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Mon, 29 Mar 2010 09:15:07 +0000

- The main objective of the project is to obtain via a modelling and simulation approach a better understanding of the structure and dynamics of metabolic pathways of gene regulatory networks involved in the morphogenesis of animals and plants. We will concentrate on the development of two kind of sponges and on the organogenesis of carpel and anthers of a flowering plant. We will tackle the complexity involved in these processes by using concepts and tools arising from complex systems science. On the one side morphogenesis of sponges and organogenesis in flowering plants share many common concerns and approaches which justify the feasability of tackling them within a common complex systems framework. On the other side they consider distinguished features and methods of analysis that will guarantee a minimal genericity in the tools designed for the modelling process. The following problems will be addressed: provide a general model allowing to describe the underlying complex systems at different hiearchical levels in the same formalism; provide tools to extract concrete models description from experimental data; provide a way to conduct in-silico experiments. These tools will be applied on real data in order to significatively progress on the initial biological problems and will also be used to develop a modelguided data collection process. Moreover, the simulation tools will be modular enough to be customised or extended in the future for modelling complex systems arising from other fields. Our global goals can be summarised by three measurable and verifiable objectives: to build patiotemporal atlases of gene expression for flowering plants (for carpel and anther) and one for sponges; to web design, implement and finely tune models of development for reproductive organs in flowering plants and for sponges; to develop a customisable modelling and simulation platform adapted to the study of ~~betsbonuscodes.com" rel="external nofollow">free~~ complex systems in the context of development biology.

+ The main objective of the project is to obtain via a modelling and simulation approach a better understanding of the structure and dynamics of metabolic pathways of gene regulatory networks involved in the morphogenesis of animals and plants. We will concentrate on the development of two kind of sponges and on the organogenesis of carpel and anthers of a flowering plant. We will tackle the complexity involved in these processes by using concepts and tools arising from complex systems science. On the one side morphogenesis of sponges and organogenesis in flowering plants share many common concerns and approaches which justify the feasability of tackling them within a common complex systems framework. On the other side they consider distinguished features and methods of analysis that will guarantee a minimal genericity in the tools designed for the modelling process. The following problems will be addressed: provide a general model allowing to describe the underlying complex systems at different hiearchical levels in the same formalism; provide tools to extract concrete models description from experimental data; provide a way to conduct in-silico experiments. These tools will be applied on real data in order to significatively progress on the initial biological problems and will also be used to develop a modelguided data collection process. Moreover, the simulation tools will be modular enough to be customised or extended in the future for modelling complex systems arising from other fields. Our global goals can be summarised by three measurable and verifiable objectives: to build patiotemporal atlases of gene expression for flowering plants (for carpel and anther) and one for sponges; to web design, implement and finely tune models of development for reproductive organs in flowering plants and for sponges; to develop a customisable modelling and simulation platform adapted to the study of free complex systems in the context of development biology.

Modelers Forums

Thu, 25 Mar 2010 13:11:58 +0000

- >>Important: Main information will be diffuse by our main newsletter. Please subscribe!
+ Important: Main information will be diffuse by our main newsletter. Please subscribe!

