FAIRDOM – FAIR Asset management and sharing experiences in Systems and Synthetic Biology

Prof Carole GobleThe FAIRDOM Consortiumcarole.goble@manchester.ac.ukhttp://fair-dom.org, http://fairdomhub.org

COMBINE 2016, Newcastle, UK 19 September 2016

FAIRFindable

Accessible

Interoperable

Reusablehttps://www.force11.org/group/fairgroup/fairprinciples

Intelligible

Reproducible

Citable

Track & Countable

FindableAccessibleInteroperableReusable

DataOperationsModels

Systems and Synthetic Biology

Projects

Sys Bio Projects ....

5

P1. BaCell-SysMOThe transition from growing to non-growing Bacillus subtilis cells - A systems biology approach

P2. COSMICSystems Biology of Clostridium acetobutylicum - a possible answer to dwindling crude oil reserves

P3. SUMOSystems Understanding of Microbial Oxygen Responses Escherichia coli

P4. KOSMOBACIon and solute homeostasis in enteric bacteria Escherichia coli

P5. SysMO-LABComparative Systems Biology: Lactic Acid Bacteria: Lactococcus lactis, Enterococcus faecalis, Streptococcus pyogenes

P6. PSYSMOSystems analysis of biotech induced stresses: towards a quantum increase in process performance in the cell factory Pseudomonas putida

P7. SCaRABSystems Biology of a genetically engineered

Pseudomonas fluorescens with inducible exo-polysaccharide production: analysis of the dynamics and robustness of metabolic networks

P8. MOSES

MicroOrganism Systems Biology: Energy and Saccharomyces cerevisiae

P9. TRANSLUCENT Gene interaction networks and models of cation homeostasis in Saccharomyces cerevisiae P10. STREAM

Global metabolic switching in

Streptomyces coelicolor P11. SulfoSYSSilicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation

P12. SysMO-DBData management group200611 projects

201512 projects

Stakeholders Stress…Sponsored to Support Projects: National level and

ERANets

Funders / Institutions• Capitalising on

investments• Skills• Justification, Audit,

Compliance• Showcase access

Publishers• Reproducibility• New publishable

assets• New services• Showcase access

Projects….Researchers’ Productivity Rhetoric

Multi-partnerDistributedDynamic membershipOverlapsSensitivities

CollaborationPublicationShowcasingComplianceRetention

Home-grown resourcesPublic resourcesMixed Skills

Projects’ “PAP-PA” People, Assets, Processes -> Publishing, Analysis

People

AssetsProcesses

Projects’ People, Assets, ProcessesOrganisation, Communication, Dissemination

Simulation

SOPs

Data Models

StandardsAnalyticsPipelines

Samples

TrackingVersioning

Validation

Articles

Strains

modeller

experimentalist

Upstream, downstream assets discovery

Organisation Communication Dissemination

Helps navigation Reuse

later

Enable team to reuse/

reproduceHelp

others find out

Reuse with new

partnersTell more and

take credit

Collecting and tracking data/modelsChoosing what to keepPreparing what to share and when

Most data/models won’t be shared• Wrong experimental method• Hidden parameter discovered • Faulty experiment

Promote standardised metadata practices

FAIR Projects & Programmes

Who is working with wh

ich 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?

What is the provenance of the parameters for this version of the model?What SOP was used for this sample?

Where is the validation data for this model?

Is there any group generating kinetic data?

Is this data available?

Track versions of my model

Whats the relationship between the data and model

Which data belong to which publications?

SOP Directory

Yellow Pages

Spreadsheettools

Auto-harvesting

FAIR Projects and Programmes

Findable Exchange & find assets and peopleCitationCredit

AccessibleShare, disseminate and publish assets sensitivelyGateway to third party tools, archivesStore assetsPackage assets

Track collection of data and metadataConsistent reporting for interpretation, interop & comparisonPromote and support standardised metadata practices.Support reproducible publications

Organise and link assetsMaintain the experimental contextRetain results beyond a projectReuse results, tools, archivesRespect local solutions

Standards! Standards!

