Discrete Modelling and Simulation of Biological Systems. MOSIMBIO

Years: 2000-2009

International journals:

 

J. Ferrer, C. Prats, D. López, J. Vives-Rego, 2009
Mathematical Modelling Methodologies in Predictive Food Microbiology: a SWOT Analysis
Int. J. Food Microbiol. 134, 2-8

P. Gómez-Moreulo, M. Ginovart, 2009
The differential equation counterpart of an individual-based model for yeast population growth
Comput Math Appl 58, 1360-1369

J. Ferrer, MD. Rosal, JM. Vidal, et al. 2008
Effect of the hematocrit layer geometry on Plasmodium falciparum static thin-layer in vitro cultures
Malaria J. 7:203
doi:10.1186/1475-2875-7-203

J. Ferrer, C. Prats, D. López, 2008
Individual-based Modelling: an essential tool for microbiology
J. Biol. Phys. 34, 19-37

C. Prats, A. Giro, J. Ferrer, et al. 2008
Analysis and IbM simulation of the stages in bacterial lag phase: Basis for an updated definition
J. Theor. Biol. 252, 56-68

M. Ginovart, JC. Canadas, 2008
INDISIM-YEAST: an individual-based simulator on a website for experimenting and investigating diverse dynamics of yeast populations in liquid media
J. Ind. Microbiol. Biotechnol. 35, 1359-1366

P. Jimenez, O. Ortiz, D. Tarrason, M. Ginovart, M. Bonmatí, 2007
Effect of differently post-treated dewatered sewage sludge on beta-glucosidase activity, microbial biomass carbon, basal respiration and carbohydrates contents of soils from limestone quarries
Biol. Fert. Soils 44, 393-398

J. Ferrer, J. Vidal, C. Prats, J. Valls, E. Herreros, D. López, A. Giró, D. Gargallo, 2007
Individual-based model and simulation of Plasmodium falciparum infected erythrocyte in vitro cultures
J. Theor. Biol. 248, 448-459

M. Ginovart, D. López, A. Giró, M. Silbert, 2006
Flocculation in brewing yeasts: a computer simulation study
Biosystems. 83, 51-55

C. Prats, D. López, A. Giró, J. Ferrer, J. Valls, 2006
Individual-based Modelling of bacterial cultures to study the microscopic causes of the lag phase
J. Theor. Biol. in press

M. Ginovart, D. López, A. Gras, 2005
Individual-based modelling of microbial activity to study mineralization of C and N and nitrification process in soil
Nonlinear Ana-Real. 6, 773-795

M. Ginovart, D. López, J. Valls, M. Silbert, 2002
Simulation modelling of bacterial growth in yoghurt
Int. J. Food Microbiol. 73, 415-425

M. Ginovart, D. López, J. Valls, M. Silbert, 2002
Individual based simulations of bacterial growth on agar plates
Physica A. 305, 604-618
doi:10.1016/S0378-4371(01)00581-7

M. Ginovart, D. López, J. Valls, 2002
INDISIM, and individual based discrete simulation model to study bacterial cultures
J. Theor. Biol. 214, 305-319

Book chapters:

C. Prats, J. Ferrer, A. Gras, M. Ginovart, 2009
Individual-based modelling and simulation of microbial processes: yeast fermentation and multi-species composting.
In: Inge Troch, Felix Breitenecker. Proceedings MATHMOD VIENNA 09. Ed. ARGESIM, Full Papers CD Volume, 1495-1506. ISBN:978-3-901608-35-3

C. Prats, A. Standaert, K. Bernaerts, J. Ferrer, D. López, J. Van Impe, 2009
Optimization methods for individual-based model parameter estimation in predictive microbiology.
In: Inge Troch, Felix Breitenecker. Proceedings MATHMOD VIENNA 09. Ed. ARGESIM, Full Papers CD Volume, 2635-2638. ISBN:978-3-901608-35-3

M. Ginovart, X. Portell, M. Silbert, 2009
Repitching of yeast in beer fermentations: Individual-based Model simulations.
In: Inge Troch, Felix Breitenecker. Proceedings MATHMOD VIENNA 09. Ed. ARGESIM, Full Papers CD Volume, 2655–2658. ISBN:978-3-901608-35-3

C. Prats, J. Ferrer, D. López, J. Vives-Rego, 2008
Individual Based Modelling and Flow Cytometry: Two Suitable Tools for PredictiveMicrobiology.
In: FoodSim’2008. Ed. E. Cummins and D. Thiel, Eurosis, Ghent, Belgium. 91-95 ISBN:978-90-77381-41-0