Events and Documents

Thu, 25 Mar 2010 12:02:35 +0000

+
+
Conferences
+
+ 1) 11th International Coral Reef Symposium, Fort Lauderdale, Florida, USA, July 7-11, 2008.
+
+ • Conference Paper :
+ Jaap Kaandorp : A computational model for gene regulation of early development in the sea anemone nematostella vectensis and the coral Acropora millepora
+
+
+ 2) HFSP meeting, Berlin, July 2008
+
+ • Conference Paper :
+ Jan Traas : "The control of plant shape."
+
+ 3) FESPB, meeting, Tampere, Finland, August 2008
+
+ • Conference Paper : Plenary lecture
+ Jan Traas : "The shoot apical meristem and organ initiation."
+
+
+ 4) COCOA 2008, 2nd Annual Confernece on Combinatorial and Applications, St. John’s, Newfoundland, Canada
+
+ • Conference Paper :
+ Leo Liberti, Automatic generation of symmetry-breaking constraints, COCOA08 Proceedings, LNCS, accepted for publication.
+ http://www.lix.polytechnique.fr/~liberti/autgensymm.pdf
+
+
+ 5) CLAIO 2008, Congreso Latino Ibero Americano de Investigacion de opraciones cartagenas de Indias, Colombia
+
+ • Conference Paper:
+ Camilo La Rota, Fabien Tarissan, Leo Liberti, Inferring parameters in Genetic Regulatory Networks, CLAIO 2008 Proceedings, accepted for publication.
+
+ http://www.lix.polytechnique.fr/~liberti/grnclaio.pdf
+ or
+
+ http://www.morphex.org/tiki-download_wiki_attachment.php?attId=326&page=Dissemination
+
+
+ 6) ECCS 08, The European Conference on Complex Systems, 2008,September 14-19 at the Hebrew University of Jerusalem, Israel.
+
+ • Conference Paper:
+ Author: Fabien Tarissan, Camilo La Rota and Leo Liberti. Title “Network reconstruction: a mathematical programming approach”, European Conference on Complex Systems (ECCS’08) accepted for publication. This article presents a method employing mathematical programming and global optimization techniques for solving inverse problems arising in biological regulatory network reconstruction. This problem consists in estimating unknown parameters of a model that describe the structure and dynamics of a biological system from a set of experimental observations and can be naturally cast as an optimization problem: choose the parameter values minimizing a given distance between the observed and estimated values of some observable variables. This minimization is subject to constraints derived from the models.
+
+ http://www.lix.polytechnique.fr/~liberti/grneccs.pdf
+ or
+ http://www.morphex.org/tiki-download_wiki_attachment.php?attId=327&page=Dissemination
+
+
+ 7) AINA’08, International Conference on Advanced Information Networking and Applications
+
+ • Conference Paper:
+ Jacques Demongeot, Michel Morvan, and Sylvain Sené. Impact of Fixed Boundary Conditions on the Basins of Attraction in the Flower’s Morphogenesis of Arabidopsis Thaliana. In IEEE Proceedings of the Workshops of the International Conference on Advanced Information Networking and Applications (AINA’08). In press.
+
+ 8) CISIS’08, International Conference on Complex, Intelligent and Software Intensive Systems 2008.
+
+ • Conference Paper:
+ Jacques Demongeot, Michel Morvan, and Sylvain Sené. Robustness of Dynamical Systems Attraction Basins Against State Perturbations: Theoretical Protocol and Application in Systems Biology. In IEEE Proceedings of the International Conference on Complex, Intelligent and Software Intensive Systems 2008 (CISIS’08). In press.
+
+ 9) ACRI 2008
+
+ • Conference Paper:
+
+ Jean-Baptiste Rouquier and Michel Morvan. Combined eﬀect of topology and synchronism perturbation on cellular automata : Preliminary results. In ACRI, 2008. accepted. This paper studies the way different structural perturbations can either sum up or nnihilate depending on the underlying dynamical system – in this case, depending on the underlying cellular automata.
+
+ 10) Journées Modélisation, optimisation et analyse statique, CIRM, Marseille, France
+
+ 11) Journée Optimeo, Université Paris-Sud XI, Orsay, France
+
+ 12) Automatic Reformulation Search Workshop (ARS08), LIX, Paris
+
+ 13) Mission in Boston, Harvard, 02 February, 2009.
+
+ • Presentation
+
+ http://www.morphex.org/tiki-download_wiki_attachment.php?attId=325&page=Dissemination
+
+ 14) CSHL meeting: PLANT GENOMES:GENES, NETWORKS & APPLICATIONS. Cold Spring Harbor, US. March 2009
+
+ • Conference Paper: Jaan Traas
+ The shoot apical meristem and organ initiation."
+
+ 15) ISNB 2009, the 6th International Symposium On Networks In Bioinformatics, Science Park Amsterdam, 22-23 April, 2009, http://isnb.amc.uva.nl/isnb2009/.
+
+ • Abstract
+
+ The 6th International Symposium on Networks in Bioinformatics (ISNB 2009) is scheduled on 22 and 23 April 2009 and is likely to continue its success from previous years in bringing different disciplines together to discuss ongoing research in bioinformatics and biology of networks. The focus of 6th International Symposium on Networks in Bioinformatics will be on biological networks such as metabolic networks, signal transduction pathways and genetic regulatory networks. This year we also aim to include topics like modeling of cells, tissues, gene regulation and biomineralisation. We also want to invite researchers working on gene networks in plants (e.g. Arabidopsis), model organisms such as Drosophila and organisms with a relatively simple and basal body plan such as sponges and scleractinian corals.
