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of Cambridge, UK Welcome Richard Kitney, Imperial College London, UK Keynote Address 1 Title – To be advised Tom Knight, Computer Science and Artificial Intelligence Lab, MIT, USA Keynote Address 2 From Molecular Machines to Gene-Regulatory Networks in Mammalian Cells Thomas Höfer, German Cancer Research Center, Heidelberg, Germany Lunch Session 1 - Synthetic Biology Chair: Jim Haseloff, University of Cambridge, UK 1.1 Title – To be advised J Haseloff, University of Cambridge, UK 1.2 Rational Design of a Set of Versatile Synthetic Biological Modules B Wang, V Rouilly, R Kitney, Imperial College London, UK, C L Poh, Nanyang Technological University, Singapore A set of modular synthetic biological parts and devices, including NOT, AND, NAND gates, Amplifier etc., are rationally designed by making use of the Hrp regulatory network of Pseudomonas syringae type III secretion system. 1.3 GenoCAD: A Formal Language Tool to Quickly Design and Verify Synthetic Genetic Constructs Y Cai, J Peccoud, Virginia Bioinformatics Institute at Virginia Tech, USA, C Gustafsson, DNA2.0, Inc., USA Genomic Computer Assisted Designer (GenoCAD) is a formal language based tool for design and verification of synthetic genetic constructs. Please visit www.genocad.org for more information. 1.4 Automatic Design Tools for Synthetic Biology G Rodrigo, J Carrera, IBMCP-UPV, Spain, M Suarez, A Jaramillo, École Polytechnique, France We describe our set of computational tools to design biological parts and devices with targeted behaviour. We also show the experimental validation of several of our
13:00 14:00 – 16:00
designs. 15:35 1.5 In Vitro Synthetic Oscillators J Kim, CbsBioscience Inc., Republic of Korea, E Winfree, California Institute of Technology, USA We constructed and characterized three kinds of artificial transcriptional oscillators comprising synthetic DNA switches regulated by RNA signals and only two enzymes. Refreshments Session 2 - Bioinformatics & Computational Biology I Chair: Jean Peccoud, Virginia Bioinformatics Institute at Virginia Tech, USA 2.1 From Registries of Biological Parts to IDE of Genetic Systems J Peccoud, Virginia Bioinformatics Institute at Virginia Tech, USA 2.2 A Spatio-Temporal Algorithm for Resolving Time-Lapse Imaging of Bacteria A Demarez, M Primet, F Taddei, A B Lindner, L Moisan, Paris Descartes University, France To reduce costly human post-processing in the image analysis of bacterial microcolony movies, we propose an automatic algorithm, based on cell shape priors and motion likelihood, that solves segmentation and tracking issues simultaneously. 2.3 Transcription Factor Heterogeneity in Single Human Embryonic Stem Cells M Hemberg, Children's Hospital Boston, USA, A Stahlberg, H Semb, Lund University, Sweden, M Bengtsson, Oxford University, UK, M Barahona, Imperial College London, UK We present a simple stochastic model which describes the distribution of mRNA of six core transcriptional regulators in single human embryonic stem cells. 2.4 Modelling the Endothelial Cell Response to Fluid Flow R J Allen, I D L Bogle, University College London, UK, A J Ridley, King's College London, UK The abstract describes my research in simulating how endothelial cells change their shape in response to a mechanical signal. Sponsors’ Reception and Poster Session 1 - Synthetic Biology P1.01 Riboswitch Development: Design of in Vivo Circuits N Kelley-Loughnane, S Harbaugh, Y Chushak, M O Stone, Applied Biotechnology Branch, Human Effectiveness Directorate, Air Force, USA Bacterial cells expressing the riboswitch containing a theophylline aptamer domain upstream of TEV protease and FRET fusion protein showed a marked optical difference and in silico studies revealed mutant riboswitches that permit novel ligand
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binding. P1.02 The E. coli Integrated Network and the Self Contained Regulatory Loops H Ma, I Goryanin, University of Edinburgh, UK We reconstructed an integrated network of E. coli which includes different types of cellular interactions. Based on it, we introduced the concept of self contained loop and studied the dynamic behaviour of such loops. P1.03 Data Integration to Constrain Computational Modelling in Synthetic Biology J S Hallinan, M Pocock, A Wipat, Newcastle University, UK This paper describes describes ongoing work using data integration and evolutionary computation for designing and modelling genetic circuits. The aim is to produce designs which are biologically plausible enough to be useful in synthetic biology. P1.04 Self-Assembly of Protein Amyloid C F Lee, Oxford University, UK This work studies the thermodynamical properties of protein amyloid self-assembly and the mechanical properties of amyloid fibrils. P1.05 An RNAi-Enhanced Logic Circuit: Cancer-Specific Detection and Destruction A Swaminathan, J Monk, P Cowgill, R Weiss, P Purnick, P Guye, Princeton University, USA We developed an RNAi based logic circuit that detects cancer by evaluating internal cell state through mRNA expression patterns. The circuit controls translation of a pro-apoptotic factor, allowing targeted destruction specific to cancer cells. P1.06 YeSOil A Yeast Sensor for Real Extra Virgin Olive Oil R Bergamasco, M Graziano, M A Ricci, G Russo, L Marucci, M di Bernardo, University of Naples Federico II, Italy, I Cantone, G Cuccato, V Siciliano, M P Cosma, D di Bernardo, TIGEM Telethon Institute of Genetics and Medicine, Italy The goal of our project is to transform Saccharomices cerevisie in a Biological Sensor able to distinguish between Extra Virgin Olive Oil and not Edible Olive Oil constructing a synthetic network. P1.07 Computational Design of Synthetic Molecular Clocks with Targeted Cell Growth G Rodrigo, J Carrera, Instituto de Biologia Molecular y Celular de Plantas, CSICUPV, Spain, B Canton, D Endy, MIT, USA, A Jaramillo, École Polytechnique, France We have designed synthetic molecular clocks following a computational evolution of circuits. In addition, we analyse the in vivo response of the chassis when hosting our synthetic constructs in plasmids P1.08 Biological Implementation of Algorithms A Becerra, F Castro, L Martinez, Y Robles, F Ramirez, P Padilla, E Samra, University of Mexico (UNAM), Mexico, R Palma, Mexican Institute of Technology
