BooleanNet

[…] Circles represent the AND function which combines several interactions. Model construction and time course simulation of MAPK signalling pathways in response to Herceptin treatment was done using the BooleanNet toolkit under Python 2.7 []. Both synchronous and asynchronous simulations were performed. In synchronous updating rules, all variables are updated at the same time, while in asynchronous s […]

[…] tep, and (ii) the state‐space is generated with all the transition history of a sufficient number of consecutive steps from a sufficient number of random initial states. R‐ABS was performed using the BooleanNet ver.1.2.6 Python package (http://code.google.com/p/booleannet/), with 700 consecutive update steps from each of 700 random initial states per condition. Five independent simulations per con […]

[…] between PSA (KLK3) and other genes: “KLK3 low => X low” and its counterpart “X high => KLK3 high” (Figure ). The resulting gene list included 57 transcripts (using s > 10, p < 0.01 threshold for the BooleanNet analysis). To filter this list, we assembled three independent publicly available prostate cancer datasets that were annotated for recurrence-free survival and tested whether the transcript […]

[…] g signal transduction pathways [], particularly when, as in the present case, relative timescales of internal processes are largely unknown. We implemented the model using the Python software library BooleanNet []. We used the stochastic asynchronous update algorithm, in which the nodes are updated in a randomly selected order in each time step. Due to the stochasticity introduced by the update me […]

[…] tinuous time description, thus providing more understandable information about general pathway dynamics under different conditions. To support these studies, publicly available software tools such as BooleanNet [], PATHOLOGIC-S [] and Odefy [] have been developed; they offer a scalable Boolean framework for modeling cellular signaling.Following these considerations, in this work we present a novel […]

[…] ible for the splice site recognition in each case.The model was simulated synchronously (i.e., all equations updated simultaneously) and asynchronously (i.e., random execution of the equations) using BooleanNet-1.2.4 software until the steady state is reached []. In this model, we also defined three functions, viz. “TH_1_response*”, “TH_2_response*”, and “NO_response*”, which reflect the type of T […]