+ Understanding of these networks is crucial for understanding molecular and cellular processes in the organism or system under study. This field is subject of lively research and both experimental and computational approaches are used to elucidate the biological networks. The bioinformatics of biological networks involves a broad range of research and approaches. Research includes the identification of regulatory elements in DNA, developmental biology, genome context analysis, modelling and simulation of pathways, reconstruction of pathways from experimental data, visualization of pathways, and the representation of pathways in database, graphs and mark-up languages.
+
+ INVITED SPEAKERS
+
+ Mark Q. Martindale (University of Hawaii, USA), Mark Biggin (Lawrence Berkely National Laboratory, USA), Noam Kaplan (Weizmann Institute Israel), Filipa Alves (Center for Developmental Biology, Portugal), Shannon K. Mcweeney (Oregon Health and Science University, USA), Yves Fomekong Nanfack (University of Amsterdam), Armand Bankhead (Knight Cancer Institute, USA)
+
+ • Conference Paper:
+ Jaan Traas
+
+
+
+ 16) NetSciCom’09, NetSciCom 2009, First IEEE International Workshop on Network Science For Communication Networks, April 24, 2009 - Rio de Janeiro, Brazil
+ http://netscicom2009.asu.edu/
+
+ SCOPE:
+ Network Science is a newly emerging discipline with applications in a variety of domains, such as, Communication Networks, Power Grid Networks, Transportation Networks, Social Networks, Biological Networks and Economics. Designing complex communication networks of the future needs a deep understanding of the interplay between the physical-, the communication- and the social networks involved. An understanding of such interdependency can only be achieved by closer interaction between Network Scientists, Communication Network Designers, and Social and Behavioral Scientists. The goal of this workshop is to a provide a forum where this diverse group of researchers can meet and exchange ideas that will lead to deeper insights into the design of robust, efficient and complex communication networks of the future.
+
+ TOPICS OF INTEREST:
+
+ The topics of this workshop lie at the intersection of Network Science and Communication Network Design - including Topology Design and Analysis, Traffic Modeling, Traffic Routing, Social Media Analysis:
+ blogs and friendship networks, Bio-inspired networks, Internet scale measurement and analysis of online communities, Social network analysis with mobile phone data, Interdependency between power grid, communication and transportation networks.
+
+ • Conference Paper:
+ Efficient Measurement of Complex Networks Using Link Queries” Fabien Tarissan, Matthieu Latapy and Christophe Prieur. In Proceedings of the IEEE International Workshop on Network Science For Communication Networks (NetSciCom’09), to appear
+
+ http://www.lix.polytechnique.fr/~tarissan/articles/eff.pdf
+
+ 17) Morphogenesis in Living Systems Conference - Paris May 14th-May 17th 2009
+ http://rnsc.fr/MLS-2009
+
+ • Abstract
+ • Presentation
+ Eric Boix and Jaap Kaandorp
+
+ http://www.morphex.org/tiki-download_wiki_attachment.php?attId=321&page=Dissemination
+
+ Jan Traas : "Morphogenesis in plants: from genes to shape".
+
+
+ 18) CTW 09, Cologne Twente Workshop 2009, Paris, France, June 2-4 2009
+ http://www.lix.polytechnique.fr/ctw09/
+
+ • Conference Paper:
+ Inferring Update Sequences in Boolean Gene Regulatory Networks” Fabien Tarissan and Camilo La Rota. In Proceedings of the Cologne-Twente Workshop on Graphs and Combinatorial Optimization 2009 (CTW’09), to appear.
+
+ http://www.morphex.org/tiki-download_wiki_attachment.php?attId=328&page=Dissemination
+
+ or
+ http://www.lix.polytechnique.fr/~tarissan/articles/asynch.pdf
+
+ 19) Séminaire du laboratoire LIFL, Lille, France
+
+ 20) Séminaire du laboratoire IBISC, Evry, France
+
+ 21) Séminaire de l'équipe Bioinformatique, LRI, Orsay, Paris, France
+
+ 22) Séminaire de l'équipe Symbiose,Irisa, Rennes, France
+
+ 23) 6th European Conference on Marine Natural Products, 19-23 July 2009, Porto, Portugal
+
+ • Conference Paper:
+ W.E.G. Müller and H.C. Schröder: The power of marine genomics. Abstract No. PL 08
+
+ 24) Honda Reseach, Offenbach, Germany, 2008
+ • Invited Presentation: Jaap Kaandorp
+
+ 25) National University of Singapore, 2009
+ • Invited Presentation: Jaap Kaandorp
+
+ 26) Centre for Scientific Computing & Complex Systems Modelling (SCI-SYM), Dublin, 2009
+ • Invited Presentation: Jaap Kaandorp
+
+ 27) International Workshop on Engineering Principles of Innovation in swarm-made Architectures, Venice, Italy, September 2009.
+ • Invited Presentation: Jaap Kaandorp
+
+ 28) University of Bologna, Italy, 2009.
+ • Invited Presentation: Jaap Kaandorp
+
+ 29) Workhop on Discrete Models of Biological Networks: from Structure to Dynamic. CIRM (Marseille Luminy), Francia. November 3-7, 2008.
+
+ • Conference Paper:
+ J. Aracena. On the number and robustness of attractors in Bolean networks.
+
+ 30) Coloquio DIM, Universidad de Concepción, Chile, October 21, 2009.
+
+ • Conference Paper:
+ Julio Aracena. Combinatoria de grafos de actualización de redes discretas.
+
+ 31) European Conference on Complex Systems. University of Warwick. September 21-25, 2009.
+
+ • Poster:
+ Aracena J., Gómez L., L. Salinas. Limit cycles and update schedules in Boolean networks,
- Leo Liberti, Sonia Cafieri and Fabien Tarissan: Reformulations in Mathematical Programming: A Computational Approach”. In A. Abraham, A.-E. Hassanien, P. Siarry (eds.), Foundations of Computational Intelligence, Vol. 3, Studies in Computational Intelligence series, 203:153-234, Springer, New York, 2009
+ 1) J.A. Kaandorp, J.G. Blom, J. Verhoef, M. Filatov, M. Postma and W.E.G. Müller, Modelling genetic regulation of growth and form in a branching sponge Proc. Roy. Soc. B. 275:2569-2577, 2008

