This FCModeler picture shows a sample metabolic network for the plant
hormone Gibberellin. For more pictures click here.
The FCModeler project focuses on the dynamic display of directed graphs for
projects such as metabolic networks and computer networks. Graph theory is used
to analyze complex networks for common cycles and path search between nodes.
The goals of this program are to:
- Capture the intuitions of biologists and provide a modeling
framework for assessing large amounts of information
- Test effects of hypotheses
- Use graph theoretic
approaches to analyze network structure and behavior and search for
critical paths in the network
- Develop simulation
tools based on fuzzy methods that model changes in the network
The graphical display program is written in Java. The modeling software is
currently implemented in Matlab with an XML interface between the packages. The
software is freely available for noncommercial use. If you improve the code,
please share your innovations with the rest of the user community.
FCModeler Current Development
- NEW Version of software
- Continue to develop
simulation tools using R
- Develop more graph theoretic
- Consistency checking for
different type of “omics” data
Software / Files / Documents Used in this Project
2.0 : Self-installing
version for windows 2000 and XP; requires the Java 2 SDK, version 1.4.1 or
above. (April 19, 2004)
version represents a major upgrade
- Different file format for files to accommodate the different
levels of information available about a graph; ranging from graph
structure to annotation and links.
- Complete subgraph selection capabilities based on pathway names,
cycles, paths, and P-neighborhoods.
- Links to the open-source program R for data computation,
generation of animation files, and performing network modeling.
- Sample Data Files (from the MetNet
Project): (Leave the files zipped for use with FCModeler)
Version 1.0 Software: (requires the Java 2 SDK version 1.3.x
Note: This software uses the dot
layout routine from the graphviz opensource software developed at
AT&T labs (http://www.research.att.com/sw/tools/graphviz/) and the diva
information software infrastructure. (http://www.gigascale.org/diva/)
Dr. Julie A. Dickerson
(Electrical and Computer Engineering)
Dr. Eve Wurtele
Mr. Zach Cox (MS,
Mr. Paul Jennings (Undergraduate Research Assistant)
Mr. Adam Tomjack
(Undergraduate Research Assistant)
Ms. Josette Etzel
(Ph.D. Student, Computational Biology)
Mr. Pan Du (Ph.D.
Student, Electrical Engineering)
This work has been supported by
- Proctor and Gamble
- National Science Foundation
(This material is based upon work supported by the National
Science Foundation under Grant No. 0209809) Any opinions, findings, and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the National Science Foundation."
- Iowa State University Plant
- J.A. Dickerson, Z. Cox, “Using
Fuzzy Measures to Group Cycles in Metabolic Networks,“ North American Fuzzy Information
Processing Society (NAFIPS) Annual Meeting, Chicago, IL, July, 2003.
- Poster from ISMB 2002
J.A. Dickerson, Z. Cox, A.W. Fulmer
- J.A. Dickerson, D.
Berleant,Z. Cox, W. Qi, D. Ashlock, E.S. Wurtele, and A.W. Fulmer, "Creating and Modeling Metabolic and
Regulatory Networks Using Text Mining and Fuzzy Expert Systems,"
in Computational Biology and Genome Informatics, edited by Jason T.
L. Wang, Cathy H. Wu, Paul Wang, World Scientific Publishing:Singapore,
- J.A. Dickerson, Z. Cox*, E.
Wurtele, A.W. Fulmer, "Creating metabolic
and regulatory network models using fuzzy cognitive maps," IFSA
World Congress and 20th North American Fuzzy Information Processing
Society (NAFIPS) International Conference, Vancouver, British Columbia,
Volume 4, 2171-2176, July, 2001.
- J.A. Dickerson, D. Berleant,
Z. Cox*, W. Qi, and E. Wurtele, "Creating Metabolic Network Models
using Text Mining and Expert Knowledge," Atlantic Symposium on
Molecular Biology and Genome Information Systems and Technology (CBGIST
2001), 26-30, Durham, North Carolina, March, 2001.
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Page last updated April 19, 2004