Programme

Programme details and conference abstracts

(For conference participants.The content is password protected)

Keynote speakers

We are very pleased that the distinguished scientists, thought leaders and excellent speakers Denis Noble, Tom Kirkwood, Peter Hunter and Yoram Rudy will each open one of the four plenary sessions of the conference:
 

Denis NobleIs the digital patient possible: What are the roadblocks and how do we negotiate them?

Professor Denis Noble, University of Oxford


 

Tom KirkwoodUntangling the complexity of ageing

Professor Tom Kirkwood, Newcastle University
 


 

Peter HunterReproducible modeling: Standards, databases and software tools

Professor Peter Hunter, University of Auckland


 

Yoram RudyMulti-scale Integration of Cardiac Excitation: From Molecular Structure to the Human Heart

Professor Yoram Rudy, Washington University in St. Louis
 

Workshops

Cardiovascular modelling

Organizer:  Arun Holden,  Multidisciplinary Cardiovascular Research Centre, University of Leeds Grodins  ( Quart Rev Biol 34 93-116 1959) began the integrated modelling of...

Cardiovascular modelling

Organizer:  Arun Holden,  Multidisciplinary Cardiovascular Research Centre, University of Leeds

Grodins  ( Quart Rev Biol 34 93-116 1959) began the integrated modelling of cardiovascular dynamics  by volumes, pressures and flows  using linear equations and analytical methods.  However, nonlinearity  is essential for explaining the phenomenology myocardial and vascular smooth muscle electrophysiology, calcium dynamics, and tissue mechanics.

Voltage-dependent channels  produce cell threshold behaviour and  allow autorhymicity. Myocytes  types are widely modelled by multiple parameter, high order systems of ordinary differential equations.  Propagation is modelled as nonlinear waves by partial differential systems.  Dysrhythmias emerge  via bifurcations (e.g. into alternans)  or by conduction blocks, and unidirectional conduction block can lead to re-entrant tachyarrhythmias and fibrillatory activity.   Detailed  3D reconstruction of cardiac activity can be partially validated by optical mapping of V and Ca++ on the surface of isolated hearts, and by clinical endo-, epi-cardial and body surface recordings, or cine- and tagged MRI. Cardiovascular tissue also includes the extracellular matrix, endothelial cells,  and fibrocytes which may be coupled to myocytes.  Vascular endothelial cells modulate vascular tone, mediate responses to oxidative stress, and endothelial dysfunction can lead to the development  and progression of  atherosclerosis. Endothelial damage leads to vascular smooth muscle proliferation and extracellular matrix synthesis  and plaque formation.

The current  challenge is to integrate these detailed electrophysiology, mechanics, fluid dynamics and biochemical signalling models into an overall model of the  cardiovascular system under autonomic control, during normal sinus rhythm, ageing, and the development of pathologies.


Computational integration of organ physiology

Organizer: Dan Beard, Department of Molecular and 
Integrative Physiology, University of Michigan, Ann Arbor Every organ in the body performs a set of specialized physiological functions...

Computational integration of organ physiology

Organizer: Dan Beard, Department of Molecular and 
Integrative Physiology, University of Michigan, Ann Arbor
Every organ in the body performs a set of specialized physiological functions that determine its contributions to whole-body function in health and disease. Yet although the organs and organ systems of the body perform distinct and diverse physiological functions, these functions emerge from a common core of basic biological/biophysical phenomena that may be captured by sophisticated multi-scale computational models. Basic cellular metabolic, mechanical, electrical, signaling, and molecular genetics processes are specialized within every organ and organ system, in which a number of types of cells are arranged in a distinct spatial pattern or patterns that determine how the cells interact chemically, mechanically, and electrically. Afferent and efferent nerves communicate with parenchymal cells via electrical, mechanical, and chemical transduction of signals between cells. Blood vessels perfuse organ tissues, transporting substrates, metabolic wastes, and endocrine factors. Simulating the combined operation of all of these processes in the individual organs of the body provides the basis for simulation virtual organisms at the level of mechanistic fidelity necessary to map from molecular function to whole-body phenotype.

Interoperability infrastructures bridging molecular- to organ-level data and models

Organizer: Bernard de Bono, CHIME Institute, University College London & Auckland Bioengineering Institute, University of Auckland The practice and research of biomedicine generates...