(IPN), Mexico We describe theoretical and experimental research on synthetic genetic regulatory networks that are in principle responsible for the creaton of space-time patterns. P1.09 Variety of Dynamics Regimes in Synthetic Genetic Oscillators A Koseska, J Kurths, Potsdam University, Germany, A Zaikin, University of Essex, UK, J Garcia-Ojalvo, Universitat Politecnica e Catalunya, Spain, E Volkov, Lebedev Physical Institute, Russia We study dynamical regimes in a population of synthetic genetic oscillators with autoinducer quorum-sensing and show that antiphase coupling leads to very complex dynamics. 2 - Bioinformatics & Computational Biology P2.01 Molecular and Comparative Modelling and Docking Analysis of CDC4 Proteinin Homo sapiens A Khanzode, PT. Ravishankar Shukla University, India Mutant CDC4 enhance high cyclin E.Over expression of cyclin E is responsible for genetic instability in Breast Cancer. The CDC4 is modeled as receptor and Inhibitors from NCI Database. P2.02 Identifying the Features of co-translational Protein Folding R J K Saunders, C M Deane, University of Oxford, UK A 2D HP model of cotranslational folding. Expected features from thought experiments were not found. New measures identified a bias towards cotranslation in the PDB. Cotranslation is characterised by N-terminal restriction in structure space. P2.03 Use of Virtual Environments and Selection of Measurement Parameters for the Application in the Phobia Treatment M P Torres, Universidad Libre de Colombia, Bogotá, Columbia The current paperwork talks about the efforts to carry out a research with the goal of determining and measuring vital signs on people who are placed a artificially environment with the use of virtual reality. P2.04 ConFunc - Functional Annotation in the Twilight Zone M N Wass, M J E Sternberg, Imperial College London, UK The abstract descirbes ConFunc, a sequence based function prediction method that uses Conserved residues to infer function. The background to the function prediction proble, ConFunc method and benchmarking results are described. P2.05 Development of an Extensible System for the Capture and Storage of Experimental Enzyme Kinetics Data N Swainston, K Smallbone, F Khan, H Messiha, I Spasic, D Kell, University of Manchester, UK, M Golebiewski, S Mir, I Rojas, EML Research, Germany We introduce a relational database repository, data model and submission too for experimental enzyme kinetics data. This provides increased confidence in kinetic parameters, allowing visualisation of the experimental data upon which they were
calculated. P2.06 Morphogenesis in Cellular Automata Models of Non-Linear Media G Juarez Martinez, P Padilla Longoria, University of the West of England, UK We must display how construct some simple Turing patterns with binary semitotalistic cellular automata (CA). Cellular constructions they are reached from macroscopic and microscopic experiments showing our results in hundred or millions of live cells. P2.07 Hierarchy, Abstraction Levels and Emergent Behaviours in Agent-based Simulations of Complex Biological Systems C C Chen, University College London, UK Two types of hierarchy are introduced and provide the basis for a formal definition of levels of abstraction. Relevance to agent-based modelling in Systems Biology is then demonstrated. P2.08 NetBuilder’ - Evolving Genetic Regulatory Networks K Wegner, J F Knabe, C L Nehaniv, M J Schilstra, University of Hertfordshire, UK Genetic regulatory networks form the basic of control for processes in living cells. The structure and dynamics of GRNs are often complex and not fully understood; we will present an evolutionary algorithm filling knowledge gaps. P2.09 Software Development in Modelling and Virtual Exploration of Proteins: An Alternative of IT in Central America A Orozco, University of Costa Rica (UCR), Costa Rica This investigation covered aspects related to the development of bio-software and the necessity that the Central American regions in general consider the activity and development of bioinformatics software oriented to the virtual protein modeling. P2.10 Predicting the Function of the Protein-Tristetraproline N Pillai, A Kumar, Deemed, India Tristetraproline is a protein whose exact function has not been clearly identified. We have used bioinformatics tools extensively to study the sequence and structure of the protein, which predicts the function of the protein. P2.11 A Process Model of Actin Polymerisation L Cardelli, A Phillips, Microsoft Research, UK, E Caron, P Gardner, O Kahramanogullari, Imperial College London, UK Actin is the monomeric subunit of actin filaments which form one of the three major cytoskeletal networks in eukaryotic cells. We give a compositional process calculus model of actin polymerisation. P2.12 Protein Network Alignment for Functional and Structural Annotation W Ali, C Deane, Oxford University, UK We are investigating using protein network alignment to identify conserved functional modules which can be used for annotation transfer.
