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Introduction to BioLab A Statistical Model Checker for BioNetGen

Introduction to BioLab A Statistical Model Checker for BioNetGen. Developer: Sumit Kumar Jha Edmund M Clarke, Sumit K. Jha, Chris Langmead, James Faeder, Andre Platzer, Paolo Zuliani. Overall Design. How to install?. Pre-compiled 64 bit binaries are available

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Introduction to BioLab A Statistical Model Checker for BioNetGen

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  1. Introduction to BioLabA Statistical Model Checker for BioNetGen Developer: Sumit Kumar Jha Edmund M Clarke, Sumit K. Jha, Chris Langmead, James Faeder, Andre Platzer, Paolo Zuliani

  2. Overall Design

  3. How to install? • Pre-compiled 64 bit binaries are available • Source code will be available once it is further cleaned (by end of this year). • Download Link: http://code.google.com/p/biolab2/ • Download these two files • http://biolab2.googlecode.com/files/simulationchecker • http://biolab2.googlecode.com/files/StatisticalModelChecker

  4. How to install? • Download SimulationChecker and SMC into the same directory (say /home/james/) • Install BioNetgen in a subdirectory called bionetgen • such that /home/james/bionetgen/BioNetGen_x.y.zz/Perl2/BNG2.pl is a valid directory entry. • Put the models to be model checked as /home/james/bionetgen/BioNetGen_x.y.zz/Models/biomodelXX.bngl • as in • /home/james/bionetgen/BioNetGen_x.y.zz/Models/biomodel1.bngl • /home/james/bionetgen/BioNetGen_x.y.zz/Models/biomodel2.bngl • …

  5. Write one or more property files • Put one LTL property each in /home/james/testX.ltl • as in • /home/james/test1.ltl • /home/james/test2.ltl • Typical LTL formulae: • [ {ppERK / totalERK < 0.1} U {time > 300} ]

  6. LTL Syntax • F : Future • G: Global • AND: And • OR: Or • U: Until • NOT: Not • <,>,=,<=,>=: Comparators • *,+,-,/: Arithmetic • {variable*variable+variable-(variable/variable) > constant-number} : example: {a/b < 100} • Formula starts with [ and ends with ]. • Use brackets () to override precedence and binding. • Typical LTL formulae: • [ {ppERK / totalERK < 0.1} U {time > 300} ]

  7. How to write a testsuite? • Write a test suite file called /home/james/testsuitewith the following entries • Sl. No. of model Sl. No. of LTL file Type I error Type II error P0 P1 BF • Example, • 1 1 0.01 0.01 0.49 0.51 1000 • Will check the model • /home/bionetgen/BioNetGen_x.y.zz/Models/biomodel1.bngl against the property in • /home/test1.ltl with Type I and II errors of 1/1000 each. • It will check whether the property is true with probability more than 0.51 or less than 0.49. The Type I and Type II errors are used to check that the BF corresponds to a value at least as tight as that specified by the Type I/II errors. The property in the LTL file must be in negation normal form – all negations must be pushed into the literals.

  8. How to start the Model Checker • ./StatisticalModelChecker • There may still be bugs lurking around. Please report crashes and wrong answers to jha@cs.cmu.edu

  9. Please send me feature requests! • Parallelization • MPI • Estimation FEATURE – LEONARD SUGGESTION • ODE Models with stochasticity parameters [loop around it can be used for parameter synthesis] - JIM] • Mustafa kamasch – russian literature (ask jim – his collaborators know about it) – correlated random sampling – correlated samples – trajectories correlated in random numbers sequence • Embedding within the BioNetGen Interface [– readfile – change bngl file] • Need your help for this to be painless for me. • How uncomfortable are these fixed file names ? • Would you prefer that you can specify their names and locations? • Write out a report file in response to the test-suite file. • Other suggestions?

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