FAIRDOM Initiative

Project Support

Community Actions

Platforms, Tools

Public Project Commons

FAIRDOM Community, Knowledge Hubhttp://www.fair-dom.org

Know-how, Guides, Templates, Workshops, Training, Webinars, Standards and Policy Forums

Policy and International Initiatives

Surveys

Stanford et al The evolution of standards and data management practices in systems biology, Molecular Systems Biology (2015) 11: 851 DOI 10.15252/msb.20156053

Community Clubshttp://www.fair-dom.org

Samples Club with ELIXIR, BBMRI-ERIC, EBI…Rework and harmonise sample metadata frameworkbioschemas.org

Developers FoundrySupport developers of Systems Biology tools and platforms 3rd Foundry meetingDec 1-2 2016, Frankfurt

FAIRDOM Platforms and Tools

FAIR Sharing Metadata CatalogueProject CommonsCross-repository gatewayTool gatewayResults repository

Web-based

Local Storage AnalyticsTrackingLIMS, Auto-archivingIn flight repositoryLocal-based

FAIRDOM Platform Installations

*Troup, E.; Clark, I; Swain, P; Millar, AJ; Zielinski, T (2015) Practical evaluation of SEEK and openBIS for biological data management in SynthSys http://hdl.handle.net/1842/12236

Local retention and In flight management, Private sharingCentres, large or national projectsLocal skills

One stop showcaseProgrammesPost-project retentionSupplementary materials

People and Project Commons FAIRDOMHub.org

self-managed workspaces

Sharing sensitivity

Investigation

Study Analysis

Data

Model

SOP(Assay)

Linking, “Packaging” & Citing Codes, Data, Models, SOPs, Samples, Strains, Articles, People, Projects….

Packaging

25

Jon Olav Vik, Norwegian University of Life Science

26

Programme Overarching research theme (The Digital Salmon)Project Research grant (DigiSal, GenoSysFat)Investigation A particular biological process, phenomenon or thing(typically corresponds to [plans for] one or more closely related papers)Study Experiment whose design reflects a specific biological research questionAssay Standardized measurement or diagnostic experiment using a specific protocol(applied to material from a study)

Jon Olav Vik, Norwegian University of Life Science

Visible, but details maybe inaccessible

Visibility controls

STUDY ASSAYINVESTIGATION

Experimental assay

Modeling assay

Publication

Maksim Zakhartsev

Glucose

Glycerol

Ethanol

GlycolysisPPP

TCA

CO2

Lactate

Carbohydrates

Nucleotides

Kinases

Pyrophosphotase

RNA

Electron transport

Maintenance

C1 metabolism

Proteines

NH4 transport Sulfur metabolism

Biomass

Lipids

Stoichiometric model

30

Stoichiometric model of Saccaromyces cerevisiae growing anaerobically at D=0.1 h¯¹Compartments 1

Pathways 35

Transformers: 254

reactions 214

transports 33

polymerization

7

Compounds 253

balanced comp.

234

Supplementary information

Annotation file

SEEK

Stoichiometric matrix

SEEK

SBML

SEEK

Stationary fluxes

SEEK

ODE-based model

32

example = glc-permease

variables: Cexglc, Cglc, Cg6p

parameters: Rmax, Kglc, KI-g6p, KII-g6p

0 500 1000 15000

2

4

6

glc-ex

Ci [

mm

ol/L

]

0 500 1000 15000

0.05

0.1

glc-in

Ci [

mm

ol/L

]

0 500 1000 15000

2

4

6

g6p

Ci [

mm

ol/L

]0 500 1000 1500

0

1

2

3f6p

time [sec]

Ci [

mm

ol/L

]

0exglc pulseex pulsex

glc glc Perm glcr

dC FCD C C t r a C

dt V

max

.1

.1 6 6

.1 .1 6 .1 .1 6 .1

.1

max

.1

.1

.1

11 1

1

11

1

perm influx efflux

exglc

permglc

influx exglc

exglc glc glc g p glc g p

glcglc glc I g p glc II g p

glc

glcperm

glcefflux

glc

glc glc

glc

r r r

CR

Kr

CC K C C C C

CK K K K KK

CR

Kr C

C KK

6 6

.1 6 .1 .1 6 .1

.1

1exglc g p glc g p

exglc glc I g p glc II g p

glc

C C C CC K K K KK

[Rizzi et al., 1997]

DATA fileEquations

Simulations

https://dx.doi.org/10.1111/febs.13237

https://doi.org/10.15490/seek.1.investigation.56

Model PublicationPublishing and data citation

reviewer

Institutional Repository

FAIRDOM Catalogue, a web of resourcesdrawing together across resources; reusing tools and repositoriesrespect local project solutions, tool plugins