P2.13 Improving Loop Prediction by Improving Loop Selection Y J Choi, C Deane, Oxford University, UK Constructing a novel score the closest to native conformation from among all the modelled structures available. P2.14 Environment-Specific Substitution Tables for Membrane Proteins S Kelm, C M Deane, University of Oxford, UK, J Shi, UCB Celltech Ltd, UK There currently exist no bioinformatics tools, which accurately predict the structure of membrane proteins. We are using environment-specific substitution tables for membrane proteins to study their molecular evolution. P2.15 Quantitative PCR Primer Database for Terpene Synthesizing Genes in Selected Aromatic Plants M Pattanayak, S K Gupta, F N Jaffery, Industrial Toxicology Research Centre, India PCR Primers database of Terpene synthesizing genes provides opportunity for researchers to analyse terpenes synthesizing pathway in more efficient way. P2.16 Error Tolerance of Gene Networks and their Robustness to Different Timescales S Yeniterzi, C Atilgan, A R Atilgan, Sabanci University, Turkey In this work, we aimed to implement the gene networks computationally and make improvements that involve gene duplication and divergence, error in the expression of genes, and different timescales for genes. P2.17 The Determination of the Basis of HLA Class I Associated Protection in HTLVI Infection A MacNamara, B Asquith, C Bangham, Imperial College London, UK We are using a variety of statistical and modelling approaches to determine the basis of HLA class I associated protection in HTLV-I infection. P2.18 HIV-1 Escape from Cytotoxic T-Lymphocytes in Gag, but not in Other Genes, is Detrimental to the Host U Kadolsky, B Asquith, Imperial College London, UK We investigate the relationship between HIV viral escape in Cytotoxic Tlymphocytes, and use novel techniques to discover and explain why viral mutations in Gag epitopes, and only Gag, are detrimental to the host. P2.19 A General Model for Inferring Boolean Networks from Sparse Gene Expression Data L Yu, S Marshall, University of Strathclyde, UK, P Ghazal, S Watterson, University of Edinburgh, UK We describe an algorithm for inferring Boolean networks with pertubation from microarray data and apply the algorithm to expression data taken from cytomegalovirus infected macrophage cells. P2.20 Statistical Analysis of Time Series of Gene Expression Response to
Mycobacterium Tuberculosis Infection M Berk, G Montana, Imperial College London, UK We apply a curve fitting method to a microarray time series data set in order to identify genes differentially expressed in response to Mycobacterium tuberculosis infection P2.21 Evolution of the G+C Content Frontier in the Rat Cytomegalovirus Genome, and its Effect on Gene Length D Gatherer, Institute of Virology, UK The RCMV genome has a marked discontinuity in its G+C content. Genes to the left of the sudden boundary are shorter. Selective constraint appears to have partially resisted mutational pressure. P2.22 A New Approach to Calculate the Measure of Similarity of 3D Structures in Proteins R Yeniterzi, S Yeniterzi, A Kucukural, U Sezerman, Sabanci University, Turkey In this project Multidimensional Linear Regression is used to find a new function to calculate the measure of similarity between model and native protein structures of CAPS experiment data. P2.23 GeneTrail - Statistical Evaluation and Visualization of Biological Pathways C B Backes, A C K Keller, J K Küntzer, H P L Lenhof, Saarland University Germany, A G Gerasch, M K Kaufmann, Eberhard Karls University, Germany We present GeneTrail, a powerful web-based application that enables users to carry out a statistical evaluation of high-throughput genomic or proteomic datasets and to visualize significant pathways with cutting-edge graph layout algorithms. P2.24 Predicting and Understanding Gene Interaction Networks based on Gene Information F Schubert, V Pancaldi, J Bahler, Wellcome Trust Sanger Institute, UK DNA sequence and other data are used to estimate the distance between genes in an interaction network. A Support Vector Machine is trained to recognize and predict whether a pair of genes is connected. P2.25 Prediction of Glycosylation Sites using Random Forests S E Hamby, J D Hirst, University of Nottingham, UK We predict glycosylation sites using random forests and pairwise patterns obtaining accuracy comparable to the state of the art. We use an aggregate tree, generated from the random forest, to derive biological information about glycosylation. P2.26 Selection of Algal Strain by Sequence Analysis for Biodiesel N Pillai, A Kumar, Deemed, India Biodiesel is the fuel of the future.We need new ways of harnessing renewable source of energy. One such way is using algae for obtaining oil needed for Biodiesel production using bioinformatics. P2.27 Placental Malaria in Different HLA Alleles
