Fernando Martin-Sanchez, PhD.Head, Medical Bioinformatics Dept.

National Institute of Health ‘Carlos III’Madrid, SPAIN

BEYOND-THE-HORIZON

TG4: Bio-ICT Synergies

Palma de Mallorca, June 8 , 2005NISIS Meeting

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Presentation

BTH-4Institute of Health “Carlos III”

Ministry of Health and Consumer Affairs

• Public Research Institute• Scientific and technological support to the

National Health System of Spain.• Competences in:

– Epidemiology, Public health laboratories (Food, Microbiology, Environmental Health)

– Health Technology Assessment– Regenerative medicine and cell therapy– Biomedical research funding and coordination– School of Public Health, Health Sciences National

Library– New technologies - Telemedicine, Bioinformatics and

genomics, Health information systems

BTH-4Medical Bioinformatics Dept.

                      

• Established in 1998 • R+D in new technologies for

the management of genetic information and its application in biomedical research and clinical practice

• Multidisciplinary group including biologists, chemists, informaticians, statisticians, pharmacists and physicians.

BTH-4Medical Bioinformatics Dept.

Microarrays & Bioinformatics Laboratory:

– Established in 2000– Affymetrix - 417 Arrayer – Affymetrix - 418 Scanner (2

channels)– Scanarray HT Scanner (20 slides

holder & 4 channels)– Hybridization ovens– Other laboratory equipment– Applications in clinical microbiology

BTH-4 Previous experience in prospective studies

•BIOINFOMED –In this European Project (2002-2003) we coordinated an international panel of 30 experts. The group produced a White Paper that, based on the study of the convergence and synergies between medical informatics and bioinformatics, yielded a research roadmap in Biomedical Informatics.

•SYMBIOMATICS – As a continuation of the previous project, this ERA-Net (2005-2006) aims to advance in the definition and research priorities in the field of applications of IT in Genomic Medicine.

•VISION BOOK – Project funded by the EC in which 20 invited authors describe their long-term vision on how IST will affect different societal aspects. Chapter corresponding to Healthcare.

•ICT-BIO – Rapporteur in the Meeting “Information Technologies at the Crossroads with Life Sciences”, organized by the European Commission. Meeting in Brussels (Oct 12th 2004).

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EC Workshop

ICT at the Crossroadswith Life Sciences

Brussels – Oct 12th, 2004

BACKGROUND

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BTH-4 Research RoadmapVision

• Higher living systems contain at least two systems that can be interpreted as ‘natural’ information processors, namely neurons and genes.

• Advances in biological and neuro-sciences of the last 20 years have enhanced our understanding of aspects like development, action, perception, homeostasis and learning.

• This vast body of knowledge can be exploited for designing and implementing new ICT systems

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Gene

Neurons

Chips ICT

Therapy

Drug

design

Faster, robust

algorithms for

applications Bi-directional

Communication

with living

systems

Complexity

A.I. Synthetic life forms

Robotics

Properties Computation algorithms

Autonomous Systems

New

algorithms

architectures

Math.

Formal Methods

Computation Modeling

Neuro Scienc

e

Life

BIO

ICT

Engineering

Uncertainty Hierarchy

Parallelism

Concurrency

Fault tolerance

Redundancy automatis

mCoding transmission (chem.)Physic

ChemistryInformation

Combinecontinuous & discrete

Immune

endocrine

Genes stem cells cells tissues organs

Genome – genome interactionNew

implants

Non linear model

environment

Membrane computing GG.AA., Cell computing

Interfacing

Chemical / Cell structure of the brain

Bio-Sensors

neurons

cortical collums

cortex

Brain consciousness

NN, Neurocomp.

plasticity

Interaction with other brain structures

Interfacing (neuro, nano, chemistry)Pattern recognition

3D structure dynamics

Display / Visualization

Information measuremnts

Physical

substrates

(biocompatible

fault tolerance)

TG5

Time / difficulty

Viruses

Building blocks:

“Genes, Brain & Chips”

Eco-computers

ROADMAP

BTH-4 Toward NBIC convergence

• Convergence of the biological, information, nano-, and cognitive sciences is accelerating.

• A major limiting roadblock is the need for researchers to be familiar with concepts in more than one discipline.

• In particular, the information technology and life science domains have developed independently with very different terminologies and concepts.

• However, over the last decade new research communities did overcome this problem and successful inter-disciplinary collaborations have emerged.

BTH-4Successful examples of convergence

• In neuro-informatics, ICT learns from the ways information is processed in our neural system and in living organisms in general, by studying for example the associative capabilities of the human brain, or the behaviour of ant colonies and bee swarms and how these self-organise.

• In computational biology, ICT is applied to model, for example, the living cell.

• Engineers and biologists join forces in ‘biomimetics’, where mechanisms found in nature are used to inspire technological design, possibly leading to ‘lifelike’ computers able to grow, self-repair and adapt.

