Transcript Presentation by Peter Hunter

CellML Workshop 2012
Overview of recent developments in the
VPH/Physiome project
Maurice
Wilkins
Centre
15 years of development ..
1997 IUPS Physiome Committee
1998 CellML, FieldML
1999 Systems Biology Markup Language
2003 IMAG (NIH, NSF, FDA, NASA, DOE, DOD, ..)
2006 STEP: Strategy for European Physiome
2008 VPH Network of Excellence
2010 Drug Disease Model Resources (DDMoRe)
2011 VPH Institute
Standards for models, data & software
Experimental measurements
Minimum information standards: MIAME, MICEE, ..
Data standards: DICOM, BioSignalML, ..
Metadata:
Ontologies
Data repositories: PhysioNet, CAPdb, CVRG, ..
Validation,
Limitations
(Journal review)
APIs, webservices
Metadata:
Model standards: SBML, CellML, FieldML Ontologies
GO, FMA,
..
Curation
Annotation
Model repositories: Biomodels, PMR2 Need modules!
Reference
APIs, webservices
description
Functional curation
Simulation standards: SED-ML
Software: OpenCOR, OpenCMISS, Continuity, Chaste, ..
Verification, Benchmarks
Workflow for reference description
MICEE etc
SED-ML
CellML, SBML
& FieldML
Benchmarks
Specification of
models & solution
techniques
Models
from
repository
Codes:
Simulation
Visualisation
Comparison
with reference
data
Data:
Initial conditions
Boundary conditions
Population
Atlas
(Cardiac, MSK, ..)
BioSignalML, DICOM
Quality control?
Physiome Projects
EU Projects
Call 2
Call 4
Call 9
NIH
NoE
euHeart
MSV (Multi-Scale Visualisation)
Ricordo
VPH-Share
TPR (Topological Physiology Resource)
OpenMOD
CAP (Cardiac Atlas Project)
…
The
challenge:
organs
to
proteins
Environment
Organism
Organ system
Heart
Lungs
Diaphragm
Knee
Colon
Liver
Eye
Organ
x 1million
Cardiac sheets
Tissue
Cell
Network
Protein
Gene
Atom
Acinus
20 generations
Osteon
Lymph node
Liver lobule Nephron
Infrastructure for linking Molecular Biology to Physiome
Cell types
Tissue types
Structure & physics
Physiome
FieldML
library
Cell function
Cell process
Meiosis
Cell cycle
Mitosis
Intracellular signalling
Apoptosis
Calcium transport
Growth
Protein trafficking
Cell
receptors
Motility
Protein degradation
Signalling
modules
Contraction
Electro-physiology
Signalling
Transport
Adhesion
ECM protein
synthesis
Cellular metabolism
Protein synthesis
Protein regulation
Gene regulation
Gene transcription
CellML
library
Molecular
Biology
Model components
annotated against
ontologies
Ion
channels
Metabolic
modules
Gene
networks
…
miRNA
Genes
mRNA
…
Proteins
Sequence
Structure
PTMs
Binding
motifs
…
Lipids
…
Carbohydrates
…
We need (and are well on the way to having):
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Model & data encoding standards
Public repositories of curated, annotated
& validated models
Reference descriptions of models
Multi-scale, multi-physics algorithms
Carefully managed, open source codes
Benchmark problems
Population atlases
We need (but have only just started):
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Better model reduction algorithms
Better ways of handling multi-scale
(as opposed to multiple-scale)
3D cell models
A comprehensive modelling
framework for metabolic pathways
A comprehensive modelling
framework for signalling pathways
Better links to bioinformatic databases
Better links to medical informatics
Thanks Andre!