P B Karau, University of Nairobi, Kenya In this abstract, bioinformatics benchmarking tools are used to predict binding affinities of pulled p. falciparum sequences. P2.28 Making Sense of Microarray Gene Lists using Text Mining and OverRepresentation Analysis H S Leong, P Giles, S Menon, D Kipling, Cardiff University, UK This study aims to expand the existing over-representation analysis protocol beyond the mining of pre-defined terminologies (e.g. GO, KEGG) to a wider mining of freetext in the form of PubMed abstracts. P2.29 Spatial Knowledge Retrieval and Discovery in Chromosomes A Martin Pittock, University of Edinburgh, UK We propose a knowledge retrieval and discovery system for cytogenetic information. P2.30 Semi Supervised Spectral Clustering for Regulatory Module Discovery A Mishra, D Gillies, Imperial College London, UK We propose semi-supervised spectral clustering, a supervised version of spectral clustering. Supervision is provided in the form of constraints derived from dnabinding data and clustering of microarray data is done in spectral domain. P2.31 Biomarker Discovery using Genetic Algorithms A Küçükural, D Yörükoğlu, U Sezerman, Sabanci University, Turkey In this work, our main focus was to discover a biomarker set using genetic algorithms based on maximization of classification accuracy to differentiate the control and patient data. P2.32 Synthetic Cis-Regulatory Bio-Logic Gates in Escherichia Coli Z Jian, Z Yun, H Y Liu, University of Science and Technology of China, China With artificial repressors based on the lac repressor as input signals, promoters with cis-regulatory elements to carry out NAND, NOR and NOT computations, are systematically constructed according to several sequence patterns. P2.33 Using Functional Annotation for the Integration and Interpretation of Microarray Data S Menon, P Giles, I Brewis, H S Leong, D Kipling, Cardiff University, UK This abstract describes a method for comparison of microarray experiments and another for exploration of data from single experiment, both of which utilise prior knowledge of biological themes represented by sets of functionally related genes. 3 - iGEM P3.01 Promoter Calibrator: One Possible Application for a Biological Comparator P Aparicio, O Cuenca, J Garzon, R Soriano, A Ferrando, J Pereto, Universidad de Valencia, Spain, D Das, S K Maiti, A Montagud, H Mosquera, M Baguena, E Navarro, P Fernandez-de-Cordoba, J Urchueguia, Universidad Politécnica de
Valencia, Spain, A Jaramillo, École Polytechnique, France Our second contribution to the iGEM competition, this time we aimed to a promoter calibrator. Critical for a correct modelling, characterizing promoters has arose as a task yet to be resolved by synthetic biology community. P3.02 ElectrEcoBlu: A Novel Self-Powering Electrochemical Biosensor X Gu, S Ramsay, D Gilbert, University of Glasgow, UK This poster presents the activities the Glasgow2007 iGEM team carried out during the summer. It illustrates the design of the novel biosensor, from both the biological and modelling point of view, complemented with substantial graphs. P3.03 University of Edinburgh iGEM 2007 Projects: A Cell Division Detector, and Self-Flavouring Yoghurt C Dahl, L Gerosa, S Hollingshead, A Marshall, P Ravindranath, J Rokicki, X Wang, D Yin, A Elfick, C French, H Ma, University of Edinburgh, UK This abstract describes the two University of Edinburgh iGEM 2007 projects: a device for detecting cell division in E. coli, and a broad host range vector for using BioBricks in bacteria other than E. coli. 4 - Systems Biology P4.01 Comparative Study of Mathematical Models for Gene Regulatory Networks A Polynikis, M di Bernardo, S J Hogan, University of Bristol, UK The aim of this talk will be to compare different mathematical modelling approaches for gene regulatory networks. We will show that different models often lead to different conclusions regarding the network dynamics. P4.02 Systematically Identifying the Key Controllers of Growth Rate in a Eukaryotic Cell K Gkargkas, S G Oliver, University of Cambridge, UK By employing the yeast deletion collection of heterozygous mutants the fitness profile of the entire yeast genome has been investigated in order to identify classes of genes encoding proteins with high flux-control coefficients. P4.03 Cold Glycerol-Saline: The Promising Quenching Solution for Accurate Intracellular Metabolite Analysis of Microbial Cells S G Villas-Boas, P Bruheim, University of Auckland, New Zealand This is an abstract focused on optimization of sample preparation for metabolome analysis of microbial cells P4.04 Dynamic Transcription Modelling Identifies Gene Networks using Time Course Expression Data and Transcript Turnover Rates M Barenco, E Papouli, M Hubank, University College London, UK, D Brewer, Institute of Cancer Research, UK, J Stark, Imperial College London, UK Our technique uses high-throughput data in conjunction with mechanistic models and uncovers global transcriptional activities and their targets hidden in a complex response. Prediction accuracy is demonstrated using independent data
P4.05 Evolution of Evolvability in Gene Regulation Networks A B M Crombach, P Hogeweg, Utrecht University, Netherlands An individual-oriented evolutionary model shows complex gene regulation networks can evolve to become more evolvable in a dynamic environment. P4.06 Glycomic Analysis of O-Gycosylation in Knockout Mice M N Ismail, M Panico, S Haslam, A Dell, Imperial College London, UK We are performing a glycomic profiling of knockout mice that is deficient in enzymes essential for a certain type of O-glycosylation towards a better understanding of the molecular defects of sugar related diseases. P4.07 Gene Regulatory Network Inference in the Fission Yeast Schizosaccharomyces Pombe S D Kane, F Schubert, L Maury, Wellcome Trust Sanger Institute, UK Using 217 microarray experiments generated by the fission yeast team at the Sanger Institute, Cambridge, different