Interoperability infrastructures bridging molecular- to organ-level data and models

Organizer: Bernard de Bono, CHIME Institute, University College London & Auckland Bioengineering Institute, University of Auckland

The practice and research of biomedicine generates considerable quantities of data and model resources. In particular, the organized archiving of high-throughput genomic and biochemical assays, as well as large scale biobanking and electronic health anonymization efforts, are starting to build a detailed, if patchy, multiscale record of tissue biology at both population and individual level. The VPH community is now faced with the challenge of interpreting this wealth of new information, and specifically to detect physiologically meaningful correlates between molecular-, subcellular-, cellular- and organ-level measurements of relevance to model construction and validation. What strategies are to be adopted to create a coherent VPH modeling framework that consistently interoperates across these levels? Do we need new forms of knowledge representation? Do we need new forms of knowledge management? This workshop draws upon real community efforts, and their solutions, to build interoperability infrastructures that address data-model integration, as well as the modular assembly of complex models, across the scale divide.


Make them run: modelling challenges identified by exercise physiology

Organizer: Trine Karlsen, 
Department of Circulation and Medical Imaging, NTNU Regular exercise training and high cardiovascular fitness are strongly associated with lifelong health, in...

Make them run: modelling challenges identified by exercise physiology

Organizer: Trine Karlsen, 
Department of Circulation and Medical Imaging, NTNU
Regular exercise training and high cardiovascular fitness are strongly associated with lifelong health, in particular protection towards cardiovascular disease. Data on epigenetic markers, mRNA expression, protein expression, metabolic signatures, and tissue and organ phenotypes show that the effects of exercise training manifest at all phenotypic levels. We are still far from a quantitative understanding of the regulatory biology underlying the observed changes; changes that are intimately linked to cellular phenotypic plasticity. If computational physiology becomes capable of describing the dynamics underlying phenotypic plasticity as a function of exercise, this will most likely have a tremendous impact on organismal biology in general. The workshop will outline state-of-the-art knowledge in exercise physiology, identify key questions being addressed in the experimental community and challenge the computational physiology community to take explanatory responsibility for exercise-related phenomena that are currently highly enigmatic and which appear to demand the construction of sophisticated mathematical representations

Mathematical challenges of multiscale modelling

Organizer: Merryn Tawhai, Auckland Bioengineering 
Institute, University of Auckland Multi-scale models attempt to simulate emergent function of a system from the interaction of their...

Mathematical challenges of multiscale modelling

Organizer: Merryn Tawhai, Auckland Bioengineering 
Institute, University of Auckland
Multi-scale models attempt to simulate emergent function of a system from the interaction of their subcomponents, which themselves may operate over vastly different length and time scales. Physiological and biological models employ a wide range of mathematical approaches that are each generally suited for a particular scale of interest or a specific task. For example network approaches for metabolic models, systems of ordinary differential equations for single cell function, partial differential equations to describe fluid and solid mechanics, and cellular automota and agent-based models that can address complexity whilst retaining physiological meaning. Now as we attempt to measure, describe, conceptualise, and model functions that occur over ranges of spatial and/or temporal scales, we generally require the simultaneous use of different types of mathematics within a single multi-scale modelling framework. The key challenge is to determine consistent and physically realistic mathematical descriptions of the coupling between scales, which is necessary for robust predictions of emergent function and synergistic interactions. Associated challenges are those of model design and size, and methods to transfer parameters both up and down between the scales. Of equal importance to the conceptualisation and mathematics of function is the mathematical description of the physical domain in which function is predicted: studying structure-function interactions requires models that capture the important geometric features of e.g. a tissue or organ. This introduces a further challenge of trade-off between geometric complexity and the ability to model function with high precision. Appropriate model reduction and parameterisation therefore remains key, alongside the need to keep models amenable to classic mathematical analysis. Approaches to address these challenges in different organ systems and across different scales will be considered.

Metamodelling methodology for easing model construction and validation

Organizer: Kristin Tøndel, Simula Research, Oslo Computational physiology models do in general contain a large number of parameters, numerous state variables, and intricate functional...

