Eric Aguado Sarrió is presenting his Master Thesis: "Modelado del proceso de difusión en próstata mediante análisis multivariante de imágenes" at Universitat Politècnica de València.
]]>Alejandro will work for three months at Tabor Lab in modeling for Synthetic Biology.
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On February 7th 2012 Alejandro Vignoni presented his work entitled: Population-level control of heterologous protein production in bacteria in the Applied Synthetic Biology in Europe. (slides)
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Alejandro Vignoni is currently Visiting Control Engineering for Synthetic Biology Group in the Centre for Synthetic Biology and Innovation, Department of Bioengineering, Faculty of Engineering, Imperial College London under the supervision of Dr. Guy-Bart Stan.
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Ana Revert currently Visiting Goupe de Modélisation et Contrôle de BioProcédés in the Centre de BioInformatique et BioModélisation, Faculté des Sciences appliquées, Université libre de Bruxelles under the supervision of Pr. Ph. Bogaerts. |
Last March 15th, two Master Thesis dissertations from the GCSC-UPV group: Control of constrained biosystems.Author: Ana Revert Supervisor: Prof. Jesús Andrés Picó Marco. Abstract Biological systems (biosystems), due to their complexity and multidisplinary character, are becoming one of the challenging research topics in the field of systems and control. In this work, several tools for dealing with control subject to constraints in the area of biosystems have been explored. Coordination of dynamical systems:
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Last March 15th, Francisco Llaneras presented his PhD Thesis dissertation: Interval and Possibilistic Methods for Constraint-Based Metabolic Models.Supervisor: Prof. Jesús Andrés Picó Marco. Abstract This thesis is devoted to the study and application of constraint-based metabolic models. The objective was to find simple ways to handle the difficulties that arise in practice due to uncertainty (knowledge is incomplete, there is a lack of measurable variables, and those available are imprecise). With this purpose, tools have been developed to model, analyse, estimate and predict the metabolic behaviour of cells. The document is structured in three parts. First, related literature is revised and summarised. This results in a unified perspective of several methodologies that use constraint-based representations of the cell metabolism. Three outstanding methods are discussed in detail, network-based pathways analysis (NPA), metabolic flux analysis (MFA), and flux balance analysis (FBA). Four types of metabolic pathways are also compared to clarify the subtle differences among them. The second part is devoted to interval methods for constraint-based models. The first contribution is an interval approach to traditional MFA, particularly useful to estimate the metabolic fluxes under data scarcity (FS-MFA). These estimates provide insight on the internal state of cells, which determines the behaviour they exhibit at given conditions. The second contribution is a procedure for monitoring the metabolic fluxes during a cultivation process that uses FS-MFA to handle uncertainty. The third part of the document addresses the use of possibility theory. The main contribution is a possibilistic framework to (a) evaluate model and measurements consistency, and (b) perform flux estimations (Poss-MFA). It combines flexibility on the assumptions and computational efficiency. Poss-MFA is also applied to monitoring fluxes and metabolite concentrations during a cultivation, information of great use for fault-detection and control of industrial processes. Afterwards, the FBA problem is addressed. A possibilistic approach is derived to get predictions under the assumption that cells have evolved to be optimal (Poss-FBA). It captures alternate optima and grades sub-optimality, thus relaxing the original assumption. The last contribution is a procedure to validate constraint-based models when data are scarce. This procedure mitigates validation problems with small metabolic networks. This thesis highlights the importance of accounting for uncertainty when modelling living cells and promotes a constraint-based perspective: if we cannot exactly model how cells operate, use the knowledge available to distinguish what is possible from what is not. Following this idea, methods are proposed that start by representing the available knowledge and its uncertainty, and then exploit this representation to generate reliable new information.
In the following site the reader will find updated information regarding this thesis. http://science.ensilicio.com/Thesis
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Participating in the Biocomplexity XI Workshop: The evolution of cooperation. Dec. 3rd-Dec. 5th, 2010 Bloomington, IN, USA
Cooperation occurs throughout the biological world, and similar Genes organize into genomes, cells into multicellular organisms,
Cooperation benefits a society, while evolution selects at the level What is an individual? Is individuality discrete or continuous? When does stable cooperation require enforcement? Can the fitness The intra-cellular cooperation of genes, molecular machines, and Is an ecosystem composed of individuals, or is an individual
This workshop will investigate these subtle and provocative issues, Talks will cover subjects ranging from cooperation inside of cells,
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Biocontrol member Alejandro Vignoni, participates in the IGEM Valencia 2010 Team, at the IGEM competition, in MIT, Cambridge, MA from 5-8 Dec 2010. The International Genetically Engineered Machine competition (iGEM) is the premiere undergraduate Synthetic Biology competition. Student teams are given a kit of biological parts at the beginning of the summer from the Registry of Standard Biological Parts. Working at their own schools over the summer, they use these parts and new parts of their own design to build biological systems and operate them in living cells. This project design and competition format is an exceptionally motivating and effective teaching method. |
Friday 19th February.