algorithms were used to infer regulatory networks based on expression data. P4.08 Reconstraction of Saccharomyces Cerevisiae and Schizosaccharomyces Pombe Metabolic Pathways Base on Enzyme Nomenclature Database K-Y Lo, A Dalby, University of Oxford, UK The aim is to establish a “species independent” network database of metabolic pathways based on the Enzyme Nomenclature and by using it to reconstruct the metabolic networks of different yeast for their metabolic evolution comparison. P4.09 Model Discrimination and Robustness for Cyanobacterial Circadian Oscillators M Hafner, H Koeppl, École Polytechnique Fédérale de Lausanne, Switzerland, A Wagner, University of Zurich, Switzerland The notion of robustness of biochemical networks is neither well established nor quantified. We propose an integrative study of robustness on the cyanobacterial circadian cycle using different complementary definitions of robustness. P4.10 Bottlenecks in Escherichia Coli-based Glyoxylate Production Revealed by 13CFlux Analysis M Kunze, S Noack, K Nöh, Research Centre Jülich, Institute of Biotechnology, Germany 13 CMFA under industrial process conditions is successfully applied on a genetically modified E. coli strain for glyoxylate production. Using LC-MS measurements of low concentrated intermediates, model validation and discrimination showed statistically firm flux limitations. P4.11 Robust Stability of Metabolic Networks H Koeppl, M Hafner, École Polytechnique Federale de Lausanne (EPFL), Switzerland, A Wagner, University of Zurich, Switzerland We are applying tools from robust control to the stability analysis of metabolic networks. Based on that we can provide intervals for the saturation level
of the enzymatic reactions that result in stable networks. P4.12 Modelling the IP3 / Calcineurin / NFAT Pathway in the Cardiac Myocyte M T Cooling, P J Hunter, E J Crampin, University of Auckland, New Zealand Here we summarise the development of mathematical models of the key IP3 / calcineurin / NFAT signal transduction pathway implicated in heart disease, and the mechanistic results and predictions from the analysis of these models. P4.13 Understanding Chemotaxis in R. Sphaeroides M A J Roberts, E August, J P Armitage, P McSharry, P K Maini, A Papachristodoulou, University of Oxford, UK This poster describes the application of control theory to develop novel approaches for designing experiments in order to elucidate the biochemical network structure of the chemotaxis mechanism in R. sphaeroides P4.14 Diffusion Simulation of Protein Molecules through the Cytoplasm of Escherichia Coli Y D Yu, Y J Choi, A Dalby, University of Oxford, UK We suggest the use of a new algorithm to study the effects of cellular architecture and inhomogeneous macromolecular crowding on the chemotaxis signalling pathway in Escherichia coli chemotaxis. P4.15 Modelling of Methylglyoxal Detoxification in Bacteria C Almeida, E Ozyamak, I R Booth, C Grebogi, A Moura, University of Aberdeen, UK Methylglyoxal is a toxic electrophile that causes cell death. We model its detoxification pathway in bacteria. This glutathione dependent pathway forms Slactylglutathione that activates potassium channels, lowering the internal pH, and thus enhance survival. P4.16 Bridging the Gap between Constraint-based and Kinetic Modelling K Smallbone, E Simeonidis, D S Broomhead, D B Kell, Manchester Centre for Integrative Systems Biology, UK We present a technique for generating kinetic models of cellular metabolism, using only information derived from reaction stoichiometries -- fluxes derived from FBA are allowed to vary according to “linlog” kinetics. P4.17 From QconCAT to Molecules per Cell: Accurate Quantification of Absolute Enzyme Concentrations in Yeast by Mass Spectrometry K M Carroll, D M Simpson, C E Eyers, C Knight, S J Gaskellm, R J Beynon, D B Kell, University of Manchester, UK We have determined absolute protein levels of glycolytic enzymes in yeast, using the well defined QconCAT approach. Our data will be used to assist in the development of a molecular model of glycolysis. P4.18 Stochastic Parameter Estimation using Minimum Entropy: Application to the RKIP Regulated ERK Signalling Pathway G Papadopoulos, M Brown, University of Manchester, UK
A novel stochastic parameter estimation method is proposed for stochastic biochemical reaction systems based on minimizing the entropy of the PDF of the residual. The method is applied in the RKIP regulated ERK pathway. P4.19 Information-Theoretic Analysis for Exploring Death-Survival Signalling in Glioblastoma Y C Tang, Singapore-MIT Alliance, Singapore, G Stephanopoulos, Massachusetts Institute of Technology, Cambridge, USA, H-P Too, National University of Singapore, Singapore A systems biology approach was applied to study the PDGF signalling network and its protective effect on TRAIL-induced cell death. Information theory was used to identify informative signals and infer relationships between them. P4.20 Global Sensitivity Methods for Identifiability Analysis and Model Reformulation in Systems Biology M Rodriguez-Fernandez, J R Banga, IIM-CSIC, Spain, A Kremling, Max-PlanckInstitute for Complex Technical Systems, Germany Global sensitivity analysis is presented here as a robust alternative for identifiability analysis and model reformulation in systems biology. The methodology is illustrated with a model describing a twocomponent