M. Ginovart, J. Xifré, D. López, M. Silbert, 2007
INDISIM-YEAST, an individual-based model to study yeast population in batch cultures.
In: Communicating Current Research and Educational Topics and Trends in Applied Microbiology. Ed. A. Méndez-Vilas. Microbiology Book Series nº 1 Vol. 1, Communicating Current Research and Educational Topics and Trends in Applied Microbiology, Formatex (Badajoz), p 401-409. ISBN-13:978-84-611-9422-3. http://www.formatex.org/microbio/

C. Prats, J. Ferrer, B. Flix, A. Giró, D. López, J. Vives-Rego, 2007
Evolution of biomass distribution during bacterial lag phase through flow cytometry, particle analysis and Individual-based Modelling.
In: 5th International Conference on Predictive Modelling in Foods. Proceedings, 301-304. Ed. G.Nychas et al., Agricultural University of Athens, Grècia. ISBN:978-960-89313-7-4

M. Ginovart, A. Gras, R. Carbó, 2007
INDISIM-YEAST, a simulator for individual-based modelling of yeast metabolism and process dynamics in asynchronous batch fermentations.
In: 5th International Conference on Predictive Modelling in Foods. Proceedings, 333-336. Ed. G.Nychas et al., Agricultural University of Athens, Grècia. ISBN:978-960-89313-7-4

M. Ginovart, A. Gras, R. Carbó, J. Vives-Rego, 2007
The use of flow cytometry and particle size analysis in the individual-based model INDISIM-YEAST, a simulator of yeast populations.
In: 5th International Conference on Predictive Modelling in Foods. Proceedings, 16-19. Ed. G.Nychas et al., Agricultural University of Athens, Grècia. ISBN:978-960-89313-7-4
Conferences' proceedings:

X. Portell, M. Ginovart, R. Carbo, J. Vives-Rego, 2009

Differences in stationary phase cells of Saccharomyces cerevisiae var. bayanus grown in aerobic and hypoxic bath cultures assessed by electric particle analysis, light diffraction and flow cytometry
In: A. Mendez-Vilas (ed), Abstracts Book of the III International Conference on Environmental, Industrial and Applied Microbiology. BioMicroWorld2009, Formatex. p. 469.

 

A. Gras, J. C. Cañadas, M. Ginovart, 2009
INDISIM-SOM: an individual-based simulator on a website for experimenting and investigating diverse dynamics of Carbon and Nitrogen in mineral soils.
In: Abstracts Book of the BioMicroWorld2009 - III International Conference on Environmental, Industrial and Applied Microbiology, Lisbon, Portugal, Ed. A. Mendez-Vilas, Formatex p. 70

X. Portell, C. Prats, M. Silbert, M. Ginovart, 2009
Effect of the inoculum characteristics on the first stages of a growing yeast population in beer fermentations by means of an Individual-based Model.
In: Abstracts Book of the BioMicroWorld2009 - III International Conference on Environmental, Industrial and Applied Microbiology, Lisbon, Portugal, Ed. A. Mendez-Vilas, Formatex p. 292

X. Portell, C. Prats, M. Silbert, M. Ginovart, 2009
Exploring lag phase and growth initiation of a yeast culture by means of an Individual-based Model.
In: Extended Abstracts of the 6th ICPMF - International Conference on Predicitive Modeling in Foods, Washington DC, United States, Ed. V.K. Juneja and D.W. Schaffner

R. Dalmau, X. Portell, C. Prats, M. Ginovart, A. Giró, 2009
Individual-based Modelling and simulation: towards a better understanding of growth dynamics from small inocula.
In: Second SAFE Consortium International Congress on Food Safety: Novel Technologies and Food Quality, Safety and Health Abstract Book, Girona, Spain, Ed. Flynn, Garriga, Hofstra, Monfort p. 153-154

J. Ferrer, C. Prats, D. López, J. Vives-Rego, 2008
Mathematical Modelling Methodologies in Predictive Food Microbiology: a SWOT Analysis.
In: The 21st International ICFMH Symposium. “Evolving Microbial Food Quality and Safety”- Abstract Book. Ed. Odgen, N. Strachan, University of Aberdeen p. 78

M. Ginovart, R. Carbó, A. Gras, X. Portell, J. Vives-Rego, 2008
A comparative study of the use of an electronic particle analyser and a flow cytometer to assess the changes of cell size distributions of Saccharomyces cerevisiae var. bayanus during aerobic and anaerobic growth in batch cultures.
In: The 21st International ICFMH Symposium. “Evolving Microbial Food Quality and Safety”, Abstract Book. Ed. Odgen, N. Strachan, University of Aberdeen p. 212

