Transcript Models - Sysmo

SysMo-DB:
Supporting Data Access and Integration
PALS kick-off
Carole Goble, University of Manchester UK
Isabel Rojas, EML Research gGmbH, Germany
Jacky Snoep, Uni of Manchester / Stellenbosch, S Africa
Goal of SysMO
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Eleven individual projects
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Different research outcomes
A cross-section of microorganisms, including
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.
DB
SysMO-DB
Web-based solution to facilitate:
 exchange
of data, models and
processes (intra- and interconsortia)
 search for data, models and
processes across the initiative
 maximisation of the "shelf life" and
utility of the data, models and
processes generated
 dissemination of results
SysMO-DB Team
Isabel Rojas
EML Research
gGmbH, Germany
Olga Krebs
Carole Goble
University of Manchester, UK
Jacky Snoep
Katy Wolstencroft
University of Stellenbosch, South Africa
University of Manchester, UK
Stuart Owen
SysMODB
Team
PALS
Falko Krause
TRANSLUCENT
Bioinformatics
Berlin, Germany
Leif Steil
BaCell-SysMO
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Walter Glaser
MOSES
Experimentalist,
databases
Bioinformatician
Malkhey Verma
MOSES + SulfoSys
Manchester, UK
Femke Mensonides
MOSES + SulfoSys
Experiment/
modeller interface
Experiment/
modeller interface
Hanan Messiha Girgis
MOSES
Experimentalist
Manchester, UK
Pawel Sierocinski
SulfoSys
Experimentalist
Wageningen, Netherlands
Maria Rodrigues
KOSMOBAC
Modeller
Vigo. Spain
Afsaneh Maleki-Dizaji
SUMO
Bioinformatician
Sheffield, UK
John Heap
COSMIC
Experimentalist
Nottingham, UK
Walid Omar
STREAM
Experimentalist
Warwick, UK
Elon Correa
Valla
Modeller
Manchester, UK
Renate Kania
SysMO-LAB
Database
EML, Germany
Mark Musters
SysMO-LAB
Modeller
Wageningen, Netherlands
Paul McDermott
PSysMO
Experimentalist
Essex, UK
Maksim Zakhartsev
MOSES
Experimentalist
Stuttgart, Germany
Jay Moore
STREAM
Bioinformatican
Jennifer ???
SysMO-LAB
Experimentalist
Vienna, Austria
Vrije University, Netherlands
Principles…
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A series of small victories
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Realistic
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Eases the real pressure points
and concerns of the groups
Works with what you have
already
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Low hanging fruit immediately
Early wins
What are these for
your project?
What are these for
your project?
Borrow, link up, spread around
Doesn‘t reinvent
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What are these for
your project?
Uses what is already available
What are these for
your project?
Sweet spots and Pains
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And what are the obstacles / barriers?
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Tell us about your experimentalists, modellers
and bioinformaticians
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What doesn’t work right now?
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What does?
So, the purpose of meeting
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Getting to know each other
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Audit and show and tell
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Wiki entries!
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Early wins
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SysMO-SEEK
New
hypothesis
Predict
New data
SysMO Data
Model
analysis
JWS
Online
Experimental
validation
Workflows
SABIORK
BioModels
External Data
and
Applications
COPASI
Construct
pathway model
in SBML
Brenda
Model
update
New data
Data analysis &
integration
Workflows
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Find people, projects and stuff
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Store experimental data
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JWS Online
Link together your own and other data and
applications into analytical pipelines
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Just Enough Results Model interface
Exchange and run models
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SABIO-RK and other systems
Exchange data
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SysMO-SEEK
Taverna workflows
Common web access point
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SysMO-HUB
Proposed solution
Discovery,
Access
Annotation &
Collaboration
DB
Results
Cache
Access Control
Interface
Service
Integration
SysMO HUB Portal (Liferay)
Taverna Workflows
JERM
Bio
Catalogue
Access Control
Web Service
Access Interface
Web Service Access Interface
SysMO Data
Models
Workflows
External Resources
Metadata
Metadata
Metadata
Metadata
Metadata
SABIORK
JWS
Online
myExperiment
Repositories
& Resources
JERM Extractor
SysMO
SEEK
Web Access - SysMO-Hub
A common web entry point to the information
created by the SysMO partners.
 How
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do you do this in your project?
