SteadyCellPhenotype: a web-based tool for the modeling of biological networks with ternary logic
Adam C Knapp1,2, Luis Sordo Vieira1, Reinhard Laubenbacher1
1Department of Medicine, University of Florida, Gainesville, FL 32611, USA.
Summary:
We introduce SteadyCellPhenotype, a browser-based interface for the analysis of ternary biological networks. It includes tools for deterministically finding all steady states of a network, as well as the simulation and visualization of trajectories with publication quality graphics. Simulations allow us to approximate the size of the basin for attractors and deterministic simulations of trajectories nearby specified points allow us to explore the behavior of the system in that neighborhood.
Availability And Implementation:
https://github.com/knappa/steadycellphenotype MIT License.
More Related Videos
Related Concept Videos
Cell Signaling Feedback Loops
Negative feedback loops
Most signaling systems have negative feedback loops that can perform different functions such as output limiter, and adaptation.
Output limiter
Upon receiving an input signal, the cellular response rapidly increases until a threshold is reached. Beyond this threshold, a negative feedback loop...
Synthetic Biology
Golden rice
Golden rice is a genetically modified...
Three-Compartment Open Model
Combinatorial Gene Control
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
Two-Compartment Open Model: Overview
The...
Interactions Between Signaling Pathways
Convergence and divergence, and cross-talk between signaling pathways
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...


