In addition, as indicated by the green buttons, the user can subsequently i) save the condition and either return to the Negative Regulation Center page or add another condition for RalBP1, ii) discard this condition, or iii) add one or more sub-conditions that will be attached to the specified condition of RalBP1. Finally, the conditioned state of Rac (“is ON”) needs to be selected. In order to specify Rac as the conditioned species, the user can drag it from the Species Palette into the indicated gray box in the main part of the screen. In order to define the condition RalBP1 is a negative regulator of Rac only when Rac is on, the user first selects the IF/THEN clause. We also show that any and all qualitative regulatory mechanisms can be built using this tool.Ī) Main page of the Negative Regulation Center. We used this tool to build a number of dynamical models, including a 130-protein large-scale model of signal transduction with over 800 interactions, influenza A replication cycle with 127 species and 200+ interactions, and mammalian and budding yeast cell cycles. The Bio-Logic Builder subsequently converts the provided information into a mathematical representation described with Boolean expressions/rules. To build/modify computational models, experimentalists provide purely qualitative information about a particular regulatory mechanisms as is generally found in the laboratory. As part of the user interface, generalized "bio-logic" modules have been defined to provide users with the building blocks for many biological processes. To help address this issue, we have developed a web-based tool, Bio-Logic Builder, that enables laboratory scientists to define mathematical representations (based on a discrete formalism) of biological regulatory mechanisms in a modular and non-technical fashion. While a large part of its potential lies in the ability to integrate it with laboratory research, modeling currently generally requires a high degree of training in mathematics and/or computer science. Computational modeling of biological processes is a promising tool in biomedical research.
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