Click on "Software" to use of download Sigmoid Model Explorer, the graphical user interface
for enhanced interaction with models in the database.
Another way to explore models in the database is to run them in Cellerator.
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
SIGMOID is initially being developed in a collaboration between
the Institute for Bioinformatics and Genomics (IGB, www.igb.uci.edu)
at the University of California Irvine, the Beckman Institute (BI,
www.bi.caltech.edu) 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.
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