signal transduction system in Escherichia coli. P4.21 Inference and Modelling of Regulatory Networks from Transcriptomic Data J Carrera, G Rodrigo, Instituto de Biologia Molecular y Celular de Plantas, CSICUPV, Spain, A Jaramillo, École Polytechnique, France The design of organisms hosting synthetic biological devices require an appropriate characterisation and modelling of the corresponding chassis. We have developed a methodology inferring a full genome transcriptional model (topology and parameters) from microarray data. P4.22 An Accelerated Algorithm for the 3D Poisson-Nernst-Planck Calculations of Ion Flux through Membrane Channels W W Dyrka, M Kotulska, Wroclaw University of Technology, Poland, A T Augousti, Kingston University, UK A novel algorithmic scheme for accelerated numerical solution of the 3D PNP model is proposed and evaluated on theoretical and real protein channel models. P4.23 Parameter Estimation for Gene and Protein Interaction Networks R K Shelton, W T Baumann, Virginia Polytechnic Institute and State University, USA, J Peccoud, Virginia Bioinformatics Institute at Virginia Tech, USA To understand a biological system we must identify parameters that are meaningful and testable from a biological perspective. We explore approaches to determining identifiability, discussing difficulties of identification and the impact of the identifiable set. P4.24 Evolutionary Algorithms and Optofluidics Chip Optimixation for System Identification in Systems Biology: The EGFR Study Case F Menolascina, G Bevilacqua, D Naso, G Mastronardi, Polytechnic of Bari, Italy This abstract describes an evolutionary method to kinetic parameter estimation in
biochemical reaction networks.
Monday, 21 April 2008 08:30 Welcome Mattias Rantalainen, General Co-chair, Imperial College London, UK Session 3 - iGEM Chairs: Richard Kitney & Paul Freemont, Imperial College London, UK 3.1 A Synthetic Biology Approach to the Design and Construction of a SelfPowered Environmental Pollutions Sensor --- A Gold-medal and First-prize project in Environmental track in the iGEM 2007 competition X Gu, S Ramsay, M Trybilo, D Gilbert, University of Glasgow, UK This abstract documents the activities the Glasgow 2007 iGEM team carried out during the summer. It contains detailed descriptions, from both biological and modelling point of view, on the engineering of the novel biosensor, called ElectrEcoBlu. 3.2 Harvesting Cellulose and Sunlight to Power Butanol Biosynthesis: A Synthetic Biology Approach to Metabolic Engineering G H McArthur, K P Hershey, A E Schell, R P Khan, E Ruhi, University of Virginia, USA The abstract describes the energy biotechnology research accomplished by the 2007 VGEM Team, the University of Virginia's iGEM team. 3.3 Inferring Closed-Loop Responses from Open-Loop Characteristics for a Family of Synthetic Transcriptional Feedback Systems N Rai, K Ramkumar, K V Venkatesh, Indian Institute of Technology Bombay, India, S Dhabolkar, M Thattai, National Centre for Biological Sciences, India, V Sreenivasan, St. Xavier's, India We predicted and experimentally validated the responses of more complex transcriptional networks called 'closed loop', by characterizing the behavior of relatively simple transcriptional networks called ‘open loops’ in bacterium E.coli. 3.4 Bacteria Online – University of Cambridge iGEM 2007 Project Y Han, N Hengrung, Y J Liew, S May, Y Miao, S Milde, X Soh, L Soirez, D F Wyatt, Z Zhao, J Ajioka, J R Brown, J M Goncalves, J Haseloff, G Micklem, T D Southall, University of Cambridge, UK, D Malyshev, University of Sheffield, UK, J Crowe, University of Nottingham, UK, L Wernisch, MRC Biostatistics Unit, UK Inter- and intra-cellular signalling systems, including PoPS amplifiers, were designed and constructed for the Cambridge 2007 iGEM project. These could be exploited to engineer complex behaviour in synthetic biological systems. 3.5 A Synthetic Genetic Circuit to Implement a Schmitt Trigger in E.coli F Ceroni, A Pasini, S Cavalcanti, University of Bologna, Italy Abstract reports the project for iGEM 2007 and concerns the design of a genetic switch that mimicks a Schmitt Trigger and that could be used to control gene
08:30 – 10:30
expression. 09:45 3.6 iGEM 2007 Grand Prize and Best Information Processing Project: Towards Self-Differentiated Bacterial Assembly-Line Y Yang, C Lou, X Liu, Peking University, China This abstract describes the project of iGEM 2007 Grand prize wining team: the Peking Team from Peking University, Beijing, China. 3.7 Creating a Copper Biosensor based on E.coli Cu-Sensitive Element and Bacteriophage Lysogenity Control System P V Afanasyev, E A Zatulovskiy, E V Kuznetsov, S V Lvovskaya, A V Sabantsev, G A Zakharov, A N Skvortsov, Saint-Petersburg State Polytechnical University, Russia, M A Ditina, Research Institute of Experimental Medicine, Russia, T N Moiseeva, V S Romanov, A V Shalygin, Institute of Cytology, Russia We provide an iGEM project of creating a copper biosensor. The bacterial cell system works as a Schmitt trigger. The cells can rapidly and reversibly choose their fluorescence colour responding to medium copper concentration change. 3.8 iGem 2007 Cell-Free Biofilm Biosensor of Catheter related Urinary Tract Infections, Built using Biobricks that Exploit AHL Signalling Pathways in Biofilms J Chappell, L Hadjilucas, J J Karcz, A Lazzaro, P Pey, D van Swaay, M T Tariq, B Y Tew, C K Tong, A R C Wong, V Rouilly, M Bultelle, K Jensen, D Lu, P Freemont, R I Kitney, Imperial College London, UK The Imperial College project entry for the 2007 iGEM synthetic biology competition. 