiation of a yeast culture by means of an individual-based model

     Ginovart Gisbert, Marta; Prats Soler, Clara; Portell Canal, Xavier; Silbert, Moises
    Food microbiology
    Date of publication: 2011
    Journal article

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    The performance of fermentation processes is greatly influenced by the size and quality of inocula. The characterization of the replicative age is decided by the number of birth scars each yeast exhibits on its cellular membrane. Yeast ageing and inoculum size are factors that affect industrial fermentation, particularly those processes in which the yeast cells are reused such as the production of beer. This process reuses yeast cropped at the end of one fermentation in the following one, in a process called “serial repitching”. The aim of this study was to explore the effects of inoculum size and ageing on the first stages of the dynamics of yeast population growth. However, only Individual-based Models (IbMs) allow the study of small, well-characterized, microbial inocula. We used INDISIM-YEAST, based on the generic IbM simulator INDISIM, to carry out these studies. Several simulations were performed to analyze the effect of the inoculum size and genealogical age of the cells that made it up on the lag phase, first division time and specific growth rate. The shortest lag phase and time to the first division were obtained with largest inocula and with the youngest inoculated parent cells. Keywords: Individual-based model; Lag phase; Growth initiation; Yeast inoculum; Inoculum size; Yeast cell age.

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    Individual-based modelling of carbon and nitrogen dynamics in soils: parameterization and sensitivity analysis of microbial components  Open access

     Gras Moreu, Anna Maria; Ginovart Gisbert, Marta; Valls Ribas, Joaquim; Baveye, Philippe C.
    Ecological modelling
    Date of publication: 2011-06-24
    Journal article

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    The fate of soil carbon and nitrogen compounds in soils in response to climate change is currently the object of significant research. In particular, there is much interest in the development of a new generation of micro-scale models of soil ecosystems processes. Crucial to the elaboration of such models is the ability to describe the growth and metabolism of small numbers of individual microorganisms, distributed in a highly heterogeneous environment. In this context, the key objective of the research described in this article was to further develop an individual-based soil organic matter model, INDISIM-SOM, first proposed a few years ago, and to assess its performance with a broader experimental data set than previously considered. INDISIM-SOM models the dynamics and evolution of carbon and nitrogen associated with organic matter in soils. The model involves a number of state variables and parameters related to soil organic matter and microbial activity, including growth and decay of microbial biomass, temporal evolutions of easily hydrolysable N, mineral N in ammonium and nitrate, CO2 and O2. The present article concentrates on the biotic components of the model. Simulation results demonstrate that the model can be calibrated to provide good fit to experimental data from laboratory incubation experiments performed on three different types of Mediterranean soils. In addition, analysis of the sensitivity toward its biotic parameters shows that the model is far more sensitive to some parameters, i.e., the microbial maintenance energy and the probability of random microbial death, than to others. These results suggest that, in the future, research should focus on securing better measurements of these parameters, on environmental determinants of the switch from active to dormant states, and on the causes of random cell death in soil ecosystems.

  • Effects of thermally dried and composted sewage sludges on the fertility of residual soils from limestone quarries.

     Marando, Graciela; Jimenez de Ridder, Patricia; Hereter Quintana, Agnès; Julia Moli, Maria; Ginovart Gisbert, Marta; Bonmati Pont, Manuel
    Applied soil ecology
    Date of publication: 2011-05-01
    Journal article

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  • Analysis of the effect of inoculum characteristics on the first stages of a growing yeast population in beer fermentations by means of an individual-based model

     Ginovart Gisbert, Marta; Prats Soler, Clara; Portell Canal, Xavier; Silbert, Moises
    Journal of industrial microbiology and biotechnology
    Date of publication: 2011
    Journal article

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  • Modelización basada en el individuo (IBM) perspectiva multidisclipinar en microbiologia aplicada: alimentos, medioambiente y salud

     Prats Soler, Clara; Valls Ribas, Joaquim; Carbo Moliner, Rosa; Ginovart Gisbert, Marta; Giro Roca, Antoni; Gras Moreu, Anna Maria; Portell Canal, Xavier; Ferrer Savall, Jordi; Silbert, Moises; Lopez Codina, Daniel
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  • An individual-based model for dealing with organic amendments and mineral nitrogen soil fertilizations

     Gras Moreu, Anna Maria; Comas Angelet, Jordi; Ginovart Gisbert, Marta
    International Conference on Environmental, Industrial and Applied Microbiology
    Presentation's date: 2011
    Presentation of work at congresses

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  • Aerobic and microaerophilic growth kinetics of Saccharomyces cerevisiae in batch cultures