Standards

Personal DataLocal Stores

ExternalDatabases

Publishing services

Modelling tools

SOPs

BiVes

Datatools

Specialist Public Repositories

General archives

Repository RepertoireStanford et al The evolution of standards and data management practices in systems biology, Molecular Systems Biology (2015) 11: 851 DOI 10.15252/msb.20156053

Local Data Stores

Laissez-Faire

openBISmetadata extraction data relationship/linkingdata processing minimal user input

*Troup, E.; Clark, I; Swain, P; Millar, AJ; Zielinski, T (2015) Practical evaluation of SEEK and openBIS for biological data management in SynthSys http://hdl.handle.net/1842/12236

Modelling standards based in browser validation and simulation

Model comparison and versioning

SBML Model simulation

[Stellenbosch, Rostock]

http://seekdb.bionet.nsc.ru/

Alexey KolodkinSiberian BranchRussian Academy of Sciences

Reproducible model simulations in papers using COMBINE Archive & SED-ML

[Jacky Snoep, Dagmar Waltemath, Martin Peters ]

Three tiered service

store DOI citable supplementary files on FAIRDOMHub

model and data curation

reproducible clickable figures in papers using SED-ML

COMBINE Archives support

Martin Peters Talk Wednesday Morning

COMBINE Archives support

Martin Peters Talk Wednesday Morning

COMBINE Archives support

Martin Peters Talk Wednesday Morning

Standards-based Structured Descriptiontemplates, register, harvest, index, search

Metadata Catalogue

Storage

Regi

ster

met

adat

a

Upl

oad

data

Regi

ster

link

Regi

ster

acc

ess m

etho

d

Closed Storage

Hooking togethertemplates, register, harvest, index, search

Just Enough Results Model

Sample

Spreadsheets!!

JBEI-ICELabCollector

LabArchivesJupyter

Galaxy / Refinery in the works….

SPARQL endpoint release

Focus – joining stuff up!- JSON read/write API- ISA-TAB output

Spreadsheet tooling for metadata templates and metadata

harvesting

Data annotation with standards

Embed ontologies into Excel templates

Excel spreadsheets enriched with ontology annotations

Upload, extract metadata and register

in browser viewing + annotations

Model annotation – in schema

Model annotation – semanticSBML

Samples Club samples framework

User defined sample models

Interlinking between sample typesSample type defines a sharable standard

Template toolingAuto extractionTied to assay processes

Spotlight: Synthetic BiologySynBioChem Centre, UK

FAIRDOM Workflows and Pathways

Project Support – Understanding ProcessPlanning, Setups, Curation, Advice, Support

Community support Special project

support Special project

support

model technical curationwith our JWS Online partners

PALs project ambassadorsco-design, tailoring, communication, requirements, review

standard, best practices

More Projects and Centres

User Meeting, Barcelona@ICSB 2016

Processes and People• 80% process, 20% tech• Structuring the ISA• PIs• Sticking to conventions

and policies• Tension with standards

take-up vs laissez faire• Time and resource• Local responsibility• Recognition• Institutional Repositories• Automagic

• Licenses• Negotiated access• Embargos• Permission controls• Staged sharing• Private walled gardens

FAIR Play

Using FAIRDOM my own lab colleagues saw what I was doing and called to collaborate!

Jurgen HannstraVrije Universiteit Amsterdam, Netherlands

FAIR Play• Drivers

– External dominate– Personal

productivity• Trading behaviours

– Tribal based– Modellers vs

Experimentalists• “enclave” sharing

– Rather than public donation

• Reciprocity & credit– Citation

affecting behavioural change through libertarian paternalism*

*Garza et al Framing the Community Data System Interface, https://dx.doi.org/10.6084/m9.figshare.1300051.v5

Stanford et al The evolution of standards and data management practices in systems biology, Molecular Systems Biology (2015) 11: 851 DOI 10.15252/msb.20156053

FAIRDOM Association e.V.

Jon Olav Vik, Norwegian University of Life ScienceMaksim ZakhartsevPlant Systems BiologyUniversity HohenheimStuttgart, GermanyAlexey KolodkinSiberian BranchRussian Academy of Sciences

Tomasz Zieliński,SynthSys CentreUniversity Edinburgh