'Infector Detector' is a biofilm biosensor that operates in a cell-free chassis and is capable of detecting infections developing on urinary catheters. Refreshments Session 4 - Systems Biology I Chair: Tom Freeman, University of Edinburgh, UK 4.1 Network Modelling of Macrophage Systems T Freeman, University of Edinburgh, UK 4.2 Human Metabolic Network-based Analysis of Drug Responses M L Mo, N Jamshidi, S A Becker, B Ø Palsson, M J Herrgard, University of California, San Diego, USA A recently constructed genome-scale network of human metabolism, Recon 1, was used to analyze gene expression profiles of drug-treated cell-lines to identify primary modes of drug metabolism. 4.3 A Systems Biology Approach to Understanding the Pathway by which a Biogenic Organophosphonate is Produced during Metabolism of 2AEP in S. Meliloti 1021 N G Ternan, University of Ulster, UK, M McAfee, Queen's University Belfast, UK This project involves an investigation of the gene expression pathway leading to
10:30 11:00 – 13:00
production of a biogenic organophosphonate, involving a process of experimental investigation and pathway modelling. 12:35 4.4 Computational Prediction of Essential Amino Acids in Streptococcus Agalactiae A Gevorgyan, D A Fell, M G Poolman, Oxford Brookes University, UK, M A Anthony, Birmingham Women's Health Care Trust, UK Genome scale metabolic models of S. agalactiae were constructed using in-house gene annotations. The essential amino acids were identified by means of stoichiometric analysis. The results were found to be consistent with experimental data. Lunch Workshop Session 1 Refreshments Workshop Session 2 Workshop Chair Alok Mishra, General Co-chair, Imperial College London, UK W1 Deciphering Metabolic Network Robustness L M Blank, B E Ebert, S Sudarsan, A Schmid, Technische Universität Dortmund and ISAS-Institute for Analytical Sciences, Germany Knockout mutants have often no detectable phenotype, which led to the concept of gene network robustness. We present the categorization of the underlying mechanisms: redundancy, modularity, and non-active reactions in yeast and E. coli. W2 Modelling and Simulation with MATLAB and SimBiology S L L Roberts, The MathWorks, UK We will introduce SimBiology, a new platform from The MathWorks for modelling, simulating and analysing biochemical pathways. W3 A Quantitative Model for the General mRNA Translation in Saccharomyces Cerevisiae T You, G M Coghill, A J P Brown, University of Aberdeen, UK An ODE model of the general mRNA translation in Saccharomyces cerevisiae that is capable of explaining various mutants under different conditions. Robustness analysis reveals new insights into the “design” of the eukaryotic translation apparatus. W4 Biobrick Applications and Management for Everyday Research R Grünberg, L Serrano, CRG, Centre de Regulacio Genomica, Spain The workshop will introduce an open source solution for local Biobrick management and discuss practical issues for using Biobricks for everyday research.
13:00 14:00 – 16:00 16:00 16:30 – 18:30
W5 A Structured Approach for the Engineering of Biochemical Network Models, Illustrated for Signalling Pathways D R Gilbert, X Gu, M Trybilo, R Donaldson, R Orton, University of Glasgow, UK, M Heiner, Brandenburg University of Technology, Germany, R Breitling, University of Groningen, Netherlands In this workshop we show how signal transduction cascades can be modelled in a modular fashion, using both a qualitative approach – Qualitative Petri nets, and quantitative approaches -- Continuous Petri Nets and Ordinary Differential Equations. W6 Science in the Open: Why? How? And where to next? A BioSysBio Workshop C Neylon, Rutherford Appleton Laboratory, UK, J B Lucks, University of California, USA, J Cumbers, Brown University, USA There is a growing interest in some sectors of the academic research community in adopting more 'open' approaches to research practice. These range from publishing in the open access literature, through research discussions on message boards to discussing the details of their research on blogs. The logical extreme of these approaches is to make the researcher's laboratory notebook freely available online or even to carry out the preparation of a research grant in public. These approaches have only recently become readily possible through the development of web based social authoring and networking tools such as Blogs, Wikis, and social bookmarking sites. While their application in academic research remains limited they nonetheless raise serious questions about the future of both the traditional format of research publication and of peer review in its current form. Responses to the advocacy of 'Open Science' therefore, understandably, run the gamut from fanatical support, through amused tolerance, to derision and, in some cases, extreme hostility. In this talk I will discuss the experience of adopting Open Science practices in my own research group, the state and usefulness of tools available to support these approaches, with a focus on our own Blog based laboratory notebook, developed in collaboration with the group of Professor Jeremy Frey, and the state and future prospects of the Open Science community more