Cellerator is a computer program that auto- matically generates and solves differential equations for complex sets of chemical reac- tions like those in living cells. Cellerator provides a mathematical and computational infra- structure for char- acterizing reaction pathways and the interactions between complex molecules (e.g., proteins and nucleic acids) and cellular environments. The user effectively defines the pathways by specifying an input set of chemical reactions. Examples include enzymatic reactions, creation and degradation of various chemical species, binding and unbinding reactions, phosphorylation reactions, and transcription and translation of nucleic acids. More complex signals, such as a chemical cascade, can also be specified. Cellerator translates the specifications of chemical reactions into the corresponding set of differential equations, then solves these equations numerically. Cellerator provides an explicit description of output at several steps through the model-generation process; this feature affords flexibility by facilitating intervention by the user to modify the computational model “on the go,” as might be desirable, for example, to correct errors.
This program was written by Bruce Shapiro, Eric Mjolsness, and Andre Levchenko of Caltech for NASA’s Jet Propulsion Laboratory.
This software is available for commercial licensing. Please contact Don Hart of the California Institute of Technology at (818) 393- 3425. Refer to NPO-21122.
This Brief includes a Technical Support Package (TSP).
Software for Modeling Biochemical Reactions
(reference NPO-21122) is currently available for download from the TSP library.
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Overview
The document presents "Cellerator," a software program developed by Bruce Shapiro, Eric Mjolsness, and Andre Levchenko at the California Institute of Technology for NASA's Jet Propulsion Laboratory. Cellerator is designed to model biochemical reactions by automatically generating and solving differential equations that represent complex sets of chemical interactions, particularly those occurring in living cells.
Cellerator allows users to define biochemical pathways through a specified set of chemical reactions, which can include various processes such as enzymatic reactions, the creation and degradation of chemical species, binding and unbinding reactions, phosphorylation, and the transcription and translation of nucleic acids. The software is capable of handling more intricate signals, such as chemical cascades, thereby providing a comprehensive tool for characterizing the interactions between proteins, nucleic acids, and their cellular environments.
The program translates user-defined chemical reactions into a corresponding set of differential equations, which it then solves numerically. This capability enables researchers to gain insights into the dynamics of cellular processes and the regulatory mechanisms that govern gene expression and protein interactions. Cellerator's design includes features that allow for real-time modifications to the computational model, offering flexibility for users to correct errors or adjust parameters as needed during the modeling process.
The document also includes a reference to a publication by the inventors, titled “Automatic Model Generation for Signal Transduction with Applications to Map Kinase Pathways,” presented at the International Conference on Systems Biology in Tokyo in November 2000. This publication highlights the application of Cellerator in the context of signal transduction pathways, emphasizing its relevance in systems biology.
Cellerator is available for commercial licensing, and interested parties are directed to contact Don Hart at Caltech for further information. The document serves as a technical support package, outlining the software's capabilities and its significance in advancing the understanding of biochemical processes, particularly in the context of cellular signaling and gene regulation.
Overall, Cellerator represents a significant advancement in computational biology, providing researchers with a robust tool for modeling and analyzing the complex interactions that define cellular behavior.
