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Reaction System Simulator

This page provides a Web interface to the brsim reaction system simulator. For more information about how to describe reaction systems and their contexts, see the project page.


 

 

 


Example 1: A Binary Counter

In Example 3 of paper [1], the authors show how binary counters can be built with reaction systems. In short, the idea is to allocate one species per binary bit and, if it is present in the system, consider that the bit is set. The following is a description of the system implementing a four-bit binary counter in the default format of the simulator, similar to the conventional notation for reactions. A reaction consuming the species a and b, producing the species c and d, and inhibited by e and i, will be written as a b, e f, c d in this format.

 

# Reactions maintaining the presence of a bit in a current state.
e1, e0, e1

e2, e0, e2
e2, e1, e2

e3, e0, e3
e3, e1, e3
e3, e2, e3

e4, e0, e4
e4, e1, e4
e4, e2, e4
e4, e3, e4

# Reactions actually doing the increment.
e0,           e1, e1
e0 e1,        e2, e2
e0 e1 e2,     e3, e3
e0 e1 e2 e3,  e4, e4

The lines starting with the hash symbols are comment lines and are ignored.

 

You can now just copy and paste these reactions into the first big text box at the top of the page. Note that you can use the small triangular grip in the bottom right corner of the text boxes to expand to whatever size you need. To provide a context sequence and thereby tell the simulator what to run the system with, and you may input the following text into the second text box:

 

e1 e4
.
e0
e0
.

 

This is exactly the sequence of contexts the authors use in [1], the lines containing full-stops corresponding to empty contexts. If you now click the button Simulate, you will see the annotated output of the simulator, providing various useful details about the evolution of the system.

Example 2: Heat Shock Response

In Table 6 of [2], the authors describe a reaction system modelling the heat shock response in eukaryotes. The following listing shows how to translate the reactions modelling the heat shock response in the format the simulator understands.

 

hsf, hsp, hsf3
hsf hsp mfp, dI, hsf3
hsf3, hse hsp, hsf
hsf3 hsp mfp, hse, hsf
hsf3 hse, hsp, hsf3:hse
hsf3 hse hsp mfp, dI, hsf3:hse
hse, hsf3, hse
hse hsf3 hsp, mfp, hse
hsf3:hse, hsp, hsf3:hse hsp
hsf3:hse hsp mfp, dI, hsf3:hse hsp

hsp hsf, mfp, hsp:hsf
hsp:hsf stress, nostress, hsp hsf
hsp:hsf nostress, stress, hsp:hsf
hsp hsf3, mfp, hsp:hsf
hsp hsf3:hse, mfp, hsp:hsf hse
prot stress, nostress, prot mfp
prot nostress, stress, prot
hsp mfp, dI, hsp:mfp
mfp, hsp, mfp
hsp:mfp, dI, hsp prot

 

The following listing gives the context sequence shown in Table 7 of [2], which describes how the reaction system models the behaviour of the cell in the absence of stress.

 

hsf prot hse nostress
nostress
nostress
nostress
nostress
nostress

 

The following listing gives the context sequence shown in Table 8 of [2], which describes how the reaction system models the behaviour of the cell in heat shock.

 

hse prot hsp:hsf stress
stress
stress
stress
stress
stress

Listing the Conserved Sets

To list the support sets, you should only provide a description of the reaction system; the list of context is not required. Since this operation may quickly become resource consuming, the simulator is set to run with a time-out.

References

[1]  A. Ehrenfeucht and G. Rozenberg. Reaction systems. Fundamenta Informaticae, 75(1):263–280, 2007.

[2]  Sepinoud Azimi, Bogdan Iancu, Ion Petre, Reaction System Models for the Heat Shock Response. Fundamenta Informaticae 131, 1–14 , 2014.

[3] Sepinoud Azimi, Cristian Gratie, Sergiu Ivanov, Luca Manzoni, Ion Petre, Antonio E. Porreca, Complexity of Model Checking for Reaction Systems. TUCS Technical Reports 1122, TUCS, 2014.

[4] Sepinoud Azimi, Cristian Gratie, Sergiu Ivanov, Ion Petre, Dependency Graphs and Mass Conservation in Reaction Systems. TUCS Technical Reports 1123, 2014.