M. Ginovart, X. Portell, M. Silbert, 2008
Reutilización de la Levadura en Fermentaciones de la Cerveza: Simulaciones por Ordenador.
In: Actas del V Congreso Español de Ingeniería de Alimentos y al II Congreso Iberoamericano sobre Seguridad Alimentaria, CIMNE, Universidad Politécnica de Cataluña, Barcelona, Ed. M. Raventos i J. Salazar, p 957 - 962 ISBN:978-84-96736-57-3

R. Carbó, M. Ginovart, M. Vias, 2008
Influencia de Brettanomyces/Dekkera en la Evolución de la Fermentación Alcohólica.
In: Actas del V Congreso Español de Ingeniería de Alimentos y del II Congreso Iberoamericano sobre Seguridad Alimentaria, CIMNE, Universidad Politécnica de Cataluña, Barcelona, Ed. M. Raventos i J. Salazar p 443 - 448 ISBN:978-84-96736-57-3

C. Prats, J. Ferrer, D. López, 2008
INDISIM, an Individual-based Model to simulate microbial cultures.
In: SwarmFest 2008, Abstracts.

J. Ferrer, C. Prats, D. López, 2007
Individual-based Modelling: an essential tool for Microbiology.
In: 6th International Conference on Biological Physics, Abstracts. p.91, Uruguai, Montevideo. ISBN:978-9974-8002-2-9

P. Gomez-Moruelo, M. Ginovart, 2006
From individual-based model to partial differential equations: an application to the study of yeast populations in batch cultures.
In: Abstracts of the ICM2006 – International Congress of Mathematicians, Madrid, Spain, p. 172-173

A. Gras, M. Ginovart, 2006
INDISIM-SOM, an individual-based model to study short-term evolutions of carbon and nitrogen pools related to microbial activity in soil organic matter.
In: Modelling Methodologies and Simulation. Key Technologies in Academia and Industry. European Conference on Modelling and Simulation - ECMS 2006, Bonn-Rhein-Sieg, Germany, Ed. W. Borutzky, A. Orsoni, R. Zobel, K. Al-Begain,  p 554-559. ISBN:0-9553018-0-7

C. Prats et al. 2006
A Mathematical Analysis of the Stages in Bacterial Lag Phase.
In: Food Micro 2006. Food safety and food biotechnology: diversity and global impact. Book of abstracts, p.550

C. Prats et al. 2006
A physical interpretation of the microbial growth rate temperature dependence.
In: XX International Conference of Physical Biology: From Molecular Interactions to Cellular Behavior. Book of abstracts, p. 161-163

A. Gras, C. Prats, M. Ginovart, 2005
An individual based model to study the main groups of microbes active in composting process.
In: 1st International conference on Environmental Industrial and Applied Microbiology, BioMicroWorld-2005. Book of abstracts, p 23

A. Gras, J. Valls, M. Ginovart, 2005
Nitrifier bacterial activity linked to mineralization of soil organic matter: individual based simulations.
In: 1st International conference on Environmental Industrial and Applied Microbiology, BioMicroWorld-2005. Book of abstracts, p 625

M. Ginovart, D. Duch, A. Gras, 2005
A discrete model to study bacterial activity of activated sludge systems in wastewater treatment.
In: Book of abstracts of the 1st International conference on Environmental Industrial and Applied Microbiology, BioMicroWorld-2005. p 6

C. Prats, D. López, A. Giró, J. Ferrer, J. Valls, 2005
Spatial properties in Individual based modelling of microbiological systems. Study of the composting process.
In: Book of abstracts of the 1st International conference on Environmental Industrial and Applied Microbiology, BioMicroWorld-2005. p 642.

M. Ginovart, M. Silbert, 2005
An individual based model to study the behaviour of yeast populations in batch cultures.
In:  Book of Abstracts 1 of The European Conference on Mathematical and Theoretical Biology, ECMTB05. Book of Abstracts, p 390.

A. Gras, C. Prats, M. Ginovart , 2005
An individual based model to study the main groups of microbes active in composting process.
In: Recent Research Developments in Multidisciplinary Applied Microbiology 2005: Understanding and Exploiting Microbes and Their Interactions - Biological, Physical, Chemical and Engineering Aspects. Wiley-VCH, Weinheim.

A. Gras, J. Valls, M. Ginovart, 2005
Nitrifier bacterial activity linked to mineralization of soil organic matter: individual based simulations.
In: Recent Research Developments in Multidisciplinary Applied Microbiology 2005: Understanding and Exploiting Microbes and Their Interactions - Biological, Physical, Chemical and Engineering Aspects. Wiley-VCH, Weinheim.

