Company presentation: Medicel - cs.helsinki.fi · Company presentation: Medicel IT platform for...

1Medicel Oy - Keilaranta 12, FIN-02150 Espoo - Finland - phone: +358-9-386 7092 - info@medicel.com

Company presentation: MedicelIT platform for integrative research

Christophe Roos – PhD, docent, Principal Analyst, christophe.roos@medicel.com

Medicel Oy – Quick Facts

• Privately held, estd. 2001• Headquartered in Espoo, Finland• ~60 person team worldwide

• 30 software engineers• 20 other engineers, mathematicians, statisticians, etc.• 5 lab technicians• 2 PhD, 1 MD

• Entering market with own products (IP, filed patents)• Out-licensing IT technology• Selling high-throughput instruments

Medicel Oy – Technology

• Supplier for research programs inthe fields of medicine,pharmacology, biology,agronomy, …

• 3 product lines• Integrator software

• Data• Methodology• Project

• High throughput multi-well bioreactor• Services

Medicel Oy – Aims

• Maximise computer readability – accelerate research• Formalise knowledge representation – data model• Centralise data – integrate data silos• Broaden understanding – multi-domain analyses• Support discovery process – modeling & simulation• Get knowledge early – pleiotropic & side effects• Long-term data accumulation – projects span years

Part 2.a – Technology

To facilitate inter-disciplinary research

Medicel Oy - Keilaranta 12, FIN-02150 Espoo - Finland - phone: +358-9-386 7092 - info@medicel.com

biology

modeling

Inter - disciplinary

Biological complexity beyond intuition –use models to produce hypotheses

Wet lab experimentation expensive –computer simulations cheap

Core technology platforms

Data warehouseI T layer

Measurement layer

Research layer

Biological applications for data refinement

Integration layer

Data management platform

Project management platform

Data -> Model -> Predict -> Measure

Experimental Theoretical

Experimental Modeling

Data Integration

It's about communication

Experimental Theoretical

Experimental Modeling

Data Integration

Very different epistemological cultures in physics and biology

Part 2.a – TechnologyTo teach and communicate biological system

descriptions

To describe biological systems

l Document and convey biological knowledge andunderstanding in computer readable format

• Use an adequate formalism• Components• System• State

• General solutions help to survive through the years

General systems theory

ComponentData

SystemData

StateData

System of lower level can be component of upper level

StateData

SystemData

Component of upper level can be system of lower level

Information model: simple overview

Biological systems

C[orotidine 5'-phosphate ]

C[UMP]

C[CO2]

P[PYRF_YEAST]

C[orotidine5'-phosphate ]

C[UMP]

C[CO2]

I[GO4590]

Pw[example_pathway]L[location]

V[rate]U[mol/s]I[GO4590]L[location]V[concentration]U[mol/L]C[CO2]L[ location]...

Component Data

System Data

State Datarelations to components relations to systems

relations to components

The model for component

I[GO4590]

C[UMP]

C[CO2]

P[PYRF_YEAST]

MGVLLGSYNVA...

IPR000...

'GlcNac'

Biological systems

C[UMP]

C[CO2]

P[PYRF_YEAST]

C[orotidine5'-phosphate ]

C[UMP]

C[CO2]

I[GO4590]

Pw[example_pathway]L[location]

V[rate]U[mol/s]I[GO4590]L[location]V[concentration]U[mol/L]C[CO2]L[ location]...

Component Data

System Data

State Datarelations to components relations to systems

relations to components

The model for the topology

C[UMP]C[CO2]

P[PYRF_YEAST]I[GO4590]

L[location]

Pw[example_pathway]

Also:stoichiometrykinetic laws

State data - Vector example

∈ RnV[concentration]U[mol/L]C[UMP]L[location2]T[ t ]

V[rate]U[mol/s]I[GO4590]L[location2]T[ t ]

Sa[gis-035/b]V[concentration]U[mol/L]P[PYRF_YEAST]L[location2]T[ t ]

V[concentration]U[mol/L]C[orotidine 5'-phosphate ]L[location2]T[ t ]

V[concentration]U[mol/L]C[CO2]L[location2]T[ t ]

V[volume]U[L]L[location2]T[ t ]

What, where and when: no data point is informative alone

The model for state

V[concentration]U[mol/L]

P[PYRF_YEAST]

T[ t ]dynamics

Sa[gis-035/b]

Information model – generic & flexible

Ca 50 tables covering biological dataCa 150 tables covering other aspects

(project, owner, version, source,evidence, etc.)

Example: Contextual(meta-) Data

Part 2.b – Technology

Data integration

Data integration – Data modeling

• The information model in a pivotal role:

• Build a data repository ’at home’ and keep it at handfor further processing and knowledge building

• Import from the most relevant data sources• Include measurement data• Export structured data to collaborators or to public

repositories

Data integration – The IT essentials

• Schema mapping• ETL: Extract, transform, load• Resolve differences (subjective, objective)• Provenance, evidence codes, ontologies• Update and maintain multiple versions• Same for public data and private data

UniProt schema mappingto Medicel schema

Data integration protocols tested

• ENSEMBL• NCBI Taxonomy• NCBI Refseq Proteins• UniProt/Swissprot• UniProt/TrEMBL• Interpro• Mammalian PhenotypeOntology

• KEGG*• Human Disease Ontology

• IntAct• GO• Cell Ontology• Chebi• Cytomer• Brenda TissueOntology

• PDB• PubMed

• ICD9• NCBI Refseq Genomes• NCBI RefSeq RNA• OMIM• SNOMED• EMBL• HapMap• GEO• ArrayExpress• Etc.

Data integration – Complex queries

• Comprehensive searches: annotate using homology

InterPro

KeggGO

UniProt

Biomarker to be annotated

Evidence from user

Integrated data -> tools -> processes

• Standards, formats• Scientific process

• Biological context• Applied methodologies

• Accumulate• Data• Methods

• Communicate• Conclusions• Hypotheses

Part 2.c – Technology

Projects and data modules (versioning)

In-silico project A

Collaboration platform

Biological data

Uniprot 1.0

Uniprot 2.0

In-silico project B

Project Data

In-silico project A

Wet-lab project C

Measurement data 1.0

Measurement data 2.0

Gene Ontology 1.0

Gene Ontology 2.0

Shared repositoryRe-usable methods 2.0

Re-usable methodsProject DataProject data

Re-usable methods 1.0

Project Data 1.0Project Data 2.0Project Data 3.0

Project A

Project B

Uniprot

Gene Ontology

Project C

Measurement data

Part 2.d – Technology

Multi-domain analysis

Research project

Mass specMeasurement technologies

Microscopy

RNAquantisation

NMR, X-ray

DNAsequencing Genotyping

Chormatin IPMolecular

biology

CustomerLibrary

Multidomain analysis

Part 3 – References

References• Medicel provides the IT infrastructure in EU FP7 framework

projects• HEALTH projects: large systems biology projects

• Apoptosis, T-cell differentiation, stem cells• KBBE projects: Food, agriculture and fisheries

• Plant parthenogenesis• ICT projects: Information and Communication Technologies

• e-Infrastructures, sustainable and personalized healthcare• Leonardo: Training in systems biology

• Evaluation of infrastructure• Academic projects (Australia, Singapore, USA)• Pharmaceutical companies

Summary – Research infrastructure

biology

modeling

Inter – disciplinary !

Company presentation: Medicel - cs.helsinki.fi · Company presentation: Medicel IT platform for...

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1 23.08.2006michael.przybilski@cs.helsinki.fi Component-based, Context-aware Software Systems Workshop on Advances in Methods of Information and Communication