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The ERATO Systems Biology Workbench. Michael Hucka, Hamid Bolouri, Andrew Finney, Herbert Sauro ERATO Kitano Systems Biology Project California Institute of Technology, Pasadena, CA, USA Principal Investigators : John Doyle, Hiroaki Kitano
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The ERATO Systems Biology Workbench Michael Hucka, Hamid Bolouri, Andrew Finney, Herbert Sauro ERATO Kitano Systems Biology Project California Institute of Technology, Pasadena, CA, USA Principal Investigators: John Doyle, Hiroaki Kitano Collaborators:Adam Arkin (BioSpice), Dennis Bray (StochSim), Igor Goryanin (DBsolve), Les Loew (Virtual Cell), Pedro Mendes (Gepasi/Copasi), Masaru Tomita (E-Cell)
Background • Modeling, simulation & analysis are critical • Huge volumes of data • Many disparate findings • Rapid rate of software tool development • Roles: data filtering, model creation, model simulation • Many groups are creating many tools • Different packages have different niche strengths reflecting expertise & preferences of the group • Strengths are often complementary to those of other packages
Tool 7 Tool 6 Tool 5 Tool 2 Tool 4 Tool 1 Tool 3 Multistate reactions/stochastic Reaction/Diffusion Optimization Bifurcation analysis Visualization of networks Handle large systems Complementary Strengths of Tools
Problems • No single package answers all needs of modelers • No single tool is likely to do so in the near future • Range of capabilities is large • New techniques ( new tools) evolving too rapidly • Researchers are likely to continue using multiple packages for the foreseeable future • Problems in using multiple tools: • Simulations & results often cannot be shared or re-used • Duplication of software development effort
Goal & Approach • Systems Biology Workbench goal: to provide software infrastructure that • Enables sharing of simulation/analysis software & models • Enables collaboration between software developers • Two-pronged approach: • Develop a common model exchange language • SBML: Systems Biology Markup Language • Develop an environment that enables tools to interact • SBW: Systems Biology Workbench
Systems Biology Markup Language • Problem: • Many software tools, few common exchange formats • Difficult to take advantage of multiple tools • Difficult to establish repositories of models • A Solution (In Principle): • Define a common exchange language • Use a simple, well-supported, textual substrate (XML) • Add components that reflect the natural conceptual constructs used by modelers in the domain
Structure of Model Definitions in SBML • Domain: biochemical network models • A model is described using a list of components: • Beginning of model definition • List of unit definitions (optional) • List of compartments • List of species • List of parameters (optional) • List of rules (optional) • List of reactions • End of model definition • Each component has a specific structure
S1 X2 X1 X0 Example k2*S1 k1*X0 k3*S1
Example (cont.) <?xml version=“1.0” encoding=“UTF-8”?> <sbml level=“1” version=“1”> <model name=“simple”> <listOfCompartments> <compartment name=“c1” /> </listOfCompartments> <listOfSpecies> <specie name=“X0” compartment=“c1” boundaryCondition=“true” initialAmount=“1”/> <specie name=“S1” compartment=“c1” boundaryCondition=“false” initialAmount=“0”/> <specie name=“X1” compartment=“c1” boundaryCondition=“true” initialAmount=“0”/> <specie name=“X2” compartment=“c1” boundaryCondition=“true” initialAmount=“0.23”/> </listOfSpecies>
Example (cont.) <?xml version=“1.0” encoding=“UTF-8”?> <sbml level=“1” version=“1”> <model name=“simple”> <listOfCompartments> <compartment name=“c1” /> </listOfCompartments> <listOfSpecies> <specie name=“X0” compartment=“c1” boundaryCondition=“true” initialAmount=“1”/> <specie name=“S1” compartment=“c1” boundaryCondition=“false” initialAmount=“0”/> <specie name=“X1” compartment=“c1” boundaryCondition=“true” initialAmount=“0”/> <specie name=“X2” compartment=“c1” boundaryCondition=“true” initialAmount=“0.23”/> </listOfSpecies>