BTH-4 Bridging the conceptual gap between the bio- and techno-disciplines

• A common conceptual basis for Bio-ICT research is needed – This can be achieved in modelling projects,

leading to: • better biological system modelling, • new types of computational architectures• new ways of computing that reflect the

‘information processing’ type of activities in living organisms (cells, neurons, genes, metabolism, etc.).

BTH-4 Bridging the temporal gap between the bio- and techno-disciplines

• The static-dynamic dichotomy between biological and ICT systems is one of the key hurdles in the natural combination of living and artificial systems.

• The static nature of ICT is incompatible with the processes of change that govern the Bio.

• This leads to biological systems having to take all the burden of adaptation in the synergistic combination, and to ICT systems prone to becoming obsolete, malfunctioning and disturbing.

BTH-4 Bridging the physical gap between the bio- and techno-disciplines

• The physical incompatibility between biological and ICT systems (‘wet-dry dichotomy’) requires work on interfacing, embedding and on hybrid combinations of biological and ICT systems.

• Not only prosthesis work, there is a much wider potential. • For instance, brain-machine and neural interfaces could

cover a large field of applications ranging from motor prostheses to any kind of sensory prostheses.

• One could even imagine ICT-based interactions directly within metabolic processes in organisms (smart drugs, for instance).

BTH-4Proposed Research Programmes

1. New Modelling Paradigms (conceptual gap)

2. Bio-Inspired Strategies of Growth, Adaptation and Evolution (temporal gap)

3. Bio-ICT Artifacts (physical gap)

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Artificial cell

Natural cell

1-Modeling

2-Strategies

3-Bio-ICTartifacts

Understanding biology

Natural world Digital world Artificial world

Hybridtissue

or muscle

Virtual cell

Replication, Growth,

Evolution, ...

Augment repair, ...

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BTH-4 Major steps towards bridging these gaps New Computational Modelling Paradigms

• New ways of computing capable of capturing, relating and integrating the different levels of complexity in biological systems — from the molecule to the cell, tissue, organ, system, individual, population and ecosystem.

• New computing systems based on life-like hardware, consisting of large numbers of simple devices operating in a highly parallel fashion at comparatively low speed and with very low power dissipation.

• New bio-inspired computation, capable of autonomy and self-organisation.

BTH-4 Major steps towards bridging these gaps Bio-Inspired Strategies of Growth, Development and

Evolution• Technological systems should mimic the capacity of

biological systems to grow, adapt, self-assemble, replicate, heal, self-organize, and evolve.

• The idea of using these strategies for problem solving is, of course, not new – think of genetic algorithms – but more recent understanding of biological processes have not been exploited yet (for example, SNPs).

• Enormous application potential, for software and hardware, to develop new types of growing, self-assembling or evolving hardware,

• For example memory growing when needed, and intelligent materials applicable in ambient interfaces (displays, active surfaces).

BTH-4 Biological concepts that can inspire ICT systems

• Ecology (colonies)

• Organisms (robots)

• Organs (Brain)

• Systems (Immune)

• Cell (pathways, interactions, networks, membranes, embryonics)

• Molecules (DNA-RNA-Proteins)

BTH-4 Major steps towards bridging these gaps Bio-ICT Artefacts

• Artificial entities seamlessly integrated into biological systems, (retinas, limbs)

• Applications include diagnostic technologies, controlled drugs release

• The main research challenges are: – new information theories and modelling techniques that

capture sensing, action, memory, adaptation, homeostasis

– to validate the results with respect to real biological systems

– to apply these theories for the design of ICT technologies, that replicate, complement or substitute for these basic capabilities of living systems or are interfaced to them

– to study how such technologies can sustainably adapt and evolve to match, over long periods of time, with evolving needs and compatible with various natural processes of change (e.g., growth, learning, aging).

BTH-4Connections with other B-T-H areas

• TG1 - Pervasive computing (evolvable systems, bionets, interfacing with human sensory system, biological sources of electric power)

• TG2 - Nanotechnology and nanoelectronics (molecular & DNA computing, self-assembly and bio-inspired fabrication, biomimetic interfaces, magnetic biomarkers, BioNEMS, LOAC, intelligent processing of biomedical signals)

• TG3 - Security (bio-inspired mechanisms – immune system, evolutionary strategies)

• TG5 - Intelligent and cognitive systems (genotype-phenotype mapping, “evo-devo”strategies, embodiment, growth)

• TG6 - Software intensive systems (Adaptation and evolution, design for emergence)

BTH-4 Thanks to all the participants

• Davide Anguita• Jerome Chailloux• Alex Dommann• Francois Fages• Eduardo Fernandez• Sten Grillner• Francois Kepes• Rod Hose• Damian Mac Randal• Bernard Manderick• Victor Maojo• Matej Oresic• Nico Rijkoff• Bernd Schuermann• Walter Van de Velde (EC)