2) Jacques Demongeot, Christelle Jézéquel, and Sylvain Sené. Boundary Conditions and Phase Transitions in Neural Networks. Theoretical Results. Neural Networks. Accepted if revised.

3) Jacques Demongeot and Sylvain Sené. Boundary Conditions and Phase Transitions in Neural Networks. Simulation Results. Neural Networks. Accepted if revised.

4) Leo Liberti, Carlile Lavor, Nelson Maculan, Marco-Antonio Chaer Nascimento, Reformulation in mathematical programming: an application to quantum chemistry, Discrete Applied Mathematics, accepted for publication.

5) Hanif Sherali, Leo Liberti, Reformulation-Linearization Methods for Global optimization, in P. Pardalos and C. Floudas (eds.), Encyclopedia of Optimization, 2nd Edition, accepted for publication. Encyclopedia entry.

6) Martin Nilsson Jacobi and Olof Görnerup: Aggregation of variables in linear dynamical systems and lumping of states in Markov chains: "We present a method for identifying coarse grained dynamics through aggregation of variables or states in linear dynamical systems. The condition for aggregation is expressed as a permutation symmetry of a set of dual eigenvectors of the matrix that defines the dynamics. The applicability of the condition is illustrated in examples from three different generic classes of reducible Markov chains: Systems consisting of independent subsystems, dynamics with symmetries, and nearly decoupled Markov chains." Under submission.

7) Martin Nilsson Jacobi and Olof Görnerup: A dual eigenvector condition for strong lumpability of Markov chains: “Necessary and sufficient conditions for identifying strong lumpability in Markov chains are presented. We show that the states in a lump necessarily correspond to identical elements in eigenvectors of the dual transition matrix. If there exist as many dual eigenvectors that respect the necessary condition as there are lumps in the aggregation, then the condition is also sufficient. The result is demonstrated with two simple examples.” Under submission.

8) Martin Nilsson Jacobi and Olof Görnerup: Ontological Simulation: Mimesis and animation. The present paper focuses on what is here termed “ontological Simulation” and argues that this class of models can be usefully defined and has enabled an epistemologically relevant scientific strategy that is becoming more and more important: A quantitative treatment of descriptive hypotheses. Ontological simulation can be differentiated from other types of modeling by that it relies on causal similarity in addition to representation: The modeling of phenomena not directly but via mimesis of the ontology (i.e. the “underlying physics”) of systems and a subsequent animation of the resulting model ontology as a dynamical system to thereby render a phenomenology. Two main types of strategies are pursued using ontological simulation: i) Direct simulation where a mimicked ontology is used basically for making complex phenomenon-level mappings or computations. ii) Inverse simulation – which is the strategy that holds epistemological significance – where the model ontology is viewed as a hypothesis regarding the ontology of the target system. Inverse ontological simulation is argued to be one of the principal tools for hypothesis-testing in the complex systems approach to science. It makes possible a quantitative approach to hypotheses about the structure and function of systems that would previously only have been amenable to qualitative study. Under submission.