Example (cont.) <?xml version=“1.0” encoding=“UTF-8”?> <sbml level=“1” version=“1”> <model name=“simple”> <listOfCompartments> <compartment name=“c1” /> </listOfCompartments> <listOfSpecies> <specie name=“X0” compartment=“c1” boundaryCondition=“true” initialAmount=“1”/> <specie name=“S1” compartment=“c1” boundaryCondition=“false” initialAmount=“0”/> <specie name=“X1” compartment=“c1” boundaryCondition=“true” initialAmount=“0”/> <specie name=“X2” compartment=“c1” boundaryCondition=“true” initialAmount=“0.23”/> </listOfSpecies>
Example (cont.) <listOfReactions> <reaction name=“reaction_1” reversible=“false”> <listOfReactants> <specieReference specie=“X0” stoichiometry=“1”/> </listOfReactants> <listOfProducts> <specieReference specie=“X0” stoichiometry=“1”/> </listOfProducs> <kineticLaw formula=“k1 * X0”> <listOfParameters> <parameter name=“k1” value=“0”/> </listOfParameters> </kineticLaw> </reaction> <reaction name=“reaction_2” reversible=“false”> <listOfReactants> <specieReference specie=“S1” stoichiometry=“1”/> </listOfReactants> . . .
Some Points About SBML • Users do not write in XML — software tools do! • SBML is being defined incrementally • SBML Level 1 covers non-spatial biochemical models • Intentionally kept simple for maximal compatibility • SBML Level 2 will extend Level 1 with more facilities • Defined in abstract form (UML) + textual descriptions • Used to define XML encoding + XML Schema E.g.: • Composition • Geometry • Arrays … others Level 3? Level 2 Level 1
Systems Biology Workbench • Open-source, integrated software environment that enables sharing of computational resources • Allows software developers to build interprocess communications facilities into their applications • From the user’s perspective: • One SBW-enabled application can interact with another • Each application or module offers services to others • E.g.: ODE solution, time-based simulation, visualization, etc.
From the Programmer’s Perspective • Desirable features • Small application programming interface (API) • Libraries that implement inter-program communications • A registry of services for applications to query • XML-based model representation (SBML) • Uses well-known, proven technologies • Communications via message-passing over plain sockets • Modular, distributed, broker-based architecture • API provides two styles: • “Low-level”: call/send operations + directory services • “High-level”: object-oriented interface layered on top
Driving Principles • Keep it language-neutral • We’ll provide C++, Java, Delphi libraries for Win, Linux • But can be implemented in any language • Keep it simple • Simple message-passing scheme • Avoid complexity & size of CORBA • Easy to make cross-platform compatible • Easy to make distributed • Simple low-level API, convenient higher-level API • Make sure contributors benefit • Open source development • Symmetric infrastructure: no application dominates
Modules Planned • Data filtering & preparation • Database support • E.g.: web searching, storage management • Model definition & manipulation • E.g.: scripting languages, visual editors • Equation solvers • E.g.: ODEs, DAEs, stochastic • Analysis & visualization tools • E.g.: bifurcation, 2-D/3-D/4-D plotting • Optimization & parameter searching
Summary & Availability • SBML • Level 1 specification is publicly available • http://www.cds.caltech.edu/erato • Support being added by other groups to their apps • SBW • Preliminary test implementation completed • Production version is now in development • Draft API definition & other info available • http://www.cds.caltech.edu/erato/sbw/docs • Expect first public release in November atICSB 2001 (http://www.icsb2001.org)
Outline 1) Background and motivations I.e., why are we doing this? 2) Systems Biology Markup Language (SBML) Model description language & exchange format 3) Systems Biology Workbench Infrastructure for connecting software tools
Vmax*S1 Km+S1 K1*X0 - S1*K2 X0 X1 X2 S3/Ki Scope of SBML • Domain: biochemical network models k7*S3*S12 k4*S2 - k5*S3 k6*S3 S1 S2 S3 k3*S2