Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle-5

Signaling Petri net. The table in (c) provides the markings for the Petri net over the course of a simulation run whose duration is two time blocks. The proteins are given the initial marking shown in the column. Each subsequent column corresponds to a single time step during which one transition fired, producing a new marking of the network. The bold number in each column indicates which protein's marking was affected by the transition that fired in that time step. The red columns – always the last time step in the block – highlight the markings whose values would be averaged and used as part of the final result. These red columns are the sources of the markings that reports.<p><b>Copyright information:</b></p><p>Taken from "Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle"</p><p>http://www.biomedcentral.com/1752-0509/2/76</p><p>BMC Systems Biology 2008;2():76-76.</p><p>Published online 19 Aug 2008</p><p>PMCID:PMC2527501.</p><p></p

Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle-1

showing the selected path highlighted.<p><b>Copyright information:</b></p><p>Taken from "Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle"</p><p>http://www.biomedcentral.com/1752-0509/2/76</p><p>BMC Systems Biology 2008;2():76-76.</p><p>Published online 19 Aug 2008</p><p>PMCID:PMC2527501.</p><p></p

Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle-0

Wo High nodes, EGF and LKB-auto. EGF will be initialized with a token-count of 10, LKB-auto with a token-count of 3. The token-count of AMPK will be zero for the duration of the simulation. (b) The setup window for the differential simulator. Two different scenarios are being compared through simulation: different token assignments are being tried with EGF and LKB-auto, with and without AMPK being fixed low. (c) The plot window for the marking series generated by a simulation. Observe that the signaling nodes whose activity-levels are plotted correspond to those selected in the checklist directly to the left of the plot.<p><b>Copyright information:</b></p><p>Taken from "Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle"</p><p>http://www.biomedcentral.com/1752-0509/2/76</p><p>BMC Systems Biology 2008;2():76-76.</p><p>Published online 19 Aug 2008</p><p>PMCID:PMC2527501.</p><p></p

Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle-3

to place and zero tokens are assigned to place . The two places are connected by a transition, . The arcs in and out of indicate the direction in which tokens move. When fires, it moves some number of tokens from and puts them in . In (b), transition has fired and moved two tokens from to .<p><b>Copyright information:</b></p><p>Taken from "Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle"</p><p>http://www.biomedcentral.com/1752-0509/2/76</p><p>BMC Systems Biology 2008;2():76-76.</p><p>Published online 19 Aug 2008</p><p>PMCID:PMC2527501.</p><p></p

Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle-2

Ghlighted in blue. (b) The color distribution for the selected marking in the group is applied to the network view in the main window. Note that signaling nodes for which values were not given are not assigned a color on the valid red to green spectrum.<p><b>Copyright information:</b></p><p>Taken from "Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle"</p><p>http://www.biomedcentral.com/1752-0509/2/76</p><p>BMC Systems Biology 2008;2():76-76.</p><p>Published online 19 Aug 2008</p><p>PMCID:PMC2527501.</p><p></p