C. Prats, D. López, A. Giró, J. Ferrer, J. Valls, 2005
Spatial properties in Individual based modelling of microbiological systems. Study of the composting process.
In: Recent Research Developments in Multidisciplinary Applied Microbiology 2005: Understanding and Exploiting Microbes and Their Interactions - Biological, Physical, Chemical and Engineering Aspects. Wiley-VCH, Weinheim.

J. Ferrer, D. López, J. Valls, C. Prats, 2005
Individual Based Model and simulation of Plasmodium falciparum Infected Erythrocytes in vitro cultures.
In: Abstract book. Medicine and health in the tropics, p. 235

J. Ferrer, E. Herreros, J. Valls, C. Prats, D. López, D. Gargallo-Viola, 2005
Individual based modelling and simulation of Plasmodium falciparum Infected erythrocytes in vitro cultures.
In: The American Journal of tropical medicine and Hygiene Vol. 73 n. 6 (Suppl.), pgs. 113-114

A. Gras, M. Ginovart, 2004
Discrete simulation model to study heterotrophic microbial activity in soil.
In: Applied Simulation and Modelling. IASTED Acta Press, Anaheim, CA USA. Ed. M.H. Hamza. p. 125-130. ISBN 0-88986-397-0

A. Giró, M. Ginovart, D. López, M. Silbert, 2004
An Individual-based Model to Study Growth Inhibitors of Yeast Cells in Batch Cultures.
In: Abstracts. 5th International Conference on Biological Physics 2004, Goteborg, Suècia, pàg. 82

C. Prats, A. Giró, D. López, J. Valls, 2004
Individual Based Modelling of Bacterial Cultures. A Lag Phase Study.
In: Abstracts. 5th International Conference on Biological Physics 2004, Goteborg, Suècia, pàg. 82

A. Giró, J. Valls, D. López, M. Ginovart, 2003
Computer Simulations of the Lag Phase.
In: Conference Proceedings of the 4th International Conference on Predictive Modelling in Foods, Ed. Van Impe J., Geeraerd I., Leguérinel I., Mafart P. p. 221-223 ISBN:90-5682-400-7

M. Ginovart, J. Valls, D. López, A. Gras, 2003
Individual Based Modelling of Microbial Activity to Study Mineralization and Nitrification Process in Soil.
In: AICME II Abstracts, Alcalá 2th International Conference on Mathematical Ecology.
Departamento de Matemáticas de la Universidad de Alcalá (Madrid, Spain) p. 09-Gin a 09-Gin b

M. Ginovart, A. Gras, D. López, 2001
Discrete simulation of bacterial activity in soils: amonification and nitrification process.
In: Modelling and Simulation 2001: 15th European Simulation Multiconference. SCS Publication, pag. 1031-1035. Erlangen (Alemanya). ISBN:1-56555-225-3

M. Ginovart, D. López, J. Valls, 2000
Simulation modelling of bacterial growth in yoghurt.
In: Conference Proceedings of the 3rd International Conference on Predictive Modelling in Foods, pag 226-228. Leuven (Belgica). ISBN:90-804818-3 -1
PhD thesis:

X. Portell (in progress), juny 2009
Modelització i simulació discreta de l'activitat dels llevats en processos d’interès biotecnològic.
Programa de doctorat “Biotecnologia agroalimentària i sostenibilitat” de DEAB
Directores: Dra. Anna Gras i Dra. Marta Ginovart

J. Ferrer, juny 2010
Individual-based modeling of Plasmodium falciparum erythrocyte infection in in vitro cultures
Directors: Dr. Daniel López i Dr. Joaquim Valls
Universitat Politècnica de Catalunya

C. Prats, 2008
Individual-based Modelling and simulation of bacterial systems in the study of the lag phase.
Tesi doctoral. Universitat Politècnica de Catalunya
TDX-0701108-105132

A. Gras, 2004
INDISIM-SOM. Un model discret per a l'estudi de la dinàmica de la matèria orgànica i la nitrificació en sòls.
Tesi doctoral. Universitat Politècnica de Catalunya
Other publications:

D. López, M. Ginovart, J. Valls, 2002
Modelització i simulació discreta: un pont entre teories matemàtiques i tecnología.
Archivos de l'Escola Superior d'Agricultura de Barcelona

M. Ginovart, M. Silbert, J. Valls, D. López, A. Giró, 2006
Modelando el Crecimiento Bacteriano.
Publicado a partir del 9 de Marzo de 2006 en la sección Expertos Invitados de Salud y Ciencia de la Sociedad Iberoamericana de Información Científica <http://www.siicsalud.com/main/expinv.htm> de la Sociedad Iberoamericana de Información Científica (SIIC) en Internet.
http://www.siicsalud.com/dato/dat047/06214010.htm