Wiki? eGroupWare? PHProject?
Does it work?
 Ideas
for getting people to use it?
 What would you like it to look like?
 What other sites might you use?
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OpenWetWare? WikiPathways? Pathway
Commons?
DB
SysMO Data
Models
Workflows
SysMO
SEEK
External Resources
Metadata
Metadata
Metadata
Metadata
SABIORK
JWS
Online
myExperiment
Metadata
Repositories and Resources
SysMO
SEEK
SysMO SEEK
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Is 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?
and many more
from you....
Discovery SysMO-SEEK
 Yellow
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People, Projects, Group
 Assets
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pages
catalogue
Data holdings, Files
 Integrated
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search
Over model and workflow catalogues
 How
do you do this in your project?
 Ideas for getting the data and maintaining it?
 How do your teams find stuff out?
 What questions would you like to ask?
 What data should we hold?
SysMO Data
Models
Workflows
External Resources
Brenda
SABIO-RK
SysMO Partner resources
Metadata
Metadata
Metadata
Metadata
JWS
Online
myExperiment
SABIORK
Metadata
Repositories and Resources
DB
SysMO
SEEK
Data Storage
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What data do you store now?
What systems do you use?
What formats?
SysMO Data
Models
Workflows
External Resources
BioModels
JWS
Model databases
Metadata
Metadata
Metadata
Metadata
JWS
Online
myExperiment
SABIORK
Metadata
Repositories and Resources
DB
SysMO
SEEK
Models
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Publish, manage, run, validate
JWS Online
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Database of curated models and a simulator
Web service enabled
Each SysMO projects will have a separate
password protected website.
DB
Data comparison and
integration
Interface
JERM
Web Service
Access Interface
Web Service Access Interface
SysMO Data
Models
Workflows
External Resources
Metadata
Metadata
Metadata
JWS
Online
myExperiment
SABIORK
Metadata
JERM Extractor
Metadata
Service
“Just Enough Results Model” (JERM) minimum
metadata for exchange, comparison and integration
SysMO
SEEK
Data and Metadata
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“Just Enough Results Model”
minimum metadata for
exchange
Ontologies, catalogues and
controlled vocabularies for
annotation
What do you annotate now?
Access Control
JERM
Web Service
Access Interface
JERM Extractor
Metadata
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SABIO-RK
SysMO Data
Data Exchange Standards
which do you use?
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MIRIAM
MIAME
MIAPE
SBML
BioPAX
FUGE
OBI
What other formats do you use?
DB
Proposed Standard: MIRIAM
Minimum Information Requested In the
Annotation of biochemical Models
Proposed guidelines for annotation and
curation of quantitative models
• Specifically about encoding & annotation
• Limited to models that can be simulated
MIRIAM approach avoids putting data
content directly into the model;
instead, it points at external resources that
contain the knowledge.
www.ebi.ac.uk/miriam
Nature Biotech. 23(12), Dec. 2005
Just Enough Results Model
Exchange
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Which data do you need / would like to know from
others?
What data would you be willing to give?
How do you annotate your data?
How do you cross relate different types of data?
What standards for data do you already use and
know about?
Can we look at the schemas of your databases?
What facilities do you have for coping with external
access – how do you export data now?
Processes - Workflows
DB
Interface
Service
Taverna Workflows
JERM
Bio
Catalogue
Access Control
Web Service
Access Interface
Web Service Access Interface
SysMO Data
Models
Workflows
External Resources
Metadata
Metadata
Metadata
Metadata
Metadata
SABIORK
JWS
Online
myExperiment
Repositories
& Resources
JERM Extractor
SysMO
SEEK
Processes - Workflows
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Automated repeatable and
shareable plan or script
Integration and analysis
pipelines
Model construction and
population
Transparent provenance log
Make data sets and tools
accessible to a workflow
engine.
Taverna Workflow
Management System
First Steps
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Simple Hub
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Simple SEEK
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Link through to your sites
Yellow pages and Assets Catalog
Identify pilots for exchange first attempt
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Three projects
Scenarios
So, the purpose of meeting
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Getting to know each other
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Audit and show and tell
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Wiki entries!
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Early wins
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SysMO-SEEK
Agenda
Today
 Pals introduction
 SEEK design
 Project Audit and Show and Tell
Tomorrow
 Data exchange brainstorm
 Collaboration planning