Boele, J. (Joost)

Maarleveld, T.R. (Timo)

Olivier, B.E.

Snoep, J.L.

Swat, M.

Wolstencroft, K.J.

English

Boele, Joost

Maarleveld, Timo

NARCIS 

Towards truly integrated modelling in Systems Biology Developing the Software and Standards

CWI's Institutional Repository

Towards truly integrated modelling in Systems Biology  Developing the Software and Standards Brett G. Olivier1,3, Maciej Swat4, Katy J. Wolstencroft2, Jacky L. Snoep2,5, Joost Boele1, Timo Maarleveld1,3 1 Systems Bioinformatics, VU University Amsterdam, Amsterdam, The Netherlands 2 Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands 3 Life Sciences, Centrum Wiskunde & Informatica (CWI), Amsterdam, The Netherlands 4 EMBL European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom 5 Triple-J Group, Stellenbosch University, Stellenbosch, South Africa b.g.olivier@vu.nl  A core principle of Systems Biology is an iterative, process that cycles between theory, modelling and experiment.  This requires the integration of new and existing software using community driven standards and application interoperability Here we present a selection of web-based and standalone modelling and data-management solutions that implement standards e.g. the Systems Biology Markup Language (SBML), SBML Flux Balance Constraints (SBML-FBC)  and Systems Biology Graphical Notation (SBGN).  The future challenge is to develop the standards and frameworks that allows the seamless integration of these and future tools. JWS Online FAME SBPKPD Web-based genome-scale modeling and visualisation environment  Model construction, analysis and visualization  Supports SBML and SBML-FBC models  Open source: PHP/Python based RightField StochPy PySCeS-CBM PySCeS Molecular Cell Physiology Systems Bioinformatics SBGN www.sbgn.org Graphical Notation SED-ML sed-ml.org Simulation experiments SBML www.sbml.org Biological models SBML-FBC www.sbml.org Constraint based models SEEK Web-based SB data and model management  Integrated platform for data, protocol management and annotation  Open source: part of the SySMO-DB project  Includes JWS Online OneStop module www.sysmo-db.org/seek Embed semantics directly into spreadsheet templates   Enables simple, standards-compliant data annotation  Open source spreadsheet add-in www.sysmo-db.org/rightfield K.Wolstencroft, et al., RightField: Embedding ontology annotation in spreadsheets. Bioinformatics (2011), May 2011. Web-based platform for Systems Biology driven Pharmacokinetics and Pharmacodynamics   Contains published and peer-reviewed models and user libraries for fitting physiological data  Implemented in R and GWT www.sbpkpd.org Swat, M. et al., What it takes to understand and cure a living system Interface Focus. (2011) 1, 16–23.  f-a-m-e.org Boele J, Olivier BG, Teusink B., FAME: the Flux Analysis and Modeling Environment, BMC Systems Biology (2012) 6, 8 Web-based Systems Biology curated database of kinetic models simulation tool  Includes simulation, steady-state, structural and metabolic control analysis  SBGN pathway representation with SED-ML support included with OneStop jjj.biochem.sun.ac.za jjj.bio.vu.nl Olivier B.G. and Snoep J.L., Web-based kinetic modelling using JWS Online, Bioinformatics (2004)  20, 2143-2144 Interactive, flexible, extendable research tool for the numerical analysis of cellular systems   Includes simulation, steady-state, bifurcation structural and metabolic control analysis  Supports SBML, provides a Python based, scriptable, open source, modelling platform Olivier, B.G., Rohwer J.M. and Hofmeyr J.-H. S. Modelling Cellular Systems with PySCeS, Bioinformatics (2005) 21, 560-561  pysces.sourceforge.net Interactive flexible package, for the stochastic simulation of biochemical systems  Includes various SSA’s and statistical analyses  Supports SBML and interfaces links to other software e.g. CAIN, StochKit and PySCeS  Open source Python implementation stompy.sourceforge.net Open source, flexible workbench for constraint based modelling of genome scale models  Includes flux balance and variability analysis, gene deletions and minimal distance methods  Has interactive, scripted and graphical user interfaces and support the SBML-FBC standard pysces.sourceforge.net/cbm 

Towards truly integrated modelling in Systems Biology Developing the Software and Standards

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