Metamodelling methodology for easing model construction and validation

Organizer: Kristin Tøndel, Simula Research, Oslo

Computational physiology models do in general contain a large number of parameters, numerous state variables, and intricate functional relationships between these state variables. Thus the parameter-to-phenotype map, i.e. the multidimensional mapping between model inputs and model outputs, can possess a very complex topography. Robust development and use of models require an explication of this topography. A metamodel of a given computational physiology model is a statistical prediction model that provides a description of the parameter-to-phenotype map. It is becoming increasingly clear that metamodels may become very useful for computational physiology in connection with model construction, model validation, parameter estimation, sensitivity analysis, model comparisons and computational compaction facilitating clinical use. The workshop will provide a state-of-the-art overview of metamodelling methodology and associated methodology for making use of metamodels in these application areas.

 


Model-guided medical device design and assessment

Organizer: Marco Viceconti, Department of 
Mechanical Engineering, University of Sheffield Traditionally, bioengineers use computational approaches in the early phases of the design of a...

Model-guided medical device design and assessment

Organizer: Marco Viceconti, Department of 
Mechanical Engineering, University of Sheffield

Traditionally, bioengineers use computational approaches in the early phases of the design of a new medical device, primarily for exploratory purposes.  Once a basic design is defined, prototypes are realised, and then tested first pre-clinically and then clinically, with multiple cycles of design revision as the product shortcomings become evident.  But in the last few years pioneering efforts have been made to explore the possibility of making much more extensive use of computer simulation to improve the medical device design process. This opens up a number of very interesting possibilities, but also raises a number of concerns on the accuracy, reliability, and certification of these in silico medicine methods when used in the development and assessment of medical devices.  Like many other industrial sectors virtual prototyping can improve the products and reduce the costs, but for medical devices this must be achieved with an extreme attention to the reliability of these simulations. The workshop will provide an overview of this pioneering work, explore innovative uses of advanced patient-specific models to guide device design, to improve the pre-clinical assessment phase and to reduce, refine and to some extent replace clinical experimentation, and discuss how to address associated model reliability issues. 


Model-guided tissue engineering and stem cell therapy

Organizer: Liesbet Geris, Biomechanical 
Engineering, University of Liege The creation of man-made living implants is the holy grail of tissue engineering (TE). As basic science...

Model-guided tissue engineering and stem cell therapy

Organizer: Liesbet Geris, Biomechanical 
Engineering, University of Liege
The creation of man-made living implants is the holy grail of tissue engineering (TE). As basic science advances, one of the major challenges in TE is the translation of the increasing biological knowledge of complex cell and tissue behavior into a predictive and robust engineering technology of clinical relevance. Considering the biological complexity involved, computational modeling is likely to become a key factor in the maturation of the TE field and its clinical impact. This workshop aims to give an overview of computational modeling efforts in the field of tissue engineering across the whole span of biomedically relevant tissues and organs. Specific attention will be given to which modelling formalisms are most appropriate to use for a given medical application and how these formalisms are connected to data-driven or hypothesis-driven approaches. Furthermore, attention will be given to issues related to specific model building, training and validation, and to issues related to how in silico work should be connected to in vitro and in vivo work in the TE field in order to ensure maximum progress.

Models for surgical decision support

Organizer: Kerstin Denecke, Innovation Center Computer Assisted Surgery (ICCAS), Medical Faculty, University of Leipzig Improved clinical examination methods and developments towards...

Models for surgical decision support

Organizer: Kerstin Denecke, Innovation Center Computer Assisted Surgery (ICCAS), Medical Faculty, University of Leipzig

Improved clinical examination methods and developments towards personalized medicine lead increasingly to complex patient data to be considered within clinical decision making processes. Clinical decision support systems aim at making the optimum use of patient data and are supposed to support in this process of information management and interpretation. They should lead to high percentages of appropriate treatment and reduce mortality and complications. However, such systems did not yet arrived sufficiently in clinical practice, since approaches often lack relationships to scientific evidence and are poorly integrated with clinician's workflow. In the last years, the idea of model-based decision support came up that bases upon two assumptions: 1) Medical knowledge can be modelled including diagnosis, treatment, and decision making processes, i.e. it can be formally described which parameter characterize a specific diagnosis or which steps are performed within a decision-making process (domain theory). 2) The observations made during physical or other clinical assessment of a patient can be described and instantiates the formal patient model (situation description).


