isab 11 for_slideshare
DESCRIPTION
This presentation describes the current status of SBSI in May 2011, and was presented at CSBE's annual scientific advisory board visit.TRANSCRIPT
Systems Biology Software Infrastructure (SBSI)
ISAB visit
May 19th 2011
Allan Clark, Nikos Tsorman, Neil Hanlon
Richard Adams, Stephen Gilmore
Talk outline
SBSI scope and purpose
Progress since last ISAB
Current priorities and future work
www.sbsi.ed.ac.uk
‘A new infrastructure to streamline the
connection between data, models, and
analysis, allowing the updating of large scale
data, models and analytic tools with greatly
reduced overhead’
SBSI objective
www.sbsi.ed.ac.uk
Goals of SBSI
Facilitate the incorporation of experimental data into modelling approaches
Develop computational capacity for analyzing larger models
Allow integration of novel scientific methods
Allow customization by external developers
Initially, focus on parameter estimation problem
www.sbsi.ed.ac.uk
Data and model results
www.sbsi.ed.ac.uk
How to get models to reproduce experimental data?
Parameter Estimation Problem
Building predictive models – a challenging problem in Systems Biology
Parameter estimation – critical stage in model development
Multiple data sets for model calibration
Global optimization needed due to complex cost landscapes
Genetic /evolutionary techniques perform well.
Circadian clock modellers have existing high-quality time-series data to fit.
www.sbsi.ed.ac.uk
Graphical Notation
Network Inference
Process Algebras
Model analysis
Existing knowledge
High-resolution data
High-throughput data
New knowledge
Static models
Kinetic models
Systems Biology Software Infrastructure™
Kinetic Parameter Facility
RNA metabolism
Systems Biology Research, CSBE view
Circadian clock Cholesterol metabolism
www.sbsi.ed.ac.uk
The SBSI Software Suite
www.sbsi.ed.ac.uk
The SBSI Software Suite
www.sbsi.ed.ac.uk
Using SBSI we can fit to oscillating data ( green line).
The SBSI Software Suite
www.sbsi.ed.ac.uk
SBSIVisual client organizes & displays resources, access SBSINumerics.
Outreach & documentation
Practical SBSI tutorial workshops at:ICSB2010, Edinburgh
EraSysBio Summer School, 2010
Several internal training sessions
Plant Systems Biology Summer School, 2011
Course material available for download from Sourceforge (http://sourceforge.net/projects/sbsi/files/SBSIVisual/).
Comprehensive HTML and pdf user manuals for SBSINumerics and SBSIVisual
Tutorial videos on YouTube ( channel sbsi23)
www.sbsi.ed.ac.uk
Integration - databases
Data sources
www.sbsi.ed.ac.uk
Integration with Plasmo & Robust databases
Integration - databases
Data sources Data Standards
High performance computing
Modelling languages
Software
www.sbsi.ed.ac.uk
Plasmo search..
HPC access
Data sources Data Standards
High performance computing
Modelling languages
BioPepa
ROBuST
ECDF
Software
www.sbsi.ed.ac.uk
SBSI installed on Hector, the UK national supercomputer
Community standards involvement
Data Standards
www.sbsi.ed.ac.uk
SED-ML purpose
Dagmar Waltemath -http://www.slideshare.net/dagwa/waltemath-onto-workshop-4326137www.sbsi.ed.ac.uk
MIASE / SED-ML contributors
> 21 collaborating institutions worldwide.http://sed-ml.org
SED-ML developments 2009 - present
www.sbsi.ed.ac.uk
MIASE paper published 2011 http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1001122
SED-ML developments 2009 - present
www.sbsi.ed.ac.uk
SED-ML specification published
SED-ML developments 2009 - present
www.sbsi.ed.ac.uk
XML schema and Java library released..
SED-ML support in SBSI
www.sbsi.ed.ac.uk
Executing SED-ML
www.sbsi.ed.ac.uk
Editing SED-ML
www.sbsi.ed.ac.uk
Integration across projects
Garuda collaborating institutions
www.sbsi.ed.ac.uk
Software
CellDesigner
Integration across projects
Garuda collaborating institutions
www.sbsi.ed.ac.uk
Garuda functionality
Pathway visualization
Model creation
Model analysis
Text mining
Pathway databases
Knowledge
Molecular databases
www.sbsi.ed.ac.ukLed by Kitano group, SBI, Tokyo
CellDesigner / Garuda plugin
www.sbsi.ed.ac.uk
Download from www.celldesigner.org
Integration across projects
Modelling languages
BioPepa
appa – RuleBase Eclipse plugin works in SBSIGaruda collaborating institutions
www.sbsi.ed.ac.uk
Integration across projects
www.sbsi.ed.ac.uk
The Kappa rule-based modelling environment
Vertical integration
Web interface to SBSI
REST-ful web service at https://mook.inf.ed.ac.uk:8083/sbsiservices/
Reuse of software components
www.sbsi.ed.ac.uk
Coding challenge
www.sbsi.ed.ac.uk
How can a fixed number of developers continue to maintain and develop new code?
Solution 1 – manage dependencies
www.sbsi.ed.ac.uk
Avoid cycles at all costs!
Solution 2 – continuous testing
Solution 3 – involve more developers
www.sbsi.ed.ac.uk
Plugin contributions can be independently developed, licensed and deployed.
Current work
Supporting core users for parameter estimation (Circadian clock and cholesterol pathway modelling)
Exploring collaboration with other computational groups in CSBE (Swain, Grima, Danos, Plotkin) for modelling language support in SBSI.
Developing external collaborations
www.sbsi.ed.ac.uk
Acknowledgements
Allan Clark
Nikos Tsorman
Neil Hanlon
Richard Adams
Stephen Gilmore
Current Development Team Past developersAzusa Yamaguchi
Millar GroupCarl TroeinSteve WattersonMaria-Louisa GuerrieroRobert SmithSimon BordageMartin BeatonTomasz Zielinski
Thanks for watching… If you’re interested follow us on Twitter@CSBE_SBSI
www.sbsi.ed.ac.uk