.. _Visualization:
 

Visualization examples
=======================

Here are the six types of reaction network motifs and some generated artificial random signaling
network examples shown as below. The figures were generated by SBcoyote version 1.5.0.

------------------------
Reaction network motifs
------------------------

The synthetic random networks were composed of six types of reactions: 

- catalyzed uni-uni (A), 
- binding and unbinding reactions (B, C), 
- exchange reactions (D),
- catalyzed phosphorylation-dephosphorylation (E),
- dual phosphorylation-dephosphorylation cycles (F). 

.. image:: Figures/Visualization/motifs.png
  :width: 700

---------------------------------------------
Artificial random signaling network examples 
---------------------------------------------

**1) Reaction networks with 15 species and 11 reactions.**

The figure below illustrates two examples of randomly generated signaling networks. Figure A 
included four types of chemical reaction motifs. Species were labeled S1 to S15. The reactions 
included four uni-uni processes: S6 → S7 catalyzed by S5, S8 → S6 catalyzed by S10, S9 → S5 
catalyzed by S15, and S11 → S9 catalyzed by S15; one bi-bi reactions: S_in + S14 → S10 + S13; 
one single phosphorylationdephosphorylation cycle: S12 ⇋ S_out catalyzed by S7 and S1; and one 
dual phosphorylation-dephosphorylation cycle S11 ⇋ S4 ⇋ S3 catalyzed by S6 and S2. Figure B 
included the other two types of chemical reaction process, namely one uni-bi reaction: 
S12 → S12 + S14 and one bi-uni reaction: S_in + S10 → S11. As shown, all the random signaling 
networks had 15 species in addition to input and output species, with 11 reactions.

.. image:: Figures/Visualization/15-11.png
  :width: 700

**2) Reaction networks with 15 species and 22 reactions.**

The figure below illustrates two examples of randomly generated signaling networks. Figure A 
included five types of chemical reaction motifs. Species were labeled S1 to S15. These include 
three uni-uni processes: S2→S9 catalyzed by S7, S14 → S5 catalyzed by S2, and S10 → S7 catalyzed 
by S11; one bi-uni reaction: S14 + S12 → S12; two bi-bi reactions: S11 + S_in → S15 + S13 and 
S12 + S15 → S12 + S14; two single phosphorylation-dephosphorylation cycles: S1 ⇋ S_out catalyzed 
by S3 and S9 and S4 ⇋ S14 catalyzed by S2 and S12; and three dual phosphorylation-dephosphorylation
cycles S2 ⇋ S8 ⇋ S6 catalyzed by S5 and S12, S3 ⇋ S10 ⇋ S11 catalyzed by S4 and S5, 
S5 ⇋ S10 ⇋ S14 catalyzed by S4 and S6. Figure B included the 6th type of chemical reaction process, 
namely one uni-bi reaction: S10 → S10 + S13. As shown, all the random signaling networks had 15 
species in addition to input and output species, with 22 reactions.

.. image:: Figures/Visualization/15-22.png
  :width: 700