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

Overall Design

Probabilistic Temporal Logic

Specification

BioNetGen Simulations

Statistical Hypothesis Testing

Either Proof of Correctness or Error

or More Samples Needed

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

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• …

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} ]

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} ]

How to write a testsuite?• Write a test suite file called /home/james/testsuite with 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.

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

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?