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Sigmoid Intro

The SIGMOID project is intended to produce a database of cellular signaling pathways and models thereof, to marshall the major forms of data and knowledge required as input to cellular modeling software and also to organize the outputs. Such cellular signaling and regulatory pathways are commonly hand-drawn in biological literature as an aid to intuitive understanding. Pathway databases can provide the same assistance in the context of attempts to achieve a quantitative understanding of cellular processes by numerical simulation. They can also serve as an aid to capturing and querying both expert knowledge and heterogeneous data sets pertaining to pathways. Cell model databases are a subject of current research. SIGMOID works at the interface of these two areas.

To this end an object schema has been designed which incorporates reactions, reactants and models. Reactions are further divided into elementary and composite biological processes, and reactants are divided into elementary and composite biological objects such as proteins (elementary in many but not all situations) and protein complexes. This coarse ontology is refined into a number of more detailed categories whose representation in common modeling software can be expected to be different.

Some tools for the SIGMOID project are currently implemented in Python and initially targeting the Linux platform, though there are plans also to provide an API in Java. SIGMOID is initially being developed in a collaboration between the Institute for Bioinformatics and Genomics (IGB, at the University of California Irvine, the Beckman Institute (BI, of the California Institute of Technology, and the Bioengineering Department at Johns Hopkins University. Most components are being made available under the MIT open source license.

Designed by Brandon King
kingb at