9) M. Morvan, and J.-B. Rouquier. Coalescing cellular automata — synchronizing CA by common random source and varying asynchronicity. Journal of Cellular Automata, to appear, 2008. This paper deals with the study of dynamical properties of cellular automata submitted to perturbations.

10) W.E.G. Mueller, A. Boreiko, U. Schloemacher, X. Wang, M. Nawaz Tahir, W. Tremel, D. Brandt, J.A. Kaandorp and H. C. Schroeder, Fractal-related assembly of the axial filament in the demosponge Suberites domuncula: relevance to biomineralization and the formation of biogenic silica, Biomaterials 28:4501-4511, 2007

11) M. Wiens, S.I. Belikov, O.V. Kaluzhnayaa, T. Adella, H.C. Schrödera, S. Perovic-Ottstadt, J.A. Kaandorp and W.E.G. Müller, Regional and modular expression of morphogenetic factors in the demosponge Lubomirskia baicalensis Micron, 39:447-460, 2008

12) Y. Fomekong Nanfack, J.A. Kaandorp and J.G. Blom Efficient parameter estimation for spatio-temporal models of pattern formation: Case study of Drosophila melanogaster Bioinformatics 23:3356-3363, 2007

13) W.E.G. Müller and I.M. Müller: Porifera: an enigmatic taxon disclosed by molecular biology/cell biology. In: Porifera Research: Biodiversity, Innovation and Sustainability (M.R. Custódio, G. Lôbo-Hajdu, E. Hajdu, G. Lôbo-Hajdu and G. Muricy, eds). Proceedings of the 7th International Sponge Symposium. Série Livros 28, Museu Nacional, Rio de Janeiro, pp. 89-106 (2007).

14) S.I. Belikov, O.V. Kaluzhnaya, H.C. Schröder, I.M. Müller and W.E.G. Müller: Lake Baikal endemic sponge Lubomirskia baicalensis: Structure and organization of the gene family of silicatein and its role in morphogenesis. In: Porifera Research: Biodiversity, Innovation and Sustainability (M.R. Custódio, G. Lôbo-Hajdu, E. Hajdu, G. Lôbo-Hajdu and G. Muricy, eds). Proceedings of the 7th International Sponge Symposium. Série Livros 28, Museu Nacional, Rio de Janeiro, pp. 179-188 (2007).

15) H.C. Schröder, F. Natalio, M. Wiens, M.N. Tahir, M.I. Shukoor, W. Tremel, S.I. Belikov, A. Krasko and W.E.G. Müller: The 2'-5'-oligoadenylate synthetase in the lowest metazoa: isolation, cloning, expression and functional activity in the sponge Lubomirskia baicalensis. Molec. Immunol. 45, 945-953 (2008).

16) Eric Goles and Lilian Salinas: Filters for Boolean networks, in progress

17) Eric Golès, Moreira: Simulation of different kinds of iteration modes and filters for Boolean networks, in progress

18) Eric Goles and Lilian Salinas: Comparison between parallel and serial dynamics of Boolean networks, Theoretical Computer Science 396 (2008), 247-253.

19) Julio Aracena, Eric Goles and Lilian Salinas, Moreira: On the robustness of update schedules in Boolean networks. Accepted. Biosystems; DOI 10.1016/j.biosystems.2009.03.006

20) O. Görnerup and M. Nilsson Jacobi, An algorithm for aggregating variables in linear dynamical systems.

21) O. Görnerup and M. Nilsson Jacobi, Inference of higher order substitution dynamics by Markov chain lumping, arXiv:0810.4860v1

22) M. Nilsson Jacobi, A robust spectral method for finding lumpings and meta stable states of non-reversible Markov chains, arXiv:0810.1127v1.”

