EXAMPLE: levchenko
==================

The following bundle of files relates to the papers:

D. Gilbert, M. Heiner, S. Lehrack:
A Unifying Framework for Modelling Biochemical Pathways Using Petri Nets;
Proc. CMSB 2007, LNCS/LNBI 4695, pp. 200-216;

M Heiner, D Gilbert, R Donaldson:
Petri Nets for Systems and Synthetic Biology;
in M Bernardo, P Degano, and G Zavattaro (eds.): SFM 2008, Springer LNCS 5016, pp. 215Ð264, 2008. 


FILES

levchenko.zip        - all the following files, including this read.me 

levchenko_N*.spped   - qpn (snoopy), N* specifies the number of levels;
levchenko_N1.pnt     - qpn (ina);
levchenko_N1.ina     - qpn, ina analysis protocol;
infinite_run.spped   - partial order run of the i/o t-invariant (snoopy) for N1;
levchenko.ctl        - ctl queries (mc bddctl);
levchenko_bddctl.log - log file (mc bddctl);
state_spaces.log     - statistics for selected level numbers (iddctl);

levchenko_1.sm       - spn (prism, process algebra coding style);
levchenko_2.sm       - spn (prism, SPN coding style);
levchenko.csl        - csl queries (mc prism) 
levchenko_prism.log  - log file (mc prism)

levchenko.spcontped  - cpn (snoopy);
levchenko.xml        - cpn (sbml);
levchenko-ode.txt    - cpn as ode in text notation;
levchenko.conltl     - ltl queries (biocham's buil-in mc);


REFERENCES

A. Levchenko, J. Bruck, and P.W. Sternberg:
Scaffold proteins may biphasically affect the levels of mitogen-activated 
protein kinase signaling and reduce its threshold properties; 
Proc Natl Acad Sci USA, 97(11):5818–5823, 2000.

S. Lehrack: 
Three Petri Net Approaches for Biochemical Network Analysis.
TR I-01, Dep. CS, BTU Cottbus, 2006.

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