Isab 11 for_slideshare

Systems Biology Software Infrastructure (SBSI) ISAB visit May 19 th 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

SBSI objective ‘ 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’ 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 C holesterol 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 ROBuST ECDF Software www.sbsi.ed.ac.uk SBSI installed on Hector, the UK national supercomputer BioPepa

Community standards involvement Data Standards www.sbsi.ed.ac.uk

SED-ML purpose Dagmar Waltemath -http://www.slideshare.net/dagwa/waltemath-onto-workshop-4326137 www.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 Knowledge www.sbsi.ed.ac.uk Led by Kitano group, SBI, Tokyo Pathway visualization Model creation Model analysis Text mining Pathway databases Molecular databases

CellDesigner / Garuda plugin www.sbsi.ed.ac.uk Download from www.celldesigner.org

Integration across projects Modelling languages Garuda collaborating institutions www.sbsi.ed.ac.uk BioPepa  appa – RuleBase Eclipse plugin works in SBSI

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 developers Azusa Yamaguchi Millar Group Carl Troein Steve Watterson Maria-Louisa Guerriero Robert Smith Simon Bordage Martin Beaton Tomasz Zielinski Thanks for watching… If you’re interested follow us on Twitter @CSBE_SBSI www.sbsi.ed.ac.uk

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Isab 11 for_slideshare

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