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Sunday, 20 April 2008

09:30 Registration and Refreshments

10:45 – 13:00 Conference Opening and Keynote Session 1
Chair: James Brown, University of Cambridge, UK

10:45 Welcome
Richard Kitney, Imperial College London, UK

11:00 Keynote Address 1
Title – To be advised
Tom Knight, Computer Science and Artificial Intelligence Lab, MIT, USA

12:00 Keynote Address 2
From Molecular Machines to Gene-Regulatory Networks in Mammalian Cells
Thomas Höfer, German Cancer Research Center, Heidelberg, Germany

13:00 Lunch

14:00 – 16:00 Session 1 - Synthetic Biology
Chair: Jim Haseloff, University of Cambridge, UK

14:00 1.1
Title – To be advised
J Haseloff, University of Cambridge, UK

14:20 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.

14:45 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.

15:10 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
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.

16:00 Refreshments

16:30 – 18:30 Session 2 - Bioinformatics & Computational Biology I
Chair: Jean Peccoud, Virginia Bioinformatics Institute at Virginia Tech, USA

16:30 2.1
From Registries of Biological Parts to IDE of Genetic Systems
J Peccoud, Virginia Bioinformatics Institute at Virginia Tech, USA

17:15 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 micro-
colony movies, we propose an automatic algorithm, based on cell shape priors and
motion likelihood, that solves segmentation and tracking issues simultaneously.

17:40 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.

18:05 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.

18:30 – 20:00 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
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, CSIC-
UPV, 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 HTLV-
I 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 T-
lymphocytes, 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 Over-
Representation 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 free-
text 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 dna-
binding 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 13C-
Flux 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 S-
lactylglutathione 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-Planck-
Institute 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, CSIC-
UPV, 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

08:30 – 10:30 Session 3 - iGEM
Chairs: Richard Kitney & Paul Freemont, Imperial College London, UK

08:30 3.1
A Synthetic Biology Approach to the Design and Construction of a Self-
Powered 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.

08:45 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.

09:00 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.

09:15 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.

09:30 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
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.

10:00 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.

10:15 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.

10:30 Refreshments

11:00 – 13:00 Session 4 - Systems Biology I
Chair: Tom Freeman, University of Edinburgh, UK

11:00 4.1
Network Modelling of Macrophage Systems
T Freeman, University of Edinburgh, UK

11:45 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.

12:10 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
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.

13:00 Lunch

14:00 – 16:00 Workshop Session 1

16:00 Refreshments

16:30 – 18:30 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.
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

08:30 – 10:30 Session 5: Bioinformatics & Computational Biology II
Chair: Colin Semple, Medical Research Council, UK

08:30 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.

09:15 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.

09:40 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.

10:05 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

10:30 Refreshments

11:00 – 13:00 Session 6 - Systems Biology II
Chair: Jaroslav Stark, Imperial College London, UK
11:00 6.1
Deducing the Unseen: The Hidden Side of Systems Biology
J Stark, Imperial College London, UK

11:45 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.

12:10 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.

12:35 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.

13:00 Lunch

14:00 – 16:00 Keynote Session 2 and Conference Closing
Chair: To be advised

14:00 Keynote Address 3
Systems Biology of the Mammalian Circadian Clock
Hanspeter Herzel, Institute of Theoretical Biology, University of Berlin, Germany

15:00 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

16:00 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