23) Y. Fomekong Nanfack, M. Postma J.A. Kaandorp, Inferring Drosophila gap gene regulatory network: a parameter sensitivity and perturbation analysis (BMC Systems Biology, 3:94, 2009)

24) Fomekong-Nanfack M. Postma and J. A. Kaandorp, Inferring Drosophila gap gene regulatory network: a systematic model analysis.

25) Leo Liberti, Sonia Cafieri and Fabien Tarissan: Reformulations in Mathematical Programming: A Computational Approach”. In A. Abraham, A.-E. Hassanien, P. Siarry (eds.), Foundations of Computational Intelligence, Vol. 3, Studies in Computational Intelligence series, 203:153-234, Springer, New York, 2009.

- Leo Liberti, Reformulations in Mathematical Programming: Definitions and Systematics, RAIRO-RO, 43(1):55-86,2009.

http://www.lix.polytechnique.fr/~liberti/defpaper.pdf
+ 26) Leo Liberti, Reformulations in Mathematical Programming: Definitions and Systematics, RAIRO-RO, 43(1):55-86,2009.

http://www.lix.polytechnique.fr/~liberti/defpaper.pdf

27) D. Krob, Y. Caseau and S. Peyronnet, Complexité des systèmes d’information : une famille de mesures de la complexité scalaire d’un schéma d’architecture, Génie Logiciel, 82, 23-30, 2007

28) D. Krob and S. Bliudze, Modeling of Complex system – System as data-flow machines, Fundamenta Informaticae, Special Issues : Machines, Computations and Universality, 91,1-24, 2009

29) M. Nilsson Jacobi and o. Görnerup, A spectral method for aggregating variables in linear dynamical systems with application to cellular automata renormalization, Advances in Complex System, 12 (2), 1-25, 2009

30) W.E.G. Müller, M.R. Custódio, M. Wiens, C. Zilberberg, A. Châtel, I.M. Müller and H.C. Schröder: Effect of bacterial infection on stem cell pattern in Porifera. In: Stem Cells in Marine Organisms (B. Rinkevich and V. Matranga, eds.). Springer-Press, Berlin, pp. 309-336 (2009).

31) M. Wiens, P. Wrede, V.A. Grebenjuk, O.V. Kaluzhnaya, S.I. Belikov, H.C. Schröder and W.E.G. Müller: Towards a molecular systematics of the Lake Baikal/Lake Tuva sponges. In: Biosilica in Evolution, Morphogenesis and Nanobiotechnology: Case Study Lake Baikal (W.E.G. Müller and M.A.Grachev, eds.). Prog. Mol. Subcell. Biol. 47, 111-144 (2009).

32) M. Wiens, V.A. Grebenjuk, H.C. Schröder, I.M. Müller and W.E.G. Müller: Identification and isolation of a retrotransposon from the freshwater sponge Lubomirskia baicalensis: implication in rapid evolution of endemic sponges. In: Biosilica in Evolution, Morphogenesis and Nanobiotechnology: Case Study Lake Baikal (W.E.G. Müller and M.A.Grachev, eds.). Prog. Mol. Subcell. Biol. 47, 207-234 (2009).

33) W.E.G. Müller, M. Kasueske, X.H. Wang, H.C. Schröder, Y. Wang, D. Pisignano and M. Wiens: Luciferase a light source for the silica-based optical waveguides (spicules) in the demosponge Suberites domuncula. Cell. Molec. Life Sci. 66, 537-552 (2009).

34) J. Cui, J.A. Kaandorp and C.M. Lloyd Simulating In Vitro Transcriptional Response of Zinc Homeostasis System in Escherichia coli, BMC Systems Biology 2:89, 2008

35) M. Ashyraliyev, Y. Fomekong Nanfack, J.A. Kaandorp, J.G. Blom Systems biology: Parameter estimation for biochemical models, FEBS journal 276:886-902, 2009

36) J.Cui, J.A. Kaandorp, P.M.A. Sloot, P. Thiagarajan, C. Lloyd, M. Filatov Calcium homeostasis and signalling in yeast cells and cardiac myocytes FEMS Yeast Research (in press)

37) Y. Fomekong Nanfack, M. Postma J.A. Kaandorp, Inferring Drosophila gap gene regulatory network: pattern analysis of gene expression profiles and stability analysis (BMC Research Notes, in press)

38) J. de Jong, M. Postma, H. Marlow, C. Magie, M.Q. Martindale and J.A. Kaandorp. Extraction and analysis of quantitative spatio-temporal gene expression in early embryogenesis in the cnidarian Nematostella vectensis (in prep.)