The workshop aims at providing an excellent opportunity for the presentation and discussion of state of the art in model-based decision support as well as for the presentation of models and concepts  specifically designed for surgical decision support. The workshop further intends to collect requirements and key challenges to be addressed in future with respect to digital patient modeling for surgical decision support.


Multiscale modelling of cancer

Organizer: Georgios S. Stamatakos, In Silico Oncology Group, Institute of Communication and Computer Systems, National Technical University of Athens Cancer is a highly complex disease...

Multiscale modelling of cancer

Organizer: Georgios S. Stamatakos, In Silico Oncology Group, Institute of Communication and Computer Systems, National Technical University of Athens
Cancer is a highly complex disease and natural phenomenon. It is manisfested at virtually all spatiotemporal scales pertinent to life, spanning from the atomic to the whole body spatial scale and from the nsec to the year temporal scale. The plethora of interdependent mechanisms jointly constituting the natural phenomenon of cancer and its response to treatment dictates the development of complex mathematical and computational multiscale models aiming at both the quantitative understanding of the phenomenon and the optimization of cancer treatment in the patient individualized context. Clinical adaptation and validation are two sine qua non processes in view of the clinical translation of such models (in silico oncology). Clinically validated cancer models  are expected to serve as platforms for performing in silico experiments by exploiting the patient's own multiscale data such as imaging, histological and molecular data in order to select the most appropriate treatment scheme. The workshop aims at providing an excellent opportunity for the presentation and discussion of state of the art multiscale cancer modelling efforts along with clinical translation activities. Since the development of cancer hypermodels of which the component models may be developed by different  modeling groups is becoming a more and more realistic scenario, aspects of the joint development of cancer hypermodels on a global scale will also be addressed.

ePoster presentations

A poster presentation is in many cases at least as valuable as an oral presentation in terms of getting people in touch with each other and conveying important results. The poster presentations therefore define a very important segment of VPH2014.We will use electronic posters (ePosters) at the VPH2014.

Find out more about the ePoster presentations.

Hands on demonstrations

On Friday September 12 there will be hands on demonstrations of VPH-compliant software.
 

Share, discover and access biomedical resources:  VPH-Share in action

Debora Testi, VPH-Share Platform

The VPH-Share is presenting the software platform currently released which allows biomedical researchers and clinicians to share data, and tools and to compose them in complex workflows to build new knowledge. The system is accessible via an easy to use web interface and allows searching for resources, the upload/creation of new resources, the remote execution of tools and workflows relying on an efficient cloud platform. The presentation will be a live demo of the system functionalities and use cases.
 

VPH tools from the Auckland Bioengineering Institute

Poul Michael Fonss Nielsen

This tutorial will highlight three VPH-compliant tools, PMR2, OpenCOR, and MAP Client. PMR2 is a software framework for providing data and knowledge repositories, with the data encapsulated in version controlled workspaces. OpenCOR is a tool for model editing, annotation, and simulation, initially based on CellML but extensible to other model encoding standards. The MAP Client is a workflow editor and execution tool being developed in order to capture the semantics of workflows.

 

EUDAT training

Adam Carter
 
In recent years, significant investments have been made by the European Commission and European member states to create a pan-European e-infrastructure supporting multiple research communities. As a result, a European e-infrastructure ecosystem is currently taking shape, with communication networks, distributed grids and HPC facilities providing European researchers from all fields with state-of-the-art instruments and services that support the deployment of new research facilities on a pan-European level. However, the accelerated proliferation of data – newly available from powerful new scientific instruments, simulations and digitization of library resources –, has created a new impetus for increasing efforts and investments in order to tackle the specific challenges of data management, and to ensure a coherent approach to research data access and preservation. EUDAT aims to address these challenges and exploit new opportunities using its vision of a Collaborative Data Infrastructure. The EUDAT hands-on demonstration at VPH2014 will familiarise the audience with the EUDAT concept and EUDAT services and support mechanisms.
 

The Flower of Life: Vessels in the human lungs (red) and first generations of branches starting from the trachea (green).

Photo: Solveig Fadnes, MI Lab and Department of Circulation and Medical Imaging, NTNU