A meeting will take place at Biopolis S.L. premises devoted to discuss on Model Reduction Techniques.
Recent work on the application of cross-validation corrected PCA ,and algebraic methods will be presented.
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In systems biology, one of the ultra goals is to engineer unnatural organic molecules
that function in living systems to investigate natural biological phenomena and for
a variety of applications. In control engineering, the overall aim is to synthesize
controllers which can achieve desired performance. The notion of feedback, which is
the core of control engineering, is now a central recurring theme in the design of
biological regulatory networks. In fact, feedback is so prevalent in biological
systems that it can be found at all levels of organization, from the molecular and
cellular levels, to the organism and ecological levels. It is impossible to overstate
the importance of feedback as a strategy for the maintenance and evolution of life.
Therefore, it is reasonable to expect that ideas from control theory will lead to new
understanding of the underlying biological processes, and therefore have potential
applications in system biology and synthetic biology.
The complexity of biological networks (BNs) poses many challenges for scientists and
engineers. In particular, the biological systems have apparently become dependent on
the complex infrastructure of the networks to such an extent that it is difficult to
analyse and control these networks thoroughly with our current capabilities. Therefore,
there is an urgent need to research into modelling, analysis, synchronization and control
of BNs using the available systems and control theory. Although many fundamental questions
have been addressed with the hope to understand network structures and dynamic properties,
some major problems have not been fully investigated, such as the behaviours of switching,
oscillating, stability, synchronization and chaos control for BNs, as well as their
applications in systems biology and bioinformatics.
This special issue aims to bring together the latest advances in analysis and control of
biological networks, which comprise gene regulatory networks, signal transduction
networks,
metabolite networks and intra-species or interspecies communication networks in microbial
communities. Topics of this special include, but are not limited to the following aspects:
(1) systems and control analysis of BNs; (2) Modelling of BNs; (3) dynamics analysis of
regulatory motifs; (4) robustness and fragility analysis of BNs; (5) synchronization of
BNs; (6) design of synthetic BNs, and (7) methods and algorithms for BN analysis.
Guest Editors:
Prof. Luonan Chen
Osaka Sangyo University
Japan
E-mail: chen@eic.osaka-sandai.ac.jp
Prof. James Lam
The University of Hong Kong
China
E-mail: james.lam@hku.hk
Prof. Zidong Wang
Brunel University
United Kingdom
E-mail: Zidong.Wang@brunel.ac.uk
Important Dates:
Jan. 1, 2010 Call for Papers
June 30, 2010 Deadline for Paper Submission
Oct. 31, 2010 Completion of First Review
Feb. 28, 2011 Completion of Final Review
Sep. 30, 2011 Publication (Tentatively Vol.13, No.5)
Potential authors are strongly encouraged to upload the electronic file of their manuscript
(in PDF format) through journal website: http://mc.manuscriptcentral.com/asjc.
If you encounter any submission problem, feel free to contact Prof. Li-Chen Fu, Editor-in-Chief:
Professor Li-Chen Fu
Department of Electrical Engineering, EE II-524
National Taiwan University
Taipei 10617, Taiwan
Tel: +886-2-3366-3558
Fax: +886-2-2365-4267
E-mail: lichen@ntu.edu.tw
All submission should include a title page containing the title of the paper, an abstract
and a list of keywords, authors’ full names and affiliations, complete postal and electronic
address, phone and fax numbers. The contacting author should be clearly identified. For detailed
submission guidelines, please visit http://www.ajc.org.tw.
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The symposium on Computer Applications in Biotechnology is organized every three years and aims at stimulating contacts between specialists active in academic research and industrial development in all major areas in biotechnology, where computers are used to support bioprocess design, supervision, diagnosis, operation, optimization and control.
Flyer: http://cab2010.org/images/documents/cab_2010.pdf
More info at: http://cab2010.org/
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The meeting will take place in the premises of the National Center of Biotechnology in Madrid, starting on December 13th and finishing on December 15th. The event will be funded by the CSIC, the Spanish Ministry of Science and Innovation as well as by the TARPOL and EMERGENCE Networks of the EC.
The meeting will bring together a panel of high-level speakers, mostly from Research Centers south the Alps or with a southern european/mediterranean background -but working in other countries. The objective of this meeting is to communicate frontline research in the fields of Systems/Synthetic Biology and to foster synergies between often fractionated SB communities in the extended southerly regions of Europe.
Contact:
]]>El curso va destinado a licenciados –un máximo de 30– implicados en un trabajo dentro de la BS. Cada alumno tendrá una beca de ayuda a estancia, y el curso será gratuito. En principio cubriría a un becario por grupo inscrito en la REBS y el resto iría a una convocatoria pública. La inscripción la deben hacer a través del correo electrónico de la REBS (info@sysbiol.net), justificando la necesidad de realizarlo y los meritos, que deberán ser acreditados en caso de concesión. Fecha límite: 15 de Abril de 2009. Podrá acceder al Programa y al Triptico en la página web de la REBS.