39) J. de Jong, M. Postma, H. Marlow, C. Magie, M.Q. Martindale and J.A. Kaandorp. A proposal for a model of spatio-temporal gene regulation expression in early embryogenesis in the cnidarian Nematostella vectensis (in prep.)

40) C. Tamulonis, M. Postma, H. Marlow, C. Magie, J. de Jong and J.A. Kaandorp Morphometrics and Modeling of Gastrulation in the starlet sea anemone – Nematostella vectensis (submitted)

41) Aracena, J., Goles, E., Moreira, A., Salinas, L. On the robustness of update schedules in Boolean networks. Biosystems 97 (2009), 1–8.

42) Aracena, J. On the number of fixed points in regulatory Boolean net- works. Bulletin of Mathematical Biology 70 (5) (2008), 1398-1409.
+ 43) Aracena, J., Gómez, L and Salinas, L. Limit cycles and update digraphs in Boolean networks,2009 (in progress)

CoSMo Methodology

Thu, 25 Mar 2010 11:40:39 +0000

- DOWNLOAD CoSMo HOWTO
+
DOWNLOAD CoSMo HOWTO (PDF)

Scientific Program

Thu, 25 Mar 2010 11:03:45 +0000

+ The Morphex project has been organised around three strongly related directions, organised around the three scientific work packages.
+
+
Collecting biological data, extracting model and problem characteristics and implementing first versions of models, tools and protocols.
+ o Data for Arabidopsis and sponges have been collected and placed in a knowledge base built by the project and easily accessible to all projects participants (morphopedia.org).
+ o A quantification of gene expression pattern tool has been implemented.
+ o A 2D cell-based model of gastrulation has been implemented. This model is currently extended in 3D.
+ o A connexionist model of gene regulation based on partial differential equations has been implemented.
+ o A model of growth and development of the adult sponge has been implemented.
+ o A geometrical model of cell has been proposed and implemented.
+ o An algorithm for inferring networks and model parameter has been implemented.
+
+
+
Proposing a definition of the meta-model, designing tools and protocols and provide results on simplified models.
+ o The meta-model has been defined.
+ o Protocols have been designed for measuring robustness of models to different kind of perturbations.
+ o Tools have been designed for finding hierarchies in models, reconstructing gene networks, inferring networks and model parameters and transforming gene networks into simpler networks having the same behaviour (network filtering).
+ o Protocols have been designed to extract gene networks from data for plants and animals.
+ o Cellular Potts model has been implemented to test the meta-model.
+
+
+
Providing a database for biological data and implement the modelling platform based on the meta-model characterisation.
+ o A technical survey on existing platform has been realised.
+ o An environment for development has been realised.
+ o The infrastructure of the biological database has been realised.
+ o A first prototype of the software architecture for the implementation of the meta-model has been conceived and implemented.
+ o A first prototype of the architecture for grid integration has been conceived and implemented.
+ o A framework for protocols design has been realised.
+
+ All the results obtained during the period have been diffused in the community, mainly by participation of researchers involved in the project to workshops and conferences and/or by publications of papers in journal or conference proceedings.
+
+ For more information, see "Events and Documents"
+