     Portell Canal, Xavier; Carbo Moliner, Rosa; Ginovart Gisbert, Marta
    International Conference on Environmental, Industrial and Applied Microbiology
    Presentation's date: 2011-09
    Presentation of work at congresses

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  • Sensitivity analysis and individual-based models in the study of yeast populations

     Ginovart Gisbert, Marta; Prats Soler, Clara; Portell Canal, Xavier
    European Conference on Modelling and Simulation
    Presentation's date: 2011-06
    Presentation of work at congresses

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    Individual-based models (IBMs), the biological agent-based models, are currently being applied to the study of microbial systems. A microbial IBM of yeast populations growing in liquid bath cultures has already been designed and implemented in the simulator called INDISIM-YEAST. In order to improve its predictive capabilities and further its development, a deeper understanding of how the variation of the output of the model can be apportioned, qualitatively or quantitatively, to different sources of variation must be investigated. The aim of this study is to show how insights into the individual cell parameters of INDISIM-YEAST can be obtained combining local and global methods using classic and well-proven methods, and to illustrate how these simple methods provide useful, reliable results with this IBM. This work deals mainly with the use of screening methods, as the main task to perform here is that of identifying the most influential factors for this microbial IBM. This screening exercise has allowed the establishment of significant input factors to this IBM on yeast population growth, and the highlighting of those that require greater attention in the parameterization and calibration processes.

  • Microbial individual-based models and sensitivity analyses: local and global methods

     Ginovart Gisbert, Marta; Prats Soler, Clara; Portell Canal, Xavier
    International Conference on Predicitive Modeling in Foods
    Presentation's date: 2011-09-13
    Presentation of work at congresses

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    A microbial Individual-based Model (IbM) to deal with yeast populations growing in liquid batch cultures has been designed and implemented in a simulator called INDISIM-YEAST. Interesting qualitative results have already been achieved with its use in the study of fermentation profiles, small inocula dynamics and lag phase, among others. Nevertheless, in order to improve its predictive capabilities and further development, a deeper comprehension of how the variation of the output of the model can be apportioned to different sources of variation must be investigated. One way to consider a sensitivity analysis for this IbM, providing an understanding of how the model response variables react to changes in the inputs, is the statistical study of well-designed computer experiments. The aim of this contribution is to show how the insights into nine individual cell parameters of INDISIMYEAST, mainly related to uptake and reproduction sub-models, can be obtained by combining local and global sensitivity analyses using simple and classic methods. From data obtained with an extensive set of computer experiments, a study of the variability observed in the evolution of two outputs of this model, ethanol production and mean biomass of the population, was performed. In addition, mono-factorial (one-at-a-time) analyses and ANOVA-based global analyses were also carried out on these two outputs. The model is clearly less sensitive to some parameters than others, depending on the output controlled. Moreover, this study allows identification of the parameters which have the greatest impact on the corresponding outputs and their significant first-order interactions. This work must be understood as an exercise to set up the procedure to be used in a sensitivity analysis study involving microbial IbMs. The knowledge gained will facilitate future parameterization and calibration of different parameters and outputs depending on the purpose of any study.

  • Upgrading the uptake and metabolism sub-models of the Individual-based Model INDISIM-YEAST to tackle the behaviour of Saccharomyces cerevisiae in different culture conditions

     Portell Canal, Xavier; Gras Moreu, Anna Maria; Carbo Moliner, Rosa; Ginovart Gisbert, Marta
    International Conference on Predicitive Modeling in Foods
    Presentation's date: 2011-09-13
    Presentation of work at congresses

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  • Discovering the power of agent-based modelling to deal with complex systems in diverse contexts

     Ginovart Gisbert, Marta; Portell Canal, Xavier; Blanco Abellan, Monica
    CIEAEM Conference
    Presentation's date: 2011-07
    Presentation of work at congresses

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    Effects of two tillage techniques on soil macroporosity in sub-humid environment.  Open access

     Josa March, Ramon Peñafort; Ginovart Gisbert, Marta; Solé, Albert
    International Agrophysics
    Date of publication: 2010
    Journal article

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  • Individual-based modelling and simulation of microbial processes: yeast fermentation and multi-species composting

     Prats Soler, Clara; Ferrer Savall, Jordi; Gras Moreu, Anna Maria; Ginovart Gisbert, Marta
    Mathematical and Computer Modelling of Dynamical Systems (online)
    Date of publication: 2010-12-06
    Journal article

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  • Individual-based modeling of carbon and nitrogen dynamics in soils: parameterization and sensitivity analysis of abiotic components

     Gras Moreu, Anna Maria; Ginovart Gisbert, Marta; Portell Canal, Xavier; Baveye, Philippe C.
    Soil science
    Date of publication: 2010
    Journal article

