SysMO-DB: A pragmatic approach to sharing information amongst Systems Biology projects in Europehttp://www.sysmo-db.org

Carole Goble, University of Manchester, UK

Pan European collaboration. Systems Biology of

Microorganisms.

The transition from growing to non-growing Bacillus subtilis cells

Energy and Saccharomyces cerevisiae

Biology of Clostridium acetobutylicum

Gene interaction networks and models of cation homeostasis in Saccharomyces cerevisiae

http://www.sysmo.net

Eleven individual projects, 91 institutes Different research outcomes A cross-section of microorganisms,

incl. bacteria, archaea and yeast.

Record and describe the dynamic molecular processes occurring in microorganisms in a comprehensive way

Present these processes in the form of computerized mathematical models.

Pool research capacities and know-how.

Running since April 2007. Two phases – more later!

http://www.sysmo.net

BaCell-SysMO COSMIC

SUMO KOSMOBAC SysMO-LAB

PSYSMO Valla

MOSES TRANSLUCENT

STREAM SulfoSYS

Types of stuff

Multiple ‘omics genomics, transcriptomics proteomics, metabolomics

Images Reaction Kinetics Models Relationships between data sets/experiments

Procedures, experiments, data, results and models Analysis of dataThe same across many Systems Biology projects

The Problem (1)

No one concept of experimentation or modelling

No planned, shared infrastructure for pooling

Started July 2008, 3 years + 3 years 4 people, 3 teams over 3 sitesSensitively retrofit a data access, model

handling and data integration platform.Support and manage the diversity of data,

models and competencies.Web-based solution:

exchange of data, models and processes.search for across the initiative‘s assets.dissemination of results.

DB SysMO-DB

Own solutions

Suspicion

Data issues

Resource Issues

Own data solutions and collaboration environments. wikis, e-Groupware, PHProjekt, BaseCamp, PLONE, Alfresco, bespoke commercial … files and spreadsheets.

Suspicion and caution over sharing.Interesting interplay between modellers, experimentalists and bioinformaticians.

Many do not have data, or follow the standards that exist or know who is doing what. Much of the data cannot be compared

Different organisms, different strains.

No extra resources for the consortiums91 institutes, 11 consortiums, some overlapping

The Problem (2)

Principles…

A series of small victories Realistic Don‘t reinvent Sustainable and extensible Migrate to community standards

Provide instant gratification Address doubt and anxiety Keep barriers low.

Social Approach PALS - Power Contributors!

18 Postdocs and PhD students All three kinds of people Design and technical

collaboration team Very intense collaboration UK and Continental PALS

Chapters

Audits and Sharing Methods, data, models,

standards, software, schemas, spreadsheets, SOPs…..

20 questions want answered

Summer Schools

Picking Pain Points. Keeping it Real. Project Directors

Data remains with us. We control who sees

what. Just enough exchange. Responsibility

PALs Spreadsheets. Yellow Pages. Standard Operating

Procedures.

SysMO SEEK Assets Catalogue. Archive. Social Network. Sharing Space. Gateway.

Yellow Pages People. Expertise. Projects. Institutions. Facilities. Studies.

Data Experimental data sets and analysed results. Gateway to data stores – SABIO-RK, ‘omics

Models Store. Stimulate. Publish. Curate. Gateway to COPASI, JWS Online, BioModels

Processes Laboratory protocols – Standard Operating Procedures Bioinformatics analyses – computational workflows - Taverna Model population and validation – workflows – Taverna Gateway to myExperiment, MolMeth, OpenWetWare….In

terli

nkin

g A

SSET

S C

ATA

LOG

UE

SysMO SEEKIs there any group generating kinetic data?

Is this data available?

Who is working with which organism?

What methods are been used to determine enzyme activity?

Under which experimental conditions are my partners working on for the measurement of glucose concentration?

???

?

Social Networks

Access Permissions

Protect: Just Enough Sharing

Reusing myExperiment

Attribution

Credit

Reward and Provenance

Reusing myExperiment

Just Enough Results Model Harvest

standards e.g. MIAME (MIBBI.org)

consortium schemas and spreadsheets

JERMs for each data type – microarray, metabolomics, proteomics

Map to projects Distribute as spreadsheet

templates

“I only want to collect and share just enough results”

COSMIC and BaCell ( Alfresco, document management system)

Keeping data safe at home

Content Management System

harvest Harvester

Extractor Register

AssetsCatalogue

SearchFetch

Project X

Quality of Data – Reliable InterpretationPublication standards by stealth

Controlled vocabulary plug inBioPortal

Observations - PALs

Dissemination of standards Debunking myths

Tools exchange Modeller – Experimentalist

Trust Like, talking together

Transcended the projects Project power politics

PALs did their jobs….

Observations - Sharing Methods sharing. Protective of models.

in progress vs published models. Access and Version management. Curator-Rival conflict

Reluctant to share data. Even within their own projects. Legacy spreadsheets dominate. Curation practices vary. Centralised archive take-up. Point to Point Exchange.

Nature 461, 145 (10 Sept09)

SysMO2 Musical Chairs Incentive Model for Sharing

Future Funding

Phase 2 - SysMO2 Projects dropped and added People dropped and added Institutions dropped and added Others reconstituted and added

Incentive Model for Sharing? Convenience, Added Value? Personal benefit? Consortium Policies?

A Platform for Systems Biology Exchange

Preservation and archiving. Widen Participation of mothership

Community Exchange Bazaar Widen adoption of platform and

enable exchange. Accelerant to standards Adoption of JERM. Curation tools CMS + JERM bundling

Widen access to External Resources, incl. publication Added value and convenience Preparation for publishing.

EMBL- EBI‘omics datasets

Public Model repositories

isatab sbml

Research Objects and e-Laboratories

Packaged Assets Workflows linked to models

linked to data linked to SOPs Community standards

Mixed resources External and central Trust

Spreadsheets Integration via RDF linked data.

myExperiment, MethodBox, NEMA, BioCatalogue

Summaryhttp://www.sysmo-db.org Reality is messy.

Extreme Technology Determinism vs Voluntarist Sociocultural shaping

Extreme and continuous partnership with users. Act Local Think Global

Agile development environment facilitated stream of features to tackle pain points. Leverage other e-Laboratories, Maintaining scientists’ buy-in.

Socio-Political Axis dominates the Technical Axis. Collaboration evolutions. Confidence in exchange Consortium Policies.

SysMO-DB Team

University of Stellenbosch, South AfricaUniversity of Manchester, UK

Jacky Snoep

EML Research gGmbH, Germany

Isabel Rojas

University of Manchester, UK

Olga Krebs

Wolfgang Müller

Sergejs Aleksejevs

Carole Goble

Stuart Owen

Katy Wolstencroft

Finn Bacall

Acknowledgements myExperiment:

http://www.myexperiment.org Taverna: http://www.mygrid.org.uk JWS Online:

http://jjj.biochem.sun.ac.za/ SABIO-RK: http://sabio.villa-bosch.de/