generally. W7 Computer Assisted Design of Synthetic Genetic Systems Session 1: A Villabos, DNA 2.0, Inc, USA, Y Cai, Virginia Bioinformatics Institute at Virginia Tech, USA, J Goler, UC Berkeley, USA Session 2: S Richardson, Johns Hopkins, USA, D Chandran, University of Washington, USA, J Carrera, G Rodrigo, École Polytechnique, France There currently is a gap between the few academic groups who have the capability of running small scale proof-of-concept projects in synthetic biology and the people who could identify and benefit from biomedical and industrial applications of this technology. Several groups are developing the infrastructure making it possible for non-specialist to design large-scale genetic systems that could be used in basic biological research or product development programs. W8 iGEM: Past, Present and Future J R Brown, University of Cambridge, UK, A Hessel, Registry of Standard Interchangeable Parts, MIT, USA, iGEM Ambassadors 19:30 – 23:00 Evening Event – Reception and Meal
Tuesday, 22 April 2008 08:30 Welcome Heather Harrington, General Co-chair, Imperial College London, UK Session 5: Bioinformatics & Computational Biology II Chair: Colin Semple, Medical Research Council, UK 5.1 Chromatin Structure and Human Genome Evolution C Semple, Medical Research Council, UK Large-scale sequencing projects and comparative genomics have provided insights into the function and evolution of many fragments of the human genome, but we still know relatively little about the overall, spatial organisation of the genome. This is a major gap in our knowledge since the physical structure of the genome is intimately involved in the spatial and temporal organisation of nuclear processes such as replication and transcription. The genome is packaged into several hierarchical layers based upon interactions between DNA and proteins to achieve compaction of the linear DNA helix, and the term ‘chromatin structure’ covers all of these layers up to the chromosome. It has long been suspected that the chromatin structure of the genome might influence its evolutionary history, and here I describe the first genome-wide analyses to confirm this. The chromatin structure of a locus affects the mutation rate, and more surprisingly, the patterns of selection seen across the genes located there. The implications for genome evolution and the genetic contribution to disease are discussed. 5.2 Towards Epigenetic Modelling: An Initial Map D Perrin, H J Ruskin, M Crane, Dublin City University, Ireland This abstract outlines early advances towards establishing the new field of “computational epigenetics”, i.e. the development of computer-based models of epigenetic mechanisms. 5.3 Improved Likelihood-Free Inference in the Evolutionary Analysis of Network Data O Ratmann, S Richardson, Imperial College London, UK, C Andrieu, University of Bristol, UK, C Wiuf, Bioinformatics Research Centre, Denmark We propose a much improved variant of likelihood-free Markov Chain Monte Carlo and apply it to an evolutionary analysis of H. pylori and S. cerevisisae protein interaction networks. 5.4 Phylogenetic Distribution of DNA-Binding Domains Across the Tree of Life V Charoensawan, D Wilson, S A Teichmann, MRC Laboratory of Molecular Biology, UK Refreshments Session 6 - Systems Biology II Chair: Jaroslav Stark, Imperial College London, UK
08:30 – 10:30
10:30 11:00 – 13:00
6.1 Deducing the Unseen: The Hidden Side of Systems Biology J Stark, Imperial College London, UK 6.2 Unwinding the Circadian Clock: Insights into Biochemical Oscillators Provided by Mathematical Models O E Akman, A Millar, Center for Systems Biology at Edinburgh, UK, J Locke, Caltech, USA, D Rand, Warwick Systems Biology Centre, UK, I Carre, University of Warwick, UK Mathematical modelling and analysis of circadian clocks provides useful insights into the relationship between the structures of biochemical networks and their functional properties. We demonstrate this with a model of the Neurospora crassa circadian network. 6.3 Design Principles of Chemotaxis Signalling Pathway D Clausznitzer, R G Endres, Imperial College London, UK Using a model of the whole pathway for chemotaxis in bacteria, we explain features found in the experimentally measured response of the flagellum to chemical stimuli. 6.4 A Logic-based Framework Diagram of Signalling Pathways Central to Macrophage Activation S Raza, K A Robertson, P A Lacaze, D Page, P Ghazal, T C Freeman, University of Edinburgh, UK, J Enright, Sanger Institute, UK In order to gain a better understanding of the macrophages role in infectious and inflammatory disease we have constructed a logically depicted, integrated pathway diagram of several pathways known to activate this cell. Lunch Keynote Session 2 and Conference Closing Chair: To be advised Keynote Address 3 Systems Biology of the Mammalian Circadian Clock Hanspeter Herzel, Institute of Theoretical Biology, University of Berlin, Germany Keynote Address 4 The Music of Life: a radical revision of the principles of biological science Denis Noble, Department of Physiology, Anatomy and Genetics, University of Oxford, UK Best Submission Awards and Conference Close BioSysBio 2008 General Co-chairs: James Brown, University of Cambridge, UK, Heather Harrington, Imperial College London, UK & Mattias Rantalainen, Imperial College London
13:00 14:00 – 16:00
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