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  • Population analysis of a commercial Saccharomyces cerevisiae wine yeast in a batch culture by electric particle analysis, light difraction and flow cytometry

     Portell Canal, Xavier; Ginovart Gisbert, Marta; Carbo Moliner, Rosa; Gras Moreu, Anna Maria; Vives Rego, J.
    Fems yeast research
    Date of publication: 2010
    Journal article

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    Data from electric particle analysis, light diffraction and flow cytometry analysis provide information on changes in cell morphology. Here, we report analyses of Saccharomyces cerevisiae populations growing in a batch culture using these techniques. The size distributions were determined by electric particle analysis and by light diffraction in order to compare their outcomes. Flow cytometry parameters forward (related to cell size) and side (related to cell granularity) scatter were also determined to complement this information. These distributions of yeast properties were analysed statistically and by a complexity index. The cell size of Saccharomyces at the lag phase was smaller than that at the beginning of the exponential phase, whereas during the stationary phase, the cell size converged with the values observed during the lag phase. These experimental techniques, when used together, allow us to distinguish among and characterize the cell size, cell granularity and the structure of the yeast population through the three growth phases. Flow cytometry patterns are better than light diffraction and electric particle analysis in showing the existence of subpopulations during the different phases, especially during the stationary phase. The use of a complexity index in this context helped to differentiate these phases and confirmed the yeast cell heterogeneity.

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    How to introduce historically the normal distribution in engineering education: a classroom experiment  Open access

     Blanco Abellan, Monica; Ginovart Gisbert, Marta
    International journal of mathematical education in science and technology (Print)
    Date of publication: 2010-01-15
    Journal article

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    Introducing the normal distribution by following a teaching approach inspired by history: an example for classroom implementation in engineering education  Open access

     Blanco Abellan, Monica; Ginovart Gisbert, Marta
    European Society for Research in Mathematics Education (ERME). Conference
    Presentation's date: 2010
    Presentation of work at congresses

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    Creating Moodle quizzes for the subjects of mathematics and statistics corresponding to the first years in engineering studies  Open access

     Blanco Abellan, Monica; Ginovart Gisbert, Marta
    EDULEARN09 (International Conference on Education and New Learning Technologies)
    Presentation's date: 2010-07
    Presentation of work at congresses

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    In 2005 the virtual campus Atenea of the Technical University of Catalonia (UPC) started to use Moodle, an open source learning management system that offers a wide variety of teaching tools [3]. One of these tools, the quiz module, represents an alternative to traditional face-to-face courses and paper-based testing. In order to explore how to apply this new strategy, in 2008 we started to carry out a project subsidised by the Institute of Education Sciences (ICE) of the UPC. The project title was “Creating Moodle quizzes for the subjects of Mathematics and Statistics corresponding to the first years in engineering studies”. It covered the compulsory undergraduate subjects in applied mathematics included in the first- and second-year syllabus for all branches of Engineering. The aims were to elaborate a substantial range of Moodle question pools and to design, implement and assess a series of quizzes, to use Moodle quizzes to promote more effective, dynamic and autonomous learning, and to change teachers’ and students’ attitude towards the campus Atenea.

  • INDISIM-YEAST, a simulator for individual-based modelling of yeast metabolism and process dynamics in asynchronous batch fermentations

     Ginovart Gisbert, Marta; Gras Moreu, Anna Maria; Carbo Moliner, Rosa
    International Conference Predictive Modelling in Food
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    Análisis de la eficiencia de cuestionarios Moodle como herramienta de evolución de asignaturas de matemáticas correspondientes a primeros cursos de titulaciones de ingeniería  Open access

     Blanco Abellan, Monica; Ginovart Gisbert, Marta
    Congrés Internacional de Docència Universitària i Innovació
    Presentation's date: 2010
    Presentation of work at congresses

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  • Modeling of Pachysolen tannophilus batch cultures by individual-based simulations

     Castro, Eulogio; Ginovart Gisbert, Marta; Gras Moreu, Anna Maria
    International Biotechnology Symposium
    Presentation's date: 2010
    Presentation of work at congresses

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    Combined use of local and global sensitivity analyses for the investigation of an individual-based model of yeast populations  Open access

     Prats Soler, Clara; Portell Canal, Xavier; Gras Moreu, Anna Maria; Ginovart Gisbert, Marta
    International ICFMH Symposium (Food Micro)
    Presentation's date: 2010-09-01
    Presentation of work at congresses

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  • Moodle quizzes for assessing statistical topics in engineering studies

     Blanco Abellan, Monica; Ginovart Gisbert, Marta
    Joint International IGIP-SEFI Annual Conference 2010
    Presentation's date: 2010-09-22
    Presentation of work at congresses

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