Morphex Partners

Wed, 24 Mar 2010 18:14:02 +0000

Overview

Wed, 24 Mar 2010 18:12:59 +0000

- Project cost ~~EU funding~~r />
€ 2 222 961.60 € 1 599 990.40

Project referencer />
+

_cost">Project cost</h2>
€ 2 222 961.60 />

EU funding

€ 1 599 990.40

_reference">Project reference</h2>

Project introduction

Wed, 24 Mar 2010 18:12:52 +0000

+ Biological organisms consist of complex systems involving genes and cells. Growth in plants or animals is governed by what happens inside the cell – regulated by genes and their interactions – and by the exchanges between cells. The goal of the MORPHEX project is to understand how these two levels of complexity combine to create the form of the final organism.
+ This shape-forming or morphogenesis is influenced by both internal and external environmental factors. So it is necessary not only to carry out experiments to see what is happening, but also to model the overall growing process mathematically, and then in the computer. This involves modelling cells, gene regulatory networks and, more difficultly, their interactions and what will emerge from these interactions.
+
+
Plant and sponge development
+
+ MORPHEX will focus on the development of the reproductive organs in the flowering plant Arabidopsis thaliana and that of two sponges, Suberites domuncula and Lubomirskia baikalensis. Sexual organs in flowering plants are formed from populations of dividing undifferentiated stem cells known as shoot apical meristems at the tips and branches of the plant, a process that continues throughout the life of the plant.
+ A great deal of data has been collected about the regulatory networks involved in the development of these organs but its analysis – without the use of modelling and simulation methods – is very difficult. This project will synthesise and expand existing gene-expression studies to determine the mechanics of morphogenesis in the plant, and so improve overall understanding of floral architecture.
+ On the animal side, major advances have been made in modelling quantitative and dynamic pattern formation in sea urchins. Currently, the interest is linking the quantitative model of gene expression in such models to a biomechanical representation, and determining the influence of the environment on the morphogenetic process.
+ The two sponges offer simpler structures than sea urchins for such a study. MORPHEX will model early development before growth in the adult sponge. Optimisation techniques will be applied to determine causal relations between genes in the regulatory networks, as well as the dynamics involved. Spatial and temporal expression patterns in the developmental processes will be simulated and compared with observed patterns. Attempts will also be made to understand the physical coupling between cells and shape formation.
+ Shape creation in the sponges and the plant share many common elements, justifying tackling their morphogenesis in the same complex systems framework. The total number of genes, for example, is around 30 000 for the sponges and about 25 000 for the plant. However, there are sufficient differences in the number of cells involved, the levels of emergence, and the development time scales, to be able to guarantee a generic approach to the design of the modelling and simulation tools.
+ The MORPHEX project will focus on establishing a general model to describe the underlying complex systems, developing tools to extract concrete models based on experimental data provided by biologists, and then determining how to describe, execute and analyse relevant protocols for computer simulation. All this will involve a highly interdisciplinary team bringing together biological development experts, mathematicians, physicists, computer scientists specialised in modelisation, as well as software specialists and engineers from across Europe.
+ Such an approach makes it possible to construct models of complex systems from incomplete, missing or inconsistent data. It also allows prediction and control of the models and the overall systems. As a result, although the focus will be on biological questions, with concrete results expected on how the sexual organs in the flower and the form of sponges develop, the concepts and software tools developed will be sufficiently generic for reuse in other biological or even non-biological domains. Moreover, the ability to model and validate such simulations will bring more rigour to the verification of results in parallel fields.
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Global benefits foreseen
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+ The results should enable us to understand why the growing process sometimes does not work, and how to overcome the problem of a missing gene by manipulating the interaction of surrounding cells. The software and procedures developed in the project will enable the development of model-driven experimentation, markedly cutting the cost of studies on genes, gene interactions and relations with cells.
+ MORPHEX should also lead to the creation of virtual plants or animals, allowing a large part of experimentation to be carried out on the computer rather than on real plants or animals – reducing risks and avoiding ethical dilemmas. This could, for example, enable crop yields and quality to be improved, and make it possible to optimise farming methods to enable us to feed an ever-growing population.
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Scientific Program

Collecting biological data, extracting model and problem characteristics and implementing first versions of models, tools and protocols.

Proposing a definition of the meta-model, designing tools and protocols and provide results on simplified models.

Providing a database for biological data and implement the modelling platform based on the meta-model characterisation.

Morphex Partners

Overview

_cost">Project cost</h2>
€ 2 222 961.60 />

EU funding

€ 1 599 990.40

_reference">Project reference</h2>

EU funding

_reference">Project reference</h2>

Project introduction

Plant and sponge development

Global benefits foreseen

Tiki RSS feed for the wiki pages

CoSMo Platform

Home

Modelers Forums

Events and Documents

Conferences

CoSMo Methodology

Scientific Program

Collecting biological data, extracting model and problem characteristics and implementing first versions of models, tools and protocols.

Proposing a definition of the meta-model, designing tools and protocols and provide results on simplified models.

Providing a database for biological data and implement the modelling platform based on the meta-model characterisation.

Morphex Partners

Overview

_cost">Project cost</h2>€ 2 222 961.60 />EU funding€ 1 599 990.40_reference">Project reference</h2>

EU funding

_reference">Project reference</h2>

Project introduction

Plant and sponge development

Global benefits foreseen

_cost">Project cost</h2>
€ 2 222 961.60 />

EU funding

€ 1